Cepf Small Grant Final Project Completion Report
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Evoregions: Mapping Shifts in Phylogenetic Turnover Across Biogeographic
bioRxiv preprint doi: https://doi.org/10.1101/650713; this version posted May 27, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 Evoregions: Mapping Shifts in Phylogenetic Turnover Across Biogeographic 2 Regions 3 Running head: Mapping evolutionary important regions 4 Renan Maestri1,* & Leandro Duarte1,* 5 1Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, 6 Av. Bento Gonçalves 9500, CP 15007, Porto Alegre RS 91501-970, Brazil 7 *Correspondence be sent to: Departamento de Ecologia, Universidade Federal do Rio 8 Grande do Sul, Av. Bento Gonçalves 9500, CP 15007, Porto Alegre RS 91501-970, 9 Brazil; E-mail: [email protected]; [email protected] 10 ABSTRACT: Biogeographic regionalization offers context to the geographical 11 evolution of clades. The positions of bioregions inform both the spatial location of 12 clusters in species distribution and where their most important boundaries are. 13 Nevertheless, defining bioregions based on species distribution alone only incidentally 14 recovers regions that are important during the evolution of the focal group. The extent 15 to which bioregions correspond to centers of independent diversification depends on 16 how clusters of species composition naturally reflect the radiation of single clades, 17 which is not the case when mixed colonization occurred. Here, we showed that using 18 phylogenetic turnover based on fuzzy sets, instead of species composition, led to more 19 adequate detection of evolutionary important bioregions, that is, regions that truly 20 account for the independent diversification of lineages. -
Subfamily Nesomyinae)
bs_bs_banner Biological Journal of the Linnean Society, 2013, ••, ••–••. With 5 figures Latitude drives diversification in Madagascar’s endemic dry forest rodent Eliurus myoxinus (subfamily Nesomyinae) JEFF J. SHI1†, LAUREN M. CHAN1*‡, ZAFIMAHERY RAKOTOMALALA2,3, AMY M. HEILMAN1, STEVEN M. GOODMAN3,4 and ANNE D. YODER1 1Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA 2Département de Biologie Animale, Université d’Antananarivo, BP 906, Antananarivo 101, Madagascar 3Association Vahatra, BP 3972, Antananarivo 101, Madagascar 4Department of Zoology, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA Received 29 March 2013; revised 14 May 2013; accepted for publication 14 May 2013 Numerous hypotheses have been proposed for the historical processes governing the rich endemism of Madagas- car’s biodiversity. The ‘watershed model’ suggests that drier climates in the recent geological past have resulted in the contraction of forests around major watersheds, thereby defining areas of endemism. We test whether this hypothesis explains phylogeographical patterns in a dry forest-dependent rodent, Eliurus myoxinus, an endemic species widely distributed through western Madagascar. We sequenced the mitochondrial cytochrome b locus and nuclear introns of the β-fibrinogen and the growth hormone receptor genes for E. myoxinus. Using a parametric bootstrapping approach, we tested whether the mitochondrial gene tree data fit expectations of local differentiation given the watershed model. We additionally estimated population differentiation and historical demographic parameters, and reconstructed the spatial history of E. myoxinus to highlight spatial and temporal patterns of differentiation. The data do not support the watershed model as a clear explanation for the genetic patterns of diversity within extant E. -
Rapid Pace of Species Extinctions Mounts to a 'Crisis'
Rapid Pace of Species Extinctions Mounts to a 'Crisis' GLAND, Switzerland, November 3, 2009 (ENS) - Nearly one-third of all known species of plants and animals are threatened with extinction, finds the International Union for the Conservation of Nature, IUCN, in the most recent update of its authoritative Red List of Threatened Species� issued today. The updated assessment shows that 17,291 species out of the 47,677 assessed species are threatened with extinction. "The scientific evidence of a serious extinction crisis is mounting," warns Jane Smart, director of IUCN's Biodiversity Conservation Group. The IUCN finds that 21 percent of all known mammals, 30 percent of all known amphibians, 12 percent of all known birds, and 28 percent of reptiles, 37 percent of freshwater fishes, 70 percent of plants, 35 percent of invertebrates assessed so far are at risk. "This year's IUCN Red List makes for sobering reading," says Craig Hilton-Taylor, manager of the IUCN Red List Unit. "These results are just the tip of the iceberg. We have only managed to assess 47,663 species so far; there are many more millions out there which could be under serious threat." "We do, however, know from experience that conservation action works so let's not wait until it's too late and start saving our species now," urged Hilton- Taylor. Threatened by climate change, the hooded grebe, Podiceps gallardoi, of Argentina, was "January sees the launch of the International Year of uplisted from Near Threatened to Biodiversity, said Smart. "The latest analysis of the Endangered in 2009. -
Morphology Captures Diet and Locomotor Types in Rodents Authors: Luis D
Royal Society Open Science Supplementary material for: Morphology captures diet and locomotor types in rodents Authors: Luis D. Verde Arregoitia, Diana O. Fisher, and Manuel Schweizer Data definition The following files can be downloaded from: http://doi.org/10.5281/zenodo.201147 Ecological data (DietLocomotion.csv) . Diet type and locomotion categories and the data sources used to assign them, following the numbered reference lists below (Reference Lists 3 and 4). Body size data (bodySizes.csv). Body size data for all 208 species with data sources, following the numbered reference list below (Reference List 2). Specimens examined (measurementsFinal.csv). Original measurements taken by LDVA. The mus field identifies the collections that house the specimens. QM = Queensland Museum (Brisbane, Australia), AusMus = Australian Museum (Sydney, Australia), MZFC = ‘‘Alfonso L. Herrera’’ Zoology Museum (UNAM, Mexico City, Mexico). See main text for measurement methods and definitions. Species means (meansMasses.csv). Mean values for all 14 measurements with their data source. Values derived from specimens measured by LDVA are identified with in the dataProv field as “LD”. Other values were collated from the sources in Reference List 1 and updated from amended tables and correspondence with the lead author (identified in the table as “AM”). Sources for body mass data are detailed separately. See main text for measurement methods and definitions. All other tables are produced as intermediate or final outputs of the analysis scripts provided The R scripts are named in the order in which they can be used. “phylo.fda.v0.2noPlotting” needs to be sourced for several of the analyses. Table S1. Taxonomic context of species examined in this study. -
Mystromys Albicaudatus – White-Tailed Rat
Mystromys albicaudatus – White-tailed Rat Fynbos biomes; Dean 1978) and is endemic to South Africa and Lesotho. Although it occurs widely across the assessment region, it has an extremely patchy and fragmented area of occupancy due to its preference for microhabitats within vegetation types and transitory habitats created after fire. Out of a total area of 417,452 km2 broadly available to the species, we inferred an effective occupancy of only 3,719–12,061 km2. They are one of the rarest species in the small mammal community, as demonstrated by consistently low trapping records. Given estimated densities ranging from 0.9– 37 colonies (breeding pairs) / km2, the most likely mature population size is 6,997–13,648 individuals. Using Patrick O’Farrell grassland vegetation type as a proxy for subpopulation delineation, subpopulation size averages 178 ± 177 colonies and ranges from 1–760 colonies, which means Red List status (2016) Vulnerable C2a(i)*† the largest subpopulation is likely to be 712–1,521 mature Red List status (2008) Endangered A3c individuals. There is an inferred continuing decline from grassland habitat loss (due to expansion in crop Reasons for change Non-genuine change: agriculture, urban and industrial development, and climate New information change) and grassland habitat degradation, primarily from Red List status (2004) Endangered A3c suppression of natural fire regimens. This may represent an emerging threat to this species if fire is increasingly TOPS listing (NEMBA) (2007) None suppressed or controlled with the rise of intensive wildlife CITES listing None breeding. Grasslands are the most threatened biome in the assessment region with at least 33% transformed Endemic No already. -
List of Vertebrate Species Recorded at Tsinjoarivo
VERTEBRATE SPECIES RECORDED AT TSINJOARIVO, MADAGASCAR Compiled by M. Irwin, 2010 SOURCE: English Name Scientific Name Local Name 1 2 3 4 MAMMALIA: PRIMATES Diademed Sifaka Propithecus diadema ssp. - EN Sadabe + + + Lesser Bamboo Lemur Hapalemur griseus - VU Kotraika + + + Brown Lemur Eulemur fulvus – NT Varika + + + Red-Bellied Lemur Eulemur rubriventer - VU Varika mena + + Woolly Lemur Avahi laniger – LC Ramiona (Avahina) + + + Sportive Lemur Lepilemur mustelinus – DD Tsidika + + + Mouse Lemur Microcebus rufus – LC Tsilamodamoka + + + Crossley’s Dwarf Lemur Cheirogaleus crossleyi - DD Matavirambo + Sibree’s Dwarf Lemur Cheirogaleus sibreei - DD Matavirambo + Aye-aye Daubentonia madagascariensis - NT Hay-hay + + Black and White Ruffed Lemur Varecia variegata variegata ? ? MAMMALIA: INSECTIVORA Common Tenrec Tenrec ecaudatus – LC Trandraka + + + Shrew Tenrecs: Microgale cowani – LC + + Microgale dobsoni – LC + + Microgale fotsifotsy – LC + Microgale gracilis – LC + + Microgale gymnorhyncha – LC + Microgale longicaudata – LC + + Microgale major 1 – LC + Microgale parvula – LC + Microgale pusilla – LC + Microgale soricoides – LC + Microgale taiva – LC + Microgale thomasi – LC + + Lowland Streaked Tenrec Hemicentetes semispinosus – LC Sora + + + Highland Streaked Tenrec Hemicentetes nigriceps – LC Sora + Greater Hedgehog Tenrec Setifer setosus – LC + + Rice Tenrec Oryzorictes hova – LC + * Musk Shrew Suncus murinus – LC + MAMMALIA: RODENTIA Tuft-tailed Rats: Eliurus grandidieri – LC + Eliurus majori – LC + Eliurus minor – LC + Voalavoanala -
Phylogenetic Relationships and Divergence Times in Rodents Based on Both Genes and Fossils Ryan Norris University of Vermont
University of Vermont ScholarWorks @ UVM Graduate College Dissertations and Theses Dissertations and Theses 2009 Phylogenetic Relationships and Divergence Times in Rodents Based on Both Genes and Fossils Ryan Norris University of Vermont Follow this and additional works at: https://scholarworks.uvm.edu/graddis Recommended Citation Norris, Ryan, "Phylogenetic Relationships and Divergence Times in Rodents Based on Both Genes and Fossils" (2009). Graduate College Dissertations and Theses. 164. https://scholarworks.uvm.edu/graddis/164 This Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks @ UVM. It has been accepted for inclusion in Graduate College Dissertations and Theses by an authorized administrator of ScholarWorks @ UVM. For more information, please contact [email protected]. PHYLOGENETIC RELATIONSHIPS AND DIVERGENCE TIMES IN RODENTS BASED ON BOTH GENES AND FOSSILS A Dissertation Presented by Ryan W. Norris to The Faculty of the Graduate College of The University of Vermont In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Specializing in Biology February, 2009 Accepted by the Faculty of the Graduate College, The University of Vermont, in partial fulfillment of the requirements for the degree of Doctor of Philosophy, specializing in Biology. Dissertation ~xaminationCommittee: w %amB( Advisor 6.William ~il~atrickph.~. Duane A. Schlitter, Ph.D. Chairperson Vice President for Research and Dean of Graduate Studies Date: October 24, 2008 Abstract Molecular and paleontological approaches have produced extremely different estimates for divergence times among orders of placental mammals and within rodents with molecular studies suggesting a much older date than fossils. We evaluated the conflict between the fossil record and molecular data and find a significant correlation between dates estimated by fossils and relative branch lengths, suggesting that molecular data agree with the fossil record regarding divergence times in rodents. -
The Input of DNA Sequences to Animal Systematics: Rodents As Study Cases
6 The Input of DNA Sequences to Animal Systematics: Rodents as Study Cases Laurent Granjon1 and Claudine Montgelard2 1Institut de Recherche Pour le Développement (IRD), CBGP(UMRIRD/INRA/CIRAD/MontpellierSupAgro), Campus de Bel-Air, Dakar, 2Biogéographie et Ecologie des Vertébrés (EPHE), Centre d’Ecologie Fonctionnelle et Evolutive (UMR 5175 CNRS), Montpellier, Cedex 5 1Senegal 2France 1. Introduction 1.1 General context The advent of molecular techniques, and especially the possibility to get DNA sequences that can then be compared between individuals of any taxon using more and more powerful algorithms of analysis, has represented a kind of revolution in systematics (Lecointre et al., 2006; Giribet et al., 2007). As in other groups, mammalian systematics was for long only based on morphological and anatomical characters. A brief history of Mammal taxonomy has been provided by Wilson & Reeder (2005: xxiii), starting by early works of Trouessart (1898-99, 1904-5) and ending by the compilation by Mc Kenna & Bell (1997). Since the latter, a huge quantity of data including a significant proportion of molecular ones has accumulated, that have greatly improved our view of the relationships between main mammalian groups (Springer et al., 2004), and increased the number of individual species in each of them (Wilson & Reeder, 2005). Rodents represent the most diverse order of Mammals, comprising around 40% of both generic and specific mammalian diversity (Wilson & Reeder, 2005). In one of the first significant contribution to the study of their classification, Tullberg (1899) subdivided them into two suborders, the Sciurognathi and Hystricognathi (see Hautier et al., 2011), based on morpho-anatomical characteristics of their skull. -
Microcebus Griseorufus) Conservation: Local Resource Utilization and Habitat Disturbance at Beza Mahafaly, Sw Madagascar
THE HUMAN FACTOR IN MOUSE LEMUR (MICROCEBUS GRISEORUFUS) CONSERVATION: LOCAL RESOURCE UTILIZATION AND HABITAT DISTURBANCE AT BEZA MAHAFALY, SW MADAGASCAR A Dissertation Presented by EMILIENNE RASOAZANABARY Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY February 2011 Anthropology © Copyright by Emilienne Rasoazanabary 2011 All Rights Reserved THE HUMAN FACTOR IN MOUSE LEMUR (MICROCEBUS GRISEORUFUS) CONSERVATION: LOCAL RESOURCE UTILIZATION AND HABITAT DISTURBANCE AT BEZA MAHAFALY, SW MADAGASCAR A Dissertation Presented By EMILIENNE RASOAZANABARY Approved as to style and content by: _______________________________________ Laurie R. Godfrey, Chair _______________________________________ Lynnette L. Sievert, Member _______________________________________ Todd K. Fuller, Member ____________________________________ Elizabeth Chilton, Department Head Anthropology This dissertation is dedicated to the late Berthe Rakotosamimanana and Gisèle Ravololonarivo (Both Professors in the DPAB) Claire (Cook at Beza Mahafaly) Pex and Gyca (Both nephews) Guy and Edmond (Both brothers-in-law) Claudia and Alfred (My older sister and my older brother) All of my grandparents Rainilaifiringa (Grandpa) All of the fellow gray mouse lemurs ACKNOWLEDGMENTS This dissertation has been more a process than a document; its completion is long anticipated and ever-so-welcome. So many people participated in and brought to me the most precious and profoundly appreciated support – academic, physical, and emotional. I would not have been able to conduct this work without leaning on those people. I am very grateful to every single one of them. In case you read the dissertation and find your name unlisted, just remember that my gratitude extends to each one of you. I am extremely grateful to Dr. -
New Findings at Andrahomana Cave, Southeastern Madagascar
Portland State University PDXScholar Anthropology Faculty Publications and Presentations Anthropology 4-1-2008 New Findings at Andrahomana Cave, Southeastern Madagascar David A. Burney National Tropical Botanical Garden Natalie Vasey Portland State University, [email protected] Laurie R. Godfrey University of Massachusetts William L. Jungers Stony Brook University Ramilisonina Musée d'Art et d'Archéologie See next page for additional authors Follow this and additional works at: https://pdxscholar.library.pdx.edu/anth_fac Part of the Anthropology Commons Let us know how access to this document benefits ou.y Citation Details D.A. Burney, N. Vasey, L.R. Godfrey, Ramilisonina, W.L. Jungers, M. Ramarolahy, and L. Raharivony – New Findings at Andrahomana Cave, Southeastern Madagascar. Journal of Cave and Karst Studies, v. 70, no. 1, p. 13–24. This Article is brought to you for free and open access. It has been accepted for inclusion in Anthropology Faculty Publications and Presentations by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Authors David A. Burney, Natalie Vasey, Laurie R. Godfrey, William L. Jungers, Ramilisonina, M. F. Ramarolahy, and L. L. Raharivony This article is available at PDXScholar: https://pdxscholar.library.pdx.edu/anth_fac/47 D.A. Burney, N. Vasey, L.R. Godfrey, Ramilisonina, W.L. Jungers, M. Ramarolahy, and L. Raharivony – New Findings at Andrahomana Cave, Southeastern Madagascar. Journal of Cave and Karst Studies, v. 70, no. 1, p. 13–24. NEW FINDINGS AT ANDRAHOMANA CAVE, SOUTHEASTERN MADAGASCAR D.A. BURNEY1,*,N.VASEY2, L.R. GODFREY3,RAMILISONINA4, W.L. JUNGERS5,M.RAMAROLAHY6, AND L. -
A Baseline Estimate of Population Size for Monitoring the Endangered Madagascar Giant Jumping Rat Hypogeomys Antimena R Ichard P
A baseline estimate of population size for monitoring the Endangered Madagascar giant jumping rat Hypogeomys antimena R ichard P. Young,Anselme T oto V olahy,Robert B ourou,Richard L ewis, J oanna D urbin,Tim J. Wright,Tim D. Hounsome and J ohn E. Fa Abstract The Endangered Madagascar giant jumping rat, Introduction Hypogeomys antimena, has suffered a major decline in dis- tribution and is now restricted to two seemingly uncon- eciduous, seasonally dry forest in western Madagascar nected sub-populations in the largest remaining fragment of Dharbours high numbers of animal and plant endemics deciduous, seasonally dry forest in Menabe, western Mada- but has been dramatically reduced in extent and become gascar. In a previous study a rapid decrease in numbers of highly fragmented through encroachment by subsistence H. antimena was observed in relatively intact forest, suggest- agriculture and timber harvesting. This habitat is now ing a factor of population decline additional to habitat loss, one of the highest conservation priorities in Madagascar 2001 and provoking fears of a negative trend occurring across its (Ganzhorn et al., ). Dry forest once covered much of 1990 3 remaining range. In the current study we conducted exten- western Madagascar but by only an estimated c. %of 1997 sive line transect surveys to estimate active H. antimena the original cover remained (Smith, ). As a result, many burrow density in 2004 and 2005 as an index of population species associated with this habitat have suffered concom- size, and trapping to estimate mean group size, as a multiplier itant declines in their distribution and population size and for population size estimation. -
The Rodent Problem in Madagascar
i Jean-Marci Duplantier and Daniel Rakotondravony Abstract In Madagascar the rodent problem is linked to one species, the black rat (Rattus rattus). This chapter will describe its population dynamics in agro-ecosystemsand its impact in agricultural crops, in stored grain, on human health and on the endemic rodent community. The black rat has spread absolutely everywhere: from sea level to more than 2,000 m-in houses, fields and also in the forests. It represents more than 95% of rodent catches in the fields and inside houses. Reproduction of rats living in fields stops during the cold season when their maximum annual abundance is observed. Irrigated rice crops suffer the greatest damage with losses estimated at 2.5% of the harvest. Rodent damage is also important for pluvial riceand to a lesser 'fi-- degree for cassava, sweet potatoes and tomatoes. Damage to cacao and sugar I cane are important only in the small, poorly-maintainedpersonal plantations. Plague ,I is undeniably the most important disease linked with rodents in Madagascar. It is endemic to the centre of the island in rural areas located above 800 m and its 5: prevalence is increasing. Rodent control in Madagascar is extremely complex because of the economic difficulties facing the country and because the black rat has displayed such successful colonisation in absolutely all habitats. Keywords Black rat, conservation biology, Madagascar, plague, rice fields, rodent control, rodent damage ! In : <( Ecologically-based rodent management $h. - Eds : Grant Singleton, Lyn Hinds, Herwig Leirs and Zhibin Zhang ACIAR editions, septembre 1999 'h, c 441 o 1O026038 Ecologically-based Rodent Management INTRODUCTION years ago.