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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The origin and evolution of Wnt signalling

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(7), P. 500 - 512

Published: Feb. 19, 2024

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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Ctenophores and parahoxozoans independently evolved functionally diverse voltage-gated K+ channels

The Journal of General Physiology, Journal Year: 2025, Volume and Issue: 157(3)

Published: Feb. 27, 2025

The ctenophore species Mnemiopsis leidyi is known to have a large set of voltage-gated K+ channels, but little about the functional diversity these channels or their evolutionary history in other species. Here, we searched genomes two additional species, Beroe ovata and Hormiphora californensis, for functionally expressed subset M. channels. We found that last common ancestor three disparate lineages probably had at least 33 Two genes belong EAG family, remaining 31 Shaker family form single clade within animal/choanoflagellate phylogeny. additionally evidence 10 transcriptome early branching lineage Euplokamis dunlapae, suggesting diversification was already underway evolution. 16 Shakers they encode diverse array conductances with orthologs many classic subtypes cnidarians bilaterians. Analysis data show are wide variety cell types, including neurons, muscle, comb cells, colloblasts. Ctenophores therefore appear independently evolved much channel shared between

Language: Английский

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Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 21, 2023

Abstract Recent advances in AI-based protein structure modeling have yielded remarkable progress predicting structures. Since structures are constrained by their biological function, geometry tends to evolve more slowly than the underlying amino acids sequences. This feature of could principle be used reconstruct phylogenetic trees over longer evolutionary timescales sequence-based approaches, but until now a reliable structure-based tree building method has been elusive. Here, we demonstrate that structure-informed phylogenies can outperform sequence-only ones not only for distantly related proteins also, remarkably, closely ones. is achieved inferring from using local structural alphabet, an approach robust conformational changes confound traditional distance measures. As illustration, decipher diversification particularly challenging family: fast-evolving RRNPPA quorum sensing receptors enabling gram-positive bacteria, plasmids and bacteriophages communicate coordinate key behaviors such as sporulation, virulence, antibiotic resistance, conjugation or phage lysis/lysogeny decision. The advent high-accuracy phylogenetics enables myriad applications across biology, uncovering deeper relationships, elucidating unknown functions, refining design bioengineered molecules.

Language: Английский

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Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(8)

Published: Aug. 1, 2023

Abstract The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% animal species half biomass. It has been subject several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack stability. Here, phylogeny estimated with expanded taxon sampling, particularly malacostracans. We small changes in sampling have large impacts phylogenetic estimation. By analyzing identical orthologs between two slightly different sets, we that differences resulting topologies are due primarily to effects reconstruction method. compare trees from our analyses those literature explore tree space pancrustacean hypotheses find statistical topology tests reject previously published favor maximum likelihood produced here. Our results clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, Syncarida. Notably, Copepoda nested Allotriocarida high support recover novel relationship decapods, euphausiids, syncarids refer as Syneucarida. With denser Stomatopoda sister this latter clade, which collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, Stomatocarida. A new Bayesian divergence time estimation conducted using 13 vetted fossils. review context other highlight 15 key taxa sample future studies.

Language: Английский

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Dicer structure and function: conserved and evolving features

EMBO Reports, Journal Year: 2023, Volume and Issue: 24(7)

Published: June 13, 2023

Abstract RNase III Dicer produces small RNAs guiding sequence‐specific regulations, with important biological roles in eukaryotes. Major Dicer‐dependent mechanisms are RNA interference (RNAi) and microRNA (miRNA) pathways, which employ distinct types of RNAs. Small interfering (siRNAs) for RNAi produced by from long double‐stranded (dsRNA) as a pool different In contrast, miRNAs have specific sequences because they precisely cleaved out hairpin precursors. Some homologs efficiently generate both, siRNAs miRNAs, while others adapted biogenesis one type. Here, we review the wealth recent structural analyses animal plant Dicers, revealed how domains their adaptations contribute to substrate recognition cleavage organisms pathways. These data imply that siRNA generation was Dicer's ancestral role miRNA relies on derived features. While key element functional divergence is RIG‐I‐like helicase domain, Dicer‐mediated also documents impressive versatility dsRNA‐binding domain.

Language: Английский

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The evolutionary history of Coleoptera (Insecta) in the late Palaeozoic and the Mesozoic

Systematic Entomology, Journal Year: 2024, Volume and Issue: 49(3), P. 355 - 388

Published: Feb. 13, 2024

Abstract Recent progress in beetle palaeontology has incited us to re‐address the evolutionary history of group. The Permian †Tshekardocoleidae had elytra that covered posterior body a loose tent‐like manner. formation elytral epipleura and tight fit abdomen were important transformations Middle Permian, resulting tightly enclosed subelytral space. families likely associated with dead wood gymnospermous trees. end‐Permian extinction event resulted turnover composition faunas, especially decline large‐bodied wood‐associated forms. Adephaga Myxophaga underwent first wave diversification Triassic. Polyphaga are very rare this period. suborder occurs Jurassic, fossils Elateriformia, Staphyliniformia Cucujiformia. Cretaceous fossil record been tremendously enriched by discovery amber inclusions. Numerous represent all major polyphagan lineages also remaining suborders. Improved analytical methods for documenting placing extinct taxa discussed. Different factors have played role beetles. enormous number species flowering plants, timing patterns phytophagous indicate angiosperm radiation macroevolution. Moreover, evolution intimate partnerships symbionts acquisition novel genes—obtained from fungi bacteria via horizontal gene transfers—facilitated use plant material as food source key innovations plant‐feeding

Language: Английский

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Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(15)

Published: April 3, 2024

Malvaceae comprise some 4,225 species in 243 genera and nine subfamilies include economically important species, such as cacao, cotton, durian, jute, with cotton an model system for studying the domestication of polyploids. Here, we use chromosome-level genome assemblies from representatives five or six (depending on placement Ochroma ) to differentiate coexisting subgenomes their evolution during family’s deep history. The results reveal that allohexaploid Helicteroideae partially derive allotetraploid Sterculioideae also form a component allodecaploid Bombacoideae Malvoideae. ancestral karyotype consists 11 protochromosomes. Four share unique reciprocal chromosome translocation, two other fusion. DNA alignments single-copy nuclear genes do not yield same relationships inferred structural traits, probably because originating different subgenomes. These illustrate how chromosome-structural data can unravel evolutionary history groups ancient hybrid genomes.

Language: Английский

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Evolution of bioluminescence in Anthozoa with emphasis on Octocorallia

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2021)

Published: April 24, 2024

Bioluminescence is a widespread phenomenon that has evolved multiple times across the tree of life, converging among diverse fauna and habitat types. The ubiquity bioluminescence, particularly in marine environments where it commonly used for communication defense, highlights adaptive value this trait, though evolutionary origins timing emergence remain elusive majority luminous organisms. Anthozoan cnidarians are group animals with numerous bioluminescent species found throughout world's oceans, from shallow waters to light-limited deep sea bioluminescence prominent. This study documents presence Anthozoa depth explores diversity Octocorallia-a major anthozoan Using phylogenomic approach ancestral state reconstruction, we provide evidence single origin Octocorallia infer age occurrence around Cambrian era, approximately 540 Ma-setting new record earliest environment. Our results further suggest trait was largely maintained descendants deep-water ancestor capabilities may have facilitated diversification sea.

Language: Английский

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