Torpor is a key survival strategy that many avian and mammalian lineages evolved in response to challenging environmental conditions. Whether the independent evolution of torpor in different lineages involved changes in the same genes remains poorly understood. Here, we performed comparative screens across 190 placental mammal genomes to comprehensively examine associations between loss, positive selection, and evolutionary rate shifts in individual protein-coding genes and evolutionary shifts in torpor use. We find that gene-torpor associations are highly clade-specific, with no gene being able to explain the majority of torpor shifts across the phylogeny of placental mammals. In contrast, there is more evidence, albeit still limited, for evolutionary convergence at the pathway level. Our results suggest that torpor emerged through several genetic routes in placental mammals, which likely explains the vast diversity of torpor use patterns that can be observed among torpor-capable species today.
Plastid genomes retain a reduced but essential translation system inherited from cyanobacterial ancestors, but the evolutionary constraints shaping their diversification remain poorly resolved. One key component ensuring translational fidelity is the tRNAIle-lysidine system, mediated by tRNAIle-lysidine synthetase (TilS), which enables accurate decoding of the AUA isoleucine codon. Here, we characterized the complete plastid genome of the Antarctic green alga Micractinium simplicissimum and investigated the evolutionary distribution of the tilS-trnI(CAU) module across green algal plastomes. Phylogenomic analyses of 35 plastomes revealed consistent retention of this module in Chlorellales, whereas partial loss or structural fragmentation occurred in core Trebouxiophyceae lineages. Comparative analyses of codon usage showed that AUA frequencies varied widely among major green algal lineages but were not tightly associated with tilS retention, suggesting partial evolutionary decoupling between tRNA modification systems and synonymous codon usage. Structural comparisons further revealed lineage-specific insertions and domain rearrangements in plastid TilS proteins relative to their cyanobacterial homologs. Candidate nuclear-encoded TilS homologs were additionally identified in several plastid tilS-lacking taxa, suggesting possible intracellular relocation of decoding functions. Together, these findings suggest that plastid decoding systems evolve through modular, lineage-specific trajectories that allow structural plasticity while maintaining translational fidelity. This study provides new insights into the evolutionary dynamics of gene expression systems in endosymbiotic organelles.
Sexual dichromatism, characterized by sex-specific differences in coloration, is widespread among birds and often involves carotenoid-based pigmentation. Despite extensive research on the social and ecological environments favoring sexual dichromatism, the molecular mechanisms underlying its development and evolution remain largely unexplored. In this study, we investigated the genetic and molecular processes giving rise to sexual dichromatism in the red ketocarotenoid-based plumage of northern cardinals (Cardinalis cardinalis). We quantified carotenoid concentrations in plasma and feather follicles, confirmed that homologs of CYP2J19, BDH1L, and TTC39B catalyze the production of C-4 ketocarotenoids, and performed gene expression analyses across tissues. Males showed significantly higher plasma and feather ketocarotenoid concentrations, upregulated CYP2J19 and TTC39B expression in liver and feather tissues, and upregulated carotenoid transport gene expression in the gut and feather follicles. Females exhibited a dramatic upregulation of BCO2 in their feather follicles, facilitating carotenoid degradation and attenuating red pigmentation. Additionally, sex-biased expression of hormonal regulators, such as HSD17B4 and ZNF131, in the feather follicle suggests hormonal modulation influences dichromatism. These findings indicate that sex-specific regulation of carotenoid processing genes underpins the vivid red coloration in males and the drab phenotype in females, likely maintained by a balance between natural and sexual selection, with mechanisms of sexual antagonism affecting divergent gene expression. This work advances understanding of the molecular basis of avian sexual dimorphism, highlighting key genetic pathways involved in carotenoid-based coloration and providing a foundation for further research into the evolution of sexually dichromatic traits.
Sex chromosome evolution is characterized by Y/W degeneration and its consequences for selection on X/Z-linked recessive mutations in the heterogametic sex, yet how functional constraints modulate the evolutionary dynamics of Z-W gametologs remains poorly resolved. We addressed this question in larks (Alaudidae), a lineage carrying enlarged neo-sex chromosomes with multiple evolutionary strata formed through repeated translocations and successive recombination-suppression events. Using whole-genome sequences of males and females of two Alauda species, we analysed 1,759 Z-W gametologs. We found that W-gene degeneration was governed primarily by evolutionary time and intrinsic gene features: long genes were lost earliest, although this tendency was mitigated by gene essentiality, as indicated by high haploinsufficiency scores. Z-linked genes lacking a functional W counterpart exhibited higher nonsynonymous divergence than Z genes retaining a functional W, consistent with selection-driven faster-Z evolution. The strongest signature of purifying selection, comparable to that of pseudoautosomal genes, was observed in haploinsufficient Z-linked genes, which were also more likely to retain W gametologs. Although W genes generally diverged faster, their selection signatures covaried with those of Z and with haploinsufficiency, suggesting partially shared Z-W evolutionary dynamics. Notably, a small subset of W genes showed intensified or positive selection, including several genes associated with putative female-specific functions. Together, our results demonstrate that gene essentiality slows functional divergence on both Z and W, modulates faster-Z dynamics and enables key W genes to remain functional-and potentially advantageous for females-for millions of generations after recombination cessation.
Genomic architecture is a key factor shaping the landscape of linkage disequilibrium between divergently selected traits. By facilitating the detection of intrachromosomal variants, long-read data fueled recent interest in the role of structural variants in adaptive radiation. The Neotropical cichlid genus Crenicichla provides a compelling system for replicated adaptive radiation in riverine environments in which at least two lineages show repeated ecomorphological evolution. The lack of South American cichlid reference genomes has thus far limited investigation of chromosomal evolution across cichlid radiations and precluded testing the role of structural variants in Crenicichla adaptive radiation. Here, we generated a complete assembly of Crenicichla tuca (iguassuensis group) collected from the type locality. To investigate structural variants within Crenicichla, we produced ultra-long reads for Crenicichla missioneira. We then conduct comparative genomics across cichlids using published chromosome-level genomes. Despite karyotypic stability in Crenicichla, intrachromosomal structural variants are abundant and enriched in repetitive genomic regions. Comparisons with other cichlid radiations indicate the predominance of intrachromosomal rearrangements. Chromosomes LG03, LG23, LG10, and LG11 show signatures of chromosomal instability, which seem to be associated with highly repetitive DNA composition and enrichment of immune-related genes. Structural variants polymorphic in both Crenicichla species are consistent with the maintenance of trans-species polymorphism through balancing selection on immune-related genes. Our results add to the growing evidence that structural variation is widespread, even when overall chromosomal morphology remains unchanged. Our approach combining field-based extractions with PacBio HiFi and ONT UL proved sufficient to generate a T2T assembly and holds great potential for evolutionary and conservation genomics in biodiversity hotspots.
Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria. Some fungal NLRs are known to control regulated cell death in the context of allorecognition, the capacity to recognize conspecific nonself. However, the function of most fungal NLR genes remains unknown. Here, we characterize the evolution of the NLRs repertoire in the Podospora anserina species complex. We show that the vast majority of the NLRs display effector domains known to be involved in regulated cell death execution. Moreover, NLRs undergo more rapid gene turnover than random genes, show higher dN/dS values, and faster evolutionary rates. A subgroup of NLRs, distinguished by superstructure-forming repeats with very high sequence identity (high internal conservation), evolved independently multiple times. We found that high internal conservation NLRs are more associated with transposable elements, exhibit higher nucleotide diversity partially driven by repeat-induced point mutation, and show elevated Tajima's D values indicative of balancing selection. Furthermore, high internal conservation NLR phylogenies do not recapitulate species relationships, which we determined is caused by both balancing selection and introgression. In addition, we identified cases of repeat exchange between distinct high internal conservation NLR genes, implying that novel binding specificities may evolve through repeat shuffling, thereby increasing allelic diversity. Finally, we determined that NLR genes with high internal conservation repeats exist outside of the fungal realm, arguing for similar dynamics in other taxa. Overall, these findings suggest that fungal NLRs evolve under diversity-enhancing mechanisms and display selective signatures consistent with a general immune function.
The common marmoset ( Callithrix jacchus ) is a biomedically important species that is characterized by two unusual biological traits - a high frequency of twin births and hematopoietic chimerism - that preclude the application of many commonly used population genomic approaches for quantifying evolutionary processes. In this study, we directly account for both factors in order to estimate fine-scale mutation and recombination rate maps, as well as to infer the demographic and selective processes shaping variation, on the common marmoset X chromosome. Comparing our findings to estimates recently inferred on the autosomes of this species, we find reduced rates of mutation and recombination on the X, as expected. Furthermore, population sex ratios are inferred to be nearly equal, and the appropriately rescaled autosomal population history fits the X chromosome well. Finally, we report evidence of recent selective sweeps targeting a number of X-linked genes, including several of significant biomedical relevance. Overall, these analyses provide novel insights into the evolutionary processes shaping X chromosome evolution in this biomedically-relevant primate model.
The dictyostelid or cellular slime molds (CSMs) are recognized as models in cell, developmental, and human disease biology. Their unusual life cycle alternates between a free-living solitary phase and an aggregative social phase. We generated short Illumina reads and assembled a consensus genome, comprising nuclear and mitochondrial genomes, representative of six naturally occurring strains of the CSM Dictyostelium giganteum. The nuclear genome has an AT content of 75.76%, accounting for 38.52 Mb with an N50 of 3.01 Mb and L50 of 5, and resolves into five chromosome-scale scaffolds consistent with the karyotype. BUSCO analysis recovered 95.5% complete single-copy orthologs and 0.6% duplicated orthologs, corresponding to an overall completeness of 96.1%, with 0.3% fragmented and 3.6% missing orthologs. Approximately 5,500 deduced gene sequences from a publicly available transcriptome further validate the genome assembly and completeness. The genome encodes 13,251 predicted proteins, including ABC transporters, polyketide synthases, Ras/Rho GTPases, and expanded families of protein kinases. A comparative analysis shows extensive conservation of syntenic blocks with Dictyostelium. discoideum and Dictyostelium. firmibasis. About 18% of the nuclear genome is made up of repetitive DNA, mostly in the form of simple repeats. Comparative proteome-level orthology analysis across Dictyostelium species and Entamoeba identifies a conserved Amoebozoan core and a substantial dictyostelid-specific gene repertoire. Domain-level comparisons indicate widespread conservation of intracellular signaling and cytoskeletal modules with animals, whereas canonical metazoan extracellular adhesion domains are absent.
Botryosphaeriaceae is an important fungal family that colonizes a wide range of woody hosts, including economically important crops, and causes serious diseases worldwide. This family has undergone substantial genomic innovations during its evolutionary history. However, the role of gene family innovations, particularly gene contractions, in shaping pathogenicity within Botryosphaeriaceae remains unclear. To address this, we generated five high-quality genomes from three species representing three genera of Botryosphaeriaceae and combined them with four previously published genomes. These nine genomes were analyzed in a comparative genomic framework together with 47 publicly available fungal genomes. Multiple rounds of gene family expansions were identified in Botryosphaeriaceae, including ancient expansions that occurred prior to the divergence of genera and genus-specific expansions that arose afterward. These expansions were associated with genes involved in host infection and virulence. In contrast, gene family contractions were less frequent but were also associated with functions potentially related to pathogenicity when they occurred after the divergence of Botryosphaeriaceae into distinct genera. Transcriptomic analysis of Lasiodiplodia theobromae further supported the functional significance of lineage-specific gene family expansions and contractions in virulence evolution. Silencing a lineage-specific expanded gene encoding a plant cell wall-degrading enzyme from the GH11 family significantly reduced the virulence of L. theobromae, confirming its role in pathogenicity. Together, these findings reveal that lineage-specific gene family innovations, including both expansions and contractions, have driven virulence diversification and adaptation among Botryosphaeriaceae species during host-pathogen interactions.
In order to investigate the genetic diversity, differentiation, gene flows, and propagation routes of Island Southeast Asian (ISEA) goats, we genotyped 50K genome-wide SNPs in 57 Philippine and 30 Indonesian Katjang goats. Correlations of the distance from the domestication center and the genetic diversities of 21 Asian populations were significantly negative. A relatively high diversity of the Philippine population (He = 0.363) against the distance from the domestication center suggests a history of admixture, notably without large effects on their Katjang phenotype. This was confirmed by supervised PCA (Principal Component Analysis), f3 coancestry and f4 admixture analyses, Treemix-inferred migrations and model-based clustering (Admixture program). The inferred differential admixture of ISEA goats agreed with previously reported fixation of mtDNA haplogroup B in Indonesia, but not in the Philippines, and with high frequencies of African or European Y-chromosomal haplogroups that were not observed in Mainland Southeast Asia. We propose that admixture of cosmopolitan European and African goats into ISEA was mediated by a unique feature of the domestic goat, the maritime transport of goats during the colonial period as a source of provisions. This was followed by more recent imports of popular breeds such as Boer, and other cosmopolitan breeds.
Colobanthus quitensis (Caryophyllaceae) is one of only two vascular plants native to Antarctica and a model species for studying adaptation to extreme environments. We report a chromosome-scale reference genome generated from PacBio HiFi and Hi-C sequencing. The final assembly spans 887.1 Mb and resolves into 40 chromosome-scale scaffolds (2n = 80), with a scaffold N50 of 20.4 Mb and a maximum scaffold length of 35.1 Mb. Assembly completeness was high, with 99.0% of Embryophyta BUSCOs recovered, the majority as duplicated (95.7%), consistent with the species' putative tetraploid origin. The genome exhibits a GC content of 36.3%. We further assembled the complete chloroplast genome (151,314 bp; 113 genes) and a draft mitochondrial assembly comprising two partial contigs totaling ∼289 kb. Repeat annotation identified 69.9% of the genome as repetitive, with long terminal repeat retrotransposons as the dominant class (34.8%), primarily of the Ty1/Copia and Gypsy/DIRS1 superfamilies. A total of 40,762 protein-coding genes were predicted, of which 95% were functionally annotated. Combined with transcriptomic resources, this genome enables functional annotation and comparative studies. This is the first chromosome-scale assembly for an Antarctic angiosperm and a resource for investigating polyploidy, genome organization, and adaptive evolution in polar environments. The C. quitensis genome will also support ecological and applied studies, including the development of crops resilient to cold and other abiotic stresses.
Gene expression bridges genotype and phenotype, shaping how organisms respond to their environments. Yet, it remains difficult to untangle how the architecture of gene regulatory networks (GRNs) influences the relationship between gene expression and fitness-especially in structured populations where genetic variants affecting both types of traits are inherited together. Here, we use publicly available data from wild Caenorhabditis elegans strains to link genome-wide gene expression levels to lifetime fecundity upon cultivation in a novel laboratory environment. Despite strong population structure caused by self-fertilization, selective sweeps, and hyperdivergent haplotypes, we find that a small subset of genes show significant covariance between their expression levels and fecundity fitness in laboratory cultivation conditions. These associations persist even after controlling for underlying genomic features. Genes that are older, show more tissue-specific expression patterns, and are particularly enriched in the germline and nervous system exhibit stronger covariance with fecundity in the new laboratory environment, consistent with known patterns of genetic divergence between wild and "domesticated" laboratory strains. Moreover, genes that are centrally positioned within GRNs, or are regulated downstream of certain transcription factors, show stronger associations with fitness. Together, these results suggest that genome structure and network topology jointly shape how variation in gene expression translates into fitness, shedding light on the early stages of adaptation to novel environments.
Bacteriophages can evolve rapidly. Mutation and recombination via horizontal gene transfer allow them to counter adaptive responses by microbial hosts. However, little is known about the genomic processes underlying phage evolution within an ecological context-especially within natural microbial communities. This is due in part to the difficulty in resolving aspects of phage ecology, such as host range. To better understand the interplay of phage ecology and evolution within natural microbial communities, we combined measures of phage host range in vivo with measures of genome evolution in order to infer the evolutionary pressures acting on phage genomes within individual honeybee worker microbiomes. We show that near-identical phage genomes, cooccurring across multiple honeybee colonies, exhibit large variation with respect to gene modules, despite retaining a highly similar core genome. Estimates of genic diversity suggest deviations from neutral evolutionary models and identify loci under putative diversifying selection. We then use HiC-resolved metagenomics and show that the honeybee gut contains a dense phage community that exhibits a wide degree of host range variation. This variation differed across individual metagenomes in both the number and phylogenetic distance of potential hosts. We show that common measures of genetic variation positively correlate with host range in bee-associated phages and that functional targets of diversifying selection are partitioned differently between broad or narrow host range phages. Our work underscores the high host range variation associated with phages within host-associated microbial communities and provides evidence that this variation impacts rates of phage evolution.
Amphibians are the most threatened group of vertebrates on the planet due to habitat loss, climate change, and the emerging disease chytridiomycosis, caused by the pathogenic fungus Batrachochytrium dendrobatidis. Axolotls, species from the genus Ambystoma endemic to Mexico, are a highly vulnerable group of salamanders with restricted distributions that are severely affected by habitat fragmentation, invasive species, and pollution. In this context, population genomic studies are urgently needed to implement adequate conservation and management decisions. In this study, we identified abiotic and biotic factors associated with the genomic diversity and structure of Ambystoma altamirani through genome-wide single-nucleotide polymorphism analyses. Based on 110,761 neutral single-nucleotide polymorphisms from 99 individuals across five populations of A. altamirani, we found that genomic diversity of individuals was positively correlated with their body condition. Moreover, patterns of genetic structure identified three main genetic clusters, which were correlated with habitat environmental differences. Specifically, Elevation and temperature-associated variables significantly contributed to the genomic structuring of A. altamirani populations. Latent factor mixed models identified 1,670 single-nucleotide polymorphisms associated with environmental variables as well as 80 and 47 single-nucleotide polymorphisms associated with the biotic variables B. dendrobatidis infection intensity and body condition, respectively. We identified single-nucleotide polymorphisms significantly associated with differences in B. dendrobatidis infection and body condition among homozygous or heterozygous genotypes. Overall, our study teases apart some of the factors likely influencing axolotl genetic diversity and population structuring, which should be considered for conservation strategies for this and other endangered amphibian species.
