CASTER: Direct species tree inference from whole-genome alignments

Science, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference tree life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, current practice leaves out large chunks genomes. As more high-quality genomes become available, we urgently need methods infer directly from a multiple genome alignment. Here, introduce CASTER, theoretically justified site-based method that eliminates predefine recombination-free loci. CASTER is scalable hundreds mammalian whole We demonstrate accuracy in simulations include recombination apply several biological datasets, showing its per-site scores can reveal both artefactual patterns discordance across genome.

Language: Английский

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A leaf-mimicking moth uses nanostructures to create 3D leaf shape appearance

Current Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

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A micro-RNA is the effector gene of a classic evolutionary hotspot locus

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

Published: Feb. 12, 2024

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

Language: Английский

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A long noncoding RNA at the cortex locus controls adaptive coloration in butterflies

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(36)

Published: Aug. 30, 2024

Evolutionary variation in the wing pigmentation of butterflies and moths offers striking examples adaptation by crypsis mimicry. The

Language: Английский

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A long non-coding RNA at thecortexlocus controls adaptive colouration in butterflies

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

Published: Feb. 12, 2024

Abstract Evolutionary variation in the wing pigmentation of butterflies and moths offers striking examples adaptation by crypsis mimicry. The cortex locus has been independently mapped as controlling colour polymorphisms 14 lepidopteran species, suggesting it acts a genomic hotspot for diversification patterns, but functional validation through protein-coding knockouts proven difficult to obtain. Our study unveils role novel long non-coding RNA (lncRNA) which we name ivory , transcribed from locus, modulating patterning butterflies. Strikingly, expression prefigures most melanic patterns during pupal development, an early developmental specifying scale identity. To test this, generated CRISPR mosaic knock-outs five nymphalid butterfly species show that mutagenesis yields transformations dark pigmented scales into white or light-coloured scales. Genotyping Vanessa cardui germline mutants associates these phenotypes small on-target deletions at conserved first exon . In contrast, mutant with confirmed null alleles lack any phenotype, exclude this adjacent gene. Overall, results lncRNA master switch pattern specification, played key roles adaptive Significance statement Deciphering genetic underpinnings is fundamental comprehensive understanding evolutionary processes. Long RNAs (lncRNAs) represent emerging category modulators within genome, yet they have overlooked source phenotypic diversity. study, unveil pivotal orchestrating transitions between light development. Remarkably, gene nested region known control multiple cases moths, including iconic natural selection. These findings highlight significant influence lncRNAs regulation, also underscore their potential players process itself.

Language: Английский

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TheivorylncRNA regulates seasonal color patterns in buckeye butterflies

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

Published: Feb. 12, 2024

Abstract Long non-coding RNAs (lncRNAs) are transcribed elements increasingly recognized for their roles in regulating gene expression. Thus far, however, we have little understanding of how lncRNAs contribute to evolution and adaptation. Here show that a conserved lncRNA, ivory , is an important color patterning the buckeye butterfly Junonia coenia . overlaps with cortex locus linked multiple cases crypsis mimicry Lepidoptera. Along companion paper by Livraghi et. al., argue not pattern interest at this locus. In J. cluster cis -regulatory (CREs) first intron genetically associated natural variation seasonal plasticity, targeted deletions these CREs phenocopy phenotypes. Deletions different produce other distinct phenotypes as well, including loss melanic eyespot rings, positive negative changes overall wing pigmentation. We transcription factors Spineless, Bric-a-brac, Ftz-f1 bind promoter during development, suggesting they directly regulate This case study demonstrates -regulation single RNA can exert diverse nuanced effects on development patterns, modulating seasonally plastic patterns. Significance The genomic hosting has been numerous adaptation moths butterflies, crypsis, mimicry, polyphenism. butterflies actual evolutionarily long (lncRNA), dubbed Compared genes, stands out because highly nuanced, quantitative pigmentation be achieved manipulating adjacent sequences. highlights underlying morphological evolution, emphasizes importance considering transcripts comparative genomics.

Language: Английский

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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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The ivory lncRNA regulates seasonal color patterns in buckeye butterflies

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(41)

Published: Oct. 1, 2024

Long noncoding RNAs (lncRNAs) are transcribed elements increasingly recognized for their roles in regulating gene expression. Thus far, however, we have little understanding of how lncRNAs contribute to evolution and adaptation. Here, show that a conserved lncRNA, ivory , is an important color patterning the buckeye butterfly Junonia coenia . overlaps with cortex locus linked multiple cases crypsis mimicry Lepidoptera. Along companion paper by Livraghi et al., argue not pattern interest at this locus. In J. cluster cis -regulatory (CREs) first intron genetically associated natural variation seasonal plasticity, targeted deletions these CREs phenocopy phenotypes. Deletions different produce other distinct phenotypes as well, including loss melanic eyespot rings, positive negative changes overall wing pigmentation. We transcription factors Spineless, Bric-a-brac, Ftz-f1 bind promoter during development, suggesting they directly regulate This case study demonstrates -regulation single RNA can exert diverse nuanced effects on development patterns, modulating seasonally plastic patterns.

Language: Английский

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Evolutionary genomics of camouflage innovation in the orchid mantis

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

Published: Aug. 10, 2023

Abstract The orchid mantises achieve camouflage with morphological modifications in body color and pattern, providing an interesting model for understanding phenotypic innovation. However, a reference genome is lacking the order Mantodea. To unveil mechanisms of plant-mimicking coloration patterns, we performed de novo assembly two chromosome-level genomes mantis its close relative, dead leaf mantis. Comparative genomic analysis revealed that Scarlet gene plays important role synthesis xanthommatin, pigment coloration. Combining developmental transcriptomic genetic engineering experiments, found cuticle was essential component ‘petal-like’ enlargement, specific expression ventral femur controlled by Wnt signaling. prolonged Ultrabithorax (Ubx) accompanied femoral expansion suggested Ubx determines leg remodeling early stage. We also evidence evolution Trypsin family insectivory adaptation ecdysone-dependent sexual dimorphism size. Overall, our study presents new catalogs reveals evolutionary underlying unique praying mantis, insights into innovation adaptation.

Language: Английский

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