Morphological species and discordant mtDNA: A genomic analysis of Phrynocephalus lizard lineages on the Qinghai-Tibetan Plateau

Jin, Yuanting; Brown, Richard P.

doi:10.1016/j.ympev.2019.106523

Cited by 9 publications

(6 citation statements)

References 37 publications

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“…The RADseq methodology has been applied in other studies of squamate (lizards and snakes), increasing understanding of the processes related to genetic divergence and the identification of genomic regions of interest. The total number of SNPs obtained in this study (288,286) agree with the SNP density found in other RADseq studies of reptiles, with relatively high levels of diversity detected 30,31 . Population structure analysis revealed a clear genetic structure among all the populations of P. lilfordi, independent of whether we used SNPs from all RAD tags or just candidates for selection 32 .…”

Section: Discussionsupporting

confidence: 90%

Genomic signatures of drift and selection driven by predation and human pressure in an insular lizard

Bassitta

Brown

Pérez‐Cembranos

et al. 2021

Sci Rep

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Genomic divergence was studied in 10 small insular populations of the endangered Balearic Islands lizard (Podarcis lilfordi) using double digest restriction-site associated DNA sequencing. The objectives were to establish levels of divergence among populations, investigate the impact of population size on genetic variability and to evaluate the role of different environmental factors on local adaptation. Analyses of 72,846 SNPs supported a highly differentiated genetic structure, being the populations with the lowest population size (Porros, Foradada and Esclatasang islets) the most divergent, indicative of greater genetic drift. Outlier tests identified ~ 2% of loci as candidates for selection. Genomic divergence-Enviroment Association analyses were performed using redundancy analyses based on SNPs putatively under selection, detecting predation and human pressure as the environmental variables with the greatest explanatory power. Geographical distributions of populations and environmental factors appear to be fundamental drivers of divergence. These results support the combined role of genetic drift and divergent selection in shaping the genetic structure of these endemic island lizard populations.

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Section: Discussionsupporting

confidence: 90%

Genomic signatures of drift and selection driven by predation and human pressure in an insular lizard

Bassitta

Brown

Pérez‐Cembranos

et al. 2021

Sci Rep

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“…Jin and Brown [86] demonstrated that morphologically different P. guinanensis is genetically indistinguishable from P. putjatai (spelled as "P. putjatia" in their work; however "P. putjatai" is the correct spelling according to Barabanov and Ananjeva [1]). Our study agrees with the results of Jin and Brown [86,122] and Jin et al [123] on the phylogenetic position of P. guinanensis (Figure 2B). The recent multilocus phylogenetic study by Chen et al [121] reported on three major lineages within P. putjatai.…”

Section: Oreosaura (Phrynocephalus Vlangalii Species Group)supporting

confidence: 93%

COI-Barcoding and Species Delimitation Assessment of Toad-Headed Agamas of the Genus Phrynocephalus (Agamidae, Squamata) Reveal Unrecognized Diversity in Central Eurasia

et al. 2023

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We provide a diversity assessment of the agamid genus Phrynocephalus Kaup, 1825. We analyze COI mtDNA barcodes from 385 individuals sampled all over Phrynocephalus range. We apply the ABGD, ASAP, bGMYC, mlPTP and hsPTP species delimitation algorithms to analyze the COI gene fragment variation and assess the species diversity in Phrynocephalus. Nine species groups are revealed in Phrynocephalus in agreement with earlier studies on the phylogenetic relationships of the genus. We demonstrate that the present taxonomy likely underestimates the actual diversity of the genus. Alternative species delimitation algorithms provide a confusingly wide range of possible number of Phrynocephalus species—from 54 to 103 MOTUs (molecular operational taxonomic units). The ASAP species delimitation scheme recognizing 63 MOTUs likely most closely fits the currently recognized taxonomic framework of Phrynocephalus. We also report on 13 previously unknown Phrynocephalus lineages as unverified candidate species. We demonstrate that the ASAP and the ABGD algorithms likely most closely reflect the actual diversity of Phrynocephalus, while the mlPTP and hsPTP largely overestimate it. We argue that species delimitation in these lizards based exclusively on mtDNA markers is insufficient, and call for further integrative taxonomic studies joining the data from morphology, mtDNA and nuDNA markers to fully stabilize the taxonomy of Phrynocephalus lizards.

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“…Interspecific gene flow can blur the morphological boundary of species because the morphology of hybrid offspring will show a parental intermediate type, resulting in errors of individual identification in a discriminant analysis (Jones et al, 2016;Flores-Rentería et al, 2017). In particular, it is difficult to classify and define species complexes with similar morphology and incomplete reproductive isolation, because interspecific hybridization can cause inconsistency between taxonomic status and phylogenetic relationships (Chan et al, 2017;Jin and Brown, 2019). In addition, due to rapid changes in the geological structure and climatic fluctuation in the middle and late Pleistocene, the rate of genetic differentiation was accelerated in O. graminea sensu stricto, and three clades evolved within a short period (2.19 MYA) (Chen et al, 2020).…”

Section: Incomplete Morphological Differentiationmentioning

confidence: 99%

Morphological variation and its correlation with bioclimatic factors in Odorrana graminea sensu stricto

Cui

Shen

et al. 2023

Front. Ecol. Evol.

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The large green cascade frog (Odorrana graminea sensu stricto) shows significant genetic differentiation in China, forming western, southern, and eastern clades. However, the morphological differentiation among the three clades is unclear, and the influence of bioclimatic factors on morphological variation among clades is unknown. Based on 20 morphological traits of 309 specimens from 28 localities, the present study explored the morphological differentiation and variation among clades and their correlation with bioclimatic factors through the multivariate statistical analysis. The results of the present study showed that O. graminea sensu stricto was divided into western, southern, and eastern morphological groups, and the gene flow between neighboring populations had caused an individual misidentification. With the three-step terrain and population distribution latitude and humidity, the annual mean temperature (Bio1) was significantly different between the southern and eastern–western clades; the maximum temperature of the hottest month (Bio5) was significantly different between the southern and western clades, and the mean temperature of the wettest quarter (Bio8) and the precipitation seasonality (Bio15) were significantly different between the eastern and western–southern clades. The southern clade that was affected by a high temperature had a smaller body size and larger sensory organs, and the eastern clade distributed in highly humid areas had a larger body size and smaller sensory organs. Moreover, the annual mean temperature range (Bio7) was the dominant factor in the morphological variation of O. graminea sensu stricto, and it had significant negative correlations with seven traits of male frogs and four traits of female frogs. The effect of precipitation factors on the morphological differentiation of each clade remained unclear. The local adaptation caused by climatic differences was the main reason for the morphological differentiation among clades. These findings will help us to understand amphibians’ abilities to adapt to environmental variation.

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Morphological species and discordant mtDNA: A genomic analysis of Phrynocephalus lizard lineages on the Qinghai-Tibetan Plateau

Abstract: The version presented here may differ from the published version or from the version of the record. Please see the repository URL above for details on accessing the published version and note that access may require a subscription.

Cited by 9 publications

References 37 publications

Genomic signatures of drift and selection driven by predation and human pressure in an insular lizard

Genomic signatures of drift and selection driven by predation and human pressure in an insular lizard

COI-Barcoding and Species Delimitation Assessment of Toad-Headed Agamas of the Genus Phrynocephalus (Agamidae, Squamata) Reveal Unrecognized Diversity in Central Eurasia

Morphological variation and its correlation with bioclimatic factors in Odorrana graminea sensu stricto

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