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PubMed2025

Host-Associated Genetic Differentiation in the Face of Ongoing Gene Flow: Ecological Speciation in a Pathogenic Parasite of Freshwater Fish.

Adaptive evolution in response to varying environments, leading to population divergence, is among the most intriguing processes of speciation. However, the extent to which these adaptive processes effectively drive population divergence amidst ongoing gene flow remains controversial. Our study addresses this by analyzing population genetic structure, gene flow, and genomic divergence between lineages of a tapeworm parasite (Ligula intestinalis) isolated from sympatric fish hosts. This parasite, which must overcome host immunological defenses for successful infection, significantly impacts host health. Utilizing genome-wide Single Nucleotide Polymorphisms (SNPs) and transcriptome data, we investigated whether host species impose distinct selection pressures on parasite populations. Genetic clustering analyses revealed clear divergence, with parasites from bream (Abramis brama) forming a distinct genetic cluster separate from those infecting roach (Rutilus rutilus), rudd (Scardinius erythrophthalmus), and bleak (Alburnus alburnus). Demographic modeling indicated isolation with continuous gene flow as the most plausible scenario for this divergence. Selection analyses identified 896 SNPs under selection, displaying low to moderate nucleotide diversity and genetic divergence compared with neutral loci. Transcriptome profiling supported these findings, revealing distinct gene expression profiles between parasite populations. Examination of selected SNPs and differentially expressed genes identified candidate genes linked to immune evasion mechanisms, potentially driving ecological speciation. This research highlights the interplay of host specificity, population demography, and disruptive selection in ecological speciation. By dissecting genomic factors, our study improves the understanding of mechanisms facilitating population divergence despite ongoing gene flow.

Animals↗
PubMed2026

A new southern limit for the distribution of African great apes: sympatric western lowland gorilla (Gorilla gorilla gorilla) and central chimpanzee (Pan troglodytes troglodytes) confirmed in Mayombe National Park, Angola.

The distribution of African great apes has remained unconfirmed regarding their southern limit, particularly on the western side of the continent. IUCN maps include the Mayombe forest of Angola as part of the estimated distribution of western lowland gorillas (Gorilla gorilla gorilla) and central chimpanzees (Pan troglodytes troglodytes). However, until now no published evidence-based records had confirmed the continued presence of both species. The Mayombe forest is a key biodiversity hotspot and a potentially important stronghold for the conservation of great ape populations in Africa. Here, we report the first systematic evidence of both species in the Mayombe National Park, Cabinda, Angola. In 2023, a grid of camera traps was systematically deployed, producing the first visual records of gorillas and chimpanzees. Building on these findings, in 2024, a pilot survey including ad libitum field observations was carried out along exploratory trails to maximise data collection. The combination of these records identified a hotspot of great ape activity where six transects were established, and systematic direct and indirect evidence was documented. Chimpanzees were recorded more times across a broader range of evidence categories, while gorillas appeared less and seemed more spatially restricted. Notably, both species were detected at overlapping sites but never simultaneously, indicating sympatric coexistence with spatio-temporal partitioning. These findings confirm the southernmost predicted distribution of both species for this part of Africa, filling critical gaps in the understanding of great ape evolution and biogeography, and providing a baseline for the first demographic and ecological census of great apes in Angola.

Animals↗
PubMed2025

Genetic Adaptation to Brackish Water and Spawning Season in European Cisco.

How species adapt to diverse environmental conditions is essential for understanding evolution and the maintenance of biodiversity. The European cisco (Coregonus albula) is a salmonid that occurs in both fresh and brackish water, and this together with the presence of sympatric spring- and autumn-spawning lacustrine populations provides an opportunity for studying the genetics of adaptation in relation to salinity and timing of reproduction. Here, we present a high-quality reference genome of the European cisco based on PacBio HiFi long read sequencing and HiC-directed scaffolding. We generated low-coverage whole-genome sequencing data from 336 individuals across 12 population samples to explore population structure and genetics of ecological adaptation. We found a major subdivision between two groups of populations most likely reflecting colonisation from different glacial refugia. Within the two major groups, we detected further genetic differentiation between spring- and autumn-spawning populations and between populations from freshwater lakes, rivers and brackish water (Bothnian Bay). A genome-wide screen for genetic differentiation among populations identified a set of outlier SNPs strongly correlated with spawning timing and salinity. Several of the genes associated with spawning time, including BHLHE40, TIMELESS and CPT1A, have previously been shown to have a role in circadian rhythm biology. As many as 17 loci were associated with genetic differentiation between populations reproducing in fresh and brackish water. This study provides insights into the genomic basis of ecological adaptation in European cisco with implications for sustainable fishery management.

Animals↗
PubMed1979

Reproductive isolation with little genetic divergence in sympatric populations of brown trout (Salmo trutta).

Two reproductively isolated demes of brown trout coexist in a small Swedish mountain lake, Lake Bunnersjörna. We electrophoretically examined 102 specimens from that lake for 27 enzymes encoded by 54 loci. The two demes are fixed for different alleles at a lactate dehydrogenase locus (LDH-1); statistically significant allele frequency differences at five other loci further support the complete lack of gene flow between these demes. There are significant differences in growth rates between fish in the two demes, but no further morphological differentiation h-s been detected.--In light of these findings, the genetic distance between these populations is surprisingly small (Nei's I = 0.975). These demes represent one of the least genetically divergent, reproductively isolated sympatric pair of vertebrate populations that have been identified. The results are discussed from both an evolutionary and ecological perspective.

Alleles↗
PubMed2025

Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.

Genetic heterogeneity exists within all microbial populations, with sympatric cells of the same species often exhibiting single-nucleotide variations that influence phenotypic traits, including metabolic efficiency. However, the evolutionary dynamics of these strain-level differences in response to environmental stress remain poorly understood. Here, we present a first-of-its-kind study tracking the adaptive evolution of an anaerobic, carbon-fixing microbiota under a controlled engineered ecosystem focused on carbon dioxide bioconversion into methane. Leveraging strain-resolved metagenomics with an ad hoc variant calling and phasing approach, we mapped mutation trajectories and observed that the two dominant Methanothermobacter species maintained distinct sweeping haplotypes over time, most likely due to niche-specific metabolic roles. By combining population genetic statistics and peptide reconstruction, mer and mcrB genes emerged as potential drivers of archaeal strain-level competition. These findings pave the way for targeted engineering of microbial communities to enhance bioconversion efficiency, with significant implications for sustainable energy and carbon management in anaerobic systems.

Metagenomics↗
PubMed2025

Rapid Divergence of Visual Systems and Signaling Traits to Contrasting Light Regimes During Early Speciation of African Crater Lake Cichlid Fish.

Sensory adaptation is widely hypothesized to drive ecological speciation, yet empirical evidence from natural populations undergoing early stage divergence remains limited. In Lake Masoko, a young crater lake in East Africa, the haplochromine cichlid Astatotilapia calliptera is undergoing early stage sympatric speciation into shallow-water littoral and deep-water benthic ecotypes that experience contrasting light environments. Here, we integrate retinal transcriptomics, phenotypic analyses, and visual modeling to uncover rapid sensory divergence associated with this ecological transition. We find striking shifts in cone opsin expression, with the benthic ecotype exhibiting a switch from short-wavelength sensitive SWS2B to SWS2A and an overall narrowing of cone sensitivity toward the center of the light spectrum, consistent with changes in deep-water light environment. In contrast, coding sequence variation in opsin genes was limited and no significant differences in allele frequencies were detected across nine polymorphic sites, pointing to expression regulation as the primary axis of early divergence in visual systems. In parallel, we observed divergence in male signaling traits, with benthic males displaying deeper red egg-spots, aligning with predictions from visual modeling of signal efficiency in different light environments. These results demonstrate rapid transcriptomic and phenotypic divergence in associated signaling traits-within ∼1,000 years-supporting a potential role for regulatory evolution in sensory adaptation during early ecological speciation.

Animals↗
PubMed2026

Life in sediments fosters 'sexual' speciation in the Shewanella baltica complex.

Understanding how intra- and interspecific differentiation arises in natural microbial populations is central to explaining the processes that drive bacterial evolution. Motivated by the co-occurrence of multiple putative genospecies closely related to Shewanella baltica in Baltic Sea sediments, we investigated the genomic structure of this species complex across fine spatial scales. We analyzed 112 genome sequences from strains collected across several sediment cores and depths (0-6 cm) at Vaxön (Stockholm archipelago, Sweden) as well as earlier isolates from this site and allopatric strains from surrounding locations obtained from both sediments and the water column. Using a reverse-ecology population genomics approach, we found unprecedented genomic diversification among sediment-associated strains, which form a species complex resolving into three cohesive evolutionary groups (G1, G2, and G3) with distinct signatures of metabolic specialization including sulfite respiration. While G1 consists predominantly of a single species (S. baltica) with high gene turnover, G2 and G3 comprise an array of divergent putative genospecies and previously reported species consistently recovered from sediments. Patterns of homologous recombination indicate that diversification of the lineages within G2 and G3 is primarily recombination-driven ('sexual') and is associated with specialization in sulfite reduction and utilization of certain carbon sources. The extent of diversity uncovered here far exceeds that reported for S. baltica from other environments, suggesting that a sediment-associated lifestyle promotes the emergence of novel genotypes. These findings expand the known limits of sympatric speciation in prokaryotes beyond subspecific ecotypes, demonstrating that bacterial species can diverge and persist as distinct lineages in the absence of spatial segregation and at microgeographic scales. Furthermore, our results suggest that collective interactions and ecological differentiation can structure sediment-associated bacterial populations strongly enough to drive divergence at the species level.

Journal Article↗
PubMed2026

Divergent evolutionary strategies in spider venoms: A comparative proteomic profiling of four sympatric species from Yunnan.

Spider venoms comprise complex cocktails of bioactive molecules evolved for predation and defense, representing a valuable resource for biological research and pharmaceutical discovery. In this study, we performed a systematic analysis of venom gland extracts from four common spider species indigenous to Yunnan, China: Agelena limbata, Hippasa lycosina, Lycosa grahami, and Sinopoda pengi. Using an integrated transcriptomic and proteomic targeted profiling approach, we successfully annotated 141 distinct toxins. Comparative analysis revealed significant interspecific heterogeneity, suggesting distinct evolutionary trajectories and "weapon system economics." Both A. limbata and L. grahami exhibited a "peptide-dominant" profile anchored by neurotoxic peptides and isomerases, optimized for rapid chemical paralysis. In contrast, S. pengi displayed a distinct "protein-dominant" signature enriched with high-molecular-weight enzymes and CAP superfamily proteins, likely functioning to facilitate tissue degradation and toxin diffusion. Occupying an intermediate position, H. lycosina demonstrated a hybrid composition. These findings suggest that although these species share the same geographical range, their venom systems have undergone divergent evolutionary adaptations driven by specific ecological niches and hunting strategies. This study represents the first systematic proteomic characterization of these venom components, providing a valuable reservoir of molecular candidates while highlighting the bioinformatic nuances of analyzing whole-gland homogenates.

Animals↗
PubMed1975

Allozymic and chromosomal similarity in two Drosophila species.

D. setosimentum and ochrobasis are a pair of very close, partly sympatric species endemic to Hawaii island. Males of the two species differ strikingly in wing-pattern and there are altitudinal and breeding-site differences. Similarity indices have been calculated for both chromosomal (C) ald allozymic (A) variants. Within the main populations of each species both kinds of data give coefficients above 0.98. Interspecific comparison of the main populations shows 0.66 (C) and 0.79 (A). An isolated population of ochrobasis from Kohala Volcano (Ohu), when compared with setosimentum, shows 0.68 (C) and 0.98 (A). Chromosomes are thus much more sensitive than allozymes in distinguishing these species; the same is true in the case of D. silvestris and heteroneura from the same forests. These morphologically distinct species, when compared, show 0.96 (A). All four species appear to be very new in the historical sense. In one area, about 2% of wild-caught D. setosimentum/ochrobasis are interspecific hybrids although adequate samples indicate that the separate gene pools have not broken down. The specific names should be retained but the two entities are perhaps best described as quite advanced semispecies in which reproductive isolation in nature is now nearly complete.

Animals↗
PubMed1975

Photobehavioral differentiation in natural populations of Drosophila pseudoobscura and Drosophila persimilis.

The photoresponses of natural populations of D. pseudoobscura and D. persimilis, occurring sympatrically, are measured in two environmental conditions ("at rest" and "disturbed"). Comparisons of the responses, intraspecifically and interspecifically, lead to the following conclusions. These must be considered within the confines of the operational nature of the measurement of laboratory photoresponses. (1) Within each species population, significant nonenvironmental differentiation has been allowed or produced by selection in the "at rest" photoresponse. No significant nonenvironmental differentiation is found in the photoresponse measured in a disturbed condition. (2) Within each species population, a higher mean "disturbed" photoresponse has been favored. The intensities or patterns of selection acting on these two photoresponses have differed such that more intrapopulation differentiation has been allowed or produced in the "at rest" photoresponse. (3) A higher mean photoresponse has been favored in D. persimilis for both conditions. The intensities or patterns of selection acting between these two species populations on the "at rest" photoresponse have differed such that more intrapopulation differentiation has been allowed or produced in D. persimilis. (4) Comparisons of this study with one on intraspecific and interspecific differentiation in wing length lead to the conclusion that the selective differences inferred above have acted at a level more specifically attuned to photobehavior.

Animals↗
PubMed2025

Molecular signatures of adaptive introgression and selection in contact zones of closely related pine species (Pinus genus).

BACKGROUND: Natural hybridization plays a key role in shaping genetic diversity, local adaptation, and the dynamics of speciation through interspecific gene flow. Hybrid zones serve as valuable natural systems for studying these processes. In this research, we used genotypic data at thousands of nuclear SNPs to investigate genomic outcomes of hybridization and selection across three contact zones of closely related pine species including Scots pine (Pinus sylvestris L.) and dwarf mountain pine (P. mugo T.). Reference allopatric stands of parental species were used to assess introgression dynamics. RESULTS: Individuals from the hybrid zones showed distinct genetic ancestry patterns and were assigned to groups including putative pure species, first-generation hybrids, and advanced backcrosses. Genotypes of the majority of hybrids were shifted towards P. mugo ancestry. Most outlier loci were shared across all sympatric populations, although some were specific to individual contact zones. The identified outliers were mainly associated with regulatory biological processes related to phosphorylation, proteolysis, and transmembrane transport. Signatures of local adaptation varied in different genetic classes in contact zones and they were strongest in pure P. sylvestris and hybrids with a majority of P. sylvestris ancestry. The pattern suggests that it may be driven by adaptation to peat bog habitats situated outside the species’ core ecological niche. CONCLUSIONS: Our findings indicate strong selective pressure acting on multiple genes in groups of hybrids and pure Pinus sylvestris individuals across all studied hybrid zones. In contrast, the weaker signal of selection observed in individuals with P. mugo ancestry suggests that relict populations of this species, which historically spread across postglacial peat bogs, were pre-adapted to such environments. While several outlier loci were shared across different contact zones, others were unique for one of them, indicating that local environmental pressures and adaptive introgression shape the genomic composition of the populations. These results highlight the role of hybridization in generating adaptive diversity and emphasize the evolutionary significance of hybrid zones in pines.

Hybridization, Genetic↗