Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 12, 2023

Heliconius butterflies, a speciose genus of Müllerian mimics, represent classic example an adaptive radiation that includes range derived dietary, life history, physiological and neural traits. However, key lineages within the genus, across broader Heliconiini tribe, lack genomic resources, limiting our understanding how neutral processes shaped genome evolution during their radiation. Here, we generate highly contiguous assemblies for nine Heliconiini, 29 additional reference-assembled genomes, improve 10 existing assemblies. Altogether, provide dataset annotated genomes total 63 species, including 58 species tribe. We use this extensive to robust dated heliconiine phylogeny, describe major patterns introgression, explore architecture, basis innovations in enigmatic group, assessment putative regulatory regions at stem. Our work illustrates increased resolution provided by such dense sampling improves power test gene-phenotype hypotheses, precisely characterize evolve.

Language: Английский

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Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(10), P. e3002847 - e3002847

Published: Oct. 9, 2024

In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype environment focal trait. these 2 fields, there are sophisticated but disparate traditions aimed at tasks. The disconnect their respective approaches becoming untenable as questions in medicine, conservation biology, evolutionary biology increasingly rely on integrating data from within among species, once-clear conceptual divisions blurred. To help bridge this divide, we lay out general model describing covariance contributions quantitative phenotypes different individuals. Taking approach shows that standard models (e.g., genome-wide association studies; GWAS) phylogenetic comparative regression) can be interpreted special cases more quantitative-genetic model. fact share same core architecture means build unified understanding strengths limitations methods for controlling structure when testing associations. We develop intuition why spurious may occur analytically conduct population-genetic simulations traits. structural similarity problems phylogenetics enables us take methodological advances one field apply them other. demonstrate by showing how GWAS technique-including relatedness matrix (GRM) well its leading eigenvectors, corresponding principal components genotype matrix, regression model-can mitigate analyses. As case study, re-examine an analysis coevolution expression levels genes across fungal phylogeny show including eigenvectors covariates decreases false positive rate while simultaneously increasing true rate. More generally, work provides foundation integrative processes shape it.

Language: Английский

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The meaning and measure of concordance factors in phylogenomics

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(11)

Published: Oct. 17, 2024

Abstract As phylogenomic datasets have grown in size, researchers developed new ways to measure biological variation and assess statistical support for specific branches. Larger more sites loci therefore less sampling variance. While we can accurately the mean signal these datasets, lower variance is often reflected uniformly high measures of branch support—such as bootstrap posterior probability—limiting their utility. also revealed substantial topologies found across individual loci, such that single species tree inferred by most phylogenetic methods represents a limited summary data many purposes. In contrast support, degree underlying topological among should be approximately constant regardless size dataset. “Concordance factors” (CFs) similar statistics become increasingly important tools phylogenetics. this review, explain why CFs thought descriptors rather than argue they provide information about predictive power not contained support. We review growing suite measuring concordance, compare them common framework reveals interrelationships, demonstrate how calculate using an example from birds. discuss might change future move beyond estimating “tree life” toward myriad evolutionary histories genomic variation.

Language: Английский

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Convergent molecular evolution associated with repeated transition to gregarious larval behaviour in Heliconiini

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

Published: Jan. 16, 2025

Abstract Collective behaviour forms the basis for many anti-predator strategies. Within Lepidoptera, larval gregariousness has evolved convergently across phylogenetically disparate lineages. While selection pressures shaping variation in social behaviours are well investigated, much less is known about mechanisms that control attraction and behavioural coordination. Similarly, little how secondary associated with living shape genome evolution. Here, using genomic data over 60 species from an adaptive radiation of Neotropical butterflies, Heliconiini, which gregarious repeatedly, we explore molecular repeated convergent shifts towards larvae. We focus on three main areas evolution: differential homologous genes, accelerated rates evolution non-coding regions key gene expression brains solitary identify strong signatures evolution, both coding loci, Heliconiini lineages behaviour. Molecular convergence also detected at transcriptomic level brains, suggesting regulation neural tissue. Among loci showing signals lineages, several candidates linked to activity, feeding behaviour, immune pathways. Our results suggest sociality profoundly changes acting multiple physiological, immunological traits.

Language: Английский

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A Phylogenetic Approach to Genomic Language Modeling

Lecture notes in computer science, Journal Year: 2025, Volume and Issue: unknown, P. 99 - 117

Published: Jan. 1, 2025

Language: Английский

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Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc

Integrative and Comparative Biology, Journal Year: 2024, Volume and Issue: 64(5), P. 1513 - 1525

Published: May 29, 2024

Synopsis Comparative genomics provides ample ways to study genome evolution and its relationship phenotypic traits. By developing testing alternate models of throughout a phylogeny, one can estimate rates molecular along different lineages in phylogeny link these with observations extant species, such as convergent phenotypes. Pipelines for work help identify when where genomic changes may be associated with, or possibly influence, We recently developed set called PhyloAcc, using Bayesian framework nucleotide substitution on branches phylogenetic tree evaluate their association pre-defined estimated PhyloAcc-ST PhyloAcc-GT both allow users define priori target then compare loci accelerating more lineages. Whereas ST considers only species across all input loci, GT topologies every locus. PhyloAcc-C simultaneously continuous trait evolution, allowing the user ask whether two are associated. Here, we describe provide tips workflows how prepare data run PhyloAcc.

Language: Английский

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Convergent and lineage-specific genomic changes contribute to adaptations in sugar-consuming birds

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

Published: Sept. 1, 2024

Although high-sugar diets are associated with metabolic diseases in humans, several bird lineages have independently evolved to primarily subsist on simple sugars from flower nectar or fruits. In this study, we address a key question of the repeatability molecular evolution by investigating convergent and lineage-specific mechanisms underlying dietary adaptations four major sugar-consuming lineages: hummingbirds, parrots, honeyeaters, sunbirds. We assembled nine new genomes for species their closely related non-sugar feeding outgroup generated 90 tissue-specific transcriptomes six species. identified signatures positive selection both protein-coding non-coding regulatory sequences, found targets same genes more frequently sugar-feeders compared controls, suggesting that adapting diet requires changes limited number genetic elements. At functional level, pathways energy homeostasis, carbohydrate metabolism, heart function, hormonal regulation showed signals evolution, while lipid amino acid metabolism demonstrated mostly evolution. Notably, observed striking evidence adaptation MLXIPL, transcription factor regulating sugar manifesting sequence across all sugar-feeders. With assays, hummingbird MLXIPL enhances sugar-induced transcriptional activity HEK239 cells, its central role diets. Our findings elucidate main genomic sugar-feeding at pathway levels.

Language: Английский

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Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations

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

Published: Feb. 12, 2024

In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype environment focal trait. these two fields, there are sophisticated but disparate traditions aimed at tasks. The disconnect their respective approaches becoming untenable as questions in medicine, conservation biology, evolutionary biology increasingly rely on integrating data from within among species, once-clear conceptual divisions blurred. To help bridge this divide, we derive general model describing covariance contributions quantitative phenotypes different individuals. Taking approach shows that standard models (e.g., Genome-Wide Association Studies; GWAS) phylogenetic comparative regression) can be interpreted special cases more quantitative-genetic model. fact share same core architecture means build unified understanding strengths limitations methods for controlling structure when testing associations. We develop intuition why spurious may occur using analytical theory conduct population-genetic simulations traits. structural similarity problems phylogenetics enables us take methodological advances one field apply them other. demonstrate by showing how GWAS technique-including relatedness matrix (GRM) well its leading eigenvectors, corresponding principal components genotype matrix, regression model-can mitigate analyses. As case study this, re-examine an analysis co-evolution expression levels genes across fungal phylogeny, show including eigenvectors covariates decreases false positive rate while simultaneously increasing true rate. More generally, work provides foundation integrative processes shape it.

Language: Английский

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Phylogenomic prediction of interaction networks in the presence of gene duplication

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

Published: Aug. 8, 2024

Abstract Assigning gene function from genome sequences is a rate-limiting step in molecular biology research. A protein’s position within an interaction network can potentially provide insights into its mechanisms. Phylogenetic analyses of evolutionary rate covariation (ERC) have been shown to be effective for large-scale prediction functional interactions protein sequence data. However, duplication, loss, and other sources phylogenetic incongruence are barriers analyzing ERC on genome-wide basis. Here, we developed ERCnet , bioinformatic program designed overcome these challenges, facilitating efficient all-vs-all large datasets. We compiled sample set 35 angiosperm genomes test the performance ERCnet, including sensitivity user-defined analysis parameters such as input dataset size, branch-length measurement strategy, significance threshold defining hits. find that our novel ‘branch-by-branch’ length measurements outperforms ‘root-to-tip’ approaches most cases, offering valuable new strategy performing even presence extensive duplication. Further, demonstrate number species composition both profound effects genes predicted interact. Our systematic exploration provides roadmap design future predict wide array genomic code freely available at https://github.com/EvanForsythe/ERCnet .

Language: Английский

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RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution

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

Published: Dec. 7, 2023

Abstract Comparative genomics approaches seek to associate evolutionary genetic changes with the evolution of phenotypes across a phylogeny. Many these methods, including our rates based method, RERconverge, lack capability analyzing non-ordinal, multicategorical traits. To address this limitation, we introduce an expansion RERconverge that associates shifts in convergent multi-categorical The categorical includes methods for performing ancestral state reconstruction, statistical tests associating relative variables, and new method phylogenetic permulations on In addition demonstrating three-category diet phenotype, compare its performance naive pairwise binary analyses two existing comparative genomic traits: simulations signal method. We also present diagnostic analysis approach how scales number species categories included analysis. Our results show outperforms at identifying genes enriched pathways significantly associated phenotype reconstruction drives improvement ability capture diet-related pathways. were able account non-uniform null distributions correct non-independence gene rank during pathway enrichment will provide strong foundation applying traits larger data sets more complex trait evolution.

Language: Английский

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