Phylogeographic and phenotypic divergence between two subspecies of Testudo graeca (T. g. buxtoni and T. g. zarudnyi) across their contact zone in Iran

Contact zones are considered as windows into the evolutionary process, allowing identification of factors influencing the evolutionary forces. Here, we combined phylogenetic and morphometric analyses to explore the evolutionary process affecting the taxonomic pattern of two subspecies of Testudo graeca (T. g. buxtoni and T. g. zarudnyi) across their contact zone in Central Iran. Our results showed high levels of phylogeographic and phenotypic variation in the contact zone. Two monophyletic clades including, clade 1 (T. g. zarudnyi) and clade 2 (T. g. buxtoni) were identified. Furthermore, four distinct subclades were found in T. g. buxtoni, across a wide geographic range. Divergence time analysis suggests that the two subspecies diverged from one another after the uplifting of the Zagros Mountains during the early Pliocene. Using neutrality tests and mismatch distribution analysis, we found no evidence of recent population expansion. Morphological associations among geographical populations in the contact zone found more distinctions, with some significant adaptive and non-adaptive morphological variations in these populations. These distinctive morphological populations can be considered as management units (MUs) to conserve the evolutionary potential of this species. Finer scale evolutionary studies are required to address the southern part of the Zagros mountain range, where the overlapping of mitochondrial clades and subclades has occurred. Such information is essential for effective conservation of T. graeca populations, preventing translocation or mixing of individuals without comprehensive genetic and morphological assessment.

The first record of the genus Microgecko Nikolskii, 1907 for Iraq

The genus Microgecko Nikolskii, 1907 (Gekkonidae) currently includes eight species distributed from western Iran to north-western India and Pakistan. During field research in Iraq, we found a population of the genus near to the Darbandikhan Lake in the north-eastern part of the country. Because members of the genus are characterized by a higher level of morphological and genetic diversity, we investigated the population using both morphological and molecular approaches. The phylogenetic analyses based on a fragment of the mitochondrial marker cytochrome b and morphological characters showed that our investigated population belongs to M. helenae fasciatus. This is the first record of the genus and species for Iraq. Moreover, the phylogenetic structure within M. helenae shows divergences that suggest the elevation of M. h. fasciatus to species level.

Population genetic structure and phylogeography of the greater horseshoe bat (Rhinolophus ferrumequinum) along Alborz and Zagros Mts. in Iran

In this paper, we investigate the genetic structure and phylogeography of Rhinolophus ferrumequinum, using the mitochondrial cytochrome b gene (1017 bp) in Iran and adjacent regions. The total haplotype and nucleotide diversity are 0.63 ± 0.055 and 0.0021 ± 0.00017, respectively which suggest that R. ferrumequinum exhibits low genetic diversity. AMOVA analysis shows that more variation of genetic differentiation is present among populations of phylogenetic groupings than within populations. Our phylogenetic results support the monophyly of R. ferrumequinum and suggest this taxon comprises three allopatric/parapatric phylogroups that are distributed in Europe-western Turkey, eastern Turkey-northern Iran, and southern Iran. The Europe-western Turkey lineage (clade 2) split from the eastern Turkey-Iran lineage (clade 1) during the middle Pleistocene (0.8534 (ca.I)-0.6454 (ca.II) Ma). The divergence time among subclades A and B occurred during the mid-Pleistocene (0.4849 (ca.I)-0.369 (ca.II) Ma). All phylogenetic analyses also indicate that the Iranian and eastern Turkey R. ferrumequinum diverged from Europe and western Turkey R. ferrumequinum, with the mean percentage sequence differences ranging from 0.92%-0.75% between them. We infer that long-term isolation of R. ferrumequinum in spatially distinct refugia in parts of southwestern and northeastern Iran has promoted distinct phylogeographic lineages during the Pleistocene.

Mitochondrial DNA sequence analysis reveals multiple Pleistocene glacial refugia for the Yellow-spotted mountain newt, Neurergus derjugini (Caudata: Salamandridae) in the mid-Zagros range in Iran and Iraq

Phylogeography is often used to investigate the effects of glacial cycles on current genetic structure of various plant and animal species. This approach can also identify the number and location of glacial refugia as well as the recolonization routes from those refugia to the current locations. To identify the location of glacial refugia of the Yellow‐spotted mountain newt, Neurergus derjugini, we employed phylogeography patterns and genetic variability of this species by analyzing partial ND4 sequences (867 bp) of 67 specimens from 15 sampling localities from the whole species range in Iran and Iraq. Phylogenetic trees concordant with haplotype networks showed a clear genetic structure among populations as three groups corresponding to the populations in the north, center, and south. Evolutionary ages of clades north and south ranging from 0.15 to 0.17 Myr, while the oldest clade is the central clade, corresponding to 0.32 Myr. Bayesian skyline plots of population size change through time show a relatively slight increase until about 25 kyr (around the last glacial maximum) and a decline of population size about 2.5 kyr. The presence of geographically structured clades in north, center, and south sections of the species range signifies the disjunct populations that have emerged in three different refugium. This study illustrates the importance of the effect of previous glacial cycles in shaping the genetic structure of mountain species in the Zagros range. These areas are important in terms of long‐term species persistence and therefore valuable areas for conservation of biodiversity.

Correlative climatic niche models predict real and virtual species distributions equally well

Climate is one of the main factors driving species distributions and global biodiversity patterns. Obtaining accurate predictions of species' range shifts in response to ongoing climate change has thus become a key issue in ecology and conservation. Correlative species distribution models (cSDMs) have become a prominent tool to this aim in the last decade and have demonstrated good predictive abilities with current conditions, irrespective of the studied taxon. However, cSDMs rely on statistical association between species' presence and environmental conditions and have rarely been challenged on their actual capacity to reflect causal relationships between species and climate. In this study, we question whether cSDMs can accurately identify if climate and species distributions are causally linked, a prerequisite for accurate prediction of range shift in relation to climate change. We compared the performance of cSDMs in predicting the distributions of 132 European terrestrial species, chosen randomly within five taxonomic groups (three vertebrate groups and two plant groups), and of 1,320 virtual species whose distribution is causally fully independent from climate. We found that (1) for real species, the performance of cSDMs varied principally with range size, rather than with taxonomic groups and (2) cSDMs did not predict the distributions of real species with a greater accuracy than the virtual ones. Our results unambiguously show that the high predictive power of cSDMs can be driven by spatial autocorrelation in climatic and distributional data and does not necessarily reflect causal relationships between climate and species distributions. Thus, high predictive performance of cSDMs does not ensure that they accurately depict the role of climate in shaping species distributions. Our findings therefore call for strong caution when using cSDMs to provide predictions on future range shifts in response to climate change.

Cryptic diversity in the smooth snake (Coronella austriaca)

The smooth snake, Coronella austriaca, is a common snake species widespread in the Western Palearctic region. It does not form conspicuous morphological variants and, although several evolutionary lineages have been distinguished based on the analyses of the mitochondrial DNA sequences, only two subspecies with very limited distribution have been traditionally recognized. Here we present an mtDNA phylogeography of the species using geographically extended sampling while incorporating biogeographically important areas that have not been analyzed before, such as Anatolia, Crimea, and Iran. We find that the smooth snake comprises 14 distinct phylogenetic clades with unclear mutual relationships, characterized by complex genetic structure and relatively deep divergences; some of them presumably of Miocene origin. In general, the biogeographic pattern is similar to other Western Palearctic reptiles and illustrates the importance of the main European peninsulas as well as the Anatolian mountains, Caucasus, and Alborz Mts. in Iran for the evolution of the present-day diversity. Considerable genetic structure present in the smooth snake populations within these large areas indicates the existence of several regional Plio-Pleistocene refugia that served as reservoirs for dispersal and population expansions after the glacial periods. The current taxonomy of C. austriaca does not reflect the rich genetic diversity, deep divergences, and overall evolutionary history revealed in our study and requires a thorough revision. This will only be possible with an even higher-resolution sampling and integrative approach, combining analyses of multiple genetic loci with morphology, and possibly other aspects of the smooth snake biology.

Historical explanation of genetic variation in the Mediterranean horseshoe bat Rhinolophus euryale (Chiroptera: Rhinolophidae) inferred from mitochondrial cytochrome-b and D-loop genes in Iran

Molecular phylogeography and species distribution modelling (SDM) suggest that late Quaternary glacial cycles have portrayed a significant role in structuring current population genetic structure and diversity. Based on phylogenetic relationships using Bayesian inference and maximum likelihood of 535 bp mtDNA (D-loop) and 745 bp mtDNA (Cytb) in 62 individuals of the Mediterranean Horseshoe Bat, Rhinolophus euryale, from 13 different localities in Iran we identified two subspecific populations with differing population genetic structure distributed in southern Zagros Mts. and northern Elburz Mts. Analysis of molecular variance (AMOVA) obtained from D-loop sequences indicates that 21.18% of sequence variation is distributed among populations and 10.84% within them. Moreover, a degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θCT = 0.68, p = .005). The positive and significant correlation between geographic and genetic distances (R² = 0.28, r = 0.529, p = .000) is obtained following controlling for environmental distance. Spatial distribution of haplotypes indicates that marginal population of the species in southern part of the species range have occupied this section as a glacial refugia. However, this genetic variation, in conjunction with results of the SDM shows a massive postglacial range expansion for R. euryale towards higher latitudes in Iran.