Out of Arabia: A Complex Biogeographic History of Multiple Vicariance and Dispersal Events in the Gecko Genus <i>Hemidactylus</i> (Reptilia: Gekkonidae)

<div><p>The geological history of the Arabian Peninsula has played a crucial role in shaping current diversity and distribution patterns of many Arabian and African faunal elements. The gecko genus <i>Hemidactylus</i> is not an exception. In this study, we provide an insight into the phylogeny and systematics of 45 recognized species of the so-called Arid clade of the genus <i>Hemidactylus</i> from Arabia, the Horn of Africa, the Levant and Iran. The material comprises 358 specimens sequenced for up to two mitochondrial (12S rRNA, cytochrome <i>b</i>) and four nuclear (<i>mc1r</i>, <i>cmos</i>, <i>rag1</i>, <i>rag2</i>) genes with 4766 bp of the concatenated alignment length. A robust calibrated phylogeny and reconstruction of historical biogeography are inferred. We link the history of this genus with major geological events that occurred in the region within the last 30 million years. Two basal divergences correspond with the break-ups of the Arabian and African landmasses and subsequent separation of Socotra from the Arabian mainland, respectively, segregating the genus by means of vicariance. Formation of the Red Sea led to isolation and subsequent radiation in the Arabian Peninsula, which was followed by multiple independent expansions: 13.1 Ma to Iran; 9.8 Ma to NE Africa; 8.2 to Socotra Archipelago; 7–7.3 Ma two colonizations to the Near East; 5.9 Ma to NE Africa; and 4.1 to Socotra. Moreover, using multiple genetic markers we detected cryptic diversity within the genus, particularly in south-western Arabia and the Ethiopian highlands, and confirmed the existence of at least seven new species in the area. These findings highlight the role of Arabia and the Horn of Africa as an important <i>Hemidactylus</i> diversity hotspot.</p></div

Summary of DNA partitions.

<p>Information on the length of all partitions used in the phylogenetic analyses, model of sequence evolution selected by jModelTest <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064018#pone.0064018-Posada1" target="_blank">[44]</a> (Model), number of variable (Var) and parsimony-informative (Pars. inf.) sites calculated for the ingroup only, and the results of the test of rate homogeneity (LRT) run in MEGA <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064018#pone.0064018-Tamura1" target="_blank">[52]</a> using only the subset of 58 sequences selected for the BEAST analysis (see Methods).</p

Detail of the phylogenetic tree of the Arid clade <i>Hemidactylus</i>: Hadhramaut and Dhofar.

<p>Red dots in the nodes indicate ML bootstrap values ≥70 and BI pp≥0.95. Numbers after species names refer to sample codes; numbers on the right correspond with the localities numbers in the map. Ages of the nodes estimated with BEAST dating analysis are indicated by the nodes, mean above in bold, 95% HPD interval in plain below.</p

Detail of the phylogenetic tree of the Arid clade <i>Hemidactylus</i>: The Persian Gulf.

<p>Red dots in the nodes indicate ML bootstrap values ≥70 and BI pp≥0.95. Numbers after species names refer to sample codes; numbers on the right correspond with the localities numbers in the map. Ages of the nodes estimated with BEAST dating analysis are indicated by the nodes, mean above in bold, 95% HPD interval in plain below.</p

Detail of the phylogenetic tree of the Arid clade <i>Hemidactylus</i>: Oman and Socotra Archipelago.

<p>Red dots in the nodes indicate ML bootstrap values ≥70 and BI pp≥0.95. Numbers after species names refer to sample codes; numbers on the right correspond with the localities numbers in the map. Ages of the nodes estimated with BEAST dating analysis are indicated by the nodes, mean above in bold, 95% HPD interval in plain below.</p

Detail of the phylogenetic tree of the Arid clade <i>Hemidactylus</i>: <i>H</i>.

<p><b> </b><b><i>robustus</i></b><b> and related species.</b><b> </b> Red dots in the nodes indicate ML bootstrap values ≥70 and BI pp≥0.95. Numbers after species names refer to sample codes; numbers on the right correspond with the localities numbers in the map. Ages of the nodes estimated with BEAST dating analysis are indicated by the nodes, mean above in bold, 95% HPD interval in plain below.</p

Detail of the phylogenetic tree of the Arid clade <i>Hemidactylus</i>: The Gulf of Aden.

<p>Red dots in the nodes indicate ML bootstrap values ≥70 and BI pp≥0.95. Numbers after species names refer to sample codes; numbers on the right correspond with the localities numbers in the map. Ages of the nodes estimated with BEAST dating analysis are indicated by the nodes, mean above in bold, 95% HPD interval in plain below.</p

Detail of the phylogenetic tree of the Arid clade <i>Hemidactylus</i>: The Levant.

<p>Red dots in the nodes indicate ML bootstrap values ≥70 and BI pp≥0.95. Numbers after species names refer to sample codes; numbers on the right correspond with the localities numbers in the map. Ages of the nodes estimated with BEAST dating analysis are indicated by the nodes, mean above in bold, 95% HPD interval in plain below.</p

A contribution to the phylogeny and taxonomy of the <i>Pachydactylus weberi</i> group (Squamata: Gekkonidae): a case of intraspecific colour polymorphism confounding taxonomy

<p><i>Pachydactylus</i> is the most species-rich reptile genus in southern Africa. Most species are habitat specialists adapted to hyper-arid conditions of the Namibian and north-western South African xeric regions. Although a fair number of phylogenetic studies and taxonomic revisions have been published, some species still remain rather enigmatic. In the ten years since the taxonomic revision of the <i>weberi</i> group, some of the species have not been recorded and our knowledge on their distribution, phylogenetic affinities, or intraspecific variability is limited or non-existent. <i>Pachydactylus goodi</i> is one such species. In this study, we report a newly discovered population of <i>P. goodi</i> in the Richtersveld National Park, South Africa, which considerably extends the known range of the species. In addition, the results of our phylogenetic analyses indicate that <i>P. goodi</i> is paraphyletic with respect to <i>P. atorquatus</i>. Although there is a striking colour polymorphism observed between these two species, the level of genetic differentiation within the <i>goodi-atorquatus</i> clade is comparable with intraspecific variability observed in other <i>Pachydactylus</i> species. As a result of these findings, which are further supported by morphological similarity of the two species, we conclude that they represent a single species and synonymise <i>P. goodi</i> with <i>P. atorquatus</i>.</p

Climate variability of Oman.

<p>(A) Map showing the distribution and extension of the 20 climatic clusters of Oman identified in this study that group 10% of the explained variance by PC1 and PC2; (B) Principal Component Analysis (PCA) of the climatic space of Oman using 12 BIOCLIM variables and with the 20 climatic clusters that group 10% of the explained variance by PC1 and PC2 with the same colors as in the map. Clusters have been numbered from 1 to 20 with the following order: from left to right and from bottom to top.</p