Incongruence in the phylogenomics era

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(12), P. 834 - 850

Published: June 27, 2023

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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An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication

Genome Research, Journal Year: 2022, Volume and Issue: 32(9), P. 1685 - 1697

Published: Aug. 12, 2022

Teleost fishes are ancient tetraploids descended from an ancestral whole-genome duplication that may have contributed to the impressive diversification of this clade. Whole-genome duplications can occur via self-doubling (autopolyploidy) or hybridization between different species (allopolyploidy). The mode tetraploidization conditions evolutionary processes by which duplicated genomes return diploid meiotic pairing, and subsequent genetic divergence genes (cytological rediploidization). How teleosts became tetraploid remains unresolved, leaving a fundamental gap in interpretation their functional evolution. As result duplication, identifying orthologous paralogous genomic regions across is challenging, hindering genome-wide investigations into polyploid history. Here, we combine tailored gene phylogeny methodology together with state-of-the-art karyotype reconstruction establish first high-resolution comparative atlas paleopolyploid 74 teleost genomes. We then leverage investigate how rediploidization occurred at level. uncover some maintained tetraploidy for more than 60 million years, three chromosome pairs diverging genetically only after separation major families. This evidence suggests ancestor was autopolyploid. Further, find biased retention along several chromosomes, contradicting current paradigms asymmetrical evolution specific allopolyploids. Altogether, our results offer novel insights genome dynamics following polyploidizations vertebrates.

Language: Английский

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Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(40)

Published: Sept. 22, 2023

The almost simultaneous emergence of major animal phyla during the early Cambrian shaped modern biodiversity. Reconstructing evolutionary relationships among such closely spaced branches in tree life has proven to be a challenge, hindering understanding evolution and fossil record. This is particularly true species-rich highly varied Mollusca where dramatic inconsistency paleontological, morphological, molecular evidence led long-standing debate about group’s phylogeny nature dozens enigmatic taxa. A critical step needed overcome this issue supplement available genomic data, which plentiful for well-studied lineages, with genomes from rare but key as Scaphopoda. Here, by presenting chromosome-level both extant scaphopod orders leveraging complete spanning Mollusca, we provide strong support Scaphopoda sister taxon Bivalvia, revitalizing morphology-based Diasoma hypothesis originally proposed 50 years ago. Our clock analysis confidently dates split between Bivalvia at ~520 Ma, prompting reinterpretation controversial laterally compressed Early fossils, including Anabarella , Watsonella, Mellopegma, stem diasomes. Moreover, show that incongruence phylogenetic placement previous phylogenomic studies was due ancient incomplete lineage sorting (ILS) occurred rapid radiation Conchifera. findings highlight need consider ILS potential source error deep reconstruction, especially context unique Explosion.

Language: Английский

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Annelid Comparative Genomics and the Evolution of Massive Lineage-specific Genome Rearrangement in Bilaterians

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(9)

Published: Aug. 13, 2024

Abstract The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained others. However, the evolutionary forces driving these differences by which they emerge have remained largely uncharacterized. Here, we analyze across phylum Annelida using 23 chromosome-level annelid genomes. We find while many lineages maintained bilaterian structure, Clitellata, group containing leeches earthworms, possesses completely scrambled develop rearrangement index to quantify extent evolution show that, compared bilaterians, earthworms among most rearranged any currently sampled species. further can be classified two distinct categories—high low rearrangement—largely influenced presence or absence, respectively, chromosome fission events. Our findings demonstrate animal variable within reveal occur both gradual, stepwise fashion, rapid, all-encompassing changes over short timescales.

Language: Английский

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Whole-genome analyses converge to support the Hemirotifera hypothesis within Syndermata (Gnathifera)

Hydrobiologia, Journal Year: 2024, Volume and Issue: 851(12-13), P. 2795 - 2826

Published: Jan. 18, 2024

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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​​Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 16, 2024

Abstract Groups of orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, is seen between bilaterian phyla divergent Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern genome evolution in Bryozoa, an understudied phylum colonial invertebrates. Using comparative genomics, reconstruct chromosomal history five bryozoans. Multiple ancient fusions followed by mixing led to near-complete loss linkage groups ancestor extant A second wave rearrangements, including fission, then occurred independently two bryozoan classes, further scrambling genomes. We also discover at least derived fusion events shared bryozoans brachiopods, supporting traditional but highly debated Lophophorata hypothesis. Finally, show that fission processes partitioning from Hox clusters onto multiple chromosomes. Our findings demonstrate canonical structure has been lost across all studied representatives entire phylum; reveal group can occur very frequently specific lineages; provide powerful source phylogenetic information.

Language: Английский

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Hox genes control homocercal caudal fin development and evolution

Science Advances, Journal Year: 2024, Volume and Issue: 10(3)

Published: Jan. 19, 2024

Ancient bony fishes had heterocercal tails, like modern sharks and sturgeons, with asymmetric caudal fins a vertebral column extending into an elongated upper lobe. Teleost fishes, in contrast, developed homocercal tail characterized by two separate equal-sized fin lobes the body axis not fin. A similar heterocercal-to-homocercal transition occurs during teleost ontogeny, although underlying genetic developmental mechanisms for either remain unresolved. Here, we investigated role of hox13 genes formation as these control posterior identity animals. Analysis expression profiles zebrafish paralogs phenotypes CRISPR/Cas9-induced mutants showed that double hoxb13a hoxc13a fail to form Furthermore, single display heterocercal-like morphologies seen since Mesozoic fossil teleosteomorphs. Relaxation functional constraints after genome duplication may have allowed duplicates neo- or subfunctionalize, ultimately contributing evolution fishes.

Language: Английский

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