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

Abstract

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.

New species of redbait from the Philippines (Teleostei, Emmelichthyidae, Emmelichthys)

“…Cleaned reads were submitted to GenBank and assigned SRA accession numbers SRR27284234–SRR27284245 under BioProject PRJNA1052721 (see Table 2 ). We assembled mitogenomes using the ‘map to reference’ function in Geneious version 11.1.5 ( Kearse et al 2012 ) with the settings described in Girard et al (2022b) and a reference mitogenome downloaded from GenBank ( E. struhsakeri , GenBank NC_004407 ; Miya et al 2003 ). Assembled mitogenomes were annotated using MitoAnnotator ( Iwasaki et al 2013 ; Sato et al 2018 ; Zhu et al 2023 ).…”

Phylogenetics of Archerfishes (Toxotidae) and Evolution of the Toxotid Shooting Apparatus

“…In addition to UCE loci, we extracted mitochondrial gene fragments of cytochrome oxidase subunit 1 (hereafter, COI) from high-throughput cleaned sequencing reads received from Arbor Biosciences. Recent studies have performed similar extractions of these data to verify identification and include additional character information in the analyses (e.g., Ghedotti et al, 2018 ; Martin et al, 2018 ; Girard et al, 2022 ). Gene fragments were extracted from cleaned reads using Geneious v11.1.5 ( Kearse et al, 2012 ) and the protocol outlined in Girard et al (2022) .…”

“…Recent studies have performed similar extractions of these data to verify identification and include additional character information in the analyses (e.g., Ghedotti et al, 2018 ; Martin et al, 2018 ; Girard et al, 2022 ). Gene fragments were extracted from cleaned reads using Geneious v11.1.5 ( Kearse et al, 2012 ) and the protocol outlined in Girard et al (2022) . Homologous regions collected were cleaned of ambiguities and inspected for stop codons using Geneious.…”

Phylogenetic Classification of Living and Fossil Ray-Finned Fishes (Actinopterygii)

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