Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Abstract

Exon markers have a long history of use in phylogenetics of ray‐finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target‐capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon‐capture sequence data into an existing data matrix of 1,104 exons and 300 ray‐finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target‐capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR‐generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR‐based exon and mitochondrial data.

Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader

“…The recovered phylogenetic position of L. sceleratus is within Tetraodontidae and is placed closer to T. nigroviridis , while the long branch length of the Tetraodontidae clade possibly suggests a faster evolutionary rate. Regarding relationships within the pufferfish group ( T. nigroviridis, T. rubripes, T. flavidus, T. bimaculatus and L. sceleratus ), the resulting topology agrees with previous studies ( Yamanoue et al, 2011 ; Meynard et al, 2012 ; Hughes et al, 2018 ; Hughes et al, 2021 ). Moreover, the Tetraodontidae group was recovered confidently as monophyletic in accordance with Yamanoue et al (2011) .…”

The impact of paleoclimatic changes on body size evolution in marine fishes

“…Target capture used the Eupercaria probe set of Hughes et al. ( 26 , 70 ) to enrich 1,105 single-copy nuclear exon markers. We assessed sequence quality and removed two exons due to high levels of missing data, leaving 1,103 exons in total.…”

Editorial 2022

“…There were also advances in DNA barcoding resources including "Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom", which used predominantly herbarium specimens to expand barcoding libraries to include over 75% of all native flowering plants in the UK for three markers (Jones et al, 2021). In addition, the study of fish phylogenomics was advanced in the study "Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics" (Hughes et al, 2021), where the authors present new probe sets that cover the diversity of teleost fishes, and a bioinformatics pipeline for the assembly of exon capture data from raw reads to alignments. prior to further analyses (Jauhal and Newcomb, 2021).…”