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Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers.
Mol Phylogenet Evol. 2013 Apr; 67(1):176-87.MP

Abstract

Determining whether a conflict between gene trees and species trees represents incomplete lineage sorting (ILS) or hybridization involving native and/or invasive species has implications for reconstructing evolutionary relationships and guiding conservation decisions. Among vertebrates, turtles represent an exceptional case for exploring these issues because of the propensity for even distantly related lineages to hybridize. In this study we investigate a group of freshwater turtles (Trachemys) from a part of its range (the Greater Antilles) where it is purported to have undergone reticulation events from both natural and anthropogenic processes. We sequenced mtDNA for 83 samples, sequenced three nuDNA markers for 45 samples, and cloned 29 polymorphic sequences, to identify species boundaries, hybridization, and intergrade zones for Antillean Trachemys and nearby mainland populations. Initial coalescent analyses of phased nuclear alleles (using (*)BEAST) recovered a Bayesian species tree that strongly conflicted with the mtDNA phylogeny and traditional taxonomy, and appeared to be confounded by hybridization. Therefore, we undertook exploratory phylogenetic analyses of mismatched alleles from the "coestimated" gene trees (Heled and Drummond, 2010) in order to identify potential hybrid origins. The geography, morphology, and sampling context of most samples with potential introgressed alleles suggest hybridization over ILS. We identify contact zones between different species on Jamaica (T. decussata × T. terrapen), on Hispaniola (T. decorata × T. stejnegeri), and in Central America (T. emolli × T. venusta). We are unable to determine whether the distribution of T. decussata on Jamaica is natural or the result of prehistoric introduction by Native Americans. This uncertainty means that the conservation status of the Jamaican T. decussata populations and contact zone with T. terrapen are unresolved. Human-mediated dispersal events were more conclusively implicated for the prehistoric translocation of T. stejnegeri between Puerto Rico and Hispaniola, as well as the more recent genetic pollution of native species by an invasive pet turtle native to the USA (T. scripta elegans). Finally, we test the impact of introgressed alleles using the multispecies coalescent in a Bayesian framework and show that studies that do not phase heterozygote sequences of hybrid individuals may recover the correct species tree, but overall support for clades that include hybrid individuals may be reduced.

Authors+Show Affiliations

John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA 92834, USA. jparham@fullerton.eduNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23353072

Citation

Parham, James F., et al. "Genetic Introgression and Hybridization in Antillean Freshwater Turtles (Trachemys) Revealed By Coalescent Analyses of Mitochondrial and Cloned Nuclear Markers." Molecular Phylogenetics and Evolution, vol. 67, no. 1, 2013, pp. 176-87.
Parham JF, Papenfuss TJ, Dijk PP, et al. Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers. Mol Phylogenet Evol. 2013;67(1):176-87.
Parham, J. F., Papenfuss, T. J., Dijk, P. P., Wilson, B. S., Marte, C., Schettino, L. R., & Brian Simison, W. (2013). Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers. Molecular Phylogenetics and Evolution, 67(1), 176-87. https://doi.org/10.1016/j.ympev.2013.01.004
Parham JF, et al. Genetic Introgression and Hybridization in Antillean Freshwater Turtles (Trachemys) Revealed By Coalescent Analyses of Mitochondrial and Cloned Nuclear Markers. Mol Phylogenet Evol. 2013;67(1):176-87. PubMed PMID: 23353072.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers. AU - Parham,James F, AU - Papenfuss,Theodore J, AU - Dijk,Peter Paul van, AU - Wilson,Byron S, AU - Marte,Cristian, AU - Schettino,Lourdes Rodriguez, AU - Brian Simison,W, Y1 - 2013/01/23/ PY - 2012/08/01/received PY - 2012/12/18/revised PY - 2013/01/06/accepted PY - 2013/1/29/entrez PY - 2013/1/29/pubmed PY - 2013/8/14/medline SP - 176 EP - 87 JF - Molecular phylogenetics and evolution JO - Mol Phylogenet Evol VL - 67 IS - 1 N2 - Determining whether a conflict between gene trees and species trees represents incomplete lineage sorting (ILS) or hybridization involving native and/or invasive species has implications for reconstructing evolutionary relationships and guiding conservation decisions. Among vertebrates, turtles represent an exceptional case for exploring these issues because of the propensity for even distantly related lineages to hybridize. In this study we investigate a group of freshwater turtles (Trachemys) from a part of its range (the Greater Antilles) where it is purported to have undergone reticulation events from both natural and anthropogenic processes. We sequenced mtDNA for 83 samples, sequenced three nuDNA markers for 45 samples, and cloned 29 polymorphic sequences, to identify species boundaries, hybridization, and intergrade zones for Antillean Trachemys and nearby mainland populations. Initial coalescent analyses of phased nuclear alleles (using (*)BEAST) recovered a Bayesian species tree that strongly conflicted with the mtDNA phylogeny and traditional taxonomy, and appeared to be confounded by hybridization. Therefore, we undertook exploratory phylogenetic analyses of mismatched alleles from the "coestimated" gene trees (Heled and Drummond, 2010) in order to identify potential hybrid origins. The geography, morphology, and sampling context of most samples with potential introgressed alleles suggest hybridization over ILS. We identify contact zones between different species on Jamaica (T. decussata × T. terrapen), on Hispaniola (T. decorata × T. stejnegeri), and in Central America (T. emolli × T. venusta). We are unable to determine whether the distribution of T. decussata on Jamaica is natural or the result of prehistoric introduction by Native Americans. This uncertainty means that the conservation status of the Jamaican T. decussata populations and contact zone with T. terrapen are unresolved. Human-mediated dispersal events were more conclusively implicated for the prehistoric translocation of T. stejnegeri between Puerto Rico and Hispaniola, as well as the more recent genetic pollution of native species by an invasive pet turtle native to the USA (T. scripta elegans). Finally, we test the impact of introgressed alleles using the multispecies coalescent in a Bayesian framework and show that studies that do not phase heterozygote sequences of hybrid individuals may recover the correct species tree, but overall support for clades that include hybrid individuals may be reduced. SN - 1095-9513 UR - https://www.unboundmedicine.com/medline/citation/23353072/Genetic_introgression_and_hybridization_in_Antillean_freshwater_turtles__Trachemys__revealed_by_coalescent_analyses_of_mitochondrial_and_cloned_nuclear_markers_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1055-7903(13)00023-7 DB - PRIME DP - Unbound Medicine ER -