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      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)

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          Abstract

          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.

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          Most cited references53

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          Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.

          T Wilcox (2002)
          Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxocemus and Xenopeltis. Additionally, uropeltids cluster strongly with Cylindrophis, and together are embedded in what has previously been considered the macrostomatan radiation. These relationships are supported by both bootstrapping (parametric and nonparametric approaches) and Bayesian analysis, although Bayesian support values are consistently higher than those obtained from nonparametric bootstrapping. Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study. Copyright 2002 Elsevier Science (USA)
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            New approaches for unravelling reassortment pathways

            Background Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment. Results The current work describes the implementation of two approaches for robustly identifying reassortment events. The algorithms rest on the idea of significance of difference between phylogenetic trees or phylogenetic tree sets, and subtree pruning and regrafting operations, which mimic the effect of reassortment on tree topologies. The first method is based on a maximum likelihood (ML) framework (MLreassort) and the second implements a Bayesian approach (Breassort) for reassortment detection. We focus on reassortment events that are found by both methods. We test both methods on a simulated dataset and on a small collection of real viral data isolated in Hong Kong in 1999. Conclusions The nature of segmented viral genomes present many challenges with respect to disease. The algorithms developed here can effectively identify reassortment events in small viral datasets and can be applied not only to influenza but also to other segmented viruses. Owing to computational demands of comparing tree topologies, further development in this area is necessary to allow their application to larger datasets.
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              seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments.

              J-F Flot (2009)
              The program phase is widely used for Bayesian inference of haplotypes from diploid genotypes; however, manually creating phase input files from sequence alignments is an error-prone and time-consuming process, especially when dealing with numerous variable sites and/or individuals. Here, a web tool called seqphase is presented that generates phase input files from fasta sequence alignments and converts phase output files back into fasta. During the production of the phase input file, several consistency checks are performed on the dataset and suitable command line options to be used for the actual phase data analysis are suggested. seqphase was written in perl and is freely accessible over the Internet at the address http://www.mnhn.fr/jfflot/seqphase. © 2009 Blackwell Publishing Ltd.
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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                peerj
                peerj
                PeerJ
                PeerJ Inc. (San Francisco, USA )
                2167-8359
                18 August 2016
                2016
                : 4
                : e2371
                Affiliations
                [1 ]Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Pompeu Fabra University) , Barcelona, Spain
                [2 ]Herpetology and Freshwater Fishes, Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority , Al Sharjah, United Arab Emirates
                [3 ]Allwetterzoo Münster , Münster, Germany
                Article
                2371
                10.7717/peerj.2371
                4994081
                27602305
                dd708eaf-3c9d-42c2-99cc-36422cb13a76
                ©2016 Carranza et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 9 June 2016
                : 26 July 2016
                Funding
                Funded by: Ministerio de Economía y Competitividad
                Award ID: CGL2012-36970
                Award ID: CGL2015-70390-P
                Award ID: BES-2013-064248
                Funded by: Ministry of Environment and Climate Affairs
                Award ID: 22412027
                Funded by: Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya
                Award ID: 2014-SGR-1532
                This work was funded by grants CGL2012-36970, CGL2015-70390-P from the Ministerio de Economía y Competitividad, Spain (cofunded by FEDER), the project ‘Field study for the conservation of reptiles in Oman’, Ministry of Environment and Climate Affairs, Oman (Ref: 22412027) and grant 2014-SGR-1532 from the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya. MSR is funded by a FPI grant from the Ministerio de Economía y Competitividad, Spain (BES-2013-064248). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Biodiversity
                Biogeography
                Evolutionary Studies
                Taxonomy
                Zoology

                phylogeny,systematics,arabia,diversification,reptiles,speciation,taxonomy,evolution,mountains,biogeography

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