Evolutionary applications of phylogenetically-informed ecological niche modelling (ENM) to explore cryptic diversification over cryptic refugia

Green lizards of the genus Lacerta have served as excellent models for studying the impact of Pleistocene climatic oscillations on genetic structures. The Caspian green lizard, Lacerta strigata , occupies various habitats across the Caucasus and the South Caspian Sea, with the Hyrcanian Forests and north of the Alborz Mountains forming the core of the range. This study aimed to re‐examine the phylogenetic relationships of L. strigata with other congeneric members and to assess the genetic structure and historical demography of the species. Furthermore, Species Distribution Models (SDMs) were performed to infer the species' potential habitat suitability and were then projected on climate scenarios reflecting current and past (6 ky and 21 ky before present) conditions. A total of 39 individuals collected from most of the distribution range, together with additional lacertid species sequences from the GenBank database, were examined using mtDNA (Cyt b and 12S ribosomal RNA) and nuclear (C‐mos and β‐fibrinogen) sequence data. Based on the phylogenetic analyses, L. strigata was found to be a sister taxon to all other members of the genus. The species included two main clades (regional western and eastern) that diverged in a period between the Early and Middle Pleistocene. Based on the BBM and S‐Diva analyses, both dispersal and vicariance events explained the phylogeographic structure of the species in the Hyrcanian Forests. The historical demographic analyses using Bayesian skyline plots showed a mild increase in the effective population size from about 120 Kya for the western regional clade. According to phylogeographic structures and SDMs evidence, as in other species within the region, it appears that the south of the Caspian Sea (Hyrcanian Forests), and the Alborz Mountains acted as multiple refugia during cold periods and promoted expansion outwards amid the warm periods. Overall, the results provided evidence that the genetic structure of the species has been influenced by the Pleistocene climatic fluctuations.

Section: Genetic Structure and Demographymentioning

confidence: 84%

Section: Evolutionary History Of Lacerta Strigatamentioning

confidence: 98%

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Pleistocene climate fluctuations as the major driver of genetic diversity and distribution patterns of the Caspian green lizard, Lacerta strigata Eichwald, 1831

Saberi-Pirooz

Rajabi-Maham

Ahmadzadeh

et al. 2021

“…Combining multiple sources of data, including genetic, ecological, and phenotypic data, can provide greater insight into the species boundaries (Ahmadi et al, 2018;Leaché et al, 2009). In this regard Lerp et al (2016), Silva et al (2017), and Fadakar et al (2020) suggested the use of morphological and nuclear genetic studies to investigate further the relatedness of gazelle populations on the two sides of the Zagros Mountains.…”

Section: Introductionmentioning

confidence: 99%

“…For many gazelle taxa, the achievements of past conservation efforts have been compromised by a lack of knowledge and confusion about the phylogeny and taxonomic status of different populations, and even species boundaries have not been certain (Groves & Grubb, 2011). Combining multiple sources of data, including genetic, ecological, and phenotypic data, can provide greater insight into the species boundaries (Ahmadi et al., 2018; Leaché et al., 2009). In this regard Lerp et al.…”

Section: Introductionmentioning

confidence: 99%

Morphological diversity and ecological niche divergence in goitered and sand gazelles

Hemami

Khosravi

Groves

et al. 2020

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The phylogeny and species boundaries of Gazella subgutturosa and G. marica have been long debated. The achievements of past conservation efforts have been compromised by a lack of knowledge about the phylogeny and taxonomic status of different populations. We integrated the recent genetic findings by previous studies with morphometric analyses and ecological niche modeling (ENM) to assess discreteness among populations of these gazelle species in Asia. Taxonomic diversity of gazelles was investigated by using principal components analysis (PCA) based on 14 cranial measures of male skulls. Ecological niche divergence was examined based on a PCA on climatic factors and a species distribution modeling (SDM) with environmental variables. Morphometric results indicated substantial differentiation in size between skulls of the western Zagros Mountains including west and south‐western Iran and Arabian Peninsula from all other samples east of the Zagros Mountains from Iran to China. ENM also revealed that gazelles in the east and west of Zagros Mountains occupy distinct niches and that there are apparent areas of disconnection across the goitered gazelle suitable range. A complete divergent niche occupation was also observed between goitered gazelles of northern Mongolia and other populations of the species, except those in China. Taking the inferences from ENM and morphology together with previous genetics results, we conclude that gazelles in the west and south‐west of Iran may represent G. marica . Also, our combined analyses revealed divergence among gazelles of Iran, Central Asia, and Mongolia/China. These results may pave the way for future studies and have conservation implications particularly for reintroduction/supplementation programs.

Ecological niche models reveal divergent habitat use of Pallas's cat in the Eurasian cold steppes

Lorestani

Hemami

Rezvani

et al. 2022

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Identifying the association between the patterns of niche occupation and phylogenetic relationships among sister clades and assisting conservation planning implications are of the most important applications of species distribution models (SDMs). However, most studies have been carried out regardless of within taxon genetic differentiation and the potential of local adaptation occurring within the species level. The Pallas's cat ( Otocolobus manul ) is a less‐studied species with unknown biogeography and phylogenetic structure across a widespread yet isolated range from the Caucasus to eastern China. In the current study, by considering a previously proposed genetic structure and based on a cluster analysis on climatic variables, we supposed three clades for this species, including O. m. manul , O. m. ferrugineus , and O. m. nigripectus . We developed SDM for each clade separately and compared it with a general distribution model of the species to determine whether the hypothesized taxonomic resolution affects the predicted ecological niche of the within‐species structures. We assessed the effect of climate change on the future distribution of the species to detect the most sensitive clades to global warming scenarios. Our results showed that for all clades' models, the AUC and TSS were greater than the general model. Access to the preferred prey of the Pallas's cat, that is, pika, had a significant effect on the distribution of O. m. manul and O. m. ferrugineus , whereas the most influential variable affecting O. m. nigripectus habitat suitability was terrain slope. Based on our future projections, we found that future climate change likely threatens the clades O. m. ferrugineus and O. m. nigripectus more than O. m. manul , findings that were hidden in the general model. Our results highlight the proficiency of SDMs in recognizing within‐taxon habitat use of widespread species and the necessity of this procedure for implementing effective conservation planning of these species.