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Large ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. While recent studies have used time-stratified aDNA for selection scans, most focus on single-locus methods. We conducted a multi-locus genotype scan on 708 samples spanning 7000 years of European history. We show that the G12 statistic, originally designed for unphased diploid data, can effectively detect selection in aDNA processed to create 'pseudo-haplotypes'. In simulations and at known positive control loci (e.g., lactase persistence), G12 outperforms the allele frequency-based selection statistic, SweepFinder2, previously used on aDNA. Applying our approach, we identified 14 candidate regions of selection across four time periods, with half the signals detectable only in the earliest period. Our findings suggest that selective events in European prehistory, including from the onset of animal domestication, have been obscured by neutral processes like genetic drift and demographic shifts such as admixture.

Mutation accumulation (MA) experiments play an important role in understanding evolution. For microbial populations, such experiments often involve periods of population growth, such that a single individual can make a visible colony, followed by severe bottlenecks. Previous work has quantified the effect of positive and negative selection on MA experiments, demonstrating for example that with 20 generations of growth between bottlenecks, big-benefit mutations can be over-represented by a factor of five or more (Wahl and Agashe, 2022). This previous work assumed a deterministic model for population growth. We now develop a fully stochastic model, including realistic offspring distributions that incorporate genetic drift and allow for the loss of rare lineages. We demonstrate that when stochastic offspring distributions are considered, selection bias is even stronger than previously predicted. We describe several analytical and numerical methods that offer an accurate correction for the effects of selection on the observed distribution of fitness effects, describe the practical considerations in implementing each method, and demonstrate the use of this correction on simulated MA data. • We quantify bias due to positive and negative selection in mutation accumulation experiments, using realistic offspring distributions. • When drift is included, selection bias is even stronger than previously predicted. • We provide analytical and numerical methods to correct MA data for selection. [ABSTRACT FROM AUTHOR]

Infinitely many distinct trait values may arise in populations bearing quantitative traits, and modeling their population dynamics is thus a formidable task. While classical models assume fixed or infinite population size, models in which the total population size fluctuates due to demographic noise in births and deaths can behave qualitatively differently from constant or infinite population models due to density-dependent dynamics. In this paper, I present a stochastic field theory for the eco-evolutionary dynamics of finite populations bearing one-dimensional quantitative traits. I derive stochastic field equations that describe the evolution of population densities, trait frequencies, and the mean value of any trait in the population. These equations recover well-known results such as the replicator-mutator equation, Price equation, and gradient dynamics in the infinite population limit. For finite populations, the equations describe the intricate interplay between natural selection, noise-induced selection, eco-evolutionary feedback, and neutral genetic drift in determining evolutionary trajectories. My work uses ideas from statistical physics, calculus of variations, and SPDEs, providing alternative methods that complement the measure-theoretic martingale approach that is more common in the literature. [ABSTRACT FROM AUTHOR]

We model natural selection for or against an anti-parasite (or anti-predator) defense allele in a host (or prey) population that is structured into many demes. The defense behavior has a fitness cost for the actor compared to non defenders ("cheaters") in the same deme and locally reduces parasite growth rates. Hutzenthaler et al. (2022) have analytically derived a criterion for fixation or extinction of defenders in the limit of large populations, many demes, weak selection and slow migration. Here, we use both individual-based and diffusion-based simulation approaches to analyze related models. We find that the criterion still leads to accurate predictions for settings with finitely many demes and with various migration patterns. A key mechanism of providing a benefit of the defense trait is genetic drift due to randomness of reproduction and death events leading to between-deme differences in defense allele frequencies and host population sizes. We discuss an inclusive-fitness interpretation of this mechanism and present in-silico evidence that under these conditions a defense trait can be altruistic and still spread in a structured population. [ABSTRACT FROM AUTHOR]

The emergence of the Omicron lineage represented a major genetic drift in SARS-CoV-2 evolution. This was associated with phenotypic changes including evasion of pre-existing immunity and decreased disease severity. Continuous evolution within the Omicron lineage raised concerns of potential increased transmissibility and/or disease severity. To address this, we evaluate the fitness and pathogenesis of contemporary Omicron variants XBB.1.5, XBB.1.16, EG.5.1, and JN.1 in the upper (URT) and lower respiratory tract (LRT). We compare in vivo infection in Syrian hamsters with infection in primary human nasal and lung epithelium cells and assess differences in transmissibility, antigenicity, and innate immune activation. Omicron variants replicate efficiently in the URT but display limited pathology in the lungs compared to previous variants and fail to replicate in human lung organoids. JN.1 is attenuated in both URT and LRT compared to other Omicron variants and fails to transmit in the male hamster model. Our data demonstrate that Omicron lineage evolution has favored increased fitness in the URT. Here the authors show that contemporary SARS-CoV-2 Omicron variants are evolving towards the upper respiratory tract while causing less severe disease in the lung. The more antigenically distinct variant JN.1 fails to transmit in the male hamster model and causes reduced pathology. [ABSTRACT FROM AUTHOR]

Simple Summary: Raccoon dogs have been farmed for economic purposes for ~100 years, and white raccoon dogs are among the most famous breeds of farmed raccoon dogs. However, white raccoon dogs are weaker in fitness than normal raccoon dogs. Purging potentially deleterious mutations while maintaining a white coat is the goal for breeders. For the first time, we performed whole-genome sequencing of a white raccoon dog population and performed a comparative analysis with normal raccoon dogs. We found a smaller effective population size for the white raccoon dogs within the last 100 years. The overall inbreeding in the two types of raccoon dogs was found to be very similar, but recently occurring inbreeding was found to be more extensive in white raccoon dogs. Interestingly, the total number of deleterious mutations in the white raccoon dogs is comparable to that in the normal raccoon dogs. However, the proportion of homozygous missense mutations in white raccoon dogs is greater than that in normal raccoon dogs, indicating that the accumulation of small-effect deleterious mutations may be facilitated during the development of white breeds. The formation of animal breeds usually begins with a small subsample from their ancestral population. Deleterious mutations accumulate in the population under genetic drift, inbreeding, and artificial selection during the development and maintenance of traits desired by humans. White raccoon dogs are among the most popular breeds of farmed raccoon dogs, but white raccoon dogs are more susceptible to disease and have a lower reproductive ability. However, the accumulation of deleterious mutations in this white breed is largely unknown. By analyzing and comparing whole-genome sequencing data from 20 white raccoon dogs and 38 normal raccoon dogs, we detected an increased occurrence of loss-of-function (LoF) mutations in white raccoon dogs compared with normal raccoon dogs. With the finding of a significantly higher dosage of homozygous missense mutations in the white raccoon dog genome, we detected a greater fitness cost in white raccoon dogs. Although a much higher FROH level for ROH fragments longer than 1 Mb has been reported in white raccoon dogs, we did not detect a genetic signal of genetic purging in white raccoon dogs. This study provides valuable genomic resources and new insights into the accumulation of mutation loads in farmed raccoon dogs. [ABSTRACT FROM AUTHOR]

In this paper, we demonstrate that neutral fractional evolution equations with finite delay possess a stable mild solution. Our model incorporates a mixed fractional derivative that combines the Riemann–Liouville and Caputo fractional derivatives with orders 0 < α < 1 and 1 < β < 2 . We identify the infinitesimal generator of the cosine family and analyze the stability of the mild solution using both Hyers–Ulam–Rassias and Hyers–Ulam stability methodologies, ensuring robust and reliable results for fractional dynamic systems with delay. In order to guarantee that the features of invariance under transformations, such as rotations or reflections, result in the presence of fixed points that remain unchanging and represent the consistency and balance of the underlying system, fixed-point theorems employ the symmetry idea. Lastly, the results obtained are applied to a fractional order nonlinear wave equation with finite delay with respect to time. [ABSTRACT FROM AUTHOR]

Despite extensive experience with influenza surveillance in humans in Senegal, there is limited knowledge about the actual situation and genetic diversity of avian influenza viruses (AIVs) circulating in the country, hindering control measures and pandemic risk assessment. Therefore, as part of the "One Health" approach to influenza surveillance, we conducted active AIV surveillance in two live bird markets (LBMs) in Dakar to better understand the dynamics and diversity of influenza viruses in Senegal, obtain genetic profiles of circulating AIVs, and assess the risk of emergence of novel strains and their transmission to humans. Cloacal swabs from poultry and environmental samples collected weekly from the two LBMs were screened by RT-qPCR for H5, H7, and H9 AIVs. Subsequently, a subset of H9-positive samples was selected for whole sequencing. From December 2023 to October 2024, 499 samples were tested, and AIV was detected in 58.3% of them. Among these, A/H9N2 was the only subtype detected in both markets, with a detection rate of 47.7% (82/172) in Thiaroye and 35.3% (42/119) in Tilene, resulting in an overall positivity rate of 42.6% (124/291). Genome sequencing of 22 A/H9N2 isolates, including 11 poultry drinking water samples, 7 carcass wash water samples, 3 fecal samples, and 1 cloacal swab, yielded 7 complete and 15 partial genomic sequences. Phylogenetic analyses of the resulting sequences showed that the A/H9N2 isolates obtained in this study formed a monophyletic cluster and were closely related to the Senegalese human strain (A/Senegal/0243/2019) identified through the national influenza sentinel surveillance program. These strains were also closely related to the A/H9N2 viruses of the G1 lineage circulating in neighboring countries, suggesting cross-border transmission. The A/H9N2 strains carried the low pathogenicity RSSR/GLF motif at the HA cleavage site and possessed several key amino acid mutations, including HA-I155T and HA-Q226L, which are associated with human host adaptation, PB2-T105V, PB2-A661T, and PB2-A588V, which are linked to the human-to-human transmission and increased polymerase activity, NS2-T14M, NS2-M100I, NS1-I106M, NS1-V222M, NS1-E223A, NS1-I226V, NS1-E227G, and NS1-P228S, which are known to alter virulence (increased or reduced) in humans or mice, and M2-S31N, which promotes drug resistance. Seven potential N-glycosylation sites were predicted in the HA protein and six in the NA protein. The selection pressure analysis revealed that the A/H9N2 isolates were primarily under neutral evolution or purifying selection pressure. Overall, our findings highlight the potential for cross-species transmission of Senegalese A/H9N2 viruses, emphasizing the need for sustained monitoring of these viruses in both animal and human populations. [ABSTRACT FROM AUTHOR]

To conserve threatened species effectively, it is crucial to map the genetic variation of the remaining populations. Thus, using 15 microsatellites markers, from which 10 were specially developed for this study, we investigated genetic structure and gene flow patterns of Herbertia zebrina Deble, a critically endangered species endemic from grasslands of southern Brazil. We also investigated the degree of habitat fragmentation and the impacts on levels of genetic diversity, mating system and pollinators of the species. STRUCTURE and discriminant analysis of principal components identified the existence of three genetic clusters. Populations were not isolated by distance, and genetic differentiation among populations was low (7.0%). Migration rates were also low, but no evidence of genetic bottlenecks was found. However, effective population-scaled mutation rates (Θ) were < 1, suggesting that populations could be experiencing genetic drift, but the reason remains unknown. The results indicate that measurements of habitat fragmentation were not significantly correlated with genetic diversity estimates, which tend to increase with fragment size. H. zebrina was identified as an outcrossing species and specialized pollinators, such as Chalepogenus goeldianus and Lanthanomelissa betinae were rarely observed. Our findings suggest that genetic differentiation across multiple populations within the entire geographic distribution of H. zebrina is very low and populations may struggle to adapt to the current environmental and pollination changes. However, habitat fragmentation is still too recent to detect significant impacts on the levels of genetic variation. Thus, conservation plans are necessary to avoid further declines of this species. [ABSTRACT FROM AUTHOR]

Genotyping 16 SNPs of C-X-C motif chemokine receptor 1 (CXCR1) gene region which affects host resistance against mastitis disease was carried out in Holstein cows raised in Türkiye. In this study, the frequency of the undesirable C allele in the CXCR1 c.771C>G polymorphic region, associated with an incomplete response, was found to be high. Additionally, the genotypes c.1016AA and c.1016GG, which contribute to mastitis resistance, were observed at low frequencies. Several SNP loci in the CXCR1 gene, including c.606G>A, c.678G>A, c.1104G>A, c.1119+6C, c.1119+7A, and c.1119+10, significantly deviated from Hardy-Weinberg equilibrium (HWE) (P<0.0001), indicating violations of HWE assumptions such as random mating and absence of selection. The deviations at c.606G>A, c.678G>A, and c.1104G>A suggest strong selection pressures, likely due to artificial selection in Holstein cattle. These variants are synonymous mutations that do not alter the amino acid sequence but may influence protein synthesis through effects on mRNA stability, splicing, or translation efficiency. Furthermore, the absence of heterozygotes at loci c.1119+6C, c.1119+7A, and c.1119+10, which are located on untranslated regions (UTRs), potentially affecting gene expression by regulating mRNA stability, localization, or translation initiation, points to genetic drift or population substructure. These findings are important for understanding genetic variability and can inform marker-assisted selection programs to enhance breeding strategies while preserving genetic diversity for traits like disease resistance and milk production. [ABSTRACT FROM AUTHOR]

Transgenic soybean [Glycine max(L.) Merrill] currently covers approximately 80% of the global crop area for this species, with the majority of transgenic plants being glyphosate resistant (Roundup Ready, GR or RR). However, there is significant concern regarding the potential effects of GM crops and their byproducts on soil microbial communities. During our research, we discovered a type of semiwild soybean that emerged due to genetic drift at a transgenic test site. Nevertheless, the ecological risk to soil rhizosphere microorganisms associated with planting semiwild soybean following genetic drift remains unclear. Therefore, we conducted a field experiment and collected soil samples at various stages of plant growth. Our results indicate that the species diversity of rhizosphere bacteria in transgenic glyphosate-resistant semiwild soybean was also not significantly different from that observed in other types of soybean. Additionally, Basidiomycota had beneficial effects on rhizosphere fungi during the flowering and maturation stages in transgenic glyphosate-tolerant semiwild soybean. These findings provide valuable insights into how genetic drift in transgenic soybean may impact the soil microenvironment. [ABSTRACT FROM AUTHOR]

Mutations can be beneficial by bringing innovation to their bearer, allowing them to adapt to environmental change. These mutations are typically unpredictable since they respond to an unforeseen change in the environment. However, mutations can also be beneficial because they are simply restoring a state of higher fitness that was lost due to genetic drift in a stable environment. In contrast to adaptive mutations, these beneficial non-adaptive mutations can be predicted if the underlying fitness landscape is stable and known. The contribution of such non-adaptive mutations to molecular evolution has been widely neglected mainly because their detection is very challenging. We have here reconstructed protein-coding-gene fitness landscapes shared between mammals, using mutation-selection models and a multi-species alignments across 87 mammals. These fitness landscapes have allowed us to predict the fitness effect of polymorphisms found in 28 mammalian populations. Using methods that quantify selection at the population level, we have confirmed that beneficial non-adaptive mutations are indeed positively selected in extant populations. Our work confirms that deleterious substitutions are accumulating in mammals and are being reverted, generating a balance in which genomes are damaged and restored simultaneously at different loci. We observe that beneficial non-adaptive mutations represent between 15% and 45% of all beneficial mutations in 24 of 28 populations analyzed, suggesting that a substantial part of ongoing positive selection is not driven solely by adaptation to environmental change in mammals. Author summary: The extent to which adaptation to changing environments is shaping genomes is a central question in molecular evolution. To quantify the rate of adaptation, population geneticists have typically used signatures of positive selection. However, mutations restoring an ancestral state of higher fitness lost by genetic drift are also positively selected, but they do not respond to a change in the environment. In this study, we have managed to distinguish beneficial mutations that are due to changing environments and those that are restoring pre-existing functions in mammals. We show that a substantial proportion of beneficial mutations cannot be interpreted as adaptive. [ABSTRACT FROM AUTHOR]

Introduction: Astragalus mongholicus Bunge is an important medicinal legume species widely cultivated in northeastern China (NEC) and northwestern China (NWC) and can establish a symbiotic relationship with nitrogen-fixing rhizobial strains. However, there are limited reports comparing the genetic diversity, differentiation, and gene flow of rhizobial strains associated with this plant in different geographic regions. Methods: We used multilocus sequence analysis (MLSA) to investigate the phylogeny and genetic diversity of rhizobia and to estimate their intra- and inter-regional gene flow and genetic differentiation based on the analysis of concatenated core genes (recA , atpD , and glnII) and the critical symbiotic gene nodC. Results: We isolated eight known and three novel genospecies representing four genera, among which Rhizobium yanglingense was the most predominant microsymbiont. Phylogenetic analysis revealed a highly diverse rhizobial community nodulating Astragalus mongholicus in NEC, consisting of the four genera Rhizobium , Bradyrhizobium , Sinorhizobium , and Mesorhizobium. This community differed markedly from the rhizobial community found in NWC. Various rhizobial genospecies with different symbiotic gene nodC sequences were capable of nodulating A. mongholicus in NEC. Therefore, A. mongholicus exhibits promiscuity in its association with symbionts in the natural environment, showing no strong preference for either the species-defining core genes or the symbiotic genes of rhizobia. We also found that the Glyco_tranf_GTA_type superfamily (Glycosyltransferase family A) is the most highly conserved and essential domain in the NodC protein, which is encoded by the symbiotic nodC gene, across nodulating rhizobia. In addition, we found independent genetic differentiation among rhizobial communities geographically, and the frequency of gene flow among microsymbionts between NEC and NWC was low. We speculate that the formation of the highly diverse rhizobial community in NEC resulted from the independent evolution of each ancestral lineage. This diversity likely arose from intraregional genetic differentiation driven by mutations rather than recombination. Conclusion: Ecogeographical isolation between NEC and NWC restricted inter-regional genetic drift and gene flow. Therefore, intraregional genetic differentiation is the major evolutionary force underlying the genetic diversity of rhizobia. [ABSTRACT FROM AUTHOR]

Summary Mate limitation in small populations can reduce reproductive fitness, hinder population growth, and increase extinction risk. Mate limitation is exacerbated in self‐incompatible (SI) taxa, where shared S‐alleles further restrict mating. Theory suggests genetic drift as a predictor of mate limitation and the breakdown of SI systems. We tested this prediction by evaluating mate availability and S‐allele number in populations of a tetraploid herb with gametophytic SI (GSI) spanning a range of effective population sizes. We performed controlled crosses in 13 populations of Argentina anserina to quantify mate availability and S‐allele diversity, which were compared with simulations of tetraploid populations with GSI. We further evaluated mechanisms at the pollen–pistil interface contributing to outcross failure and leakiness in self‐recognition. Mate availability declined in small populations, and closely fit tetraploid GSI population genetic models where maternal plants receive pollen with diverse S‐alleles generated through tetrasomic inheritance. The failure to arrest self‐pollen in the style was common in some populations. Specifically, leaky SI was more common in small populations with low mate availability, where it explained higher seed production in natural populations. The restriction of leaky self‐recognition to the smallest populations is consistent with mate limitation as a pressure driving the breakdown of self‐incompatibility. [ABSTRACT FROM AUTHOR]

AbstractNavigating the challenges in apomixis population genetics requires a comprehensive understanding of its unique genetic consequences. This review explores the population genetics of apomixis, comparing sexual and apomictic populations, research challenges, and outlining future directions. Apomictic plants form clonal seeds, and arise from sexual species through hybridization and/or polyploidy. Sexual species generate genetic variation via meiotic recombination, random mating, and gradual accumulation of beneficial mutations. In contrast, apomicts rely on similar mechanisms to generate genetic variation but at a much slower rate, primarily through ´residual´ sexuality. Clonality in apomicts also promotes the accumulation of deleterious mutations. Additionally, recurrent origins of apomicts from sexual progenitors, especially via hybridization contribute to genetic diversity in apomictic populations. These processes, with varying rates of recombination, gene flow, and genotype fixation, lead to distinct genetic structures between sexual and apomictic populations. Reevaluating the evolutionary mechanisms like gene flow, genetic drift, mutation rates, and selection pressures is, therefore, crucial for understanding the processes driving genetic differentiation and genomic structure in apomictic populations. Research on apomixis has advanced from early documentation in the 18th century to modern cytological and genomic approaches. Early theoretical models of apomixis inheritance, adjusted for polyploid and nonsexual populations, provided foundational insights, while recent genome-wide studies have shed light on the genetic basis and evolutionary dynamics of apomixis across taxa. However, significant gaps remain in understanding population-level evolutionary forces shaping apomixis. Future research in comparative genomics of apomictic and sexual relatives will help identify genes and epigenetic marks of adaptive significance. Functional evaluation of genes associated with selective advantages, coupled with specialized bioinformatic tools, will improve our understanding of genotype-phenotype interactions. Integrative approaches combining multi-omics, morphology, and ecological information are key to resolving the population genetic complexities of apomictic taxa and their adaptation and speciation processes. Moreover, machine learning offers promise for analyzing large genomic datasets and uncovering hidden patterns, while interdisciplinary collaborations could translate findings into conservation, agriculture, and biotechnology applications. [ABSTRACT FROM AUTHOR]

Background: Genomic analysis has revealed extensive contamination among laboratory-maintained microbes including malaria parasites, Mycobacterium tuberculosis, and Salmonella spp. Here, we provide direct evidence for recent contamination of a laboratory schistosome parasite population, and we investigate its genomic consequences. The Brazilian Schistosoma mansoni population SmBRE has several distinctive phenotypes, showing poor infectivity, reduced sporocyst number, low levels of cercarial shedding and low virulence in the intermediate snail host, and low worm burden and low fecundity in the vertebrate rodent host. In 2021 we observed a rapid change in SmBRE parasite phenotypes, with a 10-fold increase in cercarial production and fourfold increase in worm burden. Methods: To determine the underlying genomic cause of these changes, we sequenced pools of SmBRE adults collected during parasite maintenance between 2015 and 2023. We also sequenced another parasite population (SmLE) maintained alongside SmBRE without phenotypic changes. Results: While SmLE allele frequencies remained stable over the 8-year period, we observed sudden changes in allele frequency across the genome in SmBRE between July 2021 and February 2023, consistent with expectations of laboratory contamination. (i) SmLE-specific alleles increased in the SmBRE population from 0 to 41–46% across the genome between September and October 2021, reflecting the timing and magnitude of the contamination event. (ii) After contamination, strong selection (s ≅0.23) drove the replacement of low-fitness SmBRE with high-fitness SmLE alleles. (iii) Allele frequency changed rapidly across the whole genome, except for a region on chromosome 4, where SmBRE alleles remained at high frequency. Conclusions: We were able to detect contamination in this case because SmBRE shows distinctive phenotypes. However, this would likely have been missed with phenotypically similar parasites. These results provide a cautionary tale about the importance of tracking the identity of parasite populations, but also showcase a simple approach to monitor changes within populations using molecular profiling of pooled population samples to characterize single-nucleotide polymorphisms. We also show that genetic drift results in continuous change even in the absence of contamination, causing parasites maintained in different labs (or sampled from the same lab at different times) to diverge. [ABSTRACT FROM AUTHOR]

Ecological theory predicts that species turnover among communities (e.g. β-diversity) and genetic turnover among populations within species (e.g. FST) should be positively correlated if similar processes influence colonization and occupancy of species and gene flow and genetic drift of populations within a metacommunity. Using recently published population genomic data from multiple populations of 15 freshwater mussel (Unionidae) species across seven rivers in the Mobile and Tennessee River basins of the south-eastern USA, we conducted novel analyses examining the relationship between taxonomic turnover (β-diversity) among communities and genetic differentiation (FST) within these species. FST and β-diversity were both hierarchically structured, and strong basin effects and isolation-by-distance were observed for β-diversity and for FST among populations within most species. Furthermore, β-diversity and FST were directly correlated for the overall community and among sites for individual species, indicating that factors shaping turnover among mussel assemblages are similar at the species and genetic levels. The widespread associations between turnover metrics at the community and population genetic levels of biological organization suggest that parallel processes govern species composition and intraspecific connectivity in freshwater mussel metacommunities. [ABSTRACT FROM AUTHOR]

The amorphous/crystalline structure with superhydrophilic/superaerophobic feature has better HER activity than crystalline/crystalline phase in alkaline, neutral and simulated seawater environments. [Display omitted] The development of efficient, stable, and versatile hydrogen evolution electrocatalysts is of great meaning, but still faces challenging. Interface engineering and phase engineering have been immensely applied in the field of hydrogen evolution reaction (HER) because of their unique physicochemical properties. However, they are typically used separately, which limits their effectiveness. Herein, we propose an interface-engineered CoMo/CoTe electrocatalyst, consisting of an amorphous CoMo (a-CoMo) layer-encapsulated crystalline CoTe array, achieving the profound optimization of catalytic performance. The experimental results and density functional theory calculations show that the d-band center of the catalyst shifts further upward in contrast with its crystalline–crystalline counterpart, optimizing the electronic structure and the intermediate adsorption, thereby reducing the kinetic barrier of HER. The a-CoMo/CoTe with superhydrophilic/superaerophobic features shows excellent catalytic performance in alkaline, neutral, and simulated seawater environments. [ABSTRACT FROM AUTHOR]

The article published in the journal "Molecular Ecology" discusses the impact of chromosomal rearrangements (CRs) on evolution and speciation genomics. It highlights the role of CRs in driving evolution and species diversification, emphasizing that CRs are not randomly distributed across genomes. The article presents various studies on different organisms, such as sedges, butterflies, fishes, and mammals, to explore the evolutionary impact of CRs. It concludes by suggesting that with advancements in genomic technologies, large-scale macroevolutionary inferences can be made to understand the role of CRs in promoting speciation and biodiversity. [Extracted from the article]

Large‐scale chromosome rearrangements, such as fissions and fusions, are a common feature of eukaryote evolution. They can have considerable influence on the evolution of populations, yet it remains unclear exactly how rearrangements become established and eventually fix. Rearrangements could fix by genetic drift if they are weakly deleterious or neutral, or they may instead be favoured by positive natural selection. Here, we compare genome assemblies of three closely related Brenthis butterfly species and characterize a complex history of fission and fusion rearrangements. An inferred demographic history of these species suggests that rearrangements became fixed in populations with large long‐term effective size (Ne), consistent with rearrangements being selectively neutral or only very weakly underdominant. Using a recently developed analytic framework for characterizing hard selective sweeps, we find that chromosome fusions are not enriched for evidence of past sweeps compared to other regions of the genome. Nonetheless, we do infer a strong and recent selective sweep around one chromosome fusion in the B. daphne genome. Our results suggest that rearrangements in these species likely have weak absolute fitness effects and fix by genetic drift. However, one putative selective sweep raises the possibility that natural selection may sometimes play a role in the fixation of chromosome fusions. [ABSTRACT FROM AUTHOR]

ABSTRACT Male frogs emit stereotypical advertisement calls to attract mates and deter conspecific rivals. The evolution of these calls is thought to be linked to anatomical constraints and the acoustic characteristics of their surroundings. The acoustic adaptation hypothesis (AAH) posits that species evolve calls that maximize propagation distance and reduce signal degradation in the environment where they are emitted. We applied phylogenetic comparative analyses to study the association of body size, vegetation density, type of aquatic ecosystem, and calling site on the evolution of acoustic traits in Cophomantini, a large radiation of Neotropical treefrogs (Hylidae). We obtained and analyzed body size, acoustic, and habitat data from a total of 112 species (58% of Cophomantini), using the most inclusive available phylogeny. We found a significant negative correlation between peak frequency, body size, and calling site, but contrary to the predictions of the AAH, we did not find support for associations among call traits and environmental characteristics. Although spectral allometry is explained by an anatomical constraint, it could also be maintained by female choice. We recommend that future studies strive to incorporate factors such as female mate preferences, eavesdropping by predators or parasites, and genetic drift. [ABSTRACT FROM AUTHOR]

The electrochemical production of sustainable hydrogen under neutral conditions is advantageous, as it allows for the use of wastewater or seawater without the need for pH adjustments. However, the low ion concentration in neutral electrolytes typically results in limited adsorption of reactants on the catalyst surfaces, leading to sluggish reaction kinetics. Therefore, enhancing absorption capacity is a key challenge in the development of neutral hydrogen evolution reaction (HER) catalysts. Hetero‐structured catalysts may improve surface adsorption through extensive interfacing between phases, enabling active transportation of reaction intermediates. Integrating metal sulfides and oxides, in particular, holds the potential for generating efficient electrocatalysts with improved HER activity and surface adsorption capacity. Herein, the synthesis of CrOx‐doped Co9S8/CuCrS2 mosaic hetero‐nanostructures is reported as a proficient HER catalyst. Facile Cr‐cation migration at the Co9S8/CuCrS2 interface enables the preparation of Cr‐oxide sub‐nano domains within the sulfide matrix, boosting the HER catalysis in neutral media. The exceptional electrochemical performance is demonstrated in a pH 7.4 phosphate buffer solution, including low overpotential, small Tafel slope, and stability over 60 h. The formulation of catalyst design and synthetic approaches has the potential to pave the way for diverse catalytic applications utilizing metal oxide‐doped hetero‐nanostructures. [ABSTRACT FROM AUTHOR]

Introduction: The Faroe Islands are a small archipelago located in the North Atlantic likely colonized by a small group of founders sometime between 50 and 300 CE. Post colonization, the Faroese people have been largely isolated from admixture with mainland and other island populations in the region. As such, the initial founder effect and subsequent genetic drift are likely major contributors to the modern genetic diversity found among the Faroese. Methods: In this study, we assess the utility of Y-chromosomal microsatellites to detect founder effect in the Faroe Islands through the construction of haplotype networks and a novel empirical method, mutational distance from modal haplotype histograms (MDM), for the visualization and evaluation of population bottlenecks. Results: We compared samples from the Faroe Islands and Iceland to possible regional source populations and documented a loss of diversity associated with founder events. Additionally, within-haplogroup diversity statistics reveal lower haplotype diversity and richness within both the Faroe Islands and Iceland, consistent with a small founder population colonizing both regions. However, in the within haplogroup networks, the Faroe Islands are found within the larger set of potential source populations while Iceland is consistently found on isolated branches. Moreover, comparisons of within-haplogroup MDM histograms document a clear founder signal in the Faroes and Iceland, but the strength of this signal is haplogroup-dependent which may be indicative of more recent admixture or other demographic processes. Discussion: The results of the current study and lack of conformity between Icelandic and Faroese haplotypes implies that the two populations were founded by different paternal gene pools and there is no detectable post-founder admixture between the two groups. [ABSTRACT FROM AUTHOR]

Stephania tetrandra S. Moore (family: Menispermaceae), a dioecious herbaceous vine and the only species in the subgenus Botryodiscia of the genus Stephania of the family Menispermaceae, is mainly distributed in hilly areas south of the Huaihe River in China and found in many provinces of China, showing a high genetic diversity. This paper aimed to study genetic diversity of and genetic relationship among individuals of S. tetrandra within China to provide a basis for evaluation, exploitation, and utilization of S. tetrandra by using simple sequence repeat (SSR) molecular markers. Our results show that effective products were amplified from the 26 screened SSR gene loci, a total of 183 alleles amplified (2–16 alleles amplified by each pair of primers). Among the 26 loci, 16 had a PIC value higher than 0.5, indicating a high level of polymorphism. For most of the loci, the number of effective alleles was lower than that of the observed alleles, and the observed heterozygosity was lower than the expected heterozygosity. The genetic differentiation coefficient (0.021–0.547) was lower than 0.05 (low level of genetic differentiation) for 7 loci and higher than 0.25 (very high level of genetic differentiation) for 2 loci, and had a value representing a medium level of genetic differentiation for the remaining 17 loci. The intra-population inbreeding coefficient had a positive value for 21 loci, suggesting the presence of inbreeding and homozygous excess. The gene flow value was bigger than 1, indicating that genetic drift and natural selection played an unimportant role in population genetic differentiation of S. tetrandra. Based on discriminant analysis of principal components and Bayesian Information Criterion, K-means clustering was performed on 620 samples. These samples were divided into 9 genetic clusters, whose similarity coefficients and genetic distances were 0.755–0.918 and 0.067–0.280, respectively, indicating that these clusters were highly similar and short-distanced. The Bayesian clustering analysis was implemented in the STRUCTURE software to analyze the genetic structure of S. tetrandra and it was found that the 620 samples could be clustered into 5 ancestor groups; the 9 clusters and 40 natural populations inherited genes from the 5 groups to varying degrees, but the proportion of genes inherited from the 5 groups by each cluster and natural population differed. S. tetrandra was characterized by the presence of population structure and pronounced genetic subdivision, which, together with the presence of gene flow, may indicate a relatively stable recent state of these populations. [ABSTRACT FROM AUTHOR]

The black soldier fly (BSF), Hermetia illucens, has the ability to efficiently bioremediate organic waste into usable bio‐compounds. Understanding the impact of domestication and mass rearing on fitness and production traits is therefore important for sustainable production. This study aimed to assess patterns of genomic diversity and its association to phenotypic development across early generations of mass rearing under two selection strategies: selection for greater larval mass (SEL lines) and no direct artificial selection (NS lines). Genome‐wide single nucleotide polymorphism (SNP) data were generated using 2bRAD sequencing, while phenotypic traits relating to production and population fitness were measured. Declining patterns of genomic diversity were observed across three generations of captive breeding, with the lowest diversity recorded for the F3 generation of both selection lines, most likely due to founder effects. The SEL cohort displayed statistically significantly greater larval weight com the NS lines with pronounced genetic and phenotypic directional changes across generations. Furthermore, lower genetic and phenotypic diversity, particularly for fitness traits, were evident for SEL lines, illustrating the trade‐off between selecting for mass and the resulting decline in population fitness. SNP‐based heritability was significant for growth, but was low or non‐significant for fitness traits. Genotype–phenotype correlations were observed for traits, but individual locus effect sizes where small and very few of these loci demonstrated a signature for selection. Pronounced genetic drift, due to small effective population sizes, is likely overshadowing the impacts of selection on genomic diversity and consequently phenotypic development. The results hold particular relevance for genetic management and selective breeding for BSF in future. [ABSTRACT FROM AUTHOR]

The House Mouse, Mus musculus , is a model organism that has greatly contributed to evolutionary research. Despite its significance, there remain gaps in our understanding of its phylogeography and population genetic structure in Asian regions. This comprehensive study aims to elucidate the evolutionary history, genetic diversity, and distribution patterns of M. musculus. A diverse data set of 281 M. musculus samples was collected from across Asia, covering 101 localities in 19 countries. Phylogenetic analysis using Cytochrome b and D-Loop region unveiled well-supported lineages. These lineages correspond to: M. m. musculus , M. m. domesticus , M. m. castaneus , and M. m. bactrianus. Also, validity of M. m. bactrianus was questioned. The analysis suggests a monophyletic origin of these subspecies approximately 0.59 million years ago (Mya), followed by 2 main lineages—one consisting of M. m. domesticus (~0.59 Mya) and the other comprising M. m. castaneus , M. m. bactrianus , and M. m. musculus (~0.56 Mya). Genetic diversity varied among subspecies, with M. m. domesticus exhibiting the highest diversity due to its extensive global distribution and M. m. bactrianus exhibiting the lowest diversity due to restriction in southwest Asia. Pairwise genetic distances and F st values confirmed significant genetic differentiation among the subspecies, underlining their historical isolation. Additionally, a Mantel test indicated that geographical distance played a pivotal role in shaping genetic differentiation. Demographic analysis revealed evidence of population expansions in M. m. domesticus , M. m. musculus , and M. m. castaneus , while M. m. bactrianus showed characteristics of neutral selection and genetic drift. Species distribution modeling, assessing both Current Conditions and the Last Glacial Maximum, indicated habitat shifts and losses during glacial periods, particularly in the eastern and northern regions of Asia. However, each subspecies displayed unique responses to climatic changes, reflecting their distinct ecological adaptations. Historical biogeography analysis pointed to complex origins and a network of dispersal and vicariance events that led to the contemporary distribution of subspecies. Deserts and xeric shrublands emerged as critical areas for diversification and speciation. This study contributes to our understanding of the phylogeography and population genetics of M. musculus in Asia, highlighting the significance of geographical factors and climatic fluctuations in shaping its evolutionary history and genetic diversity. [ABSTRACT FROM AUTHOR]

Fleming–Viot diffusions are widely used stochastic models for population dynamics that extend the celebrated Wright–Fisher diffusions. They describe the temporal evolution of the relative frequencies of the allelic types in an ideally infinite panmictic population, whose individuals undergo random genetic drift and at birth can mutate to a new allelic type drawn from a possibly infinite potential pool, independently of their parent. Recently, Bayesian nonparametric inference has been considered for this model when a finite sample of individuals is drawn from the population at several discrete time points. Previous works have fully described the relevant estimators for this problem, but current software is available only for the Wright–Fisher finite-dimensional case. Here, we provide software for the general case, overcoming some nontrivial computational challenges posed by this setting. The R package FVDDPpkg efficiently approximates the filtering and smoothing distribution for Fleming–Viot diffusions, given finite samples of individuals collected at different times. A suitable Monte Carlo approximation is also introduced in order to reduce the computational cost. [ABSTRACT FROM AUTHOR]

The theory of selection fluctuation between generations has been a topic with much activities in population genetics and molecular evolution in 1970's. Most studies suggested that, as the result of fluctuating selection between generations, the frequency of an (on average) neutral mutation may fluctuate around 0.5 during the long-term evolution before it was ultimately fixed or lost. However, this pattern can only be derived from a specific type Wright-Fisher additive model, coined by the Nei-Yokoyama puzzle. In this commentary, I revisited this issue and figured out a theoretical assumption that has never been claimed explicitly, the notion of reference phenotype. Consider one locus with two-alleles: A is the wildtype allele and A' is the mutation. The fluctuating selection model actually requires a constraint that one of three genotypes (AA, AA', or A'A') must maintain a constant fitness without fluctuating between generations. It appears that the balancing selection at a frequency of 0.5 emerges only when the heterozygote (AA') is the reference genotype. Because it is difficult to determine which genotype could be the reference genotype in a real population, a desirable population genetics model should take all three possibilities into account. To this end, I propose a mixture model, where each genotype has a certain chance to be the reference genotype. My analysis showed that the emergence of balancing selection depends on the relative proportions of three different reference genotypes. [ABSTRACT FROM AUTHOR]

Island ecosystems have emerged as vital model systems for evolutionary and speciation studies due to their unique environmental conditions and biodiversity. This study investigates the population divergence, hybridization dynamics, and evolutionary history of hybridizing golden‐backed and red‐backed Dinopium flameback woodpeckers on the island of Sri Lanka, providing insights into speciation processes within an island biogeographic context. Utilizing genomic analysis based on next‐generation sequencing, we revealed that the Dinopium hybrid zone on this island is a complex three‐way hybrid zone involving three genetically distinct populations: two cryptic populations of golden‐backed D. benghalense in the north and one island‐endemic red‐backed population of D. psarodes in the south of Sri Lanka. Our findings indicate asymmetric introgressive hybridization, where alleles from the southern D. psarodes introgress into the northern D. benghalense genome while phenotype remains adapted to their respective northern arid and southern wet habitats. The discovery of two genetically distinct but phenotypically similar D. benghalense populations in northern Sri Lanka highlights the process of cryptic population differentiation within island ecosystems. These populations trace their ancestry back to a common ancestor, similar to the Indian form D. b. tehminae, which colonized Sri Lanka from mainland India during the late Pleistocene. Subsequent divergence within the island, driven by selection, isolation by distance, and genetic drift, led to the current three populations. Our findings provide evidence of cryptic diversification and within‐island population divergence, highlighting the complexity of hybridization and speciation processes. These findings further emphasize the intricate nature of evolutionary dynamics in island ecosystems. [ABSTRACT FROM AUTHOR]

We combined mitochondrial DNA sequence data and paleoclimatic distribution models to document phylogeographic patterns and investigate the historical demography of two manakins, Ceratopipra rubrocapilla and Pseudopipra pipra, as well as to explore connections between Amazonia and the Atlantic Forest. ND2 sequences of C. rubrocapilla (75 individuals, 24 sites) and P. pipra (196, 77) were used in Bayesian inference and maximum likelihood analyses. We estimated mitochondrial nucleotide diversity, employed statistical tests to detect deviations from neutral evolution and constant population sizes, and used species distribution modeling to infer the location of suitable climate for both species under present‐day conditions, the Last Glacial Maximum (LGM), and the Last Interglacial Maximum (LIG). Mitochondrial sequence data from C. rubrocapilla indicate one Amazonian and one Atlantic Forest haplogroup. In P. pipra, we recovered a highly supported and differentiated Atlantic Forest haplogroup embedded within a large Southern Amazonian clade. Genetic and taxonomic structure in Amazonia differs widely between these two species; older P. pipra has a more marked genetic structure and taxonomic differentiation relative to the younger C. rubrocapilla. Both species have similar genetic patterns in the Atlantic Forest. Paleoclimatic distribution models suggest connections between southwestern Amazonia and the southern Atlantic Forest during the LIG, but not between eastern Amazonia and the northeastern Atlantic Forest, as suggested by previous studies. This indicates that multiple corridors, and at different locations, may have been available over the Pliocene and Pleistocene between these two regions. [ABSTRACT FROM AUTHOR]

Studying intraspecific geographic variation in communication signals represents a good approach to understand the evolution of species diversification in animals. The poison frog Andinobates bombetes (Dendrobatidae) exhibits intraspecific geographic variation in the spectral traits of its advertisement call. However, it is still unknown whether there is concomitant variation in temporal call traits, and whether call variation is somehow linked to differences in warning coloration (red and yellow morphs). We analyzed spectral and temporal traits of the advertisement calls recorded from 100 males belonging to twelve populations of A. bombetes: nine bearing the red coloration, and three bearing the yellow one. After controlling for eventual effects of temperature and body size of males in call traits, we found geographic variation in both spectral and temporal call traits, yet such variation was unrelated to differences in warning coloration between populations. Previous research indicated that geographic variation in the spectral properties of this species advertisement call can be explained by concomitant differences in the acoustic abiotic environment. Nonetheless, a positive relationship between geographic distance and call divergence also supports the role of genetic drift in the evolution of acoustic signaling of A. bombetes. [ABSTRACT FROM AUTHOR]

To quantify selection acting on a trait, methods have been developed using either within or between-species variation. However, methods using within-species variation do not integrate the changes at the macro-evolutionary scale. Conversely, current methods using between-species variation usually discard within-species variation, thus not accounting for processes at the micro-evolutionary scale. The main goal of this study is to define a neutrality index for a quantitative trait, by combining within- and between-species variation. This neutrality index integrates nucleotide polymorphism and divergence for normalizing trait variation. As such, it does not require estimation of population size nor of time of speciation for normalization. Our index can be used to seek deviation from the null model of neutral evolution, and test for diversifying selection. Applied to brain mass and body mass at the mammalian scale, we show that brain mass is under diversifying selection. Finally, we show that our test is not sensitive to the assumption that population sizes, mutation rates and generation time are constant across the phylogeny, and automatically adjust for it. [ABSTRACT FROM AUTHOR]

Italy is home to several indigenous goat breeds with great economic and cultural implications, but their genetic makeup remains largely unexplored. This study used the Illumina Goat SNP chip to genotype 142 samples from four Italian goat breeds: Capestrina, Fulva, Grigia Ciociara, and Bianca Monticellana. The genotypes were combined with genome-wide SNP data from 31 Italian breeds to evaluate the genetic profile of Lazio's indigenous goats. After filtering, the dataset included 51,423 SNPs. Genetic structure and diversity were assessed using MDS, ADMIXTURE analysis and inbreeding coefficients. Focusing on the four Lazio breeds, we examined inbreeding levels (FROH), effective population size (Ne), gene exchange, and runs of homozygosity islands (ROHi). The Bianca appeared highly inbred, whereas Fulva, Capestrina, and Grigia showed heterozygosity levels comparable to other breeds. The increased sample sizes highlighted changes in genetic composition, indeed, ADMIXTURE analysis revealed genetic substructures within Bianca and Fulva. The Ne was found to be declining, with Bianca having the lowest Ne, indicating high susceptibility to inbreeding and genetic drift. The NetView analysis identified two interconnected genetic groups corresponding to: Bianca and Fulva. Key contributors to genetic structure, representing ancestral genotypes, were identified, providing targets for conservation. Moreover, ROH analysis pinpointed individuals with excessive ROH and long homozygosity stretches, particularly in Capestrina and Bianca, which could be limited from breeding to preserve genetic diversity. Finally, ROHi revealed genes linked to coat colour, disease resistance, and heat stress tolerance. These conclusions emphasise the importance of local breeds in maintaining biodiversity and enhancing breeding strategies. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate the genomic diversity of the Nero d'Aspromonte (NA) pig population. NA is a subpopulation derived from the Apulo Calabrese (AC) breed that has been reared in total isolation within the Polsi area of Aspromonte, Calabria, Italy. NA is traditionally recognised and used by local farmers for the production of typical products. The growing interest in this subpopulation has led local farmers to create a cooperative to promote NA pig meat and help preserve the cultural heritage associated with this local population. A total of 40 NA pigs were included in our study and genotyped with the Illumina GGP Porcine array. Admixture, TreeMix, and run of homozygosity (ROH) analyses were performed to investigate genetic diversity within the NA subpopulation and its relationship with the AC breed and other Italian pig breeds. The NA population clearly originated from the AC breed. The lower inbreeding and average ROH size in NA compared to AC may indicate that NA differentiated from the original AC genetic pool with the contribution of admixture from other genetic backgrounds in addition to the effects of genetic isolation and genetic drift. The analysis of the genetic diversity of the NA subpopulation showcases the utility of genomic analyses to reconstruct the genetic history of local populations. A specific conservation program for this genetic resource may further support the sustainable development of local pig production systems based on traditional farming practices as a part of agricultural cultural heritage. HIGHLIGHTS: We genetically characterised the Nero d'Aspromonte pig population using genomic data. Genomic characteristics of this population were compared with nine other Italian pig breeds. The results confirmed that Nero d'Aspromonte population originated from the Apulo Calabrese breed. An admixed genetic structure can be detected between Nero d'Aspromonte and Apulo Calabrese pigs. [ABSTRACT FROM AUTHOR]

The effective population size (Ne) is a key parameter in conservation and evolutionary biology, reflecting the strength of genetic drift and inbreeding. Although demographic estimations of Ne are logistically and time‐consuming, genetic methods have become more widely used due to increasing data availability. Nonetheless, accurately estimating Ne remains challenging, with few studies comparing Ne estimates across molecular markers types and estimators such as single‐sample methods based on linkage disequilibrium or sibship analyses versus methods based on temporal variance in allele frequencies. This study aims at bridging this gap by analysing single‐sample and temporally spaced populations in the southern damselfly (Coenagrion mercuriale), a bioindicator Odonata species of conservation concern found in southwestern Europe's freshwater stream networks. A total of 77 local populations were sampled from a semi‐urbanised area located in eastern France near Strasbourg city, yielding 2842 individuals that were genotyped with microsatellites and 958 of which were also genotyped for 2092 SNPs. Spatial genetic structure was stable over time, suggesting porosity between alternate‐year cohorts. When accounting for spatial genetic structure, single‐sample and temporal estimations of Ne were consistent for each set of molecular markers. Biologically meaningful results were obtained when the effect of migration was minimising by considering metapopulation Ne estimates based on the level of genetic differentiation and population boundaries. In terms of applied conservation and management, most depicted metapopulations displayed large Ne, indicating no immediate need for conservation measures to mitigate anthropogenic pressures, provided that a continuous suitable freshwater network is maintained. However, urbanisation negatively impacted Ne levels in populations close to Strasbourg city. Because Ne is used to inform conservation decisions, caution is crucial in interpreting Ne estimates, especially in continuously distributed populations undergoing migration. Altogether, our study highlights the challenge of obtaining robust Ne estimates and the necessity of careful interpretation to set relevant conservation guidelines. [ABSTRACT FROM AUTHOR]

Genetic mixing aims to increase the genetic diversity of small or isolated populations, by mitigating genetic drift and inbreeding depression, either by maximally increasing genetic diversity, or minimising the prevalence of recessive, deleterious alleles. However, few studies investigate this beyond a single generation of mixing. Here, we model genetic mixing using captive, low‐diversity recipient population of the threatened Southern brown bandicoot (Isoodon obesulus) over 50 generations and compare wild populations across south‐eastern Australia as candidate source populations. We first assess genetic differentiation between 12 populations, including the first genomic assessment of three mainland Australian and three Tasmanian populations. We assess genetic diversity in the 12 populations using an individualised autosomal heterozygosity pipeline, using these results to identify a candidate recipient population for genetic mixing simulations. We found that populations fell into four major groups of genetic similarity: Adelaide Hills, western Victoria, eastern Victoria, and Tasmania, but populations within these groups were also distinct, and additional substructure was observed in some populations. Our autosomal heterozygosity pipeline indicated significant variability in mean heterozygosity between populations, identifying one extremely genetically degraded population on Inner Sister Island, Tasmania. Genetic mixing simulations of a low heterozygosity captive population in Victoria suggested the greatest increase in heterozygosity would be reached by using highly differentiated populations as mixing sources. However, when removing populations that may represent taxonomically discrete lineages, neither metrics of differentiation nor heterozygosity was strongly correlated with modelled heterozygosity increase, indicating the value of simulation‐based approaches when selecting source populations for population mixing. [ABSTRACT FROM AUTHOR]

Fish stocking has been utilized for over a century to offset extirpations or declines in abundance of many native species. These historical declines and hatchery contributions have led to uncertainty surrounding whether many contemporary populations are native, introgressed with hatchery sources, or entirely of hatchery origin. Such uncertainty is problematic for the conservation of native biodiversity as it hampers management agencies' ability to prioritize the conservation of indigenous locally adapted populations. Fortunately, genetic and genomic tools have allowed researchers to investigate these questions, often through the use of clustering or assignment approaches that are predicated on identifiable and consistent divergence between native populations and hatchery sources. Here, we apply these methods to restriction‐site associated DNA (RAD) data from 643 brook trout (Salvelinus fontinalis) originating from 13 wild populations and an exogenous hatchery strain to investigate the extent of historical extirpations, hatchery contributions, and processes affecting population structure in a small area of the previously unglaciated Driftless Area of Wisconsin, USA. The results from these analyses suggest that wild populations in this region are genetically distinct even at small spatial scales, lack strong hydrologically associated population structure, rarely exchange gene flow, and have small effective population sizes. Furthermore, wild populations are substantially diverged from known hatchery strains and show minimal evidence of introgression in clustering analyses. However, we demonstrate through empirically informed simulations that distinct wild populations may potentially be hatchery‐founded and have since diverged through rapid genetic drift. Collectively, the apparent lack of hydrological population structure and potential for rapid drift in the Driftless Area suggest that many native populations may have been historically extirpated and refounded by stocking events. If this is the case, then commonly used genomic clustering methods and their associated model selection criteria may result in underestimation of hatchery introgression in the face of rapid drift. [ABSTRACT FROM AUTHOR]

The article discusses the development and release of 11 new wild-derived inbred mouse strains known as the "Nachman panel," which offer a unique genetic and phenotypic diversity platform for biological research. These strains were developed from wild-caught mice from different geographic regions in North and South America, providing a wide range of genetic and phenotypic variation. The Nachman strains have been extensively characterized genetically and phenotypically, offering a rich resource for biological discovery and disease modeling. Despite some limitations, such as smaller litter sizes and wild behavior, these strains present promising prospects for future research in basic, biomedical, and preclinical investigations. [Extracted from the article]

Livestock plays an essential role in sustaining human livelihoods, offering a diverse range of species integral to food security, economic stability, and cultural traditions. The domestication of livestock, which began over 10,000 years ago, has driven significant genetic changes in species such as cattle, buffaloes, sheep, goats, and pigs. Recent advancements in genomic technologies, including next-generation sequencing (NGS), genome-wide association studies (GWAS), and genomic selection, have dramatically enhanced our understanding of these genetic developments. This review brings together key research on the domestication process, phylogenetics, genetic diversity, and selection signatures within major livestock species. It emphasizes the importance of admixture studies and evolutionary forces like natural selection, genetic drift, and gene flow in shaping livestock populations. Additionally, the integration of machine learning with genomic data offers new perspectives on the functional roles of genes in adaptation and evolution. By exploring these genomic advancements, this review provides insights into genetic variation and evolutionary processes that could inform future approaches to improving livestock management and adaptation to environmental challenges, including climate change. [ABSTRACT FROM AUTHOR]

Background Genome size is influenced by natural selection and genetic drift acting on variations from polyploidy and repetitive DNA sequences. We hypothesized that centromere drive, where centromeres compete for inclusion in the functional gamete during meiosis, may also affect genome and chromosome size. This competition occurs in asymmetric meiosis, where only one of the four meiotic products becomes a gamete. If centromere drive influences chromosome size evolution, it may also impact post-polyploid diploidization, where a polyploid genome is restructured to function more like a diploid through chromosomal rearrangements, including fusions. We tested if plant lineages with asymmetric meiosis exhibit faster chromosome size evolution compared to those with only symmetric meiosis, which lack centromere drive as all four meiotic products become gametes. We also examined if positive selection on centromeric histone H3 (CENH3), a protein that can suppress centromere drive, is more frequent in these asymmetric lineages. Methods We analysed plant groups with different meiotic modes: asymmetric in gymnosperms and angiosperms, and symmetric in bryophytes, lycophytes and ferns. We selected species based on available CENH3 gene sequences and chromosome size data. Using Ornstein–Uhlenbeck evolutionary models and phylogenetic regressions, we assessed the rates of chromosome size evolution and the frequency of positive selection on CENH3 in these clades. Results Our analyses showed that clades with asymmetric meiosis have a higher frequency of positive selection on CENH3 and increased rates of chromosome size evolution compared to symmetric clades. Conclusions Our findings support the hypothesis that centromere drive accelerates chromosome and genome size evolution, potentially also influencing the process of post-polyploid diploidization. We propose a model which in a single framework helps explain the stability of chromosome size in symmetric lineages (bryophytes, lycophytes and ferns) and its variability in asymmetric lineages (gymnosperms and angiosperms), providing a foundation for future research in plant genome evolution. [ABSTRACT FROM AUTHOR]

Introgressive hybridization is a pivotal force influencing genetic diversity and adaptive potential of invasive species, however to date has received less attention for even the most globally destructive species. Golden apple snails (Pomacea spp.), one of the world's worst invasive species, were first introduced during the 1980s into Taiwan for commerce and have since emerged as a significant threat to regional biodiversity. Two of the most destructive invasive species of Pomacea, P. canaliculata and P. maculata, have been reported to hybridize in its native and non-native range, the latter of which has been posited to facilitate an adaptive advantage for increasing invasiveness. Thus, our study combined mitochondrial COI (Cytochrome c oxidase subunit I) barcoding and nuclear EF1-α (elongation factor 1-alpha) gene analysis to identify putative hybridization among 254 samples collected across 14 cities/counties in Taiwan. Our investigation confirmed hybridization within the sympatric but heterogeneous distribution of P. canaliculata and P. maculata in Taiwan. The results indicated that 18.9% of the total sampled population consists of hybrids, whereas 81.1% of the samples demonstrated pure P. canaliculata genetics. Remarkably, no pure P. maculata were detected across the island, and all P. maculata mtDNA samples appeared to be genetically introgressed. The dearth of pure P. maculata populations, despite the prevalence of canaliculata-maculata hybrids, invites speculation about introduction mechanisms, genetic drift and maybe the nuanced influence of environmental factors on distribution dynamics, all of which required further investigation. These findings contribute significant scientific insights into the invasive dynamics of Pomacea in Taiwan, and the results underline findings applicable for devising targeted and effective conservation strategies in regions grappling with the challenges posed by invasive species. [ABSTRACT FROM AUTHOR]

Assisted gene flow can restore genetic diversity when genetic drift has driven deleterious alleles to high frequencies in small, isolated populations. Previous crosses among 20 populations of Gymnadenia conopsea documented the strongest heterosis and the weakest inbreeding depression in sparse and small populations, consistent with fixation of mildly deleterious alleles by genetic drift. We genotyped the populations used for crosses, and used 1200–1728 SNPs to test the following predictions: (1) heterosis increases with genetic differentiation (FST) to donor populations and decreases with genetic diversity in the recipient population, (2) inbreeding depression increases with genetic diversity, and (3) genetic diversity increases, and mean FST to other populations decreases, with population size and density. Pairwise FST ranged from very low to moderate (0.005–0.20) and genetic diversity varied moderately among populations (proportion of polymorphic loci = 0.52–0.75). However, neither FST between populations, nor genetic diversity in the recipient population, were related to the strength of heterosis. There was also no association between genetic diversity and the strength of inbreeding depression. Genetic diversity increased and mean FST decreased with population size, consistent with reduced diversity and increased differentiation of small populations by genetic drift. The results indicate that the loci conferring heterosis are not mirrored by overall population differentiation, and limited additional information on potential source populations for genetic rescue is gained by the genetic data. Instead, the use of controlled crosses can directly reveal positive effects of introducing new genetic material, and is a simple method with high potential in conservation. [ABSTRACT FROM AUTHOR]

Site-selective probing of iodine 4d orbitals at 13.1 nm was used to characterize the photolysis of CH2I2 and CH2BrI initiated at 202.5 nm. Time-dependent fragment ion momenta were recorded using Coulomb explosion imaging mass spectrometry and used to determine the structural dynamics of the dissociating molecules. Correlations between these fragment momenta, as well as the onset times of electron transfer reactions between them, indicate that each molecule can undergo neutral three-body photolysis. For CH2I2, the structural evolution of the neutral molecule was simultaneously characterized along the C–I and I–C–I coordinates, demonstrating the sensitivity of these measurements to nuclear motion along multiple degrees of freedom. [ABSTRACT FROM AUTHOR]

Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.

Predator-prey interactions have been suggested as drivers of diversity in different lineages, and the presence of anti-predator defences in some clades is linked to higher rates of diversification. Warning signals are some of the most widespread defences in the animal world, and there is evidence of higher diversification rates in aposematic lineages. The mechanisms behind such species richness, however, are still unclear. Here, we test whether lineages that use aposematism as anti-predator defence exhibit higher levels of genetic differentiation between populations, leading to increased opportunities for divergence. We collated from the literature more than 3000 pairwise genetic differentiation values across more than 700 populations from over 60 amphibian species. We find evidence that over short geographical distances, populations of species of aposematic lineages exhibit greater genetic divergence relative to species that are not aposematic. Our results support a scenario where the use of warning signals could restrict gene flow, and suggest that anti-predator defences could impact divergence between populations and potentially have effects at a macro-evolutionary scale.

The forces of evolution-mutation, selection, migration, and genetic drift-shape the genetic architecture of human traits, including the genetic architecture of complex neuropsychiatric illnesses. Studying these illnesses in populations that are diverse in genetic ancestry, historical demography, and cultural history can reveal how evolutionary forces have guided adaptation over time and place. A fundamental truth of shared human biology is that an allele responsible for a disease in anyone, anywhere, reveals a gene critical to the normal biology underlying that condition in everyone, everywhere. Understanding the genetic causes of neuropsychiatric disease in the widest possible range of human populations thus yields the greatest possible range of insight into genes critical to human brain development. In this perspective, we explore some of the relationships between genes, adaptation, and history that can be illuminated by an evolutionary perspective on studies of complex neuropsychiatric disease in diverse populations.