ISOLATION BY DISTANCE

Study design and the sampling of deleterious rare variants in biobank-scale datasets

One key component of study design in population genetics is the "geographic breadth" of a sample (i.e., how broad a region across which individuals are sampled). How the geographic breadth of a sample impacts observations of rare, deleterious variants is unclear, even though such variants are of particular interest for biomedical and evolutionary applications. Here, in order to gain insight into the effects of sample design on ascertained genetic variants, we formulate a stochastic model of dispersal, genetic drift, selection, mutation, and geographically concentrated sampling. We use this model to understand the effects of the geographic breadth of sampling effort on the discovery of negatively selected variants. We find that samples which are more geographically broad will discover a greater number of variants as compared to geographically narrow samples (an effect we label "discovery"); though the variants will be detected at lower average frequency than in narrow samples (e.g., as singletons, an effect we label "dilution"). Importantly, these effects are amplified for larger sample sizes and fitness effects. We validate these results using both population genetic simulations and empirical analyses in the UK Biobank. Our results are particularly important in two contexts: the association of large-effect rare variants with particular phenotypes and the inference of negative selection from allele frequency data. Overall, our findings emphasize the importance of considering geographic breadth when designing and carrying out genetic studies, especially at biobank scale.

Pleistocene Glaciation Drove Shared Population Coexpansion in Eastern North American Snakes

Glacial cycles during the Pleistocene had profound impacts on local environments and climatic conditions. In North America, some regions that currently support diverse biomes were entirely covered by ice sheets, while other regions were environmentally unsuitable for the organisms that live there now. Organisms that occupy these regions in the present day must have expanded or dispersed into these regions since the last glacial maximum, leading to the possibility that species with similar geographic distributions may show temporally concordant population size changes associated with these warming trends. We examined 17 lineages from 9 eastern North American snake species and species complexes to test for a signal of temporally concordant coexpansion using a machine learning approach. We found that the majority of lineages show population size increases towards the present, with evidence for coexpansion in five out of fourteen lineages, while expansion in others was idiosyncratic. We also examined relationships between genetic distance and current environmental predictors and showed that genomic responses to environmental predictors are not consistent among species. We, therefore, conclude that Pleistocene warming resulted in population size increases in most eastern North American snake species, but variation in environmental preferences and other species-specific traits results in variance in the exact timing of expansion.

Exact calculation of the expected SFS in structured populations

The Site Frequency Spectrum (SFS), summary statistic of the distribution of derived allele frequencies in a sample of DNA sequences, provides information about genetic variation and can be used to make population inferences. The exact calculation of the expected SFS in a panmictic population under the infinite-site model of mutation has been known in the Markovian coalescent theory for decades, but its generalization to the structured coalescent is hampered by the almost exponential growth of the states space. We show here how to obtain this expected SFS as the solution of a linear system. More precisely, we propose a complete algorithmic procedure, from how to build a suitable state space and sort it, to how to take advantage of the sparsity of the rate matrix and to solve numerically the linear system using an iterative method. We then build a specialization for the simplest case of the symmetrical n-island model to arrive at a ready-to-use software called SISiFS from which a demographic parameters inference framework could easily be developed.

Using isolation-by-distance to jointly estimate effective population density and dispersal distance: a practical evaluation using bumble bees

Effective population density and intergenerational dispersal distance are key aspects of population biology, but obtaining empirical estimates of these parameters can be difficult. This is especially true for my study taxa, wild bees. In this paper, I apply and evaluate an existing but underutilized method to estimate effective density and dispersal distance of bumble bees (Bombus, Apidae). Specifically, using 10 datasets of bumble bees in North America, I use the relationship between genetic isolation-by-distance and Wright's neighborhood size to define a density-dispersal isocline-that is, a curve describing pairs of density and dispersal values consistent with observed rates of isolation-by-distance. These parameters are inversely related; as one increases the other decreases. I then use outside estimates of bumble bee dispersal distances to make more specific estimates of effective colony density. Compared to some prior estimates of census density (100s to 1000s colonies/km2), my estimated effective colony densities were very low (1-41 effective colonies/km2). I also hypothesize, however, that these estimates are affected by the spatial extent of sampling, due to scale-dependent patterns in the distribution of individuals. To test this hypothesis, I subsampled each dataset to simulate varying study extent, and repeated my analysis. Within populations, effective densities tended to decrease when measured across larger spatial extents. Altogether, I demonstrate a useful and under-appreciated tool for studying population biology, especially of small, mobile animals like bees, but also show that researchers must interpret their results carefully within the context of their study design.

Emergence of food webs with a multi-trophic hierarchical structure driven by nonlinear trait-matching

Food webs are a central subject in community ecology, because consumption supports the flow of matter through the system, which is at the base of many of its functions. Identifying the mechanisms that are at the origin of food web structure is useful, e.g., for restoration purposes. We investigated the extent to which trait-matching, which contributes to defining the strength of trophic interactions, can cause the emergence of food webs with a non-trivial, multi-trophic, hierarchical structure. We compared for that purpose the structural properties of food webs simulated by four food web model variants, depending whether trait-matching was linear or nonlinear and whether population dynamics and evolution were accounted for (dynamical model) or not (static model). Nonlinear trait-matching can restrict interactions in phenotypic space so as to obtain localized interactions (i.e., each species interact with a small subset of species), which is a key element for food web formation. In the static case, nonlinear trait-matching allowed for the emergence of food webs, at a relatively low connectance as with random graphs. In the dynamical case, nonlinear trait-matching combined with population dynamics and evolution allowed for the formation of groups of phenotypically close species, resulting in food webs with a multi-trophic, hierarchical structure.

The fitness effects of outcrossing distance depend on parental flowering phenology in fragmented populations of a tallgrass prairie forb

The phenomena of isolation-by-distance and isolation-by-time shapecontra mating patterns and population genetic processes, such as inbreeding and outbreeding depression, which influence progeny fitness. However, the effects of parental isolation in time on offspring fitness remain understudied, especially in combination with isolation-by-distance. We planted offspring from a common garden experiment involving 13 populations of the tallgrass prairie forb Echinacea angustifolia into a prairie restoration and tracked their fitness over 16 yr. Parental source populations were up to 9 km apart, and flowering asynchronies spanned up to 13 d. Using Aster life-history analysis, we assessed how interparent distance and asynchrony affected offspring fitness. Interparent asynchrony modified the relationship between interparent distance and offspring fitness. Offspring with the highest fitness had parents from the most distant populations, with maternal plants flowering later than paternal plants. Notably, the order of parental flowering, rather than the absolute difference in timing, better predicted fitness. Nongenetic aspects of reproductive timing, such as morphological constraints, may have contributed to these effects. We suggest management strategies to promote outcrossing over space and time, including leveraging seed production environments.

Speciation in the Peninsular Indian Flying Lizard (Draco dussumieri) Follows Climatic Transition and Not Physical Barriers

Marked with high levels of endemism and in situ radiations, the Western Ghats mountains make for a compelling backdrop to examine processes that lead to the formation and maintenance of species. Regional geographic barriers and paleoclimatic fluctuations have been implicated as drivers of speciation, but their roles have not been explicitly tested in a phylogenomic framework. We integrated mitochondrial DNA, genome-wide SNPs and climatic data to examine the influence of geographic barriers and climatic transitions in shaping phylogeography and potential speciation in the Peninsular Indian Flying lizard (Draco dussumieri). We found strong evidence for two independently evolving, geographically distinct, northern and southern lineages within D. dussumieri that diverged during the early Pleistocene, and a gradient of admixed populations across a broad hybrid zone in the Central Western Ghats. Migrations after initial divergence were continuous, but gene flow remained consistently below thresholds required to homogenise lineages. We found more support for isolation by environment (especially rainfall regimes) than by distance. The range-break between lineages occurs at a transition zone in the Central Western Ghats that separates dissimilar rainfall regimes with no physical barriers. This limit is potentially an ecological barrier, which nevertheless was permeable during glacial maxima. We hypothesise that similar phylogeographic patterns will emerge in other widespread, wet-adapted species in the Western Ghats that presumably endured the same climatic processes.

Distinguishing species boundaries from geographic variation

In an era of unprecedented biodiversity loss, the need for standardized practices to describe biological variation is becoming increasingly important. As with all scientific endeavors, species delimitation needs to be explicit, testable, and refutable. A fundamental task in species delimitation is distinguishing within-species variation from among-species variation. Many species that are distributed across large geographic areas exhibit levels of genetic variation that are as great or greater than those that exist between well-defined sympatric species. Here, we provide a workflow to distinguish between intra- and interspecific genetic variation and apply the workflow to a taxonomically problematic group of frogs (the Rana pipiens complex, or leopard frogs) that are widely distributed across Mexico and Central America. Our workflow makes use of recent advancements that pair genome-scale datasets with model-based species delimitation methods, while emphasizing the need for positive evidence of reproductive isolation to confirm the validity of geographically contiguous species boundaries. We find that intraspecific geographic variation in widespread leopard frog species has resulted in considerable taxonomic inflation of species. Ten currently recognized species are not supported in our analyses, and we here synonymize them with previously named taxa. Furthermore, we find positive evidence for the presence of three undescribed species. In addition to proposing these taxonomic changes, we provide descriptions of the data or analyses that would be needed to refute and overturn our recommendations. We recommend that all species delimitation studies (especially of geographically variable groups) clarify what new evidence would be sufficient to change the taxonomic recommendations.

Evolutionary divergence on the Qinghai-Tibet Plateau: How life-history traits shape the diversity of plateau zokor and pika populations

Understanding how species diverge and adapt is fundamental to unraveling biodiversity. While environmental impacts on species evolution are well-documented, the roles of intrinsic life-history traits remain underexplored. The Qinghai-Tibet Plateau, with its harsh conditions and unique biodiversity, offers a natural laboratory for such investigations. Here, we examined two sympatric small mammals-the solitary, low-dispersal plateau zokor (Eospalax baileyi) and the social, high-dispersal plateau pika (Ochotona curzoniae)-to elucidate how life-history traits shape population structures and adaptive strategies. Through whole-genome sequencing and cardiac-blood phenotype analyses, we reveal striking differences in their evolutionary trajectories. Despite enduring similar environmental pressures, plateau zokor populations exhibit pronounced genetic subdivisions, high inbreeding, and distinct local adaptations. In contrast, plateau pika populations display genetic panmixia, widespread diversity, and adaptive uniformity. Demographic inference highlights plateau zokors experienced severe population bottlenecks and restricted gene flow during glacial periods, underscoring the impact of dispersal capacity on evolutionary outcomes. Our findings demonstrate that intrinsic biological traits, particularly dispersal ability, fundamentally influence genetic architecture, population connectivity, and local adaptation. This study not only provides empirical evidence of how life-history traits shape evolutionary dynamics but offers a framework for integrating intrinsic and extrinsic factors in understanding biodiversity formation.

Repeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group

Mitochondrial introgression is common among animals and is often first identified through mitonuclear discordance-discrepancies between evolutionary relationships inferred from mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA). Over recent decades, genomic data have also revealed extensive nuclear introgression in many animal groups, with implications for genetic and phenotypic diversity. However, the extent to which mtDNA introgression corresponds to nuDNA introgression varies. Here, we investigated historical and recent introgression in the Gehyra nana-occidentalis clade, a complex group of Australian geckos with documented cases of mitonuclear discordance suggestive of repeated mtDNA introgression. We hypothesised that mitonuclear discordance in this clade reflects mtDNA introgression with substantial nuclear introgression. Despite evidence of repeated mtDNA introgression, however, we found little to no evidence of historical nuDNA introgression using exon capture and genome-wide single nucleotide polymorphism (SNP) data. We also found no evidence of gene flow at modern contact zones and detected only a single early generation hybrid. Unsurprisingly, given these results, we found no evidence of transgressive, intermediate, or more variable morphological phenotypes in taxa with introgressed mtDNA. These findings suggest that hybridisation in this system has, at least in some cases, resulted in repeated mitochondrial introgression with little or no nuclear introgression. This pattern aligns with other studies showing limited nuDNA introgression in taxa with mitonuclear discordance, highlighting a potentially broader trend in animal radiations.

Coupling Genetic and Demographic Data to Reveal Dispersal Processes in Emperor Penguins

Dispersal is a ubiquitous phenomenon that affects the dynamics of the population and the evolution of natural populations; however, it is challenging to measure in most species. Furthermore, the influence of informed dispersal behaviors, referring to the nonrandom selection of breeding habitats by individuals, on species' responses to rapid global change is substantial but difficult to comprehend. Here, we present a modeling framework to assess the dispersal characteristics and behaviors of a metapopulation when observations provide information on its neutral genetic structure for a restricted sampling of locations. Our mechanistic-statistical model couples a deterministic model capturing the spatio-temporal dynamics of four genetic clusters across all breeding colonies by integrating demographic processes with genetic projections, with a probabilistic observation model describing the probability to sample an individual from a given genetic cluster. We apply this new framework to the emperor penguin, a species living in Antarctica and currently experiencing habitat loss. The model estimates the species' dispersal distance, rates of emigration, and behaviors associated with dispersal (informed or random). By incorporating these estimations with satellite censuses of breeding colonies, we can identify environmental and demographic factors that influence the dispersal of emperor penguins. Finally, we provide new global population forecasts for emperor penguins that can inform conservation actions in Antarctica.

Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae

As organisms adapt to environmental changes, natural selection modifies the frequency of non-neutral alleles. For beneficial mutations, the outcome of this process may be a selective sweep, in which an allele rapidly increases in frequency and perhaps reaches fixation within a population. Selective sweeps have well-studied effects on patterns of local genetic variation in panmictic populations, but much less is known about the dynamics of sweeps in continuous space. In particular, because limited movement across a landscape leads to unique patterns of population structure, spatial dynamics may influence the trajectory of selected mutations. Here, we use forward-in-time, individual-based simulations in continuous space to study the impact of space on beneficial mutations as they sweep through a population. In particular, we show that selection changes the joint distribution of allele frequency and geographic range occupied by a focal allele and demonstrate that this signal can be used to identify selective sweeps. We then leverage this signal to identify in-progress selective sweeps within the malaria vector Anopheles gambiae , a species under strong selection pressure from vector control measures. By considering space, we identify multiple previously undescribed variants with potential phenotypic consequences, including mutations impacting known IR-associated genes and altering protein structure and properties. Our results demonstrate a novel signal for detecting selection in spatial population genetic data that may have implications for genomic surveillance and understanding geographic patterns of genetic variation.

Insights into the genetic diversity and species distribution of Oswaldocruzia nematodes (Trichostrongylida: Molineidae) in Europe: apparent absence of geographic and population structuring in amphibians

The genus Oswaldocruzia represents a taxonomically diverse group of nematodes with global distribution. Although Oswaldocruzia species are widespread and exhibit a remarkably wide host range in some species, their genetic diversity and biogeographic patterns remain poorly understood. This study investigated the genetic variability and distribution of Oswaldocruzia spp. in nine anuran species from the genera Bufo, Bufotes, Pelophylax, and Rana across Central Europe and the Balkans. Two species were identified: Oswaldocruzia filiformis and O. ukrainae, each exhibiting a different range of host associations. Phylogenetic analyses based on mitochondrial COI sequences revealed significant haplotype diversity in the generalist O. filiformis, with low geographic and host-associated genetic structuring. In contrast, O. ukrainae, which is closely associated with Bufotes viridis, exhibited only one genetic variant across all samples, highlighting its restricted genetic diversity. The findings emphasize contrasting genetic diversities among nematode parasites exhibiting different levels of host-specificity and expand the known distribution of O. filiformis into new regions of the Balkans. In addition, they highlight the need for additional studies on the ecological and evolutionary factors that influence the genetic diversity of parasites in amphibians.

Towards Genetically Informed Conservation of the Bardoka and Karakachan Sheep Breeds Autochthonous to Serbia

Bardoka and Karakachan sheep are primitive regional transboundary Pramenka-type sheep autochthonous to the Balkan Peninsula, whose populations have been reduced to a critically small size in Serbia. We genotyped 105 Bardoka animals (97 ewes and 8 rams from three flocks) and 97 Karakachan sheep (86 ewes and 11 rams from four flocks), along with 28 Ile-de-France (IDF) animals used for a comparison (25 ewes and 3 rams), using 14 nuclear microsatellites to assess their genetic status and establish a foundation for their genetically informed conservation. We utilized genetic data to assess inbreeding values of individuals (I) and pairwise relatedness (r) traditionally inferred from the pedigree data, which are incomplete in the studied autochthonous breeds. We used these data to assemble a data set of unrelated individuals for subsequent genetic analyses. Low but statistically significant genetic differentiation of Bardoka and Karakachan sheep (FST = 0.031, p < 0.01) demonstrates that these phenotypically distinct breeds differ at the genetic level as well. The I and r in ewes were higher in the Karakachan sheep (I = 0.09, r = 0.07) than in Bardoka (I = 0.06, r = 0.06). Contrary to the IDF rams, Bardoka and Karakachan sheep rams were genetically heterogeneous and those of the latter breed displayed higher average r values (0.01 vs. 0.08, respectively). Rams of both local breeds had identical I values of 0.02. Although Bardoka and Karakachan sheep still harbor rather high levels of genetic diversity (HE = 0.761 ± 0.028 and 0.761 ± 0.021, respectively), the overall genetic data demonstrate that the genetic consequences of the population decline were more severe in the latter breed. A genetic structure presenting a general trend of differentiation of flocks with low genetic exchange into separate genetic entities was observed, indicating the effects of genetic drift. The implementation of the genetically informed conservation, together with the ongoing efforts of the state to enlarge the Bardoka and Karakachan sheep populations, would increase the prospects for the long-term survival of both breeds in Serbia.

Exploring genetic diversity of local avocado (Persea americana Mill.) germplasm from the bamboutos highlands diversity centre in western cameroon: a comprehensive multivariate and phylogenetic analyses based on phenotypic descriptors

BACKGROUND

Avocado (Persea americana Mill.) is a tree of economic importance mostly grown for its fruit in home gardens and farms all over Cameroon. Plant germplasm resources are the basis for crop improvement. Analysis of complex traits and research on diversity on those resources is the first step leading to the exploration and creation of new plant varieties. The objective of this study was to assess the phenotypic variation of 206 avocado genotypes collected in ten villages across four altitude ranges in the Bamboutos highlands in western Cameroon.

RESULTS

Cross tabulation and Chi-square tests revealed differential distribution of traits variants among villages and altitude ranges. Various phenotypic features were observed among trees, pointing out the existence of several avocado races in Cameroon. For all the 46 qualitative traits, 162 phenotypic classes were detected, giving an average of 3.52 phenotypic classes per trait. The diversity index varied significantly between traits, populations and altitude ranges with a mean value of H'= 0.90 for qualitative traits and H'=1.31 for quantitative traits. The top five traits with higher diversity indices were fruit shape (H'=2.04), ripe fruit skin colour (H'=1.75), seed shape (H'=1.75), Tree shape (H'=1.74) and colour of flesh next to seed (H'=1.47). Bangang and Batcham populations were found to be more diverse. The lowest altitude range, 1100-1300 m above sea level (MASL) displayed smallest diversity when comparing altitude ranges. The partitioning of the diversity revealed more variation within population and within altitude ranges. Although this study revealed extensive variation between trees at the village and altitude range levels, no clear groupings of genotypes was identified based on geography. Dendrogram revealed that avocado trees from the same village and even from the same altitude ranges differ substantially. Altitude was negatively associated seed length, time from ripeness to deterioration and time from maturity to deterioration of fruits. Seventeen traits were significantly associated with the two main principal components of the PCA. Cluster analysis revealed four distinct clusters, associated to the existing avocado races.

CONCLUSION

The significant morphological variations combined with the high diversity observed in the avocado genotypes are likely to help in planning germplasm management, conservation, and improvement.

CLINICAL TRIAL NUMBER

Not applicable.

Correcting for Replicated Genotypes May Introduce More Problems Than it Solves

Across the tree of life, many organisms are able to reproduce clonally, via vegetative spread, budding or parthenogenesis. In population genetic analyses of clonally reproducing organisms, it is common practice to retain only a single representative per multilocus genotype. Though this practice of clone correction is widespread, the theoretical justification behind it has been very little studied. Here, I use individual-based simulations to study the effect of clone correction on the estimation of the genetic summary statistics HO, HS, FIS, FST, F''ST and Dest. The simulations follow the standard finite island model, consisting of a set of populations connected by gene flow, but with a variable rate of sexual versus asexual reproduction. The results of the simulations show that by itself, the inclusion of replicated genotypes does not lead to a deviation in the values of the summary statistics, except when the rate of sexual reproduction is less than about one in thousand. However, clone correction can introduce a strong deviation in the values of most of the statistics, when compared to a scenario of full sexual reproduction. For HS and FIS, this deviation can be informative about the process of asexual reproduction, but for FST, F''ST and Dest, clone correction can lead to incorrect conclusions. I therefore argue that clone correction is not strictly necessary, but can in some cases be insightful. However, when clone correction is applied, it is imperative that results for both the corrected and uncorrected data are presented.

Genetic structure and demographic history of house mice in western Europe inferred using whole-genome sequences

The western house mouse, Mus musculus domesticus, is a human commensal and an outstanding model organism for studying a wide variety of traits and diseases. However, we have few genomic resources for wild mice and only a rudimentary understanding of the demographic history of house mice in Europe. Here, we sequenced 59 whole genomes of mice collected from England, Scotland, Wales, Guernsey, northern France, Italy, Portugal and Spain. We combined this dataset with 24 previously published sequences from southern France, Germany and Iran and compared patterns of population structure and inferred demographic parameters for house mice in western Europe to patterns seen in humans. Principal component and phylogenetic analyses identified three genetic clusters in western European mice. Admixture and f-branch statistics identified historical gene flow between these genetic clusters. Demographic analyses suggest a shared history of population bottlenecks prior to 20 000 years ago. Estimated divergence times between populations of house mice from western Europe ranged from 1500 to 5500 years ago, in general agreement with the zooarchaeological record. These results correspond well with key aspects of contemporary human population structure and the history of migration in western Europe, highlighting the commensal relationship of this important genetic model.

Optimising Sampling Design for Landscape Genomics

Landscape genomic approaches for detecting genotype-environment associations (GEA), isolation by distance (IBD) and isolation by environment (IBE) have seen a dramatic increase in use, but there have been few thorough analyses of the influence of sampling strategy on their performance under realistic genomic and environmental conditions. We simulated 24,000 datasets across a range of scenarios with complex population dynamics and realistic landscape structure to evaluate the effects of the spatial distribution and number of samples on common landscape genomics methods. Our results show that common analyses are relatively robust to sampling scheme as long as sampling covers enough environmental and geographic space. We found that for detecting adaptive loci and estimating IBE, sampling schemes that were explicitly designed to increase coverage of available environmental space matched or outperformed sampling schemes that only considered geographic space. When sampling does not cover adequate geographic and environmental space, such as with transect-based sampling, we detected fewer adaptive loci and had higher error when estimating IBD and IBE. We found that IBD could be detected with as few as nine sampling sites, while large sample sizes (e.g., greater than 100 individuals) were crucial for detecting adaptive loci and IBE. We also demonstrate that, even with optimal sampling strategies, landscape genomic analyses are highly sensitive to landscape structure and migration-when spatial autocorrelation and migration are weak, common GEA methods fail to detect adaptive loci.

The origin, invasion history and resistance architecture of Anopheles stephensi in Africa

The invasion of Africa by the Asian urban malaria vector, Anopheles stephensi, endangers 126 million people across a rapidly urbanising continent where malaria is primarily a rural disease. Control of An. stephensi requires greater understanding of its origin, invasion dynamics, and mechanisms of widespread resistance to vector control insecticides. We present a genomic surveillance study of 551 An. stephensi sampled across the invasive and native ranges in Africa and Asia. Our findings support a hypothesis that an initial invasion from Asia to Djibouti seeded separate incursions to Sudan, Ethiopia, and Yemen before spreading inland, aided by favourable temperature, vegetation cover, and human transit conditions. Insecticide resistance in invasive An. stephensi is conferred by detoxification genes introduced from Asia. These findings, and a companion genomic data catalogue, will form the foundation of an evidence base for surveillance and management strategies for An. stephensi.

Uncovering the genetic architecture and evolutionary roots of androgenetic alopecia in African men

Androgenetic alopecia is a highly heritable trait. However, much of our understanding about the genetics of male-pattern baldness comes from individuals of European descent. Here, we examined a dataset comprising 2,136 men from Ghana, Nigeria, Senegal, and South Africa that were genotyped using the Men of African Descent and Carcinoma of the Prostate Array. We first tested how genetic predictions of baldness generalize from Europe to Africa and found that polygenic scores from European genome-wide association studies (GWASs) yielded area under the curve statistics that ranged from 0.513 to 0.546, indicating that genetic predictions of baldness generalized poorly from European to African populations. Subsequently, we conducted an African GWAS of androgenetic alopecia, focusing on self-reported baldness patterns at age 45. After correcting for age at recruitment, population structure, and study site, we identified 266 moderately significant associations, 51 of which were independent (p < 10-5, r2 < 0.2). Most baldness associations were autosomal, and the X chromosome does not seem to have a large impact on baldness in African men. Although Neanderthal alleles have previously been associated with skin and hair phenotypes, within the limits of statistical power, we did not find evidence that continental differences in the genetic architecture of baldness are due to Neanderthal introgression. While most loci that are associated with androgenetic alopecia do not have large integrative haplotype scores or fixation index statistics, multiple baldness-associated SNPs near the EDA2R and AR genes have large allele frequency differences between continents. Collectively, our findings illustrate how population genetic differences contribute to the limited portability of polygenic predictions across ancestries.

Genetic diversity and environmental adaptation in Ethiopian tef

Orphan crops serve as essential resources for both nutrition and income in local communities and offer potential solutions to the challenges of food security and climate vulnerability. Tef [Eragrostis tef (Zucc.)], a small-grained allotetraploid, C4 cereal mainly cultivated in Ethiopia, stands out for its adaptability to marginal conditions and high nutritional value, which holds both local and global promise. Despite its significance, tef is considered an orphan crop due to limited genetic improvement efforts, reliance on subsistence farming, and its nutritional, economic, and cultural importance. Although pre-Semitic inhabitants of Ethiopia have cultivated tef for millennia (4000-1000 BCE), the genetic and environmental drivers of local adaptation remain poorly understood. To address this, we resequenced a diverse collection of traditional tef varieties to investigate their genetic structure and identify genomic regions under environmental selection using redundancy analysis, complemented by differentiation-based methods. We identified 145 loci associated with abiotic environmental factors, with minimal geographic influence observed in the genetic structure of the sample population. Overall, this work contributes to the broader understanding of local adaptation and its genetic basis in tef, providing insights that support efforts to develop elite germplasms with improved environmental resilience.

Next-generation sequencing-based population genetics unravels the evolutionary history of Rhodomyrtus tomentosa in China

BACKGROUND

Rhodomyrtus tomentosa (Ait.) Hassk. is useful for its ornamental, medicinal, and ecological characteristics, and is considered a "Neglected and Underutilized Crop Species". However, our understanding of the geographic structure and evolutionary history of its wild populations is limited. To address this gap, we investigated genomic data from 284 samples of R. tomentosa from 28 wild populations in southern China.

RESULTS

The genetic diversity of populations in different regions revealed the similar trends using whole-genome and RAD-seq data, and Hainan Island having a higher genetic diversity than other regions. The 28 populations clustered into three distinct groups: (a) GROUP1 on the eastern mainland within Guangdong, Fujian, and Hunan Provinces; (b) GROUP2 on the western mainland within Guangxi and Yunnan Provinces; and (c) GROUP3 on Hainan Island. Mantel tests and redundancy analyses revealed population differentiation was affected by distance and environmental factors such as annual average radiation. Demographic history and gene flow analyses indicated the mainland populations and the Hainan Island populations diverged around 0.93 MYA, with gene flow primarily occurring from Hainan Island and the coastal regions (such as Zhanjiang in Guangdong and Fangchenggang in Guangxi) towards the mainland, reflecting an expansion trend within the species. PSMC' analyses indicated that the populations of the three groups underwent a bottleneck during the Pleistocene due to glacial-interglacial cycles and geological events. Niche analysis revealed that the ice ages caused habitat contraction for the species, and populations with higher genetic diversity are generally distributed in areas with more suitable habitats.

CONCLUSIONS

This study elucidates the current genetic distribution of the species within China and suggests that drastic Pleistocene climate change and geographical events caused population divergence and fluctuations in effective population size, shaping the current genetic distribution of R. tomentosa. These findings provide a theoretical basis for the genetic conservation and improvement of R. tomentosa.

Diversity on a small scale: phylogeography of the locally endemic dwarf succulent genus Oophytum (Aizoaceae) in the Knersvlakte of South Africa

BACKGROUND AND AIMS

Oophytum (Aizoaceae) is a locally endemic genus of the extremely fast-evolving subfamily Ruschioideae and consists of only two formally accepted species (Oophytum nanum and Oophytum oviforme). Both species are leaf-succulent dwarf shrubs and habitat specialists on quartz fields in the Knersvlakte, a renowned biodiversity hotspot in the arid winter-rainfall Succulent Karoo Biome of South Africa. Quartz fields present specialised patchy habitats with an island-like distribution in the landscape. Oophytum oviforme grows in the south-western part, whereas O. nanum covers most of the remaining Knersvlakte. These species co-occur in a small area, but within different quartz islands. We investigated the effects of the patchy distribution, environmental conditions and potential effects of palaeoclimatic changes on the genetics of Oophytum.

METHODS

Phylogenetic and population genetic analyses of 35 populations of the genus, covering its entire distribution area, were conducted using four chloroplast DNA markers and an amplified fragment length polymorphism dataset. These were combined with environmental data via a principal component analysis and comparative heatmap analyses.

KEY RESULTS

The genetic pattern of the Oophytum metapopulation is a tripartite division, with northern, central and western groups. This geographical pattern does not correspond to the two-species concept of Oophytum. Only the western O. oviforme populations form a monophyletic lineage, whereas the central populations of O. oviforme are genetic hybrids of O. nanum populations. The highly restricted gene flow often resulted in private gene pools with very low genetic diversity, in contrast to the hybrid gene pools of the central and edge populations.

CONCLUSIONS

Oophytum is an exceptional example of an extremely fast-evolving genus that illustrates the high speciation rate of the Ruschioideae and their success as one of the leading plant groups of the drought-prone Succulent Karoo Biome. The survival strategy of these dwarf quartz-field endemics is an interplay of adaptation to diverse island habitats, highly restricted gene flow, occasional long-distance dispersal, migration, founder effects and hybridisation events within a small and restricted area caused by glacial and interglacial changing climate conditions from the Pleistocene to the Present. These findings have important implications for future conservation management strategies.

Contact zones reveal restricted introgression despite frequent hybridization across a recent lizard radiation

Introgression-the exchange of genetic material through hybridization-is now recognized as common among animal species. The extent of introgression, however, can vary considerably even when it occurs: for example, introgression can be geographically restricted or so pervasive that populations merge. Such variation highlights the importance of understanding the factors mediating introgression. Here we used genome-wide SNP data to assess hybridization and introgression at 32 contact zones, comprising 21 phylogenetic independent contrasts across a recent lizard radiation (Heteronotia). We then tested the relationship between the extent of introgression (average admixture at contact zones) and genomic divergence across independent contrasts. Early-generation hybrids were detected at contact zones spanning the range of genomic divergence included here. Despite this, we found that introgression is remarkably rare and, when observed, geographically restricted. Only the two most genomically similar population pairs showed introgression beyond 5 km of the contact zone. Introgression dropped precipitously at only modest levels of genomic divergence, beyond which it was absent or extremely low. Our results contrast with the growing number of studies indicating that introgression is prevalent among animals, suggesting that animal groups will vary considerably in their propensity for introgression.

Intraspecific variation in group structure arises due to environmentally-mediated directional dispersal in a cooperative breeder

Many cooperatively breeding species live in groups with complex structure-large group sizes, low and variable kin structure, and multiple breeding pairs. Since these mixed-kin groups typically form because of immigration of unrelated individuals of both sexes in addition to limited offspring dispersal, differences in patterns of dispersal can generate variation in group structure, even within the same species or population. Here, we examine how environmentally mediated dispersal patterns influence variation in group structure in the plural breeding superb starling (Lamprotornis superbus), an avian cooperative breeder that inhabits a spatiotemporally variable savanna environment and forms mixed-kin groups with variable group sizes and more than one breeding pair per group. Using 4068 genome-wide polymorphic loci and fine-scale, remotely sensed ecological data from 22 groups sampled across a nearly 200 km2 environmental gradient in central Kenya, we find evidence of not only frequent and long-distance dispersal in both sexes (low isolation-by-distance and weak genetic structure), but also directional dispersal from small groups in lower quality habitat with low normalised difference vegetation index (NDVI) to large groups in higher quality habitat with high NDVI. Additionally, we find stronger genetic structure among groups in lower quality habitat, and higher genetic diversity and lower relatedness of groups in higher quality habitat. Previous work using long-term data from groups in the same population has shown that groups with lower relatedness are larger and have more breeding pairs. Long-distance, directional dispersal to maximise individual fitness can thus lead to smaller and simpler kin-based social groups in lower quality habitat, but larger and more complex mixed-kin groups in higher quality habitat. Such intraspecific, within-population variation in group structure, including variation in kin structure of social groups, could have profound implications for the relative importance of the evolutionary mechanisms (i.e. direct vs. indirect fitness benefits) underlying the formation of cooperative societies.

Integrative Analysis of Diphasiastrum digitatum Holub: Unveiling Genetic Variation and Ecological Adaptations for Sustainable Ecosystem Management

Understanding the diversity and ecological evolutionary history of plant species is crucial for addressing the current biodiversity crisis and comprehending the processes by which organisms fill ecological and geographic spaces. In this study, we present a comprehensive analysis of the diversity and evolutionary history of Diphasiastrum digitatum Holub from the lycophyte lineage of plants, using microsatellite genotyping data and biogeographic analyses. Based on the available transcriptome assembly, we generated numerous markers and utilized 13 robust microsatellite markers to genotype a collection of 402 specimens from the Eastern US (VT; VA; NC; TN). In accordance with the accepted phylogeny, cross-amplification tests demonstrated a closer relationship between D. digitatum and Diphasiastrum spp. compared with Lycopodium spp. Furthermore, the population genetics analyses identified two genetic clusters within the D. digitatum collection and suggested ongoing divergence and expansion. Isolation-by-distance analysis indicated that geographic distance had a minimal effect on differentiation, whereas environmental variables related to water regime were strongly associated with the genetic variance. Ecological niche modeling showed a post-Last Glacial Maximum expansion of D. digitatum from southern refugia, corroborating a similar evolutionary scenario based on our microsatellite data. Overall, this study provides valuable insights into the evolutionary history of clubmosses and highlights the migration events and the environmental factors that shaped their current distribution.

Genome-wide study for signatures of selection identifies genomic regions and candidate genes associated with milk traits in sheep

Milk production traits in sheep are influenced by complex genetic factors, and understanding these traits requires the identification of candidate genes under selection. This study employed two methods, FST and XP-EHH, to identify selection signatures and candidate genes associated with milk production traits in sheep. For this purpose, 9 different breeds from the Sheep HapMap dataset generated by the International Sheep Genomics Consortium (ISGC) based on analysis of the Ovine SNP50 BeadChip were used. The dairy breeds included Brown East Friesian (n = 39), Milk Lacaune (n = 103), Chios (n = 23), Churra (n = 120), and Comisana (n = 24), while the non-dairy breeds included Afshari (n = 37), Moghani (n = 34), Galway (n = 49), and Australian Suffolk (n = 109). Genomic regions in the top 0.1 percentile of FST values revealed 71 genes, while regions with the highest positive XP-EHH values identified 69 genes. Five overlapping genes-DHRS3, TNFRSF1B, AADACL4, ARHGEF11, and LRRC71-were detected by both methods, highlighting their relevance to milk production. Several candidate genes in regions identified from FST, such as PER2, SH3PXD2A, TMEM117, DDX6, PDCD11, CALHM2, and CALHM3, have been previously associated with milk production traits. Notably, CRABP2, PEAR1, PGM1, ALG6, COX15, and OAT were identified in regions with high XP-EHH values in the dairy group. Gene ontology analysis indicated that the identified genes are enriched in pathways related to chemokine receptor activity, gap junction channel activity, and gap junction-mediated intercellular transport, as well as cellular components like the connexin complex. Further studies on these genes may improve understanding of the genetic architecture of milk production traits in sheep.

Divergent Selection Promotes Intraspecific Genomic Differentiation in Spodoptera littoralis With Possible Involvement in Detoxification

The cotton leafworm, Spodoptera littoralis (Lepidoptera: Noctuidae), is a major agricultural pest affecting crops like cotton, maize, tomatoes, and wheat across southern Europe, Africa, the Middle East, and western Asia. Whole genome analyses have revealed adaptive evolution in chemosensation and detoxification genes in S. littoralis. However, the extent of intraspecific diversity influenced by recent adaptive evolutionary forces remains unclear. In this study, we conducted a population genomics analysis using 31 S. littoralis individuals from sub-Saharan Africa, northern Africa, and southern Europe to assess the existence of intraspecific population divergence and identify the underlying evolutionary forces. We show whole genome differentiation between populations based on geographic origin from the analyzed samples. Phylogenetic analyses indicate that sub-Saharan and southern European populations share a common ancestor, distinct from several northern African populations. FST and dXY statistics along the chromosomes reveal loci with restricted gene flow among populations. These loci are associated with population-specific selective sweeps, indicating the role of divergent natural selection in limiting gene flow. Notably, these loci are enriched with detoxification genes, including cytochrome P450, multidrug resistance, and xanthine dehydrogenase genes, all of which are potentially associated with detoxification. These results demonstrate that divergent selection limits gene flow among geographically distinct populations with the possibility of the involvement of detoxification as a key trait. We argue that this genetic heterogeneity can be considered in pest monitoring and management, as strategies tailored to specific populations may not be relevant for others.

Unraveling the potential structure of a Parnassius butterfly in Japan: Insights into the expansion history

The Japanese Archipelago consists of a series of isolated yet interconnected islands off the Eurasian continent. The linear topography of the archipelago presents a unique biogeographic context for the dispersal of organisms from the continent. In this study, mitochondrial DNA (mtDNA) and single-nucleotide polymorphism (SNP) variation were employed to elucidate the dispersal history of the Japanese clouded butterfly (Parnassius glacialis) across the Japanese Archipelago, including the northern island (Hokkaido), the main island (Honshu), and Shikoku Island. Network analysis of 1192 bp of mtDNA (cytochrome oxidase I and II) regions revealed 49 haplotypes and three distinct haplotype groups, which correspond geographically to Eastern Japan, Western Japan, and Chugoku-Shikoku. The Chugoku-Shikoku group is the most ancient lineage. Divergence time estimates using whole-genome sequencing of mtDNA suggest that the Japanese lineage diverged from the continental P. glacialis approximately 3.08 million years ago (Ma). Subsequently, the Eastern Japan and Western Japan lineages diverged from the Chugoku-Shikoku lineage around 1.06 Ma, with subsequent divergence of the Eastern and Western Japan lineages at approximately 0.62 Ma. P. glacialis is estimated to have expanded its distribution via a land bridge that once connected China and the Japanese Archipelago. Population structure analysis based on 3067 SNP genotypes revealed five distinct genetic structures within the Japanese Archipelago, indicating geographical differentiation. Through mtDNA and SNP variation analyses, four primary genetic barriers were identified: between Hokkaido and Honshu, between Eastern and Central Japan, within the Kansai region, and in the Chugoku region. The first three barriers correspond to notable geographical features, the Blakiston Line, a line parallel to the Itoigawa-Shizuoka Tectonic Line, and a boundary crossing Lake Biwa. These findings suggest that Japanese P. glacialis diverged from the continental P. glacialis and expanded its range across the Japanese Archipelago via western routes, leading to its current distribution.

Clonal interference, genetic variation and the speed of evolution in structured populations

When it comes to understanding the role that population structure plays in shaping rates of evolution, it is commonly accepted that interference between evolutionary innovations is more prevalent in structured populations compared to well-mixed, and that population structure reduces the rate of evolution, while simultaneously promoting maintenance of genetic variation. Prior models usually represent population structure using two or more connected demes or lattices with periodic boundary conditions. Fundamentally, the observed spatial evolutionary slow-down is rooted in the fact that these types of structures increase the time it takes for a selective sweep and therefore, increase the probability that multiple beneficial mutations will coexist and interfere. Here we show that systematically introducing more heterogeneity in population structure can reshape these prior conclusions and lead to a much wider range of observed evolutionary outcome, including increased rates of evolution. At a big picture level, our results showcase that the evolutionary effects of population structure crucially depend on the properties of the topology considered. Understanding these spatial properties is therefore requisite for making meaningful evolutionary comparisons across different topologies, for forming sensible null expectations about experimental or observational data or for developing an intuition for when well-mixed approximations, or approximations done using spatial models with a high degree of symmetry, might not apply.

The promise and challenge of spatial inference with the full ancestral recombination graph under Brownian motion

Spatial patterns of genetic relatedness among samples reflect the past movements of their ancestors. Our ability to untangle this history has the potential to improve dramatically given that we can now infer the ultimate description of genetic relatedness, the ancestral recombination graph (ARG). By extending spatial theory previously applied to trees, we generalize the common model of Brownian motion to full ARGs, thereby accounting for correlations in trees along a chromosome while efficiently computing likelihood-based estimates of dispersal rate and genetic ancestor locations, with associated uncertainties. We evaluate this model's ability to reconstruct spatial histories using individual-based simulations and unfortunately find a clear bias in the estimates of dispersal rate and ancestor locations. We investigate the causes of this bias, pinpointing a discrepancy between the model and the true spatial process at recombination events. This highlights a key hurdle in extending the ubiquitous and analytically-tractable model of Brownian motion from trees to ARGs, which otherwise has the potential to provide an efficient method for spatial inference, with uncertainties, using all the information available in the full ARG.

Insight into mtDNA diversity of wild forest musk deer (Moschus berezovskii) in Shanxi Province mountains

Shanxi Province is the northernmost distribution range of Chinese forest musk deer (Moschus berezovskii), with wild populations scattered across Zhongtiao (ZT), Lüliang (LL), and Taiyue (TY) mountain ranges. Using line transect surveys and local guide assistance, coupled with infrared camera data, this study systematically collected fecal samples from wild forest musk deer from five nature reserves across the three mountain ranges. Genetic diversity was analyzed using the mtDNA control region, which yielded 129 effective sequences of 656 bp and 20 distinct haplotypes. Haplotype and nucleotide diversities were 0.916 and 0.01505, respectively, indicating a relatively high overall genetic diversity in the studied populations. Significant genetic differentiation was observed between the Lüliang-Taiyue (LLTY) and ZT mountain range populations, with most of the genetic variation existing within the populations. No significant correlation was detected between the geographical and genetic distances of the samples, which may have resulted from historical agricultural activities in Shanxi impeding gene flow among populations. Therefore, genetic exchange programs are recommended to improve the genetic diversity and population fitness of forest musk deer in this region to facilitate their recovery and growth.

Population genetics meets ecology: a guide to individual-based simulations in continuous landscapes

Individual-based simulation has become an increasingly crucial tool for many fields of population biology. However, continuous geography is important to many applications, and implementing realistic and stable simulations in continuous space presents a variety of difficulties, from modeling choices to computational efficiency. This paper aims to be a practical guide to spatial simulation, helping researchers to implement individual-based simulations and avoid common pitfalls. To do this, we delve into mechanisms of mating, reproduction, density-dependent feedback, and dispersal, all of which may vary across the landscape, discuss how these affect population dynamics, and describe how to parameterize simulations in convenient ways (for instance, to achieve a desired population density). We also demonstrate how to implement these models using the current version of the individual-based simulator, SLiM. We additionally discuss natural selection - in particular, how genetic variation can affect demographic processes. Finally, we provide four short vignettes: simulations of pikas that shift their range up a mountain as temperatures rise; mosquitoes that live in rivers as juveniles and experience seasonally changing habitat; cane toads that expand across Australia, reaching 120 million individuals; and monarch butterflies whose populations are regulated by an explicitly modeled resource (milkweed).

Geography and Environment Shape Spatial Genetic Variation and Predict Climate Maladaptation Across Isolated and Disjunct Populations of Pinus muricata

Assessing the evolutionary potential of rare species with limited migration amidst ongoing climate change requires an understanding of patterns of genetic variation and local adaptation. In contrast to the large distributions and population sizes of most pines, Pinus muricata (bishop pine) occurs in a few isolated populations along coastal western North America and is listed as threatened by the IUCN. To quantify how current genetic variation is influenced by distribution and environment, we generated reduced representation DNA sequencing data for most extant populations of P. muricata (12 locations, 7828 loci). We assessed geographic variation in differentiation and diversity and used genetic-environment association (GEA) analyses to characterise the contribution of environmental variables to local adaptation and genetic structure. Based on these inferences, we quantified genomic offset as a relative estimate of potential maladaptation under mild (SSP1-2.6) and severe (SSP5-8.5) climate change scenarios across 2041-2060 and 2081-2100. Despite occurring in small, isolated populations, genetic diversity was not low in P. muricata. Population differentiation was, however, defined across a hierarchy of spatial scales, with stands generally forming genetically identifiable groups across latitude and environments. GEA analyses implicated temperature- and soil-related variables as most strongly contributing to local adaptation. Estimates of maladaptation to future climate varied non-linearly with latitude, increased with severity of projections and over time, and were predicted by increases in annual temperature. Our results suggest that isolation and local adaptation have shaped genetic variation among disjunct populations and that these factors may shape maladaptation risk under projected climate change.

The influence of elevation on genetic structure and variability in a wetland crucifer of the Rocky Mountains

PREMISE

In mountain ecosystems, environmental conditions (e.g., temperature, ultraviolet radiation) covary with elevation, potentially limiting gene flow over steep gradients. We hypothesized that, (1) due to stark elevational differences in environmental factors, populations from dissimilar elevations (e.g., montane versus alpine) are more strongly differentiated than populations from similar elevations; (2) patterns of migration reflect downslope dispersal more than upslope dispersal; and (3) alpine populations at the cold edge show evidence of expansion, while montane populations at the warm edge have declined.

METHODS

DNA polymorphisms in whole-genome sequences were studied from 6-10 genotypes each in populations of Cardamine cordifolia found at three montane sites (ranging from 2200 to 2800 m a.s.l.) and three alpine sites (ranging from 3000 to 3500 m a.s.l.). Statistical analyses assessed patterns of population structure, genetic diversity, migration, and historical demography since the Pleistocene.

RESULTS

Populations maintained very high levels of nucleotide diversity (π range: 0.062-0.071) and were weakly differentiated (pairwise FST = 0.027) on average. Migration among alpine populations was also inferred, with no directionality of migration across elevation bands. Demographic inference suggests that both montane and alpine populations have declined in size since the Pleistocene.

CONCLUSIONS

Environmental differences across elevation represent diffuse barriers to gene flow. Recent polyploidy and clonal reproduction likely explain excess heterozygosity and high nucleotide diversity within populations. The genetic similarity of populations across elevation suggests highly connected refugia during the Pleistocene; such results may indicate that montane and alpine populations will respond similarly to changing environmental conditions associated with climate change.

"Population" in biology and statistics

The development of a biological notion of "population" over the first century of the theory of evolution has been commented upon by a number of historians and philosophers of biology. Somewhat less commonly discussed, however, is the parallel development of the statistical concept of a population over precisely the same period, in some cases driven by the same historical actors (such as Francis Galton and R. A. Fisher). We explore here these parallel developments, first from the perspective of a reconstruction of the historical development of each concept, then with the aid of a digital analysis of a corpus of literature drawn from the journals Biometrika and JournalofGenetics, between 1900 and 1960. These twin analyses show both points of interesting overlap between these two historical trends as well as points of important divergence. The biological and statistical notions of "population" seem to be relatively clearly distinguishable over these six decades, in spite of the fact that a number of authors contributed clearly to both traditions. The complex interplay of continuity and discontinuity across these two notions of "population" makes them a particularly interesting case study of scientific conceptual change.

Lineage Diversification and Population Dynamics of the Qinghai Toad-Headed Agama (Phrynocephalus vlangalii) on the Qinghai-Tibet Plateau, with Particular Attention to the Northern Slope of the Kunlun-Arjin Mountains

The Kunlun, Arjin, and Qilian mountain ranges mark the northern edge of the Qinghai-Tibet Plateau (QTP), where rapid uplift and Quaternary glacial cycles have shaped a unique cold desert ecosystem and species distribution. Despite sampling challenges, phylogeographic studies are crucial for understanding reptile populations such as the Qinghai toad-headed agama (Phrynocephalus vlangalii), a viviparous lizard with limited dispersal and multiple subspecies in the northeastern QTP. Our fieldwork identified populations of P. vlangalii on the northern slope of the Kunlun-Arjin Mountains, similar to the controversial subspecies P. v. lidskii. We analyzed 130 individuals from the northern slope of the Kunlun-Arjin-Qilian Mountains and 253 individuals from GenBank, using three mitochondrial genes and two nuclear genes to assess intraspecific differentiation and demographic history. We found high haplotype diversity and low nucleotide diversity in P. vlangalii, with phylogenetic analyses revealing six distinct clades. Clade VI, confirmed as P. v. lidskii, and Clade IV, a new genetic lineage, were identified alongside three recognized subspecies. Genetic variation was largely attributed to clade splitting, indicating significant divergence. The Mantel test indicated that geographical and environmental factors drove population differentiation. Bayesian molecular clock analysis suggested that the most recent common ancestor of P. vlangalii lived 2.55 million years ago, influenced by the Qinghai-Tibet Movement and glacial cycles. Demographic history and ecological niche modeling (ENM) indicated no population decline during the Last Glacial Maximum, supporting the glacial maximum expansion model, with ENM predicting future habitat expansion for P. vlangalii. In addition, morphological data from 13 meristic and 15 metric characters confirmed clade differences. Our findings significantly advance our understanding of P. vlangalii diversification, population dynamics and response to geological and climatic changes in the QTP.

Parity-specific differences in spatial genetics and dispersal in the common lizard

Dispersal is a key demographic parameter that plays an important role in determining spatial population dynamics and genetic structure. Linking differences in dispersal patterns to life-history traits is often confounded by inconsistent environmental pressures experienced by different populations. To explore the relationship between dispersal and life history, we focus on a site where oviparous and viviparous lineages of the common lizard (Zootoca vivipara) are found adjacent to each other. We take advantage of this shared environment to investigate parity-specific dispersal patterns using high-resolution, individual-level spatial-genetic autocorrelation and population genomic approaches (11,726 single nucleotide polymorphisms; 293 oviparous and 310 viviparous individuals). We found isolation-by-distance patterns to be present in both the oviparous and viviparous populations. Density was 2.5 times higher in the oviparous population than the viviparous one, though heterozygosity and genetic diversity measures were similar in the two populations. We found marked differences in the extent of genetic neighbourhoods between the lineages, with the viviparous population showing both dispersal (σ) and spatial-genetic autocorrelation (Moran's I) at 2-fold greater geographic distances than the oviparous population. We found clear evidence of male-biased dispersal from genetic estimates in the viviparous population. In the oviparous population, evidence of male-biased dispersal was weak or absent. These differences are likely to be closely linked to specific requirements of the alternative reproductive strategies and may be the demographic consequences of mother-offspring interactions. Fine-scale geographic and individual-level measures are essential to understanding parity mode differences at microevolutionary scales and to better identifying their ecological and evolutionary impacts.

South African indigenous chickens' genetic diversity, and the adoption of ecological niche modelling and landscape genomics as strategic conservation techniques

Selection pressures found in the prevailing production environments have shaped the genetic structure of indigenous chickens we see today. Indigenous chickens, raised in villages, provide essential genetic resources and income for poverty alleviation by providing affordable protein. However, they are threatened by predators, emerging diseases, and market demand for ideal breeds and fast production which causes loss of their valuable traits. The lack of knowledge about genetic diversity and genetic mechanisms underlying adaptive variants may compromise the goal of conserving indigenous chicken breeds. The main insights of the study are that indigenous chickens are highly diversified, and environmental factors play a key role in enabling chicken adaptation and distribution. Genomic and spatial technologies have made it possible to explore the genetic structure and fully comprehend the mechanism underlying the local adaptation of indigenous chickens. These technologies can aid in creating programs that enhance productivity and promote climate-resilient breeds. This review explores the impact of natural selection on indigenous chicken, genetic diversity, population size, and the advancement of technologies in understanding local adaptation drivers. In conclusion, this review highlights the importance of studying the habitats and how this will guide in conserving local breeds in their intended production environment.

Microsatellite and Mitochondrial COI Provide Novel Insights Into the Population Genetic Structure of White Prunicola Scale (Pseudaulacaspis prunicola) in China

The white prunicola scale Pseudaulacaspis prunicola (Maskell) is an important pest of fruit and ornamental plants, characterised by its wide distribution, broad host range and distinct biological traits. In this study, a comprehensive population genetic analysis of P. prunicola in China was conducted, focusing on genetic diversity, genetic structure, relationships among geographical populations, and population dynamics. Microsatellite molecular and mitochondrial COI markers were used to examine the genetic diversity and structure of 19 P. prunicola populations across 10 provinces in China. The results revealed low genetic diversity and limited gene flow among populations. A clear geographic genetic structure was identified, with the 19 populations being, divided into four distinct groups, showing a pronounced north-south distribution pattern. Significant genetic differentiation was observed between these groups, with minimal gene exchange. COI-based diversity analyses produced results similar to those obtained from the microsatellite markers. These findings provide valuable insights into the distribution and spread of P. prunicola in China and may help inform the development of effective and targeted pest control strategies.

Floristic classifications and bioregionalizations are not predictors of intra-specific evolutionary patterns

The relationship between intra-specific and inter-specific patterns and processes over evolutionary time is key to ecological investigations. We examine this relationship taking an approach of focussing on the association between vegetation and floristic classifications, summaries of inter-specific processes, and intra-specific genetic structuring. Applying an innovative, multispecies, and standardised population genomic approach, we test the relationship between vegetation mapping schemes and structuring of genetic variation across a large, environmentally heterogenous region in eastern Australia. We show that intra-specific genetic variation shows limited correspondence to vegetation and floristic classifications and is better explained by distance between sampled populations and the location of biogeographical features which limit gene flow. Mapping schemes with contiguous mapping classes, particularly larger ones, were more predictive of genetic lineages, whether based on environmental factors or not, than geographically non-contiguous schemes. We conclude that vegetation and floristic classifications are not closely correlated with intra-specific genetic patterns, showing that intra-specific processes are not recapitulated by inter-specific floristic assembly processes. This study showcases the need to implement landscape level evolutionary patterns, based on species specific datasets, in restoration and conservation activities.

Climate and Socio-Sexual Environment Predict Interpopulation Variation in Chemical Signaling Glands in a Widespread Lizard

Many animal species show considerable intraspecific phenotypic variation. For species with broad distributions, this variation may result from heterogeneity in the strength and agents of selection across environments and could contribute to reproductive isolation among populations. Here, we examined interpopulation variation in a morphological trait related to chemical communication, femoral pore number (FP), using 3437 individuals from 55 Pyrenean populations of the common wall lizard (Podarcis muralis). Specifically, we tested the relative roles of genetic relatedness and gene flow, and adaptation to local conditions in generating this variation, with particular interest in the influence of climate and the socio-sexual environment (i.e., the intensity of sexual selection, estimated using sexual size dimorphism [SSD] and adult sex ratio as proxy measures). We found significant interpopulation variation and sexual dimorphism in FP, as well as high genomic differentiation among populations driven by both geographic and environmental distances. Specifically, FP differences across populations were best predicted by a combination of positive allometry and the local intensity of sexual selection, as determined by SSD, or local climatic conditions. Higher FP in more male-competitive environments, or with higher temperature and vegetation complexity, is consistent with adaptation to maintaining signaling efficacy of territorial scent marks. These results suggest that adaptation to local conditions contributes to interpopulation divergence in FP and thus environmental changes can potentially impact the fine-tuning of chemical communication mediating social and sexual behavior.

How fast are viruses spreading in the wild?

Genomic data collected from viral outbreaks can be exploited to reconstruct the dispersal history of viral lineages in a two-dimensional space using continuous phylogeographic inference. These spatially explicit reconstructions can subsequently be used to estimate dispersal metrics that can be informative of the dispersal dynamics and the capacity to spread among hosts. Heterogeneous sampling efforts of genomic sequences can however impact the accuracy of phylogeographic dispersal metrics. While the impact of spatial sampling bias on the outcomes of continuous phylogeographic inference has previously been explored, the impact of sampling intensity (i.e., sampling size) when aiming to characterise dispersal patterns through continuous phylogeographic reconstructions has not yet been thoroughly evaluated. In our study, we use simulations to evaluate the robustness of 3 dispersal metrics - a lineage dispersal velocity, a diffusion coefficient, and an isolation-by-distance (IBD) signal metric - to the sampling intensity. Our results reveal that both the diffusion coefficient and IBD signal metrics appear to be the most robust to the number of samples considered for the phylogeographic reconstruction. We then use these 2 dispersal metrics to compare the dispersal pattern and capacity of various viruses spreading in animal populations. Our comparative analysis reveals a broad range of IBD patterns and diffusion coefficients mostly reflecting the dispersal capacity of the main infected host species but also, in some cases, the likely signature of rapid and/or long-distance dispersal events driven by human-mediated movements through animal trade. Overall, our study provides key recommendations for the use of lineage dispersal metrics to consider in future studies and illustrates their application to compare the spread of viruses in various settings.

Multispecies genetic structure scales with β-diversity across river hierarchies in a freshwater mussel biodiversity hotspot

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.

Testing the Mating System Model of Parasite Complex Life Cycle Evolution Reveals Demographically Driven Mixed Mating

AbstractMany parasite species use multiple host species to complete development; however, empirical tests of models that seek to understand factors impacting evolutionary changes or maintenance of host number in parasite life cycles are scarce. Specifically, one model incorporating parasite mating systems that posits that multihost life cycles are an adaptation to prevent inbreeding in hermaphroditic parasites and thus preclude inbreeding depression remains untested. The model assumes that loss of a host results in parasite inbreeding and predicts that host loss can evolve only if there is no parasite inbreeding depression. We provide the first empirical tests of this model using a novel approach we developed for assessing inbreeding depression from field-collected parasite samples. The method compares genetically based selfing rate estimates to a demographic-based selfing rate, which was derived from the closed mating system experienced by endoparasites. Results from the hermaphroditic trematode Alloglossidium renale, which has a derived two-host life cycle, supported both the assumption and the prediction of the mating system model, as this highly inbred species had no indication of inbreeding depression. Additionally, comparisons of genetic and demographic selfing rates revealed a mixed mating system that could be explained completely by the parasite's demography (i.e., its infection intensities).

Variable habitat use supports fine-scale population differentiation of a freshwater piscivore (northern pike, Esox lucius) along salinity gradients in brackish lagoons

In mobile animals, selection pressures resulting from spatio-temporally varying ecological factors often drive adaptations in migration behavior and associated physiological phenotypes. These adaptations may manifest in ecologically and genetically distinct ecotypes within populations. We studied a meta-population of northern pike (Esox lucius) in brackish environments and examined intrapopulation divergence along environmental gradients. Behavioral phenotypes in habitat use were characterized via otolith microchemistry in 120 individuals sampled from brackish lagoons and adjacent freshwater tributaries. We genotyped 1514 individual pike at 33 highly informative genetic markers. The relationship between behavioral phenotype and genotype was examined in a subset of 101 pikes for which both phenotypic and genomic data were available. Thermosaline differences between juvenile and adult life stages indicated ontogenetic shifts from warm, low-saline early habitats towards colder, higher-saline adult habitats. Four behavioral phenotypes were found: Freshwater residents, anadromous, brackish residents, and cross-habitat individuals, the latter showing intermediary habitat use between brackish and freshwater areas. Underlying the behavioral phenotypes were four genotypes, putative freshwater, putative anadromous, and two putatively brackish genotypes. Through phenotype-genotype matching, three ecotypes were identified: (i) a brackish resident ecotype, (ii) a freshwater ecotype expressing freshwater residency or anadromy, and (iii) a previously undescribed intermediary cross-habitat ecotype adapted to intermediate salinities, showing limited reliance on freshwater. Life-time growth of all ecotypes was similar, suggesting comparable fitness. By combining genetic data with lifelong habitat use and growth as a fitness surrogate, our study revealed strong differentiation in response to abiotic environmental gradients, primarily salinity, indicating ecotype diversity in coastal northern pike is higher than previously believed.

Concordant Signal of Genetic Variation Across Marker Densities in the Desert Annual Chylismia brevipes Is Linked With Timing of Winter Precipitation

Climate change coupled with large-scale surface disturbances necessitate active restoration strategies to promote resilient and genetically diverse native plant communities. However, scarcity of native plant materials hinders restoration efforts, leading practitioners to choose from potentially viable but nonlocal seed sources. Genome scans for genetic variation linked with selective environmental gradients have become a useful tool in such efforts, allowing rapid delineation of seed transfer zones along with predictions of genomic vulnerability to climate change. When properly applied, genome scans can reduce the risk of maladaptation due to mismatches between seed source and planting site. However, results are rarely replicated among complimentary data sources. Here, we compared RAD-seq datasets with 819 and 2699 SNPs (in 625 and 356 individuals, respectively) from the Mojave Desert winter annual Chylismia brevipes. Overall, we found that the datasets consistently characterized both neutral population structure and genetic-environmental associations. Ancestry analyses indicated consistent spatial genetic structuring into four regional populations. We also detected a marked signal of isolation by resistance (IBR), wherein spatial genetic structure was better explained by habitat resistance than by geographic distance. Potentially adaptive loci identified from genome scans were associated with the same environmental gradients-fall precipitation, winter minimum temperature, and precipitation timing-regardless of dataset. Paired with our finding that habitat resistance best explained genetic divergence, our results suggest that isolation of populations within environmentally similar habitats-and subsequent local adaption along gradients parallel to these habitats-drive genome-wide divergence in this species. Moreover, strong genetic associations with winter precipitation timing, along with forecasted shifts in precipitation regime due to midcentury climate change, could impact future population dynamics, habitat distribution, and genetic connectivity for C. brevipes populations within the Mojave Desert.

Estimating dispersal rates and locating genetic ancestors with genome-wide genealogies

Spatial patterns in genetic diversity are shaped by individuals dispersing from their parents and larger-scale population movements. It has long been appreciated that these patterns of movement shape the underlying genealogies along the genome leading to geographic patterns of isolation-by-distance in contemporary population genetic data. However, extracting the enormous amount of information contained in genealogies along recombining sequences has, until recently, not been computationally feasible. Here, we capitalize on important recent advances in genome-wide gene-genealogy reconstruction and develop methods to use thousands of trees to estimate per-generation dispersal rates and to locate the genetic ancestors of a sample back through time. We take a likelihood approach in continuous space using a simple approximate model (branching Brownian motion) as our prior distribution of spatial genealogies. After testing our method with simulations we apply it to Arabidopsis thaliana. We estimate a dispersal rate of roughly 60 km2/generation, slightly higher across latitude than across longitude, potentially reflecting a northward post-glacial expansion. Locating ancestors allows us to visualize major geographic movements, alternative geographic histories, and admixture. Our method highlights the huge amount of information about past dispersal events and population movements contained in genome-wide genealogies.

Combined Use of Univariate and Multivariate Approaches to Detect Selection Signatures Associated with Milk or Meat Production in Cattle

OBJECTIVES

The aim of this study was to investigate the genomic structure of the cattle breeds selected for meat and milk production and to identify selection signatures between them.

METHODS

A total of 391 animals genotyped at 41,258 SNPs and belonging to nine breeds were considered: Angus (N = 62), Charolais (46), Hereford (31), Limousin (44), and Piedmontese (24), clustered in the Meat group, and Brown Swiss (42), Holstein (63), Jersey (49), and Montbéliarde (30), clustered in the Milk group. The population stratification was analyzed by principal component analysis (PCA), whereas selection signatures were identified by univariate (Wright fixation index, FST) and multivariate (canonical discriminant analysis, CDA) approaches. Markers with FST values larger than three standard deviations from the chromosomal mean were considered interesting. Attention was focused on markers selected by both techniques.

RESULTS

A total of 10 SNPs located on seven different chromosomes (7, 10, 14, 16, 17, 18, and 24) were identified. Close to these SNPs (±250 kb), 165 QTL and 51 genes were found. The QTL were grouped in 45 different terms, of which three were significant (Bonferroni correction < 0.05): milk fat content, tenderness score, and length of productive life. Moreover, genes mainly associated with milk production, immunity and environmental adaptation, and reproduction were mapped close to the common SNPs.

CONCLUSIONS

The results of the present study suggest that the combined use of univariate and multivariate approaches can help to better identify selection signatures due to directional selection.