The Ecology of Nonecological Speciation and Nonadaptive Radiations
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Novel Trophic Niches Drive Variable Progress Towards Ecological Speciation Within an Adaptive Radiation of Pupfishes
Molecular Ecology (2014) 23, 1846–1862 doi: 10.1111/mec.12658 Novel trophic niches drive variable progress towards ecological speciation within an adaptive radiation of pupfishes CHRISTOPHER H. MARTIN*† and LAURA C. FEINSTEIN†‡ *Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA, †Department of Evolution & Ecology, University of California, Davis, CA 94616, USA, ‡California Council on Science and Technology, 1130 K Street, Sacramento, CA 95814, USA Abstract Adaptive radiation is recognized by a rapid burst of phenotypic, ecological and species diversification. However, it is unknown whether different species within an adaptive radiation evolve reproductive isolation at different rates. We compared patterns of genetic differentiation between nascent species within an adaptive radiation of Cyprin- odon pupfishes using genotyping by sequencing. Similar to classic adaptive radiations, this clade exhibits rapid morphological diversification rates and two species are novel trophic specialists, a scale-eater and hard-shelled prey specialist (durophage), yet the radiation is <10 000 years old. Both specialists and an abundant generalist species all coexist in the benthic zone of lakes on San Salvador Island, Bahamas. Based on 13 912 single-nucleotide polymorphisms (SNPs), we found consistent differences in genetic differentiation between each specialist species and the generalist across seven lakes. The scale-eater showed the greatest genetic differentiation and clustered by species across lakes, whereas durophage populations often clustered with sympatric generalist populations, consistent with parallel speciation across lakes. However, we found strong evidence of admixture between durophage populations in different lakes, sup- porting a single origin of this species and genome-wide introgression with sympatric generalist populations. -
Reticulate Evolutionary History in a Recent Radiation of Montane
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426362; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Reticulate Evolutionary History in a Recent Radiation of Montane 2 Grasshoppers Revealed by Genomic Data 3 4 VANINA TONZO1, ADRIÀ BELLVERT2 AND JOAQUÍN ORTEGO1 5 6 1 Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC); Avda. 7 Américo Vespucio, 26 – 41092; Seville, Spain 8 2 Department of Evolutionary Biology, Ecology and Environmental Sciences, and 9 Biodiversity Research Institute (IRBio), Universitat de Barcelona; Av. Diagonal, 643 – 10 08028; Barcelona, Spain 11 12 13 Author for correspondence: 14 Vanina Tonzo 15 Estación Biológica de Doñana, EBD-CSIC, 16 Avda. Américo Vespucio 26, E-41092 Seville, Spain 17 E-mail: [email protected] 18 Phone: +34 954 232 340 19 20 21 22 Running title: Reticulate evolution in a grasshopper radiation bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426362; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 Abstract 24 Inferring the ecological and evolutionary processes underlying lineage and phenotypic 25 diversification is of paramount importance to shed light on the origin of contemporary 26 patterns of biological diversity. However, reconstructing phylogenetic relationships in 27 recent evolutionary radiations represents a major challenge due to the frequent co- 28 occurrence of incomplete lineage sorting and introgression. -
Adaptive Radiation
ADAPTIVE RADIATION Rosemary G. Gillespie,* Francis G. Howarth,† and George K. Roderick* *University of California, Berkeley and †Bishop Museum I. History of the Concept ecological release Expansion of habitat, or ecological II. Nonadaptive Radiations environment, often resulting from release of species III. Factors Underlying Adaptive Radiation from competition. IV. Are Certain Taxa More Likely to Undergo Adap- founder effect Random genetic sampling in which tive Radiation Than Others? only a few ‘‘founders’’ derived from a large popula- V. How Does Adaptive Radiation Get Started? tion initiate a new population. Since these founders VI. The Processes of Adaptive Radiation: Case carry only a small fraction of the parental popula- Studies tion’s genetic variability, radically different gene VII. The Future frequencies can become established in the new colony. key innovation A trait that increases the efficiency with GLOSSARY which a resource is used and can thus allow entry into a new ecological zone. adaptive shift A change in the nature of a trait (mor- natural selection The differential survival and/or re- phology, ecology, or behavior) that enhances sur- production of classes of entities that differ in one or vival and/or reproduction in an ecological environ- more hereditary characteristics. ment different from that originally occupied. sexual selection Selection that acts directly on mating allopatric speciation The process of genetic divergence success through direct competition between mem- between geographically separated populations lead- bers of one sex for mates or through choices made ing to distinct species. between the two sexes or through a combination of character displacement Divergence in a morphological both modes. -
Testing Island Biogeography Theory with an Eco-Evolutionary
bioRxiv preprint doi: https://doi.org/10.1101/100289; this version posted January 13, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 1 Original Article 2 Effects of time and isolation on plant diversity: testing island biogeography 3 theory with an eco-evolutionary model 4 Authors: Juliano Sarmento Cabral1,2,3*, Robert J. Whittaker4,5, Kerstin Wiegand6, Holger Kreft2 5 1 Ecosystem Modeling, Center of Computation and Theoretical Biology, University of Würzburg, 6 Campus Hubland-Nord, Building 32, D- 97074, Würzburg, Germany. 7 2 Department of Biodiversity, Macroecology & Biogeography, University of Göttingen, 8 Büsgenweg 1, D-37077, Göttingen, Germany. 9 3 Synthesis Centre of the German Centre for Integrative Biodiversity Research (iDiv), Deutscher 10 Platz 5e, D-04103 Leipzig, Germany. 11 4 Conservation Biogeography and Macroecology Group, School of Geography and the 12 Environment, University of Oxford, South Parks Road, Oxford, OX1 3QY, UK. 13 5 Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, 14 University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark. 15 6 Ecosystem Modelling, Büsgen-Institute, University of Göttingen, Büsgenweg 4, D-37077, 16 Göttingen, Germany. 17 *Corresponding author: Ecosystem Modeling, Center for Computation and Theoretical Biology, 18 University of Würzburg, am Hubland-Nord 32, D- 97074, Würzburg, Germany. E-mail: 19 [email protected] 20 bioRxiv preprint doi: https://doi.org/10.1101/100289; this version posted January 13, 2017. -
Graptoloid Diversity and Disparity Became Decoupled During the Ordovician Mass Extinction
Graptoloid diversity and disparity became decoupled during the Ordovician mass extinction David W. Bapsta,b,1, Peter C. Bullockc, Michael J. Melchinc, H. David Sheetsd, and Charles E. Mitchellb aDepartment of the Geophysical Sciences, University of Chicago, Chicago, IL 60637; bDepartment of Geology, University at Buffalo, The State University of New York, Buffalo, NY 14260; cDepartment of Earth Sciences, St. Francis Xavier University, Antigonish, NS, Canada B2G 2W5; and dDepartment of Physics, Canisius College, Buffalo, NY 14208 Edited by Douglas H. Erwin, Smithsonian National Museum of Natural History, Washington, DC, and accepted by the Editorial Board January 19, 2012 (received for review August 31, 2011) The morphological study of extinct taxa allows for analysis of a HME (Fig. 1), they were driven to extinction during the Hir- diverse set of macroevolutionary hypotheses, including testing for nantian glaciation (7, 15). In contrast, the Neograptina simulta- change in the magnitude of morphological divergence, extinction neously speciated rapidly after the first extinction episode of the selectivity on form, and the ecological context of radiations. Late HME (15). Ordovician graptoloids experienced a phylogenetic bottleneck at The changes in morphological diversity during this interval have the Hirnantian mass extinction (∼445 Ma), when a major clade of not been studied quantitatively. Previous work suggests that only a graptoloids was driven to extinction while another clade simulta- single morphotype survived the HME (16, 17) and that the number neously radiated. In this study, we developed a dataset of 49 eco- of morphotypes recovered in the Silurian. Mitchell (18) demon- logically relevant characters for 183 species with which we tested strated that the Silurian Neograptina evolved a number of mor- i two main hypotheses: ( ) could the biased survival of one grapto- phologies that converged upon pre-Hirnantian diplograptine loid clade over another have resulted from morphological selectiv- forms. -
(Lepidoptera: Gracillariidae: Epicephala) and Leafflower Trees (Phyllanthaceae: Phyllanthus Sensu Lato [Glochidion]) in Southeastern Polynesia
Coevolutionary Diversification of Leafflower Moths (Lepidoptera: Gracillariidae: Epicephala) and Leafflower Trees (Phyllanthaceae: Phyllanthus sensu lato [Glochidion]) in Southeastern Polynesia By David Howard Hembry A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Environmental Science, Policy, and Management in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Rosemary Gillespie, Chair Professor Bruce Baldwin Professor Patrick O’Grady Spring 2012 1 2 Abstract Coevolution between phylogenetically distant, yet ecologically intimate taxa is widely invoked as a major process generating and organizing biodiversity on earth. Yet for many putatively coevolving clades we lack knowledge both of their evolutionary history of diversification, and the manner in which they organize themselves into patterns of interaction. This is especially true for mutualistic associations, despite the fact that mutualisms have served as models for much coevolutionary research. In this dissertation, I examine the codiversification of an obligate, reciprocally specialized pollination mutualism between leafflower moths (Lepidoptera: Gracillariidae: Epicephala) and leafflower trees (Phyllanthaceae: Phyllanthus sensu lato [Glochidion]) on the oceanic islands of southeastern Polynesia. Leafflower moths are the sole known pollinators of five clades of leafflowers (in the genus Phyllanthus s. l., including the genera Glochidion and Breynia), and thus this interaction is considered to be obligate. Female moths actively transfer pollen from male flowers to female flowers, using a haired proboscis to transfer pollen into the recessed stigmatic surface at the end of the fused stylar column. The moths then oviposit into the flowers’ ovaries, and the larva which hatches consumes a subset, but not all, of the developing fruit’s seed set. -
Adaptive Radiation Versus ‘
Review Research review Adaptive radiation versus ‘radiation’ and ‘explosive diversification’: why conceptual distinctions are fundamental to understanding evolution Author for correspondence: Thomas J. Givnish Thomas J. Givnish Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA Tel: +1 608 262 5718 Email: [email protected] Received: 7 August 2014 Accepted: 1 May 2015 Summary New Phytologist (2015) 207: 297–303 Adaptive radiation is the rise of a diversity of ecological roles and role-specific adaptations within doi: 10.1111/nph.13482 a lineage. Recently, some researchers have begun to use ‘adaptive radiation’ or ‘radiation’ as synonymous with ‘explosive species diversification’. This essay aims to clarify distinctions Key words: adaptive radiation, ecological between these concepts, and the related ideas of geographic speciation, sexual selection, key keys, explosive diversification, geographic innovations, key landscapes and ecological keys. Several examples are given to demonstrate that speciation, key innovations, key landscapes, adaptive radiation and explosive diversification are not the same phenomenon, and that parallel adaptive radiations. focusing on explosive diversification and the analysis of phylogenetic topology ignores much of the rich biology associated with adaptive radiation, and risks generating confusion about the nature of the evolutionary forces driving species diversification. Some ‘radiations’ involve bursts of geographic speciation or sexual selection, rather than adaptive diversification; some adaptive radiations have little or no effect on speciation, or even a negative effect. Many classic examples of ‘adaptive radiation’ appear to involve effects driven partly by geographic speciation, species’ dispersal abilities, and the nature of extrinsic dispersal barriers; partly by sexual selection; and partly by adaptive radiation in the classical sense, including the origin of traits and invasion of adaptive zones that result in decreased diversification rates but add to overall diversity. -
Phylogenetic Comparative Methods
Phylogenetic Comparative Methods Luke J. Harmon 2019-3-15 1 Copyright This is book version 1.4, released 15 March 2019. This book is released under a CC-BY-4.0 license. Anyone is free to share and adapt this work with attribution. ISBN-13: 978-1719584463 2 Acknowledgements Thanks to my lab for inspiring me, my family for being my people, and to the students for always keeping us on our toes. Helpful comments on this book came from many sources, including Arne Moo- ers, Brian O’Meara, Mike Whitlock, Matt Pennell, Rosana Zenil-Ferguson, Bob Thacker, Chelsea Specht, Bob Week, Dave Tank, and dozens of others. Thanks to all. Later editions benefited from feedback from many readers, including Liam Rev- ell, Ole Seehausen, Dean Adams and lab, and many others. Thanks! Keep it coming. If you like my publishing model try it yourself. The book barons are rich enough, anyway. Except where otherwise noted, this book is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit https: //creativecommons.org/licenses/by/4.0/. 3 Table of contents Chapter 1 - A Macroevolutionary Research Program Chapter 2 - Fitting Statistical Models to Data Chapter 3 - Introduction to Brownian Motion Chapter 4 - Fitting Brownian Motion Chapter 5 - Multivariate Brownian Motion Chapter 6 - Beyond Brownian Motion Chapter 7 - Models of discrete character evolution Chapter 8 - Fitting models of discrete character evolution Chapter 9 - Beyond the Mk model Chapter 10 - Introduction to birth-death models Chapter 11 - Fitting birth-death models Chapter 12 - Beyond birth-death models Chapter 13 - Characters and diversification rates Chapter 14 - Summary 4 Chapter 1: A Macroevolutionary Research Pro- gram Section 1.1: Introduction Evolution is happening all around us. -
Repeated Adaptive Divergence of Microhabitat Specialization in Avian Feather Lice Kevin P Johnson1*, Scott M Shreve2 and Vincent S Smith3
Johnson et al. BMC Biology 2012, 10:52 http://www.biomedcentral.com/1741-7007/10/52 RESEARCH ARTICLE Open Access Repeated adaptive divergence of microhabitat specialization in avian feather lice Kevin P Johnson1*, Scott M Shreve2 and Vincent S Smith3 Abstract Background: Repeated adaptive radiations are evident when phenotypic divergence occurs within lineages, but this divergence into different forms is convergent when compared across lineages. Classic examples of such repeated adaptive divergence occur in island (for example, Caribbean Anolis lizards) and lake systems (for example, African cichlids). Host-parasite systems in many respects are analogous to island systems, where host species represent isolated islands for parasites whose life cycle is highly tied to that of their hosts. Thus, host-parasite systems might exhibit interesting cases of repeated adaptive divergence as seen in island and lake systems. The feather lice of birds spend their entire life cycle on the body of the host and occupy distinct microhabitats on the host: head, wing, body and generalist. These microhabitat specialists show pronounced morphological differences corresponding to how they escape from host preening. We tested whether these different microhabitat specialists were a case of repeated adaptive divergence by constructing both morphological and molecular phylogenies for a diversity of avian feather lice, including many examples of head, wing, body and generalist forms. Results: Morphological and molecular based phylogenies were highly incongruent, which could be explained by rampant convergence in morphology related to microhabitat specialization on the host. In many cases lice from different microhabitat specializations, but from the same group of birds, were sister taxa. -
Macroevolutionary Diversification with Limited Niche Disparity in a Species-Rich Lineage of Cold-Climate Lizards Ashley M
Reaney et al. BMC Evolutionary Biology (2018) 18:16 https://doi.org/10.1186/s12862-018-1133-1 RESEARCH ARTICLE Open Access Macroevolutionary diversification with limited niche disparity in a species-rich lineage of cold-climate lizards Ashley M. Reaney1,3 , Mónica Saldarriaga-Córdoba2 and Daniel Pincheira-Donoso1* Abstract Background: Life diversifies via adaptive radiation when natural selection drives the evolution of ecologically distinct species mediated by their access to novel niche space, or via non-adaptive radiation when new species diversify while retaining ancestral niches. However, while cases of adaptive radiation are widely documented, examples of non-adaptively radiating lineages remain rarely observed. A prolific cold-climate lizard radiation from South America (Phymaturus), sister to a hyper-diverse adaptive radiation (Liolaemus), has extensively diversified phylogenetically and geographically, but with exceptionally minimal ecological and life-history diversification. This lineage, therefore, may offer unique opportunities to investigate the non-adaptive basis of diversification, and in combination with Liolaemus, to cover the whole spectrum of modes of diversification predicted by theory, from adaptive to non-adaptive. Using phylogenetic macroevolutionary modelling performed on a newly created 58-species molecular tree, we establish the tempo and mode of diversification in the Phymaturus radiation. Results: Lineage accumulation in Phymaturus opposes a density-dependent (or ‘niche-filling’) process of diversification. Concurrently, we found that body size diversification is better described by an Ornstein-Uhlenbeck evolutionary model, suggesting stabilizing selection as the mechanism underlying niche conservatism (i.e., maintaining two fundamental size peaks), and which has predominantly evolved around two major adaptive peaks on a ‘Simpsonian’ adaptive landscape. -
Rates of Morphological Evolution Are Correlated with Species Richness in Salamanders
ORIGINAL ARTICLE doi:10.1111/j.1558-5646.2011.01557.x RATES OF MORPHOLOGICAL EVOLUTION ARE CORRELATED WITH SPECIES RICHNESS IN SALAMANDERS Daniel L. Rabosky1,2,3 and Dean C. Adams4,5 1Department of Integrative Biology, University of California, Berkeley, California 94750 2Museum of Vertebrate Zoology, University of California, Berkeley, California 94720 3E-mail: [email protected] 4Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011 5Department of Statistics, Iowa State University, Ames, Iowa 50011 Received July 26, 2011 Accepted November 24, 2011 Data Archived: Dryad doi:10.5061/dryad.vt41c78j The tempo and mode of species diversification and phenotypic evolution vary widely across the tree of life, yet the relationship between these processes is poorly known. Previous tests of the relationship between rates of phenotypic evolution and rates of species diversification have assumed that species richness increases continuously through time. If this assumption is violated, simple phylogenetic estimates of net diversification rate may bear no relationship to processes that influence the distribution of species richness among clades. Here, we demonstrate that the variation in species richness among plethodontid salamander clades is unlikely to have resulted from simple time-dependent processes, leading to fundamentally different conclusions about the relationship between rates of phenotypic evolution and species diversification. Morphological evolutionary rates of both size and shape evolution are correlated with clade species richness, but are uncorrelated with simple estimators of net diversification that assume constancy of rates through time. This coupling between species diversification and phenotypic evolution is consistent with the hypothesis that clades with high rates of morphological trait evolution may diversify more than clades with low rates. -
Ecological Speciation
International Journal of Ecology Ecological Speciation Guest Editors: Marianne Elias, Rui Faria, Zachariah Gompert, and Andrew Hendry Ecological Speciation International Journal of Ecology Ecological Speciation Guest Editors: Marianne Elias, Rui Faria, Zachariah Gompert, and Andrew Hendry Copyright © 2012 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “International Journal of Ecology.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial Board Mariana Amato, Italy Jean-Guy Godin, Canada Panos V. Petrakis, Greece Madhur Anand, Canada David Goldstein, USA Daniel I. Rubenstein, USA Joseph R. Bidwell, USA Shibu Jose, USA Herman H. Shugart, USA L. M. Chu, Hong Kong Chandra Prakash Kala, India Andrew Sih, USA Jean Clobert, France Pavlos Kassomenos, Greece R.C. Sihag, India Michel Couderchet, France Thomas H. Kunz, USA C. ter Braak, The Netherlands Ronald D. Delaune, USA Bruce D. Leopold, USA John Whitaker, USA Andrew Denham, Australia A. E. Lugo, USA Walter Whitford, USA Mark A. Elgar, Australia Patricia Mosto, USA J. J. Wiens, USA Jingyun Fang, China Mats Olsson, Australia Xiaozhang Yu, China Contents Factors Influencing Progress toward Ecological Speciation, Marianne Elias, Rui Faria, Zachariah Gompert, and Andrew Hendry Volume 2012, Article ID 235010, 7 pages The Role of Parasitism in Adaptive RadiationsWhen Might Parasites Promote and When Might They Constrain Ecological Speciation?, Anssi Karvonen and Ole Seehausen Volume 2012, Article ID 280169, 20 pages Parallel Ecological Speciation in Plants?, Katherine L. Ostevik, Brook T. Moyers, Gregory L. Owens, and Loren H.