The value of updating GenBank accessions for supermatrix phylogeny: The case of the New Guinean marsupial carnivore genus Myoictis

Phillips, Matthew J.; Westerman, Michael; Cascini, Manuela

doi:10.1016/j.ympev.2021.107328

Cited by 5 publications

(8 citation statements)

References 22 publications

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“…Finally, we encourage subsequent authors to perform similar comparisons between their newly generated data and those that have been previously generated to identify sequences that may be problematic, as has been shown here and in Phillips et al . (2021) and Tang et al . (2021).…”

Section: Discussionmentioning

confidence: 97%

“…(2021) and Phillips et al . (2021) highlight similar sets of mislabelled or misidentified sequences housed in public repositories for damselfishes (Pomacanthidae) and the marsupial genus Myoictis , respectively. Phillips et al .…”

Section: Discussionmentioning

confidence: 99%

“…Phillips et al . (2021) highlighted the current inability to flag or otherwise denote anomalous sequences in public repositories outside of contacting and having the sequence(s)‐submitting author(s) agree to make revisions. We echo the call to GenBank by Phillips et al .…”

Section: Discussionmentioning

confidence: 99%

“…We echo the call to GenBank by Phillips et al . (2021) and make a similar call to BOLD to allow for a flexible protocol to flag or denote anomalous sequences. This is equally critical for both databases, particularly as BOLD incorporates mitochondrial sequences from GenBank and direct links between the two databases are available for some sequences.…”

Section: Discussionmentioning

confidence: 99%

“…While such a revisionary protocol presents many challenges, such as the required level of verification needed to obtain a flag and how these flags are shown on the website, some of which are discussed with possible solutions by Phillips et al . (2021), such a system will only improve the utility of these databases and allow for the dissemination of the most accurate data possible.…”

Section: Discussionmentioning

confidence: 99%

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Molecular phylogeny of the threadfin fishes (Polynemidae) using ultraconserved elements

Girard

Davis

Baldwin

et al. 2022

Journal of Fish Biology

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Threadfins (Teleostei: Polynemidae) are a group of fishes named for their elongated and threadlike pectoral‐fin rays. These fishes are commonly found in the world's tropical and subtropical waters, and are an economically important group for people living in these regions, with more than 100,000 t harvested in recent years. However, we do not have a detailed understanding of polynemid evolutionary history such that these fishes can be monitored, managed and conserved as an important tropical food source. Recent studies hypothesize at least one genus of threadfins is polyphyletic, and no studies have focused on generating a hypothesis of relationship for the Polynemidae using DNA sequences. In this study, we analyse a genomic dataset of ultraconserved‐element and mitochondrial loci to construct a phylogeny of the Polynemidae. We recover the threadfins as a clade sister to flatfishes, with the most taxonomically rich genus, Polydactylus, being resolved as polyphyletic. When comparing our dataset to data from previous studies, we find that a few recent broad‐scale phylogenies of fishes have incorporated mislabelled, misidentified or chimeric terminals into their analyses, impacting the relationships of threadfins they recover. We highlight these problematic sequences, providing revised identifications based on the data sequenced in this study. We then discuss the intrarelationships of threadfins, highlighting morphological or ecological characters that support the clades we recover.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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