James Parham

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.► Coalescent analyses of cloned nuclear alleles provide species and gene trees. ► Mismatched alleles suggest hybridization from natural and anthropogentic contact. ► Intermediate morphology and biogeography support hybridization over ILS. ► Five contacts zones among Caribbean freshwater turtles are revealed. ► Prehistoric and ongoing exploitation of turtles result in lineage reticulations.

Three rare geoemydid turtles described from Chinese trade specimens in the early 1990s, Ocadia glyphistoma, O. philippeni, and Sacalia pseudocellata, are suspected to be hybrids because they are known only from their original descriptions and because they have morphologies intermediate between other, better-known species. We cloned the alleles of a bi-parentally inherited nuclear intron from samples of these three species. The two aligned parental alleles of O. glyphistoma, O. philippeni, and S. pseudocellata have 5–11.5 times more heterozygous positions than do 13 other geoemydid species. Phylogenetic analysis shows that the two alleles from each turtle are strongly paraphyletic, but correctly match sequences of other species that were hypothesized from morphology to be their parental species. We conclude that these rare turtles represent recent hybrids rather than valid species. Specifically, “O. glyphistoma” is a hybrid of Mauremys sinensis and M.␣cf. annamensis, “O.␣philippeni” is a hybrid of M. sinensis and Cuora trifasciata, and “S. pseudocellata” is a hybrid of C. trifasciata and S. quadriocellata. Conservation resources are better directed toward finding and protecting populations of other rare Southeast Asian turtles that do represent distinct evolutionary lineages.