Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(8), P. 1211 - 1220

Published: July 14, 2022

Language: Английский

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Genome structures resolve the early diversification of teleost fishes

Science, Journal Year: 2023, Volume and Issue: 379(6632), P. 572 - 575

Published: Feb. 10, 2023

Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts the largest and most diversified group of extant vertebrates, but relationships among their three oldest lineages remain unresolved. On basis seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited topology deepest branches teleost phylogeny using independent gene sequence chromosomal rearrangement phylogenomic approaches. These analyses converged to single scenario that unambiguously places Osteoglossomorpha (arapaima, elephantnose fish) monophyletic sister other teleosts, i.e., Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years controversy on these highlights power combining different levels genome-wide information solve complex phylogenies.

Language: Английский

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

Bulletin of the Peabody Museum of Natural History, Journal Year: 2024, Volume and Issue: 65(1)

Published: April 18, 2024

Classification of the tremendous diversity ray-finned fishes (Actinopterygii) began with designation taxonomic groups on basis morphological similarity. Starting in late 1960s phylogenetics became for classification Actinopterygii but failed to resolve many relationships, particularly among lineages within hyperdiverse Percomorpha. The introduction molecular led a dramatic reconfiguration actinopterygian phylogeny. Refined phylogenetic resolution afforded by studies revealed an uneven lineages, resulting proliferation redundant group names Linnean-ranked classifications. Here we provide unranked based summary phylogeny 830 that includes all currently recognized families and 287 fossil taxa. We definitions 90 clade review seven previously defined names. For each 97 names, etymology name, species constituent diagnostic apomorphies, synonyms, discussion clade's nomenclatural systematic history. new is free only one name describe, yielding comprehensive explicitly has emerged 21st century rests foundation previous 200 years research systematics fishes.

Language: Английский

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The promise and pitfalls of synteny in phylogenomics

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(5), P. e3002632 - e3002632

Published: May 20, 2024

Reconstructing the tree of life remains a central goal in biology. Early methods, which relied on small numbers morphological or genetic characters, often yielded conflicting evolutionary histories, undermining confidence results. Investigations based phylogenomics, use hundreds to thousands loci for phylogenetic inquiry, have provided clearer picture life’s history, but certain branches remain problematic. To resolve difficult nodes life, 2 recent studies tested utility synteny, conserved collinearity orthologous more organisms, phylogenetics. Synteny exhibits compelling phylogenomic potential while also raising new challenges. This Essay identifies and discusses specific opportunities challenges that bear value synteny data other rare genomic changes studies. Synteny-based analyses highly contiguous genome assemblies mark chapter era quest reconstruct life.

Language: Английский

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Phylogenomics of Characidae, a hyper-diverse Neotropical freshwater fish lineage, with a phylogenetic classification including four families (Teleostei: Characiformes)

Zoological Journal of the Linnean Society, Journal Year: 2024, Volume and Issue: 202(1)

Published: Sept. 1, 2024

Abstract Neotropical tetras of the family Characidae form largest and most taxonomically complex clade within order Characiformes. Previous phylogenetic relationships concur on recognition four major subclades, whereas knowledge intergeneric interspecific remains largely incomplete or nonexistent. We sampled 575 specimens 494 species 123 genera classified in Characidae, generated new molecular data ultraconserved elements (UCEs), used likelihood Bayesian analyses. The phylogeny (1348 UCE loci: 538 472 bp) yielded clades with unprecedented resolution at species- genus-levels, allowing us to propose a classification former into families: Spintherobolidae, Stevardiidae, Acestrorhamphidae. Stevardiidae includes nine subfamilies: Landoninae, Xenurobryconinae, Glandulocaudinae, Argopleurinae, Hemibryconinae, Stevardiinae, Planaltininae, Creagrutinae, Diapominae. five Aphyocharacinae, Cheirodontinae, Exodontinae, Tetragonopterinae, Characinae. Acestrorhamphidae congregates 15 Oxybryconinae, Trochilocharacinae, Stygichthyinae, Megalamphodinae, Stichonodontinae, unnamed subfamily, Stethaprioninae, Pristellinae, Jupiabinae, Tyttobryconinae, Hyphessobryconinae, Thayeriinae, Rhoadsiinae, Grundulinae, Acestrorhamphinae. resolves supports revalidation Myxiops, Megalamphodus, Ramirezella, Holopristis, Astyanacinus, synonymy Aphyodite, Genycharax, Psellogrammus, expansion Cyanogaster, Makunaima, Deuterodon, Hasemania, Hemigrammus, Bario, Ctenobrycon, Psalidodon. opens avenues for systematic reviews redefinitions included genera.

Language: Английский

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Fish Genomics and Its Application in Disease‐Resistance Breeding

Reviews in Aquaculture, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 10, 2024

ABSTRACT Global aquaculture production has been rising for several decades, with up to 76% of the total from fish. However, problem fish diseases is becoming more and prominent in today's context pursuing sustainable aquaculture. Since first genome assembly reported 2002, genomic approaches have successfully implemented breeding enhance disease resistance reduce economic losses caused by diverse diseases. Here, we present a review current progress genomics its application disease‐resistance breeding. First, data all publicly available genomes were curated statistical analysis these performed. Subsequently, genomics‐assisted (including quantitative trait loci mapping, genome‐wide association study, marker‐assisted selection, gene transfer, editing) that applied practical disease–resistance programs are outlined. In addition, candidate genetic markers could possibly be utilized summarized. Finally, remaining challenges further directions discussed. summary, this provides insight into disease‐resistant varieties.

Language: Английский

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On the relationship between extant innate immune receptors and the evolutionary origins of jawed vertebrate adaptive immunity

Immunogenetics, Journal Year: 2022, Volume and Issue: 74(1), P. 111 - 128

Published: Jan. 4, 2022

Language: Английский

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Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(43)

Published: Oct. 17, 2022

The deep sea contains a surprising diversity of life, including iconic fish groups such as anglerfishes and lanternfishes. Still, >65% marine teleost species are restricted to the photic zone <200 m, which comprises less than 10% ocean’s total volume. From macroevolutionary perspective, this paradox may be explained by three hypotheses: 1) shallow water lineages have had more time diversify deep-sea lineages, 2) faster rates speciation or 3) shallow-to-deep transition limit richness. Here we use phylogenetic comparative methods test among these non-mutually exclusive hypotheses. While found support for all hypotheses, disparity in richness is better described uneven outcome alternating phases that favored diversification over past 200 million y. Shallow teleosts became incredibly diverse 100 y ago during period warm temperatures high level, suggesting importance reefs epicontinental settings. Conversely, colonization was brief episodes when cooling increased efficiency carbon pump. Finally, time-variable ecological filters limited much history, helped maintain higher A pelagic lifestyle large jaws were associated with early colonists, while demersal tapered body plan typical later colonists. Therefore, also suggest some hallmark characteristics fishes evolved prior colonizing sea.

Language: Английский

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Distinguishing between ante factum and post factum properties of animal cell lines and demonstrating their use in grouping ray-finned fish cell lines into invitromes

In Vitro Cellular & Developmental Biology - Animal, Journal Year: 2023, Volume and Issue: 59(1), P. 41 - 62

Published: Jan. 1, 2023

Language: Английский

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A Saharan fossil and the dawn of Neotropical armoured catfishes in Gondwana

Gondwana Research, Journal Year: 2024, Volume and Issue: 132, P. 103 - 112

Published: April 26, 2024

Language: Английский

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