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Phylogenetic tree resulting from the Bayesian inference (BI) analysis of three mitochondrial and three nuclear genes concatenated. Nodes were considered supported when Bayesian posterior probability was ≥ 0.95 and maximum likelihood (ML) bootstrap values ≥ 70. Lengths of branches connecting the split between Platyceps collaris and Platyceps najadum and the crown nodes of those species are not proportional to the rest of the tree and the scale, which is indicated by their partial transparency. The two clades, the Balkan-Anatolian and the Levantine, are highlighted in the tree with the red and green shading, respectively. Four species of Telescopus used to root the tree are not shown. Each tree tip is connected by a dashed line with the locality of its sample, which is marked by a number (for details, see Table 1). Type localities are marked with stars: P. collaris collaris in green, P. collaris rubriceps in white and Coluber rubriceps thracius in pink. The potential current distribution of P. collaris based on the species distribution model with the maximum training sensitivity plus specificity threshold applied is shown in blue. Haplotype networks reconstructed for the six markers are on the right. Circles are colour coded according to the clade assignment, and their size is proportional to the number of individuals. Lines represent mutational steps. The network for the cytb gene was constructed using the 148-bp-long fragment that was available for the types of Coluber rubriceps thracius. The position of sample DJ8199 from locality 19, whose phylogenetic placement differed in the maximum likelihood and Bayesian inference analyses, is marked with the locality number in each network.
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The geological and geographical settings of the Eastern Mediterranean have resulted in complex patterns of intraspecific diversifications and phylogeographical histories that can be observed in squamates. In this study, we examined genetic differentiation of the Collared dwarf racer (Platyceps collaris) using a multilocus genetic dataset with a sam...
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... Turkey and most samples from southern Turkey (ML bootstrap = 98/BI pp = 1.00; support values are given in this order hereafter), and we term it here the Balkan-Anatolian clade. The other clade comprises samples from Israel, Jordan and Syria, and we term it the Levantine clade, although this clade has only moderate support in the ML analysis ( Fig. 1; support 65/1.00; for original ML and BI trees, see Supporting Information, Figs S1, S2, respectively). Relationships within both clades remain unresolved owing to low branch support. The position of sample DJ8199, from a locality in extreme southern Turkey (locality 19 in Fig. 1), differs in the two analyses. It was reconstructed and ...
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... although this clade has only moderate support in the ML analysis ( Fig. 1; support 65/1.00; for original ML and BI trees, see Supporting Information, Figs S1, S2, respectively). Relationships within both clades remain unresolved owing to low branch support. The position of sample DJ8199, from a locality in extreme southern Turkey (locality 19 in Fig. 1), differs in the two analyses. It was reconstructed and supported as sister to the Bulgarian and other Turkish samples in the ML analysis (support 74), but the BI analysis recovers it as sister to the Levantine clade (support 0.94). Both support values are on the edge of interpretability, but the haplotype networks constructed for each ...
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... it as sister to the Levantine clade (support 0.94). Both support values are on the edge of interpretability, but the haplotype networks constructed for each marker independently show the sample to be closer to the Levantine clade in its mitochondrial DNA, whereas the nuclear markers are more similar to the Balkan-Anatolian clade (networks in Fig. 1). When only mitochondrial markers are analysed, topologies of the ML and BI trees remain similar to those of the complete dataset, including the varying position of sample DJ8199 ( Supporting Information, Figs S3, S4). The haplotype networks clearly differentiate the two clades described above, but the nuclear ones show a certain ...
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... nuclear alleles are either ancestral or shared across multiple samples from both clades, which indicates retention of ancestral polymorphism rather than them being a result of hybridization. The boundary between the two clades corresponds well with the geographical position of the Nur Mountain range in Hatay Province of south-central Turkey (Fig. 1), which runs parallel to the Gulf of İskenderun and separates the Anatolian part of the Eastern Mediterranean from the Levant. These mountains are part of the so-called Anatolian Diagonal, a natural and probably the most important biogeographical barrier in the region, which has repeatedly been proved effective in separating closely ...
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... P. najadum, can happen (e.g. Berger- Dell'Mour, 1986). Although the range of the species spans a relatively large territory, from south-eastern Bulgaria to southern Israel and Jordan, the species distribution modelling analysis shows that the predicted suitable habitat is found only in a narrow stretch of land along the Mediterranean coast (Fig. 1). The potential distribution reaches further inland in the Levant, even beyond the Dead Sea Rift in Jordan, but there it is restricted to the Mediterranean ecozone (Disi, 1996;Disi et al., 2001). The character of the environmental variables that contribute most to the potential distribution of the species suggests that P. collaris ...
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... Turkey and most samples from southern Turkey (ML bootstrap = 98/BI pp = 1.00; support values are given in this order hereafter), and we term it here the Balkan-Anatolian clade. The other clade comprises samples from Israel, Jordan and Syria, and we term it the Levantine clade, although this clade has only moderate support in the ML analysis ( Fig. 1; support 65/1.00; for original ML and BI trees, see Supporting Information, Figs S1, S2, respectively). Relationships within both clades remain unresolved owing to low branch support. The position of sample DJ8199, from a locality in extreme southern Turkey (locality 19 in Fig. 1), differs in the two analyses. It was reconstructed and ...
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... although this clade has only moderate support in the ML analysis ( Fig. 1; support 65/1.00; for original ML and BI trees, see Supporting Information, Figs S1, S2, respectively). Relationships within both clades remain unresolved owing to low branch support. The position of sample DJ8199, from a locality in extreme southern Turkey (locality 19 in Fig. 1), differs in the two analyses. It was reconstructed and supported as sister to the Bulgarian and other Turkish samples in the ML analysis (support 74), but the BI analysis recovers it as sister to the Levantine clade (support 0.94). Both support values are on the edge of interpretability, but the haplotype networks constructed for each ...
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... it as sister to the Levantine clade (support 0.94). Both support values are on the edge of interpretability, but the haplotype networks constructed for each marker independently show the sample to be closer to the Levantine clade in its mitochondrial DNA, whereas the nuclear markers are more similar to the Balkan-Anatolian clade (networks in Fig. 1). When only mitochondrial markers are analysed, topologies of the ML and BI trees remain similar to those of the complete dataset, including the varying position of sample DJ8199 ( Supporting Information, Figs S3, S4). The haplotype networks clearly differentiate the two clades described above, but the nuclear ones show a certain ...
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... nuclear alleles are either ancestral or shared across multiple samples from both clades, which indicates retention of ancestral polymorphism rather than them being a result of hybridization. The boundary between the two clades corresponds well with the geographical position of the Nur Mountain range in Hatay Province of south-central Turkey (Fig. 1), which runs parallel to the Gulf of İskenderun and separates the Anatolian part of the Eastern Mediterranean from the Levant. These mountains are part of the so-called Anatolian Diagonal, a natural and probably the most important biogeographical barrier in the region, which has repeatedly been proved effective in separating closely ...
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... P. najadum, can happen (e.g. Berger- Dell'Mour, 1986). Although the range of the species spans a relatively large territory, from south-eastern Bulgaria to southern Israel and Jordan, the species distribution modelling analysis shows that the predicted suitable habitat is found only in a narrow stretch of land along the Mediterranean coast (Fig. 1). The potential distribution reaches further inland in the Levant, even beyond the Dead Sea Rift in Jordan, but there it is restricted to the Mediterranean ecozone (Disi, 1996;). The character of the environmental variables that contribute most to the potential distribution of the species suggests that P. collaris prefers areas of low ...
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... nov. may have occured in southern Anatolia, perhaps around the area of Nur Mountains acting as a biogeographic break 42,[46][47][48]56 . Kornilios et al. 27 discussed even older event that caused the split between E. quatuorlinata and E. sauromates than we present here, i.e., the braking-up of the southern Aegean landmass and population vicariant speciation. ...
... Total genomic DNA was extracted from the tissue samples using the E.Z.N.A.® Tissue DNA Kit (Omega Biotek, Inc., USA) and NucleoSpin Tissue Kit (Macherey-Nagel, Düren, Germany), following the manufacturer's instructions. For molecular/genetic analyses, we newly generated and/or combine sequences of four mitochondrial genes, particularly 16S rRNA (16S), cytochrome c oxidase subunit 1 (COI), the mitochondrial proteincoding segment of NADH dehydrogenase subunit 4 (ND4) (including the flanking tRNAs Serine, Histidine, and part of Leucine), cytochrome b (Cyt b) and four nuclear genes, i. e. the melanocortin 1 receptor (MC1R), the neurotrophin-3 (NT3), the nuclear protein-coding genes for the prolactin receptor (PRLR) and the recombination activation gene 1 (RAG1) following primers and conditions of PCR presented in 25,27,48 . We also obtained new sequences of NT3 for E. quatuorlineata and NT3, MC1R and RAG1 for the holotype of E. urartica that were not available previously 25 . ...
The genus Elaphe Fitzinger, 1833 includes 17 species of charismatic, large-sized, non-venomous, Eurasian snakes. In the Western Palearctic, the genus is represented by three species from the Elaphe quatuorlineata group ranging from the Apennine peninsula to Central Asia. The southernmost population of this group is distributed in the mountains of the Southern Levant, with more than 400 km gap to other Elaphe populations. This population has been known to science for only 50 years
and is virtually unstudied due to its extreme rarity. We studied these snakes’ morphological and genetic variation from the three countries where they are known to occur, i.e., Israel (Hermon, the Israeli-controlled Golan Heights), Lebanon, and Syria. We used nine mitochondrial and nuclear genes, complete mitogenome sequences, and a comprehensive morphological examination including published data, our own field observations, and museum specimens, to study its relationship to other species in the group. The three currently recognized species of the group (E. quatuorlineata, E. sauromates, E. urartica), and the Levant population, form four deeply divergent, strongly supported clades. Three of these clades correspond to the abovementioned species while the Southern Levant clade, which is genetically and morphologically distinct from all named congeners, is described here as a new species, Elaphe druzei sp. nov. The basal divergence of this group is estimated to be the Late Miocene with subsequent radiation from 5.1 to 3.9 Mya. The revealed biogeography of the E. quatuorlineata group supports the importance of the Levant as a major center of endemism and diversity of biota in Eurasia. The new species is large-sized and is one of the rarest snakes in the Western Palearctic. Because of its small mountain distribution range, in an area affected by land use and climate change, the new Elaphe urgently needs strict protection. Despite political issues, we hope this will be based on the cooperation of all countries where the new species occurs.
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.
This study presents for the first time summarized data on 759 species/taxa (628 species at least) of six classes of Quaternary vertebrates of Bulgaria: Chondrichthyes (1); Actinopterygii (34); Amphibia (18); Reptilia (33); Aves (299); and Mammalia (374). The richest fauna has been recorded in the Late Pleistocene (285 species), followed by the Calabrian (255). Bulgaria has lost 32.3% of its former total Quaternary vertebrate fauna. The number of the lost taxa is as follows: species (245), genera (80), families (16), orders (5), of them three mammalian (Perissodactyla, Proboscidea, and Primates), and two avian (Otidiformes and Pteroclidiformes). Extinct families are: one amphibian (Palaeobatrachidae); two reptilian (Varanidae and Elapidae); three avian (Gruidae, Otididae, and Pteroclididae), and ten mammalian (Dipodidae, Eomyidae, Hystricidae, Ochotonidae, Hyaenidae, Phocidae, Equidae, Rhinocerotidae, Elephantidae, and Cercopithecidae). After the small mammals (mainly Cricetidae; 52 taxa), the composition of bovids (27 taxa) and canids (13 taxa) impoverished in a higher extent. The biggest number of recorded vertebrate families is found in the Meghalayan (79), followed by the Greenlandian (63) and the Late Pleistocene (62). At order and family levels, the most varied was the vertebrate fauna in the Meghalayan (39 orders, 79 families). In the Calabrian, the number of genera was a three times greater than in the Northgrippian, which indicates more diversified paleoenvironment. One genus, 25 species, and one subspecies have been described as new to the science from the Quaternary localities in Bulgaria.
Aim
Assessment of phylogenetic diversity and biogeographical affinities of the rodent fauna from one of the most neglected areas in Africa.
Location
Angola (with biogeographical implications in adjacent areas).
Methods
Inference of mitochondrial phylogenies for rodent genera occurring in Angola, delimitation of molecular operational taxonomic units (MOTUs), assessment and comparative analysis of their geographical distribution.
Results
We provide the first genetic evidence for the presence of 44 rodent taxa from 19 genera and 5 families in Angola, including twelve MOTUs endemic to Angola, and 12 candidate new species, pending integrative taxonomic revisions. The endemic MOTUs were found almost exclusively in the Angolan Miombo Woodlands and in Angolan montane forest−grassland mosaic.
Main conclusions
The highly diverse Angolan rodent fauna is mostly composed of and shows affinities with taxa originating from three major biogeographical regions of sub‐Saharan Africa (Zambezian, South African and Congolian). It is also composed of a unique fauna comprising palaeoendemics from the Angolan Highlands. The species richness and the endemism detected in the Angolan montane forest−grassland mosaic and in the Angolan escarpment forests suggest that these are relevant for conservation, but more studies including other biological groups are needed to fundament this.
The Levant represents one of the most important reptile diversity hotspots and centers of endemism in the Western Palearctic. The region harbored numerous taxa in glacial refugia during the Pleistocene climatic oscillations. Due to the hostile arid conditions in the warmer periods they were not always able to spread or come into contact with populations from more distant regions. One large and conspicuous member of the Levantine herpetofauna is the legless anguid lizard Pseudopus apodus. This species is distributed from the Balkans to Central Asia with a portion of its range running along the eastern Mediterranean coast. Mitochondrial and nuclear DNA sequences, microsatellite genotypes, and morphology show that populations in this region differ from the two named subspecies and presumably had a long independent evolutionary history during the Quaternary. Here we describe the Levantine population as a new subspecies and present biogeographic scenarios for its origin and diversification. The new subspecies is genetically highly diverse, and it forms a sister lineage to Pseudopus from the remaining parts of the range according to mtDNA. It is the largest-bodied of the three subspecies, but occupies the smallest range.
