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Kundu S, Mukherjee T, Kamalakannan M, Barhadiya G, Ghosh C, Kim HW. Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle ( Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences. PeerJ 2023; 11:e15975. [PMID: 37692114 PMCID: PMC10492536 DOI: 10.7717/peerj.15975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
The spotted pond turtle (Geoclemys hamiltonii) is a threatened and less explored species endemic to Bangladesh, India, Nepal, and Pakistan. To infer structural variation and matrilineal phylogenetic interpretation, the present research decoded the mitogenome of G. hamiltonii (16,509 bp) using next-generation sequencing technology. The mitogenome comprises 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one AT-rich control region (CR) with similar strand symmetry in vertebrates. The ATG was identified as a start codon in most of the PCGs except Cytochrome oxidase subunit 1 (cox1), which started with the GTG codon. The non-coding CR of G. hamiltonii was determined to have a unique structure and variation in different domains and stem-loop secondary structure as compared with other Batagurinae species. The PCGs-based Bayesian phylogeny inferred strong monophyletic support for all Batagurinae species and confirmed the sister relationship of G. hamiltonii with Pangshura and Batagur taxa. We recommend generating more mitogenomic data for other Batagurinae species to confirm their population structure and evolutionary relationships. In addition, the present study aims to infer the habitat suitability and habitat quality of G. hamiltonii in its global distribution, both in the present and future climatic scenarios. We identify that only 58,542 km2 (7.16%) of the total range extent (817,341 km2) is suitable for this species, along with the fragmented habitats in both the eastern and western ranges. Comparative habitat quality assessment suggests the level of patch shape in the western range is higher (71.3%) compared to the eastern range. Our results suggest a massive decline of approximately 65.73% to 70.31% and 70.53% to 75.30% under ssp245 and ssp585 future scenarios, respectively, for the years between 2021-2040 and 2061-2080 compared with the current distribution. The present study indicates that proper conservation management requires greater attention to the causes and solutions to the fragmented distribution and safeguarding of this endangered species in the Indus, Ganges, and Brahmaputra (IGB) river basins.
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Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan, South Korea
| | - Tanoy Mukherjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata, West Bengal, India
| | | | - Gaurav Barhadiya
- Department of Environmental Studies, University of Delhi, New Delhi, New Delhi, India
| | - Chirashree Ghosh
- Department of Environmental Studies, University of Delhi, New Delhi, New Delhi, India
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan, South Korea
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, South Korea
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SINEs as Credible Signs to Prove Common Ancestry in the Tree of Life: A Brief Review of Pioneering Case Studies in Retroposon Systematics. Genes (Basel) 2022; 13:genes13060989. [PMID: 35741751 PMCID: PMC9223172 DOI: 10.3390/genes13060989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 12/31/2022] Open
Abstract
Currently, the insertions of SINEs (and other retrotransposed elements) are regarded as one of the most reliable synapomorphies in molecular systematics. The methodological mainstream of molecular systematics is the calculation of nucleotide (or amino acid) sequence divergences under a suitable substitution model. In contrast, SINE insertion analysis does not require any complex model because SINE insertions are unidirectional and irreversible. This straightforward methodology was named the “SINE method,” which resolved various taxonomic issues that could not be settled by sequence comparison alone. The SINE method has challenged several traditional hypotheses proposed based on the fossil record and anatomy, prompting constructive discussions in the Evo/Devo era. Here, we review our pioneering SINE studies on salmon, cichlids, cetaceans, Afrotherian mammals, and birds. We emphasize the power of the SINE method in detecting incomplete lineage sorting by tracing the genealogy of specific genomic loci with minimal noise. Finally, in the context of the whole-genome era, we discuss how the SINE method can be applied to further our understanding of the tree of life.
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Adrian B, Smith HF, Hutchison JH, Townsend KEB. Geometric morphometrics and anatomical network analyses reveal ecospace partitioning among geoemydid turtles from the Uinta Formation, Utah. Anat Rec (Hoboken) 2021; 305:1359-1393. [PMID: 34605614 DOI: 10.1002/ar.24792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/19/2021] [Accepted: 09/03/2021] [Indexed: 01/13/2023]
Abstract
We present new fossil records of the geoemydid turtle Bridgeremys pusilla from the Uinta Formation of Utah. Turtles are abundant throughout the unit, and known taxa are similar to those from the older strata in the Upper Green River Basin in Wyoming from the Bridger and Washakie Formations. B. pusilla is known from Bridgerian deposits but was not previously known from after the Turtle Bluff Member of the Bridger Formation. The taxon was coveal with two species of the geoemydid Echmatemys (E. callopyge and E. wyomingensis), a common genus of extinct pond turtles known primarily from lacustrine and fluvial deposits in western North America, including the Uinta Basin. In addition to previously documented morphological differences, our geometric morphometric analyses revealed significant differences in epiplastral morphology between B. pusilla and the two coeval Echmatemys species. Bridgeremys pusilla shared several morphological characters with Testudinidae. However, our anatomical network analysis suggests that the carapace of B. pusilla distributed stress forces in a manner more similar to emydids (basal and derived) than to derived testudinoids (Testudinidae and Emydidae), including Echmatemys species. This finding changes our understanding of the ecology of the species and sheds light onto how geoemydid turtles of the Uinta Formation may have partitioned the available ecospace. These new Uintan records extend the geographic range of B. pusilla into the Uinta Basin and stratigraphically through the top of the Uinta Formation, extending the temporal range of the taxon by more than 4 million years through the Uintan North American Land Mammal Age to the base of the Duchesne River Formation.
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Affiliation(s)
- Brent Adrian
- Department of Anatomy, Midwestern University, Glendale, Arizona, USA
| | - Heather F Smith
- Department of Anatomy, Midwestern University, Glendale, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - J Howard Hutchison
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, California, USA
| | - K E Beth Townsend
- Department of Anatomy, Midwestern University, Glendale, Arizona, USA
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Ascarrunz E, Claude J, Joyce WG. The phylogenetic relationships of geoemydid turtles from the Eocene Messel Pit Quarry: a first assessment using methods for continuous and discrete characters. PeerJ 2021; 9:e11805. [PMID: 34430073 PMCID: PMC8349520 DOI: 10.7717/peerj.11805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/27/2021] [Indexed: 11/30/2022] Open
Abstract
The geoemydid turtles of the Eocoene Messel Pit Quarry of Hesse, Germany, are part of a rich Western European fossil record of testudinoids. Originally referred to as "Ocadia" kehreri and "Ocadia" messeliana, their systematic relationships remain unclear. A previous study proposed that a majority of the Western European geoemydids, including the Messel geoemydids, are closely related to the Recent European representatives of the clade Mauremys. Another study hypothesised that the Western European geoemydid fauna is more phylogenetically diverse, and that the Messel geoemydids are closely related to the East Asian turtles Orlitia and Malayemys. Here we present the first quantitative analyses to date that investigate this question. We use continuous characters in the form of ratios to estimate the placement of the Messel geoemydids in a reference tree that was estimated from molecular data. We explore the placement error obtained from that data with maximum likelihood and Bayesian methods, as well as linear parsimony in combination with discrete characters. We find good overall performance with Bayesian and parsimony analyses. Parsimony performs even better when we also incorporated discrete characters. Yet, we cannot pin down the position of the Messel geoemydids with high confidence. Depending on how intraspecific variation of the ratio characters is treated, parsimony favours a placement of the Messel fossils sister to Orlitia borneensis or sister to Geoemyda spengleri, with weak bootstrap support. The latter placement is suspect because G. spengleri is a phylogenetically problematic species with molecular and morphological data. There is even less support for placements within the Mauremys clade.
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Affiliation(s)
- Eduardo Ascarrunz
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Julien Claude
- Institut des Sciences de l’Évolution de Montpellier, UMR UM/CNRS/IRD/EPHE, Montpellier, France
| | - Walter G. Joyce
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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Ascarrunz E, Claude J, Joyce WG. Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods. PeerJ 2019; 7:e7476. [PMID: 31497387 PMCID: PMC6708579 DOI: 10.7717/peerj.7476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods. METHODS We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure. RESULTS Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance of discrete characters with parsimony.
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Affiliation(s)
- Eduardo Ascarrunz
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Julien Claude
- Institut des Sciences de l’Évolution de Montpellier, UMR UM/CNRS/IRD/EPHE, Montpellier, France
| | - Walter G. Joyce
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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Garbin RC, Ascarrunz E, Joyce WG. Polymorphic characters in the reconstruction of the phylogeny of geoemydid turtles. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Rafaella C Garbin
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Eduardo Ascarrunz
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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Lalitha R, Chandavar VR. Analysis of genetic diversity in CYTB and control region sequences of Melanochelys trijuga (Schweigger, 1812) from Karnataka. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2018. [DOI: 10.1016/j.japb.2018.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Kuritzin A, Kischka T, Schmitz J, Churakov G. Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data. PLoS Comput Biol 2016; 12:e1004812. [PMID: 26967525 PMCID: PMC4788455 DOI: 10.1371/journal.pcbi.1004812] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/13/2016] [Indexed: 01/25/2023] Open
Abstract
Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p<0.05) for the branching of the third from the other two, if all three of the given species are screened equally for genome or experimental data. Five elements are necessary for significant support (p<0.05) if a diagnostic locus derived from only one of three species is screened, and no conflicting markers are detected. Most potentially conflicting patterns can be evaluated for their significance and ancestral hybridization can be distinguished from incomplete lineage sorting by considering symmetric or asymmetric distribution of rare genomic changes among possible tree configurations. Additionally, we provide an R-application to make the new KKSC insertion significance test available for the scientific community at http://retrogenomics.uni-muenster.de:3838/KKSC_significance_test/. The presence/absence patterns of transposed elements, so called jumping genes, provide invaluable information about evolution. Unfortunately, there is still no clear all-encompassing analysis of the statistical significance of insertion patterns, and the single existing model of insertion data is no longer sufficient for the emerging genomic era. Here, we have provided a comprehensive statistical framework for testing the significance of support for phylogenetic hypotheses derived from genome-level presence/absence data such as retroposon insertions and for evaluating such data for different evolutionary scenarios, including polytomy, incomplete lineage sorting, and ancestral hybridization. This statistical framework is especially important for high-throughput applications of current and upcoming genome projects due to its treatment of unlimited numbers of testable markers, and is embedded in a user-friendly R-application available to the scientific community online. Finally, a reliable, adaptable calculation for the significance of support for phylogenetic trees derived from retroposon presence/absence data is now available.
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Affiliation(s)
- Andrej Kuritzin
- Department of System Analysis, Saint Petersburg State Institute of Technology, St. Petersburg, Russia
| | - Tabea Kischka
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
- * E-mail: (JS); (GC)
| | - Gennady Churakov
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
- Institute of Evolution and Biodiversity, University of Münster, Münster, Germany
- * E-mail: (JS); (GC)
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9
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Hybridization betweenMauremys japonicaandMauremys reevesiiInferred by Nuclear and Mitochondrial DNA Analyses. J HERPETOL 2014. [DOI: 10.1670/11-320] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Fujii R, Ota H, Toda M. Genetic and Morphological Assessments of Hybridization Between Two Non-Native Geoemydid Turtles,Mauremys reevesiiandMauremys mutica,in Northcentral Japan. CHELONIAN CONSERVATION AND BIOLOGY 2014. [DOI: 10.2744/ccb-1067.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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Nishizawa H, Tabata R, Hori T, Mitamura H, Arai N. Feeding kinematics of freshwater turtles: what advantage do invasive species possess? ZOOLOGY 2014; 117:315-8. [PMID: 25156933 DOI: 10.1016/j.zool.2014.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/27/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
Abstract
The red-eared slider (Trachemys scripta) is an invasive turtle species that is displacing the populations of native freshwater turtles in many countries. However, the mechanism that makes red-eared sliders superior competitors has been less well studied. In this study, we compare the feeding kinematics of the red-eared slider with those of Reeves' pond turtle (Mauremys reevesii), a turtle native to East Asia, and offer an explanation as to why red-eared sliders are superior in food competition. Reeves' pond turtles sympatric to red-eared sliders have been reported to have a mainly durophagous diet in contrast to the preference for a soft diet in areas of allopatry to red-eared sliders, indicating the dietary shift resulted from food competition. Maximum neck extension and retraction speed are considered to be indicators of striking ability, but were not found to be superior in red-eared sliders. In fact, maximum neck extension speed was significantly higher in Reeves' pond turtles, though this advantage may be counteracted by the longer neck of Reeves' pond turtles, resulting in similar neck extension times. On the other hand, red-eared sliders had a significantly shorter gape cycle time and neck retraction time, indicating that they can complete feeding in a short time. Therefore, red-eared sliders are suggested to be superior in food competition not due to their striking ability, but due to exploiting preferable food in a shorter time.
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Affiliation(s)
- Hideaki Nishizawa
- Graduate School of Informatics, Kyoto University, Yoshida Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Runa Tabata
- Graduate School of Informatics, Kyoto University, Yoshida Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoya Hori
- Graduate School of Informatics, Kyoto University, Yoshida Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiromich Mitamura
- Graduate School of Informatics, Kyoto University, Yoshida Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Nobuaki Arai
- Field Science Education and Research Center, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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Kamath PL, Elleder D, Bao L, Cross PC, Powell JH, Poss M. The population history of endogenous retroviruses in mule deer (Odocoileus hemionus). J Hered 2013; 105:173-87. [PMID: 24336966 DOI: 10.1093/jhered/est088] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mobile elements are powerful agents of genomic evolution and can be exceptionally informative markers for investigating species and population-level evolutionary history. While several studies have utilized retrotransposon-based insertional polymorphisms to resolve phylogenies, few population studies exist outside of humans. Endogenous retroviruses are LTR-retrotransposons derived from retroviruses that have become stably integrated in the host genome during past infections and transmitted vertically to subsequent generations. They offer valuable insight into host-virus co-evolution and a unique perspective on host evolutionary history because they integrate into the genome at a discrete point in time. We examined the evolutionary history of a cervid endogenous gammaretrovirus (CrERVγ) in mule deer (Odocoileus hemionus). We sequenced 14 CrERV proviruses (CrERV-in1 to -in14), and examined the prevalence and distribution of 13 proviruses in 262 deer among 15 populations from Montana, Wyoming, and Utah. CrERV absence in white-tailed deer (O. virginianus), identical 5' and 3' long terminal repeat (LTR) sequences, insertional polymorphism, and CrERV divergence time estimates indicated that most endogenization events occurred within the last 200000 years. Population structure inferred from CrERVs (F ST = 0.008) and microsatellites (θ = 0.01) was low, but significant, with Utah, northwestern Montana, and a Helena herd being particularly differentiated. Clustering analyses indicated regional structuring, and non-contiguous clustering could often be explained by known translocations. Cluster ensemble results indicated spatial localization of viruses, specifically in deer from northeastern and western Montana. This study demonstrates the utility of endogenous retroviruses to elucidate and provide novel insight into both ERV evolutionary history and the history of contemporary host populations.
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Affiliation(s)
- Pauline L Kamath
- the US Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT 59715
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Piskurek O, Jackson DJ. Transposable elements: from DNA parasites to architects of metazoan evolution. Genes (Basel) 2012; 3:409-22. [PMID: 24704977 PMCID: PMC3899998 DOI: 10.3390/genes3030409] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 06/19/2012] [Accepted: 06/25/2012] [Indexed: 01/22/2023] Open
Abstract
One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to advances in high throughput sequencing technologies it is now clear that TEs comprise the largest molecular class within most metazoan genomes. TEs, once categorised as "junk DNA", are now known to influence genomic structure and function by increasing the coding and non-coding genetic repertoire of the host. In this way TEs are key elements that stimulate the evolution of metazoan genomes. This review highlights several lines of TE research including the horizontal transfer of TEs through host-parasite interactions, the vertical maintenance of TEs over long periods of evolutionary time, and the direct role that TEs have played in generating morphological novelty.
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Affiliation(s)
- Oliver Piskurek
- Courant Research Centre Geobiology, Georg-August-University of Göttingen, Goldschmidtstr. 3, Göttingen 37077, Germany.
| | - Daniel J Jackson
- Courant Research Centre Geobiology, Georg-August-University of Göttingen, Goldschmidtstr. 3, Göttingen 37077, Germany.
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Kindler C, Branch WR, Hofmeyr MD, Maran J, Š iroký P, Vences M, Harvey J, Hauswaldt JS, Schleicher A, Stuckas H, Fritz U. Molecular phylogeny of African hinge-back tortoises (Kinixys): implications for phylogeography and taxonomy (Testudines: Testudinidae). J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00660.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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15
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Suzuki D, Ota H, Oh HS, Hikida T. Origin of Japanese Populations of Reeves' Pond Turtle, Mauremys reevesii (Reptilia: Geoemydidae), as Inferred by a Molecular Approach. CHELONIAN CONSERVATION AND BIOLOGY 2011. [DOI: 10.2744/ccb-0885.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Suzuki D, Hikida T. Mitochondrial phylogeography of the Japanese pond turtle, Mauremys japonica (Testudines, Geoemydidae). J ZOOL SYST EVOL RES 2011. [DOI: 10.1111/j.1439-0469.2010.00577.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Han KL, Braun EL, Kimball RT, Reddy S, Bowie RCK, Braun MJ, Chojnowski JL, Hackett SJ, Harshman J, Huddleston CJ, Marks BD, Miglia KJ, Moore WS, Sheldon FH, Steadman DW, Witt CC, Yuri T. Are transposable element insertions homoplasy free?: an examination using the avian tree of life. Syst Biol 2011; 60:375-86. [PMID: 21303823 DOI: 10.1093/sysbio/syq100] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA.
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Altaba CR. Universal artifacts affect the branching of phylogenetic trees, not universal scaling laws. PLoS One 2009; 4:e4611. [PMID: 19242549 PMCID: PMC2644784 DOI: 10.1371/journal.pone.0004611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 01/21/2009] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny? METHODOLOGY In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods. PRINCIPAL FINDINGS All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees. SIGNIFICANCE There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees. Catalan Abstract in Translation S1.
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Affiliation(s)
- Cristian R Altaba
- Laboratory of Human Systematics, University of the Balearic Islands, Balearic Islands, Spain.
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Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles. Mol Phylogenet Evol 2008; 49:514-25. [PMID: 18761096 DOI: 10.1016/j.ympev.2008.08.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 08/01/2008] [Accepted: 08/05/2008] [Indexed: 11/21/2022]
Abstract
We present a strategy for phylogenetic marker development in non-model systems. Rather than using the traditional approach of comparing distantly related taxa to develop conserved primers for unknown species, we explore an alternative strategy that builds primers directly from a single, relatively well characterized species and applies those primers to increasingly distantly related taxa. We develop and test our protocol with turtles. Using a single BAC end-sequence library consisting of 3461 sequences totaling 2.43 million base pairs of data, we outline a procedure to flag repeat elements, followed by a BLAST approach to categorize sequences into high, low, and no similarity compartments compared to GenBank sequences. We developed and tested a panel of 96 primer pairs with a set of turtle tissues that forms a series of increasingly distantly related taxa with respect to the BAC reference species. Finally, we sequenced 11 of these newly discovered markers across a diverse set of 18 turtle species that spans the 210 million years of chelonian crown-group history and that includes representatives of most of the major clades of extant turtles. Our results indicate that large numbers of new, phylogenetically informative markers can be developed quickly and inexpensively from a single BAC, EST, or similar genomic resource, and that those markers provide reliable phylogenetic information across both shallow and deep levels of phylogenetic history. Our results also highlight the importance of screening for and managing repetitive elements found in randomly sequenced DNA fragments. We presume that our strategy should work well across any similarly divergent clade, suggesting that many-marker datasets can be developed quickly and efficiently for phylogenetic analysis.
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LE MINH, MCCORD WILLIAMP. Phylogenetic relationships and biogeographical history of the genusRhinoclemmysFitzinger, 1835 and the monophyly of the turtle family Geoemydidae (Testudines: Testudinoidea). Zool J Linn Soc 2008. [DOI: 10.1111/j.1096-3642.2008.00413.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Le M, McCord WP, Iverson JB. On the paraphyly of the genus Kachuga (Testudines: Geoemydidae). Mol Phylogenet Evol 2007; 45:398-404. [PMID: 17643318 DOI: 10.1016/j.ympev.2007.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 05/01/2007] [Accepted: 05/02/2007] [Indexed: 11/22/2022]
Affiliation(s)
- Minh Le
- Department of Herpetology, Division of Vertebrate Zoology, and Center for Biodiversity and Conservation, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.
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