Genomic analysis of Bornean geckos (Gekkonidae: <i>Cyrtodactylus</i>) reveals need for updated taxonomy

Davis, Hayden R.; Nashriq, Izneil; Woytek, Kyra S.; Wikramanayake, Shanelle A.; Bauer, Aaron M.; Karin, Benjamin R.; Brennan, Ian G.; Iskandar, Djoko T.; Das, Indraneil

doi:10.1111/zsc.12575

Cited by 4 publications

(1 citation statement)

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“…Traditional morphology cannot be discarded or replaced by molecular technology for the classification of species. However, molecular genetic analysis can be a powerful auxiliary tool when morphological characteristics cannot provide a clear taxonomic determination (Davis et al., 2023; Ng et al., 2023; Paz‐Sedano, Alvarez, Gosliner, & Pola, 2022; Ronque, Azevedo‐Silva, Mori, Souza, & Oliveira, 2016; Ward & Blaimer, 2022). Within the phylogenetic tree we developed, L. yarkandensis and L. timidus clustered separately and distinctly from those in the other groups (Figure 4).…”

Section: Discussionmentioning

confidence: 99%

Taxonomic status of hares (Lepus spp.) in Xinjiang, China (Lagomorpha: Leporidae): An integrative approach

Shan,

Li,

Dai

et al. 2024

Zoologica Scripta

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The taxonomic status and interspecies relationships of hares (genus Lepus) in Xinjiang, China, remain ambiguous owing to extremely similar external morphologies, introgressive hybridization between species and a lack of molecular genetic records. In this study, a total of 154 hare specimens were used to clarify their taxonomic status. Based on multiple lines of evidence, including observations and comparisons of external morphological characteristics, skull morphometrics and genome‐wide single nucleotide polymorphism (SNP) datasets, four hare species were recognised. Lepus yarkandensis and Lepus timidus, which have obvious morphological characteristics, were identified as two distinct species, as previously reported. Combining the integrated morphological and molecular datasets with the relevant literature, we proposed suggestions on the classification of the more controversial hares. Due to molecular and morphological similarities, hares in northern and central Xinjiang were divided into two subspecies of Lepus tolai, namely, Lepus tolai lehmanni and Lepus tolai centrasiaticus. Despite similar external morphological characters, hares in the southwest Pamir Plateau and its surroundings can be distinguished from L. tolai by differences in skull morphology and genetic divergence and were, therefore, considered a subspecies of Lepus tibetanus, Lepus tibetanus pamirensis. Furthermore, we found that hybridization and introgression occurred between sympatric or parapatric hares, especially between L. yarkandensis and L. tibetanus pamirensis, L. yarkandensis and L. tolai centrasiaticus, and L. tolai lehmanni and L. timidus.

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Section: Discussionmentioning

confidence: 99%

Taxonomic status of hares (Lepus spp.) in Xinjiang, China (Lagomorpha: Leporidae): An integrative approach

Shan,

Li,

Dai

et al. 2024

Zoologica Scripta

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Ecomorphology of the Locomotor Apparatus in the Genus Cyrtodactylus (Gekkota, Squamata)

Riedel,

Grismer,

Higham

et al. 2024

Evol Biol

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Adaptive radiations garner considerable interest from evolutionary biologists. Lizard radiations diversifying along structural niche space often exhibit distinct changes in body and limb proportions. One prediction is that terrestrial species inhabiting open habitats will have relatively longer hindlimbs, associated with faster running speeds, while scansorial species will have relatively shorter limbs to keep the centre of mass closer to the substratum. Alternatively, terrestrial species in densely vegetated habitats could benefit from relatively shorter limbs to prevent entanglement with more frequently encountered obstacles, whereas scansorial species could benefit from longer limbs promoting greater limb spans and static stability. Cyrtodactylus, an ecologically diverse gekkonid genus, includes numerous specialists with narrow structural niches, but the degree of morphological diversification exhibited by these specialists is largely unknown. We investigated associations between locomotor morphology and structural microhabitat use in Cyrtodactylus to test if either of the opposing predictions can be corroborated for this radiation. We measured body length and relative limb dimensions of 87 species, covering multiple independent transitions among structural microhabitat preferences. Using these data, we reconstructed the phylomorphospace and tested for associations between structural microhabitat niche and limb morphology. We found strong separation between structural niche groups in accordance with the second hypothesis, although overlap is evident among functionally related niches such as those of granite and karst specialists.

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Establishing species boundaries in Bornean geckos

Davis,

Sanford,

Das

et al. 2024

Biol. Lett.

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Species delimitation using mitochondrial DNA (mtDNA) remains an important and accessible approach for discovering and delimiting species. However, delimiting species with a single locus (e.g. DNA barcoding) is biased towards overestimating species diversity. The highly diverse gecko genus Cyrtodactylus is one such group where delimitation using mtDNA remains the paradigm. In this study, we use genomic data to test putative species boundaries established using mtDNA within three recognized species of Cyrtodactylus on the island of Borneo. We predict that multi-locus genomic data will estimate fewer species than mtDNA, which could have important ramifications for the species diversity within the genus. We aim to (i) investigate the correspondence between species delimitations using mtDNA and genomic data, (ii) infer species trees for each target species, and (iii) quantify gene flow and identify migration patterns to assess population connectivity. We find that species diversity is overestimated and that species boundaries differ between mtDNA and nuclear data. This underscores the value of using genomic data to reassess mtDNA-based species delimitations for taxa lacking clear species boundaries. We expect the number of recognized species within Cyrtodactylus to continue increasing, but, when possible, genomic data should be included to inform more accurate species boundaries.

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Genomic analysis of Bornean geckos (Gekkonidae: Cyrtodactylus) reveals need for updated taxonomy

Cited by 4 publications

References 94 publications

Taxonomic status of hares (Lepus spp.) in Xinjiang, China (Lagomorpha: Leporidae): An integrative approach

Taxonomic status of hares (Lepus spp.) in Xinjiang, China (Lagomorpha: Leporidae): An integrative approach

Ecomorphology of the Locomotor Apparatus in the Genus Cyrtodactylus (Gekkota, Squamata)

Establishing species boundaries in Bornean geckos

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