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PubMed2026

Discovering common and population-specific QTLs for leaf rust resistance in different Barley populations.

Multi-population GWAS lead to identification of common and population-specific QTLs for leaf rust resistance in barley. Genome-wide association studies (GWAS) are a powerful tool for detecting genetic markers associated with traits of interest. However, these studies are typically restricted to a single population, and transferability of identified marker effects across populations is challenged by population differences in linkage, allele frequencies, epistatic effects, and environmental context. When comparing GWAS results between populations, a lack of overlapping signals is often interpreted as a lack of common quantitative trait loci (QTLs), although such discrepancies may result from differences in statistical power to detect signals. In barley (Hordeum vulgare L.), where genetic leaf rust resistance is rapidly overcome by evolving pathogens, identification of cross-population robust and potentially transferable resistance loci is a key task. Here, we present a mixed model approach for multi-population GWAS that estimates correlated marker effects in multiple populations and use this to test for significant effects across and within populations. Applying this model to four barley breeding populations revealed both common and population-specific QTL effects for leaf rust resistance, including loci colocalizing with known Rph genes and novel regions with plausible candidate genes. Multi-population GWAS increased power, revealing signals not detected by GWAS within populations. We categorized the reported QTLs into three groups based on marker-associated allele effects: (1) consistent effect direction across populations, (2) differing effect direction across populations, and (3) present in a single population. The study highlights the transferability and limitations of leaf rust resistance QTLs across different barley populations and provides a general statistical framework to support robust marker-assisted selection across populations.

Quantitative Trait Loci↗

PubMed2025

Parallel genetic adaptation amid a background of changing effective population sizes in divergent yellow perch (Perca flavescens) populations.

Aquatic ecosystems are highly dynamic environments vulnerable to natural and anthropogenic disturbances. High-economic-value fisheries are one of many ecosystem services affected by these disturbances, and it is critical to accurately characterize the genetic diversity and effective population sizes of valuable fish stocks through time. We used genome-wide data to reconstruct the demographic histories of economically important yellow perch (Perca flavescens) populations. In two isolated and genetically divergent populations, we provide independent evidence for simultaneous increases in effective population sizes over both historic and contemporary time scales including negative genome-wide estimates of Tajima's D, 3.1 times more single nucleotide polymorphisms than adjacent populations, and contemporary effective population sizes that have increased 10- and 47-fold from their minimum, respectively. The excess of segregating sites and negative Tajima's D values probably arose from mutations accompanying historic population expansions with insufficient time for purifying selection, whereas linkage disequilibrium-based estimates of Ne also suggest contemporary increases that may have been driven by reduced fishing pressure or environmental remediation. We also identified parallel, genetic adaptation to reduced visual clarity in the same two habitats. These results suggest that the synchrony of key ecological and evolutionary processes can drive parallel demographic and evolutionary trajectories across independent populations.

Animals↗

PubMed2026

Idiopathic pulmonary fibrosis risk loci in East Asian populations mirror those of European populations.

RATIONALE: Common and rare variants that are associated with the risk of developing idiopathic pulmonary fibrosis (IPF) have been identified predominantly in European ancestry populations. OBJECTIVES: To better understand the genetic variants that contribute to IPF in individuals with Asian ancestry, we conducted a genome-wide association study of IPF in East Asian populations. METHODS: We included 1026 patients with IPF and compared them to 1723 unaffected controls of Japanese and Korean ancestry. Genome-wide association analysis was conducted in the Japanese and Korean ancestry cohorts separately and combined using meta-analysis. Restricted maximum likelihood was used to estimate the SNP-based heritability and local ancestry of chromosome 11 was inferred for each subject. MEASUREMENTS AND MAIN RESULTS: We identified loci on chromosomes 4 (FAM13A; rs7690839), 5 (TERT; rs7734992), 6 (DSP; rs2076295), and 11 (MUC5B; rs35705950) that were significantly associated with risk of IPF. Importantly, the sentinel variants in each of these loci are the same as, or in strong linkage disequilibrium with, the risk variants that have been observed in studies of European ancestry populations. In aggregate, common variants (not including the MUC5B promoter variant) account for approximately 25% of the risk of developing IPF in these East Asian ancestry cohorts. Moreover, local ancestry analysis indicates that the presence of MUC5B promoter variant in the East Asian population is not a result of admixture with European ancestry populations. CONCLUSIONS: We conclude that the IPF risk loci in East Asian populations are shared with those of European ancestry populations, although their risk allele frequencies and effect sizes differ. These findings indicate shared genetic risk factors of IPF across ancestries.

Aged↗

PubMed2026

Differences in structural color and population genetic structure of Western and Central Palearctic Polyommatus icarus populations.

The blue structural coloration of male Polyommatus icarus butterflies functions as a sexual signaling trait and exhibits remarkable spectral stability within populations despite being generated by highly complex photonic nanoarchitectures. The correlation of the blue sexual signaling color and population genetic variation of the butterflies was investigated across the Western and Central Palearctic regions. Dorsal wing reflectance spectra was measured for 95 male specimens and compared with the population genetic structure revealed in 99 specimens by 18 recently developed microsatellites. Reflectance measurements indicated a clear separation between the European and Central Asian populations, consistent with our previous findings, while the intermediate populations near the Ural Mountains exhibited distinct European spectral characteristics. In contrast, genetic variation showed limited structuring and correlated primarily with geographic distance, as indicated by a significant isolation-by-distance pattern. Thus, although both reflectance and genetic variations are geographically structured, spectral properties are only weakly correlated with genetic differentiation. Populations near the Ural Mountains exhibited genetic ancestry linked to Central Palearctic groups, while displaying distinct Western Palearctic coloration, suggesting that the focal species' sexual signaling is strongly influenced by local factors. These findings suggest that sexual signaling coloration may evolve at least partially independently of the neutral genetic background, offering additional insight into evolutionary divergence across broad geographic scales.

Animals↗

PubMed2025

Pervasive fitness trade-offs revealed by rapid adaptation to shifting population densities in large experimental populations of Drosophila melanogaster.

Trade-offs are an inherent feature of organismal biology that are expected play a fundamental role in the evolution of natural populations. Efforts to quantify trade-offs are largely confined to phenotypic measurements and the identification of negative genetic-correlations among fitness-relevant traits. Here, we use time-series genomic data collected during experimental evolution in large, genetically diverse populations of Drosophila melanogaster to directly measure the manifestation of trade-offs in response to fluctuating selection on ecological timescales. Specifically, we first conducted a lab-based selection experiment to quantify a genome-wide signal of antagonistic pleiotropy elicited in response to shifting population densities and associated with reproduction and stress tolerance selection. In doing so, we identified a putative role of two cosmopolitan inversions in these trade-offs. We then conducted an independent experiment to show that a simple manipulation of increasing population density under controlled lab-based conditions identified loci that are relevant to selection during population expansion and collapse in a complex, semi-natural setting. In concert, our results reveal how adaptation in complex, natural environments can be coarse-grained in such a manner to drive repeatable and predictable patterns of genomic variation, and further add credence to models positing a role of generic fitness trade-offs in the maintenance of variation in natural populations.

Drosophila melanogaster↗

PubMed2024

Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia.

The genetic identification of evolutionary significant units and information on their connectivity can be used to design effective management and conservation plans for species of concern. Despite having high dispersal capacity, several seabird species show population structure due to both abiotic and biotic barriers to gene flow. The Kelp Gull is the most abundant species of gull in the southern hemisphere. In Argentina it reproduces in both marine and freshwater environments, with more than 100,000 breeding pairs following a metapopulation dynamic across 140 colonies in the Atlantic coast of Patagonia. However, little is known about the demography and connectivity of inland populations. We aim to provide information on the connectivity of the largest freshwater colonies (those from Nahuel Huapi Lake) with the closest Pacific and Atlantic populations to evaluate if these freshwater colonies are receiving immigrants from the larger coastal populations. We sampled three geographic regions (Nahuel Huapi Lake and the Atlantic and Pacific coasts) and employed a reduced-representation genomic approach to genotype individuals for single-nucleotide polymorphisms (SNPs). Using clustering and phylogenetic analyses we found three genetic groups, each corresponding to one of our sampled regions. Individuals from marine environments are more closely related to each other than to those from Nahuel Huapi Lake, indicating that the latter population constitutes the first freshwater Kelp Gull colony to be identified as an evolutionary significant unit in Patagonia.

Humans↗

PubMed2026

Recovering the precolonial population structure of Khoe-San descendant populations.

San populations from Botswana and Namibia retain exceptional linguistic, cultural, and genetic diversity, but few Khoisan-speaking groups remain south of the Kalahari Desert. However, historically, far southern Africa was home to many San and Khoekhoe groups. Popular opinion often implies that such populations do not contribute to the ancestry of contemporary South Africans. Here, we characterize the genetic ancestry of self-identified South African Coloured groups and reconstruct precolonial and colonial population structures from 620 newly sampled individuals. These groups retain the majority of Khoe-San genetic ancestry (>48%), suggesting the persistence of Khoe-San ancestry to the present day. By isolating the Khoe-San ancestry component, we show that it is intermediate between the ≠Khomani San and Nama and distinct from Kalahari Khoe-San populations. We also find that signatures of the Indian Ocean slave trade can be traced to Indonesian islands such as Sulawesi, Java, and Flores, while the South Asian ancestry is regionally nonspecific.

Humans↗

PubMed2026

Mitochondrial genome-derived microsatellites reveal genetic diversity and population structure in Callery pear populations.

Callery pear (Pyrus calleryana Decne.; PC) possesses many desirable characteristics valued in managed landscapes. This has driven the release of numerous cultivars, including both hybrids and selections derived from native populations. The extensive planting of PC cultivars in managed areas has contributed to the widespread occurrence of invasive individuals across a broad range of habitats in the eastern United States (US). Self-incompatibility, tolerance to various environmental conditions, pathogen and pest resistance, intraspecific hybridization among the cultivars, possible interspecific hybridization with other Pyrus species, and seed dispersal by various vertebrates have contributed to the spread and persistence of PC across diverse environments. Because effective and environmentally appropriate management options remain limited, improved understanding of PC genetics may help inform management strategies. Previous studies have characterized PC diversity using nuclear genomic short sequence repeats (gSSRs), however, neither a mitochondrial genome resource nor mitochondrial short sequence repeats (mtSSRs) have been developed for this purpose. Here, we assembled a mitochondrial genome of 485,892 bp and used five mtSSRs to characterize mitochondrial diversity and population structure among accessions from the species' native range in Asia (n = 72), southeastern US escapees (SNesc; n = 90), Tennessee escapees (TNesc; n = 90), and US-released commercial cultivars (UScult; n = 69 representing 14 unique cultivars). We found a high genetic diversity (He = 0.728) and evidence of genetic structure in PC. In distance-based and multivariate analyses, UScult occupied an intermediate position between the Asian populations and the US escapees. The observed mitochondrial diversity among samples assigned to PC cultivars is consistent with a complex genetic landscape and may reflect distinct maternal lineages, cultivar-labeling or record-keeping discrepancies, and/or technical variation. This study underscores the need for broader genomic investigations using authenticated cultivar reference material and high-resolution nuclear markers to resolve cultivar ancestry, validate true-to-name identity, and inform species management.

Genetic Variation↗

PubMed2025

Peruvian Population Genomics: Unraveling the Genetic Landscape and Admixture Dynamics of Urban Populations.

Latin American populations exhibit high genetic and phenotypic diversity shaped by complex admixture histories, yet remain underrepresented in genomic research. Here, we analyze genome-wide data from 432 urban individuals across 13 regions of Peru, including 346 newly genotyped from the Peruvian Genome Project. We revealed fine-scale population structure and demographic patterns shaped by both ancient and recent events. Indigenous American ancestries in urban individuals trace back to ancient north-south interactions consisted with archaeological records, while admixture events occurring within the last 8-10 generations involved sources already admixed between distinct ancestral lineages. Identity-by-descent analyses reveal sustained gene flow in southern Peru, while effective population size trends highlight demographic stability in Lima over the past 25 generations. Sex-biased admixture patterns suggest Indigenous ancestry contribution preferentially mediated by females. These findings offer a comprehensive view of Peru's genetic heritage, advancing our understanding of human genetic diversity and historical demographic processes in Latin America.

Admixture↗

PubMed2025

Health conditions in adults with atrial fibrillation compared with the general population: a population-based cross-sectional analysis.

BACKGROUND: Atrial fibrillation (AF) prevalence is rising due to population ageing and comorbidity is an increasing problem. The aim of this study was to examine the prevalence and association of coexisting health conditions among adults with AF in the general population. METHODS: Cross-sectional analysis of Clinical Practice Research Datalink (CPRD) primary care electronic medical records in England linked to hospital admissions as of 30 November 2015. CPRD is broadly representative of the UK general population in terms of age, sex and ethnicity. We estimated prevalence and used logistic regression examining risk factors of age, sex and socioeconomic status (SES) to compare prevalence of 252 physical and mental health conditions and 23 higher level health condition groups in adults with AF compared with adults without AF. RESULTS: 34 338 adults with AF (57% male; 83% ≥65 years) and 907 739 without AF (49% male; 23% ≥65 years) were identified. Adjusted for age and sex, adults with AF were significantly more likely to have 20/23 (87%) health condition groups than adults without AF. The most prevalent health condition groups in adults with AF were cardiovascular (prevalence of 89% in adults with AF vs 26% in adults without AF, adjusted OR (aOR) 5.82, 95% CI 5.60 to 6.05), gastrointestinal (62% vs 37%, aOR 1.34, 95% CI 1.31 to 1.38) and orthopaedic (58% vs 24%, aOR 1.32, 95% CI 1.29 to 1.35). 151/252 individual conditions were significantly more common in adults with AF including cardiovascular conditions such as cardiomyopathy (4.5% vs 0.3%, aOR 9.58, 95% CI 8.88 to 10.35) and heart failure (18% vs 0.7%, aOR 9.07, 95% CI 8.70 to 9.46), and non-cardiovascular conditions such as pleural effusion (16% vs 1.8%, aOR 3.55, 95% CI 3.42 to 3.67) and oesophageal malignancy (0.3% vs 0.0%, aOR 2.14, 95% CI 1.69 to 2.70). Associations were similar after SES adjustment. CONCLUSIONS: While cardiovascular conditions are highly prevalent and strongly associated with AF, a wide spectrum of non-cardiovascular conditions were also strongly associated, requiring a greater understanding of managing comorbid conditions with management principles contradictory to AF.

Humans↗

PubMed2026

Genome-wide SNP-based genomic diversity and population structure analysis in alpaca populations from Europe and Peru.

This study aimed to analyze the genetic diversity and population structure of alpacas in Germany, Switzerland, and Austria (German-speaking regions, GSR) and to compare with that of the country of origin of the species (Peru). A total of 179 animals from GSR and 151 from Peru were genotyped with a species-specific 76k SNP array. The observed and expected heterozygosity was 0.305 and 0.311 for GSR and 0.310 and 0.312 for Peru. The mean FROH values were 0.029 for GSR and 0.023 for Peru. In general, results show that breeders in both analyzed regions efficiently maintain genetic diversity. Principal component analysis identified the GSR and Peru populations as separate from each other, but the relative proximity of both clusters indicates the shared genetic heritage. FST and XPEHH methods identified genomic regions under selection for traits such as coat color and adaptation. Genome-wide association studies comparing black and brown with white or gray alpacas identified associated genome regions containing the ASIP and KIT genes, respectively. The association of a recently identified keratin locus on chromosome 16 with differences in fleece type in alpacas was confirmed, while the putative causality of a TRPV3 variant was rejected.

Animals↗

PubMed2026

The Safety, Efficacy, and Feasibility of Fecal Microbiota Transplantation in a Population With Bipolar Disorder During Depressive Episodes: A Pilot Parallel Arm Randomized Controlled Trial: Sécurité, efficacité et faisabilité de la transplantation de microbiote fécal chez une population atteinte de troubles bipolaires, au cours d'épisodes dépressifs : essai pilote contrôlé à répartition aléatoire et à groupes parallèles.

BackgroundThe gut microbiome has been proposed as a potential modifiable target to treat mental illness. This double-blind randomized control trial investigated fecal microbiota transplant (FMT) in bipolar disorder (BD) to assess efficacy, safety, and feasibility. The primary outcome evaluated the effectiveness of standard approved therapy for BD depression + FMT in individuals not responding to standard treatment, measured by change in the Montgomery-Åsberg Depression Rating Scale (MADRS) score from baseline to week 24. Secondary outcomes included FMT's impact on anxiety, global function, side-effects, and safety. The feasibility of this novel intervention was also assessed. Microbial analysis utilized whole-genome shotgun metagenomic sequencing, comparing outcomes between allogenic (donor) and autologous (participants own) FMT.MethodsA total of 35 participants (28 women and 7 men) with at least moderate depressive-phase BD (MADRS) were randomized to receive either allogenic FMT (n = 17) or autologous FMT (n = 18) via colonoscopy and were followed for 24 weeks.ResultsMADRS scores significantly improved from baseline to the last visit in both treatment arms. There was no significant difference between allogenic FMT (16.74-point improvement) and autologous FMT (15.4-point improvement) regarding clinical efficacy (t = -0.47, p-value = .64, 95% confidence interval [CI] = -7.3-4.6). Microbiota analysis showed that allogenic FMT let to a bacterial profile similar to the healthy donor and increased bacterial diversity at the 6-month mark, whereas those receiving autologous FMT did not. The intervention was well tolerated with no significant adverse events. Recruitment, randomization, and retention metrics support feasibility of a larger trial.ConclusionFeasibility and tolerability data indicate further investigation into microbial manipulation in BD is warranted. The absence of efficacy differences between the two types of FMT, despite microbial change, highlights the importance of a true placebo in future studies, as well as the importance of understanding exactly what bacteria are linked to improvements. ClinicalTrials.gov, NCT0327922Plain Language Summary TitleResults of a Double-Blind Randomized Control Trial Investigating Fecal Microbiota Transplant (FMT) as an Add-on Treatment for Depression in Bipolar Disorder and Analyzing Microbial Diversity Changes Over 24 Weeks.

Humans↗

PubMed2026

Weathering the storm: Most maternal and environmental drivers of individual reproductive success do not scale up to population recruitment in a large herbivore.

Population growth depends upon individual survival and reproduction, but do drivers of individual reproductive success scale up to population recruitment? Factors affecting individuals may have little effect on population dynamics if individuals within a population experience different conditions. When seasonal resource availability is unpredictable and breeding season long, average conditions over a breeding cycle may poorly reflect the environment experienced by many individuals. We compared the drivers of individual reproductive success and population recruitment in an asynchronously breeding large herbivore, the eastern grey kangaroo (Macropus giganteus). We analysed 18 years of individual-based data using multivariate hierarchical Bayesian models to first identify the causal mechanisms relating population density, environmental conditions and maternal traits to individual success. We then assessed whether the drivers of individual reproductive success scaled up to determine population recruitment. Most maternal and environmental covariates strongly influenced individual reproductive success, with distinct effects on juvenile survival before and after pouch exit. Maternal traits had a greater influence in the pouch, whereas environmental conditions became increasingly important once young exited the pouch. Most drivers of individual reproductive success did not affect population recruitment. Recruitment increased with population density and mean body condition of adult females. Weather harshness had a weak positive effect on recruitment, which appeared independent of female age structure, previous recruitment or forage. Most drivers of individual reproductive success did not scale up to population recruitment. Birth asynchrony could buffer population recruitment against environmental variation such that variables affecting individual reproduction have little impact at the population level. Large herbivores that reproduce asynchronously may therefore be more resilient to environmental variability than synchronous breeders.

Bayesian modelling↗

PubMed2026

Genomic consequences of admixture in an experimentally founded sand lizard population.

Conservation interventions are increasingly required for species threatened by population declines and isolation due to anthropogenic pressures. Small, isolated populations are particularly vulnerable to the loss of genetic diversity, increased inbreeding, and the accumulation of deleterious mutations. Translocations or supplementation of allopatric individuals for genetic rescue may be the only way to increase genetic diversity and increase population persistence via increased adaptive potential. Here, we use an experimentally admixed population of sand lizards on a small island in Sweden as a valuable model of genetic rescue. This population was established approximately 20 years ago (5-6 generations), resulting in increased fecundity and hatchling viability. This population was founded from crossings between individuals from an inbred population from the nearby mainland and individuals sourced from populations in southern Sweden. Low-coverage whole-genome sequencing revealed elevated genetic diversity and reduced realized genetic load in this admixed population relative to the source populations. Ancestry analyses indicated a greater contribution of southern Swedish genetic variation, potentially reflecting the contribution of beneficial adaptive variation from this region that may underlie the positive population effects. This system provides valuable empirical insights into the long-term genomic consequences of genetic rescue in this model vertebrate population.

Journal Article↗

PubMed2026

Genetic rescue stabilizes diversity in small isolated populations of Bonneville cutthroat trout.

Genetic diversity loss due to anthropogenic factors is occurring rapidly on a global scale, putting many species at risk of extirpation and extinction. Different management strategies have been developed to slow this loss; however, it is often unknown whether these strategies reach their intended goals. In this study, we evaluate population structure and changes in nucleotide diversity (π) in isolated populations of Bonneville cutthroat trout (Oncorhynchus clarkii utah) from the Snake Range (Nevada, USA). Starting in the 1990s, three of these populations were used to reestablish populations in the Snake Range because many of the historic populations were extirpated. Some populations were stocked using a single-source and others were stocked using multiple-sources. Using low-coverage whole-genome sequencing coupled with historic samples (2003-2010) and contemporary samples (2019-2022), we find that single-source populations lost nucleotide diversity while mixed-source populations maintained nucleotide diversity. Further, source populations used to restore populations throughout the Snake Range lost the most nucleotide diversity over the time span evaluated. Our findings provide insight into how small, isolated populations can be managed to maintain genetic diversity.

Animals↗

PubMed2026

Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data.

The rhesus macaque (Macaca mulatta) is one of the most widely used animal models in biomedical research, both as it resembles humans in key biological aspects and as it is characterized by a broad geographic range. Most of the individuals housed in U.S. research colonies have been sampled from either China or India, though notably the source population of these animals has significantly shifted over time. Given the substantial genetic and immunological differences between these populations, a deeper understanding of the underlying population structure is critically important for biomedical interpretation. Despite this, the demographic histories of these two populations remain poorly resolved. Here, we present an analysis of whole-genome, PacBio HiFi long-read sequencing data from ten unrelated individuals of each population, applying four related model- and non-model based demographic inference approaches, in order to reconstruct their ancestral history. We evaluated the fit of the subsequently estimated models against the empirical data, and incorporated underlying uncertainty in the mutation rates used for scaling. We inferred a well-fitting population history characterized by substantial structure between Chinese and Indian populations, with a split time ∼140,000 generations ago from an ancestral population of ∼65,000 individuals. We additionally inferred the subsequent history of size change within, and gene flow between, these populations, reaching the current estimated sizes of ∼220,000 individuals in the Chinese population and ∼14,000 individuals in the Indian population. The robust baseline demographic model established in this study will serve as a valuable resource for future research on this species, including for improved fine-scale recombination mapping, selection inference, and association studies.

Cercopithecidae↗

PubMed2025

Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.

Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a population's ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusc-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, host-associated symbiont populations exhibited a notable decrease in genomic variation, including potential loss of certain habitat-specific strains. However, detection of environmental sequences resembling mollusc symbionts suggests that lost host-associated symbiont diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and pre-existing levels of connectivity, although the full extent of population bottlenecks in the host animals might only be recognisable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to both natural and anthropogenic impacts.

Animals↗

PubMed2025

Conservation genomics of a threatened subtropical Rhododendron species highlights the distinct conservation actions required in marginal and admixed populations.

With the impact of climate change and anthropogenic activities, the underlying threats facing populations with different evolutionary histories and distributions, and the associated conservation strategies necessary to ensure their survival, may vary within a species. This is particularly true for marginal populations and/or those showing admixture. Here, we re-sequence genomes of 102 individuals from 21 locations for Rhododendron vialii, a threatened species distributed in the subtropical forests of southwestern China that has suffered from habitat fragmentation due to deforestation. Population structure results revealed that R. vialii can be divided into five genetic lineages using neutral single-nucleotide polymorphisms (SNPs), whereas selected SNPs divide the species into six lineages. This is due to the Guigu (GG) population, which is identified as admixed using neutral SNPs, but is assigned to a distinct genetic cluster using non-neutral loci. R. vialii has experienced multiple genetic bottlenecks, and different demographic histories have been suggested among populations. Ecological niche modeling combined with genomic offset analysis suggests that the marginal population (Northeast, NE) harboring the highest genetic diversity is likely to have the highest risk of maladaptation in the future. The marginal population therefore needs urgent ex situ conservation in areas where the influence of future climate change is predicted to be well buffered. Alternatively, the GG population may have the potential for local adaptation, and will need in situ conservation. The Puer population, which carries the heaviest genetic load, needs genetic rescue. Our findings highlight how population genomics, genomic offset analysis, and ecological niche modeling can be integrated to inform targeted conservation.

Rhododendron↗