Molecular systematics of Pampus (Perciformes: Stromateidae) based on thousands of nuclear loci using target-gene enrichment

Yin, Guoxing; Pan, Yiling; Sarker, Anirban; Baki, Mohammad Abdul; Kim, Jin-Koo; Wu, Hao; Li, Chenhong

doi:10.1016/j.ympev.2019.106595

Cited by 13 publications

(33 citation statements)

References 21 publications

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“…Divya et al [21] described the Pampus species collected from the Arabian Sea as a new species, P. candidus, but we think further scrutiny should be made to split more species from P. cinereus lineages before distinct morphological characters are identified. On the other hand, P. liuorum, a controversial Pampus species, was defined as a synonym of P. cinereus in our previous study [15], but a recent study justified P. liuorum as a valid species using two mitochondrial DNA barcodes [66]. In their Cytb trees, P. cinereus and P. liuroum sampled in the western Pacific were separated in two lineages, which was different from our result, but their COI tree corroborated our result that P. cinereus and P. liuroum are not reciprocal in monophyletic.…”

Section: Intraspecific Diversification Of P Chinensis and P Cinereusmentioning

confidence: 98%

Diversifying of Two Pampus Species across the Indo–Pacific Barrier and the Origin of the Genus

et al. 2022

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Among marine species distributed in the Indian Ocean and the Pacific, the Indo–Pacific Barrier (IPB) has been found to be an important barrier of divergence of species distributed on both sides. Among the five species of the genus Pampus, only Pampus chinensis and P. cinereus are distributed across the western Pacific and the Indian Oceans and have not been studied comparatively using extensive sampling and gene markers. Furthermore, the origin and history of genus Pampus remain unrevealed. We used thousands of nuclear loci based on target gene enrichment to explore genetic structure of P. chinensis and P. cinereus across the western Pacific and Indian Oceans. We performed divergence dating and ancestral area reconstruction analysis and inferred the dispersal routes of the Pampus species. The results suggest that the IPB played an important role in the differentiation between populations among the two oceans for both P. chinensis and P. cinereus, dividing species into the Pacific lineage and the Indian Ocean lineage. Low sea level in the late Pleistocene may be the main cause. The result also showed that the South China Sea was the center of origin of the genus Pampus, and dispersal routes of each species may be associated with the ocean currents. Our study provided new examples for the IPB effect on marine species.

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Section: Intraspecific Diversification Of P Chinensis and P Cinereusmentioning

confidence: 98%

Diversifying of Two Pampus Species across the Indo–Pacific Barrier and the Origin of the Genus

et al. 2022

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“…High value and perpetual demand make the genus one of the most sought after in commercial targeted fisheries in its native ranges, such as India (CMFRI, 2020), 1 countries bordering the seas of China, the maritime subregion of the Bay of Bengal ("BOB"), Persian Gulf countries, and Pakistan (Froese and Pauly, 2020). Despite this, the taxonomy of the genus Pampus has been uncertain and is still debated because of synapomorphies (Yin et al, 2019), and, conversely, the taxonomic literature hinted that many of the known species probably represented misidentified ones, leading to the occurrence of synonyms (Li et al, 2019c).…”

Section: Introductionmentioning

confidence: 99%

“…Latest global reports indicate the presence of the following seven valid species in the genus including the cryptic species described herein: Pampus argenteus, Pampus minor, Pampus punctatissimus, Pampus chinensis, Pampus cinereus, Pampus candidus, and Pampus sp. In 2017, Jawad and Jig, based on detailed comparative osteology of the axial skeleton, identified eight valid species in this genus, such as Pampus liuorum (Liu and Li, 2013) and Pampus nozawae (Ishikawa, 1904), which were found to be invalid by previous and subsequent researchers who considered them as synonyms of P. cinereus (Liu et al, 2013a;Li et al, 2019c;Yin et al, 2019). The existence of a strong geographic genetic structure in P. argenteus from the Indo-Western Pacific area was indicated (Sun et al, 2013), and a COI-based analysis of Pampus specimens by Divya et al (2017) revealed the presence of seven distinct but taxonomically indecisive clades with two putative species viz.…”

Section: Introductionmentioning

confidence: 99%

“…Later, Li et al (2019c) reiterated seven species in the genus based on COI analysis and prepared a key for six, although it turned out to be inconclusive. In the same year, Yin et al (2019) provided a robust classification of Pampus based on ample nuclear markers and detailed morphological re-examination that provided a simplified identification key for the following five species: P. argenteus, P. punctatissimus, P. chinensis, P. minor, and P. cinereus. Their study confirmed that P.…”

Section: Introductionmentioning

confidence: 99%

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Postulating the Modality of Integrative Taxonomy in Describing the Cryptic Congener Pampus griseus (Cuvier) and Systematics of the Genus Pampus (Perciformes: Stromateidae)

et al. 2021

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Pomfrets (genus Pampus), a highly commercial fishery resource distributed in the Indo-Western Pacific that includes Lessepsian migrants, have witnessed a series of systematic reforms. In this study, based on comprehensive sampling spanning type localities and coevals in the Northern Indian Ocean, the cryptic and valid species Stromateus griseus is resurrected from the synonymy and re-described as Pampus griseus (New Combination) based on 35 specimens from the Bay of Bengal, corroborated by a molecular analysis, which indicated a confined distribution of the species. The Bayesian phylogeny of the genus was reconstructed, incorporating redressed barcodes (582 nucleotides) and concatenated mitochondrial gene sequence data (1,822 nucleotides) generated from the recorded species P. candidus, P. chinensis and the neophyte along with sequences from GenBank entrusting the latest literature. The phylograms differed in topology as for seven valid species, and the one predicated on the concatenated data erected a highly supported polytomous clade for the P. cinereus complex (P. griseus, P. cinereus, and P. candidus) which shares synapomorphies. Pampus argenteus and P. minor, together, formed a sister clade to the rest. Climate-driven vicariant events during glacial epochs and the Indo-Pacific Barrier effect can be the drivers behind the Indian and Pacific Ocean sister lineages in P. chinensis. A multivariate analysis isolated the cryptic species from its congeners. This article portrays the systematics revision of genus Pampus with an integrative taxonomic approach compiling distinctive molecular, morphological, and anatomical features, revised key for species identification, taxonomic archives of Indian stromateids, and winds up with specific remarks.

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“…Because exon markers tend to be more variable across the target region than UCEs or the markers used for AHE, two rounds of in vitro hybridization are optimal for their sequence capture protocols (Li et al., 2013). This improvement in laboratory techniques has resulted in a number of studies that implement exon capture for fish phylogenomics (Arcila et al., 2017; Betancur‐R et al., 2019; Ilves & López‐Fernández, 2014; Ilves et al., 2017; Kuang et al., 2018; Li et al., 2015; Rincon‐Sandoval et al., 2019; Song et al., 2017; Straube et al., 2018; Yin et al., 2019). The increase in genomic resources for fishes also has allowed for the comparison of a larger number of genomes for probe design (Li et al., 2012), and ultimately eight ray‐finned fish genomes have been used to identify > 17,000 “single‐copy” exons (Song et al., 2017) using a modification of the reciprocal BLAST approach of Li et al.…”

Section: Introductionmentioning

confidence: 99%

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

Hughes

Ortı́

Saad

et al. 2020

Molecular Ecology Resources

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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.

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Molecular systematics of Pampus (Perciformes: Stromateidae) based on thousands of nuclear loci using target-gene enrichment

Cited by 13 publications

References 21 publications

Diversifying of Two Pampus Species across the Indo–Pacific Barrier and the Origin of the Genus

Diversifying of Two Pampus Species across the Indo–Pacific Barrier and the Origin of the Genus

Postulating the Modality of Integrative Taxonomy in Describing the Cryptic Congener Pampus griseus (Cuvier) and Systematics of the Genus Pampus (Perciformes: Stromateidae)

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

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