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      Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology

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          Abstract

          Abstract

          Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutionary biogeography of southern phocids, the relationships of M. tropicalis to the two living species of critically endangered monk seals have not been resolved. In this study we present the first molecular data for M. tropicalis, derived from museum skins. Phylogenetic analysis of cytochrome b sequences indicates that M. tropicalis was more closely related to the Hawaiian rather than the Mediterranean monk seal. Divergence time estimation implicates the formation of the Panamanian Isthmus in the speciation of Caribbean and Hawaiian monk seals. Molecular, morphological and temporal divergence between the Mediterranean and “New World monk seals” (Hawaiian and Caribbean) is profound, equivalent to or greater than between sister genera of phocids. As a result, we classify the Caribbean and Hawaiian monk seals together in a newly erected genus, Neomonachus. The two genera of extant monk seals ( Monachus and Neomonachus) represent old evolutionary lineages each represented by a single critically endangered species, both warranting continuing and concerted conservation attention and investment if they are to avoid the fate of their Caribbean relative.

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          Most cited references53

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          The conditioned reconstructed process.

          We investigate a neutral model for speciation and extinction, the constant rate birth-death process. The process is conditioned to have n extant species today, we look at the tree distribution of the reconstructed trees--i.e. the trees without the extinct species. Whereas the tree shape distribution is well-known and actually the same as under the pure birth process, no analytic results for the speciation times were known. We provide the distribution for the speciation times and calculate the expectations analytically. This characterizes the reconstructed trees completely. We will show how the results can be used to date phylogenies.
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            Bayesian selection of continuous-time Markov chain evolutionary models.

            We develop a reversible jump Markov chain Monte Carlo approach to estimating the posterior distribution of phylogenies based on aligned DNA/RNA sequences under several hierarchical evolutionary models. Using a proper, yet nontruncated and uninformative prior, we demonstrate the advantages of the Bayesian approach to hypothesis testing and estimation in phylogenetics by comparing different models for the infinitesimal rates of change among nucleotides, for the number of rate classes, and for the relationships among branch lengths. We compare the relative probabilities of these models and the appropriateness of a molecular clock using Bayes factors. Our most general model, first proposed by Tamura and Nei, parameterizes the infinitesimal change probabilities among nucleotides (A, G, C, T/U) into six parameters, consisting of three parameters for the nucleotide stationary distribution, two rate parameters for nucleotide transitions, and another parameter for nucleotide transversions. Nested models include the Hasegawa, Kishino, and Yano model with equal transition rates and the Kimura model with a uniform stationary distribution and equal transition rates. To illustrate our methods, we examine simulated data, 16S rRNA sequences from 15 contemporary eubacteria, halobacteria, eocytes, and eukaryotes, 9 primates, and the entire HIV genome of 11 isolates. We find that the Kimura model is too restrictive, that the Hasegawa, Kishino, and Yano model can be rejected for some data sets, that there is evidence for more than one rate class and a molecular clock among similar taxa, and that a molecular clock can be rejected for more distantly related taxa.
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              Mitochondrial pseudogenes: evolution's misplaced witnesses.

              Nuclear copies of mitochondrial DNA (mtDNA) have contaminated PCR-based mitochondrial studies of over 64 different animal species. Since the last review of these nuclear mitochondrial pseudogenes (Numts) in animals, Numts have been found in 53 of the species studied. The recent evidence suggests that Numts are not equally abundant in all species, for example they are more common in plants than in animals, and also more numerous in humans than in Drosophila. Methods for avoiding Numts have now been tested, and several recent studies demonstrate the potential utility of Numt DNA sequences in evolutionary studies. As relics of ancient mtDNA, these pseudogenes can be used to infer ancestral states or root mitochondrial phylogenies. Where they are numerous and selectively unconstrained, Numts are ideal for the study of spontaneous mutation in nuclear genomes.
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                Author and article information

                Contributors
                Journal
                Zookeys
                Zookeys
                ZooKeys
                ZooKeys
                Pensoft Publishers
                1313-2989
                1313-2970
                2014
                14 May 2014
                : 409
                : 1-33
                Affiliations
                [1 ]Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
                [2 ]Division of Mammals, Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Ave, NW, Washington, DC 20560-0108, USA
                [3 ]Department of Paleobiology, Smithsonian Institution, National Museum of Natural History, 10th Street and Constitution Ave, NW, Washington, DC 20560-0108, USA
                [4 ]Department of Biological Sciences, Fordham University, 441 East Fordham Road, Bronx, NY 10458, USA
                [5 ]Marine Mammal Pathology Services, 19117 Bloomfield Road, Olney, MD 20832, USA
                Author notes
                Corresponding author: Alex D. Greenwood ( greenwood@ 123456izw-berlin.de ); Kristofer M. Helgen ( helgenk@ 123456si.edu )

                Academic editor: W. Bogdanowicz

                Article
                10.3897/zookeys.409.6244
                4042687
                09e744b8-b06c-4c74-9088-566733be97f1
                Dirk-Martin Scheel, Graham J. Slater, Sergios-Orestis Kolokotronis, Charles W. Potter, David S. Rotstein, Kyriakos Tsangaras, Alex D. Greenwood, Kristofer M. Helgen

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 13 September 2013
                : 19 April 2014
                Categories
                Research Article

                Animal science & Zoology
                ancient dna,extinction,mitochondrial dna,panamanian seaway,phocidae,systematics

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