A genome-based phylogeny for Mollusca is concordant with fossils and morphology

Science, Journal Year: 2025, Volume and Issue: 387(6737), P. 1001 - 1007

Published: Feb. 27, 2025

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups—gastropods, bivalves, and cephalopods—each represent diverse radiation with myriad morphological, ecological, behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed living on basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members all eight classes two high-quality genome assemblies monoplacophorans. Our analyses confirm proposed morphology show widespread genomic variation. flexibility likely explains both historic challenges their genomes evolutionary success.

Language: Английский

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Still waters run deep in large-scale genome rearrangements of morphologically conservative Polyplacophora

eLife, Journal Year: 2025, Volume and Issue: 13

Published: April 17, 2025

A major question in animal evolution is how genotypic and phenotypic changes are related, another when whether ancient gene order conserved living clades. Chitons, the molluscan class Polyplacophora, retain a body plan general morphology apparently little changed since Palaeozoic. We present comparative analysis of five reference quality genomes, including four de novo assemblies, covering all chiton clades, an updated phylogeny for phylum. constructed 20 linkage groups (MLGs) show that these relatively bivalve karyotypes, but chitons they subject to re-ordering, rearrangement, fusion, or partial duplication vary even between congeneric species. The largest number novel fusions most plesiomorphic clade Lepidopleurida, chitonid Liolophura japonica has genome duplication, extending occurrence large-scale within Mollusca. extreme dynamic rearrangements this stands contrast other animals, demonstrating have overcome evolutionary constraints acting on groups. conservative phenome belies rapid extensive genome.

Language: Английский

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A Cambrian spiny stem mollusk and the deep homology of lophotrochozoan scleritomes

Science, Journal Year: 2024, Volume and Issue: 385(6708), P. 528 - 532

Published: Aug. 1, 2024

Mollusks encompass enormous disparity, including familiar clams and snails alongside less aculiferans (chitons vermiform aplacophorans) with complex multicomponent skeletons. Paleozoic fossils trace crown mollusks to forms exhibiting a combination of biomineralized shells sclerites (e.g., scales, spines, spicules). We describe shell-less, Cambrian stem mollusk, Shishania aculeata gen. et sp. nov., conical, hollow chitinous smooth girdle, broad foot, mantle cavity. The have microstructure narrow canals consistent the impressions chaetal microvilli found in annelids brachiopods. provide morphological stepping stone between typical chaetae (chitinous bristles) external organic part aculiferan that encloses mineralized body. This discovery reinforces common origin lophotrochozoan sclerites, suggesting mollusk ancestor was densely covered chaetae.

Language: Английский

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Out of the ocean: the timescale of molluscan evolution based on phylogenomics revealed the ages of mollusks’ evolutionary transitions into the novel environment

Frontiers in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 12

Published: Feb. 12, 2024

Being the phylum with second largest biodiversity, mollusks are widely distributed in marine, freshwater, and land, conquered almost all habitats on earth. Throughout geological time, several molluscan lineages independently colonized freshwater evolving new habitats. Resolving timing of their colonization for novel environments is basis understanding complex evolution Mollusca. Herein, we obtained an elaborate single–copy orthologs set including 107 genes a total length 3,447,675 amino acid sites across 134 to reconstruct phylogeny The phylogenetic analysis recovered “Aculifera+ Conchifera” topology well–supported. By divergence times estimation fossil calibration, revealed Cambrian rapid diversification classes. What’s more, our results provided three major independent consistent previous studies. mussels (Bivalvia: Unionida) about 233 Mya, ancient origin late make this order become main represent bivalves. orders Stylommatophora Basommatophora (Gastropoda: Pulmonata) respectively land 201 Triassic–Jurassic mass extinction may have opportunities colonization. Ampullariidae (Gastropoda) 156 lungs contributed adaption tropical environment them survive. Our probably offer most comprehensive time–scale evolution, could provide some insights into habitat transition

Language: Английский

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MATEdb2, a collection of high-quality metazoan proteomes across the Animal Tree of Life to speed up phylogenomic studies

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

Published: Feb. 21, 2024

Abstract Recent advances in high throughput sequencing have exponentially increased the number of genomic data available for animals (Metazoa) last decades, with high-quality chromosome-level genomes being published almost daily. Nevertheless, generating a new genome is not an easy task due to cost sequencing, complexity assembly, and lack standardized protocols annotation. The consensus annotation publication files hinders research by making researchers lose time reformatting their purposes but can also reduce quality genetic repertoire evolutionary study. Thus, use transcriptomes obtained using same pipeline as proxy content species remains valuable resource that easier obtain, cheaper, more comparable than genomes. In previous study, we presented Metazoan Assemblies from Transcriptomic Ensembles database (MATEdb), repository transcriptomic two most diverse animal phyla, Arthropoda Mollusca. Here, present newest version MATEdb (MATEdb2) overcomes some limitations our database: (1) include all phyla where public available, (2) provide gene annotations extracted original GFF pipeline. total, proteomes inferred or 1000 species, including longest isoforms, functional based on sequence homology protein language models, well embedding representations sequences. We believe this will accelerate phylogenomics while saving thousands hours computational work plea open, greener, collaborative science.

Language: Английский

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Molluscan systematics: historical perspectives and the way ahead

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 6, 2024

ABSTRACT Mollusca, the second‐most diverse animal phylum, is estimated to have over 100,000 living species with great genetic and phenotypic diversity, a rich fossil record, considerable evolutionary significance. Early work on molluscan systematics was grounded in morphological anatomical studies. With transition from oligo gene Sanger sequencing cutting‐edge genomic technologies, molecular data has been increasingly utilised, providing abundant information for reconstructing phylogenetic tree. However, relationships among within most major lineages of Mollusca long contentious, often due limited markers, insufficient taxon sampling conflict. Fortunately, remarkable progress made recent years, which shed light how groups evolved. In this review systematics, we first synthesise current understanding Tree Life at higher taxonomic levels. We then discuss micromolluscs, adult individuals body size smaller than 5 mm, offer unique insights into Mollusca's vast diversity deep phylogeny. Despite advancements, our knowledge phylogeny still needs refinement. Further advancements will arise integrating comprehensive sets, including genome‐scale data, exceptional fossils, digital (including internal structures). Enhanced access these combined increased collaboration morphologists, palaeontologists, developmental biologists, phylogeneticists, significantly advance field.

Language: Английский

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Chronospaces: an R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

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

Published: Feb. 8, 2024

Much of our understanding the history life hinges upon time calibration, process assigning absolute times to cladogenetic events. Bayesian approaches scaling phylogenetic trees have dramatically grown in complexity, and depend today numerous methodological choices. Arriving at objective justifications for all these is difficult consuming. Thus, divergence are routinely inferred under only one or a handful parametric conditions, often chosen arbitrarily. Progress towards building robust biological timescales necessitate development better methods visualize quantify sensitivity results decisions. Here, we present an R package that assists this endeavor through use chronospaces, i.e., graphical representations summarizing variation node ages contained time-calibrated trees. We further test approach by estimating three empirical datasets-spanning widely differing evolutionary timeframes-using software PhyloBayes. Our reveal large differences impact many common decisions, with choice clock (uncorrelated vs. autocorrelated) loci having strong effects on ages. Other decisions comparatively minor consequences, including computationally intensive site-heterogeneous model CAT-GTR, whose effect might be discernible exceedingly old divergences (e.g., deepest eukaryote nodes). The chronospace implements range analytical tools assist exploration prioritization computational resources inference times.

Language: Английский

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A Phylogenomic Backbone for Acoelomorpha Inferred from Transcriptomic Data

Systematic Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 15, 2024

Abstract —Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs—which include three main groups, namely Acoela, Nemertodermatida, and Xenoturbella—have been proposed to be an early diverging Bilateria, sister protostomes deuterostomes, but phylogenomic analyses have recovered this clade nested within the as Ambulacraria. The position Xenacoelomorpha metazoan tree has understandably attracted a lot attention, overshadowing study phylogenetic relationships group. Given that Xenoturbella includes only six species whose well understood, we decided focus on most speciose Acoelomorpha (Acoela + Nemertodermatida). Here, sequenced 29 transcriptomes, doubling number species, infer backbone for based genomic data. topology is congruent with previous studies. important difference recovery Paratomella first off-shoot dramatically changing reconstruction ancestral acoel. Besides, detected incongruence between gene trees tree, likely linked incomplete lineage sorting, some signal introgression families Dakuidae Mecynostomidae, which hampers inferring correct placement family and, particularly, genus Notocelis. We also used dataset time diversification times Acoelomorpha, coincide known bilaterian extinction events. importance morphological data in acoelomorph phylogenetics, tested several partitions models. Although failed recover robust phylogeny, proven suitable alternative when reference phylogeny available.

Language: Английский

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Exploring the evolution of sex determination related genes through a cross-species genomics analysis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

Abstract The molecular basis of sex determination (SD), while being extensively studied in model organisms, remains poorly understood many animal groups. Bivalves, a diverse class molluscs with variety reproductive modes, represent an ideal yet challenging clade for investigating SD and the evolution sexual systems. However, absence comprehensive framework has limited progress this field, particularly regarding study sex-determination related genes (SRGs). In study, we performed genome-wide sequence evolutionary analysis Dmrt, Sox, Fox gene families more than 40 bivalve species. For first time, provide extensive phylogenetic-aware dataset these SRGs, find support to hypothesis that Dmrt-1L Sox-H may act as primary sex-determining genes, by showing their high levels diversity within genomic context. To validate our findings, same two well-characterized systems, mammals Drosophila . former, found male Sry exhibits pattern amino acid similar bivalves, consistent its role master regulator. contrast, no such was observed among fruit fly cascade, which is controlled chromosomic mechanism. Overall, findings highlight similarities some mammal possibly driven comparable architecture cascades. This work underscores once again importance employing comparative approach when understudied non-model

Language: Английский

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Still waters run deep: Large scale genome rearrangements in the evolution of morphologically conservative Polyplacophora

Published: April 8, 2025

A major question in animal evolution is how genotypic and phenotypic changes are related, whether ancient gene order conserved living clades. Chitons, the molluscan class Polyplacophora, retain a body plan general morphology apparently little changed since Palaeozoic. We present comparative analysis of five reference quality genomes, including four de novo assemblies, covering all chiton clades, an updated phylogeny for phylum.We constructed 20 linkage groups (MLGs) that relatively bivalve karyotypes, but subject to re-ordering, rearrangement, fusion, or partial duplication among chitons, varying even between congeneric species. The largest number novel fusions most plesiomorphic clade Lepidopleurida, chitonid Liolophura japonica has genome duplication, extending occurrence large-scale within Mollusca.The extreme dynamic rearrangements this stands contrast other animals, demonstrating chitons have overcome evolutionary constraints acting on groups. conservative phenome belies rapid extensive genome.

Language: Английский

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