Shallow genetic divergence indicates a Congo–Nile riverine connection for the softshell turtle Trionyx triunguis

WOS: 000288389500022We sequenced 20 new, field-collected individuals for up to seven genes to explore the phylogeography and conservation genetics of the threatened Nile softshell turtle Trionyx triunguis, including the first known-locality specimen from sub-Saharan Africa. Samples from Cameroon (West Africa), the Mediterranean and Nile River differed by at most a single nucleotide per gene, indicating the potential for a recent connection between these currently disjunct populations via the Nile-Congo River systems. Recently reported mitochondrial diversity between Mediterranean and "sub-Saharan" samples of the Nile softshell indicate that significant divergence exists across the species' range, but that variation cannot be fully incorporated into our analysis since those samples lack specific locality data.Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK); NSFNational Science Foundation (NSF) [DEB 0817042]; UC Davis Agricultural Experiment StationDwight Lawson collected the Cameroon turtle, and the San Diego Zoo provided a blood sample for our work, Permits were granted from the Republic of Turkey Ministry of Environment and Forestry. This work was supported by a grant from The Scientific and Technological Research Council of Turkey (TUBITAK), NSF grant DEB 0817042 and the UC Davis Agricultural Experiment Station. We thank Bob Thomson and members of the Shaffer lab for discussion. This study is a part of Muge Gidis's Ph.D. thesis

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles

<p>Abstract</p> <p>Background</p> <p>Phylogenies often contain both well-supported and poorly supported nodes. Determining how much additional data might be required to eventually recover most or all nodes with high support is an important pragmatic goal, and simulations have been used to examine this question. Most simulations have been based on few empirical loci, and suggest that well supported phylogenies can be determined with a very modest amount of data. Here we report the results of an empirical phylogenetic analysis of all 10 genera and 25 of 48 species of the new world pond turtles (family Emydidae) based on one mitochondrial (1070 base pairs) and seven nuclear loci (5961 base pairs), and a more biologically realistic simulation analysis incorporating variation among gene trees, aimed at determining how much more data might be necessary to recover weakly-supported nodes with strong support.</p> <p>Results</p> <p>Our mitochondrial-based phylogeny was well resolved, and congruent with some previous mitochondrial results. For example, all genera, and all species except <it>Pseudemys concinna</it>, <it>P. peninsularis</it>, and <it>Terrapene carolina </it>were monophyletic with strong support from at least one analytical method. The Emydinae was recovered as monophyletic, but the Deirochelyinae was not. Based on nuclear data, all genera were monophyletic with strong support except <it>Trachemys</it>, and all species except <it>Graptemys pseudogeographica</it>, <it>P. concinna</it>, <it>T. carolina</it>, and <it>T. coahuila </it>were monophyletic, generally with strong support. However, the branches subtending most genera were relatively short, and intergeneric relationships within subfamilies were mostly unsupported.</p> <p>Our simulations showed that relatively high bootstrap support values (i.e. ≥ 70) for all nodes were reached in all datasets, but an increase in data did not necessarily equate to an increase in support values. However, simulations based on a single empirical locus reached higher overall levels of support with less data than did the simulations that were based on all seven empirical nuclear loci, and symmetric tree distances were much lower for single versus multiple gene simulation analyses.</p> <p>Conclusion</p> <p>Our empirical results provide new insights into the phylogenetics of the Emydidae, but the short branches recovered deep in the tree also indicate the need for additional work on this clade to recover all intergeneric relationships with confidence and to delimit species for some problematic groups. Our simulation results suggest that moderate (in the few-to-tens of kb range) amounts of data are necessary to recover most emydid relationships with high support values. They also suggest that previous simulations that do not incorporate among-gene tree topological variance probably underestimate the amount of data needed to recover well supported phylogenies.</p

Phylogenetic relationships among the Asian tortoises of the genus Indotestudo (Reptilia: Testudines: Testudinidae)

Based on variation in 1094 bp of the mitochondrial cytochrome b gene among members of the genus Indotestudo from southern Asia ( I. elongata ), south-western India ( I. travancorica ), and eastern Indonesia ( I. forstenii ), I. travancorica is most similar genetically to I. elongata (3.7% divergence), and strongly divergent from I. forstenii (5.5 to 5.9%). Individuals of I. forstenii with and without a nuchal scute differ genetically at less than 0.7%. Our analysis offers no support for the hypothesis that Indonesian populations of I. forstenii represent introductions of I. travancorica from India. The recognition of three nominal species ( I. elongata, I. forstenii and I. travancorica ) in the genus is thus warrante

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Background: We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing.Results: Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented.Conclusions: Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders

Survival of the western pond turtle (\u3ci\u3eEmys marmorata\u3c/i\u3e) in an urban California environment

The western pond turtle Emys (formerly Clemmys) marmorata is declining throughout its range, primarily due to loss of habitat via urbanization and conversion to agriculture. Urban waterways present several important challenges to freshwater turtle populations, but they also present an opportunity to maintain declining species in a ubiquitous habitat that has high public visibility. The arboretum waterway on the University of California, Davis campus is an example of an extensively altered urban habitat that supports a relatively large E. marmorata population. Over the last 6 years, we monitored the turtle population inhabiting the arboretum waterway to determine the demographic health of the population, and the challenges and opportunities that urban environments pose for pond turtles. Since 1993, the naturally existing arboretum pond turtle population has declined by approximately 40% and has shown little natural recruitment. During this time, we also introduced 31 headstarted turtles into the arboretum. Headstarting is the process of raising juveniles in captivity until they have outgrown their period of greatest vulnerability to predators, and then releasing them into the wild. Our headstarting results demonstrate that this contentious strategy is a viable option for adding young turtles to the population, although it does not address the causes of decline. Over the course of our study, we encountered nine species of non-native turtles in the waterway, and these appear to be a serious threat to the native species. As more habitat becomes urbanized, it is increasingly important to understand how freshwater turtles, such as E. marmorata, adapt to urban waterways and the impact of non-native turtles on native turtle species. Our strong feeling is that urban waterways can provide habitat for viable populations of freshwater turtles and showcase them to the public, but both the aquatic and terrestrial habitat must be managed according to the biological requirements of individual species

Appendix S1

List of taxa, GenBank numbers and modified primer sequences used in this analysi

Data from: Phylogenetic uncertainty and taxonomic re-revisions: an example from the Australian short-necked turtles (Testudines: Chelidae)

Molecular data have greatly influenced our concepts of species and their relationships in the last few decades, and as a consequence the taxonomy of most vertebrate clades has been repeatedly revised to reflect phylogeny. However, as larger and more complete molecular data sets become available, the sometimes striking disparities between taxonomic revisions based on individual gene trees (particularly those based on mitochondrial DNA) and species trees has become increasingly apparent. Here, we present data from 13 nuclear and one mitochondrial gene. Our results demonstrate that the recent taxonomic proposal erecting the new Australian chelid genus Flaviemys (Testudines: Chelidae) was an unnecessary action, and that recognition of Flaviemys confuses, rather than clarifies, a phylogeny-based taxonomy of the group. Taxonomic actions have many broad repercussions, and we recommend that taxonomic changes should be proposed cautiously and only when they are based on the strongest possible data and analyses

Structure_Harvester_Results_Southern

This folder contains the results from the Structure Harvester analyses of all 5 replicates (K1-K10) for the Southern group (391 individuals) only