Patterns Of Genetic Variation Research Articles

Seascape Genomics of Red Abalone: Limited Range-Wide Population Structure and Evidence for Local Adaptation.

Characterising patterns of genetic diversity including evidence of local adaptation is relevant for predicting and managing species recovering from overexploitation in the face of climate change. Red abalone (Haliotis rufescens) is a species of conservation concern due to recent declines from overharvesting, disease and climate change, resulting in the closure of commercial and recreational fisheries. Using whole-genome resequencing data from 23 populations spanning their entire range (southern Oregon, USA, to Baja California, MEX) we investigated patterns of population connectivity and genotype-environment associations that would reveal local adaptation across the mosaic of coastal environments that define the California Current System (CCS). We discovered high genetic diversity that is shared within and among populations, suggesting high historical range-wide gene flow. We found little evidence for large selective sweeps between populations that occupy local habitats that vary by pH, strength of upwelling, chlorophyll, salinity and sea surface temperature. This is consistent with a broad range of species with similar life histories that show limited neutral or adaptive genetic variation across the same region and the same environments, suggesting that the mosaic of environmental variation across the CCS is insufficient to drive local adaptation in the face of high gene flow for some broad-cast spawning species. Given the high genetic connectivity across their range, state-mandated regulatory actions would be most effective if aligned across jurisdictional boundaries (i.e., Mexico, California and Oregon).

Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada

Abstract The Wolverine (Gulo gulo) is a cold-adapted species of conservation interest because it is sensitive to human development, disturbance, exploitation, and climate warming. Wolverine populations have been studied across much of their distributional range to evaluate patterns of genetic diversity, genetic structure, and gene flow. Little population structure has been detected in northwestern North America with microsatellite loci, but low genomic diversity in wolverines may limit detection of genetic differences in this highly vagile species. Here, we genotyped a relatively large sample of wolverines from across Alaska (US) and adjacent Yukon (Canada) with 12 microsatellite loci (n = 501) and 4,222 single nucleotide polymorphisms (SNPs; n = 201) identified using restriction-site associated DNA sequencing. We compared the relative ability of our microsatellite and SNP datasets to evaluate population genetic structure, genetic diversity, differentiation, and isolation by distance (IBD). We predicted that the SNP dataset would detect a higher degree of genetic structure and provide more significant support for IBD. We found evidence for multiple genetic clusters, including genetic distinctiveness of wolverines in southeast Alaska and on the Kenai Peninsula. The SNP dataset detected additional genetic clusters that align largely with ecoregions, and the SNP dataset showed stronger evidence of IBD, while the 2 datasets were generally consistent in estimates of genetic diversity and differentiation among regional groups. Our results highlight the importance of genomic methods to assess gene flow in wolverines. Identifying population genetic structure allows an assessment of the potential impacts of conservation threats and is an important precursor for designing population monitoring programs.

Concordant Patterns of Population Genetic Structure in Food-Deceptive Dactylorhiza Orchids.

The patterns of inbreeding coefficients (FIS) and fine spatial genetic structure (FSGS) were evaluated regarding the mating system and inbreeding depression of food-deceptive orchids, Dactylorhiza majalis, Dactylorhiza incarnata var. incarnata, and Dactylorhiza fuchsii, from NE Poland. We used 455 individuals, representing nine populations of three taxa and AFLPs, to estimate percent polymorphic loci and Nei's gene diversity, which are calculated using the Bayesian method; FIS; FST; FSGS with the pairwise kinship coefficient (Fij); and AMOVA in populations. We detected a relatively high proportion of polymorphic fragments (40.4-68.4%) and Nei's gene diversity indices (0.140-0.234). The overall FIS was relatively low to moderate (0.071-0.312). The average Fij for the populations of three Dactylorhiza showed significantly positive values, which were observed between plants at distances of 1-10 m (20 m). FST was significant in each Dactylorhiza taxon, ranging from the lowest values in D. fuchsii and D. majalis (0.080-0.086, p < 0.05) to a higher value (0.163, p < 0.05) in D. incarnata var. incarnata. Molecular variance was the highest within populations (76.5-86.6%; p < 0.001). We observed concordant genetic diversity patterns in three food-deceptive, allogamous, pollinator-dependent, and self-compatible Dactylorhiza. FIS is often substantially higher than Fij with respect to the first class of FSGSs, suggesting that selfing (meaning of geitonogamy) is at least responsible for homozygosity. A strong FSGS may have evolutionary consequences in Dactylorhiza, and combined with low inbreeding depression, it may impact the establishment of inbred lines of D. majalis and D. incarnata var. incarnata.

Response of Pedunculate Oak (Quercus robur L.) to Adverse Environmental Conditions in Genetic and Dendrochronological Studies.

Pedunculate oak (Quercus robur L.) is widely distributed across Europe and serves critical ecological, economic, and recreational functions. Investigating its responses to stressors such as drought, extreme temperatures, pests, and pathogens provides valuable insights into its capacity to adapt to climate change. Genetic and dendrochronological studies offer complementary perspectives on this adaptability. Tree-ring analysis (dendrochronology) reveals how Q. robur has historically responded to environmental stressors, linking growth patterns to specific conditions such as drought or temperature extremes. By examining tree-ring width, density, and dynamics, researchers can identify periods of growth suppression or enhancement and predict forest responses to future climatic events. Genetic studies further complement this by uncovering adaptive genetic diversity and inheritance patterns. Identifying genetic markers associated with stress tolerance enables forest managers to prioritize the conservation of populations with higher adaptive potential. These insights can guide reforestation efforts and support the development of climate-resilient oak populations. By integrating genetic and dendrochronological data, researchers gain a holistic understanding of Q. robur's mechanisms of resilience. This knowledge is vital for adaptive forest management and sustainable planning in the face of environmental challenges, ultimately helping to ensure the long-term viability of oak populations and their ecosystems. The topics covered in this review are very broad. We tried to include the most relevant, important, and significant studies, but focused mainly on the relatively recent Eastern European studies because they include the most of the species' area. However, although more than 270 published works have been cited in this review, we have, of course, missed some published studies. We apologize in advance to authors of those relevant works that have not been cited.

Geographical patterns of intraspecific genetic diversity reflect the adaptive potential of the coral Pocillopora damicornis species complex.

Marine heatwaves are increasing in intensity and frequency however, responses and survival of reef corals vary geographically. Geographical differences in thermal tolerance may be in part a consequence of intraspecific diversity, where high-diversity localities are more likely to support heat-tolerant alleles that promote survival through thermal stress. Here, we assessed geographical patterns of intraspecific genetic diversity in the ubiquitous coral Pocillopora damicornis species complex using 428 sequences of the Internal Transcribed Spacer 2 (ITS2) region across 44 sites in the Pacific and Indian Oceans. We focused on detecting genetic diversity hotspots, wherein some individuals are likely to possess gene variants that tolerate marine heatwaves. A deep-learning, multi-layer neural-network model showed that geographical location played a major role in intraspecific diversity, with mean sea-surface temperature and oceanic regions being the most influential predictor variables differentiating diversity. The highest estimate of intraspecific variation was recorded in French Polynesia and Southeast Asia. The corals on these reefs are more likely than corals elsewhere to harbor alleles with adaptive potential to survive climate change, so managers should prioritize high-diversity regions when forming conservation goals.

Species-Specific Traits Shape Genetic Diversity During an Expansion-Contraction Cycle and Bias Demographic History Reconstruction.

Species ranges are dynamic, experiencing expansions, contractions or shifts in response to habitat changes driven by extrinsic factors such as climate change or human activities. While existing research examines the genetic consequences of spatial processes, few studies integrate species-specific traits to analyse how habitat changes affect co-existing species. In this study, we address this gap by investigating how genetic diversity patterns vary among species with different traits (such as generation length, population density and dispersal) experiencing similar habitat changes. Using spatial simulations and a simpler panmictic population model, we investigate the temporal genetic diversity in refugium populations undergoing range expansion of their habitat, followed by stationary and contraction periods. By varying habitat contraction speed and species traits, we identified three distinct temporal dynamics of genetic diversity during contraction: (i) a decrease in genetic diversity, (ii) an initial increase followed by a decrease and (iii) a continuous increase throughout the contraction period. We show that genetic diversity trajectories during population decline can be predicted by comparing sampled population diversity to equilibrium values expected under expanded and contracted habitat ranges. Our study also challenges the belief that high genetic diversity in a refugium population is due to a recent and rapid habitat loss. Instead, we found contrasting effects of contraction speed on genetic diversity depending on the interaction between species-specific traits and the dynamics of habitat change. Finally, using simulated genetic data, we found that demographic histories inferred from effective population size estimates may vary across species, even when they experience similar habitat changes.

Orchard: Building large cancer phylogenies using stochastic combinatorial search.

Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer, i.e., cancer phylogenies, offer valuable insights about cancer development and guide treatment strategies. Many methods exist that reconstruct cancer phylogenies using point mutations detected with bulk DNA sequencing. However, these methods become inaccurate when reconstructing phylogenies with more than 30 mutations, or, in some cases, fail to recover a phylogeny altogether. Here, we introduce Orchard, a cancer phylogeny reconstruction algorithm that is fast and accurate using up to 1000 mutations. Orchard samples without replacement from a factorized approximation of the posterior distribution over phylogenies, a novel result derived in this paper. Each factor in this approximate posterior corresponds to a conditional distribution for adding a new mutation to a partially built phylogeny. Orchard optimizes each factor sequentially, generating a sequence of incrementally larger phylogenies that ultimately culminate in a complete tree containing all mutations. Our evaluations demonstrate that Orchard outperforms state-of-the-art cancer phylogeny reconstruction methods in reconstructing more plausible phylogenies across 90 simulated cancers and 14 B-progenitor acute lymphoblastic leukemias (B-ALLs). Remarkably, Orchard accurately reconstructs cancer phylogenies using up to 1,000 mutations. Additionally, we demonstrate that the large and accurate phylogenies reconstructed by Orchard are useful for identifying patterns of somatic mutations and genetic variations among distinct cancer cell subpopulations.

Gretl-variation GRaph Evaluation TooLkit.

As genome graphs are powerful data structures for representing the genetic diversity within populations, they can help identify genomic variations that traditional linear references miss, but their complexity and size makes the analysis of genome graphs challenging. We sought to develop a genome graph analysis tool that helps these analyses to become more accessible by addressing the limitations of existing tools. Specifically, we improve scalability and user-friendliness, and we provide many new statistics tailored to variation graphs for graph evaluation, including sample-specific features. We developed an efficient, comprehensive, and integrated tool, gretl, to analyze genome graphs and gain insights into their structure and composition by providing a wide range of statistics. gretl can be utilized to evaluate different graphs, compare the output of graph construction pipelines with different parameters, as well as perform an in-depth analysis of individual graphs, including sample-specific analysis. With the assistance of gretl, novel patterns of genetic variation and potential regions of interest can be identified, for later, more detailed inspection. We demonstrate that gretl outperforms other tools in terms of speed, particularly for larger genome graphs. Commented Rust source code and documentation is available under MIT license at https://github.com/MoinSebi/gretl together with Python scripts and step-by-step usage examples. The package is available at Bioconda for easy installation.

Exploring genetic diversity in Indian ginger (Zingiber officinale Rosc.) through microsatellite markers

Ginger (Zingiber officinale Rosc.) holds significant value as a rhizomatous spice known for its distinct taste and aroma. India is the worlds' largest producer, exporter, and consumer of ginger. Local names commonly know many ginger cultivars, and since the crop is propagated vegetatively, the chances of mixing are very high. This complicates the maintenance of purity and distinct characteristics of each variety. In the present study, thirty-two ginger genotypes were procured from various regions nationwide and assessed using 49 SSR (Simple Sequence Repeats) markers to evaluate their genetic diversity patterns. Among the 49 markers, 19 primers were amplified and produced 23 polymorphic bands, resulting in a polymorphism percentage of 52.63%. Additionally, the unweighted pair group method (UPGMA) cluster analysis grouped the genotypes into five distinct clusters, with similarity coefficients ranging from 0.31 to 1.00. This suggests that each genotype exhibits substantial variability. Genotypes Maran and Acc. 581 showed a similarity value 1.00, indicating perfect similarity (100%) in their genetic characteristics. These findings emphasize the critical role of SSR markers in germplasm conservation and highlight the potential for utilizing genetic diversity in breeding programs to develop improved ginger varieties with desirable traits.

Genetic diversity, genotyping and evolutionary history of the global population of Orthotospovirus tomatomaculae genomic segments

AbstractTomato spotted wilt virus (Orthotospovirus tomatomaculae; TSWV) is a destructive pathogen that affects over 1000 plant species worldwide. To elucidate its evolutionary mechanisms, genetic diversity and emergence timeline, we examined around 100 TSWV isolates with complete genome sequences available in GenBank. This study also included the complete genome of a TSWV isolate, IRP4, which has recently been implicated in an outbreak affecting greenhouse‐grown bell peppers in Iran. Pairwise genetic divergence analysis revealed varying levels of genetic differences among TSWV RNA segments. Phylogenetic and sequence analysis determined that the global TSWV population consists of three major groups based on each of the three RNA segments (L, M, and S). Results suggested multiple introductions of the virus into different regions, indicating that the geographical origin of the isolates is not the sole factor determining their phylogenetic grouping. The large incongruences observed in the phylogeny of the TSWV segments and the analysis of genetic diversity patterns highlight extensive reassortment events in TSWV. As a result, 11 genotypes were identified within the TSWV population. The Iranian IRP4 isolate, along with nine other isolates from Europe, Asia, and South America shared a common genotype designated L3‐M1‐S1. This suggests that this potentially reassortant genotype has undergone long‐distance intercontinental movement. Similar to IRP4, the majority of TSWV isolates with the L3‐M1‐S1 genotype were also obtained from pepper, suggesting a potential role of the host plant in the evolution of this genotype. Furthermore, temporal analysis suggests that the existing population of TSWV, circulating between 1996 and 2023, originated from a common ancestor that existed 107–284 years ago. The population size of TSWV experienced a significant expansion for 10–15 years since 1980 and then remained constant until recently.

Assessing the effects of land-use intensity on small mammal community composition and genetic variation in Myodes glareolus and Microtus arvalis across grassland and forest habitats

ContextLand-use intensification can alter small mammal community composition and induce loss of genetic variation in remaining populations. Fragmented landscapes favor generalist and synanthropic species, which are potential reservoirs of pathogens and pose risks to agriculture and forestry.ObjectivesThis study aimed to evaluate the effects of land-use intensity on small mammal diversity in grassland and forest habitats, as well as on genetic variation patterns driven by geographic (isolation by distance) and environmental distance (isolation by resistance) factors.MethodsWe analysed differences in small mammal community diversity on grassland and forest plots with varying land-use intensities. Genetic analyses were conducted on Myodes glareolus and Microtus arvalis populations from each habitat, using microsatellites. Maximum Likelihood Population Effects models were employed to elucidate gene flow patterns and significant differences in genetic structure based on land-use intensity.ResultsSmall mammal communities in grasslands were significantly less diverse than in forests. Land-use intensity had a significant effect on diversity within grassland but not within forest habitats. M. glareolus showed three genetic groups, while M. arvalis displayed no discernible population structure or landscape-related pattern. Land-use intensity did not significantly influence the genetic structure of either species. Gene flow in M. glareolus is best described by the IBR model.ConclusionLand-use intensity significantly affects small mammal community composition, particularly in grasslands. Neither species' genetics is directly impacted by land-use intensity but rather by landscape connectivity and distance. Risk assessments for rodent-borne zoonotic pathogens and crop damage should be framed within a habitat connectivity context.

Unraveling Genetic Variation and Inheritance Patterns in Newly Developed Maize Hybrids for Improving Late Wilt Disease Resistance and Agronomic Performance Under Artificial Inoculation Conditions.

Late wilt disease caused by the fungal pathogen Magnaporthiopsis maydis represents a major threat to maize cultivation in the Mediterranean region. Developing resistant hybrids and high-yielding offers a cost-effective and environmentally sustainable solution to mitigate yield losses. Therefore, this study evaluated genetic variation, combining abilities, and inheritance patterns in newly developed twenty-seven maize hybrids for grain yield and resistance to late wilt disease under artificial inoculation across two growing seasons. The results indicated highly significant variations among assessed hybrids for all measured traits. Combining ability analysis identified IL-306, IL-304, and IL-303 as excellent combiners for grain yield and late wilt resistance, positioning them as superior candidates for hybrid development. Additionally, IL-302 was identified as a strong general combiner for earliness, and IL-307 and IL-309 demonstrated potential for producing short-statured hybrids critical for improving lodging tolerance and maximizing yield. Specific combining ability effects indicated promising earliness, yield, and disease-resistance hybrids, including IL-303×T2 and IL-306×T1. GGE biplots presented optimal line×tester combinations, offering strategic guidance for hybrid development. The principal component analysis demonstrated strong associations between grain yield, late wilt resistance, and key agronomic traits, such as ear length and kernel number. The observed robust positive association between grain yield, late wilt resistance, and yield attributes suggests selection potential for improving maize productivity. Moreover, the genotypic correlations revealed that earlier silking, taller plants, and higher kernel counts were strongly linked to enhanced yield potential. Genetic parameter estimates indicated a predominance of non-additive genetic effects for most traits, with moderate to high broad-sense heritability suggesting substantial genetic contributions to phenotypic variance. This research provides valuable insights to support the development of disease-resistant and high-yielding maize hybrids addressing critical food security challenges.

Patterns of genetic variation and parentage in a population of desert kit foxes (Vulpes macrotis arsipus) in California

Abstract Kit foxes represent a small canid in semi-arid and arid regions in the southwestern United States. The San Joaquin Kit Fox (Vulpes macrotis mutica) is listed as federally endangered, and based on more recent studies, populations of the Nevada Kit Fox (V. m. nevadensis) are declining in Utah. These 2 subspecies show a loss of genetic variation in response to population declines. Various anthropogenic activities threaten kit foxes throughout other regions of their distribution, but less is known about the basic biology and genetics of other subspecies of kit foxes. Here, we used sequences from the mitochondrial cytochrome b (Cytb) gene and 12 DNA microsatellites to investigate patterns of genetic variation and test for mating fidelity in a population of the socially monogamous Desert Kit Fox, V. m. arsipus. In the current study, the mitochondrial haplotype diversity (Hd) was higher than or comparable to other canids and terrestrial mammals. The mitochondrial results also provided evidence for male-biased dispersal and female philopatry. Expected heterozygosity (He) and number of alleles per locus (Na) for the 12 microsatellite loci were higher relative to other species of foxes and canids. As seen for nearly all species of socially monogamous canids, 17% of the pups of the mated pairs of the Desert Kit Fox revealed evidence of extra-pair mating, a value like small canids. Additionally, we observed 1 case of mate switching between breeding seasons, even though the previous mate was still alive. These data suggest that long-term pair bonding may not be as extensive as once thought.

Phylogeography of Cold Water Soft Coral Alcyonium spp. (Anthozoa, Octocorallia: Alcyonacea) Between South America and the West Antarctic Peninsula.

The Antarctic marine environment has a unique geologic and climatic history that has contributed to the evolution of high species diversity. Given the current trend of environmental warming, understanding the history of Antarctic species is crucial for predicting the impact of climate change on ecosystem function. Soft corals are a group of striking presence in the benthic marine assemblages in the Southern Ocean, which is recognized as a biodiversity hotspot. DNA sequences (Cox1, mtMutS, and 28S rDNA) were utilized for molecular phylogenetic reconstructions, species delimitations, and divergence estimations to investigate the spatial patterns of genetic diversity in Alcyonium species in the southern South American-Antarctic region. Significant genetic divergence was observed between regions, with a clear genetic break between South America and the West Antarctic Peninsula and the identification of four putative species. Divergence time estimates indicated that Alcyonium's diversification began about 41.1 million years ago (Ma), coinciding with the opening of the Drake Passage and the formation of the Antarctic Circumpolar Current (ACC, ~42 Ma). This indicates that Alcyonium has persisted insitu for an extensive period, enduring a wide range of environmental conditions.

Genomic Evidence for the Purging of Deleterious Genetic Variation in the Endangered North Atlantic Right Whale

ABSTRACTThe reduced genetic diversity and frequent inbreeding associated with small population size may underpin the accumulation and expression of deleterious mutations (mutation load) in some declining populations. However, demographic perturbations and inbreeding coupled with purifying selection can also purge declining populations of deleterious mutations, leading to intriguing recoveries. To better understand the links between deleterious genetic variation and population status, we assess patterns of genetic diversity, inbreeding, and mutation load across the genomes of three species of Balaenidae whale with different demographic histories and recoveries following the end of commercial whaling in the 1980s. Unlike bowhead (BH) and Southern right whales (SRW), which show signs of recent recovery, reproductive rates of the endangered North Atlantic right whale (NARW) remain lower than expected. We show that the NARW is currently marked by low genetic diversity, historical inbreeding, and a high mutation load. Still, we reveal evidence that genetic purging has reduced the frequency of highly deleterious alleles in NARW, which could increase chances of future population recovery. We also identify a suite of mutations putatively linked to congenital defects that occur at high frequencies in nulliparous NARW females but are rare in NARW with high reproductive success. These same mutations are nearly absent in BH and SRW in this study, suggesting that the purging of key variants may shape the probability of population recovery. As anthropogenic disturbances continue to reduce the sizes of many populations in nature, resolving the links between population dynamics and mutation load could become increasingly important.

Local Ancestry and Adaptive Introgression in Xiangnan Cattle.

Exploring the genetic landscape of native cattle is an exciting avenue for elucidating nuanced patterns of genetic variation and adaptive dynamics. Xiangnan cattle, a native Chinese cattle breed mainly produced in Hunan Province, are well adapted to the high temperature and humidity of the local environment and exhibit strong disease resistance. Herein, we employed whole-genome sequences of 16 Xiangnan cattle complemented by published genome data from 81 cattle. Our findings revealed that Xiangnan cattle are pure East Asian indicine cattle with high genetic diversity and low inbreeding. By annotating the selection signals obtained by the CLR, θπ, FST, and XP-EHH methods, genes associated with immunity (ITGB3, CD55, OTUD1, and PRLH) and heat tolerance (COX4I2, DNAJC18, DNAJC1, EIF2AK4, and ASIC2) were identified. In addition, the considerable introgression from banteng and gaur also contributed to the rapid adaptation of Xiangnan cattle to the environment of Southern China. These results will provide a basis for the further conservation and exploitation of Xiangnan cattle genetic resources.

Broad thermal tolerance and high mitochondrial genetic connectivity in the pinfish (Lagodon rhomboides).

Pinfish (Lagodon rhomboides) are highly abundant in coastal ecosystems of the Gulf of Mexico and western Atlantic Ocean and serve as a crucial link in marine food webs. Despite their ecological relevance, little is known about this species' susceptibility to anthropogenic climate change. Here, we characterized patterns of mitochondrial genetic divergence and examined the upper thermal tolerance of pinfish across a large portion of the species' range. We found little evidence of population genetic differentiation among distant localities with divergent temperature regimes (e.g., Mexico and North Carolina), using two mitochondrial markers (cytochrome b [CytB] and cytochrome c oxidase I [COI]). This suggests high genetic connectivity, which implies low potential for local adaptation of populations to different thermal conditions along a latitudinal gradient. To further examine population-scale differences in thermal tolerance, we assessed the critical thermal maxima (CTmax) of pinfish from four localities: North Carolina, Florida Keys, Alabama, and Texas. We found that CTmax was similar across sites, with all localities showing an average CTmax within a 1°C temperature range (34.5-35.5°C). This suggests that southern populations of pinfish may be more susceptible to the detrimental effects of ocean warming, as individuals in lower latitudes regularly experience temperatures within a few degrees of their CTmax. Finally, we examined the influence of varying salinity on the upper thermal limit of the pinfish and found that pinfish show no variation in CTmax under salinity conditions ranging from hypo- to hypersaline (15-35 ppt). These results show that pinfish can tolerate a wide range of environmental parameters but may rely on phenotypic plasticity, rather than local adaptation, to distinct conditions to cope with different environmental regimes.

Within-lake isolation and reproductive strategy of Stuckenia pectinata (L.) Börner at Lake Naivasha (Kenya): About water level fluctuations and alien species

Submerged aquatic plants with mixed reproduction mode may show enhanced clonal growth explained by environmental conditions. For Stuckenia pectinata (L.) Börner this has been linked to within-lake factors, both biotic (tuber predation, herbivory, periphyton shading) and abiotic (hydrological connectivity, sediment type). We investigated the S. pectinata population from Lake Naivasha, where submerged aquatic plants tolerated strong historical water level fluctuations until introduced crayfish, shading by floating exotic weeds and increased turbidity nearly eradicated them, although some stands now rebounded in various lake areas. Using 13 nuclear microsatellite loci, we analyzed genetic diversity and structure of S. pectinata subpopulations along the southeastern shoreline of the main lake and inside Crescent Island Crater, a peripheral lake basin enclosed within the rim of an extinct volcano. Results revealed a predominantly sexual reproductive strategy with limited clonal expansion in the main lake contrasting with pronounced clonal growth in the crater basin. Each subpopulation experienced recent bottlenecks. Crater basin subpopulations exhibited the strongest divergence, lower clonal diversity and larger-sized clones. We explain this differentiation by the exposed crater rim acting as barrier, isolating the crater basin from the main lake during recent decades when low water levels prevailed, accompanied with less negative impact from alien species than in the main lake. Clonal extension occurred on steep-sloping hard sandy substrates, that likely prompted local reproductive adaptations. Genetic diversity, clonal structure and connectivity patterns are discussed in the light of the specific history and features of Lake Naivasha.

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

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

Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand.

The expansion of human settlements over the past few centuries is responsible for an unprecedented number of invasive species introductions globally. An important component of biological invasion management is understanding how introduction history and postintroduction processes have jointly shaped present-day distributions and patterns of population structure, diversity and adaptation. One example of a successful invader is the European starling (Sturnus vulgaris), which was intentionally introduced to numerous countries in the 19th century, including Aotearoa New Zealand, where it has become firmly established. We used reduced representation sequencing to characterise the genetic population structure of the European starling in New Zealand, comparing it to that present in sampling locations in the native range and invasive Australian range. The population structure and genetic diversity patterns we found suggested restricted gene flow from the majority of New Zealand to the northmost sampling location (Auckland). We also profiled genetic bottlenecks and shared outlier genomic regions, which supported historical accounts of translocations between both Australian subpopulations and New Zealand, and provided evidence of which documented translocation events were more likely to have been successful. Using these results as well as historic demographic patterns, we demonstrate how genomic analysis complements even well-documented invasion histories to better understand invasion processes, with direct implications for understanding contemporary gene flow and informing invasion management.