Molecular biology and evolution最新文献

Insects often depend on symbiotic bacteria for protection, yet the mechanisms by which these microbes target specific natural enemies remain poorly understood. In aphids, different strains of the facultative symbiont Hamiltonella defensa provide highly specific protection against particular species of parasitoid wasps. To uncover the genetic basis of this specificity, we analyzed 26 Hamiltonella genomes and their toxin-encoding APSE bacteriophages with distinct protective phenotypes. Our analyses revealed that Hamiltonella strains share a conserved core genome but differ significantly in accessory gene content, reflecting their distinct evolutionary origins. Strikingly, we show that variation in toxin types is the key distinguishing feature of APSE phages in Hamiltonella strains that protect against different parasitoid species. These toxin repertoires include several novel candidates, such as variants with MAC/perforin domains and leucine-rich repeat (LRR) proteins previously unreported in insect defensive symbionts. We also reveal cases of multiple co-integrated APSE phages carrying different toxins within a single genomic locus. These findings suggest phage-borne toxins are important determinants of enemy-specific defense and point to phage-driven toxin diversification as a major force shaping the functional evolution of this symbiosis. This work highlights how mobile genetic elements influence the ecological roles and diversification of protective symbionts.

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.

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.

Many bacteria rely on efflux pumps to survive antibiotic stress, and exposure to antibiotics often leads to mutations in pump genes or their regulators that increase pump expression. Predicting the spectrum of these mutations is important for designing effective antibiotic treatments, but the underlying regulatory networks are large and complex, making them difficult to map experimentally. To address this challenge, we developed a mathematical framework that integrates dynamical equations for efflux pump regulation with a genetic algorithm for parameter estimation and evolutionary simulations. Using this framework, we simulated in silico evolution of Pseudomonas aeruginosa under exposure to the antibiotics meropenem, tobramycin, and ciprofloxacin. The simulations revealed mutational spectra affecting the expression of four RND efflux pumps and their shared regulatory network. The most frequently mutated genes were single-target regulators that matched well with previous observations in clinical and it in vitro studies. The model also showed that the shared use of the OprM protein by two pumps is a key factor shaping their distinct mutational patterns. Mutations often produced multi-trait phenotypes, manifesting as collateral sensitivity or cross-resistance to antibiotics not used for selection. While cross-resistance evolved readily, its extent depended on initial pump expression levels and thus may vary between strains. Finally, simulations of changing environments showed that efflux pump genes tend to be lost in the absence of antibiotics, suggesting a potential strategy to steer bacterial evolution toward reduced capacity to re-evolve resistance.

Statistical methods to identify Neanderthal ancestry in modern human genomes rest on varying assumptions and inputs. Nonetheless, most studies of introgression use only a single method to define Neanderthal ancestry. Due to a lack of "ground truth," we have a limited understanding of the accuracy, comparative strengths and weaknesses, and the sensitivity of downstream conclusions for these methods. Here, we performed large-scale comparisons of 14 genome-wide introgression maps computed by 11 representative Neanderthal introgression detection algorithms: admixfrog, ArchaicSeeker2, ArchIE, ARGWeaver-D, CRF, DICAL-ADMIX, hmmix, IBDmix, SARGE, Sprime, and S*. These algorithms span statistical approaches based on summary statistics, probabilistic modeling, and machine learning, and vary in their use of archaic, modern, and simulated genomes as input. Our results highlight a core set of regions predicted by nearly all methods, as well as substantial heterogeneity in commonly used Neanderthal introgression maps, especially at the individual genome level. Furthermore, we find that downstream analyses may result in different conclusions depending on the map used. Thus, we recommend careful consideration of map(s) chosen for downstream analysis and support the use of multiple maps to ensure robustness of conclusions. We make integrated prediction sets available, enabling further understanding of Neanderthal introgression's legacy on modern humans.

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 produces 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.

A current goal of speciation research is identifying loci underlying reproductive barriers between species. Locating barrier loci in population genomic data is difficult due to the often-complex demographic history of diverged taxa and heterogeneity in evolutionary forces across the genome. We take advantage of natural hybridization between two wood ant species (Formica aquilonia and F. polyctena) to identify regions of reduced long-term gene flow using demographically explicit scans of non-admixed genomes. In addition, we identify candidate Bateson-Dobzhansky-Muller incompatibilities (BDMIs) through an imbalanced recombinant haplotype frequency analysis using a large sample of natural F. aquilonia × F. polyctena hybrid genomes. These approaches find barriers and BDMIs scattered across the genome. Furthermore, BDMIs significantly overlap with long-term barriers, indicating that some BDMIs have persisted despite divergence with gene flow. Intriguingly, the number of pairwise interactions a BDMI has correlates with its long-term barrier strength: hub-like BDMIs with many interactions reduce gene flow more effectively. Finally, we find that long-term barriers are depleted for both coding sequences (CDS) and transposable elements (TEs), while candidate BDMIs are associated with snRNAs and LTR transposons, specifically Ty1-copia. In contrast, regions where long-term barriers and BDMIs co-locate are significantly associated with introns but not CDS or TEs, implying a potential role of alternative splicing or gene regulation in long-term incompatibilities. Our results highlight the underappreciated impact of BDMI connectivity on the persistence of reproductive barriers over time.

The eastern Tianshan range in Xinjiang, serving as a crucial link between the East and the West, acts as an important channel for the eastward spread of East Asian millet and painted pottery, as well as the westward diffusion of West Asian wheat and barley, bronze wares, and livestock. However, due to the scarcity of ancient genomic data, the history of population interaction and admixture in this region remains unclear. We sequenced 23 ancient individuals from 12 archaeological sites from the Bronze Age to historical periods in Xinjiang. We identified intraregional population interactions, demonstrating that an indigenous local ancestry, represented by Tarim_EMBA1, spread to the Tianshan and persisted into the historical period. The incoming East Asian millet farmers, along with Western Steppe herders characterized by Afanasievo, contributed to the formation of the eastern Tianshan populations during the Iron Age, which is consistent with archaeological findings of painted pottery and pastoral subsistence in this area. The genetic affinity to East Asian millet farmers in the eastern Tianshan increased over time, likely reflecting geographic proximity and geopolitical changes. In contrast, in line with archaeological observations, the Iron Age individuals in the western Tianshan derived their Steppe-related ancestry from populations associated with the Andronovo culture. Our results illustrated the interplay between genetics and culture in the eastern Tianshan.

Mimicry is a manifestation of natural selection that provides a key system for exploring the evolution of complex adaptive traits. Epicopeiidae moths are strikingly diverse morphologically, having evolved resemblance to multiple butterfly and moth models despite their recent origin. To uncover the genomic basis of this rapid morphological diversification, we sequenced high-quality genomes for eight Epicopeiidae species (three at the chromosome level), and conducted comparative genomics, developmental transcriptomics, and chromatin accessibility analyses. We found that genomic structural variations and gene family expansions contributed little to morphological evolution, whereas genes under positive selection in the ancestral Epicopeiidae were enriched for neural and visual functions, likely linked to the shift from nocturnal to diurnal activity of the Epecopeiidae ancestor. In contrast, accelerated conserved noncoding elements (aCNEs) and Epicopeiidae-specific accessible chromatin regions (ACRs) were enriched near morphogenetic genes, suggesting that changes in regulatory elements played a key role in morphological innovation. Our analyses also found that Epicopeiidae experienced a pronounced burst of transposable element (TE) activity between 40-10 Mya, temporally coinciding with morphological diversification. Approximately two-thirds of ACRs overlapped with TEs, and TE-derived ACRs were enriched near morphogenetic genes. These findings suggest that TE-driven regulatory innovation rewired developmental gene networks of Epicopeiidae and facilitated the emergence of multiple mimetic forms. Epicopeiidae thus provide a compelling example for understanding how TE-mediated regulatory evolution might fuel phenotypic innovation.

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 (e.g., Filasterea and Choanoflagellata) and the metazoan phyla Porifera (sponges), Placozoa, and Cnidaria (e.g., jellyfishes, sea anemones, corals, and hydra). Herein, we review recent progress made towards 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.