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Results for “genetics”

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bioRxiv2025

Optimization of crossing strategy based on the usefulness criterion in inter-population crosses considering different genetic effects among populations

In the breeding programs of self-pollinated plants, achieving genetic improvement in multiple traits can be challenging when relying solely on a single biparental population. Interpopulation crosses are employed to integrate favorable alleles from multiple biparental populations to overcome this limitation. In this context, it is crucial to consider the distinct genetic effects in different populations. In this study, we utilized a selection method based on the usefulness criterion (UC) to identify cross pairs suitable for interpopulation crosses. We expanded this approach to enhance breeding programs accounting for varying genetic backgrounds within the genomic selection framework. Using the medicinal plant red perilla as the study material, we conducted simulations to compare the efficacy of selection based on estimated genomic breeding values with that based on UC. Our findings demonstrate that the proposed method is effective in facilitating the simultaneous improvement of multiple traits, particularly by considerably increasing genetic gains among the top-performing individuals in the population. Furthermore, we provide guidelines for implementing interpopulation crosses, including recommendations for the optimal generation for crossing and the appropriate reference generation for calculating the UC. The results obtained in this study offer valuable insights for small-scale breeding programs aimed at simultaneously enhancing multiple traits through inter-population crosses and are applicable to a wide range of crops, including neglected and underutilized species. Key MessageHerein, a method has been proposed for selecting optimal cross pairs based on the genetic potential of progeny in inter-population crosses, considering different genetic effects among populations.

bioinformatics↗

bioRxiv2025

Ancient DNA indicates 3,000 years of genetic continuity in the Northern Iranian Plateau, from the Copper Age to the Sassanid Empire

In this study, we present new ancient DNA data from prehistoric and historic populations of the Iranian Plateau. By analysing 50 samples from nine archaeological sites across Iran, we report 23 newly sequenced mitogenomes and 13 nuclear genomes, spanning 4700 BCE to 1300 CE. We integrate an extensive reference sample set of previously published ancient DNA datasets from Western and South-Central Asia, enhancing our understanding of genetic continuity and diversity within ancient Iranian populations. A new Early Chalcolithic sample, predating all other Chalcolithic genomes from Iran, demonstrates mostly Early Neolithic Iranian genetic ancestry. This finding reflects long-term cultural and biological continuity in and around the Zagros area, alongside evidence of some western genetic influence. Our sample selection prioritizes northern Iran, with a particular focus on the Achaemenid, Parthian, and Sassanid periods (355 BCE-460 CE). The genetic profiles of historical samples from this region position them as intermediates on an east-west genetic cline across the Persian Plateau. They also exhibit strong connections to local and South-Central Asian Bronze Age populations, underscoring enduring genetic connections across these regions. Diachronic analyses of uniparental lineages on the Iranian Plateau further highlight population stability from prehistoric to modern times.

genomics↗

bioRxiv2025

Whole genome sequencing reveals how plasticity and genetic differentiation underlie sympatric morphs of Arctic charr

Salmonids have a remarkable ability to form sympatric morphs after postglacial colonization of freshwater lakes. These morphs often exhibit differences in morphology, feeding, and spawning behaviour. Here we explore the genetics of morph differentiation by establishing a high-quality, annotated reference genome for the Arctic charr and use this as a resource for population genomic analysis of morphs from two Norwegian and two Icelandic lakes. The four lakes represent the spectrum of genetic differentiation between morphs from one lake with no genetic differentiation between morphs, implying phenotypic plasticity only, to two lakes with locus-specific genetic differentiation, implying incomplete reproductive isolation, and one lake with strong genome-wide divergence consistent with complete reproductive isolation. As many as 12 putative inversions ranging from 0.45 to 3.25 Mbp in size segregated among the four morphs present in one lake, Thingvallavatn, and these contributed significantly to the genetic differentiation among morphs. None of the putative inversions was found in any of the other lakes, but there were cases of partial haplotype sharing in similar morph contrasts in other lakes. The results are consistent with a highly polygenic basis of morph differentiation with limited genetic parallelism between lakes. The results support a model where morph differentiation is usually first established due to phenotypic plasticity that results in niche expansion and separation, followed by gradual development of reproductive isolation and locus-specific differentiation and eventually complete reproductive isolation and genome-wide divergence. A major explanation for salmonids ability to diversify into multiple sympatric morphs is likely the genome complexity caused by their ancient whole genome duplication that enhances evolvability.

evolutionary biology↗

bioRxiv2025

Plant genetic and root-associated microbial diversity modulate Lactuca sativa responsiveness to a soil inoculum under phosphate deficiency

O_LIMicrobial-based approaches have been proposed as a solution to decrease the use of chemical fertilizers in agriculture. Among these, the most promising candidates are arbuscular mycorrhizal fungi (AMF), with their ability to extend the root surface and absorb phosphate, and phosphate solubilizing bacteria (PSB), but their effectiveness has been shown to depend on plant genetic diversity. C_LIO_LIWith the aim of identifying genetic markers explaining plant differential responses to soil-beneficial microbes, we monitored a panel of 128 fully sequenced varieties of Lactuca sativa under controlled P starvation conditions, treated with AMF and PSB. C_LIO_LIResults showed a strong effect of the lettuce genetic variation on the plant physiological and morphological response to the inoculum. Through genome-wide association studies, we identified specific genetic regions associated with variations in leaf phosphate and shoot biomass in response to the treatment. C_LIO_LIBeyond genetic factors, we detected changes in fungal {beta}-diversity and increases in bacterial -diversity associated with phenotypic variation, and we identified 44 ASVs linked to variation in agriculturally important traits. Among these, we experimentally validated the role of six bacterial strains through both in vitro and pot experiments, in affecting the leaf phosphate concentration and plant shoot biomass. C_LIO_LIIn conclusion, we highlighted key genetic and physiological mechanisms that could play a crucial role in enhancing microbial treatments for optimizing plant phosphate management. C_LI

plant biology↗

bioRxiv2025

Unbiased genetics identifies a glutamatergic signaling network as a mediator of daily sleep patterns.

Sleep is a fundamental, conserved behavior important for survival. In many species, sleep behavior is controlled by poorly understood interactions between a system of circadian rhythms (CR), which promote sleep at ecologically appropriate times, and a homeostatic sleep drive that accumulates with time awake. The CR is a cellular phenomenon, driven by molecular oscillations of "clock genes" in nearly all cells. Emerging evidence indicates neuronal synapses are a key locus for the accumulation and resolution of sleep need, supporting a cellular basis of sleep need. Indeed, efforts to understand the genetic basis of sleep need identified Homer1a, a regulator of synapse homeostasis. To develop further insight into the genetic basis of sleep regulation, we measured daily sleep patterns in genetically diverse strains of mice from the Collaborative Cross. Strains with 1) highly consolidated light-phase sleep, or 2) fragmented, arrhythmic sleep, were identified for genetic analysis using quantitative trait loci (QTL) mapping. Excitingly, in F2 hybrids, 19 of 32 metrics of sleep and circadian behavior mapped to a narrow QTL containing GRM5, a postsynaptic glutamate receptor and binding partner of Homer1a, and GCPII, an astrocytic enzyme that regulates NAAG, a peptide agonist for the presynaptic/astrocytic glutamate receptor GRM3. Collectively, these genes form a coordinated glutamatergic signaling network across the tri-partite synapse. Pharmacology targeting GRM5, GCPII, and GRM3 strongly modulated sleep, functionally validating them as sleep-regulating genes. Our findings support a model in which synapses act as a cellular site for integration of circadian and sleep-need signals to regulate daily sleep patterns. Significance StatementSleep is a fundamental pillar of human health. Restorative sleep is supported by circadian rhythms (CR). Sleep and CR disruptions are prevalent in neuropsychiatric conditions and are increasingly understood as causal drivers of altered brain function and behavior. Therefore, sleep and CR are attractive therapeutic targets to improve health. However, the basic biological mechanisms that couple our need to sleep with the CR are not understood. Genetic discovery using diverse strains of mice identifies a glutamatergic signaling network coordinated across the synapse as an underlying genetic basis for daily sleep patterns. This work builds upon a growing body showing that excitatory synapses are a cellular site for the resolution of sleep need and interaction with the CR.

neuroscience↗

bioRxiv2025

Distinguishing Specific from Broad Genetic Associations between External Correlates and Common Factors

Within the Genomic SEM framework, common factors are often used to index shared genetic etiology across constellations of GWAS phenotypes. A standard common pathway model, in which a genetic association is estimated between an external GWAS phenotype and a common factor, assumes that all genetic associations between the external GWAS phenotype and the individual indicator phenotypes are mediated through the factor. This assumption can be tested using the QTrait statistic, which compares the common pathway model to an independent pathways model that allows for direct genetic associations between the external GWAS phenotype and the individual indicators of the factor. We expand upon the QTrait approach by describing an effect size index that quantifies the degree to which the common pathways model is violated, and we provide a systematic approach for empirically identifying specific direct pathways between an external trait and indicator traits. Our method comprises a series of omnibus tests and outlier detection algorithms indexing the heterogeneity of associations between the genetic component of external traits and the individual indicators of common factors. We provide a set of automated functions which we apply to investigate the patterns of genetic associations across a set of external correlates with respect to indicators of general cognitive ability and case-control and proxy GWAS indices of Alzheimers disease.

genomics↗

bioRxiv2025

Neurodevelopmental Impact of Bipolar Disorder Genetic Risk on Cortical Thickness and Network Topology in Adolescents

Bipolar disorder (BD) is a highly heritable psychiatric condition characterized by recurrent mood episodes that commonly manifest during adolescence. Although polygenic risk scores (PRS) effectively quantify genetic susceptibility to BD, the neurobiological correlates of this genetic risk during adolescent brain development remain unclear. Using normative modeling and longitudinal neuroimaging data from the Adolescent Brain Cognitive Development (ABCD) cohort (N = 4519), we examined cortical thickness (CT) deviations and structural covariance network (SCN) alterations in adolescents stratified into high and low BD genetic risk groups based on PRS. Adolescents with high PRS for bipolar disorder exhibited greater cortical thickening in the inferior frontal gyrus and primary visual cortex, whereas those with low PRS demonstrated greater thickening in the posterior cingulate cortex and middle precentral gyrus. These patterns suggest PRS-related variations in cortical maturation, potentially reflecting distinct neurodevelopmental trajectories associated with genetic susceptibility to bipolar disorder. Furthermore, high PRS individuals displayed altered SCN topology, characterized by decreased local clustering and enhanced global network efficiency. Longitudinal data show that these abnormal regions exhibit atypical developmental trajectories, accompanied by a global reorganization of network topology. Additionally, high genetic risk was associated with lifestyle factors, especially correlated with increased positive expectancies toward substance use. Eventually, we found three potential BD risk genes during adolescence, including PLEKHA2, ZSCAN31 and ANK3, encoding the function of the postsynaptic membrane and synaptic membrane. These findings elucidate early neurodevelopmental deviations linked to genetic risk for BD, highlighting potential biomarkers for early identification and targeted interventions.

neuroscience↗

bioRxiv2025

The genetic consequences of dispersal and immigration in a wild great tit population

Understanding how dispersal impacts the genetic makeup of populations is essential for predicting their responses to environmental change. Gene flow--via within-population dispersal and external immigration--shapes population health and evolutionary potential by boosting genetic diversity, but it can also counteract local adaptation. We investigate these processes in a population of great tits (Parus major) in Wytham Woods, United Kingdom. This system represents a large, continuous population of a vagile, widely distributed species. Using a comprehensive social pedigree alongside genomic data from two genomic datasets, one with 949 individuals genotyped at ~600,000 SNPs and another with 2,644 individuals at ~10,000 SNPs, we observe some spatial genetic structure largely driven by the spatial and temporal clustering of close kin. We quantify how temporally persistent this pattern is and find similar levels of decay of relatedness with distance across years, without a consistent genetic basis, which is frequently renewed due to high population turnover. Immigrants make up a substantial portion of the breeding population, yet are often assumed to be genetically distinct, unrelated, and outbred--assumptions that can bias population inferences. We show that immigrants are indeed outbred, as are local birds; have fewer close relatives within the population, and are less likely to be related to their neighbours than locally born birds. Despite low FST and no clear genome-wide population structure, immigrants and locals can be distinguished above chance using a Random Forest classifier trained on SNP data. Our study highlights the complex interplay between dispersal, population turnover and spatial population structure, and suggests that great tits in Wytham Woods experience substantial gene flow within the population and from immigrants, maintaining high genetic diversity and reducing the possibility of local adaptation at this spatial scale.

evolutionary biology↗

bioRxiv2025

Genetic variation in life-history traits is not correlated with estrogen-receptor positive breast cancer risk

Estrogen receptor-positive breast cancer (ER+ BC) is one of the most prevalent cancers, but the evolutionary processes shaping genetic variation in ER+ BC risk are poorly understood. Both evolutionary life-history theory and evidence from studies of individual ER+ BC risk variants suggest that increased genetic ER+ BC risk is associated with faster maturation, earlier reproduction, and/or increased reproductive success (i.e., there is a trade-off), but it is unclear how well this pattern is replicated when considering the polygenic architecture of these traits after controlling for potential biases. Here, we estimate genome-wide genetic correlations between ER+ BC risk and three reproductive traits (age at menarche, age at first birth, and the number of children) using genomic restricted maximum-likelihood analyses on Lifelines biobank data and linkage disequilibrium score regressions on population and family-based genome-wide association study data. Regardless of the data or method used, genetic correlations were low and not statistically significant. Further analyses decomposing genome-wide genetic variance into local regions detected only three loci exhibiting significant pleiotropy between ER+ BC risk and age at menarche, suggesting little shared genetic architecture between ER+ BC risk and reproductive traits. Thus, the role of life-history trade-offs in shaping ER+ BC risk in European populations appears, at most, small, and the evolutionary processes giving rise to this life-threatening disease remain unclear. Future studies could examine the impact of evolutionary mismatches in shaping ER+ BC risk, where conducting longitudinal studies on populations transitioning to reproductive patterns observed in contemporary European populations would be most useful.

evolutionary biology↗

bioRxiv2025

Genetic load proxies do not predict fitness better than inbreeding does in a wild population

A key goal in conservation is managing endangered populations in order to maximise individual and population fitness. Genetic management that reduces inbreeding and increases genetic diversity has been consistently successful, but recent attention has been drawn to managing genetic load instead. We investigated whether genetic load proxies based on evolutionary conservation predict individual fitness better than inbreeding does. We re-sequenced the genomes of 43 wild helmeted honeyeaters with lifetime fitness data, and 28 individuals of other subspecies. None of the 28 genetic load proxies we tested predicted lifetime reproductive success better than three inbreeding metrics did, and different load proxies were inconsistent regarding the occurrence of purging or accumulation of deleterious alleles. Genetic load proxies need further validation as fitness indicators for conservation management.

genomics↗

bioRxiv2025

Efficient amplicon panels for evaluating hybridization and genetic structure in the Schistosoma haematobium species group

Genetic markers for detecting hybridization and measuring population genetic parameters must be informative and cost-effective. Most population genetic studies within the Schistosoma haematobium species group rely on either a two-marker system consisting of the mitochondrial, cytochrome oxidase 1 (cox1) and the nuclear internal transcribed spacer (ITS) markers or, at the other extreme, millions of single nucleotide variants (SNVs) from whole genome/exome sequencing. cox1 and ITS studies contain minimal population genetic information but whole genome sequencing is cost-prohibitive. We examined [~]38 million previously published, whole genome SNVs genotyped in 162 S. haematobium and S. bovis sampled across Africa. We compared population genetic parameters from 4,000 panels of 10-100,000 randomly sampled SNVs to results from the whole genome dataset to test the resolution of reduced representation sequencing in schistosomes. We found that panels of 500 SNVs captured >99% of the population genetic information contained in the whole genome dataset by using Procrustes transformed principal component analyses and ancestry estimates (r{superscript 2} = 0.85). Additionally, the costs of genotyping parasites with an amplicon panel is two to three times less than whole genome sequencing. Our results show that moderately-sized amplicon panels targeting random SNVs provide an efficient approach to large scale, field-based schistosome surveillance.

evolutionary biology↗

bioRxiv2025

sox17 mutagenesis reveals microglia can be impacted by genetic maternal effects

Embryonic development is precisely shaped by maternal and zygotic factors. These maternal factors exert their influence through maternal effects, a phenomenon where an offsprings phenotype is determined, at least in part, by the mothers environment and genotype. While environmental maternal effects can cause phenotypes that present both early and later in life, genetic maternal effects generally induce phenotypes in the earliest embryonic stages. Here, we reveal a genetic maternal effect that influences the development of cells that arise after early embryogenesis, highlighting that specific cell types can be susceptible to late-onset genetic maternal effects. Using zebrafish to study microglia, the resident immune cells of the brain, we identified a mutation in sry-related HMG box gene-17 (sox17) that exhibits a maternal effect phenotype that presents as a reduction of microglia in the brain and precursors in the yolk sac. We demonstrate that sox17 is expressed in microglia and their yolk sac precursors and is maternally-loaded. We show that sox17 restoration via embryonic injection reverses the maternal effect on microglia and yolk sac cells in sox17 mutants. To identify additional genes interacting with sox17, we nominated genes from scRNA sequencing analysis of mouse embryonic microglia to perform a genetic screen using CRISPR mutagenesis and a custom-built robot that captures confocal images of the zebrafish brain in high-throughput. This screen identified f11r.1, gas6, and mpp1 as modifiers of microglia abundance in the embryonic brain, which we demonstrated are also expressed in zebrafish microglia. Transcriptional and mutant analyses with these new modifiers suggest that sox17 positively regulates mpp1 transcription. These results demonstrate that microglia are susceptible to genetic maternal effects, in addition to their known sensitivity to environmental maternal effects. Our findings reveal a late-onset phenotype associated with the maternal genotype, expanding the recognized impact of genetic maternal effects beyond initial embryo viability and into long-term vigor.

neuroscience↗

bioRxiv2025

Investigation of the molecular-genetic basis for courtship differences between Drosophila melanogaster, Drosophila simulans and their hybrids

Understanding the mechanisms driving behavioral evolution enhances our knowledge of speciation and how behavioral potentials are genetically encoded. Male courtship behaviors, which evolve rapidly, are critical for pre-mating isolation. To investigate the genetic basis of species-specific courtship, we generated hybrid males by crossing two Drosophila melanogaster strains with D. simulans Lhr males. This design allowed us to assess how genetic background and female species identity influence male courtship behavior. In both single-pair and mate-choice assays, hybrid males displayed behavioral plasticity, adjusting their courtship strategies based on the female species. The maternal D. melanogaster strain significantly shaped hybrid behavioral repertoires. To identify the neural correlates, we examined fruitless (fru)-expressing neurons in hybrids. Their projection patterns resembled those in D. melanogaster, indicating conserved circuit architecture. Using CUT&Tag, we identified FruM target genes in both species, revealing conserved core and species-specific FruM targets. Focusing on chemosensory receptors with D. melanogaster-specific FruM binding, we conducted a genetic screen in D. melanogaster, silencing neurons co-expressing fru P1 and specific receptor genes. Courtship preference assays identified three additional olfactory receptor neuron subtypes that modulate species-specific behavior. Using trans-Tango, we mapped second-order projection neurons of these subtypes, revealing their targets in higher-order brain centers. This study uncovers new molecular and neural mechanisms underlying the specification and evolution of courtship behavior, highlighting how genetic and sensory inputs shape species-specific behavioral outcomes. Article SummaryWe examined how genes and circuits shape courtship behaviors in Drosophila melanogaster and Drosophila simulans. Hybrid males adjust their behavior based on the species of female, suggesting flexible courtship. We focused on the fruitless gene, which controls male courtship. fru neurons in hybrids closely resembled those in Drosophila melanogaster. We identified both shared and species-specific FruM target genes. A genetic screen of odorant receptor neurons revealed populations that help males distinguish females. Neuroanatomical mapping shows the odor information is relayed to different higher order brain regions. The results uncover molecular and neural circuit mechanisms underlying species differences in behaviors.

neuroscience↗

bioRxiv2025

The FORGENIUS genomic resources: new genotyping tools and genomic data for 23 forest tree species and their Genetic Conservation Units

Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is precisely aimed at increasing the quality and quantity of genetic data to start monitoring the European network of forest Genetic Conservation Units (GCUs). A first step in this direction was developing standardized genomic resources for 23 forest tree species, spanning from rare and scattered (e.g., Abies nebrodensis and Torminalis glaberrima) to widespread, economically relevant ones (e.g., Fagus sylvatica, Picea abies and Pinus sylvestris). Here, we describe the development and application of targeted genotyping tools, primarily based on Single Primer Enrichment Technology (SPET), along with existing SNP arrays for the selected species. The SPET panels developed in FORGENIUS were designed to capture {square}10,000 loci per species, balancing species-specific and randomly distributed regions to ensure broad genome coverage and minimize ascertainment bias. Across 7,192 genotyped trees, we identified over 1.8 million single nucleotide polymorphisms (SNPs) covering approximately 50 Mb of DNA sequence. SPET panels demonstrated high genotyping efficiency and cross-species transferability, especially within genera such as Quercus and Abies. They represent a cost-effective, flexible, and scalable solution for population-level genetic assessments across diverse taxa, enabling standardized, genome-wide characterization of the GCU network. These resources not only promote the establishment of genetic monitoring, support genetically informed conservation strategies and improve our understanding of adaptive responses in European forests, but also enhance species delimitation and hybrid detection, and enable the characterization of phylogenetically related but previously underexplored species.

genomics↗

bioRxiv2025

Host genetic background and social environment have different effects on the establishment and structure of the adult worker honey bee gut microbiota

Many studies have highlighted the importance of gut microbiomes to many aspects of host physiology. Therefore, understanding how factors, such host genetics and social environment, impact the establishment and composition of the gut microbiota can provide insight into host biological functioning. Here, we controlled the microbial inoculation of honey bees across distinct social groups, each composed of a mixture of bees from three distinct genetic backgrounds, to determine the relative effects of host genetic background and social environment on the establishment and composition of the gut microbiota. Using 16S rRNA gene sequencing, we found that host genetic background and social environment had effects on gut microbiota structure, with each influencing gut microbiota beta diversity. In addition, host genetic background and social environment each affected the abundance of different individual gut microbes. Together, these results suggest that host genetic background and social environment may play distinct roles in shaping the establishment and structure of host gut microbiota.

ecology↗

bioRxiv2025

A programmable genetic platform for engineering noninvasive biosensors

Creating genetic sensors for noninvasive visualization of biological activities in deep, optically opaque tissues holds immense potential for basic research and the development of genetic and cell-based therapies. MRI stands out among deep-tissue imaging methods for its ability to generate high-resolution images without ionizing radiation. However, the adoption of MRI as a mainstream biomolecular technology has been hindered by the lack of adaptable methods to link molecular events with genetically encodable MRI contrast. To address this challenge, we introduce universal reporter circuit-based activatable sensors (URCAS), a highly programmable platform for the systematic creation of genetic sensors for MRI. In developing URCAS, we engineered protease-activatable MRI reporters using two distinct approaches: protein stabilization and subcellular trafficking. We established the applicability of URCAS in five diverse mammalian cell types and showcased its versatility by assembling a toolkit of genetic sensors for viral proteins, small-molecule drugs, logic gates, protein-protein interactions, and calcium, without requiring new customization for each target. Our findings suggest that URCAS provides a modular, programmable platform for streamlining the development of noninvasive, nonionizing, and genetically encoded sensors for biomedical research and in vivo diagnostics.

bioengineering↗

bioRxiv2025

Simulated climate change magnifies genetic vulnerabilities from mutation load and maladaptation

As climate change intensifies, the genetic diversity and composition of natural populations will become critical for adaptation and survival. Standing genetic diversity within populations differs across a species range, due to past demographic and natural selection processes driving the accumulation of adaptive, neutral, and deleterious variation. While accumulating genomic knowledge could be used to evaluate population extinction risk from local mal-adaptive genetic makeups, testing such approaches in natural environments remains challenging. Leveraging the genomic resources of Arabidopsis thaliana, we created experimental synthetic populations of similar genetic diversity but differing genetic makeups by mixing 245 natural accessions with different levels of potentially-climate-adaptive alleles and/or genomic burden of deleterious mutations. We planted our populations in a climate change field experiment simulating a gradient of declining rainfall. By tracking survival and reproduction of 135 synthetic experimental populations over three years, we show substantial predictability of genetic makeup on survival and population growth rate. Further, the accumulation of deleterious mutations and locally (mal)adaptive alleles synergistically reduces fitness in increasingly stressful climates. Our findings underscore that for populations to have the greatest chance of surviving climate change, the optimal combination of genomic makeups is essential.

evolutionary biology↗

bioRxiv2025

Glacial history and landscape features shape the hierarchical population genetic structure of woodland caribou (Rangifer tarandus caribou) in western Canada

Caribou, listed as a species at risk across Canada, have experienced a wide range of evolutionary and selective pressures at multiple scales, from large-scale range shifts and recolonisations driven by glacial cycles to more localized contemporary habitat degradation and fragmentation. Given these multi-scale evolutionary forces, genetic variation and diversity are expected to be hierarchically structured. Characterising hierarchical population structure is crucial to understanding a species evolutionary history and informing effective conservation and management strategies. In this study, we analysed genomic diversity and variation in woodland caribou (Rangifer tarandus caribou) across western Canada using genotypes from [~]33,000 Single Nucleotide Polymorphism (SNP) loci from 759 geo-referenced individuals spanning 45 pre-defined subpopulations. We employed genetic clustering methods and measures of genetic differentiation to characterize hierarchical population structure in the region and tested for latitudinal changes in heterozygosity resulting from post-glacial recolonisation and hybridisation. Our results confirm that woodland caribou genetic diversity and differentiation occur at multiple hierarchical levels, reflecting post-glacial recolonisation patterns and landscape heterogeneity. Notably, the major genetic clusters identified in our study do not align with current conservation units for the species in this region. We also observe elevated heterozygosity in the mid-latitudes of the sampled range, indicative of hybridisation following secondary contact during post-glacial recolonisation. These findings underscore the need to consider and include genetic diversity at all hierarchical levels in conservation planning, as wide-ranging species often experience diverse and complex evolutionary histories and pressures.

evolutionary biology↗