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Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata)
Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata) Item Type text; Electronic Dissertation Authors Lambert, Shea Maddock Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 07/10/2021 08:50:17 Link to Item http://hdl.handle.net/10150/630229 1 PHYLOGENETIC PERSPECTIVES ON VIVIPARITY, GENE-TREE DISCORDANCE, AND INTROGRESSION IN LIZARDS (SQUAMATA). by Shea Maddock Lambert ____________________________ Copyright © Shea Maddock Lambert 2018 A Dissertation Submitted to the Faculty of the DEPARTMENT OF ECOLOGY AND EVOLUTIONARY BIOLOGY In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2 THEUNIVERSITY OF ARIZONA GRADUATE COLLEGE Asmembers of the Dissertation Committee, we certify that we have read the dissertation prepared by Shea M. Lambert, titled "Phylogenetic perspectives on viviparity,gene-tree discordance, and introgressionin lizards {Squamata)" and recomme11dthat it be accepted as fulfillingthe dissertation requirem�t for the Degree of Doctor of Philosophy. _.c.---� ---------Date: May 21, 2018 _wJohn__ . �e� --�_:-_:-__:_ W_ -----�----'-------------------Date: May 21, 2018 Michael Barker M ichael ( s��t=t ��A". =----.�+o/-�i � -\.\----�--------._______ Date: May 21, 2018 Noa�man Final approval and acceptance· of this dissertation is contingent uporithe candidate's submission of the final copies of the· dissertation to the Graduate College. I hereby certify that I have read this dissertation prepared under my ditettion and recommend that it be accepted as fulfillin_;the �issertation requirement. -
Species Boundaries, Biogeography, and Intra-Archipelago Genetic Variation Within the Emoia Samoensis Species Group in the Vanuatu Archipelago and Oceania" (2008)
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2008 Species boundaries, biogeography, and intra- archipelago genetic variation within the Emoia samoensis species group in the Vanuatu Archipelago and Oceania Alison Madeline Hamilton Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Hamilton, Alison Madeline, "Species boundaries, biogeography, and intra-archipelago genetic variation within the Emoia samoensis species group in the Vanuatu Archipelago and Oceania" (2008). LSU Doctoral Dissertations. 3940. https://digitalcommons.lsu.edu/gradschool_dissertations/3940 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. SPECIES BOUNDARIES, BIOGEOGRAPHY, AND INTRA-ARCHIPELAGO GENETIC VARIATION WITHIN THE EMOIA SAMOENSIS SPECIES GROUP IN THE VANUATU ARCHIPELAGO AND OCEANIA A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Alison M. Hamilton B.A., Simon’s Rock College of Bard, 1993 M.S., University of Florida, 2000 December 2008 ACKNOWLEDGMENTS I thank my graduate advisor, Dr. Christopher C. Austin, for sharing his enthusiasm for reptile diversity in Oceania with me, and for encouraging me to pursue research in Vanuatu. His knowledge of the logistics of conducting research in the Pacific has been invaluable to me during this process. -
HCV Assessment for GPPOL
Rapid Conservation Assessment Report GPPOL, Guadalcanal A.J.F.M. Dekker Consultant, Biodiversity Final Report March 2010 Disclaimer The presentation of material in this report and the geographical designations employed do not imply the expression of any opinion whatsoever on the part of the consultant concerning the legal status of any area or territory, or the delimitation of its boundaries. The views and opinions expressed in this publication are those of the consultant and do not necessarily reflect those of GPPOL, its parent company, or the RSPO. While reasonable efforts have been made to ensure that the contents of this report are factually correct, the author does not accept responsibility for the accuracy or completeness of the contents, and shall not be liable for any loss or damage that may be occasioned directly or indirectly through the use of, or reliance on, the contents of this report. 1 EXECUTIVE SUMMARY Guadalcanal Plains Palm Oil Limited (GPPOL) is engaged in the process of obtaining certification under the Roundtable on Sustainable Palm Oil (RSPO). Certification enforces adherence to a set of Principles and Criteria (RSPO P&C), which cover operational, socio-economic, and environmental aspects. This report documents findings related to the rapid assessment of environmental conservation of the operations of GPPOL in Guadalcanal, the Solomon Islands. It is based on two short visits, from 14-25 April, and 26 July-August 3, 2009. Field surveys were carried out in five oil palm estates, and throughout the adjacent areas, with specific focus on the RSPO P&C 4.2, 4.3, 4.4, 5.1, 5.2, 5.3, 7.1, 7.2, 7.3, and 7.4 that are relevant to natural resource and biodiversity conservation, including potential High Conservation Value Areas (HCVA). -
A Phylogeny and Revised Classification of Squamata, Including 4161 Species of Lizards and Snakes
BMC Evolutionary Biology This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes BMC Evolutionary Biology 2013, 13:93 doi:10.1186/1471-2148-13-93 Robert Alexander Pyron ([email protected]) Frank T Burbrink ([email protected]) John J Wiens ([email protected]) ISSN 1471-2148 Article type Research article Submission date 30 January 2013 Acceptance date 19 March 2013 Publication date 29 April 2013 Article URL http://www.biomedcentral.com/1471-2148/13/93 Like all articles in BMC journals, this peer-reviewed article can be downloaded, printed and distributed freely for any purposes (see copyright notice below). Articles in BMC journals are listed in PubMed and archived at PubMed Central. For information about publishing your research in BMC journals or any BioMed Central journal, go to http://www.biomedcentral.com/info/authors/ © 2013 Pyron et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes Robert Alexander Pyron 1* * Corresponding author Email: [email protected] Frank T Burbrink 2,3 Email: [email protected] John J Wiens 4 Email: [email protected] 1 Department of Biological Sciences, The George Washington University, 2023 G St. -
Literary Citizen of the Andes: Gabriela Alemán and Quito 3 Next-Generation Robotic Cockroach Can Explore Under Water Environmen
Literary Citizen of the Andes: Gabriela Alemán and Quito 3 Next-generation robotic cockroach can explore under water environments 8 Extreme weather 'potentially catastrophic' for bats 11 Mistletoe Lacks Key Energy-Generating Complex 13 An Exoplanet First! Helium Spotted on Bizarre Comet-Like World 15 Nanoparticles could help rescue malnourished crops 19 Wireless 'RoboFly' Looks Like an Insect, Gets Its Power from Lasers 22 Ancient Chinese farmers sowed literal seeds of change in Southeast Asia 24 New Data: Hurricanes Will Get Worse 26 Lizards’ Green Blood Evolved Four Times 29 Zika virus may pose greater threat of miscarriages than previously thought 31 Forgotten Feminisms: Johnnie Tillmon’s Battle Against ‘The Man’ 34 Little Panic: A Literary Laboratory Exploring What It Is Like to Live in the Stranglehold of Anxiety and 47 What It Takes to Break Free Neanderthals practiced close-range hunting 120,000 years ago 55 Forgotten Feminisms: An Appeal Against ‘Domestic Despotism’ 57 Remarks on Moduli Spaces and String Theory 64 After the Fall 69 Sound-waves: Making opaque materials totally transparent 79 Toy Stories: Portraits of Children and their Toys Around the World 81 Rilke on the Lonely Patience of Creative Work 96 Smoking Ocean Vents Found in Surprisingly Shallow Water 99 Air pollution contributes significantly to diabetes globally 103 A Keith Haring Mural Painted in 1986 and Under Wraps for 30 Years Has Been Revealed in Amsterdam 106 Amanda Palmer and The Decomposers Cover Joni Mitchell’s “Big Yellow Taxi” in Tribute to Rachel 108 Carson Kate Millett: ‘Sexual Politics’ & Family Values 111 Sistema de Infotecas Centrales Universidad Autónoma de Coahuila Dreamlike Landscapes Grow from Sculptural Portraits by Yuanxing Liang 116 How Does the Summer Solstice Affect Animals? 125 Compounds found in green tea and red wine may block formation of toxic metabolites 128 Fixed vs. -
Checklist and Comments on the Terrestrial Reptile Fauna of Kau
area with a complex geologic history. Over the last 40 million Herpetological Review, 2006, 37(2), 167–170. © 2006 by Society for the Study of Amphibians and Reptiles years interplate impact resulted in considerable uplift and volcan- ism and importantly the accretion of at least 32 tectonostratigraphic Checklist and Comments on the Terrestrial terranes along the northern leading edge of the island that have Reptile Fauna of Kau Wildlife Area, Papua New influenced the biodiversity of the region (Pigram and Davies 1987; Guinea Polhemus and Polhemus 1998). To date there has been no comprehensive herpetofaunal reports from the KWA. Here I compile a list of terrestrial reptile species CHRISTOPHER C. AUSTIN present in the KWA based on fieldwork over the past 14 years. Museum of Natural Science, 119 Foster Hall, Louisiana State University Baton Rouge, Louisiana 70803, USA The KWA terrestrial reptile fauna, exclusive of crocodylians and e-mail: [email protected] turtles, currently includes 25 lizards and 7 snakes representing 8 families and 21 genera (Table 1). A similar compilation is under- The island of New Guinea has been identified as a megadiverse way for the amphibians of the region (S. Richards, pers. comm.). region because of its extraordinary biodiversity and highly en- Specific specimen and locality information as well as associated demic biota (Mittermeier and Mittermeier 1997). New Guinea, tissues can be accessed via a searchable database of the LSU Mu- the world’s largest and highest tropical island, occupies less than seum of Natural Science reptile and amphibian collection (http:// 1% of global land area yet 5–7% of the world’s biodiversity is www.lsu.edu/museum). -
Systematics of the Carlia “Fusca” Lizards (Squamata: Scincidae) of New Guinea and Nearby Islands
Systematics of the Carlia “fusca” Lizards (Squamata: Scincidae) of New Guinea and Nearby Islands George R. Zug Bishop Museum Bulletin in Zoology 5 Bishop Museum Press Honolulu, 2004 Cover: Published by Bishop Museum Press 1525 Bernice Street Honolulu, Hawai‘i 96817-2704, USA Copyright ©2004 Bishop Museum All Rights Reserved Printed in the United States of America ISSN 0893-312X Zug — Carlia “fusca” Lizards from New Guinea and Nearby Islands v TABLE OF CONTENTS Acknowledgments ......................................................................................................................... vii Abstract ........................................................................................................................................ viii Introduction ................................................................................................................................... 1 Carlia: An Analysis for Species Relationships ........................................................................... 1 Characters and Taxa .................................................................................................................. 2 Phylogenetic Analysis................................................................................................................ 8 New Guinea Carlia “fusca” ....................................................................................................... 9 Materials and Methods................................................................................................................. -
When Do Species-Tree and Concatenated Estimates Disagree? an Empirical Analysis with Higher-Level Scincid Lizard Phylogeny ⇑ Shea M
Molecular Phylogenetics and Evolution 82 (2015) 146–155 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny ⇑ Shea M. Lambert a, , Tod W. Reeder b, John J. Wiens a a Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA b Department of Biology, San Diego State University, San Diego, CA 92182, USA article info abstract Article history: Simulation studies suggest that coalescent-based species-tree methods are generally more accurate than Received 17 April 2014 concatenated analyses. However, these species-tree methods remain impractical for many large datasets. Revised 9 September 2014 Thus, a critical but unresolved issue is when and why concatenated and coalescent species-tree estimates Accepted 2 October 2014 will differ. We predict such differences for branches in concatenated trees that are short, weakly Available online 12 October 2014 supported, and have conflicting gene trees. We test these predictions in Scincidae, the largest lizard fam- ily, with data from 10 nuclear genes for 17 ingroup taxa and 44 genes for 12 taxa. We support our initial Keywords: predictions, and suggest that simply considering uncertainty in concatenated trees may sometimes Concatenated analysis encompass the differences between these methods. We also found that relaxed-clock concatenated trees Phylogenetic methods Reptile can be surprisingly similar to the species-tree estimate. Remarkably, the coalescent species-tree esti- Scincidae mates had slightly lower support values when based on many more genes (44 vs. 10) and a small Species-tree analysis (30%) reduction in taxon sampling. -
Species Richness in Time and Space: a Phylogenetic and Geographic Perspective
Species Richness in Time and Space: a Phylogenetic and Geographic Perspective by Pascal Olivier Title A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Ecology and Evolutionary Biology) in The University of Michigan 2018 Doctoral Committee: Assistant Professor and Assistant Curator Daniel Rabosky, Chair Associate Professor Johannes Foufopoulos Professor L. Lacey Knowles Assistant Professor Stephen A. Smith Pascal O Title [email protected] ORCID iD: 0000-0002-6316-0736 c Pascal O Title 2018 DEDICATION To Judge Julius Title, for always encouraging me to be inquisitive. ii ACKNOWLEDGEMENTS The research presented in this dissertation has been supported by a number of research grants from the University of Michigan and from academic societies. I thank the Society of Systematic Biologists, the Society for the Study of Evolution, and the Herpetologists League for supporting my work. I am also extremely grateful to the Rackham Graduate School, the University of Michigan Museum of Zoology C.F. Walker and Hinsdale scholarships, as well as to the Department of Ecology and Evolutionary Biology Block grants, for generously providing support throughout my PhD. Much of this research was also made possible by a Rackham Predoctoral Fellowship, and by a fellowship from the Michigan Institute for Computational Discovery and Engineering. First and foremost, I would like to thank my advisor, Dr. Dan Rabosky, for taking me on as one of his first graduate students. I have learned a tremendous amount under his guidance, and conducting research with him has been both exhilarating and inspiring. I am also grateful for his friendship and company, both in Ann Arbor and especially in the field, which have produced experiences that I will never forget. -
Animals Are Interesting a Festschrift in Honour of Anthony P
O.R.P. Bininda-Emonds, G.L. Powell, H.A. Jamniczky, A.M. Bauer & J. Theodor (eds.) All Animals are Interesting A Festschrift in Honour of Anthony P. Russell BIS-Verlag der Carl von Ossietzky Universität Oldenburg Cover Photo: Johan Marais Oldenburg, 2015 Verlag / Druck / Vertrieb BIS-Verlag der Carl von Ossietzky Universität Oldenburg Postfach 2541 26015 Oldenburg E-Mail: [email protected] Internet: www.bis-verlag.de ISBN 978-3-8142-2324-7 Anthony P. Russell, July 2012 Convergent evolution of body shape in squamate reptiles Philip J. Bergmann Department of Biology, Clark University, 950 Main Street, Worcester, Massachusetts 01610, USA; E-mail: [email protected] Abstract Convergent evolution is a common pattern in nature, with many documented examples ranging from molecular and genomic scales to organismal and possibly to ecosystem scales. Although there are many documented examples of convergence, methods for formal testing of convergence are only recently being developed and studies of mechanism are less common still. Here, I construct a phylomorphospace of squamate reptile body shape and use it to test for convergence among clades and taxa that are thought to be under sim- ilar selective regimes. I test for convergence by examining the degree of overlap among convergent taxa in the phylomorphospace and by examining the direction of evolution along convergent phylogenetic branches by com- paring non-convergent ancestors and convergent descendants. I find strong evidence for convergence in body shape among taxa that have evolved elon- gation because of fossoriality or because of inhabiting complex environ- ments, gliding, and sand-dwelling. I find some evidence for body shape con- vergence in taxa that have evolved dry adhesion, but no evidence of conver- gence among herbivores or bipedal lizards. -
Competition Poorly Correlates with Morphological Niche Partitioning In
Competition poorly correlates with morphological niche partitioning in a radiation of tropical lizards Alex Slavenko1, Allen Allison2, and Shai Meiri3 1The University of Sheffield 2Bishop Museum 3Tel Aviv University May 5, 2020 Abstract Morphology is expected to represent species' ecological niches, based on microhabitat and ecological selection pressures dictating morphological adaptations for efficient performance. However, the presence of competitor species is predicted to cause niches to contract. Therefore, an increase in species richness is expected to lead to narrower niches, and reduced overlap and distances between niches of different species. We tested these predictions on the skink fauna of New Guinea, the world's largest tropical island. We show that, while some morphospace metrics change predictably with species richness, elevation is a stronger predictor of morphospace occupancy. As elevation increases niches become narrower and closer to each other, and overall morphospace occupancy decreases. Highland skinks are, on average, smaller, thinner, and with shorter limbs than lowland species. We hypothesize that harsh climates in highland habitats impose strong selection on skinks to occupy specific areas of morphospace that facilitate efficient thermoregulation in sub-optimal thermal conditions. Competition poorly correlates with morphological niche partitioning in a radiation of tropical lizards Alex Slavenko1,2*, Allen Allison3, Shai Meiri2,4 1 { Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK 2 { School of Zoology, Tel Aviv University, Tel Aviv, Israel 3 { Bernice P. Bishop Museum, Honolulu, USA 4 { The Steinhardt Museum of Natural History, Tel Aviv, Israel * { Corresponding author; a.slavenko@sheffield.ac.uk Article type: Letters Short running title: Morphospace partitioning of tropical lizards Statement of Authorship: AS collected data and designed and performed the statistical analyses. -
Using Herpetofauna and Culture to Determine Conservation Priority Habitats on Malaita Island, Solomon Islands
EVALUATING TROPICAL FOREST ECOSYSTEMS: USING HERPETOFAUNA AND CULTURE TO DETERMINE CONSERVATION PRIORITY HABITATS ON MALAITA ISLAND, SOLOMON ISLANDS by Edgar John Maeniuta Pollard A thesis submitted in fulfilment of the requirements for the degree of Masters in Environmental Science Copyright © 2013 by Edgar John Maeniuta Pollard School of Geography, Earth Science and Environmental Sciences Faculty of Science, Technology and Environment The University of the South Pacific July, 2013 Declaration Statement by Author I, Edgar John Maeniuta Pollard, declare that this thesis is my own work and that, to the best of my knowledge, it contains no material previously published, or substantially overlapping with material submitted for the award of any other degree at any institution, except where due acknowledgment is made in the text. Signature …………………………… Date…………………………. Student ID No. ………………………………………………………. Statement by Supervisor The research in this thesis was performed under my supervision and to my knowledge is the sole work of Mr Edgar John Maeniuta Pollard. Signature…………………………….. Date ……………………….. Name..……………………………………………………………….. Designation …………………………………………………………. Acknowledgements Mauriha e hitarana rapena noni. Apu ana noni e hitarana kahu ni mauriha, susurina noni e hitarana okiraha ana mauriha, manina noni e hitarana mako e watea mauriha, ihihu ana pau na noni e hitarana ai ma maasu e watea mauriha This thesis is dedicated to the people of Are’Are, Malaita. For captured within this work is a glimpse of the richness their lands and people hold. Raemanoha Rikaa. I would like to thank the stewards, landowners and tribes of the Arata’s (land) and villages that this study was conducted in, for allowing access onto their land.