Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple nuclear loci

摘要: Asian box turtles (genus Cuora, family Geoemydidae) comprise a clade of 12 aquatic and semiaquatic nominate species distributed across southern China Southeast Asia. Over the last two decades, throughout Asia have been harvested at an unsustainable rate to satisfy demands for food, traditional Chinese medicine, pet trade. Con- sequently, all Cuora were recently placed on IUCN Red List, nine are currently listed as criti- cally endangered by IUCN, in Appendix II CITES. We compiled 67-specimen mitochondrial (~1,650 base pairs (bp) from genes) 40-specimen nuclear-plus-mitochondrial (~3,900 bp total, three nuclear introns plus additional ~860 mitochon- drial gene fragment) DNA data set reconstruct phylogeny assess genetic diversity boundaries several most problematic taxa. Our sampling included 23 C. trifas- ciata ,1 7C. zhoui 1-4 individuals remaining 10 Cuora. Maximum likelihood, maximum parsimony Bayesian analyses recovered similar, well resolved trees. Within clade, mito- chondrial sequence indicated that both mccordi represent old lineages with little or no history interspecific flow, suggesting they good genealogical species. Based mtDNA, pani was paraphyletic trifasciata composed highly divergent not each other's closest relatives; cases non-monophyly due mtDNA widespread identical aurocapitata, trifasciata. However, when combined results, our indicate is single, monophyletic taxon, introgression nuclear-mitochondrial pseudogenes led complex pattern relationships does reflect species-level histories. results imply captive ''assurance colonies'' should be genotyped identify pure, non-hybrid members taxa, we recommend introgressed pure taxa man- aged independent entities until full evolutionary histories these critically resolved.