Effective population size does not explain long-term variation in genome size and transposable element content in animals

Published: Sept. 11, 2024

Animal genomes exhibit a remarkable variation in size, but the evolutionary forces responsible for such are still debated. As effective population size (N e ) reflects intensity of genetic drift, it is expected to be key determinant fixation rate nearly-neutral mutations. Accordingly, Mutational Hazard Hypothesis postulates lineages with low N have bigger genome sizes due accumulation slightly deleterious transposable elements (TEs), and those high maintain streamlined as consequence more selection against TEs. However, existence both empirical confirmation refutation using different methods scales precludes its general validation. Using high-quality public data, we estimated TE content non-synonymous synonymous substitutions (dN/dS) proxy 807 species including vertebrates, molluscs insects. After collecting available life-history traits, tested associations among proxies, while accounting phylogenetic non-independence. Our results confirm TEs major drivers variation, endorse traits dN/dS reliable proxies . do not find any evidence increased drift result an across animals. Within closely related clades, only few isolated weak emerge fishes birds. outline scenario where dynamics vary according lineage-specific patterns, lending no support predominant force driving long-term evolution

Language: Английский

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Effective population size does not explain long-term variation in genome size and transposable element content in animals

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

Published: Feb. 29, 2024

Abstract Animal genomes exhibit a remarkable variation in size, but the evolutionary forces responsible for such are still debated. As effective population size (N e ) reflects intensity of genetic drift, it is expected to be key determinant fixation rate nearly-neutral mutations. Accordingly, Mutational Hazard Hypothesis postulates lineages with low N have bigger genome sizes due accumulation slightly deleterious transposable elements (TEs), and those high maintain streamlined as consequence more selection against TEs. However, existence both empirical confirmation refutation using different methods scales precludes its general validation. Using high-quality public data, we estimated TE content non-synonymous synonymous substitutions (dN/dS) proxy 807 species including vertebrates, molluscs insects. After collecting available life-history traits, tested associations among proxies, while accounting phylogenetic non-independence. Our results confirm TEs major drivers variation, endorse traits dN/dS reliable proxies . do not find any evidence increased drift result an across animals. Within closely related clades, only few isolated weak emerge fishes birds. outline scenario where dynamics vary according lineage-specific patterns, lending no support predominant force driving long-term evolution

Language: Английский

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Adaptive evolution of A-to-I auto-editing site in Adar of eusocial insects

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Aug. 26, 2024

Adenosine-to-inosine (A-to-I) RNA editing is a co-/post-transcriptional modification introducing A-to-G variations in RNAs. There extensive discussion on whether the flexibility of exerts proteomic diversification role, or it just acts like hardwired mutations to correct genomic allele. Eusocial insects evolved ability generate phenotypically differentiated individuals with same genome, indicating involvement epigenetic/transcriptomic regulation. We obtained genomes 104 Hymenoptera and transcriptomes representative species. Comparative analysis was performed parse evolutionary trajectory regulatory Ile > Met auto-recoding site Adar gene. At genome level, pre-editing codon conserved across node containing all eusocial hymenopterans. events are confirmed species shows considerable condition-specificity. Compared random expectation, editable avoids substitutions uneditable codons, but does not avoid other unrelated amino acids. The selectively maintained, supporting flexible hypothesis. proposed new angle view adaptation editing, providing another layer explain great phenotypical plasticity insects.

Language: Английский

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Large-scale genome analyses provide insights into Hymenoptera evolution

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

Published: July 3, 2024

Abstract The order Hymenoptera includes a large number of species with diverse lifestyles and is known for its significant contributions to natural ecosystems. To better understand the evolution this order, we performed large-scale comparative genomics on 131 from 13 superfamilies, covering most representative groups. We used these genomes reveal an overall pattern genomic change in terms gene content evolutionary rate throughout hymenopteran history. identified genes that possibly contributed several key innovations, such as parasitoidism, wasp-waist, sting, secondary phytophagy. also discovered distinct trajectories between clade containing major parasitoid wasps (Parasitoida) stinging (Aculeata) since their divergence, which are involved many aspects change, rapidly evolving families, gain loss, metabolic pathway evolution. In addition, explored features accompanying three independent Our work provides insights understanding genome basis diversification Hymenoptera.

Language: Английский

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Effective population size does not explain long-term variation in genome size and transposable element content in animals

Published: Sept. 11, 2024

Animal genomes exhibit a remarkable variation in size, but the evolutionary forces responsible for such are still debated. As effective population size (N e ) reflects intensity of genetic drift, it is expected to be key determinant fixation rate nearly-neutral mutations. Accordingly, Mutational Hazard Hypothesis postulates lineages with low N have bigger genome sizes due accumulation slightly deleterious transposable elements (TEs), and those high maintain streamlined as consequence more selection against TEs. However, existence both empirical confirmation refutation using different methods scales precludes its general validation. Using high-quality public data, we estimated TE content non-synonymous synonymous substitutions (dN/dS) proxy 807 species including vertebrates, molluscs insects. After collecting available life-history traits, tested associations among proxies, while accounting phylogenetic non-independence. Our results confirm TEs major drivers variation, endorse traits dN/dS reliable proxies . do not find any evidence increased drift result an across animals. Within closely related clades, only few isolated weak emerge fishes birds. outline scenario where dynamics vary according lineage-specific patterns, lending no support predominant force driving long-term evolution

Language: Английский

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Social family structure and biogeography contribute to genomic divergence and cryptic speciation in the only eusocial beetle species, Austroplatypus incompertus (Curculionidae: Platypodinae)

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

Published: Nov. 3, 2024

Abstract Eusociality in insects has arisen multiple times independently Hymenoptera (bees, wasps, ants), Blattodea (termites) and Coleoptera (beetles). In Blattodea, the evolution of eusociality led to massive species proliferation. hyperdiverse Coleoptera, evolved only once, ancient Australian ambrosia beetle Austroplatypus incompertus (Curculionidae: Platypodinae). This occurs mesic eucalypt forests eastern Australia, from Victoria northern New South Wales. Based on few individuals collected southern edges species’ distribution it was initially described as two distinct species; however, names were later synonymised no morphological differences found analyses more specimens. Recent mitochondrial haplotype revealed substantial latitudinal divergence across A. . To address this apparent disparity between molecular data, we sequenced analysed a SNP panel over 6,656 biallelic markers 187 11 sites 1000 km range. Our data indicate that eusocial demographic processes such low colony establishment success rate, limited dispersal reliance reproductive individuals, together with habitat fragmentation contributed population genetic structure species. We further identified Hunter Valley biogeographic barrier split into clades, both clades secondary close contact Barrington Tops plateau without any discernible admixture. results support resurrection second which important consequences for systematics Platypodinae.

Language: Английский

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Genomic architecture in social insects is more strongly associated with phylogeny than social behavior

Annals of the Entomological Society of America, Journal Year: 2024, Volume and Issue: 118(1), P. 59 - 72

Published: Nov. 5, 2024

Abstract The evolution of sociality in insects has been predicted to reduce effective population sizes, turn leading changes genome architecture, including higher recombination rates, larger genomes, increased GC-biased gene conversion (gBGC), and greater intragenomic variation GC content maintain castes through differential methylation. As the number sequenced insect genomes continues grow, it remains an open question which, if any, these genomic features are consistent across social genomes. A major challenge determining such commonalities lack phylogenetically controlled analyses independent origins sociality. Of 15 Hymenoptera species for which rate was available, had rates recombination. Next, we conducted a broader analysis architecture by analyzing assemblies 435 8 Blattodea test content, size, distribution CpG sites or codon bias repeatedly differed between nonsocial species. Overall, there little support predictable associated with Hymenoptera, after accounting phylogenetic relationships. However, found significant negative relationship within family Apidae size Halictidae. In all, results suggest that unique behavior may produce trends architecture. Our study highlights need examine behavior.

Language: Английский

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Genomic analyses of the southern and eastern yellowjacket wasps (Hymenoptera: Vespidae) reveal evolutionary signatures of social life

Annals of the Entomological Society of America, Journal Year: 2024, Volume and Issue: 117(6), P. 286 - 300

Published: Oct. 16, 2024

Abstract Insects have evolved remarkably complex social systems. Social wasps are particularly noteworthy because they display gradations in behaviors. Here, we sequence the genomes of two highly diverged Vespula wasps, V. squamosa and maculifrons Buysson (Hymenoptera: Vespidae), to gain greater insight into evolution sociality. Both that live large colonies characterized by distinct queen worker castes. However, is a facultative parasite, its frequent host. We found both species were ~200 Mbp size, similar genome sizes congeneric species. Analyses gene expression from members different castes developmental stages revealed similarities patterns among immature life stages. also evidence DNA methylation within directly analyzing reads. Moreover, genes uniformly expressed relatively methylated. further uncovered differences molecular taxa, consistent with exhibiting alterations evolutionary pressures associated facultatively parasitic or polygyne history. Finally, rates correlated variation between stages, as expected if more subject stronger levels selection. Overall, this study expands our understanding how behavior relates insects.

Language: Английский

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