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      Evolutionary history of burrowing asps (Lamprophiidae: Atractaspidinae) with emphasis on fang evolution and prey selection

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          Abstract

          Atractaspidines are poorly studied, fossorial snakes that are found throughout Africa and western Asia, including the Middle East. We employed concatenated gene-tree analyses and divergence dating approaches to investigate evolutionary relationships and biogeographic patterns of atractaspidines with a multi-locus data set consisting of three mitochondrial ( 16S, cyt b, and ND4) and two nuclear genes ( c-mos and RAG1). We sampled 91 individuals from both atractaspidine genera ( Atractaspis and Homoroselaps). Additionally, we used ancestral-state reconstructions to investigate fang and diet evolution within Atractaspidinae and its sister lineage (Aparallactinae). Our results indicated that current classification of atractaspidines underestimates diversity within the group. Diversification occurred predominantly between the Miocene and Pliocene. Ancestral-state reconstructions suggest that snake dentition in these taxa might be highly plastic within relatively short periods of time to facilitate adaptations to dynamic foraging and life-history strategies.

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          Selecting optimal partitioning schemes for phylogenomic datasets

          Background Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of fewer than 100 loci. This is a problem because datasets with thousands of loci are increasingly common in phylogenetics. Methods We develop two novel methods for estimating best-fit partitioning schemes on large phylogenomic datasets: strict and relaxed hierarchical clustering. These methods use information from the underlying data to cluster together similar subsets of sites in an alignment, and build on clustering approaches that have been proposed elsewhere. Results We compare the performance of our methods to each other, and to existing methods for selecting partitioning schemes. We demonstrate that while strict hierarchical clustering has the best computational efficiency on very large datasets, relaxed hierarchical clustering provides scalable efficiency and returns dramatically better partitioning schemes as assessed by common criteria such as AICc and BIC scores. Conclusions These two methods provide the best current approaches to inferring partitioning schemes for very large datasets. We provide free open-source implementations of the methods in the PartitionFinder software. We hope that the use of these methods will help to improve the inferences made from large phylogenomic datasets.
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            The Maximum Likelihood Approach to Reconstructing Ancestral Character States of Discrete Characters on Phylogenies

            Mark Page (1999)
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              Mitochondrial DNA Sequence Divergence and Phylogenetic Relationships among Eight Chromosome Races of the Sceloporus Grammicus Complex (Phrynosomatidae) in Central Mexico

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: ResourcesRole: Writing – review & editing
                Role: Data curationRole: Writing – review & editing
                Role: Data curationRole: Writing – review & editing
                Role: Data curationRole: Writing – review & editing
                Role: Data curationRole: Writing – review & editing
                Role: Data curationRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: InvestigationRole: Project administrationRole: ResourcesRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Project administrationRole: Writing – review & editing
                Role: Data curationRole: Project administrationRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: Data curationRole: Writing – review & editing
                Role: Data curationRole: Writing – review & editing
                Role: Data curationRole: Writing – review & editing
                Role: Data curationRole: MethodologyRole: Project administrationRole: Writing – review & editing
                Role: Data curationRole: Project administrationRole: Writing – review & editing
                Role: Data curationRole: Project administrationRole: Writing – review & editing
                Role: Data curationRole: MethodologyRole: Resources
                Role: Data curationRole: Project administrationRole: Writing – review & editing
                Role: Data curationRole: Project administrationRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: Writing – review & editing
                Role: Data curationRole: Project administrationRole: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: Writing – original draft
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                17 April 2019
                2019
                : 14
                : 4
                : e0214889
                Affiliations
                [1 ] Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
                [2 ] Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
                [3 ] Port Elizabeth Museum, Humewood, South Africa
                [4 ] Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa
                [5 ] School of Natural Resource Management, George Campus, Nelson Mandela University, George, South Africa
                [6 ] Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
                [7 ] Department of Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Germany
                [8 ] Laboratoire d’Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, Lwiro, South Kivu, Democratic Republic of the Congo
                [9 ] Institut Supérieur d'Écologie pour la Conservation de la Nature, Katana Campus, South Kivu, Democratic Republic of the Congo
                [10 ] Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
                [11 ] Laboratoire de Paludologie et Zoologie Médicale, Institut de Recherche pour le Développement, Dakar, Senegal
                [12 ] Independent Researcher, Berlin, Germany
                [13 ] Museo di Storia naturale del Salento, Calimera, Italy
                [14 ] Département des Vertébrés Récents, Institut Royal des Sciences naturelles de Belgique, Brussels, Belgium
                [15 ] Division of Biology and Conservation Ecology, School of Science and the Environment, Manchester Metropolitan University, Manchester, United Kingdom
                [16 ] Muséum National d’Histoire Naturelle, Sorbonne Universités, Département Systématique et Evolution (Reptiles), ISyEB (Institut de Systématique, Évolution, Biodiversité), Paris, France
                [17 ] African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
                [18 ] Flora Fauna & Man, Ecological Services Ltd. Tortola, British Virgin Islands
                [19 ] Institut National de Recherche en Sciences Exactes et Naturelles, Brazzaville, Republic of Congo
                [20 ] Independent Researcher, Dříteč, Czech Republic
                [21 ] Department of Biology, Whitman College, Walla Walla, Washington, United States of America
                [22 ] Department of Environmental Sciences, Makerere University, Kampala, Uganda
                State Museum of Natural History, GERMANY
                Author notes

                Competing Interests: MFB is affiliated with Flora Fauna & Man, Ecological Services Ltd. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

                Author information
                http://orcid.org/0000-0001-5257-037X
                http://orcid.org/0000-0003-0805-9683
                http://orcid.org/0000-0003-0380-981X
                http://orcid.org/0000-0003-1674-1316
                Article
                PONE-D-19-03110
                10.1371/journal.pone.0214889
                6469773
                30995262
                7b4157f8-4e88-4653-b596-78da75c6b183
                © 2019 Portillo et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 31 January 2019
                : 22 March 2019
                Page count
                Figures: 6, Tables: 3, Pages: 32
                Funding
                Funded by: National Science Foundation
                Award ID: DEB-1145459
                Award Recipient :
                Funded by: National Geographic Society
                Award ID: 8556-08
                Award Recipient :
                This work was supported by the Percy Sladen Memorial Fund, an IUCN/SSC Amphibian Specialist Group Seed Grant, K. Reed, M.D., research funds from the Department of Biology at Villanova University, and UTEP (all to EG), National Science Foundation grant DEB-1145459 (to EG and KJ), National Geographic Research and Exploration Grant no. 8556-08 (to EG), National Geographic Okavango Wilderness Project no. EC0715-15 (to WC), Belgian National Focal Point to the Global Taxonomy Initiative (to ZTN). MOR is supported by the Gorongosa Restoration Project and the Mozambican Departamento dos Serviços Cientificos (PNG/DSCi/C12/2013; PNG/DSCi/C12/2014; PNG/DSCi/C28/2015). The University of Texas at El Paso (UTEP) Border Biomedical Research Center (BBRC) Genomic Analysis Core Facility is acknowledged for services and facilities provided. This core facility is supported by grant 5G12MD007592 to the (BBRC) from the National Institutes on Minority Health and Health Disparities (NIMHD), a component of the National Institutes of Health (NIH). MFB received payment as a herpetologist consultant with Flora Fauna & Man, Ecological Services Ltd. (FFMES). The funder provided support in the form of salaries for one author [MFB], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
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                The data included in this paper can be found on GenBank and Morphosource websites (access information is contained within the paper).

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