Molecular biology and evolution最新文献

The RNA-dependent RNA polymerase (RdRP) is the only homologous gene shared among current members of the kingdom Orthornavirae in the realm Riboviria. It is therefore used as a hallmark gene to infer their evolutionary relationships and to guide their taxonomic classification. While sequence similarity between RNA viruses is often limited and sequences problematic to align, the conservation between the three-dimensional tertiary structures of viral RdRPs is notable, supporting analysis of deep evolutionary relationships. Nevertheless, the limited availability of experimental RdRP structures restricts structure-based phylogenetic analyses. We used the protein structure prediction algorithm AlphaFold to alleviate this restriction and predicted structure models for 989 viral RdRPs. Through structural alignment with Homologous Structure Finder, we identified 211 structurally equivalent residues for RdRPs, representing 96 virus genera recognized by the International Committee on Taxonomy of Viruses. These equivalent residues were used to deduce a comprehensive structure-based phylogenetic tree for viral RdRPs, which was validated using a jackknifing approach developed in this study. For comparison, structural phylogenies were inferred using alignments produced with FoldTree and FoldMason software. The resulting trees mostly support the current taxonomic assignments of RNA viruses at the class rank. However, they do not support the monophyly of phyla Pisuviricota and Duplornaviricota. Furthermore, flaviviruses frequently group apart from other members of Kitrinoviricota. The conservation of protein structures over long periods of evolutionary time, when detectable sequence homology may be lost and sequence alignment problematic, supports the use of protein structure comparison methods for demonstrating the deeper evolutionary histories of RNA viruses.

The Aedes aegypti mosquito is a vector for human arboviruses and zoonotic diseases and therefore poses a serious threat to public health. Understanding how Ae. aegypti adapts to environmental pressures-such as insecticides-is critical for developing effective mitigation strategies. However, most traditional methods for detecting recent positive selection search for signatures of classic "hard" selective sweeps, and to date no studies have examined soft sweeps in Ae. aegypti. This is a significant limitation as this is vital information for understanding the pace of adaptation-populations that can immediately respond to new selective pressures are expected to adapt more often via standing variation or recurrent adaptive mutations (both of which may produce soft sweeps) than via de novo mutations (which produce hard sweeps). To this end, we used a machine learning method capable of detecting hard and soft sweeps to investigate positive selection in Ae. aegypti population samples from Africa and the Americas. Our results reveal that soft sweeps are significantly more common than hard sweeps, which may imply that this species can respond quickly to environmental stressors. This is a particularly concerning finding for vector control methods that aim to eradicate Ae. aegypti using insecticides. We highlight genes under selection that include both well-characterized and putatively novel insecticide resistance genes. These findings underscore the importance of using methods capable of detecting and distinguishing hard and soft sweeps, implicate soft sweeps as a major selective mode in Ae. aegypti, and highlight genes that may aid in the control of Ae. aegypti populations.

In sexually dimorphic species, sex-biased gene expression plays an important role in driving morphological, physiological, and behavioral differences between males and females. Here, we examined patterns of sex-biased gene expression within and among 6 Drosophila species with divergence times ranging from 2 to 50 million years. We detected contrasting patterns of sex bias conservation and turnover between heads and bodies, with more extensive sex-biased expression and greater conservation of sex-biased expression in the body, but more species-specific turnover of sex-biased expression in the head, where conserved, unbiased expression was common. Interestingly, lineage-specific gains of sex-biased expression occurred most often via concordant expression changes in both sexes that differed only in their magnitude, with this pattern being particularly strong in the head, suggesting that the majority of lineage-specific sex bias gains do not represent a resolution of sexual antagonism, but instead reflect regulatory changes shared between the sexes. We detected an enrichment of putatively positively selected expression changes among sex-biased genes in both body parts. Altogether, our findings suggest that sex-biased expression changes are often facilitated by selection, including selection acting on the sex with lower expression, which is especially common for male expression of female-biased genes. We also detected differences in the proportion of sex-biased genes located on the X chromosome depending on sex bias and body part. Overall, our results provide novel insights into the dynamics of sex-biased gene expression, as well as the molecular mechanisms and selective forces underlying its turnover, across short and long evolutionary timescales.

In most animal species, the sex-determining pathway is typically initiated by the presence/absence of a primary genetic cue at a critical point during development. This primary genetic cue is often located on a single locus-referred to as sex chromosomes-and can be limited to females (in a ZZ/ZW system) or males (in an XX/XY system). One trademark of sex chromosomes is a restriction or cessation of recombination surrounding the sex-limited region (to prevent its inheritance in the homogametic sex). This may lead to-through a variety of mechanisms-higher amounts of genetic divergence within this region, ie between the X/Z and Y/W chromosomes, especially when compared with their autosomal counterparts. Recent advances in genome sequencing and computation have brought with them the ability to resolve haplotypes within a diploid individual, permitting assembly of previously challenging genomic regions like sex chromosomes. Leveraging these advances, we identified replicable diagnostic characteristics between typical autosomes and sex chromosomes (within a single genome assembly). Under this framework, we can use this information to identify putative sex chromosome linkage groups across divergent vertebrate taxa and simultaneously curate misassembled regions on autosomes. Here, we present this conceptual framework and associated tool for identifying candidate sex chromosome linkage groups from a single, diploid individual dubbed Sex Chromosome Identification by Negating Kmer Densities.

Copy number variants (CNVs) are DNA duplications and deletions that cause genetic variation, underlying rapid adaptive evolution. CNVs often confer selective advantages but can also incur fitness costs. Evolution of Saccharomyces cerevisiae in nutrient-limited chemostats recurrently selects for amplifications of nutrient transporter genes. However, their fate upon return to a non-selective environment remains unknown. To investigate CNV fitness and stability upon removing the original selection pressure, we studied 15 CNV lineages (11 segmental and 4 whole-chromosomal amplifications) selected in nitrogen-limited chemostats. CNV stability was monitored using fluorescent reporters during propagation in nutrient-rich batch cultures for 110 to 220 generations. All aneuploid lineages showed rapid CNV loss and reversion to a single-copy genotype, whereas segmental amplifications were remarkably stable; one of the 11 strains reverted. Pairwise fitness competitions in rich media revealed strong fitness defects associated solely with CNVs that reverted; reversion led to increased fitness. Using simulation-based inference to estimate reversion rates and fitness effects, we determined negative selection as the primary driver of CNV loss. Whole-genome sequencing revealed that reversion of aneuploids and a segmental amplification left no evidence of prior CNV existence, rendering revertant genomes indistinguishable from the single-copy ancestor. Detailed characterization of a partial revertant identified chromosomal translocation, suggesting that extant CNVs can undergo structural diversification. Our findings provide novel evidence that most segmental CNVs adapted to nitrogen limitation are stable upon removal of selection, but costly gene amplifications are readily reversible. Together, these highlight the importance of CNVs in both long-term genome evolution and rapid, reversible adaptation to transient selection.

The advent of affordable whole-genome sequencing has spurred numerous large-scale projects aimed at inferring the tree of life, yet achieving a complete species-level phylogeny remains a distant goal due to significant costs and computational demands. Traditional species tree inference methods, though effective, are hampered by the need for high-coverage sequencing, high-quality genomic alignments, and extensive computational resources. To address these challenges, this study introduces WASTER, a novel de novo tool for inferring shallow phylogenies directly from short-read sequences. WASTER employs a k-mer based approach for identifying variable sites, circumventing the need for genome assembly and alignment. Using simulations, we demonstrate that WASTER achieves accuracy comparable to that of traditional alignment-based methods, even for low sequencing depth, and has substantially higher accuracy than other alignment-free methods. We validate WASTER's efficacy on real data, where it accurately reconstructs phylogenies of eukaryotic species with as low depth as 1.5X. WASTER provides a fast and efficient solution for phylogeny estimation in cases where genome assembly and/or alignment may bias analyses or is challenging, for example due to low sequencing depth. It also provides a method for generating guide trees for tree-based alignment algorithms. WASTER's ability to accurately estimate shallow phylogenies from low-coverage sequencing data without relying on assembly and alignment will lead to substantially reduced sequencing and computational costs in phylogenomic projects.

The transition to holoparasitism in plants precipitates the loss of photosynthesis, fundamentally altering the selective landscape acting on organellar genomes. These changes raise questions about the mechanisms by which the essential, coevolved machinery of translation responds to extreme genomic erosion and metabolic dependency. Integrating comparative genomics, tRNA sequencing, and subcellular localization assays, we elucidate the extensive rewiring of organellar translation systems and the tRNA-dependent tetrapyrrole biosynthesis pathway in the holoparasitic angiosperm family Balanophoraceae, which exhibits extreme reduction of tRNA content in plastid and mitochondrial genomes. We identified a rare evolutionary event: the putative intracellular transfer of the plastid initiator tRNA (tRNA-iMet) to the nucleus, which compensates for its loss from the plastid genome. We also demonstrate that the unusual UAG-to-Trp reassignment in the Balanophora plastid genetic code is driven by the loss of release factor pRF1 and the recruitment of a mutated nuclear tRNA-Trp. Furthermore, we reveal that the retention of organellar nuclear-encoded aminoacyl-tRNA synthetases is dictated by the presence/absence of cognate organellar tRNAs, which appear to be functional regardless of their foreign (horizontal transfer from the host plant) or native origins. Finally, we uncover a striking evolutionary asymmetry in nuclear-encoded ribosomal proteins: while plastid subunits exhibit elevated substitution rates consistent with relaxed selection and compensatory coevolution, mitochondrial subunits display high sequence conservation, likely maintaining compatibility with the extensive horizontal gene transfer observed in this lineage. Collectively, these findings represent some of the most extreme changes ever identified in the anciently conserved machinery of plant organellar translation.

Ants, Formicidae, are a group of small social insects that inhabit nearly all terrestrial environments. Three competing hypotheses of ant relationships have been proposed, differing in the placement of Martialinae, a subfamily of cryptic, endogean ants. We used BUSCO genes to investigate the signals in individual and concatenated gene datasets. We found that gene trees support all three hypotheses. After concatenation, the three signals persist but their relative strength is model-dependent. The CAT-posterior mean site frequencies approach (which our model adequacy tests show best explains the across-site compositional heterogeneity of the data) finds Martialinae as the sister of all ants but Leptanillinae. We tested the effect of across-lineage compositional heterogeneity using data-recoding and excluding highly heterogeneous taxa. These tests did not lead to the emergence of significant support for alternative tree topologies. However, we identified strong gene- and site-discordance in the data and evidence that signals representing incongruent evolutionary processes exist in ant genomes supporting all three hypotheses. Incomplete lineage sorting and/or introgression seem to have significantly affected early ant evolution, which might make it impossible to establish whether Leptanillinae, Leptanillinae plus Martialinae, or Martialinae represents the sister of all the other ants.

Loss of genetic diversity threatens species survival, yet its dynamics and impacts can vary widely across species depending on their evolutionary histories, life-history traits, and demographic trajectories. To investigate these differences, we analyzed the genomes of 3 species that experienced extreme and well-documented population bottlenecks, the Mauritius parakeet, the Mauritius kestrel, and the pink pigeon, and compared them to 36 species spanning the avian phylogeny with varied IUCN Red List statuses. For each species, we assessed nucleotide diversity, genetic load, and inbreeding coefficients based on runs of homozygosity (FROH). We found a negative correlation between nucleotide diversity and FROH, but neither metric was a good predictor of the species' Red List status. Rather, the effective population size to census size ratio (Ne/Nc) showed a strong correlation to Red List status. Species with larger historical effective population sizes showed greater heterozygosity but carried a higher heterozygous load, highlighting the importance of historical demography for contextualizing species' vulnerability to genomic erosion. We also found significant differences in genetic load between taxonomic groups (parrots, pigeons, and falcons), possibly due to differences in life-history traits and demographic histories, underscoring the importance of interpreting genomic erosion dynamics in an evolutionary context. By anchoring our study on 3 evolutionarily divergent endangered species from Mauritius, we show how multispecies comparisons can contextualize extreme bottlenecks within a broader evolutionary framework, thereby identifying both general patterns of genomic erosion and species-specific vulnerabilities.

Transcription factor nuclear factor-kappa B (NF-κB) and many upstream signaling components have been identified in a diversity of holozoan taxa, including unicellular holozoans (eg Filasterea and Choanoflagellata) and the metazoan phyla Porifera (sponges), Placozoa, and Cnidaria (eg jellyfishes, sea anemones, corals, and hydra). Herein, we review recent progress made toward characterizing the structure, regulation, activity, and biological functions of NF-κB proteins found in these taxa. We also provide an updated phylogenetic sampling of NF-κB orthologs highlighting their different domain configurations among holozoans, as well as a method for comparing the computationally predicted three-dimensional structures of NF-κB dimers and relating these structures to their amino acid similarities and DNA-binding specificities. This synthesis reveals new insights regarding the evolutionarily conserved and variable domain-dependent activities and regulation of holozoan NF-κBs. Further, we provide an overview of the roles of NF-κB in pathogen responses, stress responses, symbiosis, and development, with a focus on recent findings from sponges and cnidarians. This curation of a growing body of knowledge highlights both conserved and divergent roles of NF-κB in foundational biological processes. Finally, we suggest priorities for future research on the evolution of NF-κB structure and function. Overall, investigations of NF-κB in diverse holozoan taxa will continue to provide information about the origins of this important and pervasive transcriptional regulator and will also contribute to an understanding of the responses of sentinel species to the modern-day stresses associated with changing environmental conditions and novel pathogen-based diseases.