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      A new slider turtle (Testudines: Emydidae: Deirochelyinae: Trachemys) from the late Hemphillian (late Miocene/early Pliocene) of eastern Tennessee and the evolution of the deirochelyines

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      PeerJ
      PeerJ Inc.
      Trachemys, Fossil turtle, Emydidae, Tennessee, New species, Gray Fossil Site, Deirochelyinae, Taxonomy, Hemphillian, Phylogeny

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          Abstract

          Trachemys (Testudines: Emydidae) represents one of the most well-known turtle genera today. The evolution of Trachemys, while being heavily documented with fossil representatives, is not well understood. Numerous fossils from the late Hemphillian Gray Fossil Site (GFS) in northeastern Tennessee help to elucidate its evolution. The fossil Trachemys at the GFS represent a new species. The new taxon, Trachemys haugrudi, is described, and currently represents the most thoroughly described fossil emydid species known. A phylogenetic analysis, including 31 species, focusing on the subfamily Deirochelyinae is performed that includes the new fossil species, along with numerous other modern and fossil deirochelyine species, representing the first phylogenetic analysis published that includes several fossil deirochelyines. The phylogenetic analysis, utilizing morphological evidence, provides monophyletic clades of all modern deirochelyines, including Chrysemys, Deirochelys, Pseudemys, Malaclemys, Graptemys, and Trachemys. A strict consensus tree finds the recently described fossil species Graptemys kerneri to be part of a clade of Graptemys + Malaclemys. Three fossil taxa, including one previously referred to Pseudemys ( Pseudemys caelata) and two to Deirochelys ( Deirochelys carri and Deirochelys floridana) are found to form a clade with modern Deirochelys reticularia reticularia, with D. floridana sister to the other members of the clade. Chrysemys is found to be part of a basal polytomy with Deirochelys in relation to other deirochelyine taxa. Two fossil taxa previously referred to Chrysemys ( Chrysemys timida and Chrysemys williamsi) form a paraphyly with the modern Chrysemys picta picta and Deirochelys, and may be referable to distinct genera. Additionally, fossil taxa previously attributed to Trachemys ( Trachemys hillii, Trachemys idahoensis, Trachemys inflata, and Trachemys platymarginata) and T. haugrudi are found to form a clade separate from clades of northern and southern Trachemys species, potentially suggesting a distinct lineage of Trachemys with no modern survivors. Hypotheses of phylogenetic relationships mostly agree between the present study and previous ones, although the inclusion of fossil taxa provides further clues to the evolution of parts of the Deirochelyinae. The inclusion of more fossil taxa and characters may help resolve the placement of some taxa, and further elucidate the evolution of these New World turtles.

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          Phylogenetic Relationships of Mesozoic Turtles

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            Sexual Dimorphism in Turtles with Emphasis on the Slider Turtle (Trachemys scripta)

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              Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles.

              As phylogenetic data sets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing data directly and in principle provide effective syntheses of phylogenetic information that may reveal new relationships. However, several serious difficulties exist in the construction of large supermatrices that must be overcome before these approaches will enjoy broad utility. We present analyses that examine the performance of sparse supermatrices constructed from large sequence databases for the reconstruction of species-level phylogenies. We develop a largely automated informatics pipeline that allows for the construction of sparse supermatrices from GenBank data. In doing so, we develop strategies for alleviating some of the outstanding impediments to accurate phylogenetic inference using these approaches. These include taxonomic standardization, automated alignment, and the identification of rogue taxa. We use turtles as an exemplar clade and present a well-supported species-level phylogeny for two-thirds of all turtle species based on a approximately 50 kb supermatrix consisting of 93% missing data. Finally, we discuss some of the remaining pitfalls and concerns associated with supermatrix analyses, provide comparisons to supertree approaches, and suggest areas for future research.
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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Francisco, USA )
                2167-8359
                13 February 2018
                2018
                : 6
                : e4338
                Affiliations
                [1 ]Department of Earth and Environmental Science, University of Pennsylvania , Philadelphia, PA, USA
                [2 ]Section of Paleontology and Geology, State Museum of Pennsylvania , Harrisburg, PA, USA
                [3 ]Department of Biological Sciences, Don Sundquist Center of Excellence in Paleontology , Johnson City, TN, USA
                Article
                4338
                10.7717/peerj.4338
                5815335
                2b236def-91c3-4647-844b-308987559e38
                © 2018 Jasinski

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 12 November 2016
                : 17 January 2018
                Funding
                Funded by: Department of Biological Sciences and the Department of Geosciences at East Tennessee State University
                Funded by: Don Sundquist Center of Excellence in Paleontology
                Funded by: Graduate Professional Student Association
                Funded by: The State Museum of Pennsylvania
                Funded by: National Science Foundation
                Award ID: 0958985
                Funding was provided by the Department of Biological Sciences and the Department of Geosciences at East Tennessee State University, the Don Sundquist Center of Excellence in Paleontology, and the Graduate Professional Student Association, along with The State Museum of Pennsylvania. Additional support for this study was provided by the National Science Foundation (NSF grant 0958985; PIs S.C. Wallace and B.W. Schubert), particularly for the excavation of the fossil material from the Gray Fossil Site. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Evolutionary Studies
                Paleontology
                Taxonomy
                Zoology

                trachemys,fossil turtle,emydidae,tennessee,new species,gray fossil site,deirochelyinae,taxonomy,hemphillian,phylogeny

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