Multilocus phylogeny and coalescent species delimitation in Kotschy's gecko, Mediodactylus kotschyi: Hidden diversity and cryptic species

Kotsakiozi, Panayiota; Jablonski, Daniel; Ilgaz, Çetίn; Kumlutaş, Yusuf; Avcı, Aziz; Meiri, Shai; Itescu, Yuval; Kukushkin, Oleg V.; Gvoždík, Václav; Scillitani, Giovanni; Roussos, Stephanos A.; Jandzík, Dávid; Kasapidis, Panagiotis; Lymberakis, Petros; Poulakakis, Nikos

doi:10.1016/j.ympev.2018.03.022

Cited by 48 publications

(36 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Additional samples from Iran, central Anatolia, and the Levant will be necessary to learn more about the history of this species. In particular, one might expect surprises from the Levantine region given that it hosts many endemic taxa and lineages, and several Anatolian species have their subspecies or sister species located in the region, for example, Natrix tessellata complex (Guicking, Joger & Wink, 2009), the L. trilineata complex (Ahmadzadeh et al, 2013), Z. hohenackeri (Jandzik, Avcı & Gvoždík, 2013), the Ablepharus kitaibelii complex (Skourtanioti et al, 2016), Xerotyphlops vermicularis (Kornilios, 2017), and the Mediodactylus kotschyi complex (Kotsakiozi et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

The biogeography ofElaphe sauromates(Pallas, 1814), with a description of a new rat snake species

Jablonski

Kukushkin

Avcı

et al. 2019

PeerJ

Self Cite

View full text Add to dashboard Cite

Background The rat snake genus Elaphe once comprised several dozens of species distributed in temperate through tropical zones of the New and Old World. Based on molecular-genetic analyses in early 2000s, the genus was split into several separate genera, leaving only 15 Palearctic and Oriental species as its members. One of the three species also occurring in Europe is Elaphe sauromates, a robust snake from the Balkans, Anatolia, Caucasus, Ponto-Caspian steppes, and Levant that has been suspected to be composed of two or more genetically diverse populations. Here, we studied the genetic structure and morphological variation of E. sauromates, aiming to better understand its inter-population relationships and biogeography, and subsequently revise its taxonomy. Methods We reconstructed the phylogeography and analyzed the genetic structure of E. sauromates populations originating from most of its geographic range using both mitochondrial (COI, ND4) and nuclear (C-MOS, MC1R, PRLR, RAG1) DNA gene fragments. We employed Maximum likelihood and Bayesian inference methods for the phylogenetic tree reconstructions, supplemented with species delimitation methods, analysis of haplotype networks, and calculation of uncorrected p-distances. Morphological variation in 15 metric and 18 meristic characters was studied using parametric univariate tests as well as multivariate general linearized models. In total, we analyzed sequences originating from 63 specimens and morphological data from 95 specimens of E. sauromates sensu lato. Results The molecular phylogeny identified two clearly divergent sister lineages within E. sauromates, with both forming a lineage sister to E. quatuorlineata. The genetic distance between them (5.80–8.24% in mtDNA) is similar to the distances among several other species of the genus Elaphe. Both lineages are also moderately morphologically differentiated and, while none of the characters are exclusively diagnostic, their combination can be used for confident lineage identification. Here, following the criteria of genetic and evolutionary species concepts, we describe the lineage from eastern Anatolia and parts of the Lesser and Great Caucasus as a new species E. urartica sp. nov. Discussion Elaphe urartica sp. nov. represents a cryptic species whose ancestors presumably diverged from their common ancestor with E. sauromates around the Miocene-Pliocene boundary. The intraspecific genetic structure indicates that the recent diversity of both species has been predominantly shaped by Pleistocene climatic oscillations, with glacial refugia mainly located in the Balkans, Crimea, and/or Anatolia in E. sauromates and Anatolia and/or the Caucasus in E. urartica sp. nov.

show abstract

Section: Discussionmentioning

confidence: 99%

The biogeography ofElaphe sauromates(Pallas, 1814), with a description of a new rat snake species

Jablonski

Kukushkin

Avcı

et al. 2019

PeerJ

Self Cite

View full text Add to dashboard Cite

show abstract

“…1). These mountains have provided a complex topographic and microclimatic setting that has functioned as a historical refugium for the persistence of many amphibians (Gvozdik et al, 2010;Gül, 2013;Plötner et al, 2015;van Riemsdijk et al, 2017) and reptiles (Kapli et al, 2013;Tamar et al, 2015;Candan et al, 2016;Skourtanioti et al, 2016;Stümpel et al, 2016;Kotsakiozi et al, 2018). These populations of B. verrucosissimus seem to be isolated from those in Syria and Lebanon (see Jablonski and Sadek, 2019).…”

Section: Discussionmentioning

confidence: 99%

Taxonomic assessment and distribution of common toads (Bufo bufo and B. verrucosissimus) in Turkey based on morphological and molecular data

et al. 2020

View full text Add to dashboard Cite

Abstract The Bufo bufo species group includes four species distributed in the western Palearctic: B. bufo, B. eichwaldii, B. spinosus and B. verrucosissimus. Both B. bufo and B. verrucosissimus are known to occur in Turkey, but their range boundaries and the taxonomic status of B. verrucosissimus are still uncertain. In this study, we analyzed the variation in a set of morphological characters and in two mitochondrial and two nuclear DNA markers to address these questions. Phylogenetic analyses of sequence data support two main clades of common toads in Turkey, corresponding to B. bufo and B. verrucosissimus. The latter is subdivided into two allopatric subclades including populations along the Mediterranean and Black Sea coast, respectively. Discriminant analysis of morphological data showed separation among groups as defined by molecular analyses. We discuss these results and their implications for the evolutionary history of common toads in Turkey.

show abstract

“…However, for many organisms, especially those with non-visual mating approaches (Bickford et al, 2007), if the diagnostic morphological features are subtle or even non-existent, species identification based solely on morphological differences may be problematic (Kajtoch et al, 2017;Kotsakiozi et al, 2018;Shirley et al, 2014). In addition, for some organisms, similar selection pressures or extreme environments may result in morphological features experiencing convergent evolution (Nevo, 2001).…”

Section: Introductionmentioning

confidence: 99%

“…Morphological variation may be the result of phenotypic plasticity or short-term adaptation to local conditions (Dowle et al, 2015;Svanback and Eklov, 2006;Wagner et al, 2013), a process that further makes species delimitation by morphological differences challenging. Therefore, morphology-based taxonomy may relatively underestimate species number due to the presence of cryptic species, which provide opportunities and challenges for species delimitation based on phylogenetic data (Catarina et al, 2016;Giarla et al, 2014;Kotsakiozi et al, 2018;Sheridan and Stuart, 2018).…”

Section: Introductionmentioning

confidence: 99%

Hidden species diversity in Pachyhynobius: A multiple approaches species delimitation with mitogenomes

Sun

Lai

Orozco‐terWengel

et al. 2019

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

The lack of distinct morphological features of cryptic species is a hard problem for taxonomy, especially when the taxa are closely related with considerable amounts of ancestral polymorphism. Lately, intensive coalescent-based analyses involving multiple loci have become the preferred method to assess the extent of genetic distinctivness in otherwise phenotypically similar populations. Previously, phylogenetic studies on Pachyhynobius shangchengensis uncovered five extremely deeply divergent clades, which suggested that this species may be a cryptic species complex. In this study, we used the complete mitochondrial genome data and samples from the entire range of stout salamander (Pachyhynobius), as well as publicly available mitochondrial genomes to assess species boundaries within this genus using a suite of diverse methodologies (e.g. general mixed Yule coalescent model, Automatic Barcode Gap Discovery). The phylogenetic relationships recovered two major groups within P. shangchengensis, with one group formed by four of the six extant populations and corresponding to the central and eastern range of the Dabie mountains, while the other group encompassed two other lineages in the north west of the Dabie mountain range. The species delimitation comparison within Pachyhynobius supported the presence of recognized species within the genus, and consensus was observed across methods for the existence of up to five cryptic species within what has been traditionally considered to be P. shangchengensis. While this implies the existence of four taxa in addition to the described P. shangchengensis species, morphological data and life history information are further required to contribute to the species definition. The observed pattern of genetic variation is likely the outcome of a discontinuous habitat combined with niche conservatism, which produced the sky-island effect observed in Pachyhynobius, and which led to formation of a hidden species diversity in this genus.

show abstract

Multilocus phylogeny and coalescent species delimitation in Kotschy's gecko, Mediodactylus kotschyi: Hidden diversity and cryptic species

Cited by 48 publications

References 49 publications

The biogeography ofElaphe sauromates(Pallas, 1814), with a description of a new rat snake species

The biogeography ofElaphe sauromates(Pallas, 1814), with a description of a new rat snake species

Taxonomic assessment and distribution of common toads (Bufo bufo and B. verrucosissimus) in Turkey based on morphological and molecular data

Hidden species diversity in Pachyhynobius: A multiple approaches species delimitation with mitogenomes

Contact Info

Product

Resources

About