Evolutionary history of spiny-tailed lizards (Agamidae:Uromastyx) from the Saharo-Arabian region

The evolutionary history and ancestral biogeographic range estimation of old-world Rhinolophidae and Hipposideridae (Chiroptera)

BACKGROUND

Family Rhinolophidae (horseshoe bats), Hipposideridae (leaf-nosed bats) and Rhinonycteridae (trident bats) are exclusively distributed in the Old-World, and their biogeography reflects the complex historic geological events throughout the Cenozoic. Here we investigated the origin of these families and unravel the conflicting family origin theories using a high resolution tree covering taxa from each zoogeographic realm from Africa to Australia. Ancestral range estimations were performed using a probabilistic approach implemented in BioGeoBEARS with subset analysis per biogeographic range [Old-World as whole, Australia-Oriental-Oceania (AOO) and Afrotropical-Madagascar-Palearctic (AMP)].

RESULT

Our result supports an Oriental origin for Rhinolophidae, whereas Hipposideridae originated from the Oriental and African regions in concordance with fossil evidence of both families. The fossil evidence indicates that Hipposideridae has diversified across Eurasia and the Afro-Arabian region since the Middle Eocene. Meanwhile, Rhinonycteridae (the sister family of Hipposideridae) appears to have originated from the Africa region splitting from the common ancestor with Hipposideridae in Africa. Indomalaya is the center of origin of Rhinolophidae AOO lineages, and Indomalayan + Philippines appears to be center of origin of Hipposideridae AOO lineage indicating allopatric speciation and may have involved jump-dispersal (founder-event) speciation within AOO lineage. Wallacea and the Philippines may have been used as stepping stones for dispersal towards Oceania and Australia from the Oriental region. Multiple colonization events via different routes may have occurred in the Philippines (i.e., Palawan and Wallacea) since the Late Miocene. The colonization of Rhinolophidae towards Africa from Asia coincided with the estimated time of Tethys Ocean closure around the Oligocene to Miocene (around 27 Ma), allowing species to disperse via the Arabian Peninsula. Additionally, the number of potential cryptic species in Rhinolophidae in Southeast Asia may have increased since Plio-Pleistocene and late Miocene.

CONCLUSION

Overall, we conclude an Oriental origin for Rhinolophidae, and Oriental + African for Hipposideridae. The result demonstrates that complex historical events, in addition to species specific ecomorphology and specialization of ecological niches may shape current distributions.

The false-blister beetles (Coleoptera, Oedemeridae) of Oman with the description of a new species

This paper is the first to deal with the false-blister beetle of the sultanate of Oman: it provides an overview of the biogeography of the country and an annotated checklist of the eight known species, four of which are new for Oman. In addition, a new species, Probosca (Proboxantha) coniuncta n. sp. is described.  

Habitat selection by the Spiny-tailed lizard (Uromastyx aegyptia): A view from spatial analysis

Many factors affect the habitat selection for animal species, which in turn may greatly affect their distribution in different ecosystems. Understanding the processes that affect habitat selection is also critical for guiding and managing conservation initiatives. Our study aimed to assess the habitat selection by free-ranging Spiny-tailed lizard (Uromastyx aegyptia) by analyzing a geospatial data connecting its burrow parameters to different habitat characteristics within selected sites in Hail region, Saudi Arabia. We examined evidence and patterns of significant spatial clustering for (366) active burrows by linking their parameters (burrow entrance size, burrow entrance width and burrow entrance height), their reference geographical locations and, two habitat characteristics defined by soil type and vegetation cover. The objective of the analysis was to increase the understanding on the burrows aggregation process in the space and, to describe its possible relation to other spatial habitat configurations. Analysis of distances based on the Nearest Neighbor Index (NNI) and hotspots detection in Nearest neighbor hierarchical clustering (Nnh) suggested twelve (12) spatial clusters located within the study area. In addition, a spatial ordinary least square (OLS) and Poisson regression models revealed significant effects of soil type and vegetation cover on burrow parameters (OLS, p < 0.05; Poisson, p < 0.001), which indicate a strong association between burrows parameters and habitats characteristics. Findings from the study also suggest that other factors such as elevations, highways, and human settlement concentration spots could possibly play a major role in defining burrow spatial aggregation and furthermore have a significant impact on habitat selection.

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.

Pleistocene climate fluctuations drove demographic history of African golden wolves (Canis lupaster)

Pleistocene climate change impacted entire ecosystems throughout the world. In the northern hemisphere, the distribution of Arctic species expanded during glacial periods, while more temperate and mesic species contracted into climatic refugia, where isolation drove genetic divergence. Cycles of local cooling and warming in the Sahara region of northern Africa caused repeated contractions and expansions of savannah-like environments which connected mesic species isolated in refugia during interglacial times, possibly driving population expansions and contractions; divergence and geneflow in the associated fauna. Here, we use whole genome sequences of African golden wolves (Canis lupaster), a generalist mesopredator with a wide distribution in northern Africa to estimate their demographic history and past episodes of geneflow. We detect a correlation between divergence times and cycles of increased aridity-associated Pleistocene glacial cycles. A complex demographic history with responses to local climate change in different lineages was found, including a relict lineage north of the High Atlas Mountains of Morocco that has been isolated for more than 18,000 years, possibly a distinct ecotype.

The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara)

We investigated the phylogeographic structure of the genus Saara and studied whether the Zagros Mountain ranges influence the gene flow and dispersal at the landscape scale between the Iranian Saara species, including S. asmussi in the central Iranian plateau and S. loricata in the Mesopotamian lowlands. Phylogenetic analyses clearly show three well-supported species, including S. loricata, S. asmussi and S. hardwickii, that are distinct from Uromastyx species. The S-DIVA and BBM analyses demonstrate that species of Saara originated from an ancestor somewhere in the Iranian Plateau and then dispersed to its current geographical range. Our results indicate that the separation of S. loricata from S. asmussi coincides with the orogenic events of the Zagros Mountains during the Pliocene, and thus it may show a vicariance event. Diversification within populations of S. loricata and S. assmussi are estimated to have occurred during the Pleistocene. The haplotype network indicates one haplogroup for each of the Iranian Saara species. Population genetic analyses shows signals of demographic expansions at the beginning of the Holocene for S. loricata. Our results support the hypothesis that the Zagros Mountains act as a barrier for gene flow and Quaternary climatic oscillations affected intraspecific genetic divergences of S. loricata and S. asmussi.

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.

Using multilocus approach to uncover cryptic diversity within Pseudotrapelus lizards from Saudi Arabia

The agamid Pseudotrapelus lizards inhabit the mountainous areas of the Arabian Peninsula and eastern North Africa. Currently six Pseudotrapelus species are recognised, though diagnostic morphological characters are still lacking, creating great difficulty in describing new species. Recently, two specimens of Pseudotrapelus were collected from the vicinity of Riyadh in central Saudi Arabia, an area that was not sampled in previous phylogenetic studies. In here we used both mitochondrial and nuclear data to investigate the phylogenetic position of the new samples, and assess their phylogenetic relationships with the other recognised species of Pseudotrapelus from across the distribution range of the genus. We used a multilocus approach of haplotype networks, concatenated datasets and species trees, performed mitochondrial and nuclear species delimitation analyses, and estimated divergence times. In general, our results support previous molecular studies and uncover the presence of cryptic diversity within Pseudotrapelus. The phylogenetic structure of the genus is of two major clades and within them seven distinct, delimited phylogenetic groups belonging to the six recognised species and the seventh to the individuals from Riyadh. The Riyadh specimens were distinct in all analyses performed. We suggest that the new specimens from the Riyadh area are a distinct lineage, forming a clade with their phylogenetic relatives, P. sinaitus and P. chlodnickii. The clade formed by these three species diverged during the Late Miocene around 6.4 Ma, with cladogenesis possibly facilitated by vicariance and isolation caused due to climatic fluctuations and the progression of sandy areas. Our results suggest further morphological research is necessary to revise the taxonomic status of this lineage and of the entire genus.

An integrative assessment of the diversity, phylogeny, distribution, and conservation of the terrestrial reptiles (Sauropsida, Squamata) of the United Arab Emirates

In the present study we use an unprecedented database of 5,535 distributional records to infer the diversity, ecological preferences and spatial distribution of the 60 species of terrestrial reptiles of the United Arab Emirates (UAE), and use the 57 native species to test the effectiveness of the protected areas’ network in conserving this unique vertebrate fauna. We infer a time-calibrated phylogeny with 146 species of squamates and 15 genes including all UAE terrestrial reptile species to determine the phylogenetic diversity (PD) and evolutionary distinctiveness (ED) of the native species and to compare it with the distribution of the hotspots of native species richness. The results of this study indicate that the sampling effort is remarkable, covering 75% of the country’s territory representing nearly the entire climatic space of the UAE defined by the mean annual temperature and the total annual precipitation, as well as the multivariate climatic space defined by a principal component analysis (PCA). Species richness is highest in the northeast of the country, in a transitional area from sandy desert to the mountainous terrain of the Hajar Mountains. The highest PD of a single square cell of 10 arc-minutes grid is of 2,430 million years (my) of accumulated evolutionary history and the strong correlation between PD and species richness suggests that the raw number of species is a good surrogate to quantify the evolutionary history (i.e., PD). The species with the highest values of ED are those in families represented by only one species in the UAE. Finally, the assessment of the UAE protected areas shows that, despite their relevance in protecting the terrestrial reptiles, they do not offer adequate protection for some threatened species. Therefore, a reassessment of some of the protected areas or the creation of species specific conservation action plans are recommended in order to ensure the preservation of the unique diversity of UAE terrestrial reptiles.

Ancient diversification, biogeography, and the role of climatic niche evolution in the Old World cat snakes (Colubridae, Telescopus)

The process of species diversification is often associated with niche shifts in the newly arising lineages so that interspecific competition is minimized. However, an opposing force known as niche conservatism causes that related species tend to resemble each other in their niche requirements. Due to the inherent multidimensionality of niche space, some niche components may be subject to divergent evolution while others remain conserved in the process of speciation. One such possible component is the species' climatic niche. Here, we test the role of climatic niche evolution on the diversification of the Old World cat snakes of the genus Telescopus. These slender, nocturnal snakes are distributed in arid and semiarid areas throughout Africa, southwest Asia and adjoining parts of Europe. Because phylogenetic relationships among the Telescopus species are virtually unknown, we generated sequence data for eight genetic markers from ten of the 14 described species and reconstructed a time-calibrated phylogeny of the genus. Phylogenetic analysesindicate that the genus is of considerably old origin that dates back to the Eocene/Oligocene boundary. Biogeographical analyses place the ancestor of the genus in Africa, where it diversified into the species observed today and from where it colonized Arabia and the Levant twice independently. The colonization of Arabia occurred in the Miocene, that of the Levant either in the Late Oligocene or Early Miocene. We then identified temperature and precipitation niche space and breadth of the species included in the phylogeny and examined whether there is phylogenetic signal in these climatic niche characteristics. Despite the vast range of the genus and its complex biogeographic history, most Telescopus species have similar environmental requirements with preference for arid to semiarid conditions. One may thus expect that the genus' climatic niche will be conserved. However, our results suggest that most of the climatic niche axes examined show no phylogenetic signal, being indicative of no evolutionary constraints on the climatic niche position and niche breadth in Telescopus. The only two variables with positive phylogenetic signal (temperature niche position and precipitation niche breadth) evolved under the Brownian motion model, also indicating no directional selection on these traits. As a result, climatic niche evolution does not seem to be the major driver for the diversification in Telescopus.