Spatial Distribution Of Genetic Diversity Research Articles

Relict stands of Central European oaks: Unravelling autochthony and genetic structure based on a multi-population study

Central European white oaks expanded rapidly after the last glacial period and reached their current distribution range during the early Holocene. They have been an important resource of timber, fuelwood and animal feed for humans, who actively promoted their presence in forests and other landscape types at least since the early historical times. Besides stands with intensive management, putatively relict populations of three native oak species can be found on unproductive sites with restricted accessibility. Here, we apply chloroplast and nuclear microsatellite markers in order to address the autochthony of relict and managed stands and compare the spatial distribution of genetic variation between them. Based on data from more than 150 populations, we demonstrate that oak autochthony was preserved throughout historical times which is likely the result of traditional silvicultural treatment. This is supported by the fact that the spatial pattern of chloroplast haplotype distribution still reflects the post-glacial recolonization in both relict and old managed stands. We observed significant admixture of haplotypes only in stands established after the Second World War, which is attributable to the transfer of reproductive material used for afforestation. In terms of nuclear genetic variation, we observed marked differences among species. Quercus pubescens exhibited a pronounced genetic structure. Genetic drift and limited gene flow among its small and isolated populations in our study area might have contributed to this pattern. Varying extent of genetic introgression with other sympatric oak species could offer an additional explanation. On the contrary, the gene pools of Q. petraea and Q. robur are highly homogenous, displaying only weak isolation-by-distance. We found no significant differences of genetic diversity and differentiation between relict and managed stands. This suggests that seed transfer mostly occurred within our study area, even in those stands established in post-war times, verifying previous findings which point out limited human interference. We recommend consideration of population genetic structure for gene conservation, with a finer resolution of gene conservation units needed for Q. pubescens due to its spatial genetic structure. Both relict and old managed stands, species-pure or mixed, are suitable for conservation, as they host autochthonous gene pools. Coppice-with-standard management could contribute to preservation of autochthony. In the face of climate change, it is also important to maintain the evolutionary potential of the stands, by facilitating generative reproduction and allowing for hybridization in mixed stands.

Mountains as refugia in the Dry Chaco: phylogeography and species distribution modelling of the southernmost chilli pepper, Capsicum chacoense Hunz. (Solanaceae)

Abstract Phylogeographical studies combined with species distribution modelling can provide evidence for past climate refugia. During the Pleistocene, the Chaco phytogeographical province (ChPP) underwent changes in the distribution range, and the flora might have found refugia in different habitats according to their climatic requirements. This contribution aims to infer the effects of historical geoclimatic changes on the evolutionary history of Capsicum chacoense, the southernmost chilli pepper growing in the ChPP. We analysed 27 localities with plastid markers and 23 with nuclear markers, covering the geographical range of the species. We performed statistical phylogeography, in addition to current and past species distribution modelling. We found three haploclades, diverging 2.3–1 Mya, intermingled throughout the mountain ranges of the ChPP as a consequence of glacial cycles. According to the species distribution modelling, the expansion of the species distribution occurred during interglacial periods. We found two dispersal routes from south to north of the species distribution, concomitant with the migration routes of birds that disperse their fruits. The spatial distribution of genetic diversity showed the highest genetic diversity values at higher elevations. The main orographic systems of the study area were identified as areas of presumed population stability. Consequently, mountains are priority regions for conservation because they contain areas with high genetic diversity.

Fine‐scale spatial genetic structure in a locally abundant native bunchgrass (Achnatherum thurberianum) including distinct lineages revealed within seed transfer zones

AbstractAnalyses of the factors shaping genetic variation in widespread plant species are important for understanding the evolutionary history and local adaptation and have applied significance for guiding conservation and restoration decisions. Thurber's needlegrass (Achnatherum thurberianum) is a widespread, locally abundant grass that inhabits heterogeneous arid environments of western North America and is of restoration significance. It is a common component of shrubland steppe communities in the Great Basin Desert, where drought, fire, and invasive grasses have degraded natural communities. Using a reduced representation sequencing approach, we generated SNP data at 5677 loci across 246 individuals from 17 A. thurberianum populations spanning five previously delineated seed zones from the western Great Basin. Analyses revealed a pronounced population genetic structure, with individuals forming consistent geographical clusters across a variety of population genetic analyses and spatial scales. Low levels of genetic diversity within populations, as well as high population estimates of linkage disequilibrium and relatedness, were consistent with self‐fertilization as a contributor to population differentiation. Variance partitioning and partial redundancy analysis (pRDA) indicated local adaptation to environment as additionally influencing the spatial distribution of genetic variation. The environmental variables driving these results were similar to those implicated in recent genecological work which inferred local adaptation for seed zone delineation. Our analyses also revealed a complex evolutionary history of A. thurberianum in the Great Basin, where previously delineated seed zones contain distantly related populations. Our results indicate evolutionary history, mating system, and differentiation across distinct geographic and environmental scales have shaped genetic variation in A. thurberianum and illustrate how numerous aspects of population genetic variation might require consideration for restoration planning.

Assessment of genetic and morphological differentiation among populations of the Diederik Cuckoo Chrysococcyx caprius

The Diederik Cuckoo Chrysococcyx caprius is an African species widely distributed south of the Sahara, which migrates seasonally between breeding and nonbreeding sites. It is currently unknown whether the species consists of a single panmictic population or if it is genetically structured. To investigate this, we analysed sequence variation in three mitochondrial and two nuclear gene regions in combination with morphological measurements in specimens from four localities. Phylogenetic relationships were estimated using maximum-likelihood methods and included samples of Klaas’s Cuckoo Chrysococcyx klaas, Red-chested Cuckoo Cuculus solitarius, and African Cuckoo Cuculus gularis. Haplotype networks and analysis of molecular variance were used to characterise the spatial distribution of genetic diversity. A principal component analysis was performed to investigate morphological variation among localities. Molecular analysis identified two divergent mitochondrial lineages, which were found to occur in sympatry in one South African locality (Limpopo Province). The magnitude of divergence between versus within these lineages was low (0.4–1%) yet significant (F ST: 0.84–0.88). Lack of apparent phylogeographic structure provides support for the absence of physical barriers to gene flow in this species. The divergent mitochondrial lineages did not differ in morphological measurements. The emergence and persistence of shallow mitochondrial divergence among sympatric lineages in the Diederik Cuckoo could be linked to maternal divergence in host selection of these brood parasites — a hypothesis requiring additional data to be tested.

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

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

Genetic Diversity of Five Broadleaved Tree Species and Its Spatial Distribution in Self-Regenerating Stands

European forest ecosystems are currently subject to various disturbances and shifts in land-use legacies. To be able to forecast the trends and consequences of the changes in genetic diversity following these disturbances, it is of crucial importance to understand the genetic dynamics of natural tree populations. The present study aimed at determining the extent and spatial distribution of genetic diversity in five common broadleaved tree species in Lithuania in both mature (putatively maternal) stands and in natural regeneration (juveniles) of the respective species. The genetic diversity of Quercus robur, Betula pendula, Populus tremula, Alnus glutinosa, and Fraxinus excelsior was assessed using eight nuclear microsatellite loci for each species; 417 samples of regenerating juveniles and 141 samples of putatively maternal trees were analyzed in total. The investigated populations of self-regenerating Q. robur, B. pendula, A. glutinosa, and F. excelsior juveniles showed spatially random genetic structures, while P. tremula regenerated mostly via root suckers and formed clonal groups. The genetic diversity in regenerating juveniles of all species was as high as in putatively maternal stands. The detection of adequate (substantial) genetic diversity in the studied regenerating populations of these five broadleaved tree species suggests that in Lithuania these species have a good potential to adapt to changing environmental conditions.

Taxonomic status of otter species in Nakai-Nam Theun National Park, Lao PDR, based on DNA evidence.

Otter populations are threatened by habitat loss, pollution, conflicts with humans, and illegal wildlife trade to meet the demand for pets, for their fur, and for parts used in traditional medicines. Baseline information on the distribution, population genetic diversity, and connectivity is crucial to inform conservation management decisions; however, reliable data from otter populations in Southeast Asia remain scarce. In this study, we conducted baseline otter fecal DNA surveys based on mitochondrial DNA (mtDNA) to identify species, assess the occurrence, and map the spatial distribution of genetic diversity and evolutionary relationships of otter populations using 1700 bp Cytochrome B - Control Region and mitogenome from Nakai-Nam Theun National Park in the Annamite Mountains of Lao PDR. Of the total 56 samples identified to species, the majority (87.5%) was of the widely distributed Eurasian otter with three haplotypes (Lutra lutra; LLLA01-LLLA03), with a calculated haplotype diversity of 0.600 and a nucleotide diversity of 0.00141 based on mitogenome. The second species was the Asian small-clawed otter with only one haplotype detected (Aonyx cinereus; ACLA01). All Eurasian otter haplotypes were newly characterized and clustered within the strongly supported South-Southeast-North Asian clade of Lutra lutra. Compared with the European clade, the high mtDNA diversity of Lutra lutra in Nakai-Nam Theun National Park potentially reflects long-term demographic stability and lesser degree of population bottleneck during the last glacial maxima (LGM, ~21,000 years ago). The single haplotype detected in Asian small-clawed otters had not been detected in previous genetic studies. Our research is the first otter-specific noninvasive genetic study in Lao PDR and provides baseline insights into the otter population diversity in a regional priority site for biodiversity conservation.

Genetic divergence at species boundaries of the dolphinfish (Coryphaena hippurus) in the Tropical Eastern Pacific.

Marine species constitute commercially important resources, and knowledge about mechanisms that shape phylogeographic patterns and genetic structure provides valuable information for conservation. The dolphinfish, Coryphaena hippurus, is one of the most important species caught in the Tropical Eastern Pacific (TEP). However, the lack of consensus about the existence of genetically differentiated populations in the area has hindered the adoption of management strategies to ensure its viability. We assessed genetic variation and phylogeographic structure using two mitochondrial genes and 14 nuclear DNA microsatellite loci. Population genetic tools were used to characterize the spatial distribution of genetic variation of C. hippurus in the TEP, evaluate the extent of connectivity between dolphinfish populations, infer potential barriers to gene flow, and test for signals of contemporary and historical demographic expansions. Mitochondrial DNA sequences showed genetic homogeneity across locations in the TEP, as well as a strong signal of population expansion dated to the late Pleistocene. In contrast, nuclear microsatellite markers resolved four genetically distinct groups with a remarked genetic differentiation between the most distant locations, at the northern and southern boundaries of the species' range. High mean genetic diversity was found at all localities (Hs = 0.66-0.81). Notwithstanding, positive F IS and low effective population size (Ne = 77.9-496.4) were also recorded. The distribution of genetic variation could be related to expansion-contraction cycles following seasonal temperature changes at transitional areas, promoting population subdivisions. However, we cannot rule out the effect of oceanographic dynamics to the observed patterns. Although this marine species remains highly abundant despite commercial exploitation, the low Ne values are of conservation concern and must be considered in fishery management plans.

Landscape genetics across the Andes mountains: Environmental variation drives genetic divergence in the leaf-cutting ant Atta cephalotes.

Distinguishing among the mechanisms underlying the spatial distribution of genetic variation resulting from the environmental or physical barriers from those arising due to simple geographic distance is challenging in complex landscapes. The Andean uplift represents one of the most heterogeneous habitats where multiple mechanisms may interact, confounding their relative roles. We explore this broad question in the leaf-cutting ant Atta cephalotes, a species that is distributed across the Andes mountains, using nuclear microsatellite markers and mtCOI gene sequences. We investigate spatial genetic divergence across the western range of the northern Andes in Colombia by testing the relative role of alternative scenarios of population divergence, including isolation by geographic distance (IBD), climatic conditions (IBE), and the physical barriers presented by the Andes mountains (IBB). Our results reveal substantial genetic differentiation among A. cephalotes populations for both types of markers, but only nuclear divergence followed a hierarchical pattern with multiple models of genetic divergence imposed by the western range. Model selection showed that the IBD, IBE (temperature and precipitation), and IBB (Andes mountains) models, often proposed as individual drivers of genetic divergence, interact, and explain up to 33% of the genetic divergence in A. cephalotes. The IBE model remained significant after accounting for IBD, suggesting that environmental factors play a more prominent role than IBB. These factors, in combination with the idiosyncratic dispersal patterns of ants, appear to determine the hierarchical patterns of gene flow. This study enriches our understanding of the forces shaping population divergence in complex habitat landscapes.

Genetic inference of orchid population dynamics on different‐aged lava flows in Costa Rica

AbstractColonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 vs. 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra‐ and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally smaller on the younger sites (≤3 m vs. ≤8 m).

Genetic Diversity and Population Structure of Jubaea chilensis, an Endemic and Monotype Gender from Chile, Based on SNP Markers.

Jubaea chilensis (Molina) Baill., also named Chilean palm, is an endemic species found in the coastal area of Mediterranean sclerophyllous forest in Chile. It has a highly restricted and fragmented distribution along the coast, being under intense exploitation and anthropogenic impact. Based on 1038 SNP markers, we evaluated the genetic diversity and population structure among six J. chilensis natural groups encompassing 96% of the species distribution. We observed low levels of genetic diversity, a deficit of heterozygotes (mean HE = 0.024; HO = 0.014), and high levels of inbreeding (mean FIS = 0.424). The fixation index (FST) and Nei’s genetic distance pairwise comparisons indicated low to moderate structuring among populations. There was no evidence of isolation by distance (r = −0.214, p = 0.799). In the cluster analysis, we observed a closer relationship among Culimo, Cocalán, and Candelaria populations. Migration rates among populations were low, except for some populations with moderate values. The K value that best represented the spatial distribution of genetic diversity was ∆K = 3. Habitat fragmentation, deterioration of the sclerophyllous forest, lack of long-distance dispersers, and a natural regeneration deficit may have driven inbreeding and low levels of genetic diversity in the palm groves of J. chilensis. Although extant populations are not at imminent risk of extinction, the rate of inbreeding could increase and migration could decrease if the effects of climate change and human impact become more acute.

Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size.

Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST , a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST . Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size.

Host-mediated dispersal shapes spatial distribution of genetic variability in marine symbionts

Assessing the importance of intrinsic and extrinsic factors that shape the spatial distribution of genetic diversity of symbionts has been a topic of debate for decades. While host-mediated dispersal is an important driver of gene flow in many terrestrial metazoan symbionts, few studies have identified the drivers of symbiont genetic differentiation in the marine realm, where habitats are comparatively more homogeneous and long-distance dispersal is common. In the present study, we perform a meta-analysis of existing studies examining symbiont spatial genetic diversity to determine which symbiont- and host-related traits shape the patterns of genetic differentiation of metazoan symbionts, while also considering technical aspects of each study. Specifically, we wanted to assess the influence of biological traits and/ or technical aspects in (1) detecting genetic differentiation in marine symbionts, and (2) shaping the minimum spatial scale at which genetic differentiation was detected. By assessing genetic diversity of mtDNA markers, we found that the spatial scale at which studies are conducted was a crucial predictor of both detection of genetic structure and scale at which differentiation of marine symbionts was detected. Symbiont-based traits did not influence genetic structure, however, host-mediated dispersal was the only biological trait that shaped genetic structure of marine symbionts by influencing the spatial distribution at which differentiation was detected.

Captive‐bred ancestry affects spatial patterns of genetic diversity and differentiation in brown trout (Salmo trutta) populations

AbstractIntraspecific genetic diversity is heterogeneously distributed in natural landscapes and often forms repeatable spatial patterns. For instance, in rivers, genetic diversity increases towards downstream areas, whereas genetic differentiation increases in isolated upstream areas. Nonetheless, these patterns can be modified by human‐induced perturbations, and documenting the extent to which human activities alter these natural patterns is important for conservation. Among the human pressures that affect freshwater biodiversity, stocking natural populations with captive‐bred strains is a common practice worldwide that can strongly alter the genetic integrity of wild populations.The main objectives of this study were to document the spatial distribution of captive‐bred ancestry in brown trout (Salmo trutta) populations from four French basins having been stocked according to different practices, and to quantify for each basin the effect of captive‐bred ancestry on the spatial distribution of genetic diversity and differentiation. The four basins were sampled along their upstream–downstream gradient, and a total of 1,686 individuals were genotyped at 192 single nucleotide polymorphism loci.For all basins, individuals with a strong assignment to the captive strain were mostly found in upper reaches, although the average proportion of captive‐bred ancestry varied strikingly among rivers (from 1.9 to 58.7%). Although spatial patterns of genetic differentiation were not affected by introgression and showed an expected increase with increasing distances from the river mouth in all basins, there was evidence that the classical pattern of downstream increase in genetic diversity was reversed when considering highly introgressed populations.These findings demonstrate that the stocking of captive‐bred strains can strongly modify natural spatial patterns of diversity, even when stocking occurred many generations ago and has now ended. The study illustrates the major impacts of humans on intraspecific biodiversity patterns, and emphasizes the importance of conservation plans that take into account this artificial distribution of genetic diversity.

Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments.

Ecological adaptive differentiation alters both the species diversity and intraspecific genetic diversity in forests, thus affecting the stability of forest ecosystems. Therefore, knowledge of the genetic underpinnings of the ecological adaptive differentiation of forest species is critical for effective species conservation. In this study, single-nucleotide polymorphisms (SNPs) from population transcriptomes were used to investigate the spatial distribution of genetic variation in Liriodendron to assess whether environmental variables can explain genetic divergence. We examined the contributions of environmental variables to population divergence and explored the genetic underpinnings of local adaptation using a landscape genomic approach. Niche models and statistical analyses showed significant niche divergence between L. chinense and L. tulipifera, suggesting that ecological adaptation may play a crucial role in driving interspecific divergence. We detected a new fine-scale genetic structure in L. chinense, and divergence of the six groups occurred during the late Pliocene to early Pleistocene. Redundancy analysis (RDA) revealed significant associations between genetic variation and multiple environmental variables. Environmental association analyses identified 67 environmental association loci (EALs; nonsynonymous SNPs) that underwent interspecific or intraspecific differentiation, 28 of which were associated with adaptive genes. These 28 candidate adaptive loci provide substantial evidence for local adaptation in Liriodendron. Our findings reveal ecological adaptive divergence pattern between Liriodendron species and provide novel insight into the role of heterogeneous environments in shaping genetic structure and driving local adaptation among populations, informing future L. chinense conservation efforts.

Development of tools to rapidly identify cryptic species and characterize their genetic diversity in different European kelp species

Marine ecosystems formed by kelp forests are severely threatened by global change and local coastline disturbances in many regions. In order to take appropriate conservation, mitigation, and restoration actions, it is crucial to identify the most diverse populations which could serve as a “reservoir” of genetic diversity. This requires the development of specific tools, such as microsatellite markers to investigate the level and spatial distribution of genetic diversity. Here, we tested new polymorphic microsatellite loci from the genome of the kelp, Laminaria digitata, and tested them for cross-amplification and polymorphism in four closely related congeneric species (Laminaria hyperborea, Laminaria ochroleuca, Laminaria rodriguezii, and Laminaria pallida). Adding these 20 new microsatellite loci to the ten L. digitata loci previously developed by Billot et al. (Mol Ecol 7:1778-1780, 1998) and Brenan et al. (J R Soc Interface 11:1-12, 2014) and to the ten L. ochroleuca loci previously developed by Coelho et al. (Conserv Genet Resource 6:949-950, 2014), we retained a total of 30 polymorphic loci for L. digitata, 21 for L. hyperborea, 16 for L ochroleuca, 18 for L. rodriguezii, and 12 for L. pallida. These markers have been tested for the first time in the last two species. As predicted, the proportion of markers that cross-amplified between species decreased with increasing genetic distance. In addition, as problems of species identification were reported in this family, mainly between L. digitata and Hedophyllum nigripes, but also between L. digitata, L. hyperborea, and L. ochroleuca in areas where their range distributions overlap, we report a rapid PCR identification method based on species-specific COI mitochondrial primers that allows these four species of kelp to be rapidly distinguished.

Single Independent Autopolyploidization Events From Distinct Diploid Gene Pools and Residual Sexuality Support Range Expansion of Locally Adapted Tetraploid Genotypes in a South American Grass.

Polyploidy plays a major role in plant evolution. The establishment of new polyploids is often a consequence of a single or few successful polyploidization events occurring within a species’ evolutionary trajectory. New polyploid lineages can play different roles in plant diversification and go through several evolutionary stages influenced by biotic and abiotic constraints and characterized by extensive genetic changes. The study of such changes has been crucial for understanding polyploid evolution. Here, we use the multiploid-species Paspalum intermedium to study population-level genetic and morphological variation and ecological differentiation in polyploids. Using flow cytometry, amplified fragment length polymorphism (AFLP) genetic markers, environmental variables, and morphological data, we assessed variations in ploidy, reproductive modes, and the genetic composition in 35 natural populations of P. intermedium along a latitudinal gradient in South America. Our analyses show that apomictic auto-tetraploids are of multiple independent origin. While overall genetic variation was higher in diploids, both diploids and tetraploids showed significant variation within and among populations. The spatial distribution of genetic variation provides evidence for a primary origin of the contact zone between diploids and tetraploids and further supports the hypothesis of geographic displacement between cytotypes. In addition, a strong link between the ecological differentiation of cytotypes and spatial distribution of genetic variation was observed. Overall, the results indicate that polyploidization in P. intermedium is a recurrent phenomenon associated to a shift in reproductive mode and that multiple polyploid lineages from genetically divergent diploids contributed to the successful establishment of local polyploid populations and dispersal into new environments.

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.

Geographical and environmental contributions to genomic divergence in mangrove forests

Abstract Assessing the relative importance of geographical and environmental factors to the spatial distribution of genetic variation can provide information about the processes that maintain genetic variation in natural populations. With a globally wide but very restricted habitat distribution, mangrove trees are a useful model for studies aiming to understand the contributions of these factors. Mangroves occur along the continent–ocean interface of tropical and subtropical latitudes, regions considered inhospitable to many other types of plants. Here, we used landscape genomics approaches to investigate the relative contributions of geographical and environmental variables to the genetic variation of two black mangrove species, Avicennia schaueriana and Avicennia germinans, along the South American coast. Using single nucleotide polymorphisms, our results revealed an important role of ocean currents and geographical distance in the gene flow of A. schaueriana and an isolation-by-environment pattern in the organization of the genetic diversity of A. germinans. Additionally, for A. germinans, we observed significant correlations between genetic variation with evidence of selection and the influence of precipitation regimens, solar radiation and temperature patterns. These discoveries expand our knowledge about the evolution of mangrove trees and provide important information to predict future responses of coastal species to the expected global changes during this century.

Genetic diversity and structure of Taxus baccata from the Cantabrian-Atlantic area in northern Spain: A guide for conservation and management actions

The maintenance of biological diversity at ecosystem, species and intraspecific levels is essential to ensure the survival of forests. The palaeartic yew Taxus baccata is part of a number of threatened forest types with prioritized conservation value in Europe. We investigated the spatial distribution of microsatellite genetic diversity in forty-six T. baccata populations (1,054 trees) spanning the Cantabrian-Atlantic Region (CR) in Northern Spain, framed within a conservation and restoration plan of the species in that region. Different layers of genetic structure were detected, with low structure at a global scale, suggesting historical connectivity, and a complex structure at smaller spatial scales. A low but significant regional genetic variation was also identified associated with biogeographical groups within CR, of potential interest to assist conservation and restoration programs. These genetic differences were reflected on a heterogeneous contribution to the total heterozygosity and allelic richness by the different regions. Data were contextualized within the Iberian Peninsula using previous data in this species (totaling 2,731 trees from 128 populations) after genotype standardization for a common set of seven microsatellites, confirming higher genetic diversity and more homogeneous structure in CR than in central and southeastern Iberian regions. Evidence of geographical structure between eastern (Betic Range, Catalonian Ranges, Pyrenees) and western (Cantabrian Range, Central System Range, Iberian System Range) populations was detected. This study deepens into the spatial distribution of genetic diversity in T. baccata through an intensive survey in CR as a basis for different in situ and ex situ conservation actions in the region aimed to conserve the genetic resources of this species and improve protected yew-associated natural habitats.