Hidden in the sand: Phylogenomics unravel an unexpected evolutionary history for the desert-adapted vipers of the genus Cerastes.

The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Böhme's sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we sequenced one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.

Species boundaries to the limit: Integrating species delimitation methods is critical to avoid taxonomic inflation in the case of the Hajar banded ground gecko (Trachydactylus hajarensis).

With the advent of molecular phylogenetics and the implementation of Multispecies Coalescent-based (MSC) species delimitation methods (SDM), the number of taxonomic studies unveiling and describing cryptic sibling species has greatly increased. However, speciation between early divergent lineages is often defined without evaluating population structure or gene flow, which can lead to false claims of species status and, subsequently, taxonomic inflation. In this study, we focus on the intriguing case of the Arabian gecko Trachydactylus hajarensis (Squamata: Gekkonidae). We generated mitochondrial data (12S rDNA) and genome-wide SNP data (ddRADseq) for 52 specimens to determine phylogenomic relationships, population structure and genetic diversity within this species. Then, we applied a set of different SDMs to evaluate several competing species hypotheses through the MSC. Results show that T. hajarensis is comprised by three well-defined population lineages, two of them in the Hajar Mountains of eastern Arabia, and one in Masirah Island, on the southeastern coast of Oman. Strong mito-nuclear discordances were found between populations inhabiting the Hajar Mountains, but we did not find evidence of current gene flow between them. Surprisingly, discordances in species tree topology were found when different downsampled datasets were used, and especially when linking population sizes, a commonly implemented feature in species tree reconstruction with genomic data. Different SDMs yielded different results, supporting from four species within the group, to T. hajarensis being a single species. With such contrasting results we suggest caution before splitting T. hajarensis. Overall, this study highlights the importance of sample and prior choice and the integration of several SDMs to not incur into taxonomic inflation, providing a set of already available tools to assess population structure, genetic diversity, and SDMs before describing new species.

Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past.

The geographic distribution of biodiversity is central to understanding evolutionary biology. Paleogeographic and paleoclimatic histories often help to explain how biogeographic patterns unfold through time. However, such patterns are also influenced by a variety of other factors, such as lineage diversification, that may affect the probability of certain types of biogeographic events. The complex and well-known geologic and climatic history of Afro-Arabia, together with the extensive research on reptile systematics in the region, makes Afro-Arabian squamate communities an ideal system to investigate biogeographic patterns and their drivers. Here, we reconstruct the phylogenetic relationships and the ancestral geographic distributions of several Afro-Arabian reptile clades (totaling 430 species) to estimate the number of dispersal, vicariance and range contraction events. We then compare the observed biogeographic history to a distribution of simulated biogeographic events based on the empirical phylogeny and the best-fit model. This allows us to identify periods in the past where the observed biogeographic history was likely shaped by forces beyond the ones included in the model. We find an increase in vicariance following the Oligocene, most likely caused by the fragmentation of the Afro-Arabian plate. In contrast, we did not find differences between observed and expected dispersal and range contraction levels. This is consistent with diversification enhanced by environmental processes and with the establishment of a dispersal corridor connecting Africa, Arabia and Eurasia since the middle Miocene. Finally, here we show that our novel approach is useful to pinpoint events in the evolutionary history of lineages that might reflect external forces not predicted by the underlying biogeographic model. [Dispersal; diversification; model adequacy; paleogeography; reptiles; simulations; vicariance.].

Combined Molecular and Elemental Mass Spectrometry Approaches for Absolute Quantification of Proteomes: Application to the Venomics Characterization of the Two Species of Desert Black Cobras, Walterinnesia aegyptia and Walterinnesia morgani.

We report a novel hybrid, molecular and elemental mass spectrometry (MS) setup for the absolute quantification of snake venom proteomes shown here for two desert black cobra species within the genus Walterinnesia, Walterinnesia aegyptia and Walterinnesia morgani. The experimental design includes the decomplexation of the venom samples by reverse-phase chromatography independently coupled to four mass spectrometry systems: the combined bottom-up and top-down molecular MS for protein identification and a parallel reverse-phase microbore high-performance liquid chromatograph (RP-µHPLC) on-line to inductively coupled plasma (ICP-MS/MS) elemental mass spectrometry and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-QToF MS). This allows to continuously record the absolute sulfur concentration throughout the chromatogram and assign it to the parent venom proteins separated in the RP-µHPLC-ESI-QToF parallel run via mass profiling. The results provide a locus-resolved and quantitative insight into the three desert black cobra venom proteome samples. They also validate the units of measure of our snake venomics strategy for the relative quantification of snake venom proteomes as % of total venom peptide bonds as a proxy for the % by weight of the venom toxins/toxin families. In a more general context, our work may pave the way for broader applications of hybrid elemental/molecular MS setups in diverse areas of proteomics.

Ecological specialization, rather than the island effect, explains morphological diversification in an ancient radiation of geckos.

Island colonists are often assumed to experience higher levels of phenotypic diversification than continental taxa. However, empirical evidence has uncovered exceptions to this 'island effect'. Here, we tested this pattern using the geckos of the genus Pristurus from continental Arabia and Africa and the Socotra Archipelago. Using a recently published phylogeny and an extensive morphological dataset, we explore the differences in phenotypic evolution between Socotran and continental taxa. Moreover, we reconstructed ancestral habitat occupancy to examine if ecological specialization is correlated with morphological change, comparing phenotypic disparity and trait evolution between habitats. We found a heterogeneous outcome of island colonization. Namely, only one of the three colonization events resulted in a body size increase. However, in general, Socotran species do not present higher levels or rates of morphological diversification than continental groups. Instead, habitat specialization explains better the body size and shape evolution in Pristurus. Particularly, the colonization of ground habitats appears as the main driver of morphological change, producing the highest disparity and evolutionary rates. Additionally, arboreal species show very similar body size and head proportions. These results reveal a determinant role of ecological mechanisms in morphological evolution and corroborate the complexity of ecomorphological dynamics in continent-island systems.

Systematics, biogeography and evolution of the Saharo-Arabian naked-toed geckos genus Tropiocolotes.

Plate tectonics constitute one of the main mechanisms of biological diversification on Earth, often being associated with cladogenetic events at different phylogenetic levels, as well as with exchange of faunas and floras across previously isolated biogeographic regions. North Africa and Arabia share a complex geological history that dates back to the break-up of the Arabian plate from the African plate ~30-25 Mya, followed by various geological events, such as the formation of the Red Sea or the connection between the African, Arabian and Eurasian plates. Species with Saharo-Arabian distributions have shown a close association between their evolutionary history and these geological events. In this study, we investigate the systematics, biogeography and evolution of the genus Tropiocolotes, a group of small ground-dwelling geckos, comprised by 12 species distributed from the Atlantic coast of North Africa to southwestern Iran. Species delimitation analyses uncovered the existence of high levels of undescribed diversity, with forms here considered at the species level including Tropiocolotes tripolitanus (Mauritania and southern Morocco), T. nattereri (southern Israel) and T. scorteccii (Yemen and Oman). Phylogenetic and biogeographic analyses recovered two main clades, an exclusively African clade and a Saharo-Arabian clade, that split ~25 Mya following the vicariant event mediated by the separation of the Arabian and African plates. The complex geological activity around the Red Sea is associated with the diversification within the Saharo-Arabian clade, including the colonization of North Africa from a second Tropiocolotes group. Results also provide new insights into the geographic distribution of Tropiocolotes nubicus, previously considered as exclusively associated to the Nile River valley, extending its known distribution further west, up to the Central Mountains of the Sahara. Accordingly, the Nile River seems to act as a major biogeographic barrier, separating Tropiocolotes nubicus and T. steudneri in their western and eastern margins, respectively.

Swimming through the sands of the Sahara and Arabian deserts: Phylogeny of sandfish skinks (Scincidae, Scincus) reveals a recent and rapid diversification.

Large parts of the Sahara Desert and Arabia are covered by sand seas and sand dunes, which are inhabited by specialized animal communities. For example, many lizards have developed adaptations to life in loose sand, including sand-swimming behavior. The best-known sand swimmers of the Saharo-Arabia are the sandfish skinks (genus Scincus). Although there are currently only four Scincus species recognized, their phylogenetic relationships have not yet been addressed in detail. We use eight genetic markers (three mitochondrial, five nuclear) and a complete sampling of species to infer the relationships within the genus. We employ multiple phylogenetic approaches to reconstruct the evolutionary history of these skinks and to assess the level of reticulation at the onset of their radiation. Our results indicate the presence of five strongly supported species-level lineages, four represented by the currently recognized species and the fifth by S. scincus conirostris, which does not form a clade with S. scincus. Based on these results we elevate the Iranian and northern Arabian S. conirostris to the species level. The two Saharan species, S. albifasciatus and S. scincus, are sister in all analyses. Deeper relationships within the genus, however, remained largely unresolved despite the extensive genetic data set. This basal polytomy, together with the fact that we detected no sign of hybridization in the history of the genus, indicates that the diversification of the five Scincus species was rapid, burst-like, and not followed by secondary hybridization events. Divergence time estimations show a Middle Pliocene crown radiation of the genus (3.3 Mya). We hypothesize that the aridification of the Saharo-Arabia that began in the Late Miocene triggered the initial diversification of Scincus, and that the subsequent expansion of sand deserts enabled their dispersal over the large Saharan and Arabian range. We discuss the evolution of body form in sand swimming lizards and ponder how Scincus retained their fully limbed morphology despite being sand swimmers that are typically limbless.

Parasites in a hotspot: diversity and specificity patterns of apicomplexans infecting reptiles from the Socotra Archipelago.

Although parasites represent a major component of biodiversity, they remain poorly assessed, especially in remote regions. In this study, we screened 461 reptiles from Socotra, the largest and most biologically diverse archipelago in Arabia. Using 18S rRNA primers, we detected various apicomplexan parasites, namely haemogregarines, sarcocystids and eimeriids. Haemogregarines were the most common and genetically diverse, followed by sarcocystids (genus Sarcocystis) and eimeriids (genera Isospora and Lankesterella). All were related to parasites of other reptiles, including species from Arabia, Northern Africa and Asia. Like their 29 endemic reptile hosts, almost all Socotran parasites presented high genetic divergence and ecological differences from those found elsewhere, and probably represent undescribed endemic species. Among hosts, skinks were the most parasitized, which contrasted with similar studies from other areas, probably due to their more generalist diet and habitat use. As expected due to its high species richness, geckos harboured the highest parasite diversity in the archipelago. Parasite diversity also seemed to be correlated to island size, as the largest island harboured most haplotypes. This study emphasizes the importance of screening parasites in wild hosts from remote regions and of considering host ecology to understand disease transmission across taxa.

Cryptic diversity and non-adaptive radiation of montane New Guinea skinks (Papuascincus; Scincidae).

New Guinea, the world's largest and highest tropical island, has a rich but poorly known biota. Papuascincus is a genus of skinks endemic to New Guinea's mountain regions, comprising two wide-ranging species and two species known only from their type series. The phylogeny of the genus has never been examined and the relationships among its species - as well as between it and closely related taxa - are hitherto unknown. We performed the first large-scale molecular-phylogenetic study of Papuascincus, including sampling across the genus' range in Papua New Guinea. We sequenced three mitochondrial and two nuclear markers from 65 specimens of Papuascincus and reconstructed their phylogenetic relationships. We also performed species-delimitation analyses, estimated divergence times and ancestral biogeography, and examined body-size evolution within the genus. Papuascincus was strongly supported as monophyletic. It began radiating during the mid-Miocene in the area now comprising the Central Cordillera of New Guinea, then dispersed eastward colonising the Papuan Peninsula. We found evidence of extensive cryptic diversity within the genus, with between nine and 20 supported genetic lineages. These were estimated using three methods of species delimitation and predominantly occur in allopatry. Distribution and body-size divergence patterns indicated that character displacement in size took place during the evolutionary history of Papuascincus. We conclude that the genus requires comprehensive taxonomic revision and likely represents a species-rich lineage of montane skinks.

Biogeography of Mesalina (Reptilia: Lacertidae), with special emphasis on the Mesalina adramitana group from Arabia and the Socotra Archipelago.

The lacertid lizards of the genus Mesalina inhabit the arid regions of the Old World, from North Africa to NW India. Of the 19 recognized species within the genus, eleven occur in Arabia. In this study, we explore the genetic variability and phylogeographic patterns of the less studied M. adramitana group from southern Arabia and the Socotra Archipelago within the phylogenetic and biogeographic context of the entire genus. Our unprecedented sampling extends the distribution ranges of most Mesalina species and, for the first time, sequences of M. ayunensis are included in a phylogenetic analysis. We perform analyses of concatenated multilocus datasets and species trees, conduct species delimitation analyses, and estimate divergence times within a biogeographic framework. Additionally, we inferred the environmental suitability and identified dispersal corridors through which gene flow is enabled within M. adramitana. Our results show that the Socotra Archipelago was colonized approximately 7 Mya by a single oversea colonization from mainland Arabia. Then, an intra-archipelago dispersal event that occurred approximately 5 Mya resulted in the speciation between M. balfouri, endemic to Socotra, Samha and Darsa Islands, and M. kuri, endemic to Abd al Kuri Island. Similar to previous studies, we uncovered high levels of genetic diversity within the M. adramitana species-group, with two highly divergent lineages of M. adramitana living in allopatry and adapted to locally specific climatic conditions that necessitate further investigation.

An integrative study of island diversification: Insights from the endemic Haemodracon geckos of the Socotra Archipelago.

The Socotra Archipelago in the Arabian Sea is considered one of the most geo-politically isolated landforms on earth and a center of endemism. The archipelago is located at the western edge of the Indian Ocean and comprises four islands: Socotra, Darsa, Samha, and Abd al Kuri. Here we provide an integrative study on Haemodracon geckos, the sole genus of geckos strictly endemic to the archipelago. The sympatric distribution of Haemodracon riebeckii and H. trachyrhinus on Socotra Island provides a unique opportunity to explore evolutionary relationships and speciation patterns, examining the interplay between possible sympatric and allopatric scenarios. We used molecular data for phylogenetic inference, species delimitation analyses, and to infer the diversification timeframe. Multivariate statistics were used to analyze morphological data. Ecological comparisons were explored for macro-niches using species distribution models and observations were used for micro-habitat use. Haemodracon species exhibit great levels of intraspecific genetic diversity. Our calibration estimates revealed that Haemodracon diverged from its closest relative, the mainland genus Asaccus, in the Eocene, before the detachment of the archipelago. The two Haemodracon species diversified in situ on Socotra Island during the Middle Miocene, after the archipelago's isolation, into the two reciprocally monophyletic recognized species. Their divergence is associated mostly with remarkable body size differences and micro-habitat segregation, with low levels of climatic and body shape divergences within their sympatric distributions. These results display how ecological, sympatric speciation, and allopatric speciation followed by secondary contact, may both have varying roles at different evolutionary phases.

Underground cryptic speciation within the Maghreb: Multilocus phylogeography sheds light on the diversification of the checkerboard worm lizard Trogonophis wiegmanni.

Biogeographic and evolutionary patterns in the North African portion of the Western Palaearctic are poorly known. A high fraction of undescribed diversity is expected in this region, especially in groups such as reptiles. Here we used mitochondrial (12S, 16S, cytb) and nuclear (pomc, rag2, cmos) markers and morphological data to investigate phyletic diversification and phylogeographical structure in the amphisbaenian Trogonophis wiegmanni endemic to the Maghreb. Phylogenetic and molecular dating analyses based on gene trees and species trees support three deeply divergent lineages of Pliocene origin, two in Morocco and one in central Algeria and Tunisia. Parapatry, reciprocal monophyly, high genetic divergence and limited morphological differentiation between them suggest that these lineages represent independent cryptic taxonomic units. Emerging lines of evidence from this study and from available literature on Maghreb taxa support (i) a major biogeographic break between western and eastern Maghreb and (ii) a role of the Atlas as a biogeographic divide within the western Maghreb (Morocco). The origin of these biogeographic units is probably associated with the evolutionary events prompted by the Late Miocene palaeogeographic setting and later by Plio-Pleistocene climatic changes and their interplay with prominent orographic barriers within North Africa.

The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa.

Highlands, hydrographic systems and coastal areas have been hypothesised to form corridors across the hyperarid Sahara desert in North Africa, allowing dispersal and gene flow for non-xeric species. Here we aim to provide a genetic test for the trans-Saharan corridor model, and predict the location and stability of ecological-corridors, by combining phylogeography and palaeoclimatic modelling. The model was the Psammophis schokari (Schokari sand racer) group, fast-moving and widely distributed generalist colubrids occurring mostly in arid and semiarid scrublands. We combined dated phylogenies of mitochondrial and nuclear markers with palaeoclimatic modelling. For the phylogeographic analysis, we used 75 samples of P. schokari and P. aegyptius, and Bayesian and Maximum-Likelihood methods. For the ecological models, we used Maxent over the distribution of P. schokari and West African lineages. Models were projected to past conditions (mid Holocene, Last Glacial Maximum and Last Inter-Glacial) to infer climatic stable areas. Climatic stability was predicted to be mostly restricted to coastal areas and not spatially continuous. A putative temporary trans-Saharan corridor was identified in Eastern Sahara, with a more stable one along the Atlantic coast. Six parapatric lineages were identified within P. schokari, four occurring in North Africa. These likely diverged during the Pliocene. The Tamanraset River might have been a vicariant agent. African lineages may have experienced further subsequent diversification during the late Pleistocene. The main P. schokari refugia were probably located along the northern margins of the Sahara, allowing its North-to-South colonization. Trans-Saharan corridors seem to have played a role in P. schokari biogeography, allowing colonization of central Saharan mountains and Sahel. Some might have worked as refugia, and even the most stable corridors may have sections working as filters, depending on each climatic phase. We expect the use of trans-Saharan corridors to decrease for more mesic species or with less dispersal capabilities.

Evaluating the phylogenetic signal limit from mitogenomes, slow evolving nuclear genes, and the concatenation approach. New insights into the Lacertini radiation using fast evolving nuclear genes and species trees.

Estimating the phylogeny of lacertid lizards, and particularly the tribe Lacertini has been challenging, possibly due to the fast radiation of this group resulting in a hard polytomy. However this is still an open question, as concatenated data primarily from mitochondrial markers have been used so far whereas in a recent phylogeny based on a compilation of these data within a squamate supermatrix the basal polytomy seems to be resolved. In this study, we estimate phylogenetic relationships between all Lacertini genera using for the first time DNA sequences from five fast evolving nuclear genes (acm4, mc1r, pdc, ßfib and reln) and two mitochondrial genes (nd4 and 12S). We generated a total of 529 sequences from 88 species and used Maximum Likelihood and Bayesian Inference methods based on concatenated multilocus dataset as well as a coalescent-based species tree approach with the aim of (i) shedding light on the basal relationships of Lacertini (ii) assessing the monophyly of genera which were previously questioned, and (iii) discussing differences between estimates from this and previous studies based on different markers, and phylogenetic methods. Results uncovered (i) a new phylogenetic clade formed by the monotypic genera Archaeolacerta, Zootoca, Teira and Scelarcis; and (ii) support for the monophyly of the Algyroides clade, with two sister species pairs represented by western (A. marchi and A. fitzingeri) and eastern (A. nigropunctatus and A. moreoticus) lineages. In both cases the members of these groups show peculiar morphology and very different geographical distributions, suggesting that they are relictual groups that were once diverse and widespread. They probably originated about 11-13 million years ago during early events of speciation in the tribe, and the split between their members is estimated to be only slightly older. This scenario may explain why mitochondrial markers (possibly saturated at higher divergence levels) or slower nuclear markers used in previous studies (likely lacking enough phylogenetic signal) failed to recover these relationships. Finally, the phylogenetic position of most remaining genera was unresolved, corroborating the hypothesis of a hard polytomy in the Lacertini phylogeny due to a fast radiation. This is in agreement with all previous studies but in sharp contrast with a recent squamate megaphylogeny. We show that the supermatrix approach may provide high support for incorrect nodes that are not supported either by original sequence data or by new data from this study. This finding suggests caution when using megaphylogenies to integrate inter-generic relationships in comparative ecological and evolutionary studies.

Out of Africa: Phylogeny and biogeography of the widespread genus Acanthodactylus (Reptilia: Lacertidae).

Acanthodactylus lizards are among the most diverse and widespread diurnal reptiles in the arid regions spanning from North Africa across to western India. Acanthodactylus constitutes the most species-rich genus in the family Lacertidae, with over 40 recognized species inhabiting a wide variety of dry habitats. The genus has seldom undergone taxonomic revisions, and although there are a number of described species and species-groups, their boundaries, as well as their interspecific relationships, remain largely unresolved. We constructed a multilocus phylogeny, combining data from two mitochondrial (12S, cytb) and three nuclear (MC1R, ACM4, c-mos) markers for 302 individuals belonging to 36 known species, providing the first large-scale time-calibrated molecular phylogeny of the genus. We evaluated phylogenetic relationships between and within species-groups, and assessed Acanthodactylus biogeography across its known range. Acanthodactylus cladogenesis is estimated to have originated in Africa due to vicariance and dispersal events from the Oligocene onwards. Radiation started with the separation into three clades: the Western and scutellatus clades largely distributed in North Africa, and the Eastern clade occurring mostly in south-west Asia. Most Acanthodactylus species diverged during the Miocene, possibly as a result of regional geological instability and climatic changes. We support most of the current taxonomic classifications and phylogenetic relationships, and provide genetic validity for most species. We reveal a new distinct blanfordii species-group, suggest new phylogenetic positions (A. hardyi, A. masirae), and synonymize several species and subspecies (A. lineomaculatus, A. boskianus khattensis and A. b. nigeriensis) with their phylogenetically closely-related species. We recommend a thorough systematic revision of taxa, such as A. guineensis, A. grandis, A. dumerilii, A. senegalensis and the pardalis and erythrurus species-groups, which exhibit high levels of intraspecific variability, and clear evidence of phylogenetic complexity.

The taxonomy of the Tarentola mauritanica species complex (Gekkota: Phyllodactylidae): Bayesian species delimitation supports six candidate species.

The lack of morphological diagnosable characters typical of cryptic species, poses a particular problem to taxonomists. This is especially true when taxa are closely related, sharing considerable amounts of ancestral polymorphism. Phylogenetic studies on the Moorish gecko species-complex, Tarentola mauritanica, uncovered extremely high levels of mtDNA diversity with six identified clades, including one from the Canary Islands identified as T. angustimentalis. Because of the conserved morphology of this species and its paraphyletic status with respect to T. angustimentalis, it was suggested that T. mauritanica is a cryptic species complex. Nevertheless, none of the nuclear loci used were reciprocally monophyletic regarding the mitochondrial lineages due to retention of ancestral polymorphism. In this study, we added three new intron markers to the already available dataset and used additional tools, namely phylogenetic gene trees, species tree and species limits within a Bayesian coalescent framework to confirm the support of the main lineages. Bayesian clustering analysis supports all six mtDNA lineages as independent groups, despite showing signs of ancestral polymorphism or possibly gene flow between the Maghreb/South Iberia and Central Morocco clades. The species tree recovered two major groups; one clustering taxa from Europe and Northern Maghreb and another one encompassing the lineages from Central/Southern Morocco, Central Morocco and Canary Islands, indicating that the ancestor of T. angustimentalis came from the Central/Southern Morocco region. Finally, Bayesian coalescent species delimitation analysis supports all six mitochondrial clades as "unconfirmed candidate species", pending morphological data to define them.

Patterns of diversification in islands: A comparative study across three gecko genera in the Socotra Archipelago.

In this study we used the complete fauna of geckos of the Socotra Archipelago to test whether the three gecko genera co-occurring in the islands (Pristurus, Hemidactylus and Haemodracon) produced similar outcomes of morphological and climatic diversification. To test this, we produced a time-calibrated tree of 346 geckos including all 16 endemic species of the archipelago and 26 potential close-relatives in the continent. Our dating estimates revealed that most of the diversity of geckos in the archipelago was the consequence of in situ diversification. However not all genera shared similar patterns of diversification. While in Hemidactylus and Haemodracon this involved great differences in body size and low levels of climatic diversification (mostly involving sympatric distributions), an opposite pattern appeared in Pristurus in which most of the diversification involved shifts in climatic envelopes (mostly involving allopatric and parapatric distributions) but almost no size differentiation. Consistently with this, Pristurus was the only genus in which rates of size diversification in islands were substantially lower than in the continent. This illustrates how different groups can greatly differ in their patterns of intra-island diversification and highlights the importance of taxon-dependent factors at determining different patterns of diversification in the same insular context.

Evolution around the Red Sea: Systematics and biogeography of the agamid genus Pseudotrapelus (Squamata: Agamidae) from North Africa and Arabia.

Since the Oligocene, regions adjacent to the Red Sea have experienced major environmental changes, from tectonic movements and continuous geological activity to shifting climatic conditions. The effect of these events on the distribution and diversity of the regional biota is still poorly understood. Agamid members of the genus Pseudotrapelus are diurnal, arid-adapted lizards distributed around the Red Sea from north-eastern Africa, across the mountains and rocky plateaus of the Sinai and Arabian Peninsulas northwards to Syria. Despite recent taxonomic work and the interest in the group as a model for studying biogeographic and diversity patterns of the arid areas of North Africa and Arabia, its taxonomy is poorly understood and a comprehensive phylogeny is still lacking. In this study, we analyzed 92 Pseudotrapelus specimens from across the entire distribution range of the genus. We included all known species and subspecies, and sequenced them for mitochondrial (16S, ND4 and tRNAs) and nuclear (MC1R, c-mos) markers. This enabled us to obtain the first time-calibrated molecular phylogeny of the genus, using gene trees, species trees and coalescent-based methods for species delimitation. Our results revealed Pseudotrapelus as a monophyletic genus comprised of two major clades and six independently evolving lineages. These lineages correspond to the five currently recognized species and a sixth lineage relating to the synonymized P. neumanni. The subspecific validity of P. sinaitus werneri needs further assessment as it does not form a distinct cluster relative to P. s. sinaitus. The onset of Pseudotrapelus diversification is estimated to have occurred in Arabia during the late Miocene. Radiation has likely resulted from vicariance and dispersal events due to the continued geological instability, sea level fluctuations and climatic changes within the region.

Assessing the diversity, host-specificity and infection patterns of apicomplexan parasites in reptiles from Oman, Arabia.

Understanding the processes that shape parasite diversification, their distribution and abundance provides valuable information on the dynamics and evolution of disease. In this study, we assessed the diversity, distribution, host-specificity and infection patterns of apicomplexan parasites in amphibians and reptiles from Oman, Arabia. Using a quantitative PCR approach we detected three apicomplexan parasites (haemogregarines, lankesterellids and sarcocystids). A total of 13 haemogregarine haplotypes were identified, which fell into four main clades in a phylogenetic framework. Phylogenetic analysis of six new lankesterellid haplotypes revealed that these parasites were distinct from, but phylogenetically related to, known Lankesterella species and might represent new taxa. The percentage of infected hosts (prevalence) and the number of haemogregarines in the blood (parasitaemia) varied significantly between gecko species. We also found significant differences in parasitaemia between haemogregarine parasite lineages (defined by phylogenetic clustering of haplotypes), suggesting differences in host-parasite compatibility between these lineages. For Pristurus rupestris, we found significant differences in haemogregarine prevalence between geographical areas. Our results suggest that host ecology and host relatedness may influence haemogregarine distributions and, more generally, highlight the importance of screening wild hosts from remote regions to provide new insights into parasite diversity.

Cryptic diversity within the Anatololacerta species complex (Squamata: Lacertidae) in the Anatolian Peninsula: evidence from a multi-locus approach.

The rapid development of innovative molecular tools for characterizing biodiversity is leading to an extensive and sometimes unexpected renovation of taxonomic classifications. Particularly, for species having allopatric or parapatric distributions or resulting from recent speciation processes, the absence of clear phenotypic differentiation may hinder the recognition of closely related taxa, while intraspecific polymorphism may be confused with the presence of more than one single species. In the present work, we apply different phylogenetic methods in order to infer relationships within the genus Anatololacerta, and to assess the taxonomy of this morphologically diversified group of lizards endemic to western and southern Anatolia and some neighboring Aegean islands. According to morphology, three species have been recognized (Anatololacerta anatolica, A. oertzeni and A. danfordi) as well as several subspecies, but small variation at immunological markers led some authors to join all the populations into one single taxon, A. danfordi. By selecting both mitochondrial and nuclear informative markers, we tested the effectiveness of classical "gene tree" (i.e. Bayesian Inference) vs. innovative (i.e. coalescent-based) "species tree" methods in resolving the Anatololacerta taxonomic enigma, as a case in point for similar studies on species complexes resulting from non-obvious and cryptic diversification patterns. According to our results, the gene tree method failed in resolving phylogenetic relationships among clades, whereas the multi-locus species tree approach, coupled with species delimitation methods, allowed the identification of four well distinct species. These species probably diversified in different allopatric refugia located in southern and western Anatolia, where isolated populations may have persisted during Pleistocene glacial cycles.