The molecular basis of phenotypic evolution: beyond the usual suspects

Trends in Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: May 1, 2024

Language: Английский

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A microRNA is the effector gene of a classic evolutionary hotspot locus

Science, Journal Year: 2024, Volume and Issue: 386(6726), P. 1135 - 1141

Published: Dec. 5, 2024

In Lepidoptera (butterflies and moths), the genomic region around gene cortex is a “hotspot” locus, repeatedly implicated in generating intraspecific melanic wing color polymorphisms across 100 million years of evolution. However, identity effector regulating within this locus remains unknown. We show that none four candidate protein-coding genes including , serve as major effectors. Instead, microRNA (miRNA), mir-193 serves three deeply diverged lineages butterflies, its role conserved Drosophila . Lepidoptera, derived from gigantic primary long noncoding RNA, ivory it functions by directly repressing multiple pigmentation genes. miRNA can drive repeated instances adaptive evolution animals.

Language: Английский

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Iterative evolution of supergene-based social polymorphism in ants

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1856)

Published: June 13, 2022

Species commonly exhibit alternative morphs, with individual fate being determined during development by either genetic factors, environmental cues or a combination thereof. Ants offer an interesting case study because many species are polymorphic in their social structure. Some colonies contain one queen while others queens. This variation number is generally associated suite of phenotypic and life-history traits, including mode colony founding, lifespan, queen-worker dimorphism size. The basis this polymorphism has been studied five ant lineages, remarkably morph seems to be supergene all cases. These 'social supergenes' tend large, having formed through serial inversions, comprise hundreds linked genes. They have persisted over long evolutionary timescales, multiple lineages following speciation events, spread between closely related via introgression. Their dynamics unusually complex, combining recessive lethality, spatially variable selection, selfish elements non-random mating. Here, we synthesize the cases supergene-based ants, highlighting commonalities, idiosyncrasies implications for evolution polymorphisms general. article part theme issue 'Genomic architecture supergenes: causes consequences'.

Language: Английский

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Disease outbreaks select for mate choice and coat color in wolves

Science, Journal Year: 2022, Volume and Issue: 378(6617), P. 300 - 303

Published: Oct. 20, 2022

We know much about pathogen evolution and the emergence of new disease strains, but less host resistance how it is signaled to other individuals subsequently maintained. The cline in frequency black-coated wolves ( Canis lupus ) across North America hypothesized result from a relationship with canine distemper virus (CDV) outbreaks. tested this hypothesis using cross-sectional data wolf populations that vary prevalence CDV allele makes coats black, longitudinal Yellowstone National Park, modeling. found outbreaks generates fluctuating selection results heterozygote advantage turn affects black allele, optimal mating behavior, continent.

Language: Английский

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Genetic structure, UV‐vision, wing coloration and size coincide with colour polymorphism in Fabriciana adippe butterflies

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(5)

Published: Jan. 19, 2024

Abstract Colour polymorphisms have long served as model systems in evolutionary studies and continue to inform about processes involved the origin dynamics of biodiversity. Modern sequencing tools allow for evaluating whether phenotypic differences between morphs reflect genetic differentiation rather than developmental plasticity, investigating represent intermediate stages diversification towards speciation. We investigated two colour butterfly Fabriciana adippe using a combination ddRAD‐sequencing comparisons body size, patterns optical properties bright wing spots. The silvery‐spotted form had larger darker wings reflected UV light, while yellow cleodoxa displayed more green scales very little UV, showcasing that they constitute distinct alternative integrated phenotypes. Genomic analyses revealed structuring according source population, morph, suggesting reflects modifications. report 17 outlier loci associated with including ultraviolet‐sensitive visual pigment ( UVRh1 ), which is intraspecific communication mate choice butterflies. Together demonstration (but essentially not ) morph reflectance higher females males differ this suggests these might genetically phenotypes, possibly adapted different microhabitats. propose non‐random mating contribute maintenance polymorphism.

Language: Английский

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Ecotype formation in the European anchovy fuelled by structural variants of different origins and genetic interactions with a southern lineage

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

Published: Sept. 19, 2024

Abstract The speciation of ecotypes can unfold in diverse ways and likely depends on multiple processes. variants involved ecotype divergence include new mutations as well older allelic variation that evolved different contexts. Among the types contribute to reproductive isolation between ecotypes, structural (SVs) represent candidates due their ability protect divergent haplotypes from recombination gene flow. European anchovy ( Engraulis encrasicolus ) is known be subdivided into marine coastal shows patterns are consistent with SVs. Here, we present first genome-scale study investigating genetic structure E. species complex. We generated a reference genome produced whole-genome resequencing data for anchovies North-East Atlantic Mediterranean Sea, South Africa. complemented this approach analysis RAD-seq order ecotypic across entire distribution range. found diversity not only characterised by presence two clusters, namely but also third ancestry which corresponds southern lineage. This lineage occurs off Africa Morocco Canary Islands, gradient admixture northern populations nearing Atlantic-Mediterranean transition zone. Genomic landscapes differentiation showed evidence large regions high linkage disequilibrium, representing SVs differentiate three lineages. contributing flow barrier originated lineage, suggesting lineages have partly shared evolutionary history. In addition these barriers, other appear situ . Anchovies thus an interesting case speciation, since barriers origins diverged geographic isolation.

Language: Английский

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Phenotypic and genomic dissection of colour pattern variation in a reef fish radiation

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(4)

Published: June 20, 2023

Abstract Coral reefs rank among the most diverse species assemblages on Earth. A particularly striking aspect of coral reef communities is variety colour patterns displayed by fishes. Colour pattern known to play a central role in ecology and evolution fishes through, for example, signalling or camouflage. Nevertheless, complex trait fishes—actually collection traits—that difficult analyse quantitative standardized way. This challenge that we address this study using hamlets ( Hypoplectrus spp., Serranidae) as model system. Our approach involves custom underwater camera system take orientation‐ size‐standardized photographs situ, correction, alignment fish images with combination landmarks Bézier curves, principal component analysis value each pixel aligned fish. identifies major elements contribute phenotypic variation group. Furthermore, complement image whole‐genome sequencing run multivariate genome‐wide association variation. second layer reveals sharp peaks along hamlet genome element allows characterize effect single nucleotide polymorphisms are strongly associated at peak. results suggest diversity generated modular genomic architecture.

Language: Английский

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High-quality haploid genomes corroborate 29 chromosomes and highly conserved synteny of genes in Hyles hawkmoths (Lepidoptera: Sphingidae)

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Aug. 7, 2023

Abstract Background Morphological and traditional genetic studies of the young Pliocene genus Hyles have led to understanding that despite its importance for taxonomy, phenotypic similarity wing patterns does not correlate with phylogenetic relationship. To gain insights into various aspects speciation in Spurge Hawkmoth ( euphorbiae ), we assembled a chromosome-level genome investigated some characteristics. Results The male H. was sequenced using PacBio Hi-C data, yielding 504 Mb assembly (scaffold N50 18.2 Mb) 99.9% data represented by 29 largest scaffolds forming haploid chromosome set. Consistent this, FISH analysis karyotype revealed n = chromosomes WZ/ZZ (female/male) sex system. Estimates length based on image provided an additional quality metric size. Rescaffolding published vespertilio resulted high-quality (651 Mb, scaffold 22 98% sequence chromosomes. larger size (average 1C DNA value 562 accompanied proportional increase repeats from 45% (measured as 472 almost 55% . Several pattern genes were found same two species, varying amounts positions repetitive elements inversions possibly corrupting their function. Conclusions Our two-fold comparative genomics approach high gene synteny genomes other Sphingidae correspondence intact Merian elements, ancestral linkage groups Lepidoptera, exception three simple fusion events. We propose standardized taxonomy nucleotide homology via chaining primary tool combined Oxford plots infer visualize directionality chromosomal rearrangements. identification promises future evolution forewing , although further sequencing more individuals are needed. genomic obtained provide reliable references hawkmoths (Sphingidae).

Language: Английский

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Major patterns in the introgression history of Heliconius butterflies

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Sept. 11, 2023

Gene flow between species, although usually deleterious, is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes estimation of relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach estimate phylogeny major introgression events in Heliconius butterflies from whole-genome sequence data. We obtain a robust branching order among clades genus, including ‘melpomene-silvaniform’ group, which shows extensive historical ongoing gene flow. chromosome-level estimates key parameters phylogeny, divergence times, present-day ancestral population sizes, as well direction, timing, intensity Our analysis leads with differ those obtained previous studies. find aoede most likely represents earliest-branching lineage genus ‘silvaniform’ are paraphyletic within melpomene-silvaniform group. provides new, parsimonious histories for origins traits , pollen feeding inversion involved wing pattern mimicry. results demonstrate power feasibility MSC estimating despite The methods used here should be useful other difficult groups high rates introgression.

Language: Английский

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“Divergence and gene flow history at two large chromosomal inversions involved in long-snouted seahorse ecotype formation”

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

Published: July 4, 2023

Abstract Chromosomal inversions can play an important role in divergence and reproductive isolation by building maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they take the form of balanced polymorphisms that segregate within populations over time until one arrangement becomes fixed. Many questions remain about how these different inversion arise, mechanisms responsible for their long-term maintenance interact, ultimately contribute to speciation. The long-snouted seahorse ( Hippocampus guttulatus ) is known be subdivided into partially isolated lineages marine-lagoon ecotypes differentiated structural variation. Here, we aim characterise differences along entire genome, reconstruct history ecotype formation. We generated a near chromosome-level reference genome assembly described genome-wide patterns diversity through analysis 112 whole-genome sequences from Atlantic, Mediterranean, Black Sea populations. Combined with linked-read sequencing data, found evidence two megabase-scale chromosomal showing contrasted allele frequency across species range. reveal represent ancient intraspecific polymorphisms, being likely maintained divergent selection, other associative overdominance. Haplotype characterising Mediterranean also suggest existence potential interactions inversions, possibly driven environment-dependent fitness effects. Lastly, detected gene flux eroding inverted alleles at varying levels impact on dynamics.

Language: Английский

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