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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 development of electrodes for hydrogen evolution via water splitting in a neutral electrolyte is highly desirable, especially considering that natural water resources such as seawater typically have a neutral pH. In this study, silicon nanowires (SiNWs) arrays with uniform silver (Ag) decoration are prepared as a cathode material, which exhibits excellent and stable electrochemical performance for neutral water electrolysis. Ag ions, utilized in the preparation of SiNWs through metal-assisted chemical etching technique, are retained and decorated within the SiNWs array without undergoing a dissolution process, referred to as Native SiNWs. Remained Ag+ ions on the SiNWs are activated photocathodically and reduced to Ag0, resulting in a significantly enhanced performance as an electrocatalyst for hydrogen evolution reaction (HER). Hence, this photocathodic activation of Native SiNWs (PCA-Native SiNWs) eliminates the need for additional cocatalyst deposition for HER, utilizing the Ag ions employed in the SiNWs preparation process. This enhancement in HER activity is exclusively observed by photocathodic activation, not by cathodic activation without light irradiation, indicating the crucial role of photoelectrons in SiNWs under light irradiation for the activation. Additionally, the nanowire structure serves as an ideal platform for Ag nanoparticles, providing sufficient surface area, resulting in excellent dispersion and an increased number of active sites. Furthermore, PCA-Native SiNWs demonstrates outstanding electrochemical stability for over 60 h, with no significant reduction in current density or structural degradation in a neutral electrolyte. Several characterizations and electrochemical analyses have been conducted to elucidate the in-situ decoration of Ag nanoparticles on SiNWs and investigate the surface chemistry for the activation mechanism. This work introduces a new perspective on using Ag-decorated SiNWs directly as an electrocatalyst for effective hydrogen evolution in a neutral media. Saleem et al., "A Strategy to Reutilize Silver Nanoparticles on Silicon Nanowires via Photocathodic Activation for Enhanced and Sustainable Hydrogen Evolution"Native SiNWs, which are prepared by retaining Ag nanoparticles during SiNW synthesis, exhibited better performance for HER than SiNWs. Additionally, the retained Ag can be more evenly distributed and reduced during photocathodic activation, resulting in significantly improved HER activity. [Display omitted] • Photocathodically activated Native SiNWs (PCA-Native SiNWs) are developed. • Retained Ag ions on SiNWs are reduced and activated by light irradiation and cathodic potential (photocathodic activation). • Reduced Ag enhances electrochemical performance of SiNWs as an electrocatalyst. • Ag nanoparticles are evenly distributed vis the dissolution-redeposition phenomenon. • PCA-Native SiNWs show stable activity in neutral pH. [ABSTRACT FROM AUTHOR]

The major drawback to the implementation of genomic selection in a breeding program lies in long-term decrease in additive genetic variance, which is a trade-off for rapid genetic improvement in short term. Balancing increase in genetic gain with retention of additive genetic variance necessitates careful optimization of this trade-off. In this study, we proposed an integrated index selection approach within the genomic inferred cross-selection (GCS) framework to maximize genetic gain across multiple traits. With this method, we identified optimal crosses that simultaneously maximize progeny performance and maintain genetic variance for multiple traits. Using a stochastic simulated recurrent breeding program over a 40-years period, we evaluated different GCS methods along with other factors, such as the number of parents, crosses, and progeny per cross, that influence genetic gain in a pulse crop breeding program. Across all breeding scenarios, the posterior mean variance consistently enhances genetic gain when compared to other methods, such as the usefulness criterion, optimal haploid value, mean genomic estimated breeding value, and mean index selection value of the superior parents. In addition, we provide a detailed strategy to optimize the number of parents, crosses, and progeny per cross that can potentially maximize short- and long-term genetic gain in a public breeding program. [ABSTRACT FROM AUTHOR]

How sex chromosomes evolve compared to autosomes remains an unresolved question in population genetics. Most studies focus on only a handful of taxa, resulting in uncertainty over whether observed patterns reflect general processes or idiosyncrasies in particular clades. For example, in female heterogametic (ZW) systems, bird Z chromosomes tend to evolve quickly but not adaptively, while in Lepidopterans they evolve adaptively, but not always quickly. To understand how these observations fit into broader evolutionary patterns, we explore Z chromosome evolution outside of these two well-studied clades. We utilize a publicly available genome, gene expression, population, and outgroup data in the salmon louse Lepeophtheirus salmonis , an important agricultural pest copepod. We find that the Z chromosome is faster evolving than autosomes, but that this effect is driven by increased drift rather than adaptive evolution. Due to high rates of female reproductive failure, the Z chromosome exhibits a slightly lower effective population size than the autosomes which is nonetheless to decrease efficiency of hemizygous selection acting on the Z. These results highlight the usefulness of organismal life history in calibrating population genetic expectations and demonstrate the value of the ever-expanding wealth of publicly available data to help resolve outstanding evolutionary questions. [ABSTRACT FROM AUTHOR]

Small, fragmented, or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of <100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analyzed independently of the Tasmanian scrubtit. Pairwise F ST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity, and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct. [ABSTRACT FROM AUTHOR]

Chromosome number is a fundamental genomic trait that is often the first recorded characteristic of a genome. Across large clades, a common pattern emerges: many or even most lineages exhibit relative stasis, while a handful of lineages or species exhibit striking variation. Despite recent developments in comparative methods, most of this heterogeneity is still poorly understood. It is essential to understand why some lineages have rapid rates of chromosome number evolution, as it can impact a variety of other traits. Previous research suggests that biased female meiotic drive may shape rates of karyotype evolution in some mammals. However, Carnivora exhibits variation that this female meiotic drive model cannot explain. We hypothesize that variation in effective population size may underlie rate variation in Carnivora. To test this hypothesis, we estimated rates of fusions and fissions while accounting for range size, which we use as a proxy for effective population size. We reason fusions and fissions are deleterious or underdominant and that only in lineages with small range sizes will these changes be able to fix due to genetic drift. In this study, we find that the rates of fusions and fissions are elevated in taxa with small range sizes relative to those with large range sizes. Based on these findings, we conclude that 1) naturally occurring structural mutations that change chromosome number are underdominant or mildly deleterious, and 2) when population sizes are small, structural rearrangements may play an important role in speciation and reduction in gene flow among populations. [ABSTRACT FROM AUTHOR]

Superabundant microbes (SAMs), such as marine phytoplankton, are extremely important in Earth's ecosystems. Evolutionary processes have been mainly studied in much smaller populations, and it is poorly understood how evolution works in the huge populations of SAMs. The standard tools of evolutionary genetics were developed for populations of smaller sizes, and many of these tools may not be suitable to study evolution in astronomically large SAM populations. Nucleotide sequence polymorphism is surprisingly low in SAMs, corresponding to a population of a few million individuals, but the reasons for this lack of diversity are unclear. Marine phytoplankton play crucial roles in the Earth's ecological, chemical, and geological processes. They are responsible for about half of global primary production and drive the ocean biological carbon pump. Understanding how plankton species may adapt to the Earth's rapidly changing environments is evidently an urgent priority. This problem requires evolutionary genetic approaches as evolution occurs at the level of allele frequency change within populations driven by genetic drift and natural selection (microevolution). Plankters such as the coccolithophore Gephyrocapsa huxleyi and the cyanobacterium Prochlorococcus 'marinus' are among Earth's most abundant organisms. In this opinion paper we discuss how evolution in astronomically large populations of superabundant microbes (SAMs) may act fundamentally differently than it does in the populations of more modest size found in well-studied organisms. This offers exciting opportunities to study evolution in the conditions that have yet to be explored and also leads to unique challenges. Exploring these opportunities and challenges is the goal of this article. [ABSTRACT FROM AUTHOR]

The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith), is an invasive pest species that has incurred massive economic damages in areas cultivating economically important crops like corn, rice, cotton and many others. Known to be a native of the Western Hemisphere, FAW has since then established itself in many parts of Africa, Asia and Australia and Oceania. The Philippines had been among the Asian countries vulnerable to FAW invasion, which was validated in June 2019. This study aims to characterize the existing strains and haplotypes of FAW and describe the genetic structure and the signature of its recent demographic history nationwide. COI sequences reveal the predominance of rice‐strain over the corn‐strain FAW, while Tpi sequences are more accurate in defining the corn‐strain found in corn and sugarcane. Discordant COI‐Tpi configurations frequently occur the most in the entire FAW population at 65.29%. Nucleotide and haplotype diversity are low with an average of 0.005976 and 0.4019 respectively. In addition to non‐significant values in neutrality tests suggesting neutral evolution, the low nucleotide and haplotype diversity indicate population contraction from founder effect. Variations are mostly found within regions, and genetic structure is moderate among regions (FST = 0.14375). These results can be attributed to low selective pressures accompanying its establishment, or more likely due to recent migration and/or human‐assisted factors such as trade. Implications on pest management and prospective studies in the future are also discussed in this study. [ABSTRACT FROM AUTHOR]

Philosophers of biology have recently been debating about whether random genetic drift is a distinct process from that of natural selection. One camp argues that drift is a process of “indiscriminate sampling” that is logically and ontologically distinct from the “discriminate sampling” process that is natural selection. The other camp argues that, rather than being two autonomous processes, natural selection and drift are just two aspects or facets of a single process. I argue that the two positions involved in this dispute are not mutually exclusive. Indeed, by explicitly taking into account its sources, I argue that two kinds of drift are theoretically possible. The first kind – that I call circumstantial-drift – involves a process of its own, separate from the process of natural selection, or, more specifically, it requires that differences in a circumstantial trait cause differences in reproductive output of biological entities. The second kind – that I label probabilistic-drift – requires no other process than a probabilistic causal relation between a heritable physical trait and reproductive output, i.e. requires only the causal relation on which the work of natural selection could also depend. If both of these kinds of drift are theoretically possible, then neither defining, nor empirically identifying drift need to be zero-sum games. [ABSTRACT FROM AUTHOR]

Austroasiatic (AA) speakers constitute around 4% of the population of Thailand, while the majority (89.4%) speak Kra-Dai (KD) languages. Previous forensic and population genetic studies in various Thai populations have employed a limited number of short tandem repeats (STRs). This study aims to expand the investigation of the genetic makeup of AA populations in Thailand and their relationship to KD populations using a larger number of autosomal STRs with the VeriFiler™ Plus PCR Amplification Kit. We generated 593 new genotypes from AA-speaking groups and combined them with previously reported data from AA and KD groups. A total of 1,129 genotypes across 23 STR loci were used to construct the largest allelic frequency profile for Thai and Lao populations. However, several loci deviated from Hardy–Weinberg equilibrium, likely due to the reduced genetic diversity in some highland populations, which should be considered in forensic investigations. Beyond forensic applications, our findings reveal genetic differences between AA-speaking groups in Northern and Northeastern Thailand. The AA groups from Northeastern Thailand exhibit greater genetic homogeneity and diversity, likely due to population interactions. In contrast, reduced diversity and increased heterogeneity in AA groups from Northern Thailand are possibly driven by genetic drift and cultural and geographic isolation. In conclusion, we emphasize the usefulness of increasing the number of autosomal STRs in forensic and anthropological genetic studies. Additional Y-STR and X-STR data from various AA-speaking groups in Thailand would further enhance and strengthen forensic STR databases in the region. [ABSTRACT FROM AUTHOR]

When biological populations expand into new territory, the evolutionary outcomes can be strongly influenced by genetic drift, the random fluctuations in allele frequencies. Meanwhile, spatial variability in the environment can also significantly influence the competition between subpopulations vying for space. Little is known about the interplay of these intrinsic and extrinsic sources of noise in population dynamics: When does environmental heterogeneity dominate over genetic drift or vice versa, and what distinguishes their population genetics signatures? Here, in the context of neutral evolution, we examine the interplay between a population's intrinsic, demographic noise and an extrinsic, quenched random noise provided by a heterogeneous environment. Using a multispecies Eden model, we simulate a population expanding over a landscape with random variations in local growth rates and measure how this variability affects genealogical tree structure, and thus genetic diversity. We find that, for strong heterogeneity, the genetic makeup of the expansion front is to a great extent predetermined by the set of fastest paths through the environment. The landscapedependent statistics of these optimal paths then supersede those of the population's intrinsic noise as the main determinant of evolutionary dynamics. Remarkably, the statistics for coalescence of genealogical lineages, derived from those deterministic paths, strongly resemble the statistics emerging from demographic noise alone in uniform landscapes. This cautions interpretations of coalescence statistics and raises new challenges for inferring past population dynamics. [ABSTRACT FROM AUTHOR]

The functions of proteins generally depend on their assembly into complexes. During evolution, some complexes have transitioned from homomers encoded by a single gene to heteromers encoded by duplicate genes. This transition could occur without adaptive evolution through intermolecular compensatory mutations. Here, we experimentally duplicated and evolved a homodimeric enzyme to determine whether and how this could happen. We identified hundreds of deleterious mutations that inactivate individual homodimers but produce functional enzymes when co-expressed as duplicated proteins that heterodimerize. The structure of one such heteromer reveals how both losses of function are buffered through the introduction of asymmetry in the complex that allows them to sub functionalize. Constructive neutral evolution can thus occur by gene duplication followed by only one deleterious mutation per duplicate. [ABSTRACT FROM AUTHOR]

Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's (Rhinella marina) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north‐central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic‐environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post‐introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories. [ABSTRACT FROM AUTHOR]

The article provides information on the SARS-CoV-2 variant KP.3.1.1 and its genetic characteristics. The variant has gained attention due to its global prevalence and carries multiple spike protein mutations that may affect its ability to evade immune responses and bind to ACE2 receptors. However, the significance of a deletion in site 31 of the spike protein is not well understood. The variant also has other mutations of interest, but overall, it does not appear to be particularly dangerous based on its evolutionary path. Ongoing surveillance is necessary, but currently, there is no evidence to suggest that KP.3.1.1 is an unusually concerning variant. [Extracted from the article]

Premise Methods Results Conclusions Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial–interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is Yucca, with Y. valida having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence.We assembled 4411 SNPs from 147 plants of Y. valida throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species.Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of Y. valida and its sister species.Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida. [ABSTRACT FROM AUTHOR]

Manipulating evolutionary forces imposed by hosts on pathogens like genetic drift and selection could avoid the emergence of virulent pathogens. For instance, increasing genetic drift could decrease the risk of pathogen adaptation through the random fixation of deleterious mutations or the elimination of favorable ones in the pathogen population. However, no experimental proof of this approach is available for a plant-pathogen system. We studied the impact of pepper (Capsicum annuum) lines carrying the same major resistance gene but contrasted genetic backgrounds on the evolution of Potato virus Y (PVY). The pepper lines were chosen for the contrasted levels of genetic drift (inversely related to Ne, the effective population size) they exert on PVY populations, as well as for their contrasted resistance efficiency (inversely related to the initial replicative fitness, Wi, of PVY in these lines). Experimental evolution was performed by serially passaging 64 PVY populations every month on six contrasted pepper lines during seven months. These lines exhibited highly divergent evolutionary trajectories, ranging from viral extinctions to replicative fitness gains. The sequencing of the PVY VPg cistron, where adaptive mutations are likely to occur, allowed linking these replicative fitness gains to parallel adaptive nonsynonymous mutations. Evolutionary trajectories were well explained by the genetic drift imposed by the host. More specifically, Ne, Wi and their synergistic interaction played a major role in the fate of PVY populations. When Ne was low (i.e. strong genetic drift), the final PVY replicative fitness remained close to the initial replicative fitness, whereas when Ne was high (i.e. low genetic drift), the final PVY replicative fitness was high independently of the replicative fitness of the initially inoculated virus. We show that combining a high resistance efficiency (low Wi) and a strong genetic drift (low Ne) is the best solution to increase resistance durability, that is, to avoid virus adaptation on the long term. Author summary: Given their high evolutionary potential, viruses are notoriously difficult to control by drug treatments or by breeding resistant hosts. In plants, resistance genes targeting viruses become often rapidly inefficient due to virus mutational escape. Manipulating the evolutionary forces imposed by the plant on the virus population, like selection and genetic drift, could help control virus adaptation and prevent resistance breakdown. Theoretically, a plant genotype imposing low selective pressures could slow down the fixation of adaptive viral mutations, while a plant genotype imposing strong genetic drift could decrease virus fitness by favoring the random fixation of deleterious viral mutations and/or the elimination of favorable ones. Using experimental evolution, we studied the effect of plants imposing contrasted levels of genetic drift on the emergence of resistance-adapted virus mutants. Results indicate that the level of genetic drift during plant colonization, in part controlled by the genetic background of the plant, and the plant resistance level are the main drivers of the virus evolutionary trajectories, which varied from fast adaptation to extinction. Consequently, it is possible to achieve high resistance efficiency and durability by breeding plant genotypes through the introduction of major-effect resistance genes exerting a strong selection on virus populations into a genetic background increasing genetic drift. [ABSTRACT FROM AUTHOR]

Urban environments are warmer than the rural surroundings, impacting plant phenotypic traits. When plants are present over areas with contrasted conditions such as along urbanization gradients, their phenotypes may differ, and these differences depend on different processes, including phenotypic plasticity, maternal environmental effects and genetic differentiation (local adaptation and/or genetic drift). Successful establishment of alien species along environmental gradients has been linked to high phenotypic plasticity and rapid evolutionary responses, which are easier to track for species with a known residence time. The mechanisms explaining trait variation in plants in urban versus rural microclimatic conditions have received little attention. Using the alien Veronica persica as model species, we measured leaf traits in urban and rural populations and performed a reciprocal common-garden experiment to study how germination, leaf, growth, and flowering traits varied in response to experimental microclimate (rural or urban) and population origin environment (rural or urban). Veronica persica displayed phenotypic plasticity in all measured traits, with reduced germination, development, and flowering under urban microclimate which suggests more stressful growing conditions in the urban than in the rural microclimate. No significant effect of the rural or urban origin environment was detected, providing no evidence for local adaptation to urban or rural environments. Additionally, we found limited signs of maternal environmental effects. We noted the importance of the mother plant and the population identities suggesting genetically based differences. Our results indicate that urban environments are more hostile than rural ones, and that V. persica does not show any adaptation to urban environments despite genetic differences between populations. [ABSTRACT FROM AUTHOR]

Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self‐compatible hermaphrodites, the mating system (e.g., self‐fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (Ne). This can potentially accelerate genetic drift, particularly in small populations where self‐fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (Ne) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within‐population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and Ne estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within‐population genetic diversity. [ABSTRACT FROM AUTHOR]

Genome size variation in eukaryotes has myriad effects on organismal biology from the genomic to whole-organism level. Large genome size may be associated with lower selection efficiency because lower effective population sizes allow fixation of deleterious mutations via genetic drift, increasing genome size and decreasing selection efficiency. Because of a hypothesized negative relationship between genome size and recombination rate per base pair, increased genome size could also increase the effect of linked selection in the genome, decreasing the efficiency with which natural selection can fix or remove mutations. We used a transcriptomic dataset of 15 and a subset of six Neotropical salamander species ranging in genome size from 12 to 87 pg to study the relationship between genome size and efficiency of selection. We estimated dN/dS of salamanders with small and large genomes and tested for relaxation of selection in the larger genomes. Contrary to our expectations, we did not find a significant relationship between genome size and selection efficiency or strong evidence for higher dN/dS values in species with larger genomes for either species set. We also found little evidence for relaxation of selection in species with larger genomes. A positive correlation between genome size and range size (a proxy of population size) in this group disagrees with predictions of stronger drift in species with larger genomes. Our results highlight the complex interactions between the many forces shaping genomic variation in organisms with genomic gigantism. [ABSTRACT FROM AUTHOR]

The coalescent is a stochastic process representing ancestral lineages in a population undergoing neutral genetic drift. Originally defined for a well-mixed population, the coalescent has been adapted in various ways to accommodate spatial, age, and class structure, along with other features of real-world populations. To further extend the range of population structures to which coalescent theory applies, we formulate a coalescent process for a broad class of neutral drift models with arbitrary – but fixed – spatial, age, sex, and class structure, haploid or diploid genetics, and any fixed mating pattern. Here, the coalescent is represented as a random sequence of mappings C = C t t = 0 ∞ from a finite set G to itself. The set G represents the "sites" (in individuals, in particular locations and/or classes) at which these alleles can live. The state of the coalescent, C t : G → G , maps each site g ∈ G to the site containing g 's ancestor, t time-steps into the past. Using this representation, we define and analyze coalescence time, coalescence branch length, mutations prior to coalescence, and stationary probabilities of identity-by-descent and identity-by-state. For low mutation, we provide a recipe for computing identity-by-descent and identity-by-state probabilities via the coalescent. Applying our results to a diploid population with arbitrary sex ratio r , we find that measures of genetic dissimilarity, among any set of sites, are scaled by 4 r (1 − r) relative to the even sex ratio case. [ABSTRACT FROM AUTHOR]

We study the response of a quantitative trait to exponential directional selection in a finite haploid population, both at the genetic and the phenotypic level. We assume an infinite sites model, in which the number of new mutations per generation in the population follows a Poisson distribution (with mean Θ) and each mutation occurs at a new, previously monomorphic site. Mutation effects are beneficial and drawn from a distribution. Sites are unlinked and contribute additively to the trait. Assuming that selection is stronger than random genetic drift, we model the initial phase of the dynamics by a supercritical Galton–Watson process. This enables us to obtain time-dependent results. We show that the copy-number distribution of the mutant in generation n , conditioned on non-extinction until n , is described accurately by the deterministic increase from an initial distribution with mean 1. This distribution is related to the absolutely continuous part W + of the random variable, typically denoted W , that characterizes the stochasticity accumulating during the mutant's sweep. A suitable transformation yields the approximate dynamics of the mutant frequency distribution in a Wright–Fisher population of size N. Our expression provides a very accurate approximation except when mutant frequencies are close to 1. On this basis, we derive explicitly the (approximate) time dependence of the expected mean and variance of the trait and of the expected number of segregating sites. Unexpectedly, we obtain highly accurate approximations for all times, even for the quasi-stationary phase when the expected per-generation response and the trait variance have equilibrated. The latter refine classical results. In addition, we find that Θ is the main determinant of the pattern of adaptation at the genetic level, i.e., whether the initial allele-frequency dynamics are best described by sweep-like patterns at few loci or small allele-frequency shifts at many. The number of segregating sites is an appropriate indicator for these patterns. The selection strength determines primarily the rate of adaptation. The accuracy of our results is tested by comprehensive simulations in a Wright–Fisher framework. We argue that our results apply to more complex forms of directional selection. • Accurate and tractable time-dependent results at genetic and phenotypic level. • Explicit approximations for the initial phase of polygenic adaptation. • Refined classical, quantitative genetics results for the stationary phase. • Population-wide mutation rate characterizes genetic pattern of adaptation. • Number of segregating sites is an indicator of the pattern of adaptation. [ABSTRACT FROM AUTHOR]

Fusarium stalk rot (FSR), caused by the Fusarium species complex, is an economic threat to maize cultivation all over the world. We investigated the population structure and genetic diversity of Fusarium species obtained from five major maize-growing regions in India. The Tef-1α locus was used for phylogenetic analysis of geographically distinct isolates of Fusarium verticillioides, F. andiyazi, F. proliferatum, F. nygamai, and F. acutatum causing FSR. A phylogenetic tree showed monophyletic, polyphyletic, and paraphyletic groupings reflecting the complex evolutionary history and genetic diversity within the genus. Monophyletic groupings depicting strong bootstrap support were shown to have a single common ancestor and genetic coherence with limited genetic divergence among sequences. Polyphyletic groupings also presented significant genetic differentiation within the F. verticillioides sequences from diverse ecological niches. Nucleotide diversity of moderate level 0.02471 reflected genetic variations within populations that were attributed to factors such as mutation, genetic drift, or varying selection pressures. The Fst value of 0.98205 is particularly indicative of high genetic differentiation, implying that most of the genetic variance is due to differences between populations rather than within them. F. verticillioides, with 57 sequences, showed low genetic diversity with three segregating sites and a low haplotype diversity of 0.19486, suggesting the founder effect, where a reduced population expands from a limited genetic pool. The total data estimates across all populations for haplotype analysis showed 72 sequences, 44 segregating sites, and 9 haplotypes with a haplotype diversity of 0.48513. The evolutionary dynamics showed genetic differentiations among Fusarium species causing FSR. AMOVA indicated high within-population variations, depicting a substantial genetic diversity within individual populations. The results offer a comprehensive framework for discussing the implications of genetic diversity in pathogen management and the evolutionary dynamics of the Fusarium species causing FSR in maize in the Indian subcontinent. [ABSTRACT FROM AUTHOR]

Spectra of the highest redshift galaxies taken with JWST are now allowing us to see into the heart of the reionization epoch. Many of these observed galaxies exhibit strong damping wing absorption redward of their Lyman- |$\alpha$| emission. These observations have been used to measure the redshift evolution of the neutral fraction of the intergalactic medium and sizes of ionized bubbles. However, these estimates have been made using a simple analytic model for the intergalactic damping wing. We explore the recent observations with models of inhomogeneous reionization from the Sherwood–Relics simulation suite. We carry out a comparison between the damping wings calculated from the simulations and from the analytic model. We find that although the agreement is good on the red side of the Lyman- |$\alpha$| emission, there is a discrepancy on the blue side due to residual neutral hydrogen present in the simulations, which saturates the intergalactic absorption. For this reason, we find that it is difficult to reproduce the claimed observations of large bubble sizes at |$z \sim 7$|⁠ , which are driven by a detection of transmitted flux blueward of the Lyman- |$\alpha$| emission. We suggest instead that the observations can be explained by a model with smaller ionized bubbles and larger intrinsic Lyman- |$\alpha$| emission from the host galaxy. [ABSTRACT FROM AUTHOR]

Simple Summary: Genetic diversity plays a crucial role in determining the ability of populations to evolve. We investigated the genetic variation of the black-and-white snub-nosed monkey by integrating adaptive MHC genes and neutral microsatellites. We found that neutral loci exhibited high heterozygosity and a high degree of polymorphism, while MHC genes showed high heterozygosity and moderate polymorphism. Additionally, positive selection and trans-species evolution indicated that historical balancing selection might have sustained the MHC polymorphism. This study provides valuable scientific evidence and a reference for formulating or amending conservation strategies for black-and-white snub-nosed monkeys. Genetic diversity is an essential indicator that echoes the natural selection and environmental adaptation of a species. Isolated small populations are vulnerable to genetic drift, inbreeding, and limited gene flow; thus, assessing their genetic diversity is critical in conservation. In this study, we studied the genetic diversity of black-and-white snub-nosed monkeys (Rhinopithecus bieti) using neutral microsatellites and five adaptive major histocompatibility complex (MHC) genes. Two DQA1 alleles, two DQB1 alleles, two DRB1 alleles, two DRB5 alleles, and three DPB1 alleles were isolated from a population. The results indicate that neutral microsatellites demonstrate a high degree of heterozygosity and polymorphism, while adaptive MHC genes display a high degree of heterozygosity and moderate polymorphism. The results also show that balancing selection has prominently influenced the MHC diversity of the species during evolution: (1) significant positive selection is identified at several amino acid sites (primarily at and near antigen-binding sites) of the DRB1, DRB5, and DQB1 genes; (2) phylogenetic analyses display the patterns of trans-species evolution for all MHC loci. This study provides valuable genetic diversity insights into black-and-white snub-nosed monkeys, which dwell at the highest altitude and have experienced the harshest environmental selection of all primates globally since the Pleistocene. Such results provide valuable scientific evidence and a reference for making or amending conservation strategies for this endangered primate species. [ABSTRACT FROM AUTHOR]

The evolution of suppressed recombination between sex chromosomes is widely hypothesized to be driven by sexually antagonistic selection (SA), where tighter linkage between the sex-determining gene(s) and nearby SA loci is favored when it couples male-beneficial alleles to the proto-Y chromosome, and female-beneficial alleles to the proto-X. Although difficult to test empirically, the SA selection hypothesis overshadows several alternatives, including an incomplete but often-repeated "sheltering" hypothesis which suggests that expansion of the sex-linked region (SLR) reduces the homozygous expression of deleterious mutations at selected loci. Here, we use population genetic models to evaluate the consequences of partially recessive deleterious mutational variation for the evolution of otherwise neutral chromosomal inversions expanding the SLR on proto-Y chromosomes. Both autosomal and SLR-expanding inversions face a race against time: lightly-loaded inversions are initially beneficial, but eventually become deleterious as they accumulate new mutations, after which their chances of fixing become negligible. In contrast, initially unloaded inversions eventually become neutral as their deleterious load reaches the same equilibrium as non-inverted haplotypes. Despite the differences in inheritance and indirect selection, SLR-expanding inversions exhibit similar evolutionary dynamics to autosomal inversions over many biologically plausible parameter conditions. Differences emerge when the population average mutation load is quite high; in this case large autosomal inversions that are lucky enough to be mutation-free can rise to intermediate to high frequencies where selection in homozygotes becomes important (Y-linked inversions never appear as homozygous karyotypes); conditions requiring either high mutation rates, highly recessive deleterious mutations, weak selection, or a combination thereof. [ABSTRACT FROM AUTHOR]

The article explores the concept of evolvability in evolutionary biology, highlighting different perspectives and definitions from various fields. It emphasizes the importance of historical context and conditions for evolvability, providing mathematical proofs and derivations for measurement and analysis. The article concludes by discussing the book "Evolvability" by Hansen and collaborators, which covers mutations, genotype-phenotype maps, development, body plans, and the connection between micro- and macroevolution. While the book offers a comprehensive understanding, it may lack empirical evidence and overlook concepts like phenotypic plasticity and niche construction. Overall, it provides a nuanced and updated perspective on evolvability. [Extracted from the article]

Wildlife reintroduction is an important conservation tool for threatened species, yet identifying appropriate source populations poses a challenge. In particular, the possibility of outbreeding depression is cited as a constraint limiting the range of candidate source populations for translocation. When multiple source lineages are mixed during reintroduction, genetic monitoring is necessary to evaluate whether sources contribute equally to subsequent generations and whether they are interbreeding as expected. Moreover, statistical analysis of genetic data should account for complex life histories that might affect the timescale of admixture and genetic drift. Here, we use samples collected over a 23-year period and a stochastic age-structured model to analyze the genetic mixing process in reintroduced Brook Trout (Salvelinus fontinalis) populations in the Southern Appalachians. Each restored population was seeded with two to three source populations. Previous research inferred reproductive isolation between source populations leading to a proposal of splitting the species into multiple taxa. In contrast, we found patterns of ancestry that were consistent with random mating and no advantage for one source lineage over any other. Brook Trout from different source streams are mixing as expected in the restoration sites. This result does not support the hypothesis that Brook Trout in the Southern Appalachian Mountains includes several distinct species. Mixing different sources from the same watershed seems to be an effective way to increase genetic diversity of reintroduced populations while minimizing risk to source populations. [ABSTRACT FROM AUTHOR]

Small island populations are vulnerable to genetic decline via demographic and environmental stochasticity. In the absence of immigration, founder effects, inbreeding and genetic drift are likely to contribute to local extinction risk. Management actions may also have a greater impact on small, closed populations. The demographic and social characteristics of a species can, however, delay the impact of threats. K'gari, a ~ 1 660 km2 island off the Australian east coast and UNESCO World Heritage Site (Fraser Island 1842–2023), supports an isolated population of approximately 70–200 dingoes that represent an ideal opportunity to explore the small island paradigm. To examine temporal and spatial patterns of genetic diversity in this population we analysed single nucleotide polymorphism (SNP) genotype data (72 454 SNPS) for 112 K'gari dingoes collected over a 25-year period (1996 to 2020). Genetic diversity was lower in K'gari dingoes than mainland dingoes at the earliest time point in our study and declined significantly following a management cull in 2001. We did not find any spatial genetic patterns on the island, suggesting high levels of genetic connectivity between socially discrete packs. This connectivity, combined with the social structure and behaviour of dingoes, may act in concert to buffer the population from the impacts of genetic drift in the short term. Nevertheless, a general decline in genetic variation via inbreeding and drift has occurred over the past 20 years which we suggest should be considered in any future management planning for the population. Monitoring patterns of genetic variation, together with a clearer understanding of the social ecology of K'gari dingoes, will aid in the development of measurable genetic targets set over ecologically meaningful timelines, and help ensure continued survival of this culturally important population. [ABSTRACT FROM AUTHOR]

Small populations of endangered species risk losing already eroded genetic diversity, important for adaptive potential, through the effects of genetic drift. The magnitude of drift can be mitigated by maximising the effective population size, as is the goal of genetic management strategies. Different mating systems, specifically those leading to reproductive skew, exacerbate genetic drift by distorting contributions. In the absence of an active management strategy, reproductive skew will have long-term effects on the genetic composition of a population, particularly where admixture is present. Here we examine the contrasting effects of conservation management strategies in two ex situ populations of the Critically Endangered eastern black rhino (Diceros bicornis michaeli), one managed as a semi-wild population in South Africa (SAx), and one managed under a mean-kinship breeding strategy in European zoos. We use molecular data to reconstruct pedigrees for both populations and validate the method using the zoo studbook. Using the reconstructed pedigree and studbook we show there is male sex-specific skew in both populations. However, the zoo's mean-kinship breeding strategy effectively reduces reproductive skew in comparison to a semi-wild population with little genetic management. We also show that strong male reproductive skew in SAx has resulted in extensive admixture, which may require a re-evaluation of the population's original intended role in the black rhino meta-population. With a high potential for admixture in many ex situ populations of endangered species, molecular and pedigree data remain vital tools for populations needing to balance drift and selection. [ABSTRACT FROM AUTHOR]

We calculated the found and expected frequencies of metacentrics in polymorphic populations of the Dnieper basin common rodent, resulting from hybridization of local populations with acrocentric karyotype and four chromosomal races (Neroosa, Kiev, Białowieża, and Western Dvina) with 3–5 diagnostic metacentrics in each. We have previously shown an increased frequency of acrocentric karyotype compared to that expected according to Hardy–Weinberg. The low frequency (less than 0.5) of most metacentrics of the four chromosomal races and the disappearance of some of them from the populations can be explained by the increased fitness of the acrocentric karyotype and the absence of meiotic drive. On the contrary, the preservation of high frequency (more than 0.5) of such metacentrics as gm, hk (races of Western Dvina), hi (races of Kiev), hn, ik (races of Białowieża), and, especially, the fixation of metacentric hi (races of Neroosa) in polymorphic populations can be explained by meiotic drive. The fixation of Rb compounds in the range of the common rodent may be a consequence not only of gene drift but also of meiotic drive. Most likely, meiotic drive is able to maintain the frequency of Rb compounds with the largest acrocentrics g, h, and i, which contributed to the widespread distribution of such compounds throughout the range of the common rodent. [ABSTRACT FROM AUTHOR]

Summary Polyploidy is widely recognized as an important speciation mechanism because it isolates tetraploids from their diploid progenitors. Polyploidy also provides new genetic material that may facilitate adaptive evolution. However, new mutations are more likely to arise after a neopolyploid already has successfully invaded a population. Thus, the role of adaptive forces in establishing a polyploid remains unclear. One solution to this apparent paradox may lie in the capacity of polyploids to suppress recombination among preexisting locally adapted alleles. The local adaptation mechanism requires that spatially heterogeneous selection acts on multiple loci and that gene flow introduces maladapted alleles to the population where the polyploid forms. The mechanism requires neither strong genetic drift nor any intrinsic benefit of genome doubling and can accommodate any mode of gene action. A unique prediction of the mechanism is that adaptive alleles should predate polyploidization, a pattern consistent with observations from a few well‐studied polyploids. The mechanism is also consistent with the coexistence of both diploid and tetraploid cytotypes, fitness heterogeneity among independently derived polyploids, and the prevalence of outcrossing among older polyploids. The local adaptation mechanism also makes novel predictions about circumstances favoring polyploid invasions that can be tested using molecular genetic or comparative approaches. [ABSTRACT FROM AUTHOR]

The development of efficient and long‐term stable electrodes for hydrogen evolution reaction (HER) in seawater is highly desirable for hydrogen generation but remains challenging. In this work, a highly active CrOx@Ni2P‐Ni5P4/NF electrode is developed and investigated its dynamic reconstruction for HER in neutral electrolytes. The combination of in situ Raman spectra and electrochemical measurements revealed the dynamic surface reconstruction of the catalyst during HER. The CrOx modification not only effectively facilitates water dissociation but also stabilizes the structure post‐reconstruction, enabling rapid and stable hydrogen generation in neutral media. Remarkably, CrOx@Ni2P‐Ni5P4/NF exhibits overpotentials of 109 and 263 mV at current densities of 10 and 100 mA cm−2 in 1 m PBS, respectively. Concurrently, it exhibits stable operation for 500 h in 1 m PBS and 140 h in natural seawater at current densities of 50 and 100 mA cm−2, respectively. The proposed catalytic electrode and the mechanistic insights present a significant stride toward the realization of metal phosphides for direct seawater splitting. [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 article discusses the emergence of the SARS-CoV-2 KP.2 variant, which is a descendant of the BA.2.86 variant. While the KP.2 variant has shown an increase in cases, there is no evidence suggesting that it is a significantly concerning new variant. The article provides information on the global prevalence of the KP.2 variant, highlighting regions where it has been detected and its relative prevalence in different countries. The KP.2 variant carries mutations of interest, including K417N, S477N, N501Y, and P681R, which may pose potential risks. Additionally, it shares the E484K mutation, which has been associated with the ability to evade immune responses. However, the lasting immunity conferred by natural immune responses to these mutations has not been explicitly documented. The KP.2 variant of SARS-CoV-2, also known as the Omicron variant, carries three additional mutations in the spike protein genes compared to its ancestor, the JN.1 variant. These mutations, R346T, F456L, and V1104L, have been observed in other Omicron subvariants and are associated with increased transmission and evasion of neutralizing antibodies. The F456L mutation, in particular, enhances the spike protein's affinity for the ACE2 receptor, allowing the virus to better evade immune responses. The V1104L mutation, located within a T cell epitope, may enhance protein stability. However, it is [Extracted from the article]

Over the last 5 million years, numerous species of Australian stygobiotic (subterranean and aquatic) beetles have evolved underground following independent colonization of aquifers by surface ancestors, providing a set of repeated evolutionary transitions from surface to subterranean life. We used this system as an 'evolutionary experiment' to investigate whether relaxed selection has provided a source of variability for adaptive radiations into ecosystems containing open niches and whether this variability underpins phenotypic evolution in cave animals. Linear and landmark-based measurements were used to quantify the morphology of subterranean species from different aquifers, compared to interstitial and closely related aquatic surface species. Subterranean dytiscids were observed to be morphologically distinct, suggesting they have a different lifestyle compared to their surface relatives. However, variation in the measured traits was much greater in the subterranean species, and unstructured, showing no evidence of clustering that would indicate adaptation to specific niches. Furthermore, a previously identified pattern of repeated nonoverlapping size variation in beetles across aquifers was not correlated with repeated body shape evolution. The observed variability across body shape and limb traits provides support for the hypothesis that relaxed selection and neutral evolution underlie the phenotypic evolution in these species. [ABSTRACT FROM AUTHOR]

Grapevine Roditis leaf discoloration‐associated virus (GRLDaV) is a type of virus that infects grapevines. This research aimed to determine the prevalence of GRLDaV in Turkey vineyards and investigate the genetic diversity and population structure of the selected viral isolates from Turkey compared to isolates from other countries. In this study, 800 shoot samples from Turkey vineyards were collected in late spring and autumn from different regions. The samples were analysed by RT‐PCR targeting the partial RNaseH‐like gene region of the virus genome. The overall prevalence of GRLDaV was 8.1% among the samples. Phylogenetic analysis of the GRLDaV genome showed that the GRLDaV isolates were clustered into two major lineages. The nucleotide diversity (π) value of Group I, including only Mediterranean isolates, was lower than Group II, suggesting little variation among isolates. Even though π values were low among the geographical regions in Turkey, the region with the highest nucleotide diversity was the Aegean population, followed by the Eastern and Mediterranean populations. Comparison between nonsynonymous and synonymous substitutions showed that negative selection acts on synonymous amino acids. Along with neutrality tests and gene flow analyses, it was emphasized that genetic drift played an important role in shaping the GRLDaV populations. This study provides important information on the prevalence and genetic diversity of GRLDaV in Turkey vineyards. The findings will help to develop better strategies to manage and control this virus, which can cause significant economic losses in grape industries. [ABSTRACT FROM AUTHOR]

The first record of captive-bred red foxes (Vulpes vulpes) dates to 1896 when a breeding enterprise emerged in the provinces of Atlantic Canada. Because its domestication happened during recent history, the red fox offers a unique opportunity to examine the genetic diversity of an emerging domesticated species in the context of documented historical and economic influences. In particular, the historical record suggests that North American and Eurasian farm-bred populations likely experienced different demographic trajectories. Here, we focus on the likely impacts of founder effects and genetic drift given historical trends in fox farming on North American and Eurasian farms. A total of 15 mitochondrial haplotypes were identified in 369 foxes from 10 farm populations that we genotyped (n  = 161) or that were previously published. All haplotypes are endemic to North America. Although most haplotypes were consistent with eastern Canadian ancestry, a small number of foxes carried haplotypes typically found in Alaska and other regions of western North America. The presence of these haplotypes supports historical reports of wild foxes outside of Atlantic Canada being introduced into the breeding stock. These putative Alaskan and Western haplotypes were more frequently identified in Eurasian farms compared to North American farms, consistent with historical documentation suggesting that Eurasian economic and breeding practices were likely to maintain low-frequency haplotypes more effectively than in North America. Contextualizing inter- vs. intra-farm genetic diversity alongside the historical record is critical to understanding the origins of this emerging domesticate and the relationships between wild and farm-bred fox populations. [ABSTRACT FROM AUTHOR]

For protein coding genes to emerge de novo from a non-genic DNA, the DNA sequence must gain an open reading frame (ORF) and the ability to be transcribed. The newborn de novo gene can further evolve to accumulate changes in its sequence. Consequently, it can also elongate or shrink with time. Existing literature shows that older de novo genes have longer ORF, but it is not clear if they elongated with time or remained of the same length since their inception. To address this question we developed a mathematical model of ORF elongation as a Markov-jump process, and show that ORFs tend to keep their length in short evolutionary timescales. We also show that if change occurs it is likely to be a truncation. Our genomics and transcriptomics data analyses of seven Drosophila melanogaster populations are also in agreement with the model's prediction. We conclude that selection could facilitate ORF length extension that may explain why longer ORFs were observed in old de novo genes in studies analysing longer evolutionary time scales. Alternatively, shorter ORFs may be purged because they may be less likely to yield functional proteins. [ABSTRACT FROM AUTHOR]

Species reintroductions have the potential to cause genetic bottleneck events resulting in increased genetic drift, increased inbreeding, and reduced genetic diversity creating negative fitness consequences for populations. Roosevelt elk (Cervus canadensis roosevelti Erxleben, 1777) are "at risk" in British Columbia (BC), Canada. Once widespread along the west coast, Roosevelt elk were likely extirpated from the mainland by 1900 and experienced a substantial population bottleneck on Vancouver Island at that time, and again in the 1950s. Reintroduced to the mainland from Vancouver Island in the 1980s, this re-established population became the source for subsequent mainland translocations. To understand the effects of reintroduction strategy on genetic diversity, we analyzed genetic variation in 355 Roosevelt elk from Vancouver Island and mainland BC. Using mitochondrial DNA and 10 microsatellite loci, molecular analyses showed overall reduced genetic diversity relative to other extant elk populations, genetic isolation of the southern Vancouver Island population, and increased genetic drift among reintroduced herds. Four reintroduced populations were found to have increased levels of inbreeding. Results of this study contribute to our knowledge of reintroduction biology and can be used to guide continued conservation and management of at-risk species. [ABSTRACT FROM AUTHOR]

Population diversity is crucial in evolutionary algorithms as it helps with global exploration and facilitates the use of crossover. Despite many runtime analyses showing advantages of population diversity, we have no clear picture of how diversity evolves over time. We study how the population diversity of (μ + 1) algorithms, measured by the sum of pairwise Hamming distances, evolves in a fitness-neutral environment. We give an exact formula for the drift of population diversity and show that it is driven towards an equilibrium state. Moreover, we bound the expected time for getting close to the equilibrium state. We find that these dynamics, including the location of the equilibrium, are unaffected by surprisingly many algorithmic choices. All unbiased mutation operators with the same expected number of bit flips have the same effect on the expected diversity. Many crossover operators have no effect at all, including all binary unbiased, respectful operators. We review crossover operators from the literature and identify crossovers that are neutral towards the evolution of diversity and crossovers that are not. [ABSTRACT FROM AUTHOR]

Although allelic variation is ubiquitous in natural populations, our theoretical models are poor at predicting the existence and properties of these observed polymorphisms. In this study, inspired by Van Valen's Red Queen hypothesis, we modeled the effect of viability selection in a deteriorating environment on the properties of allelic variation in populations subject to recurrent mutation. In Monte Carlo simulations, we found that levels of polymorphism consistently built up over time. We censused the simulated populations after 10,000 generations of mutation and selection, revealing that, compared with models assuming a constant environment, the mean number of alleles was greater, as was the range of allele numbers. These results were qualitatively robust to the addition of genetic drift and to the relaxation of the assumption that the viabilities of phenogenotypes containing a new mutation are independent of each other (i.e. incorporating a model of generalized dominance). The broad range of allele numbers realized in the simulated populations—from monomorphisms to highly polymorphic populations—more closely corresponds to the observed range from numerous surveys of natural populations than previously found in theoretical studies. This match suggests that, contrary to the views of some writers, selection may actively maintain genetic variation in natural populations, particularly if the selective environment is gradually becoming harsher. Our simulations also generated many populations with heterozygote advantage, a mismatch with real data that implies that this selective property must arise extremely rarely in natural populations. [ABSTRACT FROM AUTHOR]

Red algae Pterocladiella capillacea off the coast of China were investigated for genetic diversity. With 176 samples categorized into six populations based on concatenated rbcL and cox1 sequences, the results rang warning bells for the genetic diversity of Pterocladiella capillacea along the Chinese coastline: (1) a good diversity of haplotype (Hd > 0.5) in Naozhou and Hui'an populations situated along the southern coast of China, but highest in the former; (2) less nucleotide diversity in each of the six populations (Pi < 0.005); (3) genetic differentiation occurred between the north population in Changdao and the two southern grown populations in Nan'ao, and Naozhou. To identify molecular markers, an MP phylogenetic tree was used to illustrate genetic profiles in detail, with 161 concatenated sequences clustered into four branches: Changdao (north), Nan'ao (south), Naozhou (south), and the remaining regions (middle). The Fst value for each of Changdao, Nan'ao, and Naozhou was greater than 0.5, which denotes that these three populations are genetically different to those growing in the middle coast. Moreover, a 30-haplotype-based median-joining network corroborated this genetic differentiation, though variations between all the investigated populations were not very high due to the relatively smaller values of genetic distance between the six (Dxy < 0.01). Overall, red algae P. capillacea in Chinese coastal seawater showed a higher haplotype diversity and lower nucleotide diversity. Such a genetic profile indicates that both natural random genetic drift and interference from human activities have possibly affected the distribution of gene frequencies in red algae P. capillacea along the Chinese coastline. [ABSTRACT FROM AUTHOR]

In the present study, the mitochondrial genomic characteristics of Acanthopsetta nadeshnyi have been reported and have depicted the phylogenetic relationship among Pleuronectidae. Combined with a comparative analysis of 13 PCGs, the TN93 model was used to review the neutral evolution and habitat evolution catalysis of the mitogenome to verify the distancing and purification selectivity of the mitogenome in Pleuronectidae. At the same time, a species differentiation and classification model based on mitogenome analysis data was established. This study is expected to provide a new perspective on the phylogenetic relationship and taxonomic status of A. nadeshnyi and lay a foundation for further exploration of environmental and biological evolutionary mechanisms. [ABSTRACT FROM AUTHOR]

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large‐scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude – almost the entire geographical range of the European subspecies. Genome‐wide variation was consistent with a recent colonisation across Europe from a South‐East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome‐wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype‐based measures of selection were related to recombination rate, albeit less strongly, and highlighted population‐specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio‐temporal evolutionary dynamics. [ABSTRACT FROM AUTHOR]

Uncovering the mechanisms driving the genetic divergence of environmentally heterogeneous species is one of the biggest challenges in phylogeography. In the present study, the genetic variation and genetic structure of the Coilia nasus were examined by analyzing thirteen mitochondrial protein-coding genes (PCGs) among 60 individuals collected from 8 populations in affiliated waters of Yangtze River and their adjacent waters. Contrasted to the recently recognized multiple subdivision, our reconstructed phylogenetic tree, analysis of molecular variance (AMOVA), FST and haplotype networks refined only two previously recognized clades, with one clade arising from the Dongting and Poyang lakes affiliated to the upper reach of Yangtze River, and the other mainly from the remaining populations. Historical demography analysis revealed that the divergence time between the two clades could be recovered to 60.05 ka, indicating a possible role of late Pleistocene glaciers in their differentiation, possibly via isolation of diverged glaciers' refugia. Subsequent positive selection test revealed no diverged selective pressures acting on the two clades within all 13 PCGs, suggests that the observed mitochondrial lineage divergence of C. nasus in the Yangtze River and its adjacent waters was primarily driven by neutral evolution. Our results provided new insights into the spatial patterns of genetic variation in population of C. nasus and would provide valuable implications for sustainable management and utilization of this fishery resource in the future. [ABSTRACT FROM AUTHOR]

The pace of current climate change is expected to be problematic for alpine flora and fauna, as their adaptive capacity may be limited by small population size. Yet, despite substantial genetic drift following post-glacial recolonization of alpine habitats, alpine species are notable for their success surviving in highly heterogeneous environments. Population genomic analyses demonstrating how alpine species have adapted to novel environments with limited genetic diversity remain rare, yet are important in understanding the potential for species to respond to contemporary climate change. In this study, we explored the evolutionary history of alpine ground beetles in the Nebria ingens complex, including the demographic and adaptive changes that followed the last glacier retreat. We first tested alternative models of evolutionary divergence in the species complex. Using millions of genome-wide SNP markers from hundreds of beetles, we found evidence that the N. ingens complex has been formed by past admixture of lineages responding to glacial cycles. Recolonization of alpine sites involved a distributional range shift to higher elevation, which was accompanied by a reduction in suitable habitat and the emergence of complex spatial genetic structure. We tested several possible genetic pathways involved in adaptation to heterogeneous local environments using genome scan and genotype–environment association approaches. From the identified genes, we found enriched functions associated with abiotic stress responses, with strong evidence for adaptation to hypoxia-related pathways. The results demonstrate that despite rapid demographic change, alpine beetles in the N. ingens complex underwent rapid physiological evolution. [ABSTRACT FROM AUTHOR]

The role of balancing selection is a long-standing evolutionary puzzle. Balancing selection is a crucial evolutionary process that maintains genetic variation (polymorphism) over extended periods of time; however, detecting it poses a significant challenge. Building upon the Polymorphism-aware phylogenetic Models (PoMos) framework rooted in the Moran model, we introduce a PoMoBalance model. This novel approach is designed to disentangle the interplay of mutation, genetic drift, and directional selection (GC-biased gene conversion), along with the previously unexplored balancing selection pressures on ultra-long timescales comparable with species divergence times by analyzing multi-individual genomic and phylogenetic divergence data. Implemented in the open-source RevBayes Bayesian framework, PoMoBalance offers a versatile tool for inferring phylogenetic trees as well as quantifying various selective pressures. The novel aspect of our approach in studying balancing selection lies in polymorphism-aware phylogenetic models' ability to account for ancestral polymorphisms and incorporate parameters that measure frequency-dependent selection, allowing us to determine the strength of the effect and exact frequencies under selection. We implemented validation tests and assessed the model on the data simulated with SLiM and a custom Moran model simulator. Real sequence analysis of Drosophila populations reveals insights into the evolutionary dynamics of regions subject to frequency-dependent balancing selection, particularly in the context of sex-limited color dimorphism in Drosophila erecta. [ABSTRACT FROM AUTHOR]