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

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

doi:10.11646/zootaxa.3835.2.9

Cited by 8 publications

(13 citation statements)

References 20 publications

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“…Our conclusion is supported by the alternate phylogeny reported by Spinks et al (2009), a study not mentioned by Martin et al (2013Martin et al ( , 2014. Using sequences of the cyt b gene and seven nuclear loci, Spinks et al (2009) found T. c. bauri clustering with T. c. triunguis ( Fig.…”

supporting

confidence: 85%

“…Like Martin et al (2013), Spinks et al (2009) found T. carolina to be paraphyletic with respect to T. coahuila. However, for the rapidly evolving D-loop Butler et al (2011) found T. carolina not to be paraphyletic with respect to T. coahuila.…”

mentioning

confidence: 90%

“…delimitation proposed by Martin et al (2013) in that sequences of T. c. carolina, T. c. bauri, T. c. major and T. c. triunguis occurred in both clades. Consequently, we see no convincing phylogenetic evidence for splitting T. carolina sensu lato into two distinct species, regardless of the species concept applied.…”

mentioning

confidence: 93%

“…This confusing situation demands further research, and this issue is beyond the current discussion. To justify their species delimitation, Martin et al (2014) Martin et al (2014) cite, among others, a paper reporting that up to 14% of box turtles from eastern Texas are hybrids between T. carolina and T. ornata. However, if 14% are hybrids, 86% of the concerned populations must be pure, and this is evidence for the maintenance of largely distinct gene pools in sympatry.…”

mentioning

confidence: 99%

“…By contrast, T. carolina forms panmictic populations whenever different subspecies meet (Butler et al 2011), and this is fundamentally different from the situation in T. carolina and T. ornata. Consequently, the recognition of T. mexicana as a species distinct from T. carolina, as proposed by Martin et al (2013Martin et al ( , 2014, is unwarranted.…”

mentioning

confidence: 99%

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On the reclassification of Box Turtles (Terrapene): A response to Martin et al. (2014)

Fritz

Havaš²

2014

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supporting

confidence: 85%

mentioning

confidence: 90%

mentioning

confidence: 93%

mentioning

confidence: 99%

mentioning

confidence: 99%

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On the reclassification of Box Turtles (Terrapene): A response to Martin et al. (2014)

Fritz

Havaš²

2014

Zootaxa

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The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapenespp.)

Martin

Chafin

Douglas

et al. 2020

Preprint

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Model-based approaches to species delimitation are constrained both by 22 computational capacities as well as by algorithmic assumptions that are frequently violated when 23 applied to biologically complex systems. An alternate approach, demonstrated herein, employs 24 machine learning (=ML) approaches from which species limits are derived without an explicit 25 definition of an underlying species model. By doing so, we demonstrate the capacity of these 26 approaches to designate phylogenomically and biologically relevant groups, using North 27 American box turtles (Terrapene spp.) as an example. Several different ML-based and traditional 28 species delimitation algorithms were invoked to parse a large SNP dataset derived from ddRAD 29 sequencing. Our results illuminate two major findings. First, more traditional model-based 30 approaches perform poorly, a likely reflection of systematic biases inherent in their formulation. 31Multispecies coalescent methods consistently over-split Terrapene, particularly given prior 32 evidence and our own phylogenetic results. Second, results from ML and clustering algorithms 33 consistently reiterated the presence of clades that were well-supported in prior species tree 34 analyses. In summary, we highlight both the strengths and limitations of ML algorithms, and in 35 doing so, explore appropriate approaches to data manipulation and model fit. Our study was 36 accomplished within the context of a well-characterized empirical system that allowed a direct 37 contrast between ML versus traditional approaches. It allowed the utility of ML-methods to be 38 underscored for species delimitation and serves as a study case from which guidelines implicit to 39 ML methods could be applied to other study systems. 40 41

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Contrasting signatures of introgression in North American box turtle (Terrapenespp.) contact zones

Martin

Douglas

Chafin

et al. 2019

Preprint

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22Hybridization is differentially manifested across the genome, with observed introgression 23 representing a balance between selection and migration. The capacity to quantify introgression 24 and subsequently pinpoint the constituent genetic elements governing cross-species exchange has 25 been promoted by the unprecedented resolution of contemporary sequencing technologies. 26Furthermore, the availability of annotated reference genomes has allowed genomic patterns to be 27 associated with ecologically relevant phenotypes. We followed this pattern herein by harnessing 28 genomic resources to decipher the role of selection in shaping hybrid zones at the interface of 29 species-boundaries in North American box turtles (Terrapene). By so doing, we identified 30 adaptive divergence in genes related to immune system function and intrinsic thermal 31 adaptations. These, in turn, impact temperature-dependent sex determination and hypoxia 32 tolerance. Their patterns were then contrasted among inter-and intra-specific hybrid zones that 33 differed in a temporal and biogeographic context. Our results demonstrate that hybridization is 34 broadly apparent in Terrapene, but with varying levels of divergence at loci that impinge upon 35 thermal adaptation. These loci displayed signatures of adaptive introgression across intraspecific 36 boundaries, and do so despite a genome-wide selective trend against intergrades. By contrast, 37 interspecific comparisons at the same loci retained evidence of divergence. Importantly, 38 adaptations that shape species-boundaries in Terrapene not only underscore climatic boundaries 39 for these terrestrial ectotherms, but also bookmark their vulnerability to anthropogenic pressures. 40

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

Cited by 8 publications

References 20 publications

<strong>On the reclassification of Box Turtles (<em>Terrapene</em>): A response to Martin <em>et al.</em> (2014)</strong>

<strong>On the reclassification of Box Turtles (<em>Terrapene</em>): A response to Martin <em>et al.</em> (2014)</strong>

The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapenespp.)

Contrasting signatures of introgression in North American box turtle (Terrapenespp.) contact zones

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