Sequence-based molecular phylogenetics and phylogeography of the American box turtles (Terrapene spp.) with support from DNA barcoding

Martin, Bradley T.; Bernstein, Neil P.; Birkhead, Roger D.; Koukl, Jim F.; Mussmann, Steven M.; Placyk, John S.

doi:10.1016/j.ympev.2013.03.006

Cited by 36 publications

(87 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The molecular evidence of Martin et al (2013) suggest the T. mexicana clade forms a distinct species and we believe that the genetic evidence provided to support this newly recommended classification via the PSC outweighs concerns regarding hybridization utilizing a BSC framework.…”

mentioning

confidence: 78%

“…Recently, the Placyk lab reassessed the classification of Terrapene using molecular phylogenetic data, and suggested elevating a clade consisting of T. carolina triunguis (Agassiz), T. c. mexicana (Gray), and T. c. yucatana (Boulenger) to a distinct species: Terrapene mexicana ssp. (Martin et al 2013). Our dataset included all Terrapene species and almost all of the subspecies (except for T. nelsoni klauberi), as well as large sample sizes and a wide geographic sampling for both mitochondrial (mt) and nuclear (nuc) DNA.…”

mentioning

confidence: 99%

“…However, because possible introgression was detected for some of the individuals, T. mexicana was not recognized as a distinct species in a recent assessment of Testudines taxonomic updates (Fritz & Havaš 2013). The purpose of this treatise is to suggest that the possible presence of introgression seen in Martin et al (2013) does not warrant disregarding T. mexicana as a unique species.…”

mentioning

confidence: 99%

See 2 more Smart Citations

On the Reclassification of the Terrapene (Testudines: Emydidae): A Response to Fritz & Havaš

Martin

Bernstein

Birkhead

et al. 2014

Zootaxa

Self Cite

View full text Add to dashboard Cite

The American box turtles (Terrapene spp.) consist of four historically recognized species based primarily on morphological data (Minx 1996): Terrapene carolina (Linnaeus), T. ornata (Agassiz), T. nelsoni (Stejneger), and T. coahuila (Schmidt & Owens). Each of these species is polytypic except for T. coahuila. Recently, the Placyk lab re-assessed the classification of Terrapene using molecular phylogenetic data, and suggested elevating a clade consisting of T. carolina triunguis (Agassiz), T. c. mexicana (Gray), and T. c. yucatana (Boulenger) to a distinct species: Terrapene mexicana ssp. (Martin et al. 2013). Our dataset included all Terrapene species and almost all of the subspecies (except for T. nelsoni klauberi), as well as large sample sizes and a wide geographic sampling for both mitochondrial (mt) and nuclear (nuc) DNA. The mtDNA Cytochrome b (Cytb) gene and a nucDNA intron from the Glyceraldehyde-3-phosphate-dehydrogenase (GAPD) gene were used for phylogenetic analyses, and indicated that the T. mexicana clade was highly divergent from the remainder of the original T. carolina clade. In addition, the Cytochrome c oxidase subunit 1 (COI) gene, which is used in many animals for DNA barcoding, was sequenced and used to calculate pairwise percent DNA sequence divergence between taxa. The barcoding data also strongly supported our suggested classification revisions. However, because possible introgression was detected for some of the individuals, T. mexicana was not recognized as a distinct species in a recent assessment of Testudines taxonomic updates (Fritz & Havaš 2013). The purpose of this treatise is to suggest that the possible presence of introgression seen in Martin et al. (2013) does not warrant disregarding T. mexicana as a unique species.

show abstract

mentioning

confidence: 78%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

On the Reclassification of the Terrapene (Testudines: Emydidae): A Response to Fritz & Havaš

Martin

Bernstein

Birkhead

et al. 2014

Zootaxa

Self Cite

View full text Add to dashboard Cite

show abstract

“…To explore this situation in more detail, divergences of the cyt b gene of both forms of P. rhodesianus can be compared with P. carinatus and all other species of Pelusios (Table ). Uncorrected P distances of this gene, and of other mitochondrial genes, are often used as a yardstick to infer taxonomic differentiation of chelonians (e.g., Engstrom, Shaffer & McCord, ; Fritz et al ., , ; Daniels et al ., ; Ennen et al ., ; Vargas‐Ramírez et al ., ; Kindler et al ., ; Iverson, Le & Ingram, ; Martin et al ., ; Petzold et al ., ; Thomson et al ., ) and other reptiles (Torstrom, Pangle & Swanson, ), in analogy to the widely used DNA barcoding approach (e.g., Hebert, Ratnasingham & de Waard, ). The application of such divergence values is based on the observation that deeply divergent lineages correspond to distinct taxa.…”

Section: Discussionmentioning

confidence: 98%

Comparative phylogeographies of six species of hinged terrapins (Pelusiosspp.) reveal discordant patterns and unexpected differentiation in theP. castaneus/P. chapinicomplex andP. rhodesianus

Kindler

Moosig

Branch

et al. 2015

Biol. J. Linn. Soc.

View full text Add to dashboard Cite

Using up to 2117 bp of mitochondrial DNA and up to 2012 bp of nuclear DNA, we analysed phylogeographic differentiation of six widely distributed species of African hinged terrapins (Pelusios spp.) representing different habitat types. Two taxa each live in savannahs or in forests and mesic savannahs, respectively, and the remaining two species occur in intermediate habitats. The species living in forests and mesic savannahs do not enter dry savannahs, whereas the savannah species may occur in dry and wet savannahs and even in semi‐arid steppe regions. We found no obvious correlation between habitat type and phylogeographic pattern: one savannah species (P. rhodesianus) shows phylogeographic structure, i.e. pronounced genetic differences among geographically distinct populations, and the other (P. nanus) not. One species inhabiting forests and mesic savannahs (P. carinatus) has phylogeographic structure, the other (P. gabonensis) not. The same pattern is true for the two ecologically intermediate species, with phylogeographic structure present in P. castaneus and absent in P. chapini. Nuclear evidence suggests that the latter two taxa with abutting and partially overlapping ranges are distinct, while mtDNA is only weakly differentiated. Pelusios castaneus shows pronounced phylogeographic structure, which could reflect Pleistocene range interruptions correlated with the fluctuating forest cover in West and Central Africa. Our results do not support the recognition of an extinct subspecies of P. castaneus for the Seychelles. Pelusios carinatus contains two well supported clades, which are separated by the Congo River. This species is closely related to P. rhodesianus, a taxon consisting of two deeply divergent mitochondrial clades. One of these clades is paraphyletic with respect to P. carinatus, but the two clades of P. rhodesianus are not differentiated in the studied nuclear markers and, again, paraphyletic with respect to P. carinatus. Using mtDNA sequences from the type material of P. rhodesianus, we were able to allocate this name to one of the two clades. However, owing to the confusing relationships of P. rhodesianus and P. carinatus, we refrain from taxonomic decisions.

show abstract

“…(Ehret et al 2013). This has become problematic because molecular analyses of extant taxa have suggested that T. putnami should either be synonymized with T. carolina major (Butler et al 2011), or retained as a separate taxon, as an extinct subspecies of T. carolina (Martin et al 2013). To facilitate resolution of the relationships among living and fossil turtles of the T. carolina complex, Ehret et al (2013) proposed to the ICZN the designation of a more or less complete neotype specimen for T. putnami, with precise locality and stratigraphic data.…”

Section: Appendix II Fossil Taxa Synonymized With Modern Taxamentioning

confidence: 99%

Turtles and Tortoises of the World During the Rise and Global Spread of Humanity: First Checklist and Review of Extinct Pleistocene and Holocene Chelonians.

Rhodin¹,

Thomson²,

Georgalis³

et al. 2015

Chelonian Research Monographs

View full text Add to dashboard Cite

ABsTrAcT. -We provide a first checklist and review of all recognized taxa of the world's extinct Pleistocene and Holocene (Quaternary) turtles and tortoises that existed during the early rise and global expansion of humanity, and most likely went extinct through a combination of earlier hominin (e.g., Homo erectus, H. neanderthalensis) and later human (H. sapiens) exploitation, as well as being affected by concurrent global or regional climatic and habitat changes. This checklist complements the broader listing of all modern and extant turtles and tortoises by the Turtle Taxonomy Working Group (2014). We provide a comprehensive listing of taxonomy, names, synonymies, and stratigraphic distribution of all chelonian taxa that have gone extinct from approximately the boundary between the Late Pliocene and Early Pleistocene, ca. 2.6 million years ago, up through 1500 AD, at the beginning of modern times. We also provide details on modern turtle and tortoise taxa that have gone extinct since 1500 AD. This checklist currently includes 100 fossil turtle and tortoise taxa, including 84 named and apparently distinct species, and 16 additional taxa that appear to represent additional valid species, but are only identified to genus or family. Modern extinct turtles and tortoises include 8 species, 3 subspecies, and 1 unnamed taxon, for 12 taxa. Of the extinct fossil taxa, terrestrial tortoises of the family Testudinidae (including many large-bodied island forms) are the most numerous, with 60 taxa. When the numbers for fossil tortoises are combined with the 61 modern (living and extinct) species of tortoises, of the 121 tortoise species that have existed at some point since the beginning of the Pleistocene, 69 (57.0%) have gone extinct. This likely reflects the high vulnerability of these large and slow terrestrial (often insular) species primarily to human exploitation. The other large-bodied terrestrial turtles, the 000e.2 Conservation Biology of Freshwater Turtles and Tortoises • Chelonian Research Monographs, No. 5As an addition to the annual checklist of extant modern turtle taxa (Turtle Taxonomy Working Group [TTWG] 2014), we here present an annotated checklist of extinct Pleistocene and Holocene turtle and tortoise species that existed in relatively recent times, prior to 1500 AD, during the history of the rise and global spread of humanity and concurrent global climatic and habitat changes. These species, recorded from archaeological and paleontological sites from the Pleistocene and Holocene epochs (Quaternary period), approximately the last 2.6 million years, are currently considered to be valid, and not synonymous with modern (post-1500 AD) taxa.These fossil species, including some unnamed taxa of indeterminate or undescribed generic or specific allocation, represent the majority of the chelonian diversity that has gone extinct relatively recently. Many of these taxa were likely extirpated by anthropogenic exploitation over the relatively long prehistory of earlier hominin (e.g., Homo erectus, H. neanderthalensi...

show abstract

Sequence-based molecular phylogenetics and phylogeography of the American box turtles (Terrapene spp.) with support from DNA barcoding

Cited by 36 publications

References 72 publications

On the Reclassification of the Terrapene (Testudines: Emydidae): A Response to Fritz & Havaš

On the Reclassification of the Terrapene (Testudines: Emydidae): A Response to Fritz & Havaš

Comparative phylogeographies of six species of hinged terrapins (Pelusiosspp.) reveal discordant patterns and unexpected differentiation in theP. castaneus/P. chapinicomplex andP. rhodesianus

Turtles and Tortoises of the World During the Rise and Global Spread of Humanity: First Checklist and Review of Extinct Pleistocene and Holocene Chelonians.

Contact Info

Product

Resources

About

Sequence-based molecular phylogenetics and phylogeography of the American box turtles (Terrapene spp.) with support from DNA barcoding

Cited by 36 publications

References 72 publications

On the Reclassification of the Terrapene (Testudines: Emydidae): A Response to Fritz &amp; Havaš

On the Reclassification of the Terrapene (Testudines: Emydidae): A Response to Fritz &amp; Havaš

Comparative phylogeographies of six species of hinged terrapins (Pelusiosspp.) reveal discordant patterns and unexpected differentiation in theP. castaneus/P. chapinicomplex andP. rhodesianus

Turtles and Tortoises of the World During the Rise and Global Spread of Humanity: First Checklist and Review of Extinct Pleistocene and Holocene Chelonians.

Contact Info

Product

Resources

About

On the Reclassification of the Terrapene (Testudines: Emydidae): A Response to Fritz & Havaš

On the Reclassification of the Terrapene (Testudines: Emydidae): A Response to Fritz & Havaš