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

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

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 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

High Species Richness of <i>Scinax</i> Treefrogs (Hylidae) in a Threatened Amazonian Landscape Revealed by an Integrative Approach

<div><p>Rising habitat loss is one of the main drivers of the global amphibian decline. Nevertheless, knowledge of amphibian diversity needed for effective habitat protection is still highly inadequate in remote tropical regions, the greater part of the Amazonia. In this study we integrated molecular, morphological and bioacoustic evidence to evaluate the species richness of the treefrogs genus <i>Scinax</i> over a 1000 km transect across rainforest of the Purus-Madeira interfluve, and along the east bank of the upper Madeira river, Brazilian Amazonia. Analysis revealed that 82% of the regional species richness of <i>Scinax</i> is still undescribed; two nominal species, seven confirmed candidate species, two unconfirmed candidate species, and one deep conspecific lineage were detected in the study area. DNA barcoding based analysis of the 16s rRNA gene indicates possible existence of three discrete species groups within the genus <i>Scinax</i>, in addition to the already-known <i>S</i>. <i>rostratus</i> species Group. Quantifying and characterizing the number of undescribed <i>Scinax</i> taxa on a regional scale, we provide a framework for future taxonomic study in Amazonia. These findings indicate that the level to which Amazonian anura species richness has been underestimated is far greater than expected. Consequently, special attention should be paid both to taxonomic studies and protection of the still-neglected Amazonian <i>Scinax</i> treefrogs.</p></div

Specimens of <i>Scinax</i> from the Purus-Madeira interfluve and east bank of the upper Madeira River, Brazilian Amazonia.

<p>(A) <i>Scinax</i> sp. 1, male, SVL 20.2 mm, INPA-H 34688, from M-9. (B) <i>Scinax</i> sp. 2, male, SVL 18.1 mm, INPA-H 34667, from M-11. (C) <i>Scinax</i> sp. 3, male, SVL 31.3 mm, INPA-H 34584, from M-7. (D) <i>Scinax</i> sp. 5, male, not collected, from M-8. (E) <i>Scinax</i> sp. 6, male, SVL 25.2 mm, INPA-H 35562, from M-17. (F) <i>Scinax</i> sp. 7, male, SVL 23.9 mm, INPA-H 34623, from M-8. (G) <i>Scinax</i> aff. <i>cruentommus</i> BRA, male, SVL 25.4 mm, INPA-H 34596, from M-6. (H) <i>Scinax ruber</i> PM, couple, not collected. (I) <i>Scinax chiquitanus</i> BRA, female, SVL 33.7 mm, INPA-H 35554; male, 31.1 mm, INPA-H 35555, from M-14. Photographs by R. Fraga.</p