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      Phylogeography of the Indo-West Pacific maskrays (Dasyatidae, Neotrygon): a complex example of chondrichthyan radiation in the Cenozoic

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          Abstract

          Maskrays of the genus Neotrygon (Dasyatidae) have dispersed widely in the Indo-West Pacific being represented largely by an assemblage of narrow-ranging coastal endemics. Phylogenetic reconstruction methods reproduced nearly identical and statistically robust topologies supporting the monophyly of the genus Neotrygon within the family Dasyatidae, the genus Taeniura being consistently basal to Neotrygon, and Dasyatis being polyphyletic to the genera Taeniurops and Pteroplatytrygon. The Neotrygon kuhlii complex, once considered to be an assemblage of color variants of the same biological species, is the most derived and widely dispersed subgroup of the genus. Mitochondrial (COI, 16S) and nuclear (RAG1) phylogenies used in synergy with molecular dating identified paleoclimatic fluctuations responsible for periods of vicariance and dispersal promoting population fragmentation and speciation in Neotrygon. Signatures of population differentiation exist in N. ningalooensis and N. annotata, yet a large-scale geological event, such as the collision between the Australian and Eurasian Plates, coupled with subsequent sea-level falls, appears to have separated a once homogeneous population of the ancestral form of N. kuhlii into southern Indian Ocean and northern Pacific taxa some 4–16 million years ago. Repeated climatic oscillations, and the subsequent establishment of land and shallow sea connections within and between Australia and parts of the Indo-Malay Archipelago, have both promoted speciation and established zones of secondary contact within the Indian and Pacific Ocean basins.

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          Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.

          A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even in low technology laboratories. The amount of tissue required by this method is approximately 50-100 mg. The quantity and the quality of the DNA extracted by this method is high enough to perform hundreds of PCR-based reactions and also to be used in other DNA manipulation techniques such as restriction digestion, Southern blot and cloning.
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            Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations

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              Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution.

              A mismatch distribution is a tabulation of the number of pairwise differences among all DNA sequences in a sample. In a population that has been stationary for a long time these distributions from nonrecombinant DNA sequences become ragged and erratic, whereas a population that has been growing generates mismatch distributions that are smooth and have a peak. The position of the peak reflects the time of the population growth. The signature of an ancient population expansion is apparent even in the low-resolution mtDNA typings described by Merriwether et al. (1991). The smoothness of the mismatch distribution, an indicator of population expansion, is hardly affected by population structure, whereas mean sequence divergence increases in a pooled sample from highly isolated subpopulations.
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                Author and article information

                Journal
                Ecol Evol
                Ecol Evol
                ece3
                Ecology and Evolution
                Blackwell Publishing Ltd
                2045-7758
                2045-7758
                February 2013
                20 December 2012
                : 3
                : 2
                : 217-232
                Affiliations
                [1 ]Institute for Marine and Antarctic Studies, University of Tasmania Private Bag 129, Hobart, TAS, 7001, Australia
                [2 ]Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research Castray Esplanade, Hobart, TAS, 7000, Australia
                [3 ]Australian Institute of Marine Science PMB No. 3, Townsville, QLD, 4810, Australia
                Author notes
                Melody Puckridge, IMAS, University of Tasmania, Private Bag 129, Hobart TAS 7001, Australia. Tel: +613-6232-5222; Fax: +613-6226-2973; E-mail: melodyp@ 123456utas.edu.au

                Funding Information This study received financial support through the University of Tasmania, the Commonwealth Environment Research Facilities (CERF) Marine Biodiversity Hub and the Australian Centre for International Agricultural Research (ACIAR).

                Article
                10.1002/ece3.448
                3586632
                23467194
                b413aaa1-45fe-4bb2-9124-a688b358a58d
                © 2013 Published by Blackwell Publishing Ltd.

                Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.

                History
                : 07 August 2012
                : 14 November 2012
                : 15 November 2012
                Categories
                Original Research

                Evolutionary Biology
                biodiversity hotspot,cryptic species,marine speciation,maskray,neotrygon,phylogeography

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