Effects of colonization processes on genetic diversity: differences between annual plants and tree species

Conservation genetics of Notelaea lloydii (Oleaceae) in south-eastern Queensland, Australia

Habitat fragmentation can increase the chance of population bottlenecks and inbreeding, and may ultimately lead to reduced fitness and local extinction. Notelaea lloydii is a native olive species endemic to Australia and listed as vulnerable due to its restricted distribution. A recent molecular systematics study has revealed there might be some geographic structuring among N. lloydii populations. Therefore, we undertook a genome-wide single nucleotide polymorphism (SNP) analysis to determine levels and patterns of genetic diversity, inbreeding and gene flow within and among N. lloydii populations in south-eastern Queensland. Furthermore, as the reproductive phase of a plant's life history has a profound influence on genetic diversity, life history reproductive traits were also studied. Our SNP analysis revealed low genetic diversity, inbreeding and significant genetic structuring even among proximate populations. Results of a flower and fruit bagging experiment in two consecutive seasons revealed that N. lloydii produced many flowers but only a few fruits survived to maturity. There were no differences in bagged and un-bagged flowering and fruiting rates, and therefore, we conclude that the high fruit abortion rate was probably due to inbreeding depression and/or suboptimal conditions, rather than pollinator availability and insect attack. Overall, results of this study indicate that the populations of N. lloydii are small, inbred and genetically isolated and represent unique management units that require local conservation management due to ongoing threats associated with urbanisation.

Deciphering the genetic diversity and population structure of wild barley germplasm against corn leaf aphid, Rhopalosiphum maidis (Fitch)

Corn-leaf aphid (CLA-Rhopalosiphum maidis) is a major insect pest of barley (Hordeum vulgare) causing yield loss upto 30% under severe infestation. Keeping in view of the availability of very few sources of CLA resistance in barley, the present investigation was framed to assess the genetic diversity and population structure of 43 wild barley (H. vulgare subsp. spontaneum) genotypes using eight microsatellite markers against R. maidis. Three statistical methods viz. multivariate-hierarchical clustering, Bayesian clustering and PCoA, unanimously grouped genotypes into three subpopulations (K = 3) with 25.58% (SubPop1-Red), 39.53% (SubPop2-Green) and 34.88% (SubPop3-Blue) genotypes including admixtures. Based on Q ≥ 66.66%, 37.20% genotypes formed a superficial "Mixed/Admixture" subpopulation. All polymorphic SSR markers generated 36 alleles, averaging to 4.5 alleles/locus (2-7 range). The PIC and H were highest in MS31 and lowest in MS28, with averages of 0.66 and 0.71. MAF and mean genetic diversity were 0.16 and 89.28%, respectively. All these parameters indicated the presence of predominant genetic diversity and population structure amongst the studied genotypes. Based on AII, only 6 genotypes were found to be R. maidis resistant. SubPop3 had 91.66% (11) of the resistant or moderately resistant genotypes. SubPop3 also had the most pure genotypes (11), the least aphid infestation (8.78), and the highest GS (0.88), indicating its suitability for future R. maidis resistance breeding initiatives.

Antagonistic Effects of Assortative Mating on the Evolution of Phenotypic Plasticity along Environmental Gradients

AbstractPrevious theory has shown that assortative mating for plastic traits can maintain genetic divergence across environmental gradients despite high gene flow. Yet these models did not examine how assortative mating affects the evolution of plasticity. We here describe patterns of genetic variation across elevation for plasticity in a trait under assortative mating, using multiple-year observations of budburst date in a common garden of sessile oaks. Despite high gene flow, we found significant spatial genetic divergence for the intercept, but not for the slope, of reaction norms to temperature. We then used individual-based simulations, where both the slope and the intercept of the reaction norm evolve, to examine how assortative mating affects the evolution of plasticity, varying the intensity and distance of gene flow. Our model predicts the evolution of either suboptimal plasticity (reaction norms with a slope shallower than optimal) or hyperplasticity (slopes steeper than optimal) in the presence of assortative mating when optimal plasticity would evolve under random mating. Furthermore, a cogradient pattern of genetic divergence for the intercept of the reaction norm (where plastic and genetic effects are in the same direction) always evolves in simulations with assortative mating, consistent with our observations in the studied oak populations.

Population structure and genetic variation of fragmented mountain birch forests in Iceland

Betula pubescens Ehrh. (mountain birch) is the only forest-forming tree in Iceland. Since human settlement (874 AD), the continuous 25,000-30,000 km 2 forest has shrunk to 1.200 km 2 of fragmented patches, making it a good object to study population genetic consequences of habitat fragmentation and disturbance. Further, genetic studies have also shown that hybridization between the tetraploid (2n=56) B. pubescens and the diploid (2n=28) Betula nana L. (dwarf birch) occurs among Iceland's natural populations. This study assessed the genetic variation within and among eleven birch forests remaining across Iceland. Genotype-by-sequencing methodology (GBS) provided a total of 24,585 SNPs, with a minor allele frequency > 5% for genetic analyses. The analysis showed similar diversity within forests, suggesting that fragmentation and hybridization have had a limited effect on the genetic variation within sites. A clear genetic divergence is found among forests from the different regions of Iceland that may reflect historical isolation; the differentiation between forests increased with geographic distances reflecting isolation by distance. Information on the distribution of genetic variation of birch in Iceland is essential for its conservation and to establish genotype-phenotype associations to predict responses to new environmental conditions imposed by climate change and novel biotic/abiotic stressors.

Life history traits and dispersal shape neutral genetic diversity in metapopulations

Genetic diversity at population scale, depends on species life-history traits, population dynamics and local and global environmental factors. We first investigate the effect of life-history traits on the neutral genetic diversity of a single population using a deterministic mathematical model. When the population is stable, we show that semelparous species with precocious maturation and iteroparous species with delayed maturation exhibit higher diversity because their life history traits tend to balance the lifetimes of non reproductive individuals (juveniles) and adults which reproduce. Then, we extend our model to a metapopulation to investigate the additional effect of dispersal on diversity. We show that dispersal may truly modify the local effect of life history on diversity. As a result, the diversity at the global scale of the metapopulation differ from the local diversity which is only described through local life history traits of the populations. In particular, dispersal usually promotes diversity at the global metapopulation scale.

Coevolutionary theory of hosts and parasites

Host and parasite evolution are closely intertwined, with selection for adaptations and counter‐adaptations forming a coevolutionary feedback loop. Coevolutionary dynamics are often difficult to intuit due to these feedbacks and are hard to demonstrate empirically in most systems. Theoretical models have therefore played a crucial role in shaping our understanding of host–parasite coevolution. Theoretical models vary widely in their assumptions, approaches and aims, and such variety makes it difficult, especially for non‐theoreticians and those new to the field, to: (1) understand how model approaches relate to one another; (2) identify key modelling assumptions; (3) determine how model assumptions relate to biological systems; and (4) reconcile the results of different models with contrasting assumptions. In this review, we identify important model features, highlight key results and predictions and describe how these pertain to model assumptions. We carry out a literature survey of theoretical studies published since the 1950s (n = 219 papers) to support our analysis. We identify two particularly important features of models that tend to have a significant qualitative impact on the outcome of host–parasite coevolution: population dynamics and the genetic basis of infection. We also highlight the importance of other modelling features, such as stochasticity and whether time proceeds continuously or in discrete steps, that have received less attention but can drastically alter coevolutionary dynamics. We finish by summarizing recent developments in the field, specifically the trend towards greater model complexity, and discuss likely future directions for research.

Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139 candidate genes involved either in phenology or in stress responses. We inferred neutral genetic structure and processes (drift and gene flow) and performed differentiation outlier analyses and gene-environment association (GEA) analyses to detect signatures of divergent selection. Beech range-wide genetic structure was consistent with the species' previously identified postglacial expansion scenario and recolonization routes. Populations showed high diversity and low differentiation along the major expansion routes. A total of 52 loci were found to be putatively under selection and 15 of them turned up in multiple GEA analyses. Temperature and precipitation related variables were equally represented in significant genotype-climate associations. Signatures of divergent selection were detected in the same proportion for stress response and phenology-related genes. The range-wide adaptive genetic structure of beech appears highly integrated, suggesting a balanced contribution of phenology and stress-related genes to local adaptation, and of temperature and precipitation regimes to genetic clines. Our results imply a best-case scenario for the maintenance of high genetic diversity during range shifts in beech (and putatively other forest trees) with a combination of gene flow maintaining within-population neutral diversity and selection maintaining between-population adaptive differentiation.

Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.)

Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations’ resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine‐scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east‐west isolation‐by‐distance pattern consistent with the post‐glacial colonization history of the species. Genetic differentiation among sites (F_CT = 0.148) was an order of magnitude greater than between elevations within sites (F_SC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post‐glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non‐spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.

Landscape barriers to pollen and seed flow in the dioecious tropical tree Astronium fraxinifolium in Brazilian savannah

Gene flow studies provide information on gene exchange between populations, which is essential for developing genetic conservation strategies. Such analyses enable a better understanding of the life history and seed and pollen dispersal mechanisms of plant species. In this study, we investigate pollen and seed flow in a regenerant population of the pioneer species Astronium fraxinifolium in an area degraded during the construction of a hydroelectric dam. We mapped, sampled, sexed, and genotyped 386 individuals in the regenerant population (RP), as well as 128 adult trees located along two highways adjacent to the degraded area; one in Mato Grosso do Sul State (MS) and other in São Paulo State (SP). Parentage analyses was carried out for 370 individuals of the RP population, using as putative parents 348 individuals from RP and all 128 individuals sampled in MS and SP. Based on parentage analysis and eight microsatellite loci, our analyses revealed that for individuals of the RP with an identified father (pollen donor), 1.1% of the pollen was dispersed up to 532 m, while for those with an identified mother (seed donor), 0.5% of seeds were dispersed up to 4,782 m. However, a large proportion of pollen (76.5%) and seeds (57%) immigrated from trees outside the sampled populations. Pollen and seeds were dispersed through a pattern of isolation by distance. Genetic diversity was significantly similar between adults of both highway populations and individuals from RP, with significant levels of inbreeding detected only in RP. Our results demonstrate that the nearest trees contributed pollen and seeds for the recovery of the degraded area, indicating reproductive spatial isolation among the sampled populations due to the damming of the river. Such results help to understand the process of regeneration for A. fraxinifolium in regenerant populations to inform strategies for conservation and environmental recovery with this species.

Slow and steady wins the race: contrasted phylogeographic signatures in two Alpine amphibians

A deeper phylogeographic structure is expected for slow-dispersing habitat specialists compared to widespread adaptable species, especially in topographically complex regions. We tested this classic assumption by comparing the genomic (RAD-sequencing) phylogeographies of two amphibians inhabiting the Swiss Alps: the mobile, cosmopolitan common frog (Rana temporaria) against the stationary, mountain endemic Alpine salamander (Salamandra atra). Our results ran opposite of predictions: the frog displayed significantly higher genetic divergences and lower within-population variation compared to the salamander. This implies a prominent role for their distinctive glacial histories in shaping intraspecific diversity and structure: diversification and recolonization from several circum-Alpine micro-refugia for the frog versus a single refugium for the salamander, potentially combined with better population connectivity and stability. These striking differences emphasize the great variability of phylogeographic responses to the Quaternary glaciations, hence the complexity to predict general patterns of genetic diversity at the regional scale, and the forces that underlie them.

Biogeographic differences in plant-soil biota relationships contribute to the exotic range expansion of Verbascum thapsus

Exotic plant species can evolve adaptations to environmental conditions in the exotic range. Furthermore, soil biota can foster exotic spread in the absence of negative soil pathogen-plant interactions or because of increased positive soil biota-plant feedbacks in the exotic range. Little is known, however, about the evolutionary dimension of plant-soil biota interactions when comparing native and introduced ranges.To assess the role of soil microbes for rapid evolution in plant invasion, we subjected Verbascum thapsus, a species native to Europe, to a reciprocal transplant experiment with soil and seed material originating from Germany (native) and New Zealand (exotic). Soil samples were treated with biocides to distinguish between effects of soil fungi and bacteria. Seedlings from each of five native and exotic populations were transplanted into soil biota communities originating from all populations and subjected to treatments of soil biota reduction: application of (a) fungicide, (b) biocide, (c) a combination of the two, and (d) control.For most of the investigated traits, native populations showed higher performance than exotic populations; there was no effect of soil biota origin. However, plants developed longer leaves and larger rosettes when treated with their respective home soil communities, indicating that native and exotic plant populations differed in their interaction with soil biota origin. The absence of fungi and bacteria resulted in a higher specific root length, suggesting that V. thapsus may compensate the absence of mutualistic microbes by increasing its root-soil surface contact. Synthesis. Introduced plants can evolve adaptations to soil biota in their new distribution range. This demonstrates the importance of biogeographic differences in plant-soil biota relationships and suggests that future studies addressing evolutionary divergence should account for differential effects of soil biota from the home and exotic range on native and exotic populations of successful plant invaders.

Incorporating differences between genetic diversity of trees and herbaceous plants in conservation strategies

Reviews that summarize the genetic diversity of plant species in relation to their life history and ecological traits show that forest trees have more genetic diversity at population and species levels than annuals or herbaceous perennials. In addition, among-population genetic differentiation is significantly lower in trees than in most herbaceous perennials and annuals. Possible reasons for these differences between trees and herbaceous perennials and annuals have not been discussed critically. Several traits, such as high rates of outcrossing, long-distance pollen and seed dispersal, large effective population sizes (N_e ), arborescent stature, low population density, longevity, overlapping generations, and occurrence in late successional communities, may make trees less sensitive to genetic bottlenecks and more resistant to habitat fragmentation or climate change. We recommend that guidelines for genetic conservation strategies be designed differently for tree species versus other types of plant species. Because most tree species fit an LH scenario (low [L] genetic differentiation and high [H] genetic diversity), tree seeds could be sourced from a few populations distributed across the species' range. For the in situ conservation of trees, translocation is a viable option to increase N_e . In contrast, rare herbaceous understory species are frequently HL (high differentiation and low diversity) species. Under the HL scenario, seeds should be taken from many populations with high genetic diversity. In situ conservation efforts for herbaceous plants should focus on protecting habitats because the typically small populations of these species are vulnerable to the loss of genetic diversity. The robust allozyme genetic diversity databases could be used to develop conservation strategies for species lacking genetic information. As a case study of reforestation with several tree species in denuded areas on the Korean Peninsula, we recommend the selection of local genotypes as suitable sources to prevent adverse effects and to insure the successful restoration in the long term.

Oaks: an evolutionary success story

The genus Quercus is among the most widespread and species-rich tree genera in the northern hemisphere. The extraordinary species diversity in America and Asia together with the continuous continental distribution of a limited number of European species raise questions about how macro- and microevolutionary processes made the genus Quercus an evolutionary success. Synthesizing conclusions reached during the past three decades by complementary approaches in phylogenetics, phylogeography, genomics, ecology, paleobotany, population biology and quantitative genetics, this review aims to illuminate evolutionary processes leading to the radiation and expansion of oaks. From opposing scales of time and geography, we converge on four overarching explanations of evolutionary success in oaks: accumulation of large reservoirs of diversity within populations and species; ability for rapid migration contributing to ecological priority effects on lineage diversification; high rates of evolutionary divergence within clades combined with convergent solutions to ecological problems across clades; and propensity for hybridization, contributing to adaptive introgression and facilitating migration. Finally, we explore potential future research avenues, emphasizing the integration of microevolutionary and macroevolutionary perspectives.

Genetic patterns and changes in availability of suitable habitat support a colonisation history of a North American perennial plant

Climatic fluctuations during the Pleistocene influenced the geographical distribution of plant species across the southern region of California. Following an integrative approach, we combined genetic data analysis with Environmental Niche Models (ENMs) to assess the historical range expansion of Yucca schidigera, a long-lived desert perennial native of the Baja California Peninsula. We genotyped 240 individuals with seven nuclear microsatellite to investigate genetic diversity distribution across 13 populations. Indeed, we used Environmental Niche Models to examine the changes on the distribution of suitable climatic conditions for this species during the LIG (~120 ka), LGM (~22 ka) and Mid Holocene (~6 ka). We detected high genetic diversity across Y. schidigera populations (A_R = 9.94 ± 0.38 SE; H_exp = 0.791 ± 0.011 SE) with genetic variation decreasing significantly with latitude (allelic richness: R ²  = 0.38, P = 0.023; expected heterocigosity: R²  = 0.32, P = 0.042). We observed low, but significant genetic differentiation (F_ST  = 0.0678; P < 0.001) which was consistent with the parapatric distribution of the three genetic groupings detected by the Bayesian clustering algorithm. The ENMs suggest that suitable habitat for this species increased since the LGM. Our results support a range expansion of Y. schidigera across northwestern Baja California during the late Quaternary. Genetic data suggest that colonization of the current distribution followed a southward directionality as suitable climatic conditions became widely available in this region. High genetic variation across our sample suggests large historic effective population sizes for this section of the geographical range.

275 years of forestry meets genomics in Pinus sylvestris

Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA-seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long-term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.

Evaluating Population Genetic Structure and Demographic History of Quercus spinosa (Fagaceae) Based on Specific Length Amplified Fragment Sequencing

Effectively identifying the genetic structure and related factors of a species can facilitate understanding the evolutionary history of the species. Phylogeographic patterns and genetic data are essential in investigating the species historical processes and diversification that response to environmental, climatic and geological influences. In this study, Specific Length Amplified Fragment Sequencing (SLAF-seq) data and ecological niche models (ENMs) are combined to identify the genetic structure and demographic modeling of Quercus spinosa, and evaluate the impacts of historical range shifts, climatic variation, and landscape factors on this species. The population topology and genetic divergence of the Cenozoic were inferred by a site frequency spectrum based composite-likelihood approach which is a novel strategy for maximizing the utility of linked SLAF markers. The overall genetic structure using model-based and model-free clustering methods was consistently identified as two geographically distinct genetic clusters. A deep divergence between two natural lineages (i.e., a western Himalaya-Hengduan Mountains lineage and an eastern Qin-ling Mountains lineage) was observed. The demographic modeling and Niche reconstruction indicated that the two groups were diverged in the late Miocene and then presented as two distinct genetic lineages. With the Quaternary glacial climate fluctuation, two groups had continuous asymmetrical secondary contact and gene exchange in the Sichuan Basin during the last glacial maximum. Besides, a significant relationship between genetic distance and geography in all individuals was identified by the Mantel test. Overall, this study 1) contributes to a better understanding of the role played by Quaternary climatic fluctuation in the present-day distributions of Q. spinosa; 2) provides a comprehensive view of the genome-wide variation of sclerophyllous forests in ecological adaptive evolution; 3) indicates that dispersal limitation and ecological divergence contribute to the genome-wide differentiation of Q. spinosa, which supports a hypothesis that complex geography and climatic changes strongly influence the evolutionary origin and history of the species.

Genetic diversity and population divergences of an indigenous tree (Coffea mauritiana) in Reunion Island: role of climatic and geographical factors

Oceanic islands are commonly considered as natural laboratories for studies on evolution and speciation. The evolutionary specificities of islands associated with species biology provide unique scenarios to study the role of geography and climate in driving population divergence. However, few studies have addressed this subject in small oceanic islands with heterogeneous climates. Being widely distributed in Reunion Island forest, Coffea mauritiana represents an interesting model case for investigating patterns of within-island differentiation at small spatial scale. In this study, we examined the genetic diversity and population divergences of C. mauritiana using SNP markers obtained from 323 individuals across 34 locations in Reunion Island. Using redundancy analysis, we further evaluated the contribution of geographic and climatic factors to shaping genetic divergence among populations. Genetic diversity analyses revealed that accessions clustered according to the source population, with further grouping in regional clusters. Genetic relationships among the regional clusters underlined a recent process of expansion in the form of step-by-step colonization on both sides of the island. Divergence among source populations was mostly driven by the joint effect of geographic distance and climatic heterogeneity. The pattern of isolation-by-geography was in accordance with the dispersal characteristics of the species, while isolation-by-environment was mostly explained by the heterogeneous rainfall patterns, probably associated with an asynchronous flowering among populations. These findings advance our knowledge on the patterns of genetic diversity and factors of population differentiation of species native to Reunion Island, and will also usefully guide forest management for conservation.

Long-distance pollen dispersal during recent colonization favors a rapid but partial recovery of genetic diversity in Picea sitchensis

Tree species in the northern hemisphere are currently subject to rapid anthropogenic climate change and are shifting their ranges in response. This prompts questions about the mechanisms allowing tree populations to respond quickly to selection pressures when establishing into new areas. Focusing on the northern expanding range edge of Picea sitchensis, a widespread conifer of western North America, we ask how genetic structure and diversity develop during colonization, and assess the role of demographic history in shaping the evolutionary trajectory of an establishing population. We combined 500 yr of tree-ring and genotyping-by-sequencing data in 639 trees at the expansion front on the Kodiak Archipelago. We show that alleles accumulated rapidly during an increase in recruitment rate in the early 1700s. A shift from foreign to local pollen flow subsequently homogenized genetic structure at the expansion front. Taking advantage of the exceptional longevity of conifers, we highlight the major role of long-distance pollen dispersal in the rapid but incomplete recovery of genetic diversity during the initial stages of colonization. We also warn that slow initial population growth as well as long-lasting dominance of local gene flow by early founders could increase evolutionary load under a rapidly changing climate.

Release from natural enemies mitigates inbreeding depression in native and invasive Silene latifolia populations

Inbreeding and enemy infestation are common in plants and can synergistically reduce their performance. This inbreeding ×environment (I × E) interaction may be of particular importance for the success of plant invasions if introduced populations experience a release from attack by natural enemies relative to their native conspecifics. Here, we investigate whether inbreeding affects plant infestation damage, whether inbreeding depression in growth and reproduction is mitigated by enemy release, and whether this effect is more pronounced in invasive than native plant populations. We used the invader Silene latifolia and its natural enemies as a study system. We performed two generations of experimental out- and inbreeding within eight native (European) and eight invasive (North American) populations under controlled conditions using field-collected seeds. Subsequently, we exposed the offspring to an enemy exclusion and inclusion treatment in a common garden in the species' native range to assess the interactive effects of population origin (range), breeding treatment, and enemy treatment on infestation damage, growth, and reproduction. Inbreeding increased flower and leaf infestation damage in plants from both ranges, but had opposing effects on fruit damage in native versus invasive plants. Inbreeding significantly reduced plant fitness; whereby, inbreeding depression in fruit number was higher in enemy inclusions than exclusions. This effect was equally pronounced in populations from both distribution ranges. Moreover, the magnitude of inbreeding depression in fruit number was lower in invasive than native populations. These results support that inbreeding has the potential to reduce plant defenses in S. latifolia, which magnifies inbreeding depression in the presence of enemies. However, future studies are necessary to further explore whether enemy release in the invaded habitat has actually decreased inbreeding depression and thus facilitated the persistence of inbred founder populations and invasion success.

Metapop: An individual-based model for simulating the evolution of tree populations in spatially and temporally heterogeneous landscapes

Metapop is a stochastic individual-based simulation program. It uses quantitative genetics theory to produce an explicit description of the typical life cycle of monoecious and hermaphroditic plant species. Genome structure, the relationship between genotype and phenotype, and the effects of landscape heterogeneity on each individual can be finely parameterized by the user. Unlike most existing simulation packages, Metapop can simulate phenotypic plasticity, which may have a genetic component, and assortative mating, two important features of tree species. Each simulation is parameterized through text files, and raw data are generated recurrently, describing the allelic state of each quantitative trait locus involved in phenotypic variability. The data can be generated in Genepop or Fstat format, and may thus be analysed with other existing packages. Metapop also automatically computes a range of populations statistics, enabling the user to monitor evolutionary dynamics directly, from gene to metapopulation level.

Orchid colonization: multiple parallel dispersal events and mosaic genetic structure in Dactylorhiza majalis ssp. lapponica on the Baltic island of Gotland

Background and Aims

The island of Gotland in the Baltic Sea has had no contact with surrounding continental areas since the withdrawal of the Weichselian ice sheet at approx. 17 ka BP. Plants present on Gotland must have arrived by long-distance dispersal, so populations are expected to exhibit reduced levels of genetic diversity compared with populations on surrounding mainlands. However, orchids have very small seeds, which appear well adapted to long-distance dispersal, and they should therefore be less affected than other plant species by colonization bottlenecks. The aim of this study was to analyse the genetic structure of orchids colonizing isolated islands, using the marsh orchid Dactylorhiza majalis ssp. lapponica as a case study.

Methods

More than 500 samples from 27 populations were analysed for 15 plastid and eight nuclear marker loci. Population diversity and differentiation patterns were compared for nuclear and plastid marker systems and analysed in relation to geographical location.

Key Results

We found high genetic diversity but no clear geographical structure of genetic differentiation between populations on Gotland. However, the between-population differentiation in plastid and nuclear markers were correlated and the greatest diversity was found at sites at comparatively high elevations, which were the first to emerge above the water after the Ice Age.

Conclusions

The regional population on Gotland has been established by a minimum of four dispersal events from continental regions. Subsequent gene flow between sites has not yet homogenized the differentiation pattern originating from initial colonization. We conclude that long-distance seed dispersal in orchids has a strong impact on structuring genetic diversity during periods of expansion and colonization, but contributes less to gene flow between populations once a stable population structure has been achieved.

Causes and Consequences of Spatial Within-Host Viral Spread

The spread of viral pathogens both between and within hosts is inherently a spatial process. While the spatial aspects of viral spread at the epidemiological level have been increasingly well characterized, the spatial aspects of viral spread within infected hosts are still understudied. Here, with a focus on influenza A viruses (IAVs), we first review experimental studies that have shed light on the mechanisms and spatial dynamics of viral spread within hosts. These studies provide strong empirical evidence for highly localized IAV spread within hosts. Since mathematical and computational within-host models have been increasingly used to gain a quantitative understanding of observed viral dynamic patterns, we then review the (relatively few) computational modeling studies that have shed light on possible factors that structure the dynamics of spatial within-host IAV spread. These factors include the dispersal distance of virions, the localization of the immune response, and heterogeneity in host cell phenotypes across the respiratory tract. While informative, we find in these studies a striking absence of theoretical expectations of how spatial dynamics may impact the dynamics of viral populations. To mitigate this, we turn to the extensive ecological and evolutionary literature on range expansions to provide informed theoretical expectations. We find that factors such as the type of density dependence, the frequency of long-distance dispersal, specific life history characteristics, and the extent of spatial heterogeneity are critical factors affecting the speed of population spread and the genetic composition of spatially expanding populations. For each factor that we identified in the theoretical literature, we draw parallels to its analog in viral populations. We end by discussing current knowledge gaps related to the spatial component of within-host IAV spread and the potential for within-host spatial considerations to inform the development of disease control strategies.

Genetic patterns in Neotropical Magnolias (Magnoliaceae) using de novo developed microsatellite markers

Conserving tree populations safeguards forests since they represent key elements of the ecosystem. The genetic characteristics underlying the evolutionary success of the tree growth form: high genetic diversity, extensive gene flow and strong species integrity, contribute to their survival in terms of adaptability. However, different biological and landscape contexts challenge these characteristics. This study employs 63 de novo developed microsatellite or SSR (Single Sequence Repeat) markers in different datasets of nine Neotropical Magnolia species. The genetic patterns of these protogynous, insect-pollinated tree species occurring in fragmented, highly-disturbed landscapes were investigated. Datasets containing a total of 340 individuals were tested for their genetic structure and degree of inbreeding. Analyses for genetic structure depicted structuring between species, i.e. strong species integrity. Within the species, all but one population pair were considered moderate to highly differentiated, i.e. no indication of extensive gene flow between populations. No overall correlation was observed between genetic and geographic distance of the pairwise species’ populations. In contrast to the pronounced genetic structure, there was no evidence of inbreeding within the populations, suggesting mechanisms favouring cross pollination and/or selection for more genetically diverse, heterozygous offspring. In conclusion, the data illustrate that the Neotropical Magnolias in the context of a fragmented landscape still have ample gene flow within populations, yet little gene flow between populations.

Influence of Spatiotemporal Dynamics on the Fine-Scale Spatial Genetic Structure of Differently Managed Picea abies Stands

The tandem analysis of dendrochronological and genetic data is piquing forest ecologists’ interest and represents a promising approach for studying the temporal development of genetic structure in forest tree populations. Such multidisciplinary approach can help elucidate to what extent different management practices have impacted the fine-scale spatial genetic structure of forest stands through time. In this study, we jointly analysed spatial, age and genetic data from three differently managed Norway spruce permanent plots to assess: (1) possible differences among plots in the spatial distribution of individuals and their genetic structure due to different management practices, and (2) whether modifications in the age structure influenced the fine-scale spatial genetic structure within each permanent plot. With these aims, we genetically characterized at five nuclear microsatellite markers a large subset (328) of all the trees for which spatial and age data were collected (1472). We found that different management practices determined a similar spatial structure in terms of trees’ ages (r < 25 m in all plots) and neutral genetic diversity (Sp ranging from 0.002 to 0.004). Hot spots and cold spots of trees’ age were not statistically different in terms of genetic diversity, and trees’ age was not statistically different among the genetic clusters detected. On the other hand, the spatial distribution of individuals was significantly clustered up to 22 m only in the wooded pasture plot. Our main findings show that forest land use and management can indeed determine markedly different spatial layouts of Norway spruce individuals but do not produce strong distortions in the spatial structure of age and genetic parameters.

Evolution of almond genetic diversity and farmer practices in Lebanon: impacts of the diffusion of a graft-propagated cultivar in a traditional system based on seed-propagation

BACKGROUND

Under cultivation, many outcrossing fruit tree species have switched from sexual reproduction to vegetative propagation. Traditional production systems have persisted, where cultivar propagation is based on a mixed reproductive system. For millenia, almond, Prunus dulcis, has been propagated by seeds. Almond grafting remained of little importance until recently. In Lebanon, both sexual and clonal reproductions are used for almond propagation. We used 15 microsatellite markers to investigate the effect of introducing graft-propagated cultivars and associated practices, on the structure of the genetic diversity among and within the two main Lebanese cultivars.

RESULTS

As expected, the sexually propagated cultivar Khachabi exhibited more genotypic and genetic diversity than the vegetatively propagated cultivar Halwani. It also exhibited lower differentiation among populations. The distribution of clones showed that propagation modes were not exclusive: farmers have introduced clonal propagation in the seed-propagated cultivar while they have maintained a diversity of genotypes within populations that were mostly graft-propagated. These practices are also important to avoid mate limitations that hamper fruit production in a self-incompatible species. 'Khachabi' is structured into two gene pools separated by the Lebanese mountains. As to 'Halwani', two different gene pools were introduced. The most ancient one shares the same geographic range as 'Khachabi'; longtime coexistence and sexual reproduction have resulted in admixture with 'Khachabi'. In contrast, the more recent introduction of the second gene pool in the Bekaa region followed an evolution towards more extensive clonal propagation of 'Halwani' limiting hybridizations. Furthermore, some pairs of geographically distant 'Halwani' orchards, exhibited low genetic distances, suggesting that a network of exchanges between farmers was effective on a large scale and/or that farmers brought clonal plant material from a common source.

CONCLUSIONS

Almond diversification in Lebanon is clearly related to the evolution of propagation practices adapted to self-incompatible cultivars. The comparison between both cultivars demonstrated the genetic effects of the introduction of a new cultivar and the associated grafting propagation practices. Our study provided information to develop a strategy for in situ conservation of cultivars and to limit gene flow from introduced material to ancient orchards.

Are Survivors Different? Genetic-Based Selection of Trees by Mountain Pine Beetle During a Climate Change-Driven Outbreak in a High-Elevation Pine Forest

Increased mortality of forest trees, driven directly or indirectly by climate change, is occurring around the world. In western North America, whitebark pine, a high elevation keystone species, and lodgepole pine, a widespread ecologically and economically important tree, have experienced extensive mortality in recent climate-driven outbreaks of the mountain pine beetle. However, even in stands experiencing high levels of mortality, some mature trees have survived. We hypothesized that the outbreak acted as a natural selection event, removing trees most susceptible to the beetle and least adapted to warmer drier conditions. If this was the case, genetic change would be expected at loci underlying beetle resistance. Given we did not know the basis for resistance, we used inter-simple sequence repeats to compare the genetic profiles of two sets of trees, survivors (mature, living trees) and general population (trees just under the diameter preferred by the beetles and expected to approximate the genetic structure of each tree species at the site without beetle selection). This method detects high levels of polymorphism and has often been able to detect patterns associated with phenotypic traits. For both whitebark and lodgepole pine, survivors and general population trees mostly segregated independently indicating a genetic basis for survivorship. Exceptions were a few general population trees that segregated with survivors in proportions roughly reflecting the proportion of survivors versus beetle-killed trees. Our results indicate that during outbreaks, beetle choice may result in strong selection for trees with greater resistance to attack. Our findings suggest that survivorship is genetically based and, thus, heritable. Therefore, retaining survivors after outbreaks to act as primary seed sources could act to promote adaptation. Further research will be needed to characterize the actual mechanism(s) of resistance.

Genetic diversity in the candidate trees of Madhuca indica J. F. Gmel. (Mahua) revealed by inter-simple sequence repeats (ISSRs)

Madhuca indica provides livelihood to several tribal people in India, where the flowers are used for extraction of sweet juices having multiple applications. Certain trees have more value as judged by the tribal people mainly based on yield and quality performance of the trees, and these trees were selected for the genetic diversity analyses. Genetic diversity of 48 candidate Mahua trees from Etapalli, Dadagaon, and Jawhar, Maharashtra, India, was assessed using ISSR markers. Fourteen ISSR primers revealed a total of 132 polymorphic bands giving overall 92% polymorphism. Genetic diversity, in terms of expected number of alleles (Ne), the observed number of alleles (Na), Nei's genetic diversity (H), and Shannon's information index (I) was 1.921, 1.333, 0.211, and 0.337, respectively, and suggested lower genetic diversity. Region wise analysis revealed higher genetic diversity for site Etapalli (H = 0.206) and lowest at Dhadgaon (H = 0.140). Etapalli area possesses higher forest cover than Dhadgaon and Jawhar. Additionally, in Dhadgaon and Jawhar M. indica trees are restricted to field bunds; both reasons might contribute to lower genetic diversity in these regions. The dendrogram and the principal coordinate analyses showed no region-specific clustering. The clustering patterns were supported by AMOVA where higher genetic variance was observed within trees and lower variance among regions. Long-distance dispersal and/or higher human interference might be responsible for low diversity and higher genetic variance within the candidate trees.

Limited pollen dispersal, small genetic neighborhoods, and biparental inbreeding in Vallisneria americana

PREMISE OF THE STUDY

Pollen dispersal is a key process that influences ecological and evolutionary dynamics of plant populations by facilitating sexual reproduction and gene flow. Habitat loss and fragmentation have the potential to reduce pollen dispersal within and among habitat patches. We assessed aquatic pollen dispersal and mating system characteristics in Vallisneria americana-a water-pollinated plant with a distribution that has been reduced from historic levels.

METHODS

We examined pollen neighborhood size, biparental inbreeding, and pollen dispersal, based on seed paternity using the indirect paternity method KinDist, from samples of 18-39 mothers and 14-20 progeny per mother from three sites across 2 years.

KEY RESULTS

On average, fruits contained seeds sired by seven fathers. We found significant biparental inbreeding and limited pollen dispersal distances (0.8-4.34 m). However, in a number of cases, correlated paternity did not decline with distance, and dispersal could not be reliably estimated.

CONCLUSIONS

Frequent pollen dispersal is not expected among patches, and even within patches, gene flow via pollen will be limited. Limited pollen dispersal establishes genetic neighborhoods, which, unless overcome by seed and propagule dispersal, will lead to genetic differentiation even in a continuous population. Unless loss and fragmentation drive populations to extreme sex bias, local pollen dispersal is likely to be unaffected by habitat loss and fragmentation per se because the spatial scale of patch isolation already exceeds pollen dispersal distances. Therefore, managing specifically for pollen connectivity is only relevant over very short distances.

Genetic diversity and structure of an endangered desert shrub and the implications for conservation

Population genetic information can provide valuable insight for the conservation and management of threatened and endangered plant species. Tamarix taklamakanensis is an endangered shrub endemic to arid basins of northwestern China. This species serves to stabilize soils in this region, but has seen substantial loss in its abundance due to depletion of ground water. The populations of this species have become small and fragmented, warranting conservation. Seven microsatellite loci were used to assess the genetic diversity and structure of 15 populations in the Tarim Basin, China. Among populations, the expected heterozygosity and total gene diversity were both moderate (H_E = 0.392, h_T = 0.432), however the allelic diversity was low (A = 2.4). Eleven populations were detected to have experienced recent bottlenecks using Wilcoxon's test and a model-shift test. Most populations of T. taklamakanensis in the centre of Tarim Basin showed low levels of genetic differentiation, but higher levels in geographically outlying populations. Genetic structure based on Bayesian assignment, the neighbour-joining network and principal coordinates analyses produced similar results, supporting five groups in the Tarim Basin. Gene flow was high among Bayesian groups based on historical gene flow estimated by private alleles. The genetic structure of T. taklamakanensis supports a pattern where gene flow principally occurs along river corridors through hydrochory of seeds and insect-mediated pollination. Populations upstream have contributed to a more diverse mixture of populations near the confluence of several rivers near the centre of Tarim Basin. This pattern of genetic structure could be influenced by the flow of water from different river systems. Conservation efforts should focus on fostering the regeneration of this species, maintaining genetic diversity and preserving the extant genetic structure. Conservation efforts are contingent upon maintaining ground water and streamflows in this arid basin.

Genetic Structure in the Northern Range Margins of Common Ash, Fraxinus excelsior L

During post glacial colonization, loss of genetic diversity due to leading edge effects may be attenuated in forest trees because of their prolonged juvenile phase, allowing many migrants to reach the colonizing front before populations become reproductive. The northern range margins of temperate tree taxa in Europe are particularly suitable to study the genetic processes that follow colonization because they have been little affected by northern refugia. Here we examined how post glacial range dynamics have shaped the genetic structure of common ash (Fraxinus excelsior L.) in its northern range compared to its central range in Europe. We used four chloroplast and six nuclear microsatellites to screen 42 populations (1099 trees), half of which corresponded to newly sampled populations in the northern range and half of which represented reference populations from the central range obtained from previously studies. We found that northern range populations of common ash have the same chloroplast haplotypes as south-eastern European populations, suggesting that colonization of the northern range took place along a single migration route, a result confirmed by the structure at the nuclear microsatellites. Along this route, diversity strongly decreased only in the northern range, concomitantly with increasing population differentiation and complex population substructures, a pattern consistent with a leading edge colonization model. Our study highlights that while diversity is maintained in the central range of common ash due to broad colonizing fronts and high levels of gene flow, it profoundly decreases in the northern range, where colonization was unidirectional and probably involved repeated founder events and population fluctuations. Currently, common ash is threatened by ash dieback, and our results on northern populations will be valuable for developing gene conservation strategies.

A Multi-Faceted Approach to Analyse the Effects of Environmental Variables on Geographic Range and Genetic Structure of a Perennial Psammophilous Geophyte: The Case of the Sea Daffodil Pancratium maritimum L. in the Mediterranean Basin

The Mediterranean coastline is a dynamic and complex system which owes its complexity to its past and present vicissitudes, e.g. complex tectonic history, climatic fluctuations, and prolonged coexistence with human activities. A plant species that is widespread in this habitat is the sea daffodil, Pancratium maritimum (Amaryllidaceae), which is a perennial clonal geophyte of the coastal sands of the Mediterranean and neighbouring areas, well adapted to the stressful conditions of sand dune environments. In this study, an integrated approach was used, combining genetic and environmental data with a niche modelling approach, aimed to investigate: (1) the effect of climate change on the geographic range of this species at different times {past (last inter-glacial, LIG; and last glacial maximum, LGM), present (CURR), near-future (FUT)} and (2) the possible influence of environmental variables on the genetic structure of this species in the current period. The genetic results show that 48 sea daffodil populations (867 specimens) display a good genetic diversity in which the marginal populations (i.e. Atlantic Sea populations) present lower values. Recent genetic signature of bottleneck was detected in few populations (8%). The molecular variation was higher within the populations (77%) and two genetic pools were well represented. Comparing the different climatic simulations in time, the global range of this plant increased, and a further extension is foreseen in the near future thanks to projections on the climate of areas currently—more temperate, where our model suggested a forecast for a climate more similar to the Mediterranean coast. A significant positive correlation was observed between the genetic distance and Precipitation of Coldest Quarter variable in current periods. Our analyses support the hypothesis that geomorphology of the Mediterranean coasts, sea currents, and climate have played significant roles in shaping the current genetic structure of the sea daffodil especially during LGM because of strong variation in coastline caused by glaciations.

Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift

Studying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the variation of eight microsatellite loci across four study sites showed that (i) wild H. schachtii populations displayed fine-scaled genetic structure with no evidence of substantial levels of gene flow beyond the scale of the host plant, and comparisons with simulations indicated that (ii) genetic drift substantially affected the residual signals of isolation-by-distance processes, leading to departures from migration-drift equilibrium. In contrast to what can be suspected for (crop) field populations, this showed that wild cyst nematodes have very low dispersal capabilities and are strongly disconnected from each other. Our results provide some key elements for designing pest control strategies, such as decreasing passive dispersal events to limit the spread of virulence among field nematode populations.

Recent similarity in distribution ranges does not mean a similar postglacial history: a phylogeographical study of the boreal tree species Alnus incana based on microsatellite and chloroplast DNA variation

We reconstructed the historical pattern of postglacial biogeographic range expansion of the boreal tree species Alnus incana in Europe. To assess population genetic structure and diversity, we performed a combined analysis of nuclear microsatellite loci and chloroplast DNA sequences (65 populations, 1004 individuals). Analysis of haplotype and microsatellite diversity revealed that southeastern refugial populations situated in the Carpathians and the Balkan Peninsula did not spread north and cannot be considered as important source populations for postglacial recolonization of Europe; populations in Eastern Europe did not establish Fennoscandian populations; populations in Fennoscandia and Eastern Europe have no unique genetic cluster, but represent a mix with a predominant cluster typical for Central Europe; and that colonization of Fennoscandia and Eastern Europe took place from Central Europe. Our findings highlight the importance of an effective refugium in Central Europe located outside classical southern refugia confirming the existence of northern refugia for boreal trees in Europe. The postglacial range expansion of A. incana did not follow the model established for Picea abies. Fennoscandian populations are not derived from Eastern European ones, but from Central European ones.

Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication

Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops.

Simulating the Interacting Effects of Intraspecific Variation, Disturbance, and Competition on Climate-Driven Range Shifts in Trees

Climate change is expected to favor shifts in plant distributions; some such shifts are already being observed along elevation gradients. However, the rate of such shifts may be limited by their ability to reach newly suitable areas and by competition from resident species. The degree of local adaptation and genetic variation may also play a role in the interaction between migrants and residents by affecting relative fitness. We used a simulation model to explore the interacting effects of dispersal, fecundity, disturbance, and genetic variation on range-edge dynamics between a pair of demographically similar tree species. Ideal climate for an individual is determined by genotype. The simulated landscape undergoes an 80-year period of climate change in which climate bands shift upslope; subsequently, climate is held constant for 300 years. The presence of a high-elevation competitor caused a significant lag in the range shift of the low-elevation species relative to competition-free scenarios. Increases in fecundity and dispersal distance both helped to speed up the replacement of the high-elevation species by the low-elevation species at their range boundary. While some disturbance scenarios facilitated this transition, frequent canopy disturbance inhibited colonization by removing reproductive adults and led to range contractions in both species. Differences between dispersal scenarios were more pronounced when disturbance was frequent (15 vs. 25 year return interval) and dispersal was limited. When the high-elevation species lacked genetic variation, its range was more-easily invaded by the low-elevation species, while a similar lack of variation in the low-elevation species inhibited colonization-but only when this lack of variation decreased the fitness of the affected species near the range boundary. Our model results support the importance of measuring and including dispersal/fecundity, disturbance type and frequency, and genetic variation when assessing the potential for range shifts and species vulnerability to climate change.

Adapting through glacial cycles: insights from a long-lived tree (Taxus baccata)

Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long-lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation-by-distance) and selective (isolation-by-adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present-day patterns of genetic diversity.

Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent-wide lineage admixture

Genetic admixture is supposed to be an important trigger of species expansions because it can create the potential for selection of genotypes suitable for new climatic conditions. Up until now, however, no continent-wide population genetic study has performed a detailed reconstruction of admixture events during natural species expansions. To fill this gap, we analysed the postglacial history of Alnus glutinosa, a keystone species of European swamp habitats, across its entire distribution range using two molecular markers, cpDNA and nuclear microsatellites. CpDNA revealed multiple southern refugia located in the Iberian, Apennine, Balkan and Anatolian Peninsulas, Corsica and North Africa. Analysis of microsatellites variation revealed three main directions of postglacial expansion: (i) from the northern part of the Iberian Peninsula to Western and Central Europe and subsequently to the British Isles, (ii) from the Apennine Peninsula to the Alps and (iii) from the eastern part of the Balkan Peninsula to the Carpathians followed by expansion towards the Northern European plains. This challenges the classical paradigm that most European populations originated from refugial areas in the Carpathians. It has been shown that colonizing lineages have met several times and formed secondary contact zones with unexpectedly high population genetic diversity in Central Europe and Scandinavia. On the contrary, limited genetic admixture in southern refugial areas of A. glutinosa renders rear-edge populations in the Mediterranean region more vulnerable to extinction due to climate change.

Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples

Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding, and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We made use of genetic, environmental, and ecological data (microsatellite markers, apple production across landscapes and records of apple flower visitors, respectively). We provide the first evidence that both human activities, through apple production, and human disturbance, through modifications of apple flower visitor diversity, have had a significant impact on crop-to-wild interspecific introgression rates. Our analysis also revealed the impact of previous natural climate change on historical gene flow in the nonintrogressed wild apple M. sylvestris, by identifying five distinct genetic groups in Europe and a north–south gradient of genetic diversity. These findings identify human activities and climate as key drivers of gene flow in a wild temperate fruit tree and provide a practical basis for conservation, agroforestry, and breeding programs for apples in Europe.

Progressive migration and anagenesis in Drimys confertifolia of the Juan Fernández Archipelago, Chile

A common mode of speciation in oceanic islands is by anagenesis, wherein an immigrant arrives and through time transforms by mutation, recombination, and drift into a morphologically and genetically distinct species, with the new species accumulating a high level of genetic diversity. We investigate speciation in Drimys confertifolia, endemic to the two major islands of the Juan Fernández Archipelago, Chile, to determine genetic consequences of anagenesis, to examine relationships among populations of D. confertifolia and the continental species D. winteri and D. andina, and to test probable migration routes between the major islands. Population genetic analyses were conducted using AFLPs and nuclear microsatellites of 421 individuals from 42 populations from the Juan Fernández islands and the continent. Drimys confertifolia shows a wide genetic variation within populations on both islands, and values of genetic diversity within populations are similar to those found within populations of the continental progenitor. The genetic results are compatible with the hypothesis of high levels of genetic variation accumulating within anagenetically derived species in oceanic islands, and with the concept of little or no geographical partitioning of this variation over the landscape. Analysis of the probability of migration within the archipelago confirms colonization from the older island, Robinson Crusoe, to the younger island Alejandro Selkirk.