Phylogeny, biogeography, and evolution of two Mediterranean snakes, Malpolon monspessulanus and Hemorrhois hippocrepis (Squamata, Colubridae), using mtDNA sequences

Biogeography of the Iranian snakes

The events of the Cenozoic era such as mountain formation caused Iran to become one of the most amazing biodiversity hotspots in the world today. This pioneering study on Iranian snake biogeography integrates historical and ecological analyses. A phylogeographic review traces speciation and dispersal, while cluster analysis with a new snake checklist assesses faunistic similarities within Iran and its surroundings. Jaccard and Sorenson indices generate similarity dendrograms, Indicator Species Analysis pinpoints regional key species, and Endemism index calculates regional endemism rates, enriching our knowledge of Iran's species diversity. Phylogeographic analyses identify four biogeographical corridors for snake ingress into Iran: the Arabian region through southwestern Iran, the Western Asian mountainous transition zone via northwestern Iran, the Turanian region into northeastern Iran, and the Indus River Valley into southeastern and eastern Iran. Dendrogram analysis divides snake fauna into three groups. The first group associates western Zagros and Khuzestan fauna with the Sahara and Arabian regions. The second group links Kopet Dagh and Turkmen Steppe fauna with the Turanian region, and Central Plateau and Baluchistan fauna with the Iranian region. The third group connects northwest highlands, Alborz and Zagros mountains, and Caspian Sea coasts with the Western Asian Mountain transition zone. The study validates broad biogeographic patterns via ecoregional associations and indicator species analysis, providing finer resolution. Species like Platyceps najadum in Caspian Hyrcanian mixed forests exemplify ecoregional alignment, while Zagros and Alborz mountains exhibit unique faunal indicators, indicating species-level divergence. Shared indicators among widespread ecoregions reflect habitat continuity; exclusive indicators emphasize regional distinctiveness. Despite endemic species prevalence, they seldom act as significant indicators due to various factors. Our research confirms the Zagros Mountains, Khuzestan Plain, Alborz Mountains, and Persian Gulf coasts as snake diversity hotspots, marked by higher species richness compared to other Iranian regions.

Novel phylogenomic inference and 'Out of Asia' biogeography of cobras, coral snakes and their allies

Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling the biogeographic origin of elapoid snakes, which includes numerous dangerously venomous species as well as species not known to be dangerous to humans. The worldwide distribution of this lineage makes it an ideal group for testing hypotheses related to historical faunal exchanges among the many continents and other landmasses occupied by contemporary elapoid species. We developed a novel suite of genomic resources, included worldwide sampling, and inferred a robust estimate of evolutionary relationships, which we leveraged to quantitatively estimate geographical range evolution through the deep-time history of this remarkable radiation. Our phylogenetic and biogeographical estimates of historical ranges definitively reject a lingering former 'Out of Africa' hypothesis and support an 'Out of Asia' scenario involving multiple faunal exchanges between Asia, Africa, Australasia, the Americas and Europe.

Baetidae (Insecta: Ephemeroptera) of Aurès Mountains (Algeria): A New Species of the Baetis alpinus Species Group, with Notes on Baetis Laech, 1815 Biogeography within Maghreb

A new species, Baetis (Baetis) dihyaesp. nov., belonging to the Baetis alpinus species group, is described and illustrated based on larval material collected in the Aurès Mountains (northeastern Algeria) in 2020-2021. This new species is closely related to three European species, e.g., Baetis (B.) alpinus (Pictet, 1843); B. (B.) nubecularis Eaton, 1898; and B. (B.) pasquetorum Righetti & Thomas, 2002 by the combination of the following characteristics: (i) more than one short, stout bristle at the tip of segment II of the maxillary palp and (ii) a well-developed paracercus. However, the new species clearly differs from all congeners of the Baetis alpinus species group primarily by the (a) structure of mouthparts-with 14-18 long submarginal setae arranged in a single irregular row on the dorsal surface of the labrum; 2-6 short, stout bristles at the tip of segment II of the maxillary palp; and segment II of the labial palp without a considerably developed apico-internal lobe); (b) setation of abdominal terga, with a few triangular-shaped scales sparsely scattered near the posterior margin only; and (c) a well-developed paracercus, comprised of more than 50 segments. Primary data on the biology and distribution of this new species are provided, and molecular affinities are verified by the analysis of COI (barcode) sequences. Detailed notes on the distribution of mayfly species belonging to the Baetis alpinus species group common in Western Europe and the western part of North Africa are presented. The historical movement of Baetis representatives between Europe, North West Africa, and subsequently Algeria, with the land bridges 'Strait of Gibraltar' and 'Strait of Sicily' as colonization routes, is discussed in detail and identified in the present study as the Western Algeria colonization path and Eastern Algeria colonization path, respectively.

Proteomic insight into the venom composition of the largest European rear-fanged snake, Malpolon monspessulanus monspessulanus

Snake envenomations constitute a worldwide neglected tropical disease, with the vast majority of lethal bites inflicted by front-fanged snakes from the viperid and elapid groups. Rear-fanged snakes (colubrids) were often considered harmless and as a result, are much less studied, but several documented deaths have suggested potent venom in this group as well. The largest European snake (Malpolon monspessulanus monspessulanus), known as the “Montpellier snake”, is such a rear-fanged snake that belongs to the Lamprophiidae family. Its venom remains largely unknown but cases of envenomation with neurological symptoms have been reported. Here, we provide the first insights into the composition of its venom using mass spectrometry methods. First, liquid chromatography coupled mass spectrometry analysis of the manually collected venom samples reveals a complex profile, with the majority of masses encompassing the range 500–3000 Da, 4000–8000 Da, and 10 000–30 000 Da. Next, shotgun proteomics allowed the identification of a total of 42 different known families of proteins, including snake venom metalloproteinases, peptidase M1, and cysteine-rich secretory proteins, as the most prominent. Interestingly, three-finger toxins were not detected, suggesting that neurotoxicity may occur via other, yet to be determined, toxin types. Overall, our results provide the basis for a better understanding of the effects of a peculiar snake venom on human symptomatology, but also on the main prey consumed by this species.

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We investigate the venom composition of the largest European venomous snake.

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LC-MS analysis of the crude manually collected venom revealed a complex profile.

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Shotgun proteomic analysis identified 42 different protein families.

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Major components include SVMPs, consistent with the clinical features.

Reptile biodiversity in Souss-Massa National Park: an internationally important hotspot in the Mediterranean region

Souss-Massa National Park (SMNP) is Morocco’s first coastal national park, created to preserve the high diversity of its continental and marine environments. Reptiles play an essential role in balancing SMNP ecosystems, yet little work has been done to study this fauna. The present work aims at providing the first reptile inventory of SMNP since its establishment in 1991. During the period 2019 to 2020, several field surveys were carried out at 30 sites using time-constrained visual encounter surveys (TCVES), with a total sampling effort of 300 person-hours. An inventory of 23 reptile species (including four endemic species) was obtained by combining TCVES results with additional data recorded during random encounters or provided by SMNP researchers. Based on TCVES data, both sampling effort and inventory completeness were evaluated by constructing sample-based accumulation curves and calculating non-parametric estimators (Chao 1, Chao 2, Jackknife 1 and Jackknife 2). These species richness estimators suggest that the current inventory is likely to be complete. Despite its small surface area, SMNP contains nearly 20% of all known Moroccan reptile species and constitutes an important biodiversity hotspot for reptiles in the Mediterranean Region. In terms of reptile conservation concern, five species in SMNP are classified as “vulnerable”, while two species are classified as “near threatened” on the IUCN Red List, underscoring the importance of protected areas for those species.

First occurrence of Psammophis (Serpentes) from Europe witnesses another Messinian herpetofaunal dispersal from Africa - biogeographic implications and a discussion of the vertebral morphology of psammophiid snakes

We here describe abundant new snake material from the late Miocene (MN 13) of Salobreña, Spain. Vertebral morphology suggests a referral of the specimens to the extant psammophiid Psammophis, documenting the first occurrence of this genus in Europe. The diversity and disparity across the vertebral morphology of different psammophiid genera is discussed. We identify vertebral features that could diagnose Psammophis and therefore enable the recognition of the genus in the fossil record. A comparison of the new Spanish form with other taxa is conducted. We provide a detailed review of the psammophiid fossil record. Material previously described from the middle Miocene of Beni Mellal, Morocco is here tentatively referred to as? Psammophis sp., an action that renders that occurrence as the oldest (probable) record of the genus and Psammophiidae as a whole, providing thus a potential calibration point. On the other hand, Eastern European Pliocene material that had been previously supposedly referred to Psammophis is here discarded as being rather fragmentary, not affording any more precise determination. The two psammophiid genera Psammophis and Malpolon appear almost simultaneously in the European fossil record (MN 13), with the former achieving only a short-lived and apparently geographically limited distribution in the continent, while the latter still exists in its modern herpetofauna. We assess biogeographic implications of the new find, suggesting a direct dispersal event from northwestern Africa to the Iberian Peninsula during the late Miocene, facilitated by the Messinian Salinity Crisis. This article is protected by copyright. All rights reserved.

The Strait of Gibraltar is an ineffective palaeogeographic barrier for some flightless darkling beetles (Coleoptera: Tenebrionidae: Pimelia)

The geographic distribution of a species is shaped by its biology and by environmental and palaeogeographic factors that interact at different spatial-temporal scales, which leads to distributions and diversification patterns observed between and within lineages. The darkling beetle genus Pimelia has been diversifying for more than 31.2 Mya showing different colonization patterns after the opening of the Gibraltar Strait 5 Mya. Three of the 14 subgenera of Pimelia have populations on both sides of the Strait. Through extensive sampling and the analysis of three molecular markers, we determine levels of intra- and interspecific genetic variation, identify evolutionary lineages in subgenera, estimate their temporal origin and distribution ranges and discuss the historical basis for the geographic and diversification patterns of Pimelia around the Strait. This single geographical feature acted both as a barrier and as a dispersal route for different Pimelia species. The Strait has represented a strong barrier for the subgenus Magrebmelia since the Middle Miocene. However, the subgenera Amblyptera and Amblypteraca share repetitive signatures of post-Messinian colonization across the Strait, possibly driven by stochastic or ‘catastrophic’ events such as tsunamis. Our demographic analyses support Wallace’s hypothesis on insect dispersal stochasticity. Some taxonomic changes, including the designation of a lectotype for Pimelia maura, are also proposed.

Biogeographic and demographic history of the Mediterranean snakes Malpolon monspessulanus and Hemorrhois hippocrepis across the Strait of Gibraltar

BACKGROUND

The contribution of North Africa to the assembly of biodiversity within the Western Palaearctic is still poorly documented. Since the Miocene, multiple biotic exchanges occurred across the Strait of Gibraltar, underlying the high biogeographic affinity between the western European and African sides of the Mediterranean basin. We investigated the biogeographic and demographic dynamics of two large Mediterranean-adapted snakes across the Strait and assess their relevance to the origin and diversity patterns of current European and North African populations.

RESULTS

We inferred phylogeographic patterns and demographic history of M. monspessulanus and H. hippocrepis, based on range-wide multilocus data, combined with fossil data and species distribution modelling, under present and past bioclimatic envelopes. For both species we identified endemic lineages in the High Atlas Mountains (Morocco) and in eastern Iberia, suggesting their persistence in Europe during the Pleistocene. One lineage is shared between North Africa and southern Iberia and likely spread from the former to the latter during the sea-level low stand of the last glacial stage. During this period M. monspessulanus shows a sudden demographic expansion, associated with increased habitat suitability in North Africa. Lower habitat suitability is predicted for both species during interglacial stages, with suitable areas restricted to coastal and mountain ranges of Iberia and Morocco. Compiled fossil data for M. monspessulanus show a continuous fossil record in Iberia at least since the Pliocene and throughout the Pleistocene.

CONCLUSIONS

The previously proposed hypothesis of Pleistocene glacial extinction of both species in Europe is not supported based on genetic data, bioclimatic envelopes models, and the available fossil record. A model of range retraction to mountain refugia during arid periods and of glacial expansion (demographic and spatial) associated to an increase of Mediterranean habitats during glacial epochs emerges as a general pattern for mesic vertebrates in North Africa. Moreover, the phylogeographic pattern of H. hippocrepis conforms to a well-established biogeographic partition between western and eastern Maghreb.

Molecular biogeography of the Mediterranean Buthus species complex (Scorpiones: Buthidae) at its southern Palaearctic margin

Neogene orogenesis and climatic cycles strongly influenced inter- and intraspecific differentiation and variability of taxa. In this study, we focused on the southern margin of the western Palaearctic, known to be a geographically complex region. We performed mitochondrial DNA analyses of Buthus scorpions from the Moroccan Atlas Mountains, from the Hoggar Mountains in Algeria and from Tunisia, Iberia and Israel. Molecular species delimitation suggests the existence of ≥ 24 molecular operational taxonomic units. The data confirm complex differentiation patterns across the Atlas Mountains of Morocco, but structures in Iberia, Algeria and Tunisia have considerably lower complexity. This identifies the Atlas Mountain region as the most important differentiation centre of Buthus scorpions. Samples from the Hoggar Mountains (southern Algeria) cluster with those from the southernmost parts of Morocco in the middle and upper parts of the Draa Valley. This reinforces a recent connection of these regions. Samples from Israel are genetically similar to individuals from eastern Algeria and Tunisia. This suggests a widespread group across major parts of North Africa. Divergence time estimates indicate that differentiation in the genus began during the late Miocene, a period characterized by strong tectonic activities in this region. Further differentiation could be linked to subsequent climatic changes that have occurred since the end of the Miocene, with an increasing aridification of the Moroccan area. This also produced many microrefugia in the mountains of the area during the Pleistocene climatic fluctuations.

Collapse of the endemic lizard Podarcis pityusensis on the island of Ibiza mediated by an invasive snake

The invasive snake Hemorrhois hippocrepis colonized the island of Ibiza (Balearic Islands) in 2003 as stowaways inside trunks of olive trees imported for gardening. It has quickly spread since 2010, posing a threat to the island’s only remaining endemic vertebrate, the Ibiza wall lizard Podarcis pityusensis. We map the yearly expansion rate of the snake and estimate via transect surveys how severely it affects the distribution and abundance of the endemic lizard. As well, we surveyed 9 of 30 small lizard populations on islets surrounding Ibiza that have been isolated since the Last Glacial Maximum. Snakes had invaded 49% of Ibiza’s land area by 2018, and censuses show a critical contrast in lizard abundance between areas with and without snakes; almost all censuses in areas without snakes show lizard presence whereas nearly all censuses in areas with H. hippocrepis lack lizard sightings. Moreover, at least one subspecies previously thriving on one of the offshore islets has become extinct, and there have been several snakes recorded swimming between Ibiza and the surrounding islets. Therefore, lizard populations have been dramatically reduced or have vanished within the range of the snake, and our results quantitatively support upgrading this species’ threat level for extinction. This study can inform to programs to manage invasive snake populations and to conservation actions to recover the endemic lizard.

Speciation patterns in the Forficula auricularia species complex: cryptic and not so cryptic taxa across the western Palaearctic region

Forficula auricularia (the European earwig) is possibly a complex of cryptic species. To test this hypothesis, we performed: (1) a phylogeographic study based on fragments of the mitochondrial COI and the nuclear ITS2 markers on a wide geographic sampling, (2) morphometric analyses of lineages present in Spain and (3) niche overlap analyses. We recovered five reciprocally monophyletic ancient phylogroups with unique historical patterns of distribution, climatic niches and diversification. External morphology was conserved and not correlated with speciation events, except in one case. Phylogenetic placement of the morphologically distinct taxon renders F. auricularia paraphyletic. Based on the congruence of the phylogenetic units defined by mtDNA and nuclear sequence data, we conclude that phylogroups have their own historical and future evolutionary trajectory and represent independent taxonomic units. Forficula auricularia is a complex of at least four species: the morphologically diagnosable Forficula aeolica González-Miguéns & García-París sp. nov., and the cryptic taxa: Forficula mediterranea González-Miguéns & García-París sp. nov., Forficula dentataFabricius, 1775stat. nov. and Forficula auriculariaLinnaeus, 1758s.s. We also provide new synonymy for F. dentata.

Reproduction ecology of the recently invasive snake Hemorrhois hippocrepis on the island of Ibiza

Knowing the causes of biological invasion success can be relevant to combat future invasive processes. The recent invasion of the horseshoe whip snake Hemorrhois hippocrepis on the island of Ibiza provides the opportunity to compare natural history traits between invasive and source populations, and to unravel what makes this snake a successful invader that is threatening the only endemic vertebrate of the island, Podarcis pityusensis. This study compares the basic reproductive traits of mainland native and invasive populations of the snake. Our results revealed that invasive populations were characterized by female maturity at a smaller size, extended reproductive period, and much lower reproduction frequency compared to the native population. In contrast, some major reproductive traits-the abdominal fat body cycle, clutch size, hatchling body size, and hatchling body condition, did not differ between the two populations. Some of these results must reflect the environmental differences in the recently invaded island with respect to the source area, and overall plasticity of reproductive traits. Plasticity is evolutionarily interesting, and may aid the successful growth of this species in their invasiveness of Mediterranean islands like Ibiza. The most significant finding is that this expression of phenotypic plasticity occurred rapidly in this invasive population, within a period of 14 years maximum. Our results on the reproduction ecology of the invasive population were not conclusive regarding the factors determining the invasiveness of the snake and pointed to alternative causes.

Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patterns of Ibero-Maghrebian and Cyrenaican populations

The Mediterranean Basin represents a Global Biodiversity Hotspot where many organisms show high inter- and intraspecific differentiation. Extant phylogeographic patterns of terrestrial circum-Mediterranean faunas were mainly shaped through Pleistocene range shifts and range fragmentations due to retreat into different glacial refugia. Thus, several extant Mediterranean bird species have diversified by surviving glaciations in different hospitable refugia and subsequently expanded their distribution ranges during the Holocene. Such a scenario was also suggested for the Eurasian Wren (Nannus troglodytes) despite the lack of genetic data for most Mediterranean subspecies. Our phylogenetic multi-locus analysis comprised 18 out of 28 currently accepted subspecies of N. troglodytes, including all but one subspecies which are present in the Mediterranean Basin. The resulting phylogenetic reconstruction dated the onset of the entire Holarctic radiation of three Nannus species to the early Pleistocene. In the Eurasian Wren, two North African subspecies represented separate basal lineages from the Maghreb (N. t. kabylorum) and from the Libyan Cyrenaica (N. t. juniperi), being only distantly related to other Mediterranean populations. Although N. troglodytes appeared to be paraphyletic with respect to the Nearctic Winter Wren (N. hiemalis), respective nodes did not receive strong statistical support. In contrast, paraphyly of the Ibero-Maghrebian taxon N. t. kabylorum was strongly supported. Southern Iberian populations of N. t. kabylorum did not clade with Maghrebian populations of the same subspecies but formed a sister clade to a highly diverse European clade (including nominate N. t. troglodytes and eight further taxa). In accordance with a pattern also found in other birds, Eurasian populations were split into a western clade (Europe, Caucasus) and an eastern clade (Central Asia, Sino-Himalayas, East Asia). This complex phylogeographic pattern revealed cryptic diversification in N. troglodytes, especially in the Iberio-Maghrebian region.

Comparative phylogeography of amphibians and reptiles in Algeria suggests common causes for the east-west phylogeographic breaks in the Maghreb

A series of phylogeographic studies in the Maghreb identified a repeated pattern of deep genetic divergence between an eastern (Tunisia) and western (Morocco) lineage for several taxa but lack of sampling in Algeria made it difficult to know if the range limits between the eastern and western lineages were shared among taxa or not. To address this question, we designed a comparative phylogeographic study using 8 reptile and 3 amphibian species with wide distribution in the Maghreb as models. We selected species where previous studies had identified an East-West phylogeographic divide and collected sampled in Algeria to 1) examine whether the simple East-West divergence pattern still holds after filling the sampling gap in Algeria or if more complex diversity patterns emerge; 2) if the E-W pattern still holds, test whether the limits between the E and W clades are shared between species, suggesting that common historical process caused the E-W divergences; 3) if E-W limits are shared between species, use information on the age of the divergence to identify possible geological or climatic events that could have triggered these E-W differentiations. We found that the E-W pattern was generally maintained after additional sampling in Algeria and identified two common disjunction areas, one around the Algeria-Morocco border, the other one in Kabylia (central Algeria), suggesting that common historical mechanisms caused the E-W divergences in the Maghreb. Our estimates for the times to most common recent ancestors to the E and W clades span a wide range between the Messinian salinity crisis and the Plio-Pleistocene limit (except for one older split), suggesting different origins for the initial divergences and subsequent preservation of the E and W lineages in common climatic refugia in the west and the east of the Maghreb.

Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species

Recent studies found major conflicts between traditional taxonomy and genetic differentiation of grass snakes and identified previously unknown secondary contact zones. Until now, little is known about gene flow across these contact zones. Using two mitochondrial markers and 13 microsatellite loci, we examined two contact zones. One, largely corresponding to the Rhine region, involves the western subspecies Natrix natrix helvetica and the eastern subspecies N. n. natrix, whereas in the other, more easterly, contact zone two lineages meet that are currently identified with N. n. natrix and N. n. persa. This second contact zone runs across Central Europe to the southern Balkans. Our analyses reveal that the western contact zone is narrow, with parapatrically distributed mitochondrial lineages and limited, largely unidirectional nuclear gene flow. In contrast, the eastern contact zone is very wide, with massive nuclear admixture and broadly overlapping mitochondrial lineages. In combination with additional lines of evidence (morphology, phylogeny, divergence times), we conclude that these differences reflect different stages in the speciation process and that Natrix helvetica should be regarded as a distinct species. We suggest a nomenclatural framework for presently recognized grass snake taxa and highlight the need for reconciling the conflicts between genetics and taxonomy.

Does Sexual Selection Influence Ornamentation of Hemipenes in Old World Snakes?

In the present study, we investigated and documented the morphology of the male copulatory organs (hemipenes) in fifteen wide-ranging snake species. The species represent four families (Boidae, Colubridae, Lamprophiidae, and Viperidae) and ten genera. We applied the same preparation techniques for all species, successfully everting and expanding the organs completely. The detailed description of the general morphology of the male copulatory organs was based on 31 specimens. Our data were compared with published observations and we point out some incorrectly described details in previous investigations. We provide the first description of the hemipenial morphology for three ophidian species (Elaphe sauromates, Telescopus fallax, and Malpolon insignitus). In addition to the morphological characteristics of the hemipenes presented in the research, we propose the adoption of a standardized index describing the hemipenial proportions. The immense variation in hemipenial morphology presupposes its dynamic evolution, but we suggest that many of the significant structures observed here may have escaped previous researchers due to differing methodologies. Some of the highly ornamented morphologies that we describe are consistent with a locking mechanism during copulation. However, other morphologies may relate to the variety of mating behaviors observed. As a result, we propose that sexual selection is the major driver affecting the hemipenial ornamentation in snakes. Anat Rec, 300:1680-1694, 2017. © 2017 Wiley Periodicals, Inc.

Pre-Quaternary divergence and subsequent radiation explain longitudinal patterns of genetic and morphological variation in the striped skink, Heremites vittatus

Background

Many animal and plant species in the Middle East and northern Africa have a predominantly longitudinal distribution, extending from Iran and Turkey along the eastern Mediterranean coast into northern Africa. These species are potentially characterized by longitudinal patterns of biological diversity, but little is known about the underlying biogeographic mechanisms and evolutionary timescales. We examined these questions in the striped skink, Heremites vittatus, one such species with a roughly longitudinal distribution across the Middle East and northern Africa, by analyzing range-wide patterns of mitochondrial DNA (mtDNA) sequence and multi-trait morphological variation.

Results

The striped skink exhibits a basic longitudinal organization of mtDNA diversity, with three major mitochondrial lineages inhabiting northern Africa, the eastern Mediterranean coast, and Turkey/Iran. Remarkably, these lineages are of pre-Quaternary origin, and are characterized by p-distances of 9–10%. In addition, within each of these lineages a more recent Quaternary genetic diversification was observed, as evidenced by deep subclades and high haplotype diversity especially in the Turkish/Iranian and eastern Mediterranean lineages. Consistent with the genetic variation, our morphological analysis revealed that the majority of morphological traits show significant mean differences between specimens from northern Africa, the eastern Mediterranean coast, and Turkey/Iran, suggesting lineage-specific trait evolution. In addition, a subset of traits exhibits clinal variation along the eastern Mediterranean coast, potentially indicating selection gradients at the geographic transition from northern Africa to Anatolia. The existence of allopatric, morphologically and genetically divergent lineages suggests that Heremites vittatus might represent a complex with several taxa.

Conclusions

Our work demonstrates that early divergence events in the Pliocene, likely driven by both climatic and geological factors, established the longitudinal patterns and distribution of Heremites vittatus. Subsequent radiation during the Pleistocene generated the genetic and morphological diversity observed today. Our study provides further evidence that longitudinal diversity patterns and species distributions in the Middle East and northern Africa were shaped by complex evolutionary processes, involving the region’s intricate geological history, climatic oscillations, and the presence of the Sahara.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0969-0) contains supplementary material, which is available to authorized users.

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

BACKGROUND

With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61).

RESULTS

Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades.

CONCLUSION

Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.

Snakes on the Balearic islands: an invasion tale with implications for native biodiversity conservation

Biological invasions are a major conservation threat for biodiversity worldwide. Islands are particularly vulnerable to invasive species, especially Mediterranean islands which have suffered human pressure since ancient times. In the Balearic archipelago, reptiles represent an outstanding case with more alien than native species. Moreover, in the last decade a new wave of alien snakes landed in the main islands of the archipelago, some of which were originally snake-free. The identification of the origin and colonization pathways of alien species, as well as the prediction of their expansion, is crucial to develop effective conservation strategies. In this study, we used molecular markers to assess the allochthonous status and the putative origin of the four introduced snake species (Hemorrhois hippocrepis, Malpolon monspessulanus, Macroprotodon mauritanicus and Rhinechis scalaris) as well as ecological niche models to infer their patterns of invasion and expansion based on current and future habitat suitability. For most species, DNA sequence data suggested the Iberian Peninsula as the potential origin of the allochthonous populations, although the shallow phylogeographic structure of these species prevented the identification of a restricted source-area. For all of them, the ecological niche models showed a current low habitat suitability in the Balearic, which is however predicted to increase significantly in the next few decades under climate change scenarios. Evidence from direct observations and spatial distribution of the first-occurrence records of alien snakes (but also lizards and worm lizards) suggest the nursery trade, and in particular olive tree importation from Iberian Peninsula, as the main pathway of introduction of alien reptiles in the Balearic islands. This trend has been reported also for recent invasions in NE Spain, thus showing that olive trees transplantation may be an effective vector for bioinvasion across the Mediterranean. The combination of molecular and ecological tools used in this study reveals a promising approach for the understanding of the complex invasion process, hence guiding conservation management actions.

Out of Africa: did Emys orbicularis occidentalis cross the Strait of Gibraltar twice?

The narrow Strait of Gibraltar has separated the African and European continents since the Miocene (5.3 Mya), with a different degree of permeability for Mediterranean taxa. Southern and northern regions of the Iberian Peninsula and Morocco, respectively, are key areas to evaluate the colonization dynamics and biogeographic history of taxa occurring at both sides of this strait. The Ibero-Maghrebian subspecies of the European pond turtle, Emys orbicularis occidentalis, is patchily distributed and threatened throughout most of the Iberian Peninsula and northern Morocco and its origin is thought to be in North Africa. Here we expand the geographic sampling across the Iberian Peninsula and Morocco, with special emphasis in the southern tip of the peninsula and northern Morocco, and analyze mtDNA sequences of 183 E. o. occidentalis to better understand the complex biogeographic history of this subspecies. We provide for the first time evidence for shared haplotypes of Iberian and North African pond turtles, with an additional haplotype in the southern Iberian Peninsula derived from Moroccan haplotypes. This supports the hypothesis that the Strait of Gibraltar constitutes no significant biogeographic barrier for E. orbicularis. However, the newly discovered shared, or extremely similar, haplotypes of European pond turtles from the southern Iberian Peninsula and Morocco suggest either that at least two independent natural colonization waves from Morocco have reached the Iberian Peninsula or that Moroccan turtles were accidentally or deliberately introduced there.

Refugia, colonization and diversification of an arid-adapted bird: coincident patterns between genetic data and ecological niche modelling

Phylogeographical studies are common in boreal and temperate species from the Palaearctic, but scarce in arid-adapted species. We used nuclear and mitochondrial markers to investigate phylogeography and to estimate chronology of colonization events of the trumpeter finch Bucanetes githagineus, an arid-adapted bird. We used 271 samples from 16 populations, most of which were fresh samples but including some museum specimens. Microsatellite data showed no clear grouping according to the sampling locations. Microsatellite and mitochondrial data showed the clearest differentiation between Maghreb and Canary Islands and between Maghreb and Western Sahara. Mitochondrial data suggest differentiation between different Maghreb populations and among Maghreb and Near East populations, between Iberian Peninsula and Canary Islands, as well as between Western Sahara and Maghreb. Our coalescence analyses indicate that the trumpeter finch colonized North Africa during the humid Marine Isotope Stage 5 (MIS5) period of the Sahara region 125 000 years ago. We constructed an ecological niche model (ENM) to estimate the geographical distribution of climatically suitable habitats for the trumpeter finch. We tested whether changes in the species range in relation to glacial-interglacial cycles could be responsible for observed patterns of genetic diversity and structure. Modelling results matched with those from genetic data as the species' potential range increases in interglacial scenarios (in the present climatic scenario and during MIS5) and decreases in glacial climates (during the last glacial maximum, LGM, 21 000 years ago). Our results suggest that the trumpeter finch responded to Pleistocene climatic changes by expanding and contracting its range.

Conquering the Sahara and Arabian deserts: systematics and biogeography of Stenodactylus geckos (Reptilia: Gekkonidae)

Background

The evolutionary history of the biota of North Africa and Arabia is inextricably tied to the complex geological and climatic evolution that gave rise to the prevalent deserts of these areas. Reptiles constitute an exemplary group in the study of the arid environments with numerous well-adapted members, while recent studies using reptiles as models have unveiled interesting biogeographical and diversification patterns. In this study, we include 207 specimens belonging to all 12 recognized species of the genus Stenodactylus. Molecular phylogenies inferred using two mitochondrial (12S rRNA and 16S rRNA) and two nuclear (c-mos and RAG-2) markers are employed to obtain a robust time-calibrated phylogeny, as the base to investigate the inter- and intraspecific relationships and to elucidate the biogeographical history of Stenodactylus, a genus with a large distribution range including the arid and hyper-arid areas of North Africa and Arabia.

Results

The phylogenetic analyses of molecular data reveal the existence of three major clades within the genus Stenodactylus, which is supported by previous studies based on morphology. Estimated divergence times between clades and sub-clades are shown to correlate with major geological events of the region, the most important of which is the opening of the Red Sea, while climatic instability in the Miocene is hypothesized to have triggered diversification. High genetic variability is observed in some species, suggesting the existence of some undescribed species. The S. petrii - S. stenurus species complex is in need of a thorough taxonomic revision. New data is presented on the distribution of the sister species S. sthenodactylus and S. mauritanicus.

Conclusions

The phylogenetic hypothesis for the genus Stenodactylus presented in this work permits the reconstruction of the biogeographical history of these common desert dwellers and confirms the importance of the opening of the Red Sea and the climatic oscillations of the Miocene as major factors in the diversification of the biota of North Africa and Arabia. Moreover, this study traces the evolution of this widely distributed and highly specialized group, investigates the patterns of its high intraspecific diversity and elucidates its systematics.

Early Oligocene to Pliocene Colubridae of Europe: a review

The paper reviews the entire fossil record of the Colubridae coming from the European Early Oligocene (MP21) to late Early Pliocene (MN15) localities. Prior to the end of the Early Miocene, European colubrids were rare and dominated by booid snakes. At the end of the Early Miocene (MN4), the archaic ophidian fauna of Europe was literally flooded by eastern immigrants, principally representatives of the colubroid families Colubridae, Elapidae, and Viperidae. Since then, the Colubridae became a dominant group in snake assemblages, both in Europe and elsewhere. The rich colubrid fauna inhabiting the European continent in the Middle Miocene (MN5 to 7+8) was composed exclusively of extinct species, representing mainly fossil genera, although members of living genera were also quite common. At the beginning of the Late Miocene (MN9), almost all fossil genera became extinct, but living genera were represented exclusively by fossil species. In the late Early Pliocene (MN15), almost all European colubrids were living species. The Late Pliocene (MN16) and Pleistocene colubrid snakes did not differ from those inhabiting Europe today.