2018
DOI: 10.1016/j.mgene.2017.10.003
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Mitochondrial recovery from shotgun metagenome sequencing enabling phylogenetic analysis of the common thresher shark (Alopias vulpinus)

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Cited by 14 publications
(17 citation statements)
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“…This might be the result of the heavy pruning of these clades whose relationships were not well supported in the original tree either and, according to the authors, needed further exploration. In contrast to the original tree of Naylor et al () in which the genus Alopias did not represent a monophyletic group, we decided to treat this clade as a monophyly, since this is supported by previous molecular analyses based on cytochrome b (Martin & Naylor, )) and whole mitochondrial genomes (Doane et al ), as well as morphological analyses (Compagno, ; Shimada, ). The topology of the resulting tree was used for stochastic character mapping with the make.simmap function in phytools (Revell, ) to perform ancestral state reconstructions of the three different tooth histotypes.…”
Section: Methodsmentioning
confidence: 99%
“…This might be the result of the heavy pruning of these clades whose relationships were not well supported in the original tree either and, according to the authors, needed further exploration. In contrast to the original tree of Naylor et al () in which the genus Alopias did not represent a monophyletic group, we decided to treat this clade as a monophyly, since this is supported by previous molecular analyses based on cytochrome b (Martin & Naylor, )) and whole mitochondrial genomes (Doane et al ), as well as morphological analyses (Compagno, ; Shimada, ). The topology of the resulting tree was used for stochastic character mapping with the make.simmap function in phytools (Revell, ) to perform ancestral state reconstructions of the three different tooth histotypes.…”
Section: Methodsmentioning
confidence: 99%
“…Such studies have the potential to also provide insight into the host's genomics. For example, shotgun sequencing of community DNA from the skin of the common thresher allowed reconstruction of the host mitochondrial genome, helping to clarify the position of this species in the elasmobranch phylogeny [129]. Metagenomic analysis can also characterize other microbiome members, potentially including fungi, other small eukaryotic organisms, and viruses.…”
Section: Discussionmentioning
confidence: 99%
“…Microbiome samples from the sharks were collected using a microbial collection tool, which flushes the epidermis with ~250 ml of sterile seawater and dislodges the microbes. The microbial slurry is collected into the back end of the microbial tool, as we have conducted previously (Doane et al 2017;Doane et al 2018;Doane et al 2020;Johri et al 2019;Lima et al 2020). Each epidermal microbiome sample was taken from the flank region below the dorsal fin and above the lateral line.…”
Section: Epidermal Microbiome Samplingmentioning
confidence: 99%