Genetic introgression and hybridization in Antillean freshwater turtles (Trachemys) revealed by coalescent analyses of mitochondrial and cloned nuclear markers.

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.

Multiple sources, admixture, and genetic variation in introduced anolis lizard populations.

Invasive species are classically thought to suffer from reduced within-population genetic variation compared to their native-range sources due to founder effects and population bottlenecks during introduction. Reduction in genetic variation in introduced species may limit population growth, increase the risk of extinction, and constrain adaptation, hindering the successful establishment and spread of an alien species. Results of recent empirical studies, however, show higher than expected genetic variation, rapid evolution, and multiple native-range sources in introduced populations, which challenge the classical scenario of invasive-species genetics. With mitochondrial DNA (mtDNA) sequence data, we examined the molecular genetics of 10 replicate introductions of 8 species of Anolis lizards. Eighty percent of introductions to Florida and the Dominican Republic were from multiple native-range source populations. MtDNA haplotypes restricted to different geographically distinct populations in the native range of a species commonly occurred as intrapopulation polymorphisms in introduced populations. Two-thirds of introduced populations had two or more sources, and admixture elevated genetic variation in half of the introduced populations above levels typical of native-range populations. The mean pairwise sequence divergence among haplotypes sampled within introduced populations was nearly twice that within native-range populations (2.6% vs. 1.4%). The dynamics of introductions from multiple sources and admixture explained the observed genetic contrasts between native and introduced Anolis populations better than the classical scenario for most introduced populations. Elevated genetic variation through admixture occurred regardless of the mode or circumstances of an introduction. Little insight into the number of sources or amount of genetic variation in introduced populations was gained by knowing the number of physical introductions, the size of a species' non-native range, or whether it was a deliberate or accidental introduction. We hypothesize that elevated genetic variation through admixture of multiple sources is more common in biological invasions than previously thought. We propose that introductions follow a sequential, two-step process involving a reduction in genetic variation due to founder effects and population bottlenecks followed by an increase in genetic variation if admixture of individuals from multiple native-range sources occurs.

Partial island submergence and speciation in an adaptive radiation: a multilocus analysis of the Cuban green anoles.

Sympatric speciation is often proposed to account for species-rich adaptive radiations within lakes or islands, where barriers to gene flow or dispersal may be lacking. However, allopatric speciation may also occur in such situations, especially when ranges are fragmented by fluctuating water levels. We test the hypothesis that Miocene fragmentation of Cuba into three palaeo-archipelagos accompanied species-level divergence in the adaptive radiation of West Indian Anolis lizards. Analysis of morphology, mitochondrial DNA (mt DNA) and nuclear DNA in the Cuban green anoles (carolinensis subgroup) strongly supports three pre dictions made by this hypothesis. First, three geographical sets of populations, whose ranges correspond with palaeo-archipelago boundaries, are distinct and warrant recognition as independent evolutionary lineages or species. Coalescence of nuclear sequence fragments sampled from these species and the large divergences observed between their mtDNA haplotypes suggest separation prior to the subsequent unification of Cuba ca. 5 Myr ago. Second, molecular phylogenetic relationships among these species reflect historical geographical relationships rather than morphological similarity. Third, all three species remain distinct despite extensive geographical contact subsequent to island unification, occasional hybridization and introgression of mtDNA haplotypes. Allopatric speciation initiated during partial island submergence may play an important role in speciation during the adaptive radiation of Anolis lizards.