Within-population Genetic Diversity Research Articles

Genomic epidemiology and evolutionary dynamics of the Omicron variant of SARS-CoV-2 during the fifth wave of COVID-19 in Pakistan.

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has posed extraordinary challenges to global health systems and economies. The virus's rapid evolution has resulted in several variants of concern (VOCs), including the highly transmissible Omicron variant, characterized by extensive mutations. In this study, we investigated the genetic diversity, population differentiation, and evolutionary dynamics of the Omicron VOC during the fifth wave of COVID-19 in Pakistan. A total of 954 Omicron genomes sequenced during the fifth wave of COVID-19 in Pakistan were analyzed. A Bayesian framework was employed for phylogenetic reconstructions, molecular dating, and population dynamics analysis. Using a population genomics approach, we analyzed Pakistani Omicron samples, revealing low within-population genetic diversity and significant structural variation in the spike (S) protein. Phylogenetic analysis showed that the Omicron variant in Pakistan originated from two distinct lineages, BA.1 and BA.2, which were introduced from South Africa, Thailand, Spain, and Belgium. Omicron-specific mutations, including those in the receptor-binding domain, were identified. The estimated molecular evolutionary rate was 2.562E-3 mutations per site per year (95% HPD interval: 8.8067E-4 to 4.1462E-3). Bayesian skyline plot analysis indicated a significant population expansion at the end of 2021, coinciding with the global Omicron outbreak. Comparative analysis with other VOCs showed Omicron as a highly divergent, monophyletic group, suggesting a unique evolutionary pathway. This study provides a comprehensive overview of Omicron's genetic diversity, genomic epidemiology, and evolutionary dynamics in Pakistan, emphasizing the need for global collaboration in monitoring variants and enhancing pandemic preparedness.

Population genetic structure in a self-compatible hermaphroditic snail is driven by drift independently of its contemporary mating system.

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 (N e). 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 (N e) 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 N e 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.

Within population plastic responses to combined thermal-nutritional stress differ from those in response to single stressors, and are genetically independent across traits in both males and females.

Phenotypic plasticity helps animals to buffer the effects of increasing thermal and nutritional stress created by climate change. Plastic responses to single and combined stressors can vary among genetically diverged populations. However, less is known about how plasticity in response to combined stress varies among individuals within a population or whether such variation changes across life-history traits. This is important because individual variation within populations shapes population-level responses to environmental change. Here, we used isogenic lines of Drosophila melanogaster to assess plasticity of egg-to-adult viability and sex-specific body size for combinations of two temperatures (25°C or 28°C) and three diets (standard diet, low caloric diet, or low protein:carbohydrate ratio diet). Our results reveal substantial within-population genetic variation in plasticity for egg-to-adult viability and wing size in response to combined thermal-nutritional stress. This genetic variation in plasticity was a result of cross-environment genetic correlations that were often < 1 for both traits, as well as changes in the expression of genetic variation across environments for egg-to-adult viability. Cross-sex genetic correlations for body size were weaker when the sexes were reared in different conditions, suggesting that the genetic basis of traits may change with the environment. Further, our results suggest that plasticity in egg-to-adult viability is genetically independent from plasticity in body size. Importantly, plasticity in response to diet and temperature individually differed from plastic shifts in response to diet and temperature in combination. By quantifying plasticity and the expression of genetic variance in response to combined stress across traits, our study reveals the complexity of animal responses to environmental change, and the need for a more nuanced understanding of the potential for populations to adapt to ongoing climate change.

Too simple, too complex, or just right? Advantages, challenges, and guidance for indicators of genetic diversity

Abstract Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritizing species and populations to preserve and recover genetic diversity (e.g., via genetic rescue). Recently, indicators were developed for tracking and reporting genetic diversity status and trends for hundreds of species. The indicators quantify two simple proxies of within-population and among-population genetic diversity and adaptive potential: small effective population size (Ne &amp;lt; 500) and the loss of genetically distinct populations. The indicators must balance scientific credibility, practicality, and simplicity. In the present article, we summarize the advantages of these pragmatic indicators, address critiques by scientists for simplifying assumptions and by policymakers for complexity, and propose potential solutions and next steps. We aim to support practitioners putting indicators into policy, action, legislation, and reporting.

Stronger genetic differentiation among within-population genetic groups than among populations in Scots pine provides new insights into within-population genetic structuring

We investigated the presence of spatial genetic groups within forest tree populations and determined if the genetic divergence among these groups is greater than that between populations using Scots pine (Pinus sylvestris) as a model species. We genotyped 890 adult trees of Scots pine in six natural populations in Lithuania at 11 nuclear microsatellite loci. We used a Bayesian clustering approach to identify the within-population genetic groups within each of the six populations. We calculated the differentiation indexes among the genetic groups within each population and among the six populations by ignoring the genetic groups. The Bayesian clustering revealed 2 to 6 distinct genetic groups of varying size as the most likely genetic structures within populations. The genetic differentiation indexes among the genetic groups within populations were nearly tenfold greater (FST = 0.012–0.070) than those between the populations (FST = 0.003). We conclude on the existence of markedly stronger structuring of genetic variation within populations than between populations of Scots pine in large forest tracts of northern Europe. Such genetic structures serve as a contributing factor to large within population genetic diversity in northern conifers. We assume that within population mating in Scots pine is not completely random but rather is stratified into genetic clusters. Our study provides pioneering novel key insights into structuring of genetic variation within populations. Our findings have implications for examining within-population genetic diversity and genetic structure, conservation, and management of genetic resources.

Phenotypic plasticity of a winter-diapause mechanism copes with the effects of summer global warming in an ectothermic predator.

To adapt to changes in temperature, animals tend to invest more energy in thermal tolerance to enhance survival, which can have simultaneous costs on plastic traits. Would a decrease in genetic variability, due to global warming, affect the ability of populations with existing metabolic regulatory mechanisms to cope with extreme temperatures? To address this question, we conducted a series of experiments based on the A1B scenario of global warming, assessing within-population genetic variance in (a) morphological traits, (b) metabolic rate allometries, and (c) survival of a winter-diapausing predator ectotherm. Our study focused on the lacewing species Chrysoperla pallida, using both exogamic and endogamic artificial genetic lines. We discovered that both lines use their winter-diapausing phenotype to adapt to summer extreme temperatures caused by extreme heating conditions, but the exogamic line is prone to express phenotypic plasticity in metabolic scaling, with a trade-off between body size and mandible size, i.e. larger individuals tended to develop smaller mandibles to better survive. These findings highlight the significance of substantial phenotypic plasticity and pre-existing metabolic regulatory mechanisms in enabling ectotherms to cope with potential extreme heating occurring in global warming.

Differential patterns of within- and between-population genetically based trait variation in Lupinus angustifolius.

Within-population genetic and phenotypic variation play a key role in the development of adaptive responses to environmental change. Between-population variation is also an essential element in assessing the evolutionary potential of species in response to changes in environmental conditions. In this context, common garden experiments are a useful tool to separate the genetic and environmental components of phenotypic variation. We aimed to assess within- and between-population phenotypic variation of Lupinus angustifolius L. in terms of its evolutionary potential to adapt to ongoing climate change. We evaluated populations' phenotypic variation of foliar, phenological and reproductive traits with a common garden experiment. Patterns of functional trait variation were assessed with (1) mixed model analyses and coefficients of variation (CVs) with confidence intervals, (2) principal component analyses (PCAs) and (3) correlations between pairs of traits. Analyses were performed at the population level (four populations) and at the latitude level (grouping pairs of populations located in two latitudinal ranges). Phenotypic variation had a significant genetic component associated with a latitudinal pattern. (1) Mixed models found lower specific leaf area, advanced flowering phenology and lower seed production of heavier seeds in southern populations, whereas CV analyses showed lower within-latitude variation especially in phenological and reproductive traits in southern populations. (2) PCAs showed a clearer differentiation of phenotypic variation between latitudes than between populations. (3) Correlation analyses showed a greater number of significant correlations between traits in southern populations (25 vs. 13). Between-population phenotypic variation was determined by contrasting temperature and drought at different latitude and elevation. Southern populations had differential trait values compatible with adaptations to high temperatures and drought. Moreover, they had lower within-population variation and a greater number of trait correlations probably as a result of these limiting conditions, making them more vulnerable to climate change.

Why fake death? Environmental and genetic control of tonic immobility in larval lacewings (Neuroptera: Chrysopidae).

Tonic immobility is a passive antipredator strategy employed late in the predation sequence that may decrease individual mortality in prey animals. Here, we investigate how energetic state and genetic predisposition influence antipredator decision-making in green lacewing larvae, Chrysoperla plorabunda (Fitch), using simulated predatory encounters. We demonstrate that tonic immobility is a plastic response influenced by energetic resource limitation. Larvae exposed to 1 or 2 days of food deprivation initiate tonic immobility more often and with less physical provocation than individuals fed ad libitum. Recently molted individuals exposed to food deprivation, the individuals most energetically challenged, engage in tonic immobility at a higher rate than any other group. We also find that variation in antipredator strategy between individuals is partly the result of within-population genetic variation. We estimate the propensity to enter tonic immobility to have a broad-sense heritability of 0.502. Taken together our results suggest that larval lacewings under energetic stress are more likely to engage in tonic immobility. Yet, energetic state does not explain all within-population variation, as individuals can have a genetic predisposition for tonic immobility.

Development of SSR molecular markers and genetic diversity analysis of Clematis acerifolia from Taihang Mountains.

Investigating the genetic diversity and population structure is important in conserving narrowly distributed plants. In this study, 90 Clematis acerifolia (C. acerifolia) plants belonging to nine populations were collected from the Taihang Mountains in Beijing, Hebei, and Henan. Twenty-nine simple sequence repeats (SSR) markers developed based on RAD-seq data were used to analyze the genetic diversity and population structure of C. acerifolia. The mean PIC value for all markers was 0.2910, indicating all SSR markers showed a moderate degree of polymorphism. The expected heterozygosity of the whole populations was 0.3483, indicating the genetic diversity of both C. acerifolia var. elobata and C. acerifolia were low. The expected heterozygosity of C. acerifolia var. elobata (He = 0.2800) was higher than that of C. acerifolia (He = 0.2614). Genetic structure analysis and principal coordinate analysis demonstrated that C. acerifolia and C. acerifolia var. elobata showed great genetic differences. Molecular variance analysis (AMOVA) demonstrated that within-population genetic variation (68.31%) was the main contributor to the variation of the C. acerifolia populations. Conclusively, C. acerifolia var. elobata had higher genetic diversity than C. acerifolia, and there are significant genetic differences between C. acerifolia and C. acerifolia var. elobata, and small genetic variations within the C. acerifolia populations. Our results provide a scientific and rational basis for the conservation of C. acerifolia and provide a reference for the conservation of other cliff plants.

Morphological, Molecular, and Nutritional Characterisation of the Globe Artichoke Landrace "Carciofo Ortano".

The present study focused on the molecular, morphological, and nutritional characterisation of a globe artichoke landrace at risk of genetic erosion still cultivated in the municipality of Orte (Lazio Region, Central Italy) and therefore named "Carciofo Ortano". Molecular analysis based on SSR and ISSR markers was carried out on 73 genotypes selected at random from 20 smallholdings located in the Orte countryside and 17 accessions of landraces/clones belonging to the main varietal types cultivated in Italy. The results confirmed that "Carciofo Ortano" belongs to the "Romanesco" varietal typology and revealed the presence within the landrace of two distinct genetic populations named Orte 1 and Orte 2. Despite the high level of within-population genetic variation detected, the two populations were genetically differentiated from each other and from the landraces/clones of the main varietal types cultivated in Italy. Morphological and nutritional characterisation was performed on representative genotypes for each of the two populations of the "Carciofo Ortano" and the four landraces/clones included in the varietal platform of the PGI "CARCIOFO ROMANESCO DEL LAZIO" used as reference genotypes ("Campagnano", "Castellammare", "C3", and "Grato 1"). Principal component analysis showed that, of the 43 morphological descriptors considered, 12, including plant height, head shape index, head yield, and earliness, allowed a clear grouping of genotypes, distinguishing Orte 1 and Orte 2 populations from the reference genotypes. Regarding the nutritional composition of heads, particular attention should be devoted to the Orte 2 genotypes for their high dietary fibre, inulin, flavonoid, and phenol content, a feature that could be highly appreciated by the market.

Genetic diversity of the threatened &lt;i&gt;Saussurea dorogostaiskii&lt;/i&gt; (Asteraceae) in the Khuvsgul region of Mongolia

&lt;i&gt;Saussurea dorogostaiskii&lt;/i&gt; Palib. (Asteraceae) is a critically endangered medicinal plant in Mongolia and Russia. We studied the genetic variation of &lt;i&gt;S. dorogostaiskii&lt;/i&gt; from three mountains of northern Mongolia. The genetic profile was assessed in 70 individuals from eight populations using five inter-simple sequence repeat markers, producing 53 loci with 96.4% polymorphism across all bands. Shannon’s index (&lt;i&gt;I&lt;/i&gt;) and Nei’s gene diversity (&lt;i&gt;H&lt;/i&gt;) value at the species level of &lt;i&gt;S. dorogostaiskii&lt;/i&gt; are 0.25 and 0.17, respectively. An AMOVA showed high genetic variation among the populations (22% of populations and 32% of mountains), consistent with the high genetic differentiation (&lt;i&gt;G&lt;sub&gt;ST&lt;/sub&gt;&lt;/i&gt; = 0.49) and low gene flow (&lt;i&gt;N&lt;sub&gt;m&lt;/sub&gt;&lt;/i&gt; = 0.51) in &lt;i&gt;S. dorogostaiskii&lt;/i&gt; populations. Eight populations were clustered into two groups, corresponding to their geographic locations. The low within-population genetic diversity and high genetic differentiation among &lt;i&gt;S. dorogostaiskii&lt;/i&gt; populations factor into their endangered designation. This genetic analysis reveals that all populations are equally threatened, and community-based conservation is appropriate for these species.

Historical biogeography and local adaptation explain population genetic structure in a widespread terrestrial orchid.

Historical changes in environmental conditions and colonization-extinction dynamics have a direct impact on the genetic structure of plant populations. However, understanding how past environmental conditions influenced the evolution of species with high gene flow is challenging when signals for genetic isolation and adaptation are swamped by gene flow. We investigated the spatial distribution and genetic structure of the widespread terrestrial orchid Epipactis helleborine to identify glacial refugia, characterize postglacial population dynamics and assess its adaptive potential. Ecological niche modelling was used to locate possible glacial refugia and postglacial recolonization opportunities of E. helleborine. A large single-nucleotide polymorphism (SNP) dataset obtained through genotyping by sequencing was used to define population genetic diversity and structure and to identify sources of postglacial gene flow. Outlier analyses were used to elucidate how adaptation to the local environment contributed to population divergence. The distribution of climatically suitable areas was restricted during the Last Glacial Maximum to the Mediterranean, south-western Europe and small areas in the Alps and Carpathians. Within-population genetic diversity was high in E. helleborine (mean expected heterozygosity, 0.373 ± 0.006; observed heterozygosity, 0.571 ± 0.012; allelic richness, 1.387 ± 0.007). Italy and central Europe are likely to have acted as important genetic sources during postglacial recolonization. Adaptive SNPs were associated with temperature, elevation and precipitation. Forests in the Mediterranean and Carpathians are likely to have acted as glacial refugia for Epipactis helleborine. Postglacial migration northwards and to higher elevations resulted in the dispersal and diversification of E. helleborine in central Europe and Italy, and to geographical isolation and divergent adaptation in Greek and Italian populations. Distinguishing adaptive from neutral genetic diversity allowed us to conclude that E. helleborine has a high adaptive potential to climate change and demonstrates that signals of adaptation and historical isolation can be identified even in species with high gene flow.

Genetic structuring and invasion status of the perennial Ambrosia psilostachya (Asteraceae) in Europe

The perennial western ragweed (Ambrosia psilostachya DC.) arrived from North America to Europe in the late nineteenth century and behaves invasive in its non-native range. Due to its efficient vegetative propagation via root suckers, A. psilostachya got naturalized in major parts of Europe forming extensive populations in Mediterranean coastal areas. The invasion history, the spreading process, the relationships among the populations as well as population structuring is not yet explored. This paper aims to give first insights into the population genetics of A. psilostachya in its non-native European range based on 60 sampled populations and 15 Simple Sequence Repeats (SSR). By AMOVA analysis we detected 10.4% of genetic variation occurring among (pre-defined) regions. These regions represent important harbors for trading goods from America to Europe that might have served as source for founder populations. Bayesian Clustering revealed that spatial distribution of genetic variation of populations is best explained by six groups, mainly corresponding to regions around important harbors. As northern populations show high degrees of clonality and lowest levels of within-population genetic diversity (mean Ho = 0.40 ± 0.09), they could preserve the initial genetic variation levels by long-lived clonal genets. In Mediterranean populations A. psilostachya expanded to millions of shoots. Some of those were obviously spread by sea current along the coast to new sites, where they initiated populations characterized by a lower genetic diversity. For the future, the invasion history in Europe might get clearer after consideration of North American source populations of western ragweed.

Genetic Characterization of Nile Tilapia (&amp;lt;i&amp;gt;Oreochromis niloticus&amp;lt;/i&amp;gt;) Strains from Senegal for Sustainable Local Aquaculture Production

The optimization of aquaculture production requires the selection of efficient strains. Thus, genetic improvement has become one of the important levers to boost the development of aquaculture. The objective of this study was to carry out genetic characterization of Nile tilapia Oreochromis niloticus, one of the most cultivated fish species in Senegal, in order to select an efficient strain to optimize local fish production. Thus, fish from five different populations (Richard-Toll, ANA, ITACA, Mbodiene and Sauvage) were analyzed, with 15 individuals per population. Genetic diversity and population structure were assessed using molecular genetic analyses by sequence characterized amplified region (SCAR) and microsatellite (SSR) markers. The analyses of the SCARII marker were conducted on four populations (ANA, ITACA, Sauvage and Mbodiene) while microsatellite analyses were conducted on all five populations. The results show high levels of polymorphism of SSR markers, and a high level of observed heterozygosity (Ho), indicating a high within-population genetic variability. These results are in agreement with the AMOVA results, which indicated a high within-population genetic variability (94%). The genetic structure analysis by DAPC indicates that the five populations analyzed are structured into four groups, which are highly heterogeneous because they share common allele individuals. The analysis of the genetic structure by AMOVA showed a low degree of differentiation between the populations (6%), in agreement with the genetic differentiation index (Fst = 0.059). The heterogeneity of studied populations implies a genetic flow over time, which may have existed between the original populations. The overall negative Tajima D values and low genetic differentiation indicate an excess of rare mutations in the populations studied, resulting from a recent population expansion from a limited number of initial breeders isolated in locale hatcheries. Thus, further studies with a much larger panel of markers are required to better differentiate the strains and identify the most efficient ones for sustainable local aquaculture production.

Genetic diversity and gene expression diversity shape the adaptive pattern of the aquatic plant Batrachium bungei along an altitudinal gradient on the Qinghai-Tibet plateau.

It is an intriguing issue of evolutionary biology how genetic diversity and gene expression diversity shape the adaptive patterns. Comparative transcriptomic studies of wild populations in extreme environments provide critical insights into the relative contribution of genetic and expressive components. In this study, we analyzed the genetic diversity and gene expression diversity of 20 populations of the aquatic plant Batrachium bungei along elevations ranging from 2690 to 4896m on the Qinghai-Tibet plateau (QTP). Based on single nucleotide polymorphisms (SNPs) and gene expression data from 100 individuals of B. bungei, we found that variation in genetic sequence was more sensitive to detect weak differentiation than gene expression. Using 292,613 high-quality SNPs, we documented a significant phylogeographical structure, a low within-population genetic diversity, and a high inter-population genetic differentiation in B. bungei populations. Analysis of relationship between geographic distance, genetic distance, and gene expression similarity showed that geographic isolation shaped gene flow patterns but not gene expression patterns. We observed a negative relationship between genetic diversity and gene expression diversity within and among B. bungei populations, and we demonstrated that as environmental conditions worsen with increasing altitude, genetic diversity played an increased role in maintaining the stability of populations, while the corresponding role of gene expression diversity decreased. These results suggested that genetic diversity and gene expression diversity might act as a complementary mechanism contributing to the long-term survival of B. bungei in extreme environments.

Are populations less genetically diverse and more differentiated at the species range edges? Analysis of the quantitative trait and molecular variation in wild oat Avena sterilis

Abstract Although understanding factors determining the genetic makeup of natural populations has long been an important goal of evolutionary biology, the effect of population position within the species range (i.e., interior vs. edge) on species genetic variation is still unclear. According to the ‘abundant center’ hypothesis, the range edge populations are expected to exhibit lower genetic variation and higher differentiation than core populations because of their greater spatial isolation and smaller size. We tested these predictions by comparing the extent and structure of neutral (SSR) and quantitative trait genetic variation in 20 populations of an annual grass Avena sterilis hierarchically sampled at the species range core and two opposite edges. Within-population genetic diversity was reduced at the desert range edge compared to the range core as assessed by six SSR markers but not by eight quantitative traits; no reduction was detected at the mountain edge. Genetic differentiation among populations was higher at the desert range edge than the range core in both molecular markers and quantitative traits, but not at the mountain edge. Our results imply that the pattern of population genetic variation at the species range edges largely depends on the steepness of the environmental cline that has a major effect on species fitness. The more gradual the environmental cline from the species interior towards the edge, the higher the probability of detecting reduced genetic diversity and increased differentiation of peripheral populations as predicted by the ‘abundant center’ hypothesis.

Genetic diversity pattern reveals the primary determinant of burcucumber (Sicyos angulatus L.) invasion in Korea.

Biological invasion is a complex process associated with propagule pressure, dispersal ability, environmental constraints, and human interventions, which leave genetic signatures. The population genetics of an invasive species thus provides invaluable insights into the patterns of invasion. Burcucumber, one of the most detrimental weeds for soybean production in US, has recently colonized Korea and rapidly spread posing a great threat to the natural ecosystem. We aim to infer the determinants of the rapid burcucumber invasion by examining the genetic diversity, demography, and spread pattern with advanced genomic tools. We employed 2,696 genome-wide single-nucleotide polymorphisms to assess the level of diversity and the spatial pattern associated with the landscape factors and to infer the demographic changes of 24 populations (364 genotypes) across four major river basins with the east coastal streams in South Korea. Through the approximate Bayesian computation, we inferred the likely invasion scenario of burcucumber in Korea. The landscape genetics approach adopting the circuit theory and MaxEnt model was applied to determine the landscape contributors. Our data suggested that most populations have experienced population bottlenecks, which led to lowered within-population genetic diversity and inflated population divergences. Burcucumber colonization in Korea has strongly been affected by demographic bottlenecks and multiple introductions, whereas environmental factors were not the primary determinant of the invasion. Our work highlighted the significance of preventing secondary introductions, particularly for aggressive weedy plants such as the burcucumber.

Climate change threatens unique genetic diversity within the Balkan biodiversity hotspot – The case of the endangered stone crayfish

The stone crayfish Austropotamobius torrentium is globally endangered due to anthropogenic pressure on its habitats, climate change and the invasive crayfish species, particularly the signal crayfish Pacifastacus leniusculus . Aiming to guide A. torrentium conservation within the hotspot of its genetic diversity in the western Balkan Peninsula, we combined population genetics and species distribution models (SDMs) to reveal the impact of climate change and the invasive P. leniusculus on A. torrentium diversity. Population genetic analyses based on newly developed microsatellites revealed moderate within-population genetic diversity and high differentiation among populations, reflecting isolated populations with limited gene flow. Alongside strong genetic structuring, we discovered high level of inbreeding coefficient indicating homozygote excess within the majority of populations. The SDMs results predicted substantial reductions of suitable habitats for A. torrentium by 2070; 80 % of its currently suitable habitat is predicted to be lost under high‐warming climate change scenario. Obtained results indicated that 44 % of populations with high and/or unique genetic diversity, including three highly divergent and geographically restricted evolutionary lineages, are located in the areas predicted to become unsuitable in the future, highlighting their vulnerability to extinction. Further, SDMs revealed considerable decrease of future habitat suitability for P. leniusculus , suggesting that climate change represents greater threat to A. torrentium . Our study highlights the importance of conserving remnant A. torrentium populations, among other, through assisted migration and population mixing that could help populations overcome the risks of inbreeding and maladaptation, and thus enabling A. torrentium to withstand the ongoing climate change. • Native freshwater crayfish decline is a global conservation concern. • The first study of Austropotamobius torrentium genetic diversity in its hotspot (Balkan Peninsula). • Climate change poses a higher risk to A. torrentium than invasive crayfish species. • Transboundary conservation actions needed for species long-term preservation. • . Conservation strategies should include assisted migration and population reinforcement.

Phylogeography and genetic variation in Western Jacob's ladder (Polemonium occidentale) provide insights into the origin and conservation of rare species in the Great Lakes region.

The perennial herb Western Jacob's Ladder (Polemonium occidentale, Polemoniaceae) is widespread in the mountains of western North America but reappears as a disjunct in the Great Lakes Region in Minnesota and Wisconsin, USA as the narrow endemic P. occidentale subsp. lacustre. This distribution is shown by a diverse assemblage of angiosperms. It has been hypothesized that these species became isolated just after the Last Glacial Maximum, but this has not been tested. Additionally, the genetic diversity and population connectivity of the endemic Great Lakes flora has been understudied, with important conservation implications. Using genotyping-by-sequencing, we examined the relationship of P. occidentale subsp. lacustre to its closest relatives, relationships among all known populations, and genetic diversity within these populations. Polemonium occidentale subsp. lacustre represents an isolated, unique lineage that diverged from its closest relatives 1.3Ma and arrived in the Great Lakes Region by at least 38 ka. Nearly all extant populations diverged prior to the Last Glacial Maximum, are genetically distinct, and show little within-population genetic diversity. Clonality may mitigate reduction in diversity due to drift. Mixed population signal between Wisconsin and some Minnesota populations may be due to gene flow during the Late Pleistocene. While populations of P. occidentale subsp. lacustre may be relictual from a now extinct western relative, it is best treated as a distinct species. Conservation efforts should focus more on ensuring that current populations remain rather than maintaining large populations sizes across a few populations. However, encouraging habitat heterogeneity may accomplish both simultaneously.

Genetic and spatial variation in vegetative and floral traits across a hybrid zone.

Genetic variation influences the potential for evolution to rescue populations from impacts of environmental change. Most studies of genetic variation in fitness-related traits focus on either vegetative or floral traits, with few on floral scent. How vegetative and floral traits compare in potential for adaptive evolution is poorly understood. We measured variation across source populations, planting sites, and genetic families for vegetative and floral traits in a hybrid zone. Seeds from families of Ipomopsis aggregata, I. tenuituba, and F1 and F2 hybrids of the two species were planted into three common gardens. Measured traits included specific leaf area (SLA), trichomes, water-use efficiency (WUE), floral morphology, petal color, nectar, and floral volatiles. Vegetative traits SLA and WUE varied greatly among planting sites, while showing weak or no genetic variation among source populations. Specific leaf area and trichomes responded plastically to snowmelt date, and SLA exhibited within-population genetic variation. All aspects of floral morphology varied genetically among source populations, and corolla length, corolla width, and sepal width varied genetically within populations. Heritability was not detected for volatiles due to high environmental variation, although one terpene had high evolvability, and high emission of two terpenes, a class of compounds emitted more strongly from the calyx than the corolla, correlated genetically with sepal width. Environmental variation across sites was weak for floral morphology and stronger for volatiles and vegetative traits. The inheritance of three of four volatiles departed from additive. Results indicate stronger genetic potential for evolutionary responses to selection in floral morphology compared with scent and vegetative traits and suggest potentially adaptive plasticity in some vegetative traits.