Distinct host adaptation strategies and conserved biosynthetic potential are revealed in Clostridia, with Oscillospirales showing extensive specialization and Lachnospirales maintaining versatility.
Molecular Biology and Evolution
Oxford University Press · Genomics & Bioinformatics · ISSN 0737-4038, 1537-1719
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Accounting for genotype uncertainty and structured migration reduces false negatives in identifying adaptive variation in low-coverage genome data of Fringilla species.
DNA methylation shows limited association with gene expression and wing pattern differences in Bicyclus anynana butterflies' seasonal forms.
Deep-branching ciliates experienced massive intron loss and predominantly retain tiny 3n introns, revealing contrasting intron evolution modes in unicellular eukaryotes.
Kamino rapidly generates accurate proteome-wide amino acid phylogenomic alignments, outperforming classical methods with speeds several orders of magnitude faster.
Ancient whole genome duplication in vertebrates led to the divergence of cytochrome c genes, with testis-type proteins showing 2.5 times greater resistance to hydrogen peroxide.
Ultra-short introns under 30 base pairs independently evolved in at least two parasitic animal lineages, with median lengths as short as 22 bp in Myxozoa.
Natural selection significantly influences metabolite abundance in Saccharomyces cerevisiae, with about 28.58% of metabolites under directional selection, shaping the metabolome's evolution.
Mito-nuclear incompatibility in black soldier flies disrupts mitochondrial and peroxisomal metabolism, reducing ACOX1/ACOX3 activity and impairing organismal fitness.
Long-read sequencing revealed 5.7 million structural variants in three conifer species, with significant impacts on genome structure and evolution.
DAIseg, a new reference-free HMM-based method, outperforms existing tools by jointly detecting Neanderthal and Denisovan introgressed segments in modern human genomes, revealing two Denisovan events in Papuans.
Male-female expression imbalance of X-linked genes is widespread across phrynosomatid lizards, with females overexpressing ancestral X genes and males underexpressing neo-X genes.
Gene-level complexity, measured by genomic features, explains variation in the distribution of fitness effects across genomes of multiple species.
Arabis alpina populations in Northern Spain show genetic divergence and adaptation to drought, driven by demographic history and climatic shifts since the last glacial maximum.
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Nonsense-mediated mRNA decay effectively degrades PTV transcripts in wild yeast diploids but shows no widespread evidence of transcriptional adaptation.
Redesign of frustrated regions in the T4 clamp loader restores function, with fitness improvements up to 2.5-fold in defective variants.
A highly prevalent Mega-NUMT with up to 60 mitochondrial genomes is stably integrated into the nuclear genome of Drosophila paulistorum, found in 40% of populations.
Genomic analysis reveals that Chinese and Indian rhesus macaque populations diverged approximately 140,000 generations ago, with current sizes of about 220,000 and 14,000 individuals respectively.
Extreme dietary shifts in carnivorous Miletinae butterflies cause disrupted mitonuclear coadaptation, with mitochondrial evolution accelerating 2-3 times compared to relatives.
Over 20 independent recruitment events transformed neuropeptide genes into venom toxins in Conus textile, driven by diverse genomic mechanisms rather than whole-genome duplication.
snpArcher pipeline produces high-quality, analysis-ready variant callsets from raw sequencing data in non-model organisms, demonstrated with 137 burrowing owl genomes.
Bayesian analysis refutes explosive diversification models, showing they have near-zero probability for the origin of animals and placental mammals.
Recurrent artefactual within-host SARS-CoV-2 variants are common and can distort diversity and transmission estimates, even at low minor allele frequencies.
Local ancestry inference reveals strong evidence of selection at FADS1/2 in Neolithic Europe, with consistent signals across multiple datasets and methods.
Bacterial chromosomes acquire and lose toxin-antitoxin systems rapidly, with most TAs being short-lived and often lost through deletion or pseudogenization.
Fission yeasts evolved distinct invertase paralogs, with Inv2 uniquely coupling carbon metabolism to sexual reproduction in S. pombe, enabling adaptation to diverse sugar environments.
High rD values in yeast genetic correlations indicate more stable, polygenic-driven trait relationships across environments, with some correlations influenced by few large-effect loci.
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