Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny.

Slade, Robert; Moritz, Craig; Heideman, A.

doi:10.1093/oxfordjournals.molbev.a040117

Cited by 45 publications

(8 citation statements)

References 36 publications

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“…Indeed, the genome of the Weddell seal (family Phocidae ) has not been completed ( http://software.broadinstitute.org/allpaths-lg/blog/?p=647 ). In addition, most phylogenetic studies of pinnipeds have used limited marker sequences, such as that of the mitochondrial genome 10 – 12 .…”

Section: Introductionmentioning

confidence: 99%

Deciphering the evolutionary signatures of pinnipeds using novel genome sequences: The first genomes of Phoca largha, Callorhinus ursinus, and Eumetopias jubatus

Park

Kim

Sohn

et al. 2018

Sci Rep

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The pinnipeds, which comprise seals, sea lions, and walruses, are a remarkable group of marine animals with unique adaptations to semi-aquatic life. However, their genomes are poorly characterized. In this study, we sequenced and characterized the genomes of three pinnipeds (Phoca largha, Callorhinus ursinus, and Eumetopias jubatus), focusing on site-wise sequence changes. We detected rapidly evolving genes in pinniped lineages and substitutions unique to pinnipeds associated with amphibious sound perception. Phenotypic convergence-related sequence convergences are not common in marine mammals. For example, FASN, KCNA5, and IL17RA contain substitutions specific to pinnipeds, yet are potential candidates of phenotypic convergence (blubber, response to hypoxia, and immunity to pathogens) in all marine mammals. The outcomes of this study will provide insight into targets for future studies of convergent evolution or gene function.

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Section: Introductionmentioning

confidence: 99%

Deciphering the evolutionary signatures of pinnipeds using novel genome sequences: The first genomes of Phoca largha, Callorhinus ursinus, and Eumetopias jubatus

Park

Kim

Sohn

et al. 2018

Sci Rep

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show abstract

“…Intron sequences, while not obviously functional, are not junk DNA [15] and affect a number of eukaryotic gene expression pathways [16]–[18]. However, they are considered largely neutral [19], [20] and tend to accumulate informative mutations across sites more equally, with less homoplasy, and lower transition∶transversion ratios than coding regions [21]–[23]. Priming within the exon region allows for relatively robust primer design and enhances the ability for primers to be used across closely related taxa.…”

Section: Introductionmentioning

confidence: 99%

Next-Generation Phylogeography: A Targeted Approach for Multilocus Sequencing of Non-Model Organisms

2012

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The field of phylogeography has long since realized the need and utility of incorporating nuclear DNA (nDNA) sequences into analyses. However, the use of nDNA sequence data, at the population level, has been hindered by technical laboratory difficulty, sequencing costs, and problematic analytical methods dealing with genotypic sequence data, especially in non-model organisms. Here, we present a method utilizing the 454 GS-FLX Titanium pyrosequencing platform with the capacity to simultaneously sequence two species of sea star (Meridiastra calcar and Parvulastra exigua) at five different nDNA loci across 16 different populations of 20 individuals each per species. We compare results from 3 populations with traditional Sanger sequencing based methods, and demonstrate that this next-generation sequencing platform is more time and cost effective and more sensitive to rare variants than Sanger based sequencing. A crucial advantage is that the high coverage of clonally amplified sequences simplifies haplotype determination, even in highly polymorphic species. This targeted next-generation approach can greatly increase the use of nDNA sequence loci in phylogeographic and population genetic studies by mitigating many of the time, cost, and analytical issues associated with highly polymorphic, diploid sequence markers.

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“…The second mtDNA sequence was a 456 bp fragment of the control region of D-loop ( DLOOP ). The primers used were forward TDKD [ 31 ] ( ) and reverse L15926 [ 32 ] ( ). The 12.5 μL reaction volume contained: 1 μL tDNA, 4 pmol of each primer, 2 mM of MgCl 2 , 0.6 U of Taq polymerase (Thermo Scientific ™ ), 0.2 mM of each dNTP, reaction buffer (Thermo Scientific ™ ).…”

Section: Methodsmentioning

confidence: 99%

New data on Weddell seal (Leptonychotes weddellii) colonies: A genetic analysis of a top predator from the Ross Sea, Antarctica

et al. 2017

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In this paper, we studied the genetic variability in Weddell seal from colonies in Terra Nova Bay and Wood Bay, both sites located in the Ross Sea area, Antarctica. Two mitochondrial genes and one nuclear gene, with different mutation rates, were sequenced to investigate the haplotype diversity of the colonies and to test for a possible recent expansion. Fifteen microsatellites were used to analyze their genetic structure. Sequenced genes and microsatellites were also used to estimate the effective population size of the studied colonies and the Ross Sea seal population. The Ross Sea has a high density population of Weddel seals, with an estimated effective number of 50,000 females, and 1,341 individuals for the sampling area, possibly due to its high primary production. The colonies showed high diversity (Hd > 0.90) and many exclusive haplotypes (> 75%), likely a consequence of the surprisingly high site fidelity of Weddell seals, despite the proximity of the colonies. Nevertheless, there was low microsatellite differentiation between colonies, suggesting that they are part of a single larger population. Their expansion seemed to have started during the last glacial cycle (around 58,000 years ago), indicating that the Ross Sea seal populations have been present in the area for long time, probably due to the lack of hunting by humans and terrestrial predation. As a top predator, the role of Weddell seals in the Ross Sea ecology is crucial, and its demographic dynamics should be monitored to follow the future changes of such an important ecosystem.

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Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny.

Cited by 45 publications

References 36 publications

Deciphering the evolutionary signatures of pinnipeds using novel genome sequences: The first genomes of Phoca largha, Callorhinus ursinus, and Eumetopias jubatus

Deciphering the evolutionary signatures of pinnipeds using novel genome sequences: The first genomes of Phoca largha, Callorhinus ursinus, and Eumetopias jubatus

Next-Generation Phylogeography: A Targeted Approach for Multilocus Sequencing of Non-Model Organisms

New data on Weddell seal (Leptonychotes weddellii) colonies: A genetic analysis of a top predator from the Ross Sea, Antarctica

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