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Cenozoic Palaeoecology, Phylogeography and Ecosystem Dynamics of South American Mammals (Sparassodonta and Chiroptera)

Cenozoic Palaeoecology, Phylogeography and Ecosystem Dynamics of South American Mammals (Sparassodonta and Chiroptera)

palaeoecology, phylogeography and ecosystem dynamics of South American ( and Chiroptera)

Camilo López-Aguirre

A thesis in fulfilment of the requirements for the degree of Master by Research

University of New South Wales School of Biological, Earth and Environmental Sciences Faculty of Science

February, 2017 PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet

Surname or Family name: Lopez-Aguirre

First name: Camilo Other name/s: Ernesto

Abbreviation for degree as given in the University calendar: MSc

School: BEES Faculty: Science

Title: Cenozoic palaeoecology, phylogeography and ecosystem dynamics of South American mammals (Sparassodonta and Chiroptera)

Abstract 350 words maximum: (PLEASE TYPE)

Biogeographic studies of South American mammals have typically shown a mismatch between latitudinal trends of extant and extinct richness. shows modern mammal biodiversity increasing towards the Equator, whereas evidence of extinct South American mammals is concentrated at higher latitudes. Consequently, most studies focusing on the ecology and evolution of the South American mammal fauna have been limited temporally (to either extinct or extant taxa) or spatially (specific localities or ecosystems only). In this study, new methodologies were implemented to include both extinct and extant taxa in analyses of two orders of South American mammals: the Sparassodonta and the Chiroptera. A novel multivariate statistical approach was used to study the endemic metatherian order Sparassodonta and to test several competing hypotheses about the of this group. Non-competitive ecological interactions within the South American mammal assemblage appear to have been the main drivers for sparassodontan extinction rather than, as commonly assumed, the result of competition and/or abiotic fluctuations. Diversity loss and eventual demise of the sparassodontans was a gradual process that followed family-specific patterns which changed over time. New statistical tools were also developed to examine phylogenetic diversity and phylogenetic spatially and temporally in New World chiroptera. Trans-continental migrations proved to be most significant in the evolution of the South American fauna. Multiple centres of significant endemism were found across the New World for most bat families, extending the hypothesis of dual centres of diversification, previously proposed for Emballonuridae, Phyllostomidae and Mormoopidae, to Molossidae and Vespertilionidae. and southern played particularly important roles in the diversification of New World , as did the in South America.

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I hereby grant to the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or in part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all property rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation.

I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstracts International (this is applicable to doctoral theses only).

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Date ……………………………………………...... February 15, 2017 COPYRIGHT STATEMENT

‘I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstract International (this is applicable to doctoral theses only). I have either used no substantial portions of copyright material in my thesis or I have obtained permission to use copyright material; where permission has not been granted I have applied/will apply for a partial restriction of the digital copy of my thesis or dissertation.'

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February 15, 2017 Date ……………………………………………...... List of Contents CHAPTER 1 ...... 9 INTRODUCTION ...... 10 CHAPTER 2 ...... 20 EXTINCTION OF SOUTH AMERICA’S SPARASSODONTANS (): ENVIRONMENTAL FLUCTUATIONS OR COMPLEX ECOLOGICAL PROCESSES? ...... 21 CHAPTER 3 ...... 22 GEOGRAPHICAL REGIONALISATION, PHYLOGENETIC DIVERSITY, DIFFERENTIAL ENDEMISM AND THE EVOLUTIONARY HISTORY OF NEW WORLD BATS ...... 23 Introduction ...... 23 Methods ...... 28 Results ...... 34 Discussion ...... 40 CHAPTER 4 ...... 70 SUMMARY OF FINDINGS ...... 71 REFERENCES ...... 76 APPENDICES ...... 131

List of Figures

Figure 1. Geographical distribution of all published records of Cenozoic mammal in South America as compiled by the Paleobiology Database (PBDB): Location of sites (A); mean abundance of published fossil records within a 100 km radius (B)...... 19

Figure 8. Family-level spatial patterns of PD of New World bat families. Emballonuridae (A), Molossidae (B), Mormoopidae (C), (D), Phyllostomidae (E), Vespertilionidae (F)...... 57

Figure 9. Geographical distribution of statistical significance of family-level PD of New World bats. Order Chiroptera (A), Emballonuridae (B), Molossidae (C), Mormoopidae (D), Natalidae (E), Phyllostomidae (F) and Vespertilionidae (G)...... 58

Figure 10. Scatterplot of empirical family-level PD values and significance values of PD obtained from the randomization analysis...... 59

Figure 11. Geographical distribution of statistical significance of family-level RPD of New World bats. Order Chiroptera (A), Emballonuridae (B), Molossidae (C), Mormoopidae (D), Natalidae (E), Phyllostomidae (F) and Vespertilionidae (G)...... 60

Figure 12. Family-level spatial patterns of PE of New World bat families. Emballonuridae (A), Molossidae (B), Mormoopidae (C), Natalidae (D), Phyllostomidae (E), Vespertilionidae (F)...... 61

Figure 13. Geographical distribution of statistical significance of family-level PE of New World bats. Order Chiroptera (A), Emballonuridae (B), Molossidae (C), Mormoopidae (D), Natalidae (E), Phyllostomidae (F) and Vespertilionidae (G)...... 62

Figure 14. Scatterplot of empirical family-level PE values and significance values of PD obtained from the randomization analysis...... 63

Figure 15. Geographical distribution of statistical significance of family-level RPE of New World bats. Order Chiroptera (A), Emballonuridae (B), Molossidae (C), Mormoopidae (D), Natalidae (E), Phyllostomidae (F) and Vespertilionidae (G)...... 64 Figure 16. Multi-family spatial patterns of PD (A) and PE (B) of New World bats. ... 65

Figure 17. Bootstrapping hierarchical clustering analysis of PD and PE of New World bat families. Statistically significant clusters retrieved from 1000 iterations are highlighted in squares. Emballonuridae (Emb), Molossidae (Mol), Mormoopidae (Mor), Natalidae (Nat), Phyllostomidae (Phy) and Vespertilionidae (Ves)...... 66

Figure 18. Zoogeographical regions for New World bat families identified for each corresponding cluster. Emballonuridae (A), Molossidae (B), Mormoopidae (C), Natalidae (D), Phyllostomidae (E), Vespertilionidae (F)...... 67

Figure 19. Geographical distribution of statistically significant centres of endemism of New World bats. Order Chiroptera (A), Emballonuridae (B), Molossidae (C), Mormoopidae (D), Natalidae (E), Phyllostomidae (F) and Vespertilionidae (G)...... 68

Figure 20. Clustering analysis of phylogenetic similarity across statistically significant centres of endemism of New World bats. Emballonuridae (A), Molossidae (B), Mormoopidae (C), Natalidae (D), Phyllostomidae (E) and Vespertilionidae (F)...... 69

Acknowledgments

Firstly, I would like to acknowledge the unconditional support of my family in my pursuit of personal achievement. Thanks to my parents for teaching me the importance of always living under my own beliefs. To my sister Ana for her example and support that taught me how to deal with inconveniences and unforeseen difficulties. To Laura, accomplice and confident in every major part of my life, thanks for being an example and an inspiration as a professional, a person and a partner. Special thanks go to Chris “Chrysomelid” for his interest and attention everytime we sat down to talk about my project.

I would like to thank my supervisors Drs. Suzanne Hand, Michael Archer and Shawn Laffan for their trust and support.

Many people have helped me in different ways over the years to improve the quality of my thesis: Laura Wilson, Troy Myers, Robin Beck, Brent Mishler, Anjali Goswami, Sally Thomas, Juan Carrillo, Pierre Oliver-Antoine, and Andrew Smith. CHAPTER 1

9 INTRODUCTION

Representing less than 15% of Earth’s total land area, South America was the cradle of the adaptive radiation of several different mammal groups (e.g. xenarthrans, and noctilionoid bats; Patterson and Pascual 1968). Its geography encompasses contrasting ecosystems across both latitudinal and altitudinal gradients. Latitudinally it stretches from temperate ecosystems, such as and xeric shrublands in southern South America, to tropical rainforests such as the Amazon in northern South America (Fergnani and Ruggiero 2015).

Altitudinal gradients range from mangroves in lowland coastal areas to mountain forests and wetlands at higher altitudes in the Andes (Sanders and Rahbek 2012).

Some of these ecosystems are among the most productive and diverse on Earth

(Jarvis et al. 2010), but they also are some of the most endangered ecosystems, facing many anthropogenic threats (Jarvis et al. 2010). Grasslands, savannas and shrublands are under the greatest threat, being particularly susceptible to fires and pressure (Jarvis et al. 2010).

Numbering over 1300 , South American mammals represent almost 30% of the global mammal fauna, one of the highest concentrations of mammalian biodiversity in the world (Gardner 2007, Patton et al. 2015). South American mammals provide an example of a group adapting and diversifying to multiple niches available within the geological and environmental landscape of this region

(Gaudin and Croft 2015; Appendix One).

10 Modern South American mammals include numerous emblematic species that embody an exceptional adaptive radiation during the .

Mammals such as felids (species of Panthera, Leopardus and Puma),

(genera Choloepus and Bradypus), ( Tapirus) and the Andean bear

(Tremarctos ornatus) have been the focus of many conservation and research programs (Costa et al. 2005; Marco et al. 2012). Most of the biodiversity within the group is concentrated in the intertropical region (Neotropics; Johnson 1998;

Rosauer and Jetz 2015), following a general latitudinal pattern found worldwide.

Palaeontological and molecular evidence posits platyrrhine monkeys, caviomorph , noctilionoid bats, xenarthrans and marsupials as endemic South American mammal lineages (Woodburne 2010; Woodburne and Martin 2012; Woodburne et al. 2013). The ancestors of some of these groups, as well as the non-native modern South American lineages, are thought to have colonised the Neotropics after independent dispersals from , the Caribbean, North America, and (Lim 2009; Woodburne and Martin 2012).

South American mammals represent not only a large number of species, but also a broad taxonomic range, including 14 mammalian orders (Antoine et al. 2016). This is thought to result from a series of geological and ecological events that began approximately 150 million years ago, with the fragmentation of in the later (Hoorn et al. 2010).

The spatial arrangement of South American ecosystems and associated mammalian faunas reflect the geological history of the continent. Five hundred million years ago, South America was part of the supercontinent Gondwana, along

11 with continents such as Antarctica, Africa, and Australia (Parrish 1990; Jokat et al.

2003).

Later, during the Jurassic, Gondwana began fragmenting into the landmasses that eventually formed modern continents of the Southern Hemisphere (Parrish 1990).

About 145 million years ago, geological rifting resulted in a marine transgression that separated South America from Africa, with the drifting westwards (Riccardi 1987).

South America reached its current position during the early , after its collision with the Nazca plate, an event that also triggered the of the

Andes due to the subduction of the Nazca plate (Riccardi 1987). At this point South

America was an island continent, facilitating the evolution of endemic taxa.

This insular condition lasted for over 60 million years, up until the Isthmus formed and the was closed (Montes et al. 2015).

Intermittent land connections with Antarctica, via the Weddellian Isthmus, were the only cases where South America was connected to another large landmass (Gelfo et al. 2015). Although current evidence does not provide compelling evidence for a between Australia and South America via Antarctica after the late

Cretaceous, several fossil findings strongly suggest that all three landmasses were somehow connected during the , until as late as the

(Reguero et al. 2013). Several fossil specimens of Nothofagus from the early

Paleocene of (Romero 1986), as well as representatives of native South

American mammal groups present in Antarctica around the same period (Gelfo et

12 al. 2015), clearly indicate active South America-Antarctica migration and interchange of flora and fauna (Reguero et al. 2013).

The unique discovery of a outside Australia in Argentinean

(Pascual et al. 1992), as well as the restricted South American distribution of the australidelphian order (D’Elía et al. 2016), add evidence of a shared evolutionary history between Australia, Antarctica and South America

(Pascual et al. 1992; Forasiepi and Martinelli 2003; D’Elía et al. 2016).

Simultaneously, geological events and ecological processes between South and

North America took place during the and (Weir et al. 2009;

Pinto-Sánchez et al. 2012; Wilson et al. 2014). Mammalian diversity increased markedly during the Paleo-Eocene when a major radiation of native South

American took place. Along with an overall increase in litoptern diversity, the first representatives of appeared during the , followed by the first appearance of astrapotherians and notoungulates during the early

Eocene (Gelfo et al. 2008; Bond et al. 2011; Welker et al. 2015).

Polydolopimorphians and sparassodontans also increased in diversity during this period.

Intermittent land connections between the Americas and the Caribbean facilitated both migration and colonization of different groups across the New World, processes that shaped modern biogeographical patterns at an inter-continental scale (Forasiepi et al. 2014, 2015; Prothero et al. 2014; Suarez et al. 2015;

Vucetich et al. 2015; Amson et al. 2016). Among these, the Great American Biotic

13 Interchange (GABI) was one of the most important, due to its temporal and biological range.

Originally hypothesized by Alfred Wallace (1876), the first concrete evidence and analysis of a major bilateral biotic migration across the Americas was provided by

Marshall (1981). GABI was a set of migration waves across Central America that marked the final event that would shape the distribution and composition of modern mammals in the New World (Woodburne 2010). This latitudinal exchange of biodiversity was only possible with the formation of the Panama Isthmusbetween

North and South America (Montes et al. 2015). Traditional interpretation of available palaeontological and geological evidence placed the onset of the GABI during the late ~3.0 Ma (Bacon et al. 2016; O'Dea et al. 2016). During the decades following Marshall’s (1981) paper, several studies compiled both geological and biological evidence that supported an onset of the GABI and the formation of the Panama Isthmus around 2.8 Ma, in the late Pliocene (O’Dea et al.

2016). However, recent palaeontological and geological studies have accumulated considerable evidence to push back the onset of the GABI by ~ 10 My (Carrillo et al. 2015; Bacon et al. 2015; Amson et al. 2016; Bloch et al. 2016).

Lagomorphs, sciuromorph rodents, vespertilionid bats, carnivorans, gomphotheres and modern ungulates (artiodactyls and perissodactyls) migrated southwards in four different dispersal pulses from North America (Woodburne 2010; Woodburne et al. 2014a, 2014b). South American emigrants were mostly caviomorph rodents, platyrrhine , xenarthrans, and marsupials, which also arrived in North

America in separate waves (Woodburne et al. 2014a, 2014b).

14 North American migrants were more effective at adapting to Neotropical ecosystems than their South American counterparts to more temperate latitudes

(Faurby and Svenning 2016). Of the principal North American migrant groups, only proboscideans disappeared from South America, after their only representatives in the New World (family Gomphotheriidae) went extinct during the late megafaunal mass extinction (MacFadden et al. 2015). The other groups (e.g. carnivorans and ungulates) diversified and spread across South America, where they are now key components of the trophic arrangement in many ecosystems

(Fergnani and Ruggiero 2015). Although most of the South American migrant groups have modern representatives in North America, higher levels of extinction are recorded for South American lineages present in North America, with mass extinction of xenarthrans in North America (Vizcaíno and Bargo 2015). Of the North

American migrants, only proboscideans disappeared completely, whereas the

South American migrant notoungulates and some xenarthrans went extinct in

North America.

The recent discovery of the Panamacebus transitus from the early

Miocene (20.8 Ma) of Panama provides the oldest evidence of faunal interchange between the landmasses, 15 Ma earlier than GABI (Bloch et al. 2016). Other fossil findings, such as a specimen of from Florida (Flynn et al. 2003), suggest older dispersals across the Americas that predated GABI, as part of the so-called First American Biotic Interchange (FABI) (Gelfo et al. 2015; Rincon et al.

2015). FABI comprises an early stage of the South American mammal evolution before GABI during which several North American and Australo-Antarctic taxa

15 colonized insular South America (Ali 2012; Fabre et al. 2014; Rincon et al. 2015).

Some of these groups include extinct (e.g. Monotremata and

Gondwanatheria) that disappeared before the radiation of modern groups (e.g.

Condylarthra and Dryolestoidea) and the oldest ancestors of some of the living orders (e.g. caviomorph rodents, platyrrhine monkeys and noctilionoid bats).

Prior to the FABI and GABI, and as a result of an isolated marine migration, the first North American mammal recorded from South America is the phocid

Properiptychus argentines from the late of the Entre Ríos province in eastern (Muizon and Bond 1982). However, current estimates suggest that several procyonid , river dolphins and trichechid sirenians species most likely predated the arrival of Properiptychus argentines in South America

(Antoine pers. comm).

Extinct South American mammals are generally less well known than their living counterpart. Although South American sparassodontans, giant ground sloths and are widely recognised extinct mammals (Bacon et al. 2015; Carrillo et al. 2015), other native groups, such as ungulates (e.g. , ,

Notoungulata and ) and Ameridelphian marsupials (e.g.

Polydolopimorphia), are not (Welker et al. 2015; Lorente et al. 2016). Together they comprise the diverse extinct mammal fauna that characterised South America during most of the Cenozoic (Woodburne et al. 2013; ODea et al. 2016), until the

Pleistocene, when the extinction of the mammalian occurred, with the exceptions of some toxodontid notoungulates and giant sloths that briefly survived the Pleistocene- transition (Metcalf et al. 2016; Plotnick et al. 2016).

16 Review of the South American fossil mammal record reveals a clear bias leading to an incomplete understanding of its evolutionary history. Unlike modern distributional patterns, many South American fossil mammals have been discovered in the Southern Cone (mostly Argentina, Chile, southern and

Uruguay), leaving the Neotropics highly underrepresented (Fig. 1). More recently, international efforts have resulted in a new wave of palaeontological discoveries in the lower latitudes of South America and these have added significantly to the interpretation of the natural history of the New World (Rincon et al. 2015; Suarez et al. 2015; Amson et al. 2016). These Neotropical fossil sites include: Urumaco

(), (), Acre (), Fitzcarrald (Peru), Inchasi and

Quebrada Honda () (Carrillo et al. 2015).

Important palaeontological discoveries from these Neotropical fossil sites have helped to rewrite the evolutionary history of South American mammals. For example, description of Perupithecus ucayaliensis and Cachiyacuy and

Canaanimys species from Peru has pushed back the arrival of the African ancestors of modern platyrrhin monkeys and caviomorph rodents by several million years (Antoine et al. 2011; Bond et al. 2015).

This research uses novel approaches to investigate the palaeobiology of the

Cenozoic mammalian fauna of South America, a region with a geological history and geographic position that holds key information about the dynamics between

South American and North American mammals. It focuses on two orders of South

American mammals: the extinct sparassodontans, endemic apex mammal predators throughout most of the Cenozoic (Prevosti et al. 2011); and the extant

17 chiropterans, a morphologically and ecologically diverse group of mixed origins

(Arita et al. 2014).

In this thesis, Chapter Two implements a novel multivariate statistical approach, structural equation modelling, to study the drivers behind the extinction of the

South American native metatherian order Sparassodonta. To achieve this objective, three different extinction scenarios simultaneously were tested; 1)

Environmental fluctuations; 2) competition with other predators; 3) ecological interactions within the mammalian assemblage. Chapter Three uses a novel statistical framework that study phylogenetic measures of biodiversity to study the evolutionary history of New World bats, a highly diverse group with a highly heterogeneous natural history. Chapter Four summarises all findings and provides a compiling list of conclusions.

18

Figure 1. Geographical distribution of all published records of Cenozoic mammal fossils in South America as compiled by the Paleobiology Database (PBDB): Location of fossil sites (A); mean abundance of published fossil records within a 100 km radius (B).

19 CHAPTER 2

20 EXTINCTION OF SOUTH AMERICA’S SPARASSODONTANS (METATHERIA): ENVIRONMENTAL FLUCTUATIONS OR COMPLEX ECOLOGICAL PROCESSES? 1

1 A version of this has been accepted for publication: LOPEZ-AGUIRRE, C., ARCHER, M., HAND, S. J. and LAFFAN, S. 2017. Extinction of South America’s sparassodontans (metatheria): environmental fluctuations or complex ecological processes?. Palaeontology, 60: 91-115.* * This paper is the direct result of my thesis research, including the design, analysis and interpretation of results. I acknowledge my co-authors for their supervisory guidance and their contributions to the publication.

21 CHAPTER 3

22 GEOGRAPHICAL REGIONALISATION, PHYLOGENETIC DIVERSITY, DIFFERENTIAL ENDEMISM AND THE EVOLUTIONARY HISTORY OF NEW WORLD BATS

Introduction

Understanding geographical patterns in the distribution of biodiversity provides key insights into the evolution and macroecology of taxa over wide spatial and temporal scales (Springer et al. 2011; Leigh et al. 2014). In this context, one of the most important tools is the delimitation of biogeographical zones (Holt et al. 2013; Rueda et al. 2013; Morrone 2014a,b). Defined as areas delimited by geological and geographical features that show similar faunal or floral composition, biogeographic regions are a key concept for the study of biodiversity. Progress in the study of biogeographic regions has broadened its applicability to fields including conservation biology and evolutionary studies (Mishler et al. 2014; González‐Orozco et al. 2014; Sanginés-Franco et al. 2015). Contrary to other concepts in community ecology (e.g. biome, biota, etc.), biogeographic areas can be easily tested for both plants (phytogeographical zones) and (zoogeographical zones), and can be compared across multiple taxa (Holt et al. 2013).

Biogeographic patterns for taxa have been widely studied, showing consistent zoogeographic regionalisation (i.e. spatial partitioning of a specific region based on similarities in species composition) at a global scale (Holt et al. 2013). The study of biogeographic regionalisation has evolved from intuitive analysis of distribution patterns of higher taxa on geographically similar areas, to

23 incorporate biodiversity indexes and similarity analysis (Procheş and Ramdhani 2012; Holt et al. 2013; Mishler et al. 2014).

Recent advances in the implementation of phylogenetic data in the delimitation of biogeographical zones have enabled extension of this approach to the study of evolutionary processes (Melo et al. 2009; Smith et al. 2012; Pereira and Palmeirim 2013; Patrick and Stevens 2016), as well as the development of new measures of biodiversity that successfully combine the evidence that palaeontological and biogeographic analyses provide, shedding light on the historical trajectory linking extinct and extant biodiversity (Bininda-Emonds et al. 2007; Davalos et al. 2014; Rojas et al. 2016).

Consequently, biogeography is no longer limited to the description of biodiversity based on species distribution, richness and abundance. Phylogenetic structuring, phylogenetic fields of species, and phylogenetic diversity (PD) and phylogenetic endemism (PE) are increasingly investigated and have revolutionised the understanding of macroecological processes in deep time (Villalobos et al. 2013, in press; Daru et al. 2015; Fergnani and Ruggiero 2015; Rosauer and Jetz 2015; Aguirre et al. 2016). These methodologies have proven to be especially effective when analysing higher taxonomic groups or widely distributed taxa (González‐ Orozco et al. 2015; Rosauer and Jetz 2015).

With over 1100 species, bats (Mammalia: Chiroptera) are the second most diverse group of mammals in the world, reflecting a complex evolutionary history involving diversification, migration and extinction processes (Simmons 2005; Teeling et al. 2012); within ~55 Ma bats evolved the capability of self-powered flight, colonised every continent except Antarctica, and radiated to occupy the greatest niche diversity among mammals. Wide ecological plasticity and morphological disparity are considered to be the main drivers of the adaptive radiation of bats (Santana et al. 2012; Dumont et al. 2014).

Among bats, the evolutionary history of the New World fauna is probably one of the most complex. Home to almost a third of the world’s bat species, the New World

24 includes the most varied terrestrial ecosystems on the planet (Crowther et al. 2015). The extant New World bat fauna comprises more than 350 species across nine families representing three superfamilies (Emballonuroidea, and Vespertilionoidea), each with a different evolutionary history (Arita et al. 2014; Peixoto et al. 2014). Current understanding suggests that the Emballonuridae (the only New World emballonuroid family) and the vespertilionoid family Molossidae could have colonised South America via sweepstakes migration from Africa in the Early (Lim 2008; Arita et al. 2014). Noctilionoid fossils from Africa and Australia suggest a Gondwanan origin for the , and that the ancestor of New World noctilionoids possibly colonised South America after migrating from Australia via Antarctica (Gunnell et al. 2014). New World noctilionoids may have migrated subsequently to North America and the Caribbean, where diversification evidently occurred (Gunnell et al. 2014; Rojas et al. 2016). Finally, the vespertilionoid families Natalidae and Vespertilionidae are thought to have originated in the Caribbean and North America respectively, both eventually migrating southwards (Dávalos 2005; Lack et al. 2010).

Traditional interpretations of the evolutionary history of bats in the New World, based on incomplete modern distribution models and a scarce fossil record, hypothesised that each family had a single centre of diversification (e.g. Koopman 1982). More recently, with the development of phylogenetic measures of diversity and the implementation of Bayesian statistics, studies have challenged this traditional view, arguing for dual centres of diversification for several families of New World bats (Arita et al. 2014; Pereira and Palmeirim 2013; Rojas et al. 2016). Addressing the increasing interest in understanding the evolution of this group, comparing zoogeographical regionalisation across clades could help elucidate common evolutionary trajectories, while accounting for the evolutionary history specific to each clade (Morrone 2014a, b; Absolon et al. 2016).

Fossil and phylobiogeographic evidence suggests that the evolution of New World bats is more complex than previously thought. For example, the early presence of noctilionoids, molossids and emballonuroids in North America points to either a

25 North American origin for these clades or an early northward migration from South America (Gunnell and Simmons 2005; Eiting and Gunnell 2009), before the onset of the rising of the and the Great American Biotic Interchange (GABI; Arita et al. 2014; Rojas et al. 2016). Phylogenetic analyses suggest that natalid diversification did occur in the Caribbean, but that this family’s origin was in North America (Dávalos 2005).

Also, biogeographic studies have successfully uncovered large-scale patterns in modern bat biodiversity by testing the role that ecological and environmental processes had on shaping that biodiversity (Villalobos and Arita 2010; Villalobos et al. 2013, in press; Arita et al. 2014; Olalla‐Tárraga et al. 2016). Latitudinal gradients in the distribution of bats, density-dependent community structuring, tropical niche conservatism and limiting similarity are some of the evolutionary processes that have been widely studied in bats (York and Papes 2007; Stevens 2011; Pereira and Palmeirim 2013; Patrick and Stevens 2016).

Geographic regionalisation of bat diversity has been previously studied at a global scale (Procheş 2005). Overall, a total of 9-11 biogeographic zones of mammal diversity have been described worldwide (Procheş 2006; Holt et al. 2013). These regions have been found to correspond with other currently accepted faunal and floral regions and subregions (Holt et al. 2013, Morrone 2014b). Procheş (2006) suggested that the longitudinal separation between the Old and New Worlds has been the main biogeographical barrier that shaped modern bat diversity worldwide.

Nonetheless, the evolutionary processes behind modern bat diversity were remarkably different between the Old and New Worlds, leaving the evolutionary framework in which bat diversity evolved in each region and the mechanisms underlying its current status untested (Procheş 2006, Morrone 2014a). Different multi-taxa biogeographical studies are consistent in dividing the New World in two broad biogeographical regions (Procheş 2005; Holt et al. 2013, Morrone 2014b); the Nearctic, and the Neotropics (also referred to as the Panamanian Realm), the

26 latter comprised of three subregions (Antillean, Brazilian and Chacoan) and two transition zones (Mexican and South American).

Interpreting PD and PE in a way that can account for the place and relative time of specific events could be particularly useful in this group. Mishler et al. (2014) developed a methodological framework designed to identify the spatial phylogenetic structure of an assemblage and to classify areas of endemism based on phylogenetic relationships, implemented within a Categorical Analysis of Neo- and Palaeo-Endemism (CANAPE). This approach has been applied to several biotic groups (Mishler et al. 2014; González-Orozco et al. 2015; Schmidt-Lebuhn et al. 2015; Gonzalez-Orozco et al. 2016; Thornhill et al. 2016), but its applicability for the interpretation and comparison of complex evolutionary processes in multiple lineages remains largely untested.

In order to better understand possible differences in the biogeographic patterns of diversity of New World bat families, and their correlation with the evolutionary history of each family, we analyse the geographic patterns of PD and PE to further study the biogeographic regionalisation of the New World based on bat diversity and endemism. Our goals were to: 1) describe the spatial distribution and statistical significance of PD and PE of New World bats; 2) identify and compare areas of differential endemism across the Americas; 3) depict differences in the geographical delimitation of zoogeographical zones of different New World bat families.

We tested the following hypotheses:

 Geographic patterns of distribution of PD and PE for each New World bat family match the expected patterns under a niche conservatism scenario. Prediction: Values of PD and PE will be higher across families, closer to the putative centre of origin of each family.

27  Contrary to the traditional interpretation of single centres of diversification, New World bat families Molossidae, Phyllostomidae and Vespertilionidae have multiple centres of diversification across the Americas. Prediction: Significant levels of any kind of endemism will be found in at least two different, isolated areas for each of these families.  Family-specific patterns of zoogeographic regionalisation of PD and PE can be found across New World bat families that better reflect the evolutionary differences between groups. Prediction: Rather than following the general regionalisation of the New World demonstrated for other groups, each family will show distinctive patterns of regionalisation.

Methods

Taxonomic sampling and spatial data

To build a geographic dataset of New World bats, distribution maps were retrieved from the IUCN data repository and the Nature Serve database (IUCN 2016, accessed from http://www.iucnredlist.org; Appendix Four). Taxonomic identities of all sampled species were corroborated and, when necessary, taxonomically updated based on Simmons (2005). Species with deficient distributional data (i.e. isolated records instead of polygons of distribution) or doubtful taxonomic identity were excluded. The final dataset included a total of 325 species, spanning six families and three superfamilies (Emballonuroidea, Noctilionoidea and Vespertilionoidea). To transform the distribution maps into presence records, ArcMap 10 was used to intersect each distribution polygon with a grid of 6602 cells (100 km ×100 km grid cells), using an equal area Mollweide projection. Presence was assumed as the mid-point of each cell that falls in the polygon. This resulted in

28 a matrix of 372,156 presence records for all species combined, which were then imported into Biodiverse 1.0 (Laffan et al. 2010) at the same resolution for spatial analyses, resulting in a data set of 6602 cells. Subsets of records for each family level clade were also imported for analysis at the same resolution.

Phylogenetic data

Phylogenetic information for all New World bats was obtained from a time- calibrated species-level supertree covering all major chiropteran clades, as updated by Fritz et al. (2009). The taxonomic identities of each of the species included in the supertree were updated to match the current taxonomic arrangement used by IUCN. The phylogenetic supertree was imported to Biodiverse 1.0 and trimmed to match the spatial data (Laffan et al. 2010). Of the 325 species with distribution data, 320 were included in the phylogeny. To obtain subtrees for each family (Appendix Two), the supertree was trimmed to the most recent common ancestor (MRCA) of the clade.

Spatial distribution of diversity and endemism

To analyse family-level patterns of diversity and endemism, PD and PE were calculated. All analyses were performed for the six most diverse families (Emballonuridae, Molossidae, Mormoopidae, Phyllostomidae, Natalidae, Vespertilionidae) to elucidate family-specific patterns. All analyses of diversity were conducted using Biodiverse 1.0 (Laffan et al. 2010), and results were plotted for each taxonomic group separately using ArcMap 10.

29 As used here, PD is a measure of biodiversity that accounts for the amount of evolutionary history shared by a pool of taxa in a specific area (Faith 1992). It is calculated for a cell by summing the branch lengths of the set of taxa present in that cell. Here we also standardised the PD score as a proportion of the tree’s total length by dividing PD by the sum of all branch lengths in the tree.

푃퐷 = ∑ 퐿푐 {푐∈퐶}

Where C is the set of branches in the minimum spanning path joining the taxa to the root of the tree; c is a single branch in the spanning path (C); and Lc is the length of the branch c, expressed as a proportion of the total length of the tree.

PE integrates PD with traditional measures of endemism based on taxonomic richness (i.e. weighted endemism; Faith et al. 2004). PE is a measure of relative range restriction of the branches of a phylogenetic tree (Rosauer et al. 2009). This is distinct from PD-endemism that is an absolute endemism measure that represents the amount of PD that is found in an area and nowhere else (Faith et al. 2004). We used Rosauer et al.’s relative definition of PE, with relative PE resulting from range-weighting PD by the distribution of each clade. PE was also standardised to the total sum of branch lengths.

퐿푐 푃퐸 = ∑ 푅푐 {푐∈퐶}

Where Rc is the union of the combined ranges of the taxa that are descendants of branch c in a phylogeny, such that overlapping areas are considered only once.

It has been noted that raw values of phylogenetic measures of biodiversity are not highly informative and could be difficult to analyse, highlighting the need to test their statistical significance (Mishler et al. 2014; Zupan et al. 2014; Zhang et al. 2015). To do so, the distributional data were randomised 999 times, using a null

30 model that assigned taxa randomly to grid cells, while holding richness in each cell and the range size (number of cells where present) of each species constant (Mishler et al. 2014; González‐Orozco et al. 2015; Nagalingum et al. 2015; Schmidt‐Lebuhn et al. 2015; Thornhill et al. 2016). This results in random selections of the same number of terminal branches on the tree for each grid cell. PD, PE, RPD and RPE were then calculated for each randomisation, and the rank relative significance of each cell’s score was calculated by comparing the observed score to the randomly generated distribution. Classification of ecosystems of the New World is based on Graham (2011) and Wiken et al. (2011).

Comparisons across New World bat groups

Gonzalez-Orozco et al. (2015) established a methodology to compare different levels of biodiversity among groups. These multi-clade measures can be applied to quantify the congruence in PD and PE between different clades (referred to as

PDmulti and PEmulti in this study). Following Gonzalez-Orozco et al. (2015), PDmulti and PEmulti were calculated to estimate the spatial correspondence between observed values of PD and PE across bat clades. The PD/PE surfaces were range-standardised into the interval 0 to 1 and then averaged across taxon groups to generate PDmulti and PEmulti values that represent agreement in the geographic distribution of diversity and endemism. Because the range and distribution of the families included in our study were uneven, analysing only grid cells where all families were present would have excluded vast areas of the distribution of some families. Instead, PDmulti and PEmulti were obtained for all grid cells where at least two families were present.

Bootstrapping hierarchical clustering analysis was used to study similarities in PD and PE values across families; Euclidian distances and Ward’s agglomerative method were used based on 1000 iterations. This approach allows testing the

31 statistical significance of each cluster within analysis dendrograms with approximately unbiased (AU) p-values. Clustering analysis was performed in the pvclust package for the programming environment R version 3.2.3 (Suzuki and Shimodaira, 2015; R Core Team, 2016).

Delimitation of zoogeographical zones of New World bats

Zoogeographical zones were assessed with pairwise comparisons of phylogenetic relatedness between pairs of grid cells, using the phylo-jaccard dissimilarity index. Phylo-jaccard index estimates phylogenetic dissimilarity based on the proportion of branch lengths from a phylogeny that are shared between pairs of assemblages (grid cells in this study). Hierarchical clustering analysis was used to evaluate the geographical distribution of phylogenetically similar grid cells, using matrices of phylo-jaccard dissimilarity and a weighted average linkage. Based on previous studies that have identified three to five biogeographical regions in the New World (Procheş 2012; Holt et al. 2013), we set a minimum of four clusters. Zoogeographic regions were also identified as clades clearly separated from other sister or parental clusters.

It has been suggested that clustering algorithms based on dissimilarity measures are vulnerable to topological bias (Dapporto et al. 2013). A tiebreaker condition was hence implemented: when two clusters had the same phylogenetical turnover, the pair with the highest Corrected Weighted Endemism (CWE) was selected (Mishler et al. 2014). CWE is a modification to the traditional Weighted Endemism (WE) index that controls for species richness bias by dividing WE by the species richness of the target area (Laffan et al. 2013).

32 CANAPE

CANAPE is a two-step analysis that tests the relative contribution of all short and long branches to PE, based on randomisation analyses (Mishler et al. 2014). First, CANAPE retrieves grid cells with significantly high endemism (one-tailed test, α=0.05), detecting grid cells with a significantly high numerator, denominator or both in the RPE score. Second, grid cells that passed step one are tested for the statistical significance of the RPE ratio (two-tailed test α=0.05). Accordingly, grid cells are then subdivided into four independent, non-overlapping categories: neo- endemism (i.e. grids cells with high concentration of rare short branches of the tree, significantly low RPE); palaeo-endemism (grids cells with high concentration of rare long branches of the tree, significantly high RPE); mixed-endemism (concentration of both rare long and rare short branches, non-significant RPE); and super-endemism (highly significant RPE numerator and denominator from step one at α=0.01).

To elucidate family-specific patterns of endemism, all analyses were first completed for the entire order and then compared with the results for the six most diverse families (Emballonuridae, Molossidae, Mormoopidae, Phyllostomidae, Natalidae, Vespertilionidae). All analyses were performed using Biodiverse 1.0 (Laffan et al. 2010).

To depict zoogeographical areas of endemism, we compared grid cells that were identified as statistically significant based on the phylogenetic dissimilarity between grid cells. The ‘phylojaccard’ dissimilarity was used in a hierarchical clustering analysis to group cells based on the length of the branches shared between grid cells (Mishler et al. 2014).

33 Results

Diversity and endemism analysis

The geographic distribution of PD was different across vespertilionoid families: tropical South America (SA) and eastern Brazil were the main areas of high PD for molossids, whereas PD was higher in the Caribbean and North America (NA) for natalids and vespertilionids, respectively (Fig. 8B, D, F).

The noctilionoid family Mormoopidae has three main areas of high PD, one in southern NA, one in the Caribbean, and one in tropical areas of Colombia and Venezuela (Fig. 8C). High PD for phyllostomids was evenly distributed across tropical and subtropical SA, with a relative increase in PD in the Pacific coast and the Andes of Colombia, and Peru (Fig. 8E).

Large areas of significantly low PD were identified in several Neotropical ecosystems including the Caatinga and the Amazon, Atlantic and Pantanal rainforests, and North American ecosystems including the Great Plains, the Eastern Temperate Forests and the Northern Forests. Significantly high PD was found in the Caribbean, the Pacific coast of the central and southern Andes, the Baja California Peninsula and the forests of Sierra Madre del Sur (Fig. 9A).

Different patterns of diversity and endemism are evident from analysing individual families within the order. Significantly low PD areas were considerably more common than significantly high areas, most commonly associated with the distributional limits of the families (Fig. 9). Moreover, areas of significant PD (both high and low) are only a fraction of the range of the species, meaning that the PD values obtained for the other non-significant areas are values that could be expected by randomly assigning any taxa to that area. In Molossidae, Mormoopidae and Natalidae, significantly low PD was found across the Amazon 34 rainforest and the Atlantic coast of South America (Fig. 9C-E). The Pacific coast and the central Andes of Peru formed the only region of significantly high PD for Molossidae (Fig. 9C), and mainland North America formed a small region of significantly high PD for Vespertilionidae (Fig. 9G). Scatterplots of PD and significance values showed no correlation that could suggest a tendency to find significant areas based on the PD empirical values (Fig. 10).

RPD, on the other hand, did not follow the same spatial pattern. Significantly high RPD was found in the Eastern Temperate Forests of North America, the southern Andes and the Caribbean lowlands of Colombia (Fig. 11A). Emballonuridae showed areas of significantly low RPD in the Brazilian Pampa and the Yucatan Peninsula (Fig. 11B). Molossidae showed significantly high RPD in the Baja California Peninsula and the Pacific coast of the central Andes, and significantly low RPD in the Guiana Shield (Fig. 11C). Phyllostomidae and Vespertilionidae did not exhibit clear patterns in the distribution of significantly low RPD values, showing small areas scattered throughout their distributions (Fig. 11F-G). Mormoopidae showed three main areas of significantly low RPD, in Central America, the central Andes and the Cerrado of Brazil, whereas Natalidae showed significantly low RPD in the Caribbean, the Atlantic coast of Brazil, and throughout Central America and southern North America (Fig. 11D-E).

The families Mormoopidae and Natalidae were highly endemic to the Caribbean (Fig. 12C-D). Distribution of molossid PE was geographically restricted to the Pacific coast of SA and Central America (CA), with its highest values in the Pacific coast of Ecuador and Peru (Fig. 12B). For phyllostomids, several highly endemic areas were detected across the Caribbean, CA and SA. The Guajira Peninsula and the Orinoquean regions between Colombia and Venezuela, the Biogeographic Chocó, the Colombian Amazon and the tropical forests of Costa Rica and Panamá contain the highest endemism of phyllostomids of the continental regions (Fig. 12E). Insular endemism was homogeneous across the Caribbean, with peaks of PE values in Jamaica, Puerto Rico and Lesser Antilles.

35 The highest values of PE for vespertilionids were distributed between Mexico, the Andean region of Colombia and the Guajira Peninsula. Intermediate, isolated areas of vespertilionid endemism were found in the southern Andes, some Caribbean islands (Jamaica and Lesser Antilles), and an area comprising and the Brazilian Pampa (Fig. 12F).

The Caribbean and the southern and central Andes were the main areas of significantly high PE, whereas the Amazon and Atlantic forests formed a large area of significantly low PE (Fig. 13A). It is worth noting that, although these areas contain the larger endemic regions, many areas with high PE values are not significant. This is because although these areas harbour high levels of endemism such values are not higher than expected by chance. The central and northern Andes were areas of significantly high PE for the families Emballonuridae, Molossidae and Phyllostomidae (Fig. 13B-C, F). In contrast, the Brazilian Amazon, Cerrado and Caatinga were areas of significantly low PE for Emballonuridae, Natalidae, Phyllostomidae and Vespertilionidae (Fig. 13B, E-G). Central America and North America included several areas of significantly high PE across families (Fig. 13B, F-G). The Caribbean was an area of significantly high PE for all families with a Caribbean distribution, with the exception of the Natalidae in the Lesser Antilles where significantly low PE was detected. Similar to our findings for PD, scatterplots showed no correlation between empirical PE values and their significance values obtained from the randomization analysis (Fig. 14).

Patterns of significant RPE resemble those of PE at the order level, with significantly low RPE in the Amazon and Atlantic forests and significantly high RPE in the Caribbean and the southern Andes (Fig. 15A). Areas of significantly high RPE were detected for all families except Emballonuridae and Natalidae (Fig. 15B, E). The Peruvian Andes and the latitudinal limits for molossids are large areas of significantly high RPE (Fig. 15C). Mormoopid RPE was significantly high only in the xeric environments of the Sonora and the Chihuahua deserts (Fig. 15D).

The Pacific coast of and Nicaragua, and the Sierra Madre mountain range of Mexico showed significantly low phyllostomid RPE (Fig. 15F). Significantly 36 high phyllostomid RPE was found on the northern boundary of the family’s distribution, in the Amazon of Colombia and Venezuela, and in southern Peru. Vespertilionid RPE was significantly high in several areas across the Americas: the Llano Estacado in southwestern United States, the Baja California Peninsula and British Columbia in Canada (Fig. 15F). Significantly low RPE, on the other hand, was evident in the Yucatan Peninsula and northern Mexico, and the islands of British Columbia in Canada.

Comparison across New World bat groups

Multi-taxon metrics of diversity and endemism showed concordant areas of high PD and PE values across the six New World bat families studied (Fig. 16). High concentrations of PDmulti were evident in the Amazon and central-to-northern

Andes, whereas high levels of PEmulti were more evenly distributed across the tropical and subtropical region (Fig. 16A). The Caribbean, CA and the Pacific coast of equatorial SA showed comparatively elevated PEmulti (Fig. 16B). High

PEmulti was also found in a small area of the southern Andes.

Similarities in the spatial patterns of PD and PE were tested with the hierarchical clustering analysis. PD and PE clustered families differently (Fig.17). Overall, similarity values ranged from 0 to 0.3 for PD and from 0 to 0.025 for PE, suggesting that PE values were similar among families (Fig. 17). PD separated Phyllostomidae from other families, which grouped as one cluster (p < 0.05). Mormoopidae and Natalidae formed a subcluster, while Emballonuridae and Molossidae grouped with Vespertilionidae (Fig. 17). PE clustered the six families differently. Mormoopidae and Natalidae formed the only statistically significant group (p < 0.05), part of a bigger cluster with Emballonuridae and Phyllostomidae.

37 Delimitation of zoogeographical zones of New World bats

Despite the fact that the boundaries of the regions vary across families, by combining the results of all six families, it is possible to recover the presence of the four zoogeographic regions and two subregions identified by Procheş and Ramdhani (2012): Nearctic, Neotropical (Central American and La Plata subregions), Caribbean and Andean regions (Fig. 18). The Nearctic region is evident for vespertilionids (Fig. 18F), the Caribbean region for all families but Natalidae (Fig. 18A-C, E-F) and the Andean for molossids, phyllostomids and vespertilionids (Fig. 18B,E-F). The Central American subregion is more clearly depicted by families Emballonuridae, Molossidae and Phyllostomidae (Fig. 18A-B, E).

In four of the six families analysed (Emballonuridae, Molossidae, Phyllostomidae and Vespertilionidae), clustering analysis grouped the areas representing the boundaries of their distributions within a single cluster (Fig. 18A-B, E-F). It is worth noting that, for these taxa, the Caribbean always clustered with the temperate zoogeographic zone. The tropical and subtropical regions of the New World formed a single zoogeographic zone across families.

Vespertilionidae is the only family with a cosmopolitan distribution across the New World. NA formed a cluster, separate from CA, with an independent zone between southern NA and northern CA (Fig. 18F). For Mormoopidae and Natalidae, no clear pattern of regionalisation was found; the tropical-intertropical region was divided into two zones with no spatial continuity (Fig. 18C-D).

38 CANAPE

At the ordinal level, palaeo-endemism was found in the Caribbean and southern Andes, with small areas in the Baja California Peninsula and central Andes (Fig. 19A). Areas of mixed and super endemism were repeatedly found across the northern and central Andes and the tropical forests of Mexico. Across families, the Pacific coast of the Americas harboured the greatest concentrations of endemism. Areas of all types of endemism were found throughout the tropical zone of the New World between the Pacific coast and the Andes. It is also remarkable that, for all families studied, the Amazon and in eastern South America had no significant level of endemism of any kind. Analysing each family separately showed unique patterns of endemism with respect to the evolutionary history of each taxon. Emballonuridae was found to be super-endemic in southern Mexico and different ecosystems in the tropical Andes of Ecuador, Colombia and Peru (Fig. 19B). Mixed endemism was always found in adjacent areas associated with these super- endemic areas.

Similar geographical patterns were evident for molossids; the tropical forests of Central America and southern North America on the Pacific coast were areas of mixed-endemism, along with the tropical Andes, the Bolivian Altiplano and Cuba (Fig. 19C). The most extensive area of palaeo-endemism was found across the tropical Andes and Pacific coast of Peru. Additional smaller areas of palaeo- endemism were detected in southern Central America. Super-endemism was scattered across several small areas of South America and the Caribbean.

Mormoopids are endemic to the Caribbean. In particular, the Greater Antilles in the Caribbean showed the greatest concentration of super-endemism, whereas the Lesser Antilles showed smaller areas of palaeo-endemism (Fig. 19D). A similar pattern was evident for natalids, with the only endemic regions being in the Greater Antilles of the Caribbean, where all types of endemism were found (Fig.19E).

39 Patterns of endemism in Phyllostomidae and Vespertilionidae were the most complex. The Caribbean was an important area of high levels of super- and mixed- endemism for phyllostomids and vespertilionids respectively (Fig. 19F-G). Phyllostomid super-endemism was also found in the Baja California Peninsula, the Chihuahua and Sonora deserts and the Western Cordillera of the Andes of Peru (Fig. 19F). Pacific tropical forests of Mexico, Central America and northern South America showed extensive areas of neo- and mixed-endemism. Phyllostomidae was the only family endemic to the Bolivian Altiplano and the Argentinian Puna, with a contiguous area of mixed-endemism across both. Unique areas of phyllostomid endemism were detected in isolated areas of the Colombian Amazon and the Brazilian Pampa.

Two areas of mixed-endemism were of vespertilionid endemism only: the area comprised by the Guajira Peninsula and , and the temperate forest of southern Andes in Chile and Argentina (Fig. 19G).

Zoogeographic zones of endemism tended to form clusters according to geographic proximity (Fig. 20). In South America, several clusters representing different zoogeographic zones were detected throughout the Andes. Families endemic solely to the Caribbean (i.e. Mormoopidae and Natalidae) presented endemic zones in the Greater Antilles exclusive to each family (Fig. 20C-D). Hence, Haiti and the Dominican Republic grouped together, and Cuba and Jamaica as a separate cluster. Other families also endemic to the Caribbean (i.e. Molossidae, Phyllostomidae and Vespertilionidae) showed a consistent pattern where all Caribbean endemic areas were grouped within a Caribbean cluster and these Caribbean clusters consistently grouped with endemic areas in North America (Fig. 20B, E and F).

Discussion

40 Diversity and endemism analysis across taxa

Niche conservatism is one of the main hypotheses proposed to explain geographical patterns of bat biodiversity in the New World (Pereira and Palmeirim 2013; Olalla‐Tárraga et al. 2016). This hypothesis states that the geographical expansion and cladogenic diversification of taxa will be restricted towards the centre of origin for those groups where several traits of the niche are historically inherited from their ancestor, limiting niche evolution.

To test this, several studies have focused on latitudinal patterns of biodiversity richness across the New World, with contrasting results. Similar to previous findings, our results showed that PD is greater in the tropical and intertropical regions across taxa, following a latitudinal gradient that could be consistent with niche conservatism (Pereira and Palmeirim 2013; Arita et al. 2014). Superfamilies with possible tropical to intertropical origins (i.e. Emballonuroidea and Noctilionoidea; Lim 2008; Arita et al. 2014; Rojas et al. 2016) are not as widespread as Vespertilionoidea, which is present in both tropical and temperate areas of the New World (Pereira and Palmeirim, 2013). This pattern in the distribution of superfamilies could be consistent with a general interpretation of niche conservatism; the presumed tropical origin of emballonuroids and most noctilionoid families would limit the adaptability of these species to more temperate environments and hibernation, promoting the concentration of centres of radiation in the tropical and intertropical region (Pereira and Palmeirim, 2013).

Vespertilionoid PD tended to decrease at higher latitudes, a pattern that appeared to be consistent with those of tropical superfamilies that had higher PD in the tropical and subtropical regions (Appendix Three). Such gradients are difficult to interpret without considering the evolutionary history of the superfamily. Although disputed, the origin of New World vespertilionoids appears to be the result of independent, family-specific events. Natalids and Vespertilionids are thought to have originated in NA from a Eurasian ancestor (Gunnell and Simmons 2005),

41 followed by diversification in NA and the Caribbean. Molossids are thought to have migrated from Africa to the proto-Amazonia of SA, subsequently diversifying there (Ammerman and Lee 2012; Gregorin and Cirranello 2016). The wider geographic range and highest PD in temperate and high-altitude tropical regions for Vespertilionoidea suggest an evolutionary process in which the specialisation in temperate niches could have enabled vespertilionoids to successfully disperse into the Neotropics and temperate SA, using the high-altitude Andes as ecological corridors (Pereira and Palmeirim 2013). Another possible explanation of these results is that PD is higher in these areas because regional took place in more tropical areas of the Neotropics. However, my results do not provide evidence that support this hypothesis, and further studies are needed to test it.

It is worth noting that intra-tropical PD values showed inverse patterns across superfamilies (Appendix Three). Emballonuroid PD is higher towards the Amazonian region and the Guiana Shield, while noctilionoid and vespertilionoid PD is higher towards the western coast of SA and northern and central Andes. Vespertilionoid PD peaks in both tropical SA and southern NA and drops in CA, whereas noctilionoid PD peaks in CA and decreases in southern NA (i.e. Mexico). These patterns cannot be expected to be a result of niche conservatism and, instead, it has been suggested that competition between superfamilies could have been a powerful driver of geographical patterns of bat diversity in the New World (Pereira and Palmeirim 2013).

Insectivory is the most common dietary adaptation in New World bats, being predominant in all vespertilionoid and emballonuroid families, the noctilionoid families Mormoopidae, Furipteridae, and Thyropteridae, as well as some phyllostomid species (Dumont 2007; Santana et al. 2012; Dumont et al. 2014). Such high diversity of insectivorous species could have saturated available niches, leading to resource partitioning and distributional exclusion to avoid competition (Bloch et al. 2011; Lima-Ribeiro et al. 2013; Formoso et al. 2015; Prufrock et al. 2016).

42 Vespertilionid PD is unevenly distributed across the Americas, with a disproportionate concentration of diversity in NA. Peaks of PD are found across the Andes and the Brazilian Pampa, regions that include ecosystems with temperate- like climates where vespertilionids could potentially find similar conditions to those in their temperate centres of origin (Pereira and Palmeirim 2013). Mormoopid and natalid PD is heavily concentrated in the Caribbean, suggesting that these families might have colonised and diversified in the Caribbean before migrating towards SA (Lewis-Oritt et al. 2001; Dávalos 2005; Pavan and Marroig 2016). New World families of putative tropical origin (Emballonuridae, Molossidae and Phyllostomidae; Lim 2008; Arita et al. 2014) show similar latitudinal patterns of diversity that tend to support the concept of niche conservatism (Arita et al. 2014) (i.e. high concentration of PD near their centre of origin).

Comparing the intertropical distribution of PD across insectivorous families reveals similar trends to those observed for superfamilies (i.e. geographical partitioning of insectivorous family diversity possibly reducing competition). Such trends at both taxonomical levels suggests a scenario where a general interpretation of niche conservatism could be considered because it corresponds to the distribution of New World bats in a wider geographical context, and that more specific patterns are the result of more complex evolutionary processes (Rodríguez and Arita 2004; Stevens 2011). Insectivorous families of putative tropical origin are highly diverse in the intertropical region, but their diversity appears to be partitioned in a way that would be predicted by the evolutionary tendency to avoid niche overlapping and ecological competition (Pereira and Palmeirim 2013). Moreover, vespertilionid PD in tropical SA is disproportionately lower, compared with its North American PD, possibly as a result of competitive displacement with tropical insectivorous families that were established in the region well before vespertilionids colonised SA (Cione et al. 2003; Dávalos and Russell 2012; Pereira and Palmeirim 2013; Soto-Centeno and Steadman 2015; Metcalf et al. 2016).

This restricted interpretation of niche conservatism in New World bats has been previously supported by other studies. Arita et al. (2014) found specific latitudinal

43 gradients in genus richness and endemism and suggested that not only do they obey niche conservatism but also that several New World bat families have dual centres of diversification. Pereira and Palmeirim (2013) concluded that latitudinal gradients in New World bat diversity could not be completely explained by niche conservatism alone, emphasising evolutionary history differences between tropical and temperate clades, and suggested that competitive displacement could have played an important role in New World bat evolution.

Additional key evidence of the limited extent of niche conservatism is in our results for PE. Emballonuroidea exhibits areas of high endemism across the Americas. The Amazonia and the Guiana Shield harbour a high PE, corresponding with PD values. High endemism of noctilionoids and vespertilionoids in the Caribbean reflects the evolutionary history of families Mormoopidae and Natalidae respectively. High PE in CA and southern NA across all superfamilies reflects the importance of the Panamanian Realm during the evolution of New World bats, regardless of their putative origin (Arita et al. 2014). Previous studies provided evidence for the importance of the Panamanian Realm during the diversification of phyllostomids (Arita et al. 2014; Rosauer and Jetz 2015; Rojas et al. 2016), and our results extend its importance to all three New World bat superfamilies and the order as a whole.

Analysing PE for each family provides additional information about the mechanisms shaping its biogeographical distribution. Natalids and mormoopids are highly endemic to the Caribbean, reflecting the historical importance of the Caribbean for the radiation and colonisation of the continental representatives of these families (Arita et al. 2014; Rosauer and Jetz 2015). Another important finding from our results is the spatial clustering of endemic areas in the Pacific coast of the Americas. High endemism in this area was found for emballonurids, molossids, phyllostomids and vespertilionids, suggesting that endemism of New World bats responds to abiotic variables, rather than ecological factors (Estrada-Villegas et al. 2012; Yu et al. 2014; Shi and Rabosky 2015). Some of these abiotic drivers could be precipitation and rainfall, which have been identified as being correlated with the

44 diversification of New World bat species (Marchan‐Rivadeneira 2012), and are particularly high on the Pacific coast of SA and CA, especially in the biogeographic Chocó (tropical SA), a region with the highest historical rainfall regimes in SA (Poveda et al. 2004).

Testing the statistical significance of PD showed trends common to most families; observed PD was significantly low at the higher latitudinal limits of familial distributions, and significantly high in the tropics (with the exception of emballonurids). However, these areas of significantly high PD do not cover the entire Neotropics, only between 1-20% depending on the family. Significantly low PD can represent phylogenetic clustering under two different scenarios: 1) elevated concentrations of derived species resulting from recent diversification processes; or 2) conservative evolutionary habitat filtering which favors the prevalence of closely-related taxa that share an advantageous trait, and disfavors the presence of other taxa. Areas with significantly high PD found for vespertilionoid and noctilionoid families in South America suggest a greater representation of distantly related taxa. This could be interpreted as indicative of historical refugia or as a ‘mixing-pot’ where a phylogenetically heterogeneous local fauna (as a consequence of ecological exclusion of closely related taxa) could have converged with recent migrants (Mishler et al. 2014; González-Orozco et al. 2015; Nagalingum et al. 2015; Schmidt-Lebuhn et al. 2015).

At family level, the results were strikingly different from those for the order. This indicates that, in order to better understand patterns of endemism in New World bats, it is necessary to work at the taxonomic level that better reflects both differences between and similarities within taxa, and their evolutionary history. Although significantly low PD was evident at the distributional limits of all families, additional areas were identified for each family. It is important to note that PD was significantly low for natalids across their entire continental distribution. Current understanding of natalid evolutionary history does not support a scenario of recent diversification on the mainland, further suggesting that the modern distribution of natalids resulted from evolutionary habitat filtering that favoured continental

45 colonisation by the lineage (Dávalos 2005; Lim 2009; Arita et al. 2014; Mishler et al. 2014).

Emballonuridae exhibits areas of significantly high endemism across the Americas. The rainforests of CA and the Pacific coast of SA host a significantly high level of PE, consistent with their PD values. High endemism in the Caribbean reflects the insular diversification of families Mormoopidae and Natalidae, supporting the hypothesis of a subsequent southward migration to South America (Dávalos 2005, 2006; Arita et al. 2014). High PE in Central America and southern North America across all families reflects the importance that the Panamanian Realm had as a cradle for adaptive radiation during the evolution of New World bats, regardless of their putative origin. Previous studies provided evidence suggesting that the Panamanian Realm was an important area of speciation during the diversification of phyllostomids (Arita et al. 2014). Based on our results we suggest that this finding can be extended to the diversification processes of all three New World bat superfamilies.

Analysing the significance of PE in each family provides additional evidence of the historical events that shaped their modern distribution. Natalids and mormoopids are highly endemic in the Caribbean, reflecting a Caribbean centre of diversification in the Antilles followed by a radiation and colonisation of South America by some representatives of these families (Dávalos 2005, 2006). One important finding from our results is the spatial clustering of endemic areas in the Pacific coast of the Americas. High endemism in this area was found for emballonurids, molossids, phyllostomids and vespertilionids, suggesting that endemism of New World bats responds to both biotic and abiotic variables associated with altitudinal gradients (Velazco and Patterson 2013; Aguirre et al. 2016). These abiotic drivers could include precipitation and rainfall, which have been identified as being correlated with the diversification of bats (Lars et al. 2010; Stoffberg et al. 2012). Bat diversity is particularly high in the Pacific coast of South America and Central America, especially in the biogeographic Chocó (tropical SA),

46 a region with some of the highest historical rainfall regimes in South America (Poveda et al. 2006; Grimm and Tedeschi 2009).

Areas of significantly high RPD represent areas with greater than expected concentrations of long branches of a tree. Such unpredicted accumulation of long branches indicates the presence of relictual taxa, possibly as a result of historical range reduction processes or as survivors of local extinction events (Thornhill et al. 2016). Low RPD, on the other hand, characterises areas with an unexpectedly high concentration of taxa representing short branches of a tree. This may indicate diversification events resulting from recent adaptive radiations (Thornhill et al. 2016).

Low RPD and PD were found in the Yucatan Peninsula for families Emballonuridae, Natalidae and Vespertilionidae. These results suggest that the Yucatan Peninsula was the scene of recent diversification in these families, and that the species present are related as a result of recent speciation. This interpretation is supported by our CANAPE results that identify neo- and mixed- endemic areas in the same region. The Yucatan Peninsula has been characterised as having a particularly high concentration of endemic biota that are part of a unique ecosystem different from other similar tropical ecosystems, such as the tropical deciduous forests of the western Sierra Madre (Manrique et al. 2003; Alonso et al. 2013).

Low mormoopid RPD in the central Andes, the Brazilian Cerrado, the Caribbean and Central America also coincides with low values of PD, suggesting an early diversification event for the family in these regions. Our results underscore recent findings that have revised the of the mormoopid genus Pteronotus and suggested a greater diversity than expected, with the number of species in the genus raised from six to 16 (Pavan and Marroig 2016). The proposed distributions of some of these newly recognised species match areas of low RPD and PD we detected on both the mainland and the Caribbean, supporting a scenario of phylogenetic clustering as a result of recent diversification processes.

47 Noteworthy areas of high RPD were evident only for molossids, phyllostomids and vespertilionids. For molossids, the Baja California Peninsula and the central Andes had higher concentrations of long branches than expected. Both regions host more deep-rooted taxa than expected, suggesting that they represent refugia ( González-Orozco et al. 2014, 2015) for this family. Additionally, based on the CANAPE results, the central Andes and Pacific coast of South America are also the most significant areas of molossid palaeo-endemism, supporting a refugia hypothesis inferred by the RPD analysis. Most of the species present in these regions represent long branches that could have gone through historical range reductions to the point where each was restricted to its modern distribution (Penone et al. 2016).

The xeric shrublands of southern North America also comprise an important area of high phyllostomid and vespertilionid RPD. This pattern might be explained differently for each family. Phyllostomids, on one hand, have major areas of endemism across southern North and Central America. In particular, super- endemism was heavily concentrated in the Sonoran and Chihuahuan deserts in southern USA and northern Mexico. As noted above for other families, this congruence between RPD and CANAPE suggests the areas represent historical refugia for ancestral taxa (Thornhill et al. 2016). Vespertilionids, on the other hand, showed endemic areas in the Sonora desert only. One explanation could be that, instead of these areas being refugia for ancestral taxa, short branches of the vespertilionid tree could have disappeared from these regions as a result of selective local extinctions (Mishler et al. 2014). Long-branched lineages that colonised these ecosystems earlier could be better adapted to subsequent biotic or abiotic fluctuations in the region. This hypothesis is of special interest considering the geological age of the Chihuahuan desert and the historical environmental changes during the Pleistocene, when cycles of high precipitation alternated with cycles of desertification (Chavez-Lara et al. 2012).

48 Delimitation of zoogeographical zones of New World bats

Comparing values of PD and PE (from the previous section) with the zoogeographic zones depicted across families (current section), it is clear that regionalisation reflects patterns of PD more than patterns of PE. Temperate zoogeographic zones correspond with areas where only families Molossidae, Phyllostomidae and Vespertilionidae are present. This temperate America cluster has been identified in previous studies, and cannot be considered a zoogeographic zone in the sense that a biogeographic region can only be identified if obeys the principle of spatial continuity (Procheş 2005). Rather, this temperate cluster found across these families suggests two possible interpretations: 1) that each temperate zone should be interpreted as an independent zoogeographic zone and that these temperate zones converge in phylogenetic diversity composition, or 2) that spatial continuity is not as important as biological composition and phylogenetic similarity when delimiting zoogeographic zones.

Our results not only support previous findings of biological similarity between temperate areas in the Americas (Procheş and Ramdhani 2012; Holt et al. 2013), but they also reveal a general pattern where the limits of the geographic range of a family are more similar to each other than to any other area where the family is present, regardless of their latitudinal separation. The fact that this pattern is found for all families with broad distributions emphasises that there are strong environmental variables behind this trend that affect all taxa equally, irrespective of their natural history or centres of origin (Procheş 2006; Holt et al. 2013).

The southern limit in the distribution of some families (i.e. Molossidae, Phyllostomidae and Vespertilionidae) coincides with the Andean zoogeographic region in SA. The validity of this region has been debated, some studies including it within the Neotropical region and others keeping it as an isolated region. For the three bat families distributed in this region, the Andean region always clustered with the Nearctic region, separate from the Neotropical region. This pattern

49 suggests that for New World bats the southern Andes represent an independent region with a specific faunal composition and abiotic characteristics, compared with the rest of SA.

Clustering of the Caribbean with NA supports previous findings of world zoogeographic zones for bats (Procheş 2005, 2006). Although our results differ across families, the Caribbean consistently constituted an independent cluster within a larger cluster containing NA and temperate SA. Studies analysing phytogeographic and zoogeographic regionalisation have not considered the Caribbean as an independent zoogeographic zone, it commonly being associated with CA. Procheş (2005) suggested that the Caribbean may represent a unique biological composition within the Neotropics, and that this area does not reflect strong biological similarity with CA and tropical SA and NA. In our results the Caribbean always clustered with temperate and non-tropical areas, and appears to represent a distinct zoogeographic zone, especially considering the habitat differences between the areas that form this cluster (Iturralde-Vinent and MacPhee 1999; Procheş 2005; Dávalos 2010; Ali 2012; Matos-Maraví et al. 2014).

The Neotropical region has been described as a zoogeographical zone that includes all the continental land area from southern NA to temperate SA (da Rocha et al. 2015). Two subregions have been designated for this zone; the Central American subregion and the La Plata subregion (Procheş and Ramdhani 2012; Holt et al. 2013; Mishler et al. 2014). For all families studied both regions are recognised as independent zones, but they group with the Neotropical region as part of a super-cluster. Since the degree of dissimilarity between the regions included in this super-cluster varies among families, a cautious interpretation of our results would support this super-cluster as the Neotropical region, including both subregions.

Finally, the regionalisation of the distribution of the family Vespertilionidae provides evidence that supports the extension of the Palearctic realm to the northern part of the Western Hemisphere (Hawkins et al. 2012; Holt et al. 2013; Rueda et al. 2013). Based on the vespertilionid regionalisation of its distribution, the phylogenetic 50 dissimilarity between the Nearctic region and the proposed Palearctic region is the same as that between the Nearctic and the Andean and Caribbean regions. Considering the environmental differences between these three regions (Holt et al. 2013; Morrone 2015), it is possible to argue that the northernmost part of NA is in fact part of the Palearctic realm, traditionally considered to be limited to the Eastern Hemisphere (Holt et al. 2013).

CANAPE

Using CANAPE we tested the statistical significance of the spatial distribution of endemism, and deconstructed it into different categories of endemism. Across families and at the ordinal level, high concentrations of statistically significant endemism were detected in three main areas of the New World: the Panamanian Realm, the Caribbean, and the Pacific coast of South America. These findings are supported by our results for the randomisation analysis of PD, PE, RPD and RPE. Our data also supports evidence provided by Arita et al. (2014) for dual centres of diversification for Emballonuridae, with super-endemic areas in both South America and southern North America. As evidenced by the endemic genus Balantiopteryx, a minor southern North American emballonurid radiation has been proposed, compared to the major radiation in northern South America (Arita et al. 2014). However, we found palaeo-, mixed- and super-endemic areas were located within the Panamanian Realm, which suggests that, although emballonurids have a putative tropical origin, dual radiations in tropical South and North America could have occurred (Arita et al. 2014).

As noted above, families Mormoopidae and Natalidae are the only families exclusively endemic to the Caribbean. Palaeo-, mixed- and super-endemic cells were detected for these families in Cuba, Jamaica, Haiti, Dominican Republic and Puerto Rico. Several studies support the idea of a land bridge connecting the

51 Greater Antilles with continental America (i.e. GAARlandia) for a 1-2 million interval around the Eocene-Oligocene boundary (c. 30-34 Ma) (Ali 2012; Weaver et al. 2016).

This connection provided an opportunity for a wide variety of lineages to colonise and diversify in different ecosystems across the complex of islands (Ali 2012). Given the antiquity and relatively long duration of GAARlandia, many cladogenic events potentially occurred as migrant taxa diverged from their putative continental ancestral populations (Ali 2012; Říčan et al. 2013; Esposito et al. 2015; Weaver et al. 2016). Subsequently, long-lasting isolation from the mainland from the Oligocene onwards limited geographic distribution of these populations. As a result, the Caribbean islands have been a cradle of unique biodiversity, with among the highest levels of endemism in the world (Rosauer and Jetz 2015; Cano-ortiz et al. 2016; Cervantes et al. 2016; Crews and Yang 2016). This, in consequence, might have resulted in distinctive faunal and floral composition of Caribbean ecosystems, where both mormoopids and natalids specialized and diversified to fill empty niches in these unique ecosystems (Dávalos 2004). However, as Dávalos (2004) has pointed out, Caribbean mammal diversity at the ordinal level shows patterns that cannot be explained by GAARlandia, and further studies should be family specific.

Considering their relatively high species diversity and wide distribution, New World molossids are of great interest to biogeographers (Gregorin and Cirranello 2016). It has been argued that New World molossids have African ancestors and colonised South America as a result of a sweepstakes migration across the Atlantic during the early Oligocene (Arroyo-Cabrales et al. 2002; Lim 2009; Gregorin and Cirranello 2016). Analysis of modern patterns of diversity indicates that tropical South America is the centre of diversification of New World molossids, and that some of these taxa are endemic to the Neotropics of South America (Arita et al. 2014). Our CANAPE results contradict this traditional interpretation, and suggest a scenario of multiple centres of diversification for molossids across the New World. As suggested by tropical niche conservatism, wide areas of all kinds of endemism

52 throughout South America (especially the palaeo-endemic area on the Pacific coast) support the idea of South America being the first centre of diversification for this family (Stevens 2011; Pereira and Palmeirim 2013; Olalla-Tárraga et al. 2016). Nonetheless, the presence outside South America of palaeo- (i.e. Central America) and mixed-endemism (i.e. northern North America and the Greater Antilles) suggests the possibility of additional centres of endemism. Moreover, palaeo- endemism in Central and North America also suggests that the northward migration of molossids could have occurred earlier than thought, supporting the idea that GABI does not explain patterns of modern molossid biodiversity (Arita et al. 2014).

Similar conclusions can be drawn from the results obtained for the family Phyllostomidae. The presence of significant areas of all kinds of endemism in Central and North America not only support the “dual centre hypothesis” postulated by Arita et al. (2014) but also argue against GABI as a model to explain the modern distribution of phyllostomids. Combined palaeo- and neo-endemism in this area could imply that modern phyllostomid diversity is the result of multiple geological and biological processes during the Cenozoic. Areas of palaeo- endemism corresponded with the occurrence of taxa with restricted distributions such as species of the subfamilies Macrotinae and Glossophaginae (Rojas et al. 2016). Neo-endemic areas, on the other hand, suggest recent divergence of species such as Artibeus hirsutus, Choeronycteris mexicana and Musonycteris harrisoni. This array of endemism outside the putative South American centre of origin coincides with the proposed historical distributions of the MRCA of several phyllostomid lineages. Rojas et al. (2016) concluded that the MRCA of the subfamilies Macrotinae and Carolliinae could have had a Central to North American distribution, a conclusion in part supported by our results CANAPE.

It is worth noting that the xeric ecosystems of southern North America (i.e. the Baja California, Sonora and Chihuahuan deserts) hosted the most extensive super- endemic areas for emballonurids and phyllostomids, evidence that these ecosystems played an important role during the evolution of both families (Penone

53 et al. 2016). The MRCA of the subfamily Glossophaginae and subtribe Stenodermatina is thought to have had an Antillean distribution (Rojas et al. 2016) and the super-endemic Caribbean areas we detected probably reflect that history. Concentration of endemism in the Andean region indicates that this area played an important role by providing refugia for long-branched taxa (e.g. palaeo-endemism of Lonchophylla, Platalina, Rhinophylla, Vampyressa and Vampyrodes), and as the centre of recent speciation of short-branched taxa (i.e. neo-endemism of Artibeus, Platyrrhinus and Sturnira) (Arita et al. 2014; Rojas et al. 2016).

Vespertilionid neo-endemism in the Yucatan Peninsula corresponds to the presence of species Corynorhinus mexicanus and Rhogeessa aeneus (Roehrs et al. 2010). The Baja California desert is another large area of mixed endemism. Several species of Lasiurus and Myotis are neo-endemic to this desert, whereas M. peninsularis and M. vivesi are palaeo-endemic (Stadelmann et al. 2007). The significant endemic areas in the tropical and coniferous forests of the Pacific coast of Mexico and Central America portrait a cradle of mixed endemism in Rhogeessa (e.g. R. allena, R. genowaysi, R. gracilis and R. mira). South American areas of vespertilionid endemism are particularly interesting because they contradict the idea that North America was the only centre of diversification for vespertilionids in the New World, opposing previous studies (Arita et al. 2014). Species of Histiotus, Lasiurus and Myotis are endemic to the southern Andes (e.g. H. macrotus, L. varius, M. aelleni and M. chiloensis), implying that diversification in this family has taken place outside North America. Moreover, this region was significant for more than one type of endemism, meaning that modern levels of endemism are the result of separate events (i.e. Myotis species are probably palaeo-endemic, whereas L. varius and H. macrotus are likely neo-endemic). Our results provide evidence to suggest that the “dual centre hypothesis” could explain the patterns of diversification in this family.

Our clustering analysis of significantly endemic cells revealed geographic structuring of the phylogenetic similarity between areas of endemism. A common trend reflecting latitudinal gradient was detected for most families. Phylogenetic

54 similarity between endemic areas tended to be higher towards the Neotropics, and to decrease as latitude increased. An example is the grouping of vespertilionid temperate endemic areas into a single cluster, and the tropical endemic areas grouped in a different isolated cluster (Fig. 25F). For those families with endemic centres in both continental and insular New World, Caribbean clusters consistently grouped with North American endemic areas. A possible interpretation of these results is that the processes behind patterns of endemism in the Caribbean and North America for these families (i.e. Molossidae, Phyllostomidae and Vespertilionidae) reflect a similar evolutionary history in these regions. Combined, these results seem to reflect biogeographic regionalisation of the New World; temperate clusters represent the Nearctic and Palearctic zones, whereas the tropical clusters represent the Neotropical zone (equivalent to the Panamanian Realm).

Implications for understanding of the fossil record and the evolutionary history of New World bats

Although the participation of bats in the GABI has not been directly tested, based on the fossil record of both North and South America it has been suggested that the GABI was a three-phase event for bats (Morgan and Czaplewski 2012). As posited by Morgan and Czaplewski (2012), the first phase was a Plio-Pleistocene migration of both vespertilionoid and noctilionoid bat species (southward and northward, respectively). Evidence for this includes Pliocene fossils of Desmodus and Eumops found in North America, as well as several Pleistocene records of natalids and mormoopids in South America. The second phase involves the interruption of bat migration across the Americas during the Late Miocene, during which time an important aquatic barrier has been suggested. Finally, a third wave includes a southward Oligocene- migration wave into South

55 America, although no additional evidence for this phase has been identified from non-volant mammal groups (Morgan and Czaplewski 2012).

Our results provide indirect evidence that may lend support to both migration waves. Presence of vespertilionid palaeo-endemic areas in SA suggests early diversification of vespertilionid taxa in the region, which could also imply early migration events. Similar conclusions may be drawn by the presence of phylllostomid neo- and palaeo-endemic areas in North America, supporting a Pleistocene northward migration of Desmodus and other genera. Additionally, the presence of palaeo-endemic areas for Emballonuridae, Molossidae and Phyllostomidae suggest that these families might have colonised NA earlier than current understood.

56

Figure 2. Family-level spatial patterns of PD of New World bat families. Emballonuridae (A), Molossidae (B), Mormoopidae (C), Natalidae (D), Phyllostomidae (E), Vespertilionidae (F).

57

Figure 3. Geographical distribution of statistical significance of family-level PD of New World bats. Order Chiroptera (A), Emballonuridae (B), Molossidae (C), Mormoopidae (D), Natalidae (E), Phyllostomidae (F) and Vespertilionidae (G).

58

Figure 4. Scatterplot of empirical family-level PD values and significance values of PD obtained from the randomization analysis.

59

Figure 5. Geographical distribution of statistical significance of family-level RPD of New World bats. Order Chiroptera (A), Emballonuridae (B), Molossidae (C), Mormoopidae (D), Natalidae (E), Phyllostomidae (F) and Vespertilionidae (G).

60

Figure 6. Family-level spatial patterns of PE of New World bat families. Emballonuridae (A), Molossidae (B), Mormoopidae (C), Natalidae (D), Phyllostomidae (E), Vespertilionidae (F).

61

Figure 7. Geographical distribution of statistical significance of family-level PE of New World bats. Order Chiroptera (A), Emballonuridae (B), Molossidae (C), Mormoopidae (D), Natalidae (E), Phyllostomidae (F) and Vespertilionidae (G).

62

Figure 8. Scatterplot of empirical family-level PE values and significance values of PD obtained from the randomization analysis.

63

Figure 9. Geographical distribution of statistical significance of family-level RPE of New World bats. Order Chiroptera (A), Emballonuridae (B), Molossidae (C), Mormoopidae (D), Natalidae (E), Phyllostomidae (F) and Vespertilionidae (G).

64

Figure 10. Multi-family spatial patterns of PD (A) and PE (B) of New World bats.

65

Figure 11. Bootstrapping hierarchical clustering analysis of PD and PE of New World bat families. Statistically significant clusters retrieved from 1000 iterations are highlighted in squares. Emballonuridae (Emb), Molossidae (Mol), Mormoopidae (Mor), Natalidae (Nat), Phyllostomidae (Phy) and Vespertilionidae (Ves).

66

Figure 12. Zoogeographical regions for New World bat families identified for each corresponding cluster. Emballonuridae (A), Molossidae (B), Mormoopidae (C), Natalidae (D), Phyllostomidae (E), Vespertilionidae (F).

67

Figure 13. Geographical distribution of statistically significant centres of endemism of New World bats. Order Chiroptera (A), Emballonuridae (B), Molossidae (C), Mormoopidae (D), Natalidae (E), Phyllostomidae (F) and Vespertilionidae (G).

68

Figure 14. Clustering analysis of phylogenetic similarity across statistically significant centres of endemism of New World bats. Emballonuridae (A), Molossidae (B), Mormoopidae (C), Natalidae (D), Phyllostomidae (E) and Vespertilionidae (F).

69 CHAPTER 4

70

SUMMARY OF FINDINGS

This thesis has explored aspects of the Cenozoic evolutionary history of South

American mammals, and in particular extinction in the marsupial order

Sparassodonta and diversity, endemism and phylogeography in the placental order

Chiroptera.

Chapter 1 provided a short introduction to the thesis and its contents.

In Chapter 2, multivariate statistical modelling of data from the fossil record proved to be a useful way to test alternative hypotheses about the causes of mammal extinctions. In spite of bias inherent in the fossil record, this study supports the hypothesis that the extinction of sparassodontans may have been the result of deep-time non-competitive interactions and to a lesser degree environmental factors. Diversity loss and eventual demise of the sparassodontans was a gradual process that followed family-specific patterns which changed over time. After testing four competing hypotheses to explain this extinction, non-competitive ecological interactions could not be rejected, which supports the assumption that there was a correlation between sparassodontan extinction and the diversity of other mammal groups over time. Statistical models were congruent and highlight the importance of seeking to understand the reasons for extinction within a framework of diverse ecological variables. Sensitivity analysis and Path Analysis

71 identified specific predictors within the models as the most relevant, such as the potential role of native South American ungulates and African migrants in driving or precipitating sparassodontan extinction. The results suggest that didelphimorphians probably also played a role in this process.

Post-Eocene sparassodontan beta diversity increased, indicating that this guild of marsupial carnivores was relatively unstable over time. Deconstruction of beta diversity into turnover and nestedness provided further insights into intraordinal dynamics and indicates that most significant component was turnover. Because turnover tended to increase with richness, it suggests that intraguild interactions may have contributed to the replacement and instability of genera over time.

The models developed here explored a range of diverse biological and environmental variables in order to assess the probability that any particular one or combination was most likely to have been involved in the extinction of the sparassodontans. Although the analysis produced some highly significant results, to increase confidence that this process has indeed identified the most important factors driving sparassodontan extinction, inclusion of more early to mid Cenozoic sites from the Neotropics of South America will be important.

As illustrated in Chapter 3, regionalisation analysis based on phylogenetic diversity

(PD) and phylogenetic endemism (PE) of a specific group is an insightful tool that allows investigation of macro-ecological interactions within that group, accounting for the evolutionary history shared by its members. This study is the first comprehensive analysis of phylogenetic diversity and endemism for the order

72 Chiroptera. Families are used as taxonomic units in a novel application of phylogenetic measures of biodiversity at infraordinal levels to investigate the evolutionary history of New World bats. This was found to be particularly useful considering that the assembly of this bat fauna resulted from a series of migrations from different continents throughout the Cenozoic.

Most bat families followed a latitudinal diversity gradient, with PD and PE gradually increasing at lower latitudes. The Neotropics harbours the highest bat evolutionary diversity across the New World. Vespertilionidae was the only family showing a different pattern, with the highest values of PD found in North America. This may be associated with the temperate niche to which vespertilionids adapted during their evolutionary history in NA, in contrast with the tropical niche conservatism hypothesis applicable to other New World bat families. As a result, my results support the hypothesis that the geographic distribution of PD and PE follows patterns that seems to agree with niche conservatism. Contrary to my hypothesis of family-specific patterns of regionalisation, biogeographic regionalisation was consistent across families and corresponded with other biogeographic studies that found similar biogeographic zones (i.e. Nearctic, Neotropical) for other taxonomic groups. Bat families with wider distributions (e.g. Molossidae, Phyllostomidae and

Vespertilionidae) showed other biogeographic zones (e.g. Andean and Caribbean zones). Vespertilionid regionalisation found here confirms previous studies arguing for extension of the Palearctic biogeographic zone into the northernmost part of the

New World.

73 The statistical framework developed for CANAPE (categorical analysis of neo- and palaeo-endemism) was for the first time implemented to assess the statistical significance of phylogenetic values of biodiversity of New World bats. Using this analysis, it was possible for key evolutionary theories to be tested and compared.

The diversification of New World bats was examined within a geological and ecological framework. This allowed a better understanding of the relative importance of specific events, such as the rifting of South America from

Antarctica and the Neogene formation of the Isthmus of Panama.

The results support the “dual centre of diversification” hypothesis as a model to explain the evolutionary history of the bat families Emballonuridae, Mormoopidae and Phyllostomidae in the New World, as suggested by Arita et al. (2014). They also suggest that this same model can shed light on the evolution of molossids and vespertilionids, hence extending this hypothesis to the diversification of lineages in all New World bat superfamilies. The Great American Biotic Interchange does not appear to explain the presence of centres of diversification in both South and North

America for five of the nine New World bat families, suggesting that before the formation of the Isthmus of Panama, the Central American Seaway did not represent a geographic barrier that prevented latitudinal migration across the

Americas. The results of the study suggest that the Andes acted as a centre of diversification and refugia for some vespertilionid species and were important during the evolution of South American bat families overall. Phylogenetic similarity across significant endemic zones followed the broader biogeographic regionalisation of the New World.

74 Nevertheless, given the high dispersal capacity of bats, and in order to better understand their evolution in the New World, an analysis of global bat diversity and endemism is recommended, particularly based on updated phylogenies including recently described taxa and new taxonomic rearrangements. Implementing

CANAPE methodology to study patterns of endemism for South American mammals more broadly would no doubt reveal further information about evolutionary histories. By comparing lineages of different origins and endemism in taxa with different centres of diversification, interesting new hypotheses could be generated and tested.

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130 APPENDICES

131

APPENDIX 1

South American Cenozoic mammal genera compiled for this of study. †, extinct taxon; SA, South American; NA, North American.

171

Locomotor Infraclass Order Family Genus Origin Trophic guild habit Incertae sedis Incertae sedis Lophiodolodus† SA Scansorial Gondwanatheria Sudamericidae † SA Insectivore Scansorial Epanorthidae Callomenus† SA Arboreal Epanorthus† SA Herbivore Arboreal Metatheria Incertae sedis Jaskhadelphydae Jaskhadelphys† SA Scansorial Protodidelphidae Carolocoutoia† SA Omnivore Scansorial Guggenheimia† SA Omnivore Scansorial Periprotodidelphis† SA Omnivore Scansorial Protodidelphis† SA Omnivore Scansorial Zeusdelphys† SA Omnivore Scansorial Sternbergiidae

172

Didelphopsis† SA Omnivore Scansorial Pediomyidae Monodelphopsis† SA Omnivore Scansorial Didelphimorphia Incertae sedis Szalinia† SA Omnivore Scansorial Peradectidae Caroloameghinia† SA Omnivore Scansorial † SA Omnivore Scansorial Procaroloameghinia† SA Omnivore Scansorial Derorhynchidae Derorhynchus† SA Omnivore Scansorial Pucadelphydae Andinodelphys† SA Omnivore Scansorial † SA Omnivore Scansorial Didelphidae Caluromys SA Omnivore -Carnivore Scansorial Caluromysiops SA Omnivore-Carnivore Scansorial Chironectes SA Omnivore-Carnivore Amphibious Coona† SA Omnivore-Carnivore Scansorial Didelphis SA Omnivore-Carnivore Scansorial Eobrasilia† SA Omnivore Scansorial Gaylordia† SA Omnivore-Carnivore Scansorial Gracilinanus SA Omnivore-Carnivore Scansorial Hyperdidelphys† SA Omnivore-Carnivore Scansorial Incadelphys† SA Omnivore-Carnivore Scansorial Ischyrodidelphis† SA Omnivore-Carnivore Scansorial 173

Lestodelphys† SA Omnivore-Carnivore Scansorial Lutreolina SA Omnivore-Carnivore Scansorial SA Carnivore Scansorial Marmosops SA Omnivore-Carnivore Scansorial Marmosopsis† SA Omnivore Scansorial Metachirus SA Omnivore-Carnivore Scansorial Micoureus SA Insectivore-Carnivore Scansorial Minusculodelphis† SA Omnivore Scansorial Monodelphis SA Insectivore Scansorial Paradidelphys† SA Omnivore-Carnivore Scansorial Philander SA Omnivore-Carnivore Scansorial Sairadelphys† SA Omnivore-Carnivore Scansorial SA Omnivore-Carnivore Scansorial Thylatheridium† SA Insectivore-Carnivore Scansorial Thylophorops† SA Omnivore-Carnivore Scansorial Tiulordia† SA Omnivore-Carnivore Scansorial Xenodelphis† SA Omnivore-Carnivore Scansorial Zygolestes† SA Insectivore-Carnivore Scansorial Caluromyopsis SA Herbivore Arboreal Chacodelphys SA Insectivore Ground Dwelling Cryptonanus SA Omnivore Scansorial Glironia SA Omnivore Scansorial Hyladelphys SA Insectivore-Omnivore Arboreal Mayulestidae † SA Carnivore Scansorial Sparassocynidae Sparassocynus† SA Carnivore Scansorial 1 74

Hesperocynus† SA Carnivore Scansorial

Polydolopimorphia Incertae sedis Bobbschaefferia† SA Omnivore Scansorial Chulpasia† SA Omnivore Scansorial Cocatherium† SA Omnivore Scansorial Hondonadia† (= Pascuadelphys) SA Omnivore Scansorial Wamradolops† SA Omnivore Scansorial Argyrolagidae Argyrolagus† SA Omnivore Saltatorial Hondalagus† SA Omnivore Scansorial Klohnia† SA Omnivore Scansorial Microtragulus† SA Omnivore Scansorial Proargyrolagus† SA Omnivore Scansorial Bonapartheriidae Bonapartherium† SA Omnivore Scansorial Epidolops† SA Omnivore Scansorial Polydolopidae Amphidolops† SA Omnivore Scansorial Eudolops† SA Omnivore Scansorial Polydolops† SA Omnivore Scansorial Seumadia† SA Omnivore Scansorial Prepidolopidae Incadolops† SA Omnivore Scansorial Prepidolops† SA Omnivore Scansorial 175

Sillustanidae Roberthoffstetteria† SA Omnivore Scansorial Sillustania† SA Omnivore Scansorial Incertae sedis Bardalestes† SA Omnivore Ground Dwelling Evolestes† SA Omnivore Scansorial Riolestes† SA Omnivore Scansorial Caenolestidae Perulestes† SA Insectivore Scansorial Pliolestes† SA Insectivore Scansorial Caenolestes SA Insectivore Ground Dwelling Lestoros SA Insectivore-Omnivore Scansorial Rhyncholestes SA Insectivore-Herbivore Groeberiidae Groeberia† SA Omnivore Scansorial Palaeothentidae Abderites† SA Frugivore Scansorial Palaeothentes† SA Omnivore Scansorial Parabderites† SA Frugivore Scansorial Sasawatsu† SA Omnivore Scansorial Hondathentes† SA Omnivore Scansorial Pichipilidae Pichipilus SA Omnivore Scansorial Sparassodonta Incertae sedis Hondadelphys† SA Carnivore Scansorial 176

Patene† SA Carnivore Scansorial Stylocynus† SA Carnivore Scansorial Ground Dwelling- † SA Carnivore Cursorial Borhyaenidae Acrocyon† SA Ground dwelling Allqokirus† SA Omnivore Scansorial Angelocabrerus† SA Hypercarnivore Scansorial Arctodictis† SA Hypercarnivore Ground dwelling Argyrolestes† SA Hypercarnivore Scansorial Australohyaena† SA Hypercarnivore Scansorial Ground Borhyaena† Hypercarnivore dwelling- SA Cursorial Callistoe† SA Hypercarnivore Scansorial Dukecynus† SA Hypercarnivore Scansorial Eutemnodus† SA Hypercarnivore Scansorial Fredszalaya† SA Hypercarnivore Scansorial Nemolestes† SA Hypercarnivore Scansorial Plesiofelis† SA Hypercarnivore Scansorial Prothylacynus† SA Hypercarnivore Ground dwelling Pseudolycopsis† SA Hypercarnivore Scansorial Pseudothylacynus† SA Hypercarnivore Scansorial Simpsonia† SA Mesocarnivore Scansorial Hathliacynidae Acyon† SA Mesocarnivore Ground dwelling Borhyaenidium† SA Hypercarnivore Scansorial Chasicostylus† SA Hypercarnivore Scansorial † SA Hypercarnivore Scansorial

177

Notictis† SA Hypercarnivore Scansorial Notocynus† SA Hypercarnivore Scansorial Notogale† SA Hypercarnivore Scansorial Perathereutes† SA Mesocarnivore Ground dwelling Procladosictis† SA Hypercarnivore Scansorial Pseudonotictis† SA Mesocarnivore Ground dwelling Sallacyon† SA Hypercarnivore Scansorial Sipalocyon† SA Mesocarnivore Ground dwelling Proborhyaenidae Arminiheringia† SA Hypercarnivore Scansorial Paraborhyaena† SA Hypercarnivore Scansorial Pharsophorus† SA Hypercarnivore Scansorial Proborhyaena† SA Hypercarnivore Scansorial Anachlysictis† SA Hypercarnivore Scansorial Patagosmilus† SA Hypercarnivore Scansorial Thylacosmilus† SA Hypercarnivore Scansorial Wangliidae Alcidedorbignya† SA Herbivore Ground Dwelling Cimolestidae † SA Carnivore -Insectivore Scansorial Cetartiodactyla Incertae sedis Prosqualodon† - Carnivore Aquatic Pontivaga† - Carnivore Aquatic 178

Acrophyseter† - Carnivore Aquatic Atocetus† - Carnivore Aquatic Chilcacetus† - Carnivore Aquatic † - Carnivore Aquatic Piscocetus† - Suspension Feeder Aquatic Saurocetes† - Piscivore Aquatic Bos NA Grazer -Browser Ground Dwelling Ovis NA Grazer-Browser Ground Dwelling Eulamaops† NA Browser Ground Dwelling Hemiauchenia† NA Browser-Grazer Ground Dwelling Lama NA Grazer-Browser Ground Dwelling Palaeolama† NA Browser Ground Dwelling Vicugna† NA Grazer Ground Dwelling Cervidae Agalmaceros† NA Grazer -Browser Ground Dwelling Antifer† NA Grazer-Browser Ground Dwelling Blastocerus NA Grazer-Browser Ground Dwelling Charitoceros† NA Grazer-Browser Ground Dwelling Epieurycerus† NA Grazer-Browser Ground Dwelling Hippocamelus NA Grazer-Browser Ground Dwelling Mazama NA Grazer-Browser Ground Dwelling Morenelaphus† NA Grazer-Browser Ground Dwelling Odocoileus NA Browser Ground Dwelling Ozotoceros NA Grazer-Browser Ground Dwelling Pudu NA Browser Ground Dwelling 179

Paraceros† NA Grazer-Browser Ground Dwelling Palaeomerycidae Surameryx† NA Browser Ground Dwelling Tayassuidae Catagonus NA Herbivore -Omnivore Ground Dwelling Pecari NA Herbivore-Omnivore Ground Dwelling Platygonus† NA Browser-Grazer Ground Dwelling Selenogonus† NA Browser-Grazer Ground Dwelling Sylvochoerus† NA Herbivore-Omnivore Ground Dwelling Tayassu NA Herbivore-Omnivore Ground Dwelling Balaenidae Balaena - Suspension Feeder Aquatic Eubalaena - Suspension Feeder Aquatic Balaenopteridae Balaenoptera - Suspension Feeder Aquatic Megaptera - Suspension Feeder Aquatic Notiocetus† - Suspension Feeder Aquatic Basilosauridae Cynthiacetus† - Carnivore Aquatic Ocucajea† - Carnivore Aquatic Supayacetus† - Carnivore Aquatic Miocaperea† - Suspension Feeder Aquatic Palaeobalaena† - Suspension Feeder Aquatic † - Suspension Feeder Aquatic Delphinidae Delphinus - Piscivore -Carnivore Aquatic 180

Feresa - Piscivore-Carnivore Aquatic Hemisyntrachelus† - Piscivore-Carnivore Aquatic Lagenodelphis - Piscivore-Carnivore Aquatic Orcinus - Piscivore-Carnivore Aquatic Peponocephala† - Piscivore-Carnivore Aquatic Pseudorca - Piscivore-Carnivore Aquatic Sotalia - Piscivore-Carnivore Aquatic Stenella - Piscivore-Carnivore Aquatic Steno - Piscivore-Carnivore Aquatic Tursiops - Piscivore-Carnivore Aquatic Cephalorhynchus - Aquatic Globicephala - Carnivore Aquatic Grampus - Carnivore Aquatic Lagenorhynchus - Carnivore Aquatic Lissodelphis - Aquatic Prionodelphis† - Carnivore Aquatic Iniidae Ischyrorhynchus† - Piscivore Aquatic Plicodontinia† - Piscivore Aquatic Inia - Piscivore Aquatic Kentriodontidae Belonodelphis† - Carnivore Aquatic Incacetus† - Carnivore Aquatic Kentriodon† - Carnivore Aquatic Kogiidae Kogia - Carnivore Aquatic Scaphokogia† - Carnivore Aquatic 181

Neobalaenidae Caperea - Suspension Feeder Aquatic Odobenocetopsidae † - Carnivore Aquatic Phocoenidae Australithax† - Piscivore Aquatic Lomacetus† - Piscivore Aquatic Phocoena - Piscivore Aquatic Piscolithax† - Piscivore Aquatic Physeteridae Physeter - Carnivore Aquatic Platanistidae Pomatodelphis† - Piscivore Aquatic Pontoporiidae † - Carnivore Aquatic Pliopontos† - Carnivore Aquatic Pontistes† - Carnivore Aquatic Pontoporia - Piscivore Aquatic Squalodelphinidae Huaridelphis† - Carnivore Aquatic Notocetus† - Carnivore Aquatic Ziphiidae Indopacetus - Piscivore -Carnivore Aquatic Mesoplodon - Piscivore-Carnivore Aquatic † - Piscivore-Carnivore Aquatic Nazcacetus† - Piscivore-Carnivore Aquatic Ninoziphius† - Piscivore-Carnivore Aquatic 182

Ziphius - Piscivore-Carnivore Aquatic Berardius - Carnivore Aquatic Hyperoodon - Carnivore Aquatic Tasmacetus - Carnivore Aquatic Astrapotheria Astrapotheriidae Albertogaudrya† SA Herbivore Scansorial † SA Herbivore Scansorial Granastrapotherium† SA Herbivore Scansorial Hilarcotherium† SA Herbivore Scansorial Parastrapotherium† SA Herbivore Scansorial Xenastrapotherium† SA Herbivore Cursorial Astraponotus† SA Herbivore Scansorial † SA Herbivore Cursorial Maddenia† SA Herbivore Scansorial Astrapodon† SA Herbivore Cursorial Astrapothericulus† SA Herbivore Scansorial Comahuetherium† SA Herbivore Cursorial Liarthrus† SA Herbivore Scansorial Uruguaytherium† SA Herbivore Cursorial Eoastrapostylopidae Eoastrapostylops† SA Herbivore Scansorial Trigonostylopidae Shecenia† SA Herbivore Scansorial Tetragonostylops† SA Herbivore Scansorial Trigonostylops† SA Herbivore Scansorial Carnivora 183

Canidae Canis NA Carnivore -Omnivore Ground Dwelling Cerdocyon NA Carnivore-Omnivore Ground Dwelling Chrysocyon NA Carnivore-Omnivore Ground Dwelling Dusicyon† NA Carnivore-Omnivore Ground Dwelling Protocyon† NA Carnivore-Omnivore Ground Dwelling Speothos NA Carnivore-Omnivore Ground Dwelling Theriodictis† NA Carnivore-Omnivore Ground Dwelling Urocyon NA Omnivore-Carnivore Scansorial Atelocynus NA Carnivore-Omnivore Ground Dwelling Pseudalopex NA Carnivore Ground Dwelling Felidae Felis NA Carnivore Scansorial Herpailurus NA Carnivore Scansorial Homotherium† NA Carnivore Scansorial Leopardus NA Carnivore Scansorial Panthera NA Carnivore Scansorial Puma NA Carnivore Scansorial Smilodon† NA Carnivore Scansorial Mustelidae Conepatus NA Carnivore -Omnivore Scansorial Eira NA Carnivore-Omnivore Scansorial NA Carnivore-Omnivore Scansorial Lontra NA Carnivore-Omnivore Amphibious Lyncodon NA Carnivore-Omnivore Scansorial Pteronura NA Carnivore-Omnivore Amphibious Mustela NA Carnivore Ground Dwelling 184

Otariidae Arctocephalus NA Piscivore Amphibious Eumetopias NA Piscivore Amphibious Hydrarctos† NA Piscivore Amphibious Otaria NA Piscivore Amphibious Zalophus NA Piscivore Amphibious Phocidae Acrophoca† NA Piscivore Amphibious Hadrokirus† NA Piscivore-Carnivore Amphibious Mirounga NA Piscivore Amphibious Piscophoca† NA Piscivore-Carnivore Amphibious Properiptychus† NA Piscivore-Carnivore Amphibious Bassaricyon NA Frugivore -Carnivore Arboreal Chapalmalania† NA Frugivore-Carnivore Scansorial † NA Omnivore Scansorial Nasua NA Carnivore-Omnivore Scansorial Parahyaenodon† NA Frugivore-Carnivore Scansorial Potos NA Frugivore-Carnivore Arboreal Procyon NA Omnivore-Carnivore Scansorial Nasuella NA Omnivore Scansorial Ursidae Arctodus† NA Carnivore -Omnivore Ground Dwelling † NA Carnivore-Omnivore Ground Dwelling Tremarctos NA Omnivore Ground Dwelling Chiroptera Emballonuridae 185

Diclidurus SA Insectivore Volant Rhynchonycteris SA Insectivore Volant Balantiopteryx SA Insectivore Volant Centronycteris SA Insectivore Volant Cormura SA Insectivore Volant Cyttarops SA Insectivore Volant Peropteryx SA Insectivore Volant Saccopteryx SA Insectivore Volant Furipteridae Amorphochilus SA Insectivore Volant Furipterus SA Insectivore Volant Molossidae Eumops SA Insectivore Volant Kiotomops† SA Insectivore Volant Molossops SA Insectivore Volant Molossus SA Insectivore Volant Mormopterus† SA Insectivore Volant Potamops† SA Insectivore Volant Tadarida SA Insectivore Volant Cynomops SA Insectivore Volant Nyctinomops SA Insectivore Volant Promops SA Insectivore Volant Tomopeas SA Insectivore Volant Mormoopidae Mormoops SA Insectivore Volant Pteronotus SA Insectivore Volant Natalidae 186

Chilonatalus NA Insectivore Volant Natalus NA Insectivore Volant Noctilionidae Noctilio SA Piscivore -Insectivore Volant Phyllostomidae Artibeus SA Frugivore -Omnivore Volant Carollia SA Frugivore-Omnivore Volant Chrotopterus SA Omnivore Volant Desmodus SA Sanguivorous Volant Glossophaga SA Nectarivorous Volant Leptonycteris SA Nectarivorous Volant Lonchophylla SA Nectarivorous Volant Lophostoma SA Insectivore Volant Micronycteris SA Insectivore Volant Notonycteris† SA Insectivore Volant Palynephyllum† SA Nectarivorous Volant Phyllostomus SA Omnivore Volant Sturnira SA Frugivore Volant Tonatia SA Insectivore Volant Trachops SA Insectivore-Carnivore Volant Ametrida SA Frugivore Volant Anoura SA Nectarivorous Volant Centurio SA Frugivore Volant Chiroderma SA Frugivore Volant Choeroniscus SA Nectarivorous Volant Dermanura SA Frugivore Volant Diaemus SA Sanguivorous Volant 187

Diphylla SA Sanguivorous Volant Enchisthenes SA Frugivore Volant Glyphonycteris SA Insectivore Volant Lampronycteris SA Omnivore Volant Lichonycteris SA Nectarivorous Volant Lionycteris SA Nectarivorous Volant Lonchorhina SA Insectivore Volant Macrophyllum SA Insectivore Volant Mesophylla SA Frugivore Volant Mimon SA Insectivore Volant Neonycteris SA Insectivore Volant Phylloderma SA Omnivore Volant Platalina SA Nectarivorous Volant Platyrrhinus SA Frugivore Volant Pygoderma SA Frugivore Volant Rhinophylla SA Frugivore Volant Scleronycteris SA Nectarivorous Volant Sphaeronycteris SA Frugivore Volant Trinycteris SA Insectivore-Herbivore Volant Uroderma SA Frugivore Volant Vampyressa SA Frugivore Volant Vampyriscus SA Frugivore Volant Vampyrodes SA Frugivore Volant Vampyrum SA Carnivore Volant Xeronycteris SA Nectarivorous Volant Thyropteridae SA Insectivore Volant 188

Vespertilionidae Eptesicus NA Insectivore Volant Lasiurus NA Insectivore Volant Myotis NA Insectivore-Carnivore Volant Rhogeessa NA Insectivore Volant Histiotus NA Insectivore Volant Condylarthra Incertae sedis Perutherium† SA Insectivore Scansorial Ernestokokenia† SA Insectivore Scansorial Lamegoia† SA Insectivore Scansorial Ricardocifellia† (=Paulacoutoia) SA Insectivore Scansorial Salladolodus† SA Insectivore Scansorial Umayodus† SA Insectivore Scansorial Andinodus† SA Omnivore Scansorial Asmithwoodwardia† SA Omnivore Scansorial Molinodus† SA Omnivore Scansorial Pucanodus† SA Omnivore Scansorial Simoclaenus† SA Omnivore Scansorial Tiuclaenus† SA Omnivore Scansorial Lagomorpha Leporidae Kerodon NA Grazer -Browser Ground Dwelling Lepus NA Grazer-Browser Ground Dwelling

189

Sylvilagus NA Grazer-Browser Ground Dwelling Litopterna Adianthidae Indalecia† SA Herbivore Scansorial Notopithecus† SA Herbivore Scansorial Thadanius† SA Herbivore Scansorial Cramauchenia† SA Herbivore Scansorial Cullinia† SA Herbivore Scansorial † SA Herbivore Scansorial Macraucheniopsis† SA Herbivore Scansorial Macrauchenopsis† SA Herbivore Scansorial Notodiaphorus† SA Herbivore Scansorial Paranauchenia† SA Herbivore Scansorial Promacrauchenia† SA Herbivore Scansorial Pseudomacrauchenia† SA Herbivore Scansorial Scalabrinitherium† SA Herbivore Scansorial † SA Herbivore Scansorial Victorlemoineia† SA Herbivore Scansorial Windhausenia† SA Herbivore Scansorial † SA Herbivore Scansorial Mesorhinidae Coelosoma† SA Herbivore Scansorial Coniopternium† SA Herbivore Scansorial Oxyodontherium† SA Herbivore Scansorial Protheosodon† SA Herbivore Scansorial Tricoelodus† SA Herbivore Scansorial 190

Notonychopidae Notonychops† SA Herbivore Scansorial Requisia† SA Herbivore Scansorial Wainka† SA Herbivore Scansorial Proterotheridae Anisolambda† SA Herbivore Scansorial Bounodus† SA Herbivore Scansorial Brachytherium† SA Herbivore Scansorial Deuterotherium† SA Herbivore Scansorial † SA Herbivore Scansorial Eoauchenia† SA Herbivore Scansorial Epecuenia† SA Herbivore Scansorial Epitherium† SA Herbivore Scansorial Lambdaconus† SA Herbivore Scansorial Licaphrium† SA Herbivore Scansorial Megadolodus† SA Herbivore Scansorial Neobrachytherium† SA Herbivore Scansorial Neolicaphrium† SA Herbivore Scansorial Picturotherium† SA Herbivore Scansorial Prolicaphrium† SA Herbivore Scansorial Proterotherium† SA Herbivore Scansorial Prothoatherium† SA Herbivore Scansorial Tetramerorhinus† SA Herbivore Scansorial † SA Herbivore Scansorial Villarroelia† SA Herbivore Scansorial Sparnotheriodontidae Sparnotheriodon† SA Herbivore Scansorial 191

Notoungulata Incertae sedis Satshatemnus† SA Herbivore Scansorial Seudenius† SA Herbivore Scansorial † SA Herbivore Scansorial Archaeotypotherium† SA Herbivore Scansorial Plagiarthrus† SA Herbivore Scansorial Protarchaeohyrax† SA Herbivore Scansorial Pseudhyrax† SA Herbivore Scansorial † SA Herbivore Scansorial Hemihegetotherium† SA Herbivore Scansorial Paedotherium† SA Herbivore Scansorial Prohegetotherium† SA Herbivore Scansorial Propachyrucos† SA Herbivore Scansorial Prosotherium† SA Herbivore Scansorial Pseudohegetotherium† SA Herbivore Scansorial Sallatherium† SA Herbivore Scansorial Tremacyllus† SA Herbivore Scansorial Henricosbornidae Henricosbornia† SA Omnivore Arboreal Peripantostylops† SA Herbivore Ground Dwelling Acamana† SA Herbivore Scansorial Homalodotheriidae Asmodeus† SA Herbivore Scansorial Homalodontotherium† SA Herbivore Scansorial 192

Trigonolophodon† SA Herbivore Scansorial Periphragnis† SA Insectivore Scansorial Antepithecus† SA Herbivore Scansorial Argyrohyrax† SA Herbivore Scansorial Brucemacfaddenia† SA Herbivore Scansorial Cochilius† SA Herbivore Scansorial Eopachyrucos† SA Herbivore Scansorial Federicoanaya† SA Herbivore Scansorial † SA Herbivore Scansorial Miocochilius† SA Herbivore Cursorial Munizia† SA Herbivore Scansorial Proargyrohyrax† SA Herbivore Scansorial † SA Herbivore Scansorial Punapithecus† SA Herbivore Scansorial Santiagorothia† SA Herbivore Scansorial Isotemnus† SA Herbivore Scansorial Pleurostylodon† SA Herbivore Scansorial Leontiniidae Anayatherium† SA Herbivore Scansorial Huilatherium† SA Herbivore Scansorial † SA Herbivore Scansorial Purperia† SA Herbivore Scansorial Scarrittia† SA Herbivore Scansorial Taubatherium† SA Herbivore Scansorial Mesotheriidae 193

Altitypotherium† SA Herbivore Scansorial Eotypotherium† SA Herbivore Scansorial Eutypohterium† SA Insectivore Scansorial Eutrachytherus† (= Trachytherus) SA Herbivore Scansorial Hypsitherium† SA Herbivore Scansorial Microtypotherium† SA Herbivore Scansorial Plesiotypotherium† SA Herbivore Scansorial Trachytherus† SA Herbivore Scansorial Typotheriopsis† SA Herbivore Scansorial Typotherium† SA Herbivore Scansorial Pseudotypotherium† SA Herbivore Scansorial Coresodon† SA Herbivore Scansorial Eomorphippus† SA Herbivore Scansorial Eurygeniops† SA Herbivore Scansorial Eurygenium† SA Herbivore Scansorial Moqueguahippus† SA Herbivore Scansorial Pampahippus† SA Herbivore Scansorial Pascualihippus† SA Herbivore Scansorial † SA Herbivore Scansorial Notostylopidae Homalostylops† SA Herbivore Scansorial † SA Herbivore Scansorial Colbertia† SA Herbivore Scansorial Dolichostylodon† SA Herbivore Scansorial

194

Kibenikhoria† SA Herbivore Scansorial Suniodon† SA Herbivore Scansorial Abothrodon† SA Herbivore Scansorial † SA Herbivore Scansorial Alitoxodon† SA Herbivore Scansorial Berroia† SA Herbivore Scansorial Calchaquitherium† SA Herbivore Scansorial Dilobodon† SA Herbivore Scansorial Dinotoxodon† SA Herbivore Scansorial Eutomodus† SA Herbivore Scansorial Gyrinodon† SA Herbivore Scansorial Haplodontherium† SA Herbivore Scansorial Mesenodon† SA Herbivore Scansorial Mesotoxodon† SA Herbivore Scansorial Minitoxodon† SA Herbivore Scansorial † SA Herbivore Scansorial Neotoxodon† SA Herbivore Scansorial Neotrigodon† SA Herbivore Scansorial † SA Herbivore Scansorial Ocnerotherium† SA Herbivore Scansorial Pachynodon† SA Herbivore Scansorial Palaeotoxodon† SA Herbivore Scansorial Palyeidodon† SA Herbivore Scansorial Paratrigodon† SA Omnivore Scansorial Pericotoxodon† SA Herbivore Scansorial Pisanodon† SA Herbivore Scansorial 195

Plesiotoxodon† SA Herbivore Scansorial Posnanskytherium† SA Herbivore Scansorial Proadinotherium† SA Herbivore Scansorial Stenotephanos† SA Herbivore Scansorial † SA Grazer Scansorial Toxodontherium† SA Herbivore Scansorial Trigodon† SA Grazer Scansorial Trigodonops† SA Herbivore Scansorial Xotodon† SA Grazer Scansorial Campanorcidae Campanorco† SA Herbivore Scansorial Perissodactyla Equus NA Grazer Ground Dwelling Hippidion† NA Grazer-Browser Ground Dwelling Onohippidion† NA Grazer-Browser Ground Dwelling Onohippidium† NA Grazer-Browser Ground Dwelling Tapiridae Tapirus NA Browser Amphibious Primates Incertae sedis Branisella† SA Omnivore Arboreal Perupithecus† SA Omnivore Arboreal Aotidae Aotus SA Omnivore Arboreal Alouatta SA Omnivore Arboreal 196

Ateles SA Omnivore Arboreal Lagothrix SA Omnivore Arboreal Miocallicebus† SA Omnivore Arboreal † SA Omnivore Arboreal Solimoea† SA Omnivore Arboreal † SA Folivore Arboreal Brachyteles SA Herbivore Arboreal Oreonax SA Herbivore Arboreal Cebuella SA Insectivore Arboreal Mico SA Herbivore Arboreal Acrecebus† SA Frugivore Arboreal Callimico SA Insectivore-Herbivore Arboreal SA Insectivore-Herbivore Arboreal Cebus SA Frugivore-Omnivore Arboreal Chilecebus† SA Omnivore Arboreal Dolichocebus† SA Frugivore-Omnivore Arboreal Killikaike† SA Frugivore-Omnivore Arboreal † SA Herbivore-Frugivore Arboreal Leontopithecus† SA Insectivore-Herbivore Arboreal † SA Insectivore-Herbivore Arboreal Neosaimiri† SA Frugivore-Omnivore Arboreal † SA Frugivore-Insectivore Arboreal Saguinus SA Insectivore-Herbivore Arboreal Saimiri SA Frugivore-Omnivore Arboreal Sapajus SA Frugivore-Insectivore Arboreal 197

Caipora† SA Herbivore Arboreal Homo NA Omnivore Ground Dwelling SA Omnivore Arboreal Carlocebus† SA Omnivore Arboreal † SA Omnivore Arboreal Chiropotes SA Omnivore Arboreal † SA Herbivore Arboreal Pithecia SA Omnivore Arboreal Propithecia† SA Frugivore-Granivore Arboreal Soriacebus† SA Omnivore Arboreal Cacajao SA Herbivore Arboreal Gomphotheriidae Amahuacatherium† NA Browser Ground Dwelling Cuvieronius† NA Browser Ground Dwelling Haplomastodon† NA Browser Ground Dwelling Notiomastodon† NA Browser Ground Dwelling Rhynchotherium† NA Browser-Grazer Ground Dwelling Stegomastodon† NA Grazer Ground Dwelling Pyrotheria Colombitheridae Colombitherium† SA Herbivore Scansorial Proticia† SA Herbivore Scansorial Pyrotheriidae Propyrotherium† SA Herbivore Scansorial 198

Pyrotherium† SA Herbivore Scansorial Baguatherium† SA Herbivore Scansorial Carolozittelia† SA Herbivore Scansorial Rodentia Incertae sedis Acarechimys† SA Herbivore Ground Dwelling Aenigmys† SA Herbivore Ground Dwelling Cachiyacuy† SA Herbivore Ground Dwelling Canaanimys† SA Herbivore Ground Dwelling Guiomys† SA Herbivore Ground Dwelling Marisela† SA Herbivore Ground Dwelling Microcardiodon† SA Herbivore Ground Dwelling Luribayomys† SA Herbivore Ground Dwelling Abrocomidae Protabrocoma† SA Herbivore Ground Dwelling Abrocoma SA Herbivore Scansorial Cuscomys SA Herbivore Arboreal Acaremyidae Acaremys† SA Herbivore Ground Dwelling Galileomys† SA Herbivore Ground Dwelling Protacaremys† SA Herbivore Ground Dwelling Caviidae Anatochoerus† SA Grazer Amphibious Cardiatherium† SA Grazer Ground Dwelling Cardiomys† SA Herbivore Ground Dwelling Cavia SA Herbivore Ground Dwelling Caviodon† SA Herbivore Ground Dwelling 199

Chubutomys† SA Herbivore Ground Dwelling Contracavia† SA Grazer Amphibious Dolicavia† SA Herbivore Ground Dwelling Dolichotis SA Herbivore Ground Dwelling Eocardia† SA Herbivore Ground Dwelling Eodolichotis† SA Herbivore Ground Dwelling Galea SA Herbivore Ground Dwelling Hydrochoeropsis† SA Herbivore Ground Dwelling Hydrochoerus SA Herbivore Amphibious Luantus† SA Herbivore Ground Dwelling Microcavia SA Herbivore Ground Dwelling Neocavia† SA Herbivore Ground Dwelling Neochoerus† SA Herbivore Ground Dwelling Orthomyctera† SA Herbivore Ground Dwelling Palaeocavia† SA Herbivore Ground Dwelling Parodimys† SA Herbivore Ground Dwelling Pascualia† SA Herbivore Ground Dwelling Pediolagus† SA Herbivore Ground Dwelling Phanomys† SA Herbivore Ground Dwelling Phugatherium† SA Grazer Amphibious Pliodolichotis† SA Herbivore Ground Dwelling Prodolichotis† SA Herbivore Ground Dwelling Rhodanodolichotis† SA Herbivore Ground Dwelling Schistomys† SA Herbivore Ground Dwelling Cavia SA Herbivore Ground Dwelling Cephalomyidae Asteromys† SA Herbivore Ground Dwelling 200

Banderomys† SA Herbivore Ground Dwelling Cephalomys† SA Herbivore Ground Dwelling Eoviscaccia† SA Herbivore Ground Dwelling Lagidium SA Herbivore Ground Dwelling Lagostomus SA Herbivore Ground Dwelling Prolagostomus† SA Herbivore Ground Dwelling Scotamys† SA Herbivore Ground Dwelling Chinchilla SA Herbivore-Insectivore Ground Dwelling Cricetidae Abrothrix NA Herbivore Ground Dwelling Akodon NA Herbivore Ground Dwelling Andinomys† NA Herbivore Ground Dwelling Auliscomys† NA Herbivore Ground Dwelling Bolomys NA Herbivore-Insectivore Ground Dwelling Calomys NA Herbivore Ground Dwelling Eligmodontia NA Herbivore Ground Dwelling Graomys† NA Herbivore Ground Dwelling Holochilus NA Herbivore Ground Dwelling Kunsia NA Herbivore Ground Dwelling Neacomys NA Herbivore Ground Dwelling Necromys NA Herbivore Ground Dwelling Nectomys NA Insectivore Amphibious Neotomys NA Herbivore Ground Dwelling Oecomys NA Herbivore Ground Dwelling Oligoryzomys NA Herbivore Ground Dwelling Oryzomys NA Herbivore Ground Dwelling 201

Oxymycterus NA Herbivore Fossorial Phyllotis NA Herbivore Ground Dwelling Reithrodon NA Herbivore Ground Dwelling Rhipidomys NA Herbivore Ground Dwelling Scapteromys NA Herbivore Ground Dwelling Sigmodon NA Herbivore Ground Dwelling Tafimys NA Herbivore Ground Dwelling Zygodontomys† NA Herbivore Ground Dwelling Abrawayaomys NA Aegialomys NA Herbivore Scansorial Aepeomys NA Omnivore Ground Dwelling Amphinectomys NA Carnivore Amphibious Andalgalomys NA Herbivore Ground Dwelling Anotomys NA Piscivore Amphibious Bibimys NA Omnivore Ground Dwelling Blarinomys NA Insectivore Fossorial Brucepattersonius NA Insectivore Ground Dwelling Cerradomys NA Frugivore Ground Dwelling Chelemys NA Herbivore Fossorial Chibchanomys NA Piscivore Amphibious Chilomys NA Omnivore Ground Dwelling Chinchillula NA Grazer Ground Dwelling Delomys NA Omnivore Deltamys NA Omnivore Ground Dwelling Eremoryzomys NA Herbivore Arboreal Euneomys NA Herbivore-Granivore Cursorial Euryoryzomys NA Omnivore Ground Dwelling 202

Fossorial-Ground Galenomys NA Herbivore-Granivore Dwelling Geoxus NA Insectivore Fossorial Handleyomys NA Herbivore Ground Dwelling Hylaeamys NA Omnivore Ground Dwelling Ichthyomys NA Piscivore Amphibious Irenomys NA Frugivore-Granivore Arboreal Isthmomys NA Herbivore Ground Dwelling Juliomys NA Frugivore-Granivore Arboreal Juscelinomys NA Fossorial Lenoxus NA Loxodontomys NA Herbivore Ground Dwelling Lundomys NA Herbivore Scansorial Megaoryzomys NA Melanomys† NA Omnivore Ground Dwelling Microakodontomys NA Ground Dwelling Microryzomys NA Omnivore Ground Dwelling Mindomys NA Amphibious Nephelomys NA Omnivore Ground Dwelling Nesoryzomys NA Omnivore Ground Dwelling Neusticomys NA Piscivore-Carnivore Amphibious Noronhomys NA Omnivore Ground Dwelling Notiomys† NA Insectivore-Herbivore Fossorial Oreoryzomys NA Ground Dwelling Paralomys NA Ground Dwelling Pearsonomys NA Herbivore -Insectivore Fossorial Phaenomys NA Arboreal

203

Podoxymys NA Pseudoryzomys NA Punomys NA Herbivore Scansorial Reithrodontomys NA Herbivore-Insectivore Ground Dwelling Rhagomys NA Herbivore-Insectivore Arboreal Salinomys NA Ground Dwelling Scolomys NA Herbivore Ground Dwelling Sigmodontomys NA Herbivore Amphibious Sooretamys NA Tapecomys NA Arboreal Thalpomys NA Herbivore Ground Dwelling Thaptomys NA Herbivore Ground Dwelling Thomasomys NA Herbivore Ground Dwelling Transandinomys NA Herbivore-Insectivore Ground Dwelling Tylomys NA Herbivore Arboreal Wiedomys NA Herbivore-Insectivore Scansorial Wilfredomys NA Herbivore Arboreal Ctenomyidae Actenomys† SA Herbivore Fossorial Ctenomys SA Herbivore Fossorial Eucelophorus† SA Herbivore Fossorial Cuniculidae Cuniculus SA Herbivore Ground Dwelling Eobranisamys† SA Frugivore-Herbivore Ground Dwelling Eoincamys† SA Frugivore-Herbivore Ground Dwelling Eopicure† SA Frugivore-Herbivore Ground Dwelling 204

Australoprocta† SA Herbivore Ground Dwelling Dasyprocta SA Herbivore Ground Dwelling Incamys† SA Herbivore Ground Dwelling Mesoprocta† SA Herbivore Ground Dwelling Microscleromys† SA Herbivore Ground Dwelling Myoprocta SA Herbivore Ground Dwelling Neoreomys† SA Herbivore Ground Dwelling Arazamys† SA Frugivore -Folivore Ground Dwelling Artigasia† SA Frugivore-Folivore Ground Dwelling Branisamys† SA Frugivore-Folivore Ground Dwelling Briaromys† SA Frugivore-Folivore Ground Dwelling Carlesia† SA Frugivore-Folivore Ground Dwelling Colpostemma† SA Frugivore-Folivore Ground Dwelling Diaphoromys† SA Frugivore-Folivore Ground Dwelling Dinomys SA Frugivore-Folivore Ground Dwelling Doellomys† SA Frugivore-Folivore Ground Dwelling Drytomomys† SA Frugivore-Folivore Ground Dwelling Eumegamys† SA Frugivore-Folivore Ground Dwelling Eumegamysops† SA Frugivore-Folivore Ground Dwelling Gyriabrus† SA Frugivore-Folivore Ground Dwelling Isostylomys† SA Frugivore-Folivore Ground Dwelling Olenopsis† SA Frugivore-Folivore Ground Dwelling Paranamys† SA Frugivore-Folivore Ground Dwelling Pentastylomys† SA Frugivore-Folivore Ground Dwelling Perimys† SA Herbivore Ground Dwelling Potamarchus† SA Frugivore-Folivore Ground Dwelling 205

Protomegamys† SA Frugivore-Folivore Ground Dwelling Pseudosigmomys† SA Frugivore-Folivore Ground Dwelling Scleromys† SA Frugivore-Folivore Ground Dwelling Simplimus† SA Herbivore Ground Dwelling Telicomys† SA Frugivore-Folivore Ground Dwelling Tetrastylus† SA Frugivore-Folivore Ground Dwelling Adelphomys† SA Herbivore Scansorial Carterodon† SA Herbivore Scansorial Caviocricetus† SA Herbivore Scansorial Clyomys† SA Herbivore Scansorial Echimys SA Herbivore Scansorial Eodelphomys† SA Herbivore Scansorial Eoespina† SA Herbivore Scansorial Eosachacui† SA Herbivore Scansorial Eosallamys† SA Herbivore Scansorial Eumysops† SA Herbivore Scansorial Euryzygomatomys SA Herbivore Scansorial Haplostropha† SA Herbivore Scansorial Maruchito† SA Herbivore Scansorial Prostichomys† SA Herbivore Scansorial Quebradahondomys† SA Herbivore Scansorial Ricardomys† SA Herbivore Scansorial Sallamys† SA Herbivore Scansorial Spaniomys† SA Herbivore Scansorial Thrichomys† SA Herbivore Scansorial Callistomys SA Herbivore Arboreal 206

Diplomys SA Herbivore Arboreal Hoplomys SA Omnivore Ground Dwelling Kannabateomys SA Herbivore Arboreal Lonchothrix SA Makalata SA Herbivore Scansorial Olallamys SA Herbivore Arboreal Pattonomys SA Herbivore Arboreal Phyllomys SA Herbivore Arboreal Santamartamys SA Herbivore Arboreal Toromys SA Arboreal Trinomys SA Herbivore -Insectivore Ground Dwelling Erethizontidae Branisamyopsis† SA Herbivore Arboreal Coendou SA Herbivore Arboreal Eopululo† SA Herbivore Arboreal Eosteiromys† SA Herbivore Ground Dwelling Erethizon SA Herbivore Arboreal Microsteiromys† SA Herbivore Arboreal Neosteiromys† SA Herbivore Arboreal Paradoxomys† SA Herbivore Arboreal Steiromys† SA Herbivore Arboreal Chaetomys SA Herbivore Ground Dwelling Echinoprocta SA Herbivore Arboreal Sphiggurus SA Herbivore-Insectivore Arboreal Geomyidae Orthogeomys SA Herbivore Fossorial Heteromyidae 207

Heteromys SA Omnivore Ground Dwelling Myocastoridae Myocastor SA Herbivore Amphibious Paramyocastor† SA Herbivore Amphibious Strophostephanos† SA Herbivore Amphibious Neoepiblemidae Neoepiblema† SA Herbivore Ground Dwelling Perumys† SA Herbivore Ground Dwelling Phoberomys† SA Herbivore Ground Dwelling Octodontidae Chasichimys† SA Herbivore Scansorial Dactylomys SA Herbivore Ground Dwelling Dicolpomys† SA Herbivore Ground Dwelling Isothrix SA Herbivore Ground Dwelling Mesomys SA Herbivore Ground Dwelling Migraveramus† SA Herbivore Ground Dwelling Neophanomys† SA Herbivore Ground Dwelling Palaeoctodon† SA Herbivore Ground Dwelling Phtoramys† SA Herbivore Ground Dwelling Pithanotomys† SA Herbivore Ground Dwelling Platypittamys† SA Herbivore Ground Dwelling Praectenomys† SA Herbivore Ground Dwelling Proechimys SA Herbivore Ground Dwelling Pseudoplataeomys† SA Herbivore Ground Dwelling Sciamys† SA Herbivore Ground Dwelling Xenodontomys† SA Herbivore Ground Dwelling Aconaemys SA Herbivore Scansorial 208

Octodon SA Herbivore Fossorial Octodontomys SA Herbivore Scansorial Octomys SA Herbivore Ground Dwelling Pipanacoctomys SA Herbivore Scansorial Salinoctomys SA Herbivore Ground Dwelling Spalacopus SA Herbivore Fossorial Tympanoctomys SA Herbivore Fossorial Sciuridae Sciurus NA Granivore -Frugivore Arboreal Microsciurus NA Herbivore Scansorial Sciurillus NA Herbivore Arboreal Incertae sedis Sirenotherium† - Herbivore Aquatic Dioplotherium† - Herbivore Aquatic † - Herbivore Aquatic † - Herbivore Aquatic Rytiodus† - Herbivore Aquatic Trichechidae Potamosiren† - Herbivore Aquatic † - Herbivore Aquatic Trichechus - Herbivore Aquatic Soricomorpha Soricidae Cryptotis NA Omnivore Ground Dwelling Xenarthra 209

Incertae sedis † SA Omnivore Ground Dwelling Hiskatherium† SA Omnivore Ground Dwelling † SA Omnivore Ground Dwelling Pseudoglyptodon† SA Omnivore Ground Dwelling Bradypodidae Bradypus SA Omnivore Ground Dwelling Dasypodidae Acantharodeia† SA Insectivore Ground Dwelling Anadasypus† SA Insectivore Ground Dwelling Cabassous† SA Insectivore Semifossorial Chaetophractus SA Insectivore Ground Dwelling Chasicotatus SA Insectivore Ground Dwelling Chorobates† SA Insectivore Ground Dwelling Dasypus† SA Insectivore-Frugivore Fossorial Doellotatus SA Insectivore Ground Dwelling Euphractus† SA Insectivore Ground Dwelling Eutatus SA Insectivore Ground Dwelling Kuntinaru† SA Insectivore Ground Dwelling Macrochorobates† SA Insectivore Ground Dwelling † SA Insectivore Ground Dwelling Nanoastegotherium† SA Insectivore Ground Dwelling Paleuphractus† SA Insectivore Ground Dwelling Paraeuphractus† SA Insectivore Ground Dwelling Pedrolypeutes† SA Insectivore Ground Dwelling Pliodasypus† SA Insectivore Ground Dwelling Priodontes SA Insectivore Fossorial 210

Proeuphractus† SA Insectivore Ground Dwelling Proeutatus† SA Insectivore Ground Dwelling Propraopus† SA Insectivore Ground Dwelling Prozaedyus† SA Insectivore Ground Dwelling Ringueletia† SA Insectivore Ground Dwelling Stegotherium† SA Omnivore Ground Dwelling Stenotatus† SA Insectivore Ground Dwelling Tolypeutes SA Insectivore Ground Dwelling Vetelia† SA Insectivore Ground Dwelling Zaedyus† SA Insectivore Ground Dwelling Calyptophractus SA Omnivore Arboreal Chlamyphorus SA Insectivore Fossorial Glyptodontidae Aspidocalyptus† SA Omnivore Ground Dwelling Berthawyleria† SA Omnivore Ground Dwelling † SA Omnivore Ground Dwelling Chlamydotherium† SA Omnivore Ground Dwelling Chlamyphractus† SA Omnivore Ground Dwelling Comaphorus† SA Omnivore Ground Dwelling Coscinocercus† SA Omnivore Ground Dwelling Cranithlastus† SA Omnivore Ground Dwelling † SA Omnivore Ground Dwelling Eleutherocercus† SA Omnivore Ground Dwelling Eosclerocalyptus† SA Herbivore Ground Dwelling Glyptatelus† SA Omnivore Ground Dwelling † SA Omnivore Ground Dwelling † SA Omnivore Ground Dwelling 211

Hoplophorus† SA Omnivore Ground Dwelling Lomaphorops† SA Omnivore Ground Dwelling Neoglyptatelus† SA Omnivore Ground Dwelling Neosclerocalyptus† SA Omnivore Ground Dwelling Neothoracophorus† SA Omnivore Ground Dwelling Neuryurus† SA Omnivore Ground Dwelling Palaeohoplophorus† SA Omnivore Ground Dwelling Panochthus† SA Omnivore Ground Dwelling Paraglyptodon† SA Omnivore Ground Dwelling Parahoplophorus† SA Omnivore Ground Dwelling Parapanochthus† SA Omnivore Ground Dwelling Parapropalaehoplophorus† SA Omnivore Ground Dwelling Phlyctaenopyga† SA Omnivore Ground Dwelling Plaxhaplous† SA Omnivore Ground Dwelling Plohophorops† SA Omnivore Ground Dwelling Plohophorus† SA Omnivore Ground Dwelling Prodaedicurus† SA Omnivore Ground Dwelling Protoglyptodon† SA Omnivore Ground Dwelling Pseudoeuryurus† SA Omnivore Ground Dwelling Pseudoplohophorus† SA Omnivore Ground Dwelling Sclerocalyptus† SA Omnivore Ground Dwelling Stromaphorus† SA Omnivore Ground Dwelling Trachycalyptoides† SA Omnivore Ground Dwelling Trachycalyptus† SA Omnivore Ground Dwelling Urotherium† SA Omnivore Ground Dwelling Xiphuroides† SA Omnivore Ground Dwelling Lomaphorus† SA Omnivore Ground Dwelling 212

Megalonychidae Ahytherium† SA Herbivore Ground Dwelling Amphiocnus† SA Herbivore Ground Dwelling Australonyx† SA Herbivore Ground Dwelling Choloepus SA Herbivore Ground Dwelling Megalonychops† SA Herbivore Ground Dwelling Nothropus† SA Herbivore Ground Dwelling Ocnopus† SA Herbivore Ground Dwelling Ortotherium† SA Herbivore Ground Dwelling Paranabradys† SA Herbivore Ground Dwelling Pliomorphus† SA Herbivore Ground Dwelling Protomegalonyx† SA Herbivore Ground Dwelling Torcellia† SA Herbivore Ground Dwelling Eucholoeops† SA Omnivore Ground Dwelling Megatheriidae Eomegatherium† SA Herbivore Ground Dwelling † SA Herbivore Ground Dwelling Megathericulus† SA Herbivore Ground Dwelling Megatherium† SA Herbivore Ground Dwelling Planops† SA Herbivore Ground Dwelling Plesiomegatherium† SA Herbivore Ground Dwelling Pliomegatherium† SA Herbivore Ground Dwelling Proeremotherium† SA Herbivore Ground Dwelling Promegatherium† SA Herbivore Ground Dwelling Pyramiodontherium† SA Herbivore Ground Dwelling Urumaquia† SA Herbivore Ground Dwelling Prepotherium† SA Herbivore Ground Dwelling 213

Analcimorphus† SA Herbivore Ground Dwelling Schismotherium† SA Omnivore Ground Dwelling Bolivartherium† SA Herbivore Ground Dwelling Brievabradys† SA Herbivore Ground Dwelling † SA Herbivore Ground Dwelling Elassotherium† SA Herbivore Ground Dwelling Glossotheriopsis† SA Herbivore Ground Dwelling Glossotherium† SA Herbivore Ground Dwelling Kiyumylodon† SA Herbivore Ground Dwelling Lestobradys† SA Herbivore Ground Dwelling † SA Herbivore Ground Dwelling Megabradys† SA Herbivore Ground Dwelling Mirandabradys† SA Omnivore Ground Dwelling † SA Herbivore Ground Dwelling Mylodonopsis† SA Herbivore Ground Dwelling Nematherium† SA Herbivore Ground Dwelling Neonematherium† SA Herbivore Ground Dwelling Octodontotherium† SA Herbivore Ground Dwelling Octomylodon† SA Herbivore Ground Dwelling Paroctodontotherium† SA Herbivore Ground Dwelling Prolestodon† SA Herbivore Ground Dwelling Promylodon† SA Herbivore Ground Dwelling Proscelidodon† SA Herbivore Ground Dwelling Pseudoprepotherium† SA Herbivore Ground Dwelling Ranculcus† SA Herbivore Ground Dwelling † SA Herbivore Ground Dwelling 214

Scelidotheridium† SA Herbivore Ground Dwelling † SA Herbivore Ground Dwelling Sphenotherus† SA Herbivore Ground Dwelling Stenodon† SA Herbivore Ground Dwelling Strabosodon† SA Herbivore Ground Dwelling Urumacotherium† SA Herbivore Ground Dwelling † SA Herbivore Ground Dwelling Analcitherium† SA Herbivore Ground Dwelling Cyclopes SA Insectivore Arboreal Myrmecophaga SA Insectivore Ground Dwelling Neotamandua† SA Insectivore Arboreal Tamandua SA Insectivore Ground Dwelling Nothrotheriidae Chasicobradys† SA Herbivore Ground Dwelling Neohapalops† SA Herbivore Ground Dwelling † SA Herbivore Ground Dwelling † SA Herbivore Ground Dwelling † SA Herbivore Aquatic Xyophorus† SA Herbivore Ground Dwelling Orophodontidae Octodontobradys† SA Herbivore Ground Dwelling Paleopelthidae Paleopeltis† SA Omnivore Ground Dwelling Chlamytherium† SA Omnivore Ground Dwelling † SA Omnivore Ground Dwelling 215

Kraglievichia† SA Omnivore Ground Dwelling Pampatherium† SA Omnivore Ground Dwelling Plaina† SA Omnivore Ground Dwelling Scirrotherium† SA Omnivore Ground Dwelling Vassallia† SA Omnivore Ground Dwelling Peltephilidae Peltephilus† SA Omnivore Ground Dwelling

Propalaehoplophoridae Asterostemma† SA Omnivore Ground Dwelling † SA Omnivore Ground Dwelling Xenungulata Carodniidae † SA Insectivore Scansorial Etayoa† SA Insectivore Scansorial Notoetayoa† SA Insectivore Scansorial

216

APPENDIX 2

Family-level phylogenies of New World bat families used in

Chapter Three

217

218

219

220

221

222 APPENDIX 3

Spatial distribution of Phylogenetic Diversity and Endemism for three superfamilies of New World bats

223

224 APPENDIX FOUR

Distribution maps of all New World bat species included for analyses of chapter 3

225 All 325 maps are included in CD attached to the thesis as raster files

Example map for distribution of Myotis riparius

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