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

References

• Afrasiab, S. R., & Mohamad, S. I. (2009). A study on cave-dwelling geckos in Iraq, with the description of a new species from Saffine mountain: (Reptilia: Gekkonidae). Zoology in the Middle East, 47, 49–56.
   Web of Science ®Google Scholar
• Ahmadzadeh, F., Flecks, M., Carretero, M. A., Böhme, W., Ihlow, F., Kapli, P., … Rödder, D. (2016). Separate histories in both sides of the Mediterranean: Phylogeny and niche evolution of ocellated lizards. Journal of Biogeography, 43, 1242–1253.
   Web of Science ®Google Scholar
• Arnold, E. N. (1972). Lizards with northern affinities from the mountains of Oman. Zoologische Meded Leiden, 47, 111–128.
   Google Scholar
• Arnold, E. N. (1977). The scientific results of the Oman flora and fauna survey 1975. Little-known geckoes (Reptilia: Gekkonidae) from Arabia with descriptions of two new species from the Sultanate of Oman. Journal of Oman Studies Special Report, 1, 81–110.
   Google Scholar
• Arnold, E. N. (1986). A key and annotated checklist to the lizards and amphisbaenians of Arabia. Fauna of Saudi Arabia, 8, 385–435.
   Google Scholar
• Arnold, E. N., & Gallagher, M. D. (1977). The scientific results of the Oman flora and fauna survey 1975. Reptiles and amphibians from the mountains of northern Oman with special reference to the Jebel Akhdar region. Journal of Oman Studies Special Report, 1, 59–80.
   Google Scholar
• Arnold, E. N., & Gardner, A. S. (1994). A review of the middle eastern leaf-toed geckoes (Gekkonidae: Asaccus) with descriptions of two new species from Oman. Fauna of Saudi Arabia, 14, 424–441.
   Google Scholar
• Badiane, A., Garcia-Porta, J., Červenka, J., Kratochvíl, L., Sindaco, R., Robinson, M. D., … Carranza, S. (2014). Phylogenetic relationships of Semaphore geckos (Squamata: Sphaerodactylidae: Pristurus) with an assessment of the taxonomy of Pristurus rupestris. Zootaxa, 3835, 33–58.
   PubMed Web of Science ®Google Scholar
• Balletto, E., Cherchi, M. A., & Gasperetti, J. (1985). Amphibians of the Arabian Peninsula. Fauna of Saudi Arabia, 7, 318–392.
   Google Scholar
• Blonder, B., Lamanna, C., Violle, C., & Enquist, B. J. (2014). The n‐dimensional hypervolume. Global Ecology and Biogeography, 23, 595–609.
   Web of Science ®Google Scholar
• Bosworth, W., Huchon, P., & McClay, K. (2005). The Red Sea and Gulf of Aden Basins. Journal of African Earth Sciences, 43, 334–378.
   Web of Science ®Google Scholar
• Brinkmann, K., Patzelt, A., Dickhoefer, U., Schlecht, E., & Buerkert, A. (2009). Vegetation patterns and diversity along an altitudinal and a grazing gradient in the Jabal al Akhdar mountain range of northern Oman. Journal of Arid Environments, 73, 1035–1045.
   Web of Science ®Google Scholar
• Busais, S., & Joger, U. (2011a). Molecular phylogeny of the gecko genus Hemidactylus Oken, 1817 on the mainland of Yemen: (Reptilia: Gekkonidae). Zoology in the Middle East, 53, 25–34.
   Web of Science ®Google Scholar
• Busais, S. M., & Joger, U. (2011b). Three new species and one new subspecies of Hemidactylus Oken, 1817 from Yemen (Squamata, Gekkonidae). Vertebrate Zoology, 61, 267–280.
   Web of Science ®Google Scholar
• Carranza, S., & Arnold, E. N. (2012). A review of the gecko genus Hemidactylus (Squamata: Gekkonidae) from Oman based on morphology, mitochodrial and nuclear data, with descriptions of eight new species. Zootaxa, 95, 1–95.
   Google Scholar
• Carranza, S., Simó-Riudalbas, M., Jayasinghe, S., Wilms, T., & Els, J. (2016). 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). PeerJ, 4, e2371.
   PubMed Web of Science ®Google Scholar
• Clement, M., Posada, D., & Crandall, K. A. (2000). TCS: A computer program to estimate gene genealogies. Molecular Ecology, 9, 1657.
   PubMed Web of Science ®Google Scholar
• Dakhteh, S. M. H., Kami, H. G., & Anderson, S. C. (2007). Stenodactylus khobarensis (Haas, 1957): An addition to the Iranian herpetofauna (Reptilia: Squamata: Gekkonidae). Russian Journal of Herpetology, 14, 229–231.
   Google Scholar
• de Pous, P., Machado, L., Metallinou, M., Červenka, J., Kratochvíl, L., Paschou, N., … Carranza, S. (2016a). Taxonomy and biogeography of Bunopus spatalurus (Reptilia; Gekkonidae) from the Arabian Peninsula. Journal of Zoological Systematics and Evolutionary Research, 54, 67–81.
   Web of Science ®Google Scholar
• de Pous, P., Simó-Riudalbas, M., Els, J., Jayasinghe, S., Amat, F., & Carranza, S. (2016b). Phylogeny and biogeography of Arabian populations of the Persian Horned Viper Pseudocerastes persicus (Duméril, Bibron & Duméril, 1854). Zoology in the Middle East, 62, 231–238.
   Web of Science ®Google Scholar
• de Queiroz, K. (1998). The general lineage concept of species, species criteria, and the process of speciation: A conceptual unification and terminological recommendations. In D. J. Howard & S. H. Berlocher (Eds.), Endless forms: Species and speciation (pp. 57–75). Oxford: Oxford University Press.
   Google Scholar
• de Queiroz, K. (2007). Species concepts and species delimitation. Systematic Biology, 56, 879–886.
   PubMed Web of Science ®Google Scholar
• Dixon, J. R., & Anderson, S. C. (1973). A new genus and species of gecko (Sauria: Gekkonidae) from Iran and Iraq. Bulletin of the Southern California Academy of Sciences, 72, 155–160.
   Google Scholar
• Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012). Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969–1973.
   PubMed Web of Science ®Google Scholar
• Edgell, H. S. (2006). Arabian deserts: Nature, origin and evolution. Springer Science & Business Media.
   Google Scholar
• Ezard, T., Fujisawa, T., & Barraclough, T. G. (2009). Splits: Species’ limits by threshold statistics. R package version, 1.0-19/r51. Retrieved from http://R-Forge.R-project.org/projects/splits/ (accessed 7 November 2017).
   Google Scholar
• Felsenstein, J. (1985). Confidence-limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783.
   PubMed Web of Science ®Google Scholar
• Flot, J. F. (2010). Seqphase: A web tool for interconverting phase input/output files and fasta sequence alignments. Molecular Ecology Resources, 10, 162–166.
   PubMed Web of Science ®Google Scholar
• Fujisawa, T., & Barraclough, T. G. (2013). Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: A revised method and evaluation on simulated data sets. Systematic Biology, 62, 707–24.
   PubMed Web of Science ®Google Scholar
• Gamble, T., Bauer, A. M., Colli, G. R., Greenbaum, E., Jackman, T. R., Vitt, L. J., & Simons, A. M. (2011). Coming to America: Multiple origins of New World geckos. Journal of Evolutionary Biology, 24, 231–244.
   PubMed Web of Science ®Google Scholar
• Gamble, T., Bauer, A. M., Greenbaum, E., & Jackman, T. R. (2008). Evidence for Gondwanan vicariance in an ancient clade of gecko lizards. Journal of Biogeography, 35, 88–104.
   Web of Science ®Google Scholar
• Gamble, T., Greenbaum, E., Jackman, T. R., & Bauer, A. M. (2015). Into the light: Diurnality has evolved multiple times in geckos. Biological Journal of the Linnean Society, 115, 896–910.
   Web of Science ®Google Scholar
• Gamble, T., Greenbaum, E., Jackman, T. R., Russell, A. P., & Bauer, A. M. (2012). Repeated origin and loss of adhesive toepads in geckos. Public Library of Science ONE, 7, e39429.
   Google Scholar
• Garcia-Porta, J., Morales, H. E., Gómez-Díaz, E., Sindaco, R., & Carranza, S. (2016). Patterns of diversification in islands: A comparative study across three gecko genera in the Socotra Archipelago. Molecular Phylogenetics and Evolution, 98, 288–299.
   PubMed Web of Science ®Google Scholar
• Garcia-Porta, J., Simó‐Riudalbas, M., Robinson, M., & Carranza, S. (2017). Diversification in arid mountains: Biogeography and cryptic diversity of Pristurus rupestris rupestris in Arabia. Journal of Biogeography, 44, 1694–1704.
   Web of Science ®Google Scholar
• Gardner, A. (1999). The Reptiles and Amphibians of Oman: Herpetological history and current status. In The Natural History of Oman: A Festschrift for Michael Gallagher (pp. 65–88). Leiden: Backhuys Publishers.
   Google Scholar
• Gardner, A. S. (1994). A new species of Asaccus (Gekkonidae) from the mountains of northern Oman. Journal of Herpetology, 28, 141–145.
   Web of Science ®Google Scholar
• Gardner, A. S. (2013). The Amphibians and Reptiles of Oman and the UAE. Frankfurt am Main: Chimaira.
   Google Scholar
• Gasperetti, J. (1988). Snakes of Arabia. Fauna of Saudi Arabia, 9, 169–450.
   Google Scholar
• Gasperetti, J., Stimson, A. F., Miller, J. D., Ross, J. P., & Gasperetti, P. R. (1993). Turtles of Arabia. Fauna of Saudi Arabia, 13, 70–367.
   Google Scholar
• Ghazanfar, S. A. (1991). Vegetation structure and phytogeography of Jabal Shams, an arid mountain in Oman. Journal of Biogeography, 18, 299–309.
   Web of Science ®Google Scholar
• Glennie, K. (2006). Oman's Geological Heritage. London: Stacey International Publishers.
   Google Scholar
• Gómez-Díaz, E., Sindaco, R., Pupin, F., Fasola, M., & Carranza, S. (2012). Origin and in situ diversification in Hemidactylus geckos of the Socotra Archipelago. Molecular Ecology, 21, 4074–4092.
   PubMed Web of Science ®Google Scholar
• Harrigan, R. J., Mazza, M. E., & Sorenson, M. D. (2008). Computation vs. cloning: Evaluation of two methods for haplotype determination. Molecular Ecology Resources, 8, 1239–1248.
   PubMed Web of Science ®Google Scholar
• Harrison, D. (1976). The Oman Flora and Fauna Survey 1975. Journal of Oman Studies, 1, 181–186.
   Google Scholar
• Harrison, D. (1977). The scientific results of the Oman Flora and Fauna Survey 1975. Journal of Oman Studies Special Report, 1, 10–11.
   Google Scholar
• Hawlitschek, O., & Glaw, F. (2013). The complex colonization history of nocturnal geckos (Paroedura) in the Comoros Archipelago. Zoologica Scripta, 42, 135–150.
   Web of Science ®Google Scholar
• Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G., & Jarvis, A. (2005). Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965–1978.
   Web of Science ®Google Scholar
• Huelsenbeck, J. P., & Rannala, B. (2004). Frequentist properties of bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology, 53, 904–913.
   PubMed Web of Science ®Google Scholar
• Kapli, P., Lymberakis, P., Crochet, P., Geniez, P., Brito, J. C., Almutairi, M., … Poulakakis, N. (2015). Historical biogeography of the lacertid lizard Mesalina in North Africa and the Middle East. Journal of Biogeography, 42, 267–279.
   Web of Science ®Google Scholar
• Kapli, P., Lymberakis, P., Poulakakis, N., Mantziou, G., Parmakelis, A., & Mylonas, M. (2008). Molecular phylogeny of three Mesalina (Reptilia: Lacertidae) species (M. guttulata, M. brevirostris and M. bahaeldini) from North Africa and the Middle East: Another case of paraphyly? Molecular Phylogenetics and Evolution, 49, 102–110.
   PubMed Web of Science ®Google Scholar
• Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30, 772–780.
   PubMed Web of Science ®Google Scholar
• Krause, V., Ahmadzadeh, F., Moazeni, M., Wagner, P., & Wilms, T. M. (2013). A new species of the genus Tropiocolotes Peters, 1880 from western Iran (Squamata: Sauria: Gekkonidae). Zootaxa, 3716, 22–38.
   PubMed Web of Science ®Google Scholar
• Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874.
   PubMed Web of Science ®Google Scholar
• Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., & Calcott, B. (2016). PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution, 34, 772–773.
   Web of Science ®Google Scholar
• Lemey, P., Rambaut, A., Drummond, A. J., & Suchard, M. A. (2009). Bayesian phylogeography finds its roots. Public Library of Science Computational Biology, 5, e1000520.
   PubMed Web of Science ®Google Scholar
• Mandaville, J. (1977). The scientific results of the Oman flora and fauna survey 1975. Plants. Journal Oman Studies Special Report, 1, 229–267.
   Google Scholar
• Metallinou, M., Arnold, E. N., Crochet, P.-A., Geniez, P., Brito, J. C., Lymberakis, P., … Carranza, S. (2012). Conquering the Sahara and Arabian deserts: Systematics and biogeography of Stenodactylus geckos (Reptilia: Gekkonidae). BioMed Central Evolutionary Biology, 12, 1–17.
   PubMed Web of Science ®Google Scholar
• Metallinou, M., & Carranza, S. (2013). New species of Stenodactylus (Squamata: Gekkonidae) from the Sharqiyah Sands in northeastern Oman. Zootaxa, 3745, 449–468.
   PubMed Web of Science ®Google Scholar
• Metallinou, M., Červenka, J., Crochet, P.-A., Kratochvíl, L., Wilms, T., Geniez, P., … Carranza, S. (2015). Species on the rocks: Systematics and biogeography of the rock-dwelling Ptyodactylus geckos (Squamata: Phyllodactylidae) in North Africa and Arabia. Molecular Phylogenetics and Evolution, 85, 208–220.
   PubMed Web of Science ®Google Scholar
• Metallinou, M., Vasconcelos, R., Šmíd, J., Sindaco, R., & Carranza, S. (2014). Filling in the gap: Two new records and an updated distribution map for the Gulf Sand gecko Pseudoceramodactylus khobarensis Haas, 1957. Biodiversity Data Journal. 2, e4011. doi:10.3897/BDJ.2.e4011
   Google Scholar
• Milá, B., Surget-Groba, Y., Heulin, B., Gosá, A., & Fitze, P. S. (2013). Multilocus phylogeography of the common lizard Zootoca vivipara at the Ibero-Pyrenean suture zone reveals lowland barriers and high-elevation introgression. BioMed Central Evolutionary Biology, 13, 1.
   PubMed Web of Science ®Google Scholar
• Papenfuss, T. J., Jackman, T. R., Bauer, A. M., Stuart, B. L., Robinson, M. D., & Parham, J. F. (2010). Phylogenetic relationships amongst species of Southwest Asian Leaf-toed geckos (Asaccus). Proceedings of the California Academy of Sciences, 61, 587–596.
   Google Scholar
• Pons, J., Barraclough, T. G., Gomez-Zurita, J., Cardoso, A., Duran, D. P., Hazell, S., … Vogler, A. P. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55, 595–609.
   PubMed Web of Science ®Google Scholar
• R Development Core Team. (2016 ). R: A language and environment for statistical computing. Vienna: The R Foundation for Statistical Computing. ISBN: 3-900051-07-0. http://www.R-project.org/ (accessed 5 December 2017).
   Google Scholar
• Rambaut, A., Suchard, M. A., Xie, D., & Drummond, A. J. (2014). Tracer v1.6. Retrieved from http://beast.bio.ed.ac.uk/Tracer (accessed 7 November 2017).
   Google Scholar
• Rastegar-Pouyani, N. (1996). A new species of Asaccus (Sauria: Gekkonidae) from the Zagros mountains, Kermanshahan province, western Iran. Russian Journal of Herpetology, 3, 11–17.
   Google Scholar
• Rastegar-Pouyani, N., Nilson, G., & Faizi, H. (2006). A new species of Asaccus (Sauria: Gekkonidae) from Kurdistan province, western Iran. Hamadryad, 30, 141–150.
   Google Scholar
• Reid, N. M., & Carstens, B. C. (2012). Phylogenetic estimation error can decrease the accuracy of species delimitation: A Bayesian implementation of the general mixed Yule-coalescent model. BioMed Central Evolutionary Biology, 12, 196.
   PubMed Web of Science ®Google Scholar
• Silvestro, D., & Michalak, I. (2012). raxmlGUI: A graphical front-end for RAxML. Organisms Diversity & Evolution, 12, 335–337.
   Web of Science ®Google Scholar
• Simó-Riudalbas, M., Metallinou, M., de Pous, P., Els, J., Jayasinghe, S., Péntek-Zakar, … Carranza, S. (2017). Cryptic diversity in Ptyodactylus (Reptilia: Gekkonidae) from the northern Hajar Mountains of Oman and the United Arab Emirates uncovered by an integrative taxonomic approach. Public Library of Science ONE, 12, e0180397.
   Google Scholar
• Sindaco, R., Metallinou, M., Pupin, F., Fasola, M., & Carranza, S. (2012). Forgotten in the ocean: Systematics, biogeography and evolution of the Trachylepis skinks of the Socotra Archipelago. Zoologica Scripta, 41, 346–362.
   Web of Science ®Google Scholar
• Šmíd, J., Carranza, S., Kratochvíl, L., Gvoždík, V., Nasher, A. K., & Moravec, J. (2013). Out of Arabia: A complex biogeographic history of multiple vicariance and dispersal events in the Gecko Genus Hemidactylus (Reptilia: Gekkonidae). Public Library of Science ONE, 8, e64018.
   Google Scholar
• Šmíd, J., Moravec, J., Kratochvíl, L., Nasher, A. K., Mazuch, T., Gvoždík, V., & Carranza, S. (2015). Multilocus phylogeny and taxonomic revision of the Hemidactylus robustus species group (Reptilia, Gekkonidae) with descriptions of three new species from Yemen and Ethiopia. Systematics and Biodiversity, 13, 346–368.
   Web of Science ®Google Scholar
• Šmíd, J., Shobrak, M., Wilms, T., Joger, U., & Carranza, S. (2016). Endemic diversification in the mountains: Genetic, morphological, and geographical differentiation of the Hemidactylus geckos in southwestern Arabia. Organisms Diversity & Evolution, 17, 267–2865.
   Web of Science ®Google Scholar
• Stamatakis, A. (2006). RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688–2690.
   PubMed Web of Science ®Google Scholar
• Stephens, M., Smith, N. J., & Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. The American Journal of Human Genetics, 68, 978–989.
   PubMed Web of Science ®Google Scholar
• Tamar, K., Carranza, S., Sindaco, R., Moravec, J., Trape, J.-F., & Meiri, S. (2016a). Out of Africa: Phylogeny and biogeography of the widespread genus Acanthodactylus (Reptilia: Lacertidae). Molecular Phylogenetics and Evolution, 103, 6–18.
   PubMed Web of Science ®Google Scholar
• Tamar, K., Scholz, S., Crochet, P.-A., Geniez, P., Meiri, S., Schmitz, A., … Carranza, S. (2016b). Evolution around the red sea: Systematics and biogeography of the agamid genus Pseudotrapelus (Squamata: Agamidae) from North Africa and Arabia. Molecular Phylogenetics and Evolution, 97, 55–68.
   PubMed Web of Science ®Google Scholar
• Tamar, K., Šmíd, J., Göçmen, B., Meiri, S., & Carranza, S. (2016c). An integrative systematic revision and biogeography of Rhynchocalamus snakes (Reptilia, Colubridae) with a description of a new species from Israel. PeerJ, 4, e2769.
   PubMed Web of Science ®Google Scholar
• Torki, F. (2010). Beschreibung eines neuen Asaccus (Reptilia: Phyllodactylidae) aus der Provinz Lorestan, Iran. Sauria, 32, 3–16.
   Google Scholar
• Torki, F., Ahmadzadeh, F., Ilgaz, Ç., Avcı, A., & Kumlutaş, Y. (2011a). Description of four new Asaccus Dixon and Anderson, 1973 (Reptilia: Phyllodactylidae) from Iran and Turkey. Amphibia-Reptilia, 32, 185–202.
   Web of Science ®Google Scholar
• Torki, F., Fathinia, B., Rostami, H. A., Gharzi, A., & Nazari-Serenjeh, F. (2011b). Beschreibung eines neuen Asaccus (Sauria: Phyllodactylidae) aus dem Iran. Sauria, 33, 51–62.
   Google Scholar
• Uetz, P., Goll, J., & Hallerman, J. (2017). The reptile database. Retrieved from http://www.reptile–database.org (accessed 24 March 2016).
   Google Scholar
• Vasconcelos, R., & Carranza, S. (2014). Systematics and biogeography of Hemidactylus homoeolepis Blanford, 1881 (Squamata: Gekkonidae), with the description of a new species from Arabia. Zootaxa, 3835, 501–527.
   PubMed Web of Science ®Google Scholar
• Warren, D. L., Glor, R. E., & Turelli, M. (2008). Environmental niche equivalency versus conservatism: Quantitative approaches to niche evolution. Evolution, 62, 2868–2883.
   PubMed Web of Science ®Google Scholar
• Werner, Y. (2006). Retraction of Ptyodactylus Goldfuss from the fauna of Iran and its replacement by a new species of Asaccus Dixon and Anderson (Reptilia: Sauria: Gekkonidae). Hamadryad, 30, 135–140.
   Google Scholar
• Wilcox, T. P., Zwickl, D. J., Heath, T. A., & Hillis, D. M. (2002). Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution, 25, 361–371.
   PubMed Web of Science ®Google Scholar
• Yousofi, S., Rastegar-Pouyani, E., & Hojati, V. (2015). Phylogenetic relationships amongst populations of Pristurus rupestris Blanford, 1874 (Sauria: Sphaerodactylidae) in southern Iran. Turkish Journal of Zoology, 39, 1–6.
   Web of Science ®Google Scholar