Incongruence in the phylogenomics era

Nature Reviews Genetics, Год журнала: 2023, Номер 24(12), С. 834 - 850

Опубликована: Июнь 27, 2023

Язык: Английский

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

Bulletin of the Peabody Museum of Natural History, Год журнала: 2024, Номер 65(1)

Опубликована: Апрель 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.

Язык: Английский

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The promise and pitfalls of synteny in phylogenomics

PLoS Biology, Год журнала: 2024, Номер 22(5), С. e3002632 - e3002632

Опубликована: Май 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.

Язык: Английский

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

Genome Research, Год журнала: 2022, Номер 32(9), С. 1685 - 1697

Опубликована: Авг. 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.

Язык: 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, Год журнала: 2023, Номер 120(40)

Опубликована: Сен. 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.

Язык: Английский

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

Molecular Biology and Evolution, Год журнала: 2024, Номер 41(9)

Опубликована: Авг. 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.

Язык: Английский

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

Hydrobiologia, Год журнала: 2024, Номер 851(12-13), С. 2795 - 2826

Опубликована: Янв. 18, 2024

Язык: Английский

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Fish Genomics and Its Application in Disease‐Resistance Breeding

Reviews in Aquaculture, Год журнала: 2024, Номер unknown

Опубликована: Сен. 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.

Язык: Английский

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

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Фев. 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.

Язык: Английский

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The Caudal Neurosecretory System: A Still Enigmatic Second Neuroendocrine Complex in Fish

Neuroendocrinology, Год журнала: 2024, Номер unknown, С. 1 - 41

Опубликована: Янв. 16, 2024

The caudal neurosecretory system (CNSS) is a neuroendocrine complex, whose existence specific to fishes. In teleosts, it consists of cells (Dahlgren cells) fibers are associated with neurohemal terminal tissue (urophysis). other actinopterygians as well in chondrichthyes, the devoid urophysis, so that Dahlgren end diffuse region. Structurally, has many similarities hypothalamic-neurohypophysial system. However, differs regarding its position at spinal cord and nature hormones secretes, most notable ones being urotensins. CNSS was first described more than 60 years ago, but embryological origin still hypothetical, role poorly understood. Observations experimental data gave some evidences possible involvement osmoregulation, stress reproduction. But one may question benefit for fish possess this second system, while central hypothalamic-pituitary complex already controls such functions. As an introduction our review, brief report on discovery given. A description organization follows, review then focuses neuroendocrinology different factors produces secretes. current knowledge ontogenesis developmental also reported, evolution. special focus finally given what known potential physiological roles.

Язык: Английский

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