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PubMed2026

Comparative Transcriptomic Analyses Identify Candidate Genes for Convergent Reproductive Shifts in a Bimodal Viviparous Amphibian.

Shifts in reproductive mode represent key evolutionary innovations that shape species' life histories and evolutionary trajectories. Species showing bimodal reproductive strategies with multiple independent origins offer a rare opportunity to gain insights into the adaptive processes and mechanisms underlying convergent traits. The fire salamander, Salamandra salamandra, is the only amphibian exhibiting intraspecific variation in reproductive mode across multiple independent reproductive shifts, enabling investigation of the transition between larviparity (females give birth to aquatic larvae) and pueriparity (females give birth to fully developed terrestrial juveniles) within a single species and across different timescales. Pueriparity is an adaptive innovation that skips the aquatic larval stage, allowing individuals to exploit habitats with no available water bodies. The fire salamander is larviparous across most of its range, but pueriparity has evolved independently at least three times: once in the early Pleistocene within S. s. bernardezi in the mountains of northern Spain, and more recently on two land-bridge islands (NW Spain) inhabited by S. s. gallaica. To identify candidate genes associated with these distinct reproductive modes, we compared gene expression profiles of the uterus and oviduct of pregnant females across two independent evolutionary transitions using RNA-sequencing. We detected shared changes in maternal gene expression among pueriparous S. s. bernardezi and S. s. gallaica relative to their larviparous counterparts, in addition to differences unique to each independent evolutionary transition. Functional enrichment analyses indicated that differentially expressed genes were associated with reproductive timing, angiogenesis, and maternal signalling, consistent with the phenotypic differences observed in the uterine environment and embryonic development between the two reproductive modes. This study represents an important first step towards understanding the genomic basis of the evolution of pueriparity in a remarkable bimodal reproductive system, and provides transcriptomic resources and candidate genes for future research into the genomic architecture underlying this poorly understood adaptive trait.

Animals↗

PubMed2026

Primula pingwuensis (Primulaceae), a new species in Primula sect. Auganthus from Sichuan, China.

Primula pingwuensis sp. nov., a new species of Primula sect. Auganthus from Sichuan, China, is described. It resembles P. sinensis in having palmately lobed leaves and multi-whorled inflorescences but differs by its multi-branched stems, more densely short-pubescent surfaces, thicker chartaceous leaves, narrower leaf blades, and indistinct translucent nectar guides. A taxonomic key covering all nine known species of Primula sect. Auganthus is compiled herein to support field morphological discrimination. A chloroplast genome-based phylogeny shows that P. pingwuensis is sister to P. rongrong, and this clade is sister to P. fujiangensis. Incongruence between morphology and molecular phylogeny is observed within the section. Leaf-lobing patterns have undergone multiple independent evolutionary transitions during adaptive radiation in karst habitats, indicating that a few morphological traits cannot be used to reliably infer interspecific relationships. The new species is assessed as Data Deficient (DD) following IUCN criteria, owing to the lack of long-term observations of its threat status and population dynamics. This study provides new data for the taxonomy and evolution of Primula sect. Auganthus.

Primula↗

PubMed2026

From Southeast Asia to global: phylogeny, biogeography and character evolution of the thread-legged bug tribe Leistarchini (Hemiptera: Reduviidae: Emesinae).

The thread-legged bug tribe Leistarchini (Hemiptera: Reduviidae: Emesinae) is a cosmopolitan and diverse group characterized by a highly disproportionate spatial distribution across zoogeographic regions. Due to a historical lack of phylogenetic focus, the internal relationships and evolutionary history of the tribe remain poorly understood. In this study, we provide the first robust phylogenetic framework for Leistarchini by integrating molecular data from mitochondrial genomes and nuclear rDNA (88 taxa, 19 937 bp) with universal single-copy orthologs (24 taxa, 667 loci). Our results support the monophyly of Leistarchini and identify five major clades, including a newly described genus Calliemesa gen. n. Our findings further reveal that the five most species-rich genera (Nesita, Orthunga, Pleias, Ploiaria and Tinna) are either paraphyletic or polyphyletic as currently circumscribed. Molecular dating and biogeographic reconstructions suggest a Southeast Asian origin for the Leistarchini crown group during the late Palaeocene (ca. 57 Ma). Early diversification appears to have been driven by Paleogene geological and climatic shifts in Southeast Asia, while multiple intercontinental dispersals since the middle Eocene into the Afrotropics, Madagascar and the New World shaped the current global distribution. Ancestral state reconstructions indicate that the Leistarchini ancestor possessed a well-developed posterior pronotal lobe and a three-segmented protarsus. Subsequent evolutionary trajectories involved four independent transitions toward a shortened posterior pronotal lobe, and four separate reductions in protarsal segmentation.

Animals↗

PubMed2025

The evolution of the plastid genomes in the holoparasitic Balanophoraceae.

The independent transition to a heterotrophic lifestyle in plants drove remarkably convergent evolutionary trajectories, characterized by morphological modifications and reductions in their plastomes. The characteristics of the minimum plastome required for survival, if they exist, remain a topic of debate. The holoparasitic family Balanophoraceae was initially presumed to have entirely lost their plastids, however, recent reports revealed the presence of reduced and aberrant plastids with odd genomes. Among the outstanding features of these genomes are the highest nucleotide composition bias across the tree of life and the only two genetic code changes ever recorded among plants. In this study, we assembled the plastomes from five genera, four of which had never been studied. Major common features include extremely high AT content, the lack of a typical quadripartite structure and extensive size reduction due to gene elimination and genome compaction. The family exhibits multiple gene and intron losses, and a broad range of scenarios regarding the evolution of the plastid trnE, a gene considered essential because of its dual function in tetrapyrrole biosynthesis and translation within the plastid. In addition, phylogenetic analyses suggest that the genus Scybalium is not monophyletic. An evolutionary model for the plastomes of the Balanophoraceae is proposed.

Genome, Plastid↗

PubMed2025

Transposable Element-Mediated Cis-Regulation Drives the Evolution of dmrt1 as a Candidate Master Sex-Determining Gene in Black Carp.

Sex determination in vertebrates exhibits remarkable evolutionary plasticity, with diverse mechanisms and master sex-determining (MSD) genes arising independently across lineages. Among these, dmrt1, a dosage-sensitive gene, has repeatedly been recruited as an MSD gene through gene duplication or allelic diversification. However, the biochemical basis of such evolutionary transitions, particularly those driven by allelic diversification, remains largely unexplored. Here, we generated haplotype-resolved genome assemblies for both XX and XY black carp (Mylopharyngodon piceus) and identified a ∼40-kb region on chromosome 4, containing only dmrt1, as the candidate sex-determining locus. We discovered two Y-specific insertions in the dmrt1 promoter: a 13.4-kb highly repetitive element and an 11-bp motif. Functional assays revealed that these insertions act as enhancer and a promoter element, respectively, driving early, allele-specific upregulation of dmrt1 prior to gonadal differentiation. Notably, the 13.4-kb insertion contains transposable elements (TEs) functioning as cis-regulatory modules with transcription factor binding sites that mediate Y-specific activation. Our findings reveal a TE-mediated regulatory innovation that promoted dmrt1's evolution as a male-determining gene via allelic diversification, providing new insights into how mobile genetic elements drive the origin and diversification of sex-determining systems in vertebrates.

Animals↗

PubMed2024

Illuminating the coevolution of photosynthesis and Bacteria.

Life harnessing light energy transformed the relationship between biology and Earth-bringing a massive flux of organic carbon and oxidants to Earth's surface that gave way to today's organotrophy- and respiration-dominated biosphere. However, our understanding of how life drove this transition has largely relied on the geological record; much remains unresolved due to the complexity and paucity of the genetic record tied to photosynthesis. Here, through holistic phylogenetic comparison of the bacterial domain and all photosynthetic machinery (totally spanning >10,000 genomes), we identify evolutionary congruence between three independent biological systems-bacteria, (bacterio)chlorophyll-mediated light metabolism (chlorophototrophy), and carbon fixation-and uncover their intertwined history. Our analyses uniformly mapped progenitors of extant light-metabolizing machinery (reaction centers, [bacterio]chlorophyll synthases, and magnesium-chelatases) and enzymes facilitating the Calvin-Benson-Bassham cycle (form I RuBisCO and phosphoribulokinase) to the same ancient Terrabacteria organism near the base of the bacterial domain. These phylogenies consistently showed that extant phototrophs ultimately derived light metabolism from this bacterium, the last phototroph common ancestor (LPCA). LPCA was a non-oxygen-generating (anoxygenic) phototroph that already possessed carbon fixation and two reaction centers, a type I analogous to extant forms and a primitive type II. Analyses also indicate chlorophototrophy originated before LPCA. We further reconstructed evolution of chlorophototrophs/chlorophototrophy post-LPCA, including vertical inheritance in Terrabacteria, the rise of oxygen-generating chlorophototrophy in one descendant branch near the Great Oxidation Event, and subsequent emergence of Cyanobacteria. These collectively unveil a detailed view of the coevolution of light metabolism and Bacteria having clear congruence with the geological record.

Photosynthesis↗

PubMed2026

Environmental Gradients as a Dominant Force in the Macroevolution of a Host-Associated Marine Bacterium.

Natural selection is imposed by both abiotic environmental filtering and biotic interactions, yet their relative roles in shaping the deep phylogeny of widespread, generalist host-associated bacteria remain unclear. Here, we integrate large-scale phylogenomics, environmental sequencing, functional genomics, and global metagenomic analysis to demonstrate that tidal zonation overrides host association as the dominant macroevolutionary force structuring the marine bacterial genus Ruegeria. Analysis of 533 genomes and 74 global coastal metagenomes reveals that the intertidal-subtidal boundary structures the deepest phylogenetic splits, driving the repeated evolution of distinct ecotypes through independent zonation transitions across global coastlines. These ecotypes possess divergent genomic toolkits: intertidal strains are enriched for genes coding for stress resistance and anaerobic metabolism, whereas subtidal strains specialize in high-affinity nutrient scavenging. Our findings establish that predictable physicochemical gradients act as filters that generate foundational diversity from which specialized host symbionts subsequently emerge, reframing how environmental gradients shape microbial evolution at the eco-evolutionary interface.

Journal Article↗

PubMed2025

Tracing the evolution and genomic dynamics of mating-type loci in Cryptococcus pathogens and closely related species.

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in C. decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in K. mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

MAT genes↗

PubMed2025

The complex evolution and genomic dynamics of mating-type loci in Cryptococcus and Kwoniella.

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in Cryptococcus decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in Kwoniella mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

Genes, Mating Type, Fungal↗

PubMed2026

Genome-wide barriers to gene flow reveal the genetic basis of viviparity evolution in a lizard.

Viviparity (live-bearing) is a major evolutionary transition repeatedly linked with ecological and evolutionary diversification throughout vertebrates. Live-bearing reproduction entails a novel suite of phenotypes and life history traits, but the genetic processes by which such a reproductive innovation evolves are unknown. Remarkable among amniotes, the common lizard (Zootoca vivipara) has extant oviparous (egg-laying) and viviparous lineages and a to-date unresolved history of parity mode emergence. This species represents an ideal model to reconstruct the evolutionary and genetic mechanisms of how viviparity arises. By analyzing whole genomes of individuals from across the species' distribution, we robustly show that viviparity evolved once. However, gene flow from oviparous to viviparous populations is found to be long-term and extensive, causing pronounced gene tree discordance. We inferred signals of selection for viviparity in many independent regions across the genome, and these were recruited over considerable time. Genomic barriers to gene flow between oviparity and viviparity were found genome wide. These are enriched for regions under selection for parity mode and for genes known to be involved in pregnancy and parturition in squamates and mammals. Further implicating their functional role in viviparity, we show that genes in genomic regions under selection and resisting gene flow are more highly expressed in the uterus of viviparous lizards during pregnancy. Our study demonstrates that viviparity in an amniote evolved by selection in the face of gene flow and primarily by the genome-wide accumulation of functional regulatory variants. These results reveal how complex adaptive innovations can arise and be maintained.

Animals↗

PubMed2026

Museum genomics links MC1R alleles to adaptive winter coat color polymorphism in the long-tailed weasel.

Understanding the architecture of biological adaptations is a major endeavor of evolutionary biology. Using Natural History collections, we study the genetic basis and evolution of white/brown winter coat color variation in the long-tailed weasel (Neogale frenata), a crucial phenological adaptation for camouflage in habitats with seasonal snow. We produced whole-genome sequencing data for museum specimens, along two winter color morph transition areas in North America, at the West and East coasts. Genome-wide association scans identified a single genomic region linked to color variation polymorphism with approximately 300 kb and 200 kb in the West and East regions, respectively, which included the pigmentation gene MC1R. We identified three MC1R alleles, two of which with deletions of nine or eight amino acids, alternatively associated with the winter brown morphs in the West and East, respectively. These deletions affect the second transmembrane domain, and in one case also the first extracellular loop, which in silico analyses predicted to impact the protein's function. Our findings show alternative intraspecific evolutionary solutions for environmental adaptation in long-tailed weasels, building on the evidence that major genes of the melanin production pathway are hotspots for recurrent and independent evolution of winter camouflage adaptation. This adaptive variation may be crucial to anchor adaptive responses facing future environmental change.

Receptor, Melanocortin, Type 1↗

PubMed2025

RNA Pol I activity is required for meiotic chromatin organization and the H3K4me3 gradient essential for oogenesis, independent of ribosome synthesis.

Oogenesis requires extensive and dynamic chromatin remodeling that primes gene promoters for later transcriptional activation during embryonic development. Here, we uncover a pivotal, non-canonical role for RNA Polymerase I (Pol I) in driving these chromatin state transitions during Caenorhabditis elegans oogenesis. Using the auxin-inducible degron system to selectively deplete either Pol I catalytic subunits or ribosome assembly factors, we disentangle the consequences of impaired nucleolar integrity from reductions in ribosome biogenesis. Strikingly, although disrupting ribosome assembly caused minimal effects on oocyte production, loss of Pol I activity led to widespread changes in chromatin accessibility, a dampening of the distal-proximal H3K4me3 gradient required for oogenesis, reduced synapsis, and elevated ATM/ATR phosphorylation, resulting in fewer but significantly larger oocytes. Despite their promoters becoming more accessible, oogenesis genes did not show large changes in steady-state mRNA, consistent with transcriptional repression prior to fertilization. Instead, Pol I depletion prematurely remodeled oogenic chromatin, through a misdirection of H3K4me3 deposition towards promoters normally primed for zygotic genome activation. These findings reveal an epigenetic gating function for nucleolar integrity in oocyte maturation: Pol I preserves three-dimensional chromatin organization and maintains proper spatiotemporal regulation of histone modifications, independent of ribosome production. Given the evolutionary conservation of nucleolar dynamics and histone modifications during gametogenesis, our work suggests that nucleolar stress, whether from environmental factors, aging, or genetic disorders, could broadly compromise fertility by disrupting oogenic chromatin priming.

Journal Article↗

PubMed2026

A Cis-Regulatory Duplication in a Hox Hotspot Implicated in Mimetic Convergence in the Bumble Bee Bombus flavifrons.

Several species of North American bumble bees spanning the Pacific Coastal and Rocky Mountain regions converge onto distinct mimetic abdominal colour forms for each region by switching abdominal coloration from black to red. Previous genome-wide association studies (GWAS) of red and black transitions in two mimics (Bombus melanopygus and Bombus vancouverensis) revealed that black forms were generated by independently deleting a portion of the same cis-regulatory region near the Hox gene Abdominal-B (Abd-B). Here, we test the genetic basis of these mimetic colour forms in a third co-mimic, Bombus flavifrons, that has continuous variation in red and black that is shifted posteriorly one segment compared to its co-mimics. Using genome-wide association of red and black forms, we identified a structural variant < 50 bp away from the deletions in B. melanopygus and B. vancouverensis that was strongly associated with the colour phenotype. Sequencing across mimicry zones and closely related taxa revealed that all red forms of B. flavifrons and monomorphic red close relative Bombus centralis have a 319 bp tandem duplication at this locus that has extensive modification to the duplicated copy. Black forms of B. flavifrons from the Cascades also have this duplication but without the modifications, while black forms in the western Rockies mostly lack this duplication, similar to ancestral black forms. This suggests independent mechanisms may regulate the black phenotypes in different populations and that ancestral sorting of variation and/or adaptive introgression generated these phenotypes. This study strengthens support for this Abd-B cis-regulatory region being a hotspot for regulating abdominal coloration in bumble bees, and features the role of regulatory region duplication in creating novel phenotypes.

Animals↗