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Ancestral range estimation for the G. halys/G. intermedius complex using BioGeoBEARS under DIVALIKE + J model on the concatenated mtDNA + nDNA dataset. Colours are correspondent to the seven regions (explained in section 2.4.2). Yellow star indicates ML estimation of the center of origin of all taxa (latitude 43.308 and longitude 96.388, estimated by PhyloMapper 1b1) in the complex, the orange circle shows G. shedaoensis locality in Shedao Island, China, and black and red arrows present a hypothetical direction of dispersal supported by BioGeoBEAR results. Numbers refer to divergence times among taxa in million years (see Fig. 3). Polygons show approximate range of distribution of each species/subspecies. The red circle in Afghanistan refers to G. h. boehmei (Nilson, 1983), which is not included in our study.
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It has been generally acknowledged that glacial climates at the time of the Pleistocene altered the patterns of species distributions, prompting latitudinal and altitudinal distribution shifts in several species, including poikilothermic species commonly known for their thermal sensitivity. However, the historical hylogeographic patterns of such sp...
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... + J model holds the strongest support compared to other analyses performed in BioGeoBEARS (Table S2) and dis- persal, extinction, and cladogenesis parameters were estimated at 0.000431, 0.022, and 1.00E-12, respectively. We have found some allopatric speciation and founder-event speciation in evolution of this complex in different time slices (Fig. 4). Furthermore, among the four different scenarios tested, the second one (Scenario HB in Table S2) is characterized by the highest AICc value, under the DIVALIKE + J model (Fig. 4). The best hypothesis suggests that the ancestor of the complex was widespread through regions A and G at 3.62 (2.30-5.32 Coalescent analyses and simulations ...
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... 0.000431, 0.022, and 1.00E-12, respectively. We have found some allopatric speciation and founder-event speciation in evolution of this complex in different time slices (Fig. 4). Furthermore, among the four different scenarios tested, the second one (Scenario HB in Table S2) is characterized by the highest AICc value, under the DIVALIKE + J model (Fig. 4). The best hypothesis suggests that the ancestor of the complex was widespread through regions A and G at 3.62 (2.30-5.32 Coalescent analyses and simulations of G. h. caucasicus. Both ABC coalescence simulations (direct and the logistic approaches) using the concatenated mtDNA + nDNA dataset led to the conclusion that the Scenario EH 3 ...
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... latitudes (40-50 degrees of latitude) and lower elevations 59 . Given that G. rickmersi and G. caraganus are sister clades to G. caucasicus (Fig. 1), it could be inferred that as a consequence of the cooling of high latitudes, one could expect gene flow to be driven toward more southerly latitudes such as Afghanistan and northeastern Iran (Fig. 4). The first divergence due to vicariance in populations of G. caucasicus in northern Iran is estimated to have occurred around 1.25 Myr (95% HPD: 0.73-1.83 Myr). At that time, populations of central and western Alborz diverged from populations of the north-east. Results of ABC analyses suggested a bi-directional gene flow from ...
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... was performed using two independent runs of 40 million gener- ations, sampled every 1000 generations, with the first 25% discarded as burn-in. Tracer was used to evaluate acceptable levels of MCMC chain mixing, the stationary likelihoods and appropriate lengths of burn-in (25%), as well as to estimate effective sample sizes for all parameters. (Fig. 4). We used BEAST 1.8.2 58 to construct an ultrametric tree, then pruned all outgroups using Mesquite v.3.04 111 . We chose four time slices (0-0.30, 0.30-1.20, 1.20-2.50 and 2.50-3.45 Mya), corresponding to divergence times within the complex. First, we ran the S0 scenario in which dispersal between regions was not penalized. Then, we ...
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... four time slices (0-0.30, 0.30-1.20, 1.20-2.50 and 2.50-3.45 Mya), corresponding to divergence times within the complex. First, we ran the S0 scenario in which dispersal between regions was not penalized. Then, we tested four alternative scenarios (Scenario HB 0-3), where we tested colonization of the complex lineages from other adjacent regions (Fig. 4). We also estimated the geographic location of the ancestors of the G. halys/G. intermedius complex, employing a statistical method implemented in PhyloMapper 1b1 112 , optimized by 10,000 ...
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... + J model holds the strongest support compared to other analyses performed in BioGeoBEARS (Table S2) and dis- persal, extinction, and cladogenesis parameters were estimated at 0.000431, 0.022, and 1.00E-12, respectively. We have found some allopatric speciation and founder-event speciation in evolution of this complex in different time slices (Fig. 4). Furthermore, among the four different scenarios tested, the second one (Scenario HB in Table S2) is characterized by the highest AICc value, under the DIVALIKE + J model (Fig. 4). The best hypothesis suggests that the ancestor of the complex was widespread through regions A and G at 3.62 (2.30-5.32 Coalescent analyses and simulations ...
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... 0.000431, 0.022, and 1.00E-12, respectively. We have found some allopatric speciation and founder-event speciation in evolution of this complex in different time slices (Fig. 4). Furthermore, among the four different scenarios tested, the second one (Scenario HB in Table S2) is characterized by the highest AICc value, under the DIVALIKE + J model (Fig. 4). The best hypothesis suggests that the ancestor of the complex was widespread through regions A and G at 3.62 (2.30-5.32 Coalescent analyses and simulations of G. h. caucasicus. Both ABC coalescence simulations (direct and the logistic approaches) using the concatenated mtDNA + nDNA dataset led to the conclusion that the Scenario EH 3 ...
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... latitudes (40-50 degrees of latitude) and lower elevations 59 . Given that G. rickmersi and G. caraganus are sister clades to G. caucasicus (Fig. 1), it could be inferred that as a consequence of the cooling of high latitudes, one could expect gene flow to be driven toward more southerly latitudes such as Afghanistan and northeastern Iran (Fig. 4). The first divergence due to vicariance in populations of G. caucasicus in northern Iran is estimated to have occurred around 1.25 Myr (95% HPD: 0.73-1.83 Myr). At that time, populations of central and western Alborz diverged from populations of the north-east. Results of ABC analyses suggested a bi-directional gene flow from ...
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... was performed using two independent runs of 40 million gener- ations, sampled every 1000 generations, with the first 25% discarded as burn-in. Tracer was used to evaluate acceptable levels of MCMC chain mixing, the stationary likelihoods and appropriate lengths of burn-in (25%), as well as to estimate effective sample sizes for all parameters. (Fig. 4). We used BEAST 1.8.2 58 to construct an ultrametric tree, then pruned all outgroups using Mesquite v.3.04 111 . We chose four time slices (0-0.30, 0.30-1.20, 1.20-2.50 and 2.50-3.45 Mya), corresponding to divergence times within the complex. First, we ran the S0 scenario in which dispersal between regions was not penalized. Then, we ...
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... four time slices (0-0.30, 0.30-1.20, 1.20-2.50 and 2.50-3.45 Mya), corresponding to divergence times within the complex. First, we ran the S0 scenario in which dispersal between regions was not penalized. Then, we tested four alternative scenarios (Scenario HB 0-3), where we tested colonization of the complex lineages from other adjacent regions (Fig. 4). We also estimated the geographic location of the ancestors of the G. halys/G. intermedius complex, employing a statistical method implemented in PhyloMapper 1b1 112 , optimized by 10,000 ...
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... + J model holds the strongest support compared to other analyses performed in BioGeoBEARS (Table S2) and dis- persal, extinction, and cladogenesis parameters were estimated at 0.000431, 0.022, and 1.00E-12, respectively. We have found some allopatric speciation and founder-event speciation in evolution of this complex in different time slices (Fig. 4). Furthermore, among the four different scenarios tested, the second one (Scenario HB in Table S2) is characterized by the highest AICc value, under the DIVALIKE + J model (Fig. 4). The best hypothesis suggests that the ancestor of the complex was widespread through regions A and G at 3.62 (2.30-5.32 Coalescent analyses and simulations ...
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... 0.000431, 0.022, and 1.00E-12, respectively. We have found some allopatric speciation and founder-event speciation in evolution of this complex in different time slices (Fig. 4). Furthermore, among the four different scenarios tested, the second one (Scenario HB in Table S2) is characterized by the highest AICc value, under the DIVALIKE + J model (Fig. 4). The best hypothesis suggests that the ancestor of the complex was widespread through regions A and G at 3.62 (2.30-5.32 Coalescent analyses and simulations of G. h. caucasicus. Both ABC coalescence simulations (direct and the logistic approaches) using the concatenated mtDNA + nDNA dataset led to the conclusion that the Scenario EH 3 ...
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... latitudes (40-50 degrees of latitude) and lower elevations 59 . Given that G. rickmersi and G. caraganus are sister clades to G. caucasicus (Fig. 1), it could be inferred that as a consequence of the cooling of high latitudes, one could expect gene flow to be driven toward more southerly latitudes such as Afghanistan and northeastern Iran (Fig. 4). The first divergence due to vicariance in populations of G. caucasicus in northern Iran is estimated to have occurred around 1.25 Myr (95% HPD: 0.73-1.83 Myr). At that time, populations of central and western Alborz diverged from populations of the north-east. Results of ABC analyses suggested a bi-directional gene flow from ...
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... was performed using two independent runs of 40 million gener- ations, sampled every 1000 generations, with the first 25% discarded as burn-in. Tracer was used to evaluate acceptable levels of MCMC chain mixing, the stationary likelihoods and appropriate lengths of burn-in (25%), as well as to estimate effective sample sizes for all parameters. (Fig. 4). We used BEAST 1.8.2 58 to construct an ultrametric tree, then pruned all outgroups using Mesquite v.3.04 111 . We chose four time slices (0-0.30, 0.30-1.20, 1.20-2.50 and 2.50-3.45 Mya), corresponding to divergence times within the complex. First, we ran the S0 scenario in which dispersal between regions was not penalized. Then, we ...
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... four time slices (0-0.30, 0.30-1.20, 1.20-2.50 and 2.50-3.45 Mya), corresponding to divergence times within the complex. First, we ran the S0 scenario in which dispersal between regions was not penalized. Then, we tested four alternative scenarios (Scenario HB 0-3), where we tested colonization of the complex lineages from other adjacent regions (Fig. 4). We also estimated the geographic location of the ancestors of the G. halys/G. intermedius complex, employing a statistical method implemented in PhyloMapper 1b1 112 , optimized by 10,000 ...
Citations
... The Gloydius halys-G. intermedius species complex is a group of pit vipers widely distributed in the Palaearctic with 23 rows mid-back scales, which consists of 9 taxa of the Crotalinae subfamily (Viperidae family), including G. halys, G. cognatus, G. caucasicus, G. caraganus, G. stejnegeri, G. rickmersi, G. shedaoensis, G. changaoensis, and G. intermedius [33,34]. These pit vipers' distribution area starts from Azerbaijan and Iran in the west and passes through several countries of Central Asia to Mongolia and China [35][36][37]. ...
... For instance, the Caucasian pit viper (G. caucasicus) has been elevated recently to species rank based on phylogeographic analyses and its four documented evolutionary significant units (ESUs) [33]; the Alay pit viper (G. rickmersi) was ...
... PartitionFinder was used to select the best partition and evolutionary models in our analysis based on AICc. Following Asadi et al. [33], three calibration points were chosen to estimate divergence times of Gloydius: (i) the divergence of three populations of the genus Porthidium in South America, some 3.5 million years ago (Mya), using a normal distribution model (mean = 3.5, SD = 0.51), (ii) the divergence between Crotalus and Sistrurus before 9 Mya, using a lognormal prior model with a zero offset of 9 Mya (mean = 1.0, SD = 1.0), and, finally, (iii) the divergence of the Eurasian vipers clade (genera Macrovipera, Montivipera, and Vipera) about 20 Mya, as suggested by fossil data, using a lognormal prior model with a zero offset of 17 Mya (mean = 1.0, ...
Simple Summary
Northwest China is characterized by unique geological and historical dynamics and endemic biota, but the joint influence of geography and past climate changes on the evolutionary history of endemic animals is poorly understood. We used two mtDNA genes (ND4 and Cytb) and ecological niche modeling (ENM) to explore how the Quaternary climatic fluctuations and complex geography in Northwest China have shaped genetic diversity, genetic structure, and demographic history of the Alashan pit viper (Gloydius cognatus). Our results clearly show that the lineage diversification of G. cognatus is related to the expansions of deserts and/or the early Pleistocene integration of the Yellow River. The strong spatial genetic structure fits an isolation-by-distance model. The signature of demographic and range contractions during the last glacial maximum (LGM) is rejected by both mitochondrial evidence and ENM. In addition, the suitable habitat of G. cognatus is predicted to be decreased in the future, suggesting that conservation and management of evolutionary significant units (ESUs) should be a priority. Our findings provide the first insights on the evolutionary history of G. cognatus in arid Northwest China and adjacent areas throughout the Quaternary.
Abstract
The joint impacts of historical geological events and Quaternary climatic oscillations in Northwest China on species evolution have been examined extensively in plant under a phylogeographic perspective. However, animal phylogeographic analyses in this region are still limited. The Alashan pit viper, Gloydius cognatus, occurs primarily in arid Northwest China and adjacent areas. Based on variation at two mtDNA genes (ND4 and Cytb) in 27 individuals representing 24 populations, the spatial genetic structure and demographic history of G. cognatus were examined across its geographic range. Phylogenetic analyses revealed two well-supported allopatric clades (each with two distinct subclades/lineages), distributed across the southern (Qaidam Basin, Lanzhou Basin, and Zoige Basin [S1]; Loess Plateau [S2]) and northern (Ily Basin [N1]; Junggar Basin and Mongolian Plateau [N2]) regions. AMOVA analysis demonstrated that over 76% of the observed genetic variation was related to these lineage splits, indicating substantial genetic differentiation among the four lineages. A strong pattern of isolation-by-distance across the sampling populations suggested that geographic distance principally shaped the genetic structure. The four lineages diverged by 0.9–2.2% for the concatenated data, which were estimated to have coalesced ~1.17 million years ago (Mya), suggesting that the expansions of the Badain Jaran, Tengger, and Mu Us deserts during the Xixiabangma glaciation likely interrupted gene flow and triggered the observed divergence in the southern and northern regions. Subsequently, the early Pleistocene integration of the Yellow River and associated deserts expansion promoted the differentiation of S1 and S2 lineages (~0.9 Mya). Both mitochondrial evidence and ecological niche modeling (ENM) reject the signature of demographic and range contractions during the LGM for G. cognatus. In addition, ENM predicts that the suitable habitat of G. cognatus will contract in the future. As such, the conservation and management of ESUs should be a priority. Our findings provide the first insights on the lineage diversification and population dynamics of the Alashan pit viper in relation to geological history and Pleistocene climatic oscillations in arid Northwest China.
... The Volga River region of Russia which represents the source area of the Eneolithic migration wave to Europe (see above) is inhabited by the Karaganda pit viper (Gloydius caraganus). It is a small-sized moderately venomous species belonging to the genus Gloydius of Central Asian origin that diverged about 2.5 million years ago (Asadi et al., 2019). Smaller insectivorous species of adders from the Vipera ursini-renardi complex (Mizsei et al., 2017) resemble other viper species, but due to their smaller size, they are much less venomous. ...
Snakes are known as highly fear-evoking animals, eliciting preferential attention and fast detection in humans. We examined the human fear response to snakes in the context of both current and evolutionary experiences, conducting our research in the cradle of humankind, the Horn of Africa. This region is characterized by the frequent occurrence of various snake species, including deadly venomous viperids (adders) and elapids (cobras and mambas). We conducted experiments in Somaliland and compared the results with data from Czech respondents to address the still unresolved questions: To which extent is human fear of snakes affected by evolutionary or current experience and local culture? Can people of both nationalities recognize venomous snakes as a category, or are they only afraid of certain species that are most dangerous in a given area? Are respondents of both nationalities equally afraid of deadly snakes from both families (Viperidae, Elapidae)? We employed a well-established picture-sorting approach, consisting of 48 snake species belonging to four distinct groups. Our results revealed significant agreement among Somali as well as Czech respondents. We found a highly significant effect of the stimulus on perceived fear in both populations. Vipers appeared to be the most salient stimuli in both populations, as they occupied the highest positions according to the reported level of subjectively perceived fear. The position of vipers strongly contrasts with the fear ranking of deadly venomous elapids, which were in lower positions. Fear scores of vipers were significantly higher in both populations, and their best predictor was the body width of the snake. The evolutionary, cultural, and cognitive aspects of this phenomenon are discussed.
... The only pit viper species occurring in Iran is the Caucasian pit viper Gloydius caucasicus (Nikolsky, 1916) (Asadi et al., 2019). This is found in montane habitats at altitudes up to 3,000 m a.s.l. and belongs to the Gloydius halys/Gloydius intermedius species complex, a group of closely related vipers in the subfamily Crotalinae (Alencar et al., 2016). ...
... This is found in montane habitats at altitudes up to 3,000 m a.s.l. and belongs to the Gloydius halys/Gloydius intermedius species complex, a group of closely related vipers in the subfamily Crotalinae (Alencar et al., 2016). The Caucasian pit viper is a viviparous, diurnal snake distributed from the northwest of Afghanistan and southern Turkmenistan to Azerbaijan and northern parts of Iran (Rastegar et al., 2008;Khani et al., 2017;Asadi et al., 2019;Uetz et al., 2022). In Iran, the species is distributed along the Alborz Mountains, from the Hezar Masjed Mountains in Khorasan Razavi province to the western regions of Gilan province (Mozaffari et al., 2016). ...
... The Caucasian pit viper is threatened by several anthropogenic impacts that include habitat loss due to agricultural development, urbanisation, livestock overgrazing, indiscriminate and irrational killing by local people, and most importantly, excessive collection and over exploitation by antivenom co-operatives in Iran (Rastegar-Pouyani et al., 2018;Asadi et al., 2019;Kaboli, pers. obs.). ...
The Caucasian pit viper Gloydius caucasicus is one of six snake species that is frequently reported as a cause of venomous snakebite in Iran. We present the results of successful captive breeding of 20 Caucasian pit vipers (10 males and 10 females) collected in August 2018 from the Lar National Park, northern Iran. Mating and copulatory behaviours were observed from mid-June to early July 2019. Five of the ten females gave birth with parturition occurring from 10 to 13 September, when 17 vipers were born in litter sizes ranging from 2 to 5. The present captive breeding programme has been successful and shows potential for both venom production and support for conservation by reducing the demand for wild caught specimens.
... Knowledge of the snake fauna of Middle and Southwest Asia (here considered the countries of Afghanistan, Iran, western China, Mongolia and the former Soviet Middle Asian republics fide Berg, 1931;Geptner, 1938;Chernov, 1949) has improved over the past decade as researchers continue to contribute species descriptions, range extensions, and natural history observations (Wagner et al., 2016a;Rajabizadeh, 2018;Shestopal & Rustamov, 2018a;Shestopal & Rustamov, 2018b;Orlov et al., 2018;Asadi et al., 2019;Rajabizadeh et al., 2020;Eskandarzadeh et al., 2020;Chen et al., 2021). Biogeographically, most snakes inhabiting Middle-Southwest Asia are elements of the Palearctic; however, a few species traditionally associated with the Indo-Malayan (Oriental) realm reach their westernmost distributional limits in this region (Wagner et al., 2016b;Orlov et al., 2018). ...
The kukri snakes of the genus Oligodon Fitzinger, 1826 reach the westernmost limits of their distribution in Middle and Southwest Asia (Afghanistan, Iran, and Turkmenistan), and the Palearctic portions of Pakistan. In this article, we review the systematics and distribution of the two species native to this region, Oligodon arnensis (Shaw, 1802) and Oligodon taeniolatus (Jerdon, 1853) based on an integrative approach combining morphological, molecular, and species distribution modeling (SDM) data. Phylogenetic analyses recover O. taeniolatus populations from Iran and Turkmenistan in a clade with the O. arnensis species complex, rendering the former species paraphyletic relative to O. taeniolatus sensu stricto on the Indian subcontinent. To correct this, we resurrect the name Contia transcaspica Nikolsky, 1902 from the synonymy of O. taeniolatus and assign it to populations in Middle–Southwest Asia. So far, Oligodon transcaspicus comb. et stat. nov. is known only from the Köpet–Dag Mountain Range of northeast Iran and southern Turkmenistan, but SDM mapping suggests it may have a wider range. Genetic samples of O. “arnensis” from northern Pakistan are nested in a clade sister to the recently described Oligodon churahensis Mirza, Bhardwaj & Patel, 2021, and are phylogenetically separate from O. arnensis sensu stricto in south India and Sri Lanka. Based on morphological similarity, the Afghanistan and Pakistan populations are assigned to Oligodon russelius (Daudin, 1803) and we synonymize O. churahensis with this species. Our investigation leads us to remove O. taeniolatus from the snake fauna of Afghanistan, Iran, and Turkmenistan, with the consequence that only Oligodon transcaspicus comb. et stat. nov. and O. russelius are present in these countries. Additional studies are needed to resolve the taxonomy of the O. taeniolatus and O. arnensis species complexes on the Indian subcontinent, and an updated key for both groups is provided.
... Additionally, Gloydius himalayanus (Günther, 1864) has long been regarded as a full species within the G. strauchi complex based on its unique morphological characters (e.g., the conspicuous rostralis and the triangular head in dorsal view; Gloyd and Conant 1990). In spite of numerous recent studies focused on the molecular phylogeny of the genus Gloydius (Xu et al. 2012;Eskandar et al. 2018;Shi et al. 2016Shi et al. , 2018Asadi et al. 2019;Wang et al. 2019), the systematic and taxonomic position of G. himalayanus in relation to the G. strauchi complex is still unclear due to lack of the sequence data for this species. ...
We provide a molecular phylogeny of Asian pit vipers (the genus Gloydius ) based on four mitochondrial genes (12S, 16S, ND4, and cytb). Sequences of Gloydius himalayanus , the only member of the genus that occurs south of the Himalayan range, are included for the first time. In addition, two new species of the genus Gloydius are described based on specimens collected from Zayu, Tibet, west of the Nujiang River and Heishui, Sichuan, east of the Qinghai-Tibet Plateau. The new species, Gloydius lipipengi sp. nov., can be differentiated from its congeners by the combination of the following characters: the third supralabial not reaching the orbit (separated from it by a suborbital scale); wide, black-bordered greyish postorbital stripe extending from the posterior margin of the orbit (not separated by the postoculars, covering most of the anterior temporal scale) to the ventral surface of the neck; irregular black annular crossbands on the mid-body; 23-21-15 dorsal scales; 165 ventral scales, and 46 subcaudal scales. Gloydius swild sp. nov. can be differentiated from its congeners by the narrower postorbital stripe (only half the width of the anterior temporal scale, the lower edge is approximately straight and bordered with white); a pair of arched stripes on the occiput; lateral body lakes black spots; a pair of round spots on the parietal scales; 21 rows of mid-body dorsal scales; zigzag dark brown stripes on the dorsum; 168–170 ventral scales, and 43–46 subcaudal scales. The molecular phylogeny in this study supports the sister relationship between G. lipipengi sp. nov. and G. rubromaculatus , another recently described species from the Qinghai-Tibet Plateau, more than 500 km away, and indicate the basal position of G. himalayanus within the genus and relatively distant relationship to its congeners.
... During the Quaternary stadials, the prevalent climate of the region was cold/dry and the species was likely sheltered in the southern refugia until interstadials when the climate became warmer and moist (Kehl, 2009). The Alborz Mountains and the southern Caspian Sea have been reported as refugia for many other species (Ahmadzadeh, Flecks, Carretero, Mozaffari, Böhme, et al., 2013;Asadi et al., 2019;Saberi-Pirooz et al., 2018;Veith et al., 2003;Zohary, 1973), acting as sources of subsequent diversifications , which eventually promoted haplotype admixture. ...
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.
... These studies have shown that impact of climate fluctuation is more complicated and may not follow a prevailing scenario of glacial retraction and postglacial expansion as has been reported from the more northerly located regions of the western Palaearctic (Chiocchio, Bisconti, Zampiglia, Nascetti, & Canestrelli, 2017). Indeed, Southern Europe, Turkey, the southern parts of the Caucasus and Alborz act as multiple glacial refugia due to topographical heterogeneity and low latitude (Ahmadzadeh, Flecks, et al., 2013a;Asadi et al., 2019;Rossiter, Benda, Dietz, Zhang, & Jones, 2007). In Iran, some species experienced range contractions to glacial refugia located, for example, in the Zagros, Alborz, and Kope Dagh Mountains, which were followed by postglacial expansion for Brandt's Persian lizard, Iranolacerta brandtii (Ahmadzadeh, Carretero, et al., 2013b), oriental green lizards of the Lacerta trilineata (Ahmadzadeh, Flecks, et al., 2013a), two sympatric moth species, Gnopharmia colchidari and G. kasrunensis (Rajaei Sh et al., 2013), Persian jird, Meriones persicus (Dianat, Darvish, Cornette, Aliabadian, & Nicolas, 2017), greater horseshoe bat, Rhinolophus ferrumequinum (Shahabi, Akmali, & Sharifi, 2017), Asian pit viper, Gloydius halys caucasicus , and Eastern rock nuthatch, Sitta tephronota, (Yousefi, Shabani, & Azarnivand, 2019). ...
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.
Influenced by rapid changes in climate and landscape features since the Miocene, widely distributed species provide suitable models to study the environmental impact on their evolution and current genetic diversity. The dice snake Natrix tessellata, widely distributed in the Western Palearctic is one such species. We aimed to resolve a detailed phylogeography of N. tessellata with a focus on the Central Asian clade with 4 and the Anatolia clade with 3 mitochondrial lineages, trace their origin, and correlate the environmental changes that affected their distribution through time. The expected time of divergence of both clades began at 3.7 Mya in the Pliocene, reaching lineage differentiation approximately 1 million years later. The genetic diversity in both clades is rich, suggesting different ancestral areas, glacial refugia, demographic changes, and colonization routes. The Caspian lineage is the most widespread lineage in Central Asia, distributed around the Caspian Sea and reaching the foothills of the Hindu Kush Mountains in Afghanistan, and Eastern European lowlands in the west. Its distribution is limited by deserts, mountains, and cold steppe environments. Similarly, Kazakhstan and Uzbekistan lineages followed the Amu Darya and the Syr Darya water systems in Central Asia, with ranges delimited by the large Kyzylkum and Karakum deserts. On the western side, there are several lineages within the Anatolia clade that converged in the central part of the peninsula with 2 being endemic to Western Asia. The distribution of both main clades was affected by expansion from their Pleistocene glacial refugia around the Caspian Sea and in the valleys of Central Asia as well as by environmental changes, mostly through aridification.
Aim
Many biogeographic analyses require some form of automated state assignment to tips of phylogenetic trees, reflecting a species presence or absence in a particular area, e.g., a biome. As datasets get exponentially larger, such procedures may increasingly induce errors (here called tip‐state‐error), but the specific algorithmic cause and consequence on downstream estimation of dispersal and extinction rates remains poorly known. We aim to improve automated tip‐scoring methods in the context of the alpine biome by leveraging elevation information. We document the profound effect of tip‐state‐errors on Dispersal‐Extirpation‐Cladogenesis (DEC) models.
Location
The European Alpine Arc.
Taxon
Three thousand three hundred seventeen vascular plant species, emphasizing six focal genera: Campanula , Carex , Festuca , Ranunculus , Saxifraga , and Viola .
Methods
We use GBIF data to classify whether species occur above the upper climatic treeline using a newly developed algorithm ElevDistr or a gridded landscape model of thermal belts, under various filtering thresholds. We compared classification performance using the Flora Alpina as validation data. To determine if tip‐state‐error biases the dispersal and extirpation rate estimation, we fit DEC models for selected clades using tip‐states from different classification models.
Results
ElevDistr is less error prone than other approaches. Filtering thresholds lower the false positive rate but increase the false negative rate. Inflated false positive rates bias the dispersal rate estimation upward, while inflated false negative rates lead to upward bias in extirpation rate estimation.
Main Conclusions
Even moderate tip‐state‐error may lead to profound systematic bias in dispersal and extinction rate estimation if an unbalanced ratio between false positive and false negative rates occurs. Therefore, careful validation is imperative, though ElevDistr alleviates this problem in the context of the alpine environment. Overall, our results suggest contrasting rates of alpine biome shifts across the studied genera and have major implications for studies addressing the likelihood of niche evolution versus geographic dispersal.
The potential for population genomics to elucidate invasion pathways of a species is limited by taxonomic identification issues. The Oriental fruit fly pest, Bactrocera dorsalis (Hendel) belongs to a complex in which several sympatric species are attracted to the same lure used in trapping and are morphologically cryptic and/or reported to hybridize. In this study, we evaluated the taxonomic ambiguity between B. dorsalis and 2 major cryptic species, based on morphological expertise and 289 target specimens sampled across the whole distribution range. Specimens were then subjected to DNA sequence analyses of the COI mitochondrial barcode and the EIF3L nuclear marker to evaluate the potential for molecular identification, in particular for specimens for which morphological identification was inconclusive. To this aim, we produced reference datasets with DNA sequences from target specimens whose morphological identification was unambiguous, which we complemented with 56 new DNA sequences from closest relatives and 76 published and curated DNA sequences of different species in the complex. After the necessary morphological observation, about 3.5% of the target dataset and 47.6% of the specimens from Southeast Asian islands displayed ambiguous character states shared with B. carambolae and/or B. occipitalis. Critical interpretation of DNA sequence data solved morphological ambiguities only when combining both mitochondrial and nuclear markers. COI discriminated B. dorsalis from 5 species; EIF3L and ITS from another species. We recommend this procedure to ensure correct identification of B. dorsalis specimens in population genetics studies and surveillance programs.
