8
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Phylogenetic relationships and biogeographic range evolution in cat-eyed snakes, Boiga (Serpentes: Colubridae)

      Read this article at

      ScienceOpenPublisher
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The genus Boiga includes 35, primarily arboreal snake species distributed from the Middle East to Australia and many islands in the western Pacific, with particularly high species diversity in South-East Asia. Despite including the iconic mangrove snakes (Boiga dendrophila complex) and the brown tree snake (Boiga irregularis; infamous for avian extinctions on small islands of the Pacific), species-level phylogenetic relationships and the biogeographic history of this ecologically and morphologically distinct clade are poorly understood. In this study, we sequenced mitochondrial and nuclear DNA for 24 Boiga species and used these data to estimate a robust phylogenetic inference, in order to (1) test the hypothesis that Boiga is monophyletic, (2) evaluate the validity of current species-level taxonomy and (3) examine whether geographic range evolution in Boiga is consistent with expectations concerning dispersal and colonization of vertebrates between continents and islands. Our results support the prevailing view that most dispersal events are downstream – from continents to oceanic islands – but we also identify a role for upstream dispersal from oceanic islands to continents. Additionally, the novel phylogeny of Boiga presented here is informative for updating species-level taxonomy within the genus.

          Related collections

          Most cited references103

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

          Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            MUSCLE: multiple sequence alignment with high accuracy and high throughput.

            We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              A new look at the statistical model identification

              IEEE Transactions on Automatic Control, 19(6), 716-723
                Bookmark

                Author and article information

                Journal
                Zoological Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4082
                1096-3642
                May 01 2021
                April 30 2021
                August 15 2020
                May 01 2021
                April 30 2021
                August 15 2020
                : 192
                : 1
                : 169-184
                Affiliations
                [1 ]Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
                [2 ]Department of Biology, University of Hawai’i at Mānoa, Honolulu, HI, USA
                [3 ]Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
                [4 ]Zoological Institute, Russian Academy of Science, Universitetskaya nab., St. Petersburg, Russia
                [5 ]Department of Biological Sciences, Auburn University, Auburn, AL, USA
                [6 ]Department of Herpetology, American Museum of Natural History, New York, NY, USA
                Article
                10.1093/zoolinnean/zlaa090
                d0daa146-99e9-438e-9a6f-661a8bfae59e
                © 2020

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

                History

                Comments

                Comment on this article