Phylogeny, biogeography and diversification patterns of side-necked turtles (Testudines: Pleurodira) (original) (raw)
Related papers
Biological Journal of The Linnean Society, 1999
Aspects of the phylogeny of pleurodiran turtles are contentious, particularly within the Chelidae. Morphological analyses group the long-necked Australasian Chelodina and the long-necked South American Chelus and Hydromedusa into a single clade, suggesting a common derived origin of the long neck and associated habits that predated the separation of Australia from South America. In contrast, published analyses of 12SrRNA and cytochrome b sequences suggest that the long-necked Chelodina are more closely related to the short-necked Australasian genera than to either Chelus or Hydromedusa. This paper adds partial sequences of 16S rRNA and CO1 mitochondrial genes and partial sequences of the nuclear oncogene c-mos to test a range of previous hypotheses on the phylogenetic relationships among chelid turtles. In total, 1382 nucleotides were available for each of 25 taxa after elimination of ambiguously aligned regions. These taxa included representatives of all the genera of the turtle families Chelidae and Pelomedusidae, the three sub-genera of Phrynops, and recognized sub-generic groups of Elseya and Chelodina. Of the four genes examined, 12S rRNA was the most informative, followed by c-mos with 16S rRNA and CO1 the least informative. The molecular data support the currently accepted arrangement for pelomedusid genera, that is, a sister relationship between the African Pelusios and Pelomedusa and a clade comprising the South American Peltoceplhalus and Podocnemis with the Madagascan Erymnochelys. However, there is also support for Erymnochelys and Podocnemis as sister taxa to the exclusion of Peltocephalus (bootstrap values of 69–80%) which is at odds with the most commonly accepted arrangement. The South American chelids are monophyletic (76–82%). This clade includes the long-necked Chelus and Hydromedusa, but excludes the Australasian long-necked Chelodina. Furthermore, the South American long-necked chelids are not themselves monophyletic, with 98–100% bootstrap values for the node supporting Chelus and the remaining South American chelids to the exclusion of Hydromedusa. Hence, the hypothesis of a monophyletic grouping of the long-necked genera of South America and Australasia is not supported by the molecular data. Although reciprocal monophyly of the South American and Australasian chelid faunas was the most likely and the most parsimonious arrangement in all but one analysis, bootstrap support for the monophyly of the Australasian chelids was low (52–66%). The South American chelids, Chelodina and the short-necked Australasian chelids form an unresolved trichotomy. The genera Phrynops and Elseya are paraphyletic, leading to a recommendation to elevate the three sub-genera of Phrynops to generic status and support for previous suggestions to erect a new genus for Elseya latistermum and close relatives. A revised classification of the extant Pleurodira is presented, consistent with the phylogenetic relationships that emerge from this study.
1999
Aspects of the phylogeny of pleurodiran turtles are contentious, particularly within the Chelidae. Morphological analyses group the long-necked Australasian Chelodina and the longnecked South American Chelus and Hydromedusa into a single clade, suggesting a common derived origin of the long neck and associated habits that predated the separation of Australia from South America. In contrast, published analyses of IZSrRNA and cytochrome b sequences suggest that the long-necked Chelodina are more closely related to the short-necked Australasian genera than to either Chelus or Hydromedusa. This paper adds partial sequences of 16s rRNA and CO1 mitochondria1 genes and partial sequences of the nuclear oncogene c-mos to test a range of previous hypotheses on the phylogenetic relationships among chelid turtles. In total, 1382 nucleotides were available for each of 25 taxa after elimination of ambiguously aligned regions. These taxa included representatives of all the genera of the turtle fam...
Diversity
Turtles are one of the most threatened groups of vertebrates, with about 60% of species classified at some level of extinction risk. Compounding this extinction crisis are cryptic species and species complexes that are evaluated under a single species epithet but harbor multiple species, each of which needs to be evaluated independently. The Phrynops geoffroanus species group is a classic example. Described first in 1812, it is currently thought to harbor multiple species. To test this hypothesis, we collected mitochondrial and nuclear genomic data, morphometric data, and distribution and associated biome information. We applied statistically rigorous species delimitation analyses, taxonomic hypotheses tests, and fully coalescent phylogenetic reconstruction methods, concluding that the Phrynops geoffroanus species complex comprises four geographically structured species/lineages that diverged during the Pleistocene and are currently geographically structured along the main South Ame...
Ecological diversification and phylogeny of emydid turtles
Ecological diversification is a central topic in ecology and evolutionary biology. We undertook the first comprehensive species-level phylogenetic analysis of Emydidae (an ecologically diverse group of turtles), and used the resulting phylogeny to test four general hypotheses about ecological diversification. Phylogenetic analyses were based on data from morphology (237 parsimony-informative characters) and mitochondrial DNA sequences (547 parsimony-informative characters) and included 39 of the 40 currently recognized emydid species. Combined analyses of all data provide a well-supported hypothesis for intergeneric relationships, and support monophyly of the two subfamilies (Emydinae and Deirochelyinae) and most genera (with the notable exception of Clemmys and Trachemys ). Habitat and diet were mapped onto the combined-data tree to test fundamental hypotheses about ecological diversification. Using continuous coding of ecological characters showed that lineages changed in habitat before diet, ecological change was most frequently from generalist to specialist, and habitat and diet rarely changed on the same branch of the phylogeny. However, we also demonstrate that the results of ancestral trait reconstructions can be highly sensitive to character coding method (i.e. continuous vs. discrete). Finally, we propose a simple model to describe the pattern of ecological diversification in emydid turtles and other lineages, which may reconcile the (seemingly) conflicting conclusions of our study and two recent reviews of ecological diversification. Wiens JJ. 2003a. Missing data, incomplete data, and phylogenetic accuracy. Systematic Biology 52: in press. Wiens JJ. 2003b. Incomplete taxa, incomplete characters, and phylogenetic accuracy: is there a missing data problem? Journal of Vertebrate Paleontology 23: 297-310. Wiens JJ, Hollingsworth BD. 2000. War of the iguanas: conflicting molecular and morphological phylogenies and longbranch attraction in iguanid lizards. Systematic Biology 49: 143-159. Wiens JJ, Morris MR. 1996. Character definitions, sexual selection, and the evolution of swordtails. American Naturalist 147: 866-869. Wiens JJ, Reeder TW. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Systematic Biology 44: 548-558. Wiens JJ, Reeder TW. 1997. Phylogeny of the spiny lizards (Sceloporus) based on molecular and morphological evidence. Herpetological Monographs 11: 1-101. Wiens JJ, Reeder TW, Nieto Montes de Oca A. 1999. Molecular phylogenetics and evolution of sexual dichromatism among populations of the Yarrow's spiny lizard (Sceloporus jarrovii). Evolution 53: 1884-1897. Wiens JJ, Servedio MR. 1997. Accuracy of phylogenetic analysis including and excluding polymorphic characters. Systematic Biology 46: 332-345. Wiens JJ, Servedio MR. 1998. Phylogenetic analysis and intraspecific variation: performance of parsimony, distance, and likelihood methods. Systematic Biology 47: 228-253. Wilgenbusch J, de Queiroz K. 2000. Phylogenetic relationships among phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Systematic Biology 49: 592-612. Wilkinson M. 1995. A comparison of two methods of character construction. Cladistics 11: 297-308. Williams EE. 1972. The origin of faunas: evolution of lizard congeners in a complex island fauna -a trial analysis. Evolutionary Biology 6: 47-89. Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods.
Abstract Adding new taxa to morphological phylogenetic analyses without substan- tially revising the set of included characters is a common practice, with drawbacks (undersampling of relevant characters) and potential benefits (character selection is not biased by preconceptions over the affinities of the ‘retrofitted’ taxon). Retrofitting turtles (Testudines) and other taxa to recent reptile phylogenies consistently places turtles with anapsid-grade parareptiles (especially Eunotosaurus and/or pareiasauromorphs), under both Bayesian and parsimony analyses. This morphological evidence for turtle–parareptile affinities appears to contradict the robust genomic evidence that extant (liv- ing) turtles are nested within diapsids as sister to extant archosaurs (birds and crocodilians). However, the morphological data are almost equally con- sistent with a turtle–archosaur clade: enforcing this molecular scaffold onto the morphological data does not greatly increase tree length (parsimony) or reduce likelihood (Bayesian inference). Moreover, under certain analytic conditions, Eunotosaurus groups with turtles and thus also falls within the turtle–archosaur clade. This result raises the possibility that turtles could simultaneously be most closely related to a taxon traditionally considered a parareptile (Eunotosaurus) and still have archosaurs as their closest extant sister group.
Molecular systematics of Old World stripe-necked turtles (Testudines: Mauremys)
2004
Nine extant species of Mauremys (including Ocadia and Chinemys) represent a geographically widespread yet morphologically and ecologically conservative group of batagurid turtles. Here we examine the evolutionary relationships of Mauremys using 1539 base pairs of mitochondrial DNA encoding portions of COI, ND4, and three adjacent tRNA genes. These data contain 246 parsimony informative characters that we use to erect hypotheses of relationships for Mauremys. Both maximum parsimony and Bayesian methods suggest that Mauremys japonica, M. sinensis, M. nigricans, and M. reevesii form a well-supported monophyletic clade, as do M. mutica and M. annamensis. Furthermore, our analyses show that M. mutica is paraphyletic with respect to M. annamensis. The western taxa M. leprosa, M. caspica, and M. rivulata remain problematic and do not form a monophyletic group sister to the Asian taxa. Nevertheless, an east-west biogeographic hypothesis cannot be discounted with our molecular genetic data.
Organisms Diversity & Evolution, 2014
Several important aspects of the evolution of the softshell turtle (family Trionychidae) have not been addressed thoroughly in previous studies, including the pattern and timing of diversification of major clades and species boundaries of the critically endangered Shanghai Softshell Turtle, Rafetus swinhoei. To address these issues, we analyzed data from two mitochondrial loci (cytochrome b and ND4) and one nuclear intron (R35) for all species of trionychid turtles, except Pelochelys signifera, and for all known populations of Rafetus swinhoei in Vietnam and one from China. Phylogenetic analyses using three methods (maximum parsimony, maximum likelihood, and Bayesian inference) produce a well resolved and strongly supported phylogeny. The results of our time-calibration and biogeographic optimization analyses show that trionychid dispersals out of Asia took place between 45 and 49 million years ago in the Eocene. Interestingly, the accelerated rates of diversification and dispersal within the family correspond surprisingly well to global warming periods between the mid Paleocene and the early Oligocene and from the end of the Oligocene to the mid Miocene. Our study also indicates that there is no significant genetic divergence among monophyletic populations of Rafetus swinhoei, and that previous taxonomic revision of this species is unwarranted.
The American Naturalist, 2003
Speciation is the process that ultimately generates species richness. However, the time required for speciation to build up diversity in a region is rarely considered as an explanation for patterns of species richness. We explored this "time-for-speciation effect" on patterns of species richness in emydid turtles. Emydids show a striking pattern of high species richness in eastern North America (especially the southeast) and low diversity in other regions. At the continental scale, species richness is positively correlated with the amount of time emydids have been present and speciating in each region, with eastern North America being the ancestral region. Within eastern North America, higher regional species richness in the southeast is associated with smaller geographic range sizes and not greater local species richness in southern communities. We suggest that these patterns of geographic range size variation and local and regional species richness in eastern North America are caused by glaciation, allopatric speciation, and the time-for-speciation effect. We propose that allopatric speciation can simultaneously decrease geographic range size and increase regional diversity without increasing local diversity and that geographic range size can determine the relationship between a, b, and g diversity. The time-forspeciation effect may act through a variety of processes at different spatial scales to determine diverse patterns of species richness.
Marine turtle mitogenome phylogenetics and evolution
Molecular Phylogenetics and Evolution, 2012
The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution.