The Scandinavian wolf population (Norway and Sweden) is intensively managed at a population size considered sustainable by managing authorities. As these authorities have decided to reduce the population to only 170 individuals, it is timely to evaluate this population size goal and to scrutinize underlying assumptions of recent simulation studies that inform population management. The effective size of a population determines the pace at which genetic diversity declines and inbreeding increases and plays a crucial role in short- and long-term extinction risks. Here, we use the complete published pedigree of the Scandinavian wolf population to precisely calculate the effective size Ne since the founding of the population, per year. Our results indicate the Ne is unsustainably low. Moreover, we find that recent simulation studies commissioned by the managing authorities greatly overestimate the effective size of the Scandinavian wolf population, questioning their usefulness to inform population management.
Understanding recent change in effective population size is crucial to evaluate how specie respond to environmental modifications and their ability to adapt to global changes. However, the impact of past environmental change on the demography history of species communities has rarely been studied across multiple species, members of the same community sharing the same habitat. In this study, we compare historical change in effective population size across eight species of coastal sand dune plant communities along the coastal dune in Southwest France. We developed and sequenced species-specific microsatellite markers to genotype 3116 individuals. In an attempt to increase temporal resolution, we integrate both fast (microsatellite repeat number) and slow (substitution in flanking sequence) mutating polymorphisms to infer demographic parameters of a simple model of a single population size change in the past using coalescent simulations and approximate Bayesian computations. Recent and ancient effective population sizes were well inferred and informed by allelic richness at microsatellites and heterozygosity at flanking sequence respectively. The timing of event was more difficult to estimate, but benefit from summary statistics combining microsatellite variation and flanking substitutions. Most species showed a synchronous and strong decline dating back from 135 to 450 years ago, overlapping with the Little Ice Age during which high storminess caused sand drift that probably wiped out most of the open sand dune vegetation, which is now restricted along the shoreline. Historical habitat loss led to community level decline in effective population size that will constrain future sand dune plant responses.
Despite the economic and scientific importance of Bombyx mori, its satellite DNA (satDNA) fraction remains poorly characterized. Here, we present the first comprehensive analysis of the B. mori satellitome, through the analysis of seven strains, plus the analysis of genome reference assembly. A total of 35 satDNAs were detected, all of which were present across the studied strains, with 29 also shared with B. mandarina, its wild ancestor. We revealed low abundance of satDNAs (mean abundance between strains of ~0.85% for males and 0.91% for females), A + T enrichment, high monomer size variability, and predominantly dispersed chromosomal organization. Divergence landscapes of satDNA sequences indicate predominantly ancient amplifications with few recent homogenization events. SatDNA families exhibited low strain differentiation across seven B. mori reference strains. The W sex chromosome was identified as a hotspot for satDNA accumulation, which showed female-specific amplification and higher sequence homogeneity, suggesting functional or structural roles in W sex chromosome evolution. In contrast, the Z sex chromosome displayed similar satDNA content to autosomes, with few families slightly amplified in this chromosome. Remarkably, some of the B. mori satDNAs were found to be derived from transposable elements (TEs), i.e four families covering ~63% of total satDNA content, supporting the hypothesis of TE-driven satDNA origin via multiple mechanisms, including tandemization of TE fragments. Our findings underscore the dynamic interplay between satDNAs and TEs in shaping genome architecture, the stability of the satellitome through strains diversification, and the sex chromosome-specific accumulation patterns. These insights lay the groundwork for future studies investigating the functional roles of satDNAs in genome regulation and chromatin dynamics in Lepidoptera.
Highway construction often leads to habitat fragmentation, altering the genetic features of wild populations. While compensatory measures are commonly implemented to mitigate their negative demographic and genetic impacts, their effectiveness remains species-dependent and difficult to assess. We analysed the short-term impact of a newly built highway in eastern France and the associated restoration measures on population genetic structure in the protected southern damselfly (Coenagrion mercuriale). We genotyped 46 populations collected after the highway construction using microsatellite and SNP markers over two successive years to detect potential genetic discontinuities across the highway. We also evaluated the effectiveness of watercourse restoration and identified the likely origin of recolonising individuals. We found no significant barrier effect of the highway construction on gene flow. However, these encouraging results should be interpreted with caution, considering the likely time-lag in populations’ responses to genetic drift effects. We observed a gradual recolonisation of restored watercourses that had undergone compensatory measures, suggesting positive effects of reproductive habitat recovery. Recolonisation involved nearby populations but also long-distance dispersal events occurring overland. Detected migrant individuals may come from geographically distant populations belonging to a different watercourse. This mirrors a migrant-pool model of colonisation that leaves high levels of genetic diversity and no evident spatial patterns in populations located close to the highway. Altogether, our study highlights both the potential and limitations of genetic tools to assess the impacts of linear infrastructure on gene flow and for understanding watercourse recolonisation processes after ecological management restoration.
Anthropogenic selective pressures imposed by intensive anthelmintic use provide a powerful framework to investigate rapid evolutionary responses in natural populations. The study described here applied the deep amplicon sequencing of ITS2 rDNA and isotype-1 β-tubulin genes, alongside the Faecal Egg Count Reduction Test, to identify gastrointestinal nematode (GIN) species and assess benzimidazole (BZD) resistance, in six commercial beef cattle farms in Argentina. Seven nematode species were identified, with communities dominated by Haemonchus placei and Cooperia punctata. Screening for isotype-1 β-tubulin (tbb-isotype-1) polymorphisms identified four SNPs known to be associated with BZD resistance: F167Y(TTC>TAC), E198A(GAA>GCA), E198L(GAA>TTG), and F200Y(TTC>TAC), which were identified in C. punctata, Ostertagia ostertagi, H. contortus, and C. oncophora. Treatment failures following BZD administration were mainly associated with C. punctata and, to a lesser extent, O. ostertagi carrying 71.4% of β-tubulin resistance-associated ASVs, consistent with strong directional selection at this locus. Surprisingly, C. punctata survivors frequently carried predominantly susceptible alleles, revealing a marked discordance between genotype and phenotype. In contrast, under combined BZD + macrocyclic lactone treatments, surviving C. punctata predominantly harbored β-tubulin resistance-associated alleles, consistent with enhanced selection under multidrug pressure. Together, these patterns suggest that variation in treatment outcome cannot be fully explained by tbb-isotype-1 alone, and likely involves additional genetic mechanisms, ecological factors such as parasite niche, and/or pharmacokinetic interactions. This study provides the first genetic characterization of GIN communities and BZD resistance in large-scale cattle systems in Argentina, revealing complex resistance dynamics and underscoring the importance of molecular surveillance to guide sustainable parasite control.
Conservation interventions are increasingly required for species threatened by population declines and isolation due to anthropogenic pressures. Small, isolated populations are particularly vulnerable to the loss of genetic diversity, increased inbreeding, and the accumulation of deleterious mutations. Translocations or supplementation of allopatric individuals for genetic rescue may be the only way to increase genetic diversity and increase population persistence via increased adaptive potential. Here, we use an experimentally admixed population of sand lizards on a small island in Sweden as a valuable model of genetic rescue. This population was established approximately 20 years ago (5-6 generations), resulting in increased fecundity and hatchling viability. This population was founded from crossings between individuals from an inbred population from the nearby mainland and individuals sourced from populations in southern Sweden. Low-coverage whole-genome sequencing revealed elevated genetic diversity and reduced realized genetic load in this admixed population relative to the source populations. Ancestry analyses indicated a greater contribution of southern Swedish genetic variation, potentially reflecting the contribution of beneficial adaptive variation from this region that may underlie the positive population effects. This system provides valuable empirical insights into the long-term genomic consequences of genetic rescue in this model vertebrate population.
The Asellus aquaticus species complex, a freshwater isopod crustacean, includes surface and cave ecomorphs that differ markedly in eye and pigmentation phenotypes. Previous genetic studies in Slovenian cave populations revealed that the same genomic regions underlie eye and pigment loss across multiple cave populations, suggesting strong genetic constraints on these traits. To test the generality of this pattern, we examined Asellus infernus, a cave population from Mangalia, Romania, that inhabits thermal, sulfidic waters and is geographically distant from the Slovenian cave populations. Based on its distinct ecology and likely different ancestral surface population, we hypothesized that A. infernus would rely on different genomic regions for similar traits. Using hybrid crosses, we uncovered novel hybrid phenotypes unique to A. infernus, highlighting the presence of additional genetic variation not observed in Slovenian cave populations. However, we found that the same genomic regions previously implicated in Slovenian populations were also associated with similar eye and pigmentation phenotypes in A. infernus. Eye and pigment phenotypes examined were pigmented vs. unpigmented individuals, orange vs. red/brown and red vs. orange/brown eye pigment, stellate vs. diffuse head pigmentation pattern, and presence vs. absence of ommatidia and/or their fragments. These results point to shared genetic mechanisms of eye and pigment reduction between different cave populations. Whether these parallels reflect shared standing genetic variation in ancestral surface populations or convergent evolution through recurrent changes at the same loci due to pleiotropic fitness benefits remains unresolved.
Reproductive isolation; Genomic divergence; Introgression; Seaweed, Hawai’i. Speciation in marine environments is inherently complex, and the mechanisms underlying the evolution of reproductive isolation remain a fundamental yet understudied challenge in macroalgae. This study investigates two lineages of the marine red alga Amansia glomerata around Oʻahu, Hawaiʻi, to test the hypothesis that lineage boundaries are maintained by strong reproductive barriers. Using genomic sequencing (ddRAD), fine-scale spatial transects, and demographic modeling, we characterized lineage spatial structure and genomic divergence. Our results revealed that lineages form extensive sympatric populations and remain strongly differentiated across the genome, even when co-occurring at fine spatial scales. Demographic analyses supported a scenario of allopatric divergence followed by secondary contact, likely driven by Pleistocene sea-level fluctuations within the Hawaiian Archipelago. The absence of backcrosses and second-generation hybrids, combined with numerous loci acting as barriers to gene flow, is consistent with a lack of contemporary admixture. Nevertheless, genomic footprints of introgression were detected, and their spatial configuration around Oʻahu may indicate past, geographically restricted episodes of asymmetric gene flow during secondary contact. While our findings highlight allopatric divergence as a major driver of speciation in this system, the potential role of ecological differentiation remains to be explored. Overall, this study offers additional genomic perspectives on algal speciation and underscores the potential of Hawaiian seaweeds to yield new insights into this process.
A vast portion of genes in microbial genomes, termed the “unknome,” remains functionally uncharacterised. This genetic “dark matter” represents a significant bottleneck in microbiology, as it is often excluded from genomic studies. We argue that a substantial part of the unknome encodes functions critical for biotic interactions, the complex dialogues among microbes or between microbes and their hosts. These functions are rarely observed under standard laboratory conditions, which rely on simplified pure cultures. Unlocking the unknome therefore calls for a stronger emphasis on ecologically relevant experimental systems. By embracing complexity through co-culture and in situ analyses, we can begin to decipher this hidden genetic repertoire, deepening our understanding of microbial communication, adaptation, and evolution. Crucially, the conceptual and methodological challenges raised by the microbial unknome resonate well beyond microbiology: parallel “dark” fractions of uncharacterised genes and proteins pervade eukaryotic genomes, from lineage-specific (orphan) genes underpinning novelties in plants and animals, including humans. Embracing ecological and systems-level approaches to dissect the unknome therefore has the potential to reframe how we link genotype to phenotype in context-dependent, interaction-driven biological systems.
Interspecific hybridization can reshape patterns of genetic variation and alter evolutionary trajectories, but the implications of naturally occurring hybridization for endangered species remain uncertain. Understanding how species boundaries are maintained or eroded in the presence of hybridization is therefore essential for managing endangered species in altered ecosystems. In the San Juan River, three native catostomids (bluehead sucker Catostomus discobolus, flannelmouth sucker C. latipinnis, and the endangered razorback sucker Xyrauchen texanus) form a hybridizing assemblage in an ecosystem transformed by anthropogenic disturbance. Despite annual reproduction, razorback sucker recruitment is exceptionally rare, whereas adult flannelmouth x razorback sucker hybrids are regularly encountered. We applied double digest restriction site-associated DNA sequencing and mitochondrial DNA barcoding to characterize hybridization dynamics and evaluate whether introgression threatens razorback sucker persistence. Analysis of 30,774 loci from 1128 individuals revealed that 98.8% of hybrids involved crosses between flannelmouth and razorback sucker. F1 (68.4%) and third-generation (28.4%) hybrids were most prevalent, while second-generation hybrids were rarely detected (3.2%). All second and third-generation hybrids resulted from backcrossing. Razorback sucker mitochondrial haplotypes occurred in 92.7% of hybrids, suggesting asymmetric mating or potential mitonuclear incompatibilities. Genomic cline analyses identified loci with non-neutral introgression patterns, including a large chromosomal region consistent with overdominance and others reflecting potential Dobzhanzky-Muller incompatibilities or genetic drift. These patterns, combined with a scarcity of later-generation intermediate hybrids, suggest that disruption of co-adapted gene complexes limits hybridization beyond the F1 generation. Although hybridization occurs regularly, introgression appears constrained, and formation of a hybrid swarm remains unlikely under current conditions.
Biological invasions provide opportunities for previously isolated lineages to come into secondary contact, often resulting in hybridization. This process can generate admixed genomes and novel phenotypes, potentially contributing to invasion success. Here, we investigated invasive saltcedar (Tamarix spp.) in the southwestern United States using genome-wide SNP data from 319 individuals, including the parental lineages Tamarix chinensis and T. ramosissima. By integrating population genomics, ecological niche modeling, and demographic inference, we reconstructed the origins of invasive populations and characterized admixture across major river basins. Our results reveal that introduced populations are predominantly admixed, with varying ancestry contributions from both parental lineages. Multiple lines of evidence, including hybrid indices, f3-statistics, and phylogenetic network analyses, support extensive admixture among US populations. Demographic inference indicates a recent origin consistent with historical introduction records and suggests that admixed propagules were likely introduced and subsequently expanded. Furthermore, ecological niche analyses suggest significant differentiation and niche expansion in the introduced populations compared to their native parental counterparts. Together, these results demonstrate that hybridization, together with multiple introductions and demographic processes, contributed to the maintenance of neutral genetic diversity and may have facilitated the successful establishment of these invasive populations. More broadly, this study highlights how integrating genomic data with ecological niche analyses clarifies the evolutionary dynamics during biological invasions.
It is generally accepted that non-coding DNA constitutes the vast majority of most eukaryotic genomes and is concentrated at the nuclear periphery and nucleolar surface. Building upon this spatial organization, we have previously proposed that this layer of abundant, peripherally localized non-coding DNA functions as a 3D buffer that transiently absorbs or permanently excludes DNA damage to protect the genome and the relatively central exome from external and internal mutagens in somatic cells. This review explores the potential role of non-coding DNA as a physical barrier in genome safeguarding during early developmental stages and major evolutionary transitions. During gametogenesis and early embryogenesis the barrier is first provided by abundant non-coding DNA; as heterochromatin matures from non-coding DNA, many species programmatically eliminate the now-redundant non-coding DNA. Across evolution, whole-genome duplications and repeat amplification expand the shield, facilitating major evolutionary transitions such as vertebrate origins, water-to-land colonization and survival through mass-extinction crises. Conversely, in stable ecosystems selection favors genome streamlining: redundant non-coding DNA is lost to reduce fitness costs. Thus, the dosage of non-coding DNA is negatively correlated with the strength of apomorphic safeguards (adaptive immunity, viviparity) and positively correlated with ecological or developmental stress. By integrating comparative genomics, 3D nuclear architecture and evolution, we unify a single conceptual framework: non-coding DNA acts as a malleable fortress whose thickness is tuned to the variable need for genome protection during both ontogeny and phylogeny. This perspective offers new explanatory power for the accumulation or loss of non-coding DNA and can predict genome-size trajectories.
Hybridization between closely related forest tree species is a major concern for assisted migration decisions. Historical introductions, such as the repeated introduction of Caucasian beech (Fagus hohenackeriana) into European beech (Fagus sylvatica) forests over 100 years ago, provide insight into potential outcomes. In two such forest stands in Central Europe, we exhaustively genotyped adults (N = 216 and 226) and surrounding seedlings and juveniles (N = 639 and 423). We found that the two species interbred successfully, with interspecific F1 hybrids comprising 10.4% and 34.2% of the seedlings in the two stands, respectively. However, their proportion decreased in later age classes, and advanced-generation hybrids were rare (<4%), despite up to three possible generations of introgression. Parentage analyses revealed a tendency toward assortative mating, likely driven by the, on average, 2.3-day earlier spring bud break of Caucasian beech, based on five years of observations. In agreement with this finding, F1 seedlings grew near adult Caucasian beeches, which acted as seed donors. To assess whether these patterns could arise from demographic processes alone or reflect outbreeding depression, we used spatially explicit individual-based simulations with mating and demographic parameters specific to the study system and sites, including selection against F1s. All simulated scenarios underestimated F1 frequencies and overestimated advanced-generation hybrid frequencies, suggesting that life-stage-specific selection may alter hybrid persistence. We conclude that Caucasian beech introductions do not pose a risk of invasiveness, and that mild seedling-stage-specific heterosis effect overridden by outbreeding depression at the adult stage is the most parsimonious explanation for the observed patterns. Our simulation pipeline can be used for other species and contexts to evaluate potential outcomes of assisted gene flow.
While inbreeding is known to affect individual fitness and thus population extinction risk, studies often under-represent non-model species of conservation concern and rarely examine the conditionality of inbreeding depression. Here, using genomic markers (SNPs), we determined inbreeding depression in a threatened bird, the aquatic warbler Acrocephalus paludicola - a habitat specialist with depleted genetic diversity that went through a steep recent decline. We also explored whether the magnitude of inbreeding depression depends on phenotypic (tarsus and wing length) and environmental (timing of breeding and brood size) factors. In adult males, the relationship between genomic inbreeding and breeding success depended on tarsus length, a proxy for body size, being strongly negative in small-tarsus males. We also detected a weak interaction effect between genomic inbreeding and wing length on male survival, with short-winged males being negatively affected by inbreeding. By contrast, models that did not include these interactions provided little evidence for inbreeding effects on male fitness, and estimates of inbreeding load were highly uncertain for both survival and breeding success. In adult females, we found little support for associations between genomic inbreeding and clutch size, hatching success, nestling survival, or fledged brood size, and no evidence that these relationships were conditional on the phenotypic and environmental variables examined. Accordingly, estimates of inbreeding load in females were close to zero. We conclude that inbreeding depression on fitness components is phenotype-dependent, being stronger in small-bodied males, and that considering interactions with phenotypic variables enables more accurate estimation of inbreeding depression.
The responses of anurans to paleogeology, climate variability and anthropogenic factors play a crucial role in understanding their diversity and population dynamics. Despite substantial phylogeographic studies existing for northeast Asia, a region-wide synthesis linking divergence timing with major evolutionary drivers is lacking. To address this gap, we synthesised published divergence-time estimates for northeast Asian anurans from 1998 to present, and linked basal, stem and crown ages to their associated drivers and regional contexts. We integrated the data with time-calibrated genomic species trees, diversification analyses, and three key trait data (body size, elevation and latitude range) to assess temporal patterns of lineage divergence and compare diversification dynamics among the major anuran families in northeast Asia. Our synthesis identifies four recurrent evolutionary drivers: (1) paleogeology and landscape barriers, (2) climate fluctuations and latitudinal gradients, (3) glaciations and past sea-level change, and (4) anthropogenic influences. Across families, we highlight unresolved species boundaries, detect the genetic imprint of human-mediated disturbance, synthesise phenotypic, ecological, and macroevolutionary patterns using openly available datasets, and identify cases where multiple drivers interact within species complexes. Bayesian Analysis of Macroevolutionary Mixtures (BAMM) trait reconstructions showed that across all three traits, Ranidae had the highest trait values through time, indicating broader ecological breadth and greater macroevolutionary expansion than Bufonidae and Microhylidae. Our synthesis integrates divergence timing, trait evolution, and environmental drivers, providing a general framework for understanding biodiversity responses to long-term environmental change.
Availability of de novo mutation rate (µ) estimates based on approaches that rely on bioinformatic validations has increased tremendously during the past few years, but the accuracy and precision of these estimates often remain unclear as Sanger sequencing validation of the mutations is often lacking. We used both long- and short-read sequencing data and different bioinformatic pipelines to estimate µ, as well as false positive (FPR) and negative (FNR) rates, for family trios of flat-headed loaches (Oreonectes platycephalus). By comparing estimates against PCR-verified mutations, we observed that the top-performing approach (as ranked by the F1 score of seven approaches at the same depth) still exhibited a 4% false positive rate (FPR) alongside a 12% false-negative rate (FNR). Across the remaining methods, FPR values ranged from 4-12%, and FNRs from 8-19%. Irrespective of the bioinformatic approach used, long-read data yielded consistently lower µ estimates than short-read data because of the larger callable genome sizes. In addition, a higher mapping depth resulted in a lower FNR. These results call for caution regarding de novo mutations without Sanger sequencing validation in non-model organisms and raise the possibility that many published µ-estimates, especially those based on low mapping depths, might be biased.
Genomic prediction (GP) has become an essential tool for accelerating modern plant breeding, particularly for complex traits. We evaluated different GP approaches for pre-breeding in thirteen biparental strawberry families derived from crosses between Fragaria virginiana and Fragaria chiloensis, focusing on resistance to powdery mildew (PM) in both leaves and fruits. Five-fold cross-validation using Genomic Best Linear Unbiased Prediction (GBLUP) for combined-year data yielded mean predictive abilities (PAs) of 0.56 and 0.36 for leaf and fruit resistance, respectively. Family-based GBLUP analyses showed higher PAs for closely related families, ranging from 0.10 to 0.89. Simulations identified key parameters: training sets comprising 40% of the population provided stable predictions for both traits, while ≈8300 SNPs were sufficient for predicting leaf resistance. However, PA for fruit resistance remained consistently low regardless of marker density. We then compared GBLUP with a marker-assisted model that iteratively incorporated the major resistance loci as fixed effects. This strategy increased PA by ≈10-30% for leaf resistance and ≈25-47% for fruit resistance across models. We further applied cross-environment forward prediction in independent greenhouse and separate field validation trials. The GBLUP model maintained substantial PA when trained on either the full population or a 40% subset, demonstrating robustness in predicting new genotypes across distinct environments. Our findings highlight the importance of taking trait genetic architecture into account to enhance PAs for PM resistance in strawberry. Together, these results provide evidence-based thresholds for training population size and marker density, offering a framework for efficient implementation of genomic selection in strawberry pre-breeding populations.
Large, cold-adapted ungulates are particularly sensitive to environmental changes and human pressure. Despite a decline in its geographic range and population size, the moose (Alces alces) remains one of the few extant representatives of Eurasian megafauna. We analysed the complete mitochondrial genomes (mtDNA) of 95 subfossil and 137 modern Eurasian moose specimens in order to assess how genetic diversity, effective population size (Nef), and phylogeographic patterns of the species have changed over the last 50,000 years in response to climatic oscillations and human impact. The European and Asiatic-American moose mtDNA lineages diverged approximately 100,000 years BP, occurring in regions with different environmental conditions. All extant mtDNA groups of the Eurasian moose originated before the Last Glacial Maximum (LGM), and subsequently diversified into several subgroups. Bayesian coalescent analyses indicate that Nef was lowest immediately after the LGM, and increased to a maximum during the Middle Holocene. Following this peak, Nef declined towards the present day, decreasing by approximately half in the Asiatic-American lineage and fourfold in the European lineage. The Central European group experienced the strongest range contraction, while the Eastern group remained largely stable and the Western group shifted geographically. The Nef in the Western group fluctuated the least, while that in the Central and Eastern groups declined substantially from the mid-Holocene. Although moose are cold-adapted and sensitive to high temperatures, the most significant factor contributing to the decline of their Nef during the Holocene was likely human impact (overhunting, habitat degradation) rather than climate warming.
