Marc Simó-Riudalbas

Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago.

Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra’s most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8–54.4%. This has implications in the species’ ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.

Microendemicity in the northern Hajar Mountains of Oman and the United Arab Emirates with the description of two new species of geckos of the genus Asaccus (Squamata: Phyllodactylidae)

Background The Hajar Mountains of Oman and the United Arab Emirates (UAE) is the highest mountain range in Eastern Arabia. As a result of their old geological origin, geographical isolation, complex topography and local climate, these mountains provide an important refuge for endemic and relict species of plants and animals with strong Indo-Iranian affinities. Among vertebrates, the rock climbing nocturnal geckos of the genus Asaccus represent the genus with the highest number of endemic species in the Hajar Mountains. Recent taxonomic studies on the Zagros populations of Asaccus have shown that this genus is much richer than it was previously thought and preliminary morphological and molecular data suggest that its diversity in Arabia may also be underestimated. Methods A total of 83 specimens originally classified as Asaccus caudivolvulus (including specimens of the two new species described herein), six other Asaccus species from the Hajar and the Zagros Mountains and two representatives of the genus Haemodracon were sequenced for up to 2,311 base pairs including the mitochondrial 12S and cytb and the nuclear c-mos, MC1R and ACM4 genes. Phylogenetic relationships were inferred using both Bayesian and maximum-likelihood approaches and the former method was also used to calibrate the phylogenetic tree. Haplotype networks and phylogenetic trees were inferred from the phased nuclear genes only. Sixty-one alcohol-preserved adult specimens originally classified as Asaccus caudivolvulus from the northern Hajar Mountains were examined for 13 morphometric and the five meristic variables using multivariate methods and were also used to diagnose and describe the two new species. Results The results of the molecular and morphological analyses indicate that the species originally classified as Asaccus caudivolvulus is, in fact, an assemblage of three different species that started diversifying during the Mid-Miocene. The molecular phylogenies consistently recovered the Hajar endemic A. montanus as sister taxon to all the other Asaccus species included in the analyses, rendering the Arabian species of Asaccus polyphyletic. Discussion Using this integrative approach we have uncovered a very old diversification event that has resulted in a case of microendemicity, where three morphologically and ecologically similar medium-sized lizard species coexist in a very short and narrow mountain stretch. Asaccus caudivolvulus is restricted to a small coastal area of the UAE and at risk from heavy development, while the two new species described herein are widely distributed across the northern tip of the Hajar Mountains and seem to segregate in altitude when found in close proximity in the Musandam Peninsula (Oman). Similarly to other integrative analyses of Hajar reptiles, this study highlights the high level of diversity and endemicity of this arid mountain range, underscoring its status as one of the top hotspots of reptile diversity in Arabia.

Cryptic diversity in Ptyodactylus (Reptilia: Gekkonidae) from the northern Hajar Mountains of Oman and the United Arab Emirates uncovered by an integrative taxonomic approach

The Hajar Mountains of south-eastern Arabia form an isolated massif surrounded by the sea to the east and by a large desert to the west. As a result of their old geological origin, geographical isolation, complex topography and local climate, these mountains provide an important refuge for endemic and relict species of plants and animals. With 19 species restricted to the Hajar Mountains, reptiles are the vertebrate group with the highest level of endemicity, becoming an excellent model for understanding the patterns and processes that generate and shape diversity in this arid mountain range. The geckos of the Ptyodactylus hasselquistii species complex are the largest geckos in Arabia and are found widely distributed across the Arabian Mountains, constituting a very important component of the reptile mountain fauna. Preliminary analyses suggested that their diversity in the Hajar Mountains may be higher than expected and that their systematics should be revised. In order to tackle these questions, we inferred a nearly complete calibrated phylogeny of the genus Ptyodactylus to identify the origin of the Hajar Mountains lineages using information from two mitochondrial and four nuclear genes. Genetic variability within the Hajar Mountains was further investigated using 68 specimens of Ptyodactylus from 46 localities distributed across the entire mountain range and sequenced for the same genes as above. The molecular phylogenies and morphological analyses as well as niche comparisons indicate the presence of two very old sister cryptic species living in allopatry: one restricted to the extreme northern Hajar Mountains and described as a new species herein; the other distributed across the rest of the Hajar Mountains that can be confidently assigned to the species P. orlovi. Similar to recent findings in the geckos of the genus Asaccus, the results of the present study uncover more hidden diversity in the northern Hajar Mountains and stress once again the importance of this unique mountain range as a hot spot of biodiversity and a priority focal point for reptile conservation in Arabia.

Phylogeny and biogeography of Arabian populations of the Persian Horned Viper Pseudocerastes persicus (Duméril, Bibron & Duméril, 1854)

The Persian Horned Viper (Pseudocerastes persicus) is distributed from northeast Iraq through the Iranian Plateau to western Pakistan with isolated populations in the Hajar Mountains of south-eastern Arabia. Like the other members of the genus Pseudocerastes, P. persicus is a sit-and-wait ambush feeder with low vagility, a characteristic that often results in high levels of population differentiation. In order to clarify the level of genetic variability, phylogenetic relationships, and biogeography of the Arabian populations of P. persicus we sequenced 597 base pairs of the mitochondrial cytochrome b of four individuals from the Hajar Mountains in south-eastern Arabia and inferred their phylogenetic relationships including 10 samples of P. persicus from Iran and Pakistan, four P. urarachnoides and one P. fieldi downloaded from GenBank. The four Arabian samples are genetically very similar in the gene fragment analysed and are phylogenetically very closely related to populations of P. persicus from coastal south Iran. Biogeographically, it appears that colonisation of the Hajar Mountains by P. persicus took place from Iran very recently, most probably during the last glaciation, when most of the Persian Gulf was above sea level and did not represent a barrier for dispersal.

Diversity, distribution and conservation of the terrestrial reptiles of Oman (Sauropsida, Squamata)

In the present work, we use an exceptional database including 5,359 records of 101 species of Oman’s terrestrial reptiles together with spatial tools to infer the spatial patterns of species richness and endemicity, to infer the habitat preference of each species and to better define conservation priorities, with especial focus on the effectiveness of the protected areas in preserving this unique arid fauna. Our results indicate that the sampling effort is not only remarkable from a taxonomic point of view, with multiple observations for most species, but also for the spatial coverage achieved. The observations are distributed almost continuously across the two-dimensional climatic space of Oman defined by the mean annual temperature and the total annual precipitation and across the Principal Component Analysis (PCA) of the multivariate climatic space and are well represented within 17 out of the 20 climatic clusters grouping 10% of the explained climatic variance defined by PC1 and PC2. Species richness is highest in the Hajar and Dhofar Mountains, two of the most biodiverse areas of the Arabian Peninsula, and endemic species richness is greatest in the Jebel Akhdar, the highest part of the Hajar Mountains. Oman’s 22 protected areas cover only 3.91% of the country, including within their limits 63.37% of terrestrial reptiles and 50% of all endemics. Our analyses show that large areas of the climatic space of Oman lie outside protected areas and that seven of the 20 climatic clusters are not protected at all. The results of the gap analysis indicate that most of the species are below the conservation target of 17% or even the less restrictive 12% of their total area within a protected area in order to be considered adequately protected. Therefore, an evaluation of the coverage of the current network of protected areas and the identification of priority protected areas for reptiles using reserve design algorithms are urgently needed. Our study also shows that more than half of the species are still pending of a definitive evaluation by the International Union for Conservation of Nature (IUCN).

Systematics of the Mesalina guttulata species complex (Squamata: Lacertidae) from Arabia with the description of two new species

Mesalina are small diurnal lacertid lizards inhabiting arid areas from North Africa to northwestern India. Previous phylogenetic studies have shown the existence of several species complexes within the genus, some of them with high levels of undiscovered diversity. In the present study, we carry out an integrative systematic revision of the Mesalina guttulata species complex using both molecular and morphological data from across its entire distribution range in North Africa, the Middle East and Arabia. The results of the genetic analyses indicate that M. guttulata and M. bahaeldini are two allopatric sister taxa separated by the Suez Canal and that the species complex includes a further three unnamed deep phylogenetic lineages, two of them restricted to southern and southwestern Arabia and described herein as Mesalina austroarabica sp. nov. and Mesalina arnoldi sp. nov., respectively. As a result of the lack of enough material, the third deep lineage, distributed across Kuwait, Saudi Arabia and Jordan, is provisionally left undescribed. The two newly described species are characterized by their size, scale counts and tail coloration, as well as differences at the three mitochondrial and one nuclear gene analyzed in the present study.

Systematics, biogeography and evolution of Asaccus gallagheri (Squamata, Phyllodactylidae) with the description of a new endemic species from Oman

The Hajar Mountains are the highest mountain range in eastern Arabia. Despite being classified as a mountain desert, it is considered one of the top biodiversity hotspots of Arabia. As a result of its relatively old geological origin, complex topography, environmental heterogeneity and geographic isolation from other mountain ranges, its fauna and flora have diversified significantly producing high levels of endemicity, particularly amongst reptiles. Several genetic studies indicate that this diversity may still be underestimated, especially within some groups containing morphologically similar species like the nocturnal geckos of the genus Asaccus. These have radiated extensively on both sides of the Gulf of Oman, in the Hajar Mountains and the Zagros Mountains of south-west Asia, and are a good example of the faunal affinities between these two mountain ranges. In the present work, we analyse A. gallagheri, the smallest species of the Arabian radiation, using an unprecedented sampling across its entire distribution range and an integrative approach combining morphological, macroecological and multilocus molecular data with the objective of clarifying its systematics and phylogeography. The results support the presence of two allopatric species within A. gallagheri that split approximately 6 Ma. The newly discovered species is endemic to the Eastern Hajars and is described herein mainly on the basis of its smaller size and high genetic divergence from A. gallagheri. The molecular analyses also uncovered remarkable levels of genetic diversity within both species. The present study highlights the diversity of the genus Asaccus in south-east Arabia and stresses its relevance from a conservation point of view. http://www.zoobank.org/urn:lsid:zoobank.org:pub:62EB3146-9F79-4857-8CC6-36FE235D84D4

The complete mitochondrial genome of Pristurus rupestris rupestris

Abstract Pristurus rupestris rupestris is a gecko of the family Sphaerodactylidae adapted to the arid habitat found in the Hajar Mountains of southeastern Arabia. The complete mitochondrial genome was obtained with Illumina sequencing. The sequenced mitogenome has 13 protein-coding genes, 22 tRNAs, two rRNA genes and two non-coding regions, totalling 16,993 bp. The AT content of the obtained sequence is 52.1% (A:28.7%, T:23.4%, G:14.7%, C:33.2%). The control region has an AT content of 54.3% and a length of 1558 bp.