Three-dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity.

Estimating connectivity among fragmented habitat patches is crucial for evaluating the functionality of ecological networks. However, current estimates of landscape resistance to animal movement and dispersal lack landscape-level data on local habitat structure. Here, we used a landscape genetics approach to show that high-fidelity habitat structure maps derived from Light Detection and Ranging (LiDAR) data critically improve functional connectivity estimates compared to conventional land cover data. We related pairwise genetic distances of 128 Capercaillie (Tetrao urogallus) genotypes to least-cost path distances at multiple scales derived from land cover data. Resulting ß values of linear mixed effects models ranged from 0.372 to 0.495, while those derived from LiDAR ranged from 0.558 to 0.758. The identification and conservation of functional ecological networks suffering from habitat fragmentation and homogenization will thus benefit from the growing availability of detailed and contiguous data on three-dimensional habitat structure and associated habitat quality.

Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri.

Numerous landscape genomic studies have identified single-nucleotide polymorphisms (SNPs) and genes potentially involved in local adaptation. Rarely, it has been explicitly evaluated whether these environmental associations also hold true beyond the populations studied. We tested whether putatively adaptive SNPs in Arabidopsis halleri (Brassicaceae), characterized in a previous study investigating local adaptation to a highly heterogeneous environment, show the same environmental associations in an independent, geographically enlarged set of 18 populations. We analysed new SNP data of 444 plants with the same methodology (partial Mantel tests, PMTs) as in the original study and additionally with a latent factor mixed model (LFMM) approach. Of the 74 candidate SNPs, 41% (PMTs) and 51% (LFMM) were associated with environmental factors in the independent data set. However, only 5% (PMTs) and 15% (LFMM) of the associations showed the same environment-allele relationships as in the original study. In total, we found 11 genes (31%) containing the same association in the original and independent data set. These can be considered prime candidate genes for environmental adaptation at a broader geographical scale. Our results suggest that selection pressures in highly heterogeneous alpine environments vary locally and signatures of selection are likely to be population-specific. Thus, genotype-by-environment interactions underlying adaptation are more heterogeneous and complex than is often assumed, which might represent a problem when testing for adaptation at specific loci.

Expert-based versus habitat-suitability models to develop resistance surfaces in landscape genetics.

Landscape genetics aims to investigate functional connectivity among wild populations by evaluating the impact of landscape features on gene flow. Genetic distances among populations or individuals are generally better explained by least-cost path (LCP) distances derived from resistance surfaces than by simple Euclidean distances. Resistance surfaces reflect the cost for an organism to move through particular landscape elements. However, determining the effects of landscape types on movements is challenging. Because of a general lack of empirical data on movements, resistance surfaces mostly rely on expert knowledge. Habitat-suitability models potentially provide a more objective method to estimate resistance surfaces than expert opinions, but they have rarely been applied in landscape genetics so far. We compared LCP distances based on expert knowledge with LCP distances derived from habitat-suitability models to evaluate their performance in landscape genetics. We related all LCP distances to genetic distances in linear mixed effect models on an empirical data set of wolves (Canis lupus) from Italy. All LCP distances showed highly significant (P ≤ 0.0001) standardized ß coefficients and R 2 values, but LCPs from habitat-suitability models generally showed higher values than those resulting from expert knowledge. Moreover, all LCP distances better explained genetic distances than Euclidean distances, irrespective of the approaches used. Considering our results, we encourage researchers in landscape genetics to use resistance surfaces based on habitat suitability which performed better than expert-based LCPs in explaining patterns of gene flow and functional connectivity.

Isolation-by-distance in landscapes: considerations for landscape genetics.

In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern). We investigated if landscape configuration influenced the rate at which a case-IV pattern changed to a case-I pattern. We also determined at what interdeme distance the highest correlation was measured between genetic differentiation and geographic distance and whether this distance corresponded to the maximum migration distance. We set up a population genetic simulation study and assessed the development of IBD patterns for several habitat configurations and maximum migration distances. We show that the rate and likelihood of the transition of case-IV to case-I FST-distance relationships was strongly influenced by habitat configuration and maximum migration distance. We also found that the maximum correlation between genetic differentiation and geographic distance was not related to the maximum migration distance and was measured across all deme pairs in a case-I pattern and, for a case-IV pattern, at the distance where the FST-distance curve flattens out. We argue that in landscape genetics, separate analyses should be performed to either assess IBD or the landscape effects on gene flow.

The structural and functional connectivity of the grassland plant Lychnis flos-cuculi.

Understanding the relationship between structural and functional connectivity is essential for successful restoration and conservation management, particularly in intensely managed agricultural landscapes. We evaluated the relationship between structural and functional connectivity of the wetland plant Lychnis flos-cuculi in a fragmented agricultural landscape using landscape genetic and network approaches. First, we studied the effect of structural connectivity, such as geographic distance and various landscape elements (forest, agricultural land, settlements and ditch verges), on gene flow among populations as a measurement of functional connectivity. Second, we examined the effect of structural graph-theoretic connectivity measures on gene flow among populations and on genetic diversity within populations of L. flos-cuculi. Among landscape elements, forests hindered gene flow in L. flos-cuculi, whereas gene flow was independent of geographic distance. Among the structural graph-theoretic connectivity variables, only intrapopulation connectivity, which was based on population size, had a significant positive effect on gene flow, that is, more gene flow took place among larger populations. Unexpectedly, interpopulation connectivity of populations, which takes into account the spatial location and distance among populations, did not influence gene flow in L. flos-cuculi. However, higher observed heterozygosity and lower inbreeding was observed in populations characterised by higher structural interpopulation connectivity. This finding shows that a spatially coherent network of populations is significant for maintaining the genetic diversity of populations. Nevertheless, lack of significant relationships between gene flow and most of the structural connectivity measures suggests that structural connectivity does not necessarily correspond to functional connectivity.

Widespread phenotypic and genetic divergence along altitudinal gradients in animals.

Altitudinal gradients offer valuable study systems to investigate how adaptive genetic diversity is distributed within and between natural populations and which factors promote or prevent adaptive differentiation. The environmental clines along altitudinal gradients tend to be steep relative to the dispersal distance of many organisms, providing an opportunity to study the joint effects of divergent natural selection and gene flow. Temperature is one variable showing consistent altitudinal changes, and altitudinal gradients can therefore provide spatial surrogates for some of the changes anticipated under climate change. Here, we investigate the extent and patterns of adaptive divergence in animal populations along altitudinal gradients by surveying the literature for (i) studies on phenotypic variation assessed under common garden or reciprocal transplant designs and (ii) studies looking for signatures of divergent selection at the molecular level. Phenotypic data show that significant between-population differences are common and taxonomically widespread, involving traits such as mass, wing size, tolerance to thermal extremes and melanization. Several lines of evidence suggest that some of the observed differences are adaptively relevant, but rigorous tests of local adaptation or the link between specific phenotypes and fitness are sorely lacking. Evidence for a role of altitudinal adaptation also exists for a number of candidate genes, most prominently haemoglobin, and for anonymous molecular markers. Novel genomic approaches may provide valuable tools for studying adaptive diversity, also in species that are not amenable to experimentation.

Contemporary gene flow and mating system of Arabis alpina in a Central European alpine landscape.

BACKGROUND AND AIMS: Gene flow is important in counteracting the divergence of populations but also in spreading genes among populations. However, contemporary gene flow is not well understood across alpine landscapes. The aim of this study was to estimate contemporary gene flow through pollen and to examine the realized mating system in the alpine perennial plant, Arabis alpina (Brassicaceae). METHODS: An entire sub-alpine to alpine landscape of 2 km(2) was exhaustively sampled in the Swiss Alps. Eighteen nuclear microsatellite loci were used to genotype 595 individuals and 499 offspring from 49 maternal plants. Contemporary gene flow by pollen was estimated from paternity analysis, matching the genotypes of maternal plants and offspring to the pool of likely father plants. Realized mating patterns and genetic structure were also estimated. KEY RESULTS: Paternity analysis revealed several long-distance gene flow events (≤1 km). However, most outcrossing pollen was dispersed close to the mother plants, and 84 % of all offspring were selfed. Individuals that were spatially close were more related than by chance and were also more likely to be connected by pollen dispersal. CONCLUSIONS: In the alpine landscape studied, genetic structure occurred on small spatial scales as expected for alpine plants. However, gene flow also covered large distances. This makes it plausible for alpine plants to spread beneficial alleles at least via pollen across landscapes at a short time scale. Thus, gene flow potentially facilitates rapid adaptation in A. alpina likely to be required under ongoing climate change.

Diversity of S-alleles and mate availability in 3 populations of self-incompatible wild pear (Pyrus pyraster).

Small populations of self-incompatible plants may be expected to be threatened by the limitation of compatible mating partners (i.e., S-Allee effect). However, few empirical studies have explicitly tested the hypothesis of mate limitation in small populations of self-incompatible plants. To do so, we studied wild pear (Pyrus pyraster), which possesses a gametophytic self-incompatibility system. We determined the S-genotypes in complete samplings of all adult trees from 3 populations using a PCR-RFLP approach. We identified a total of 26 different S-alleles, homologous to S-alleles of other woody Rosaceae. The functionality of S-alleles and their Mendelian inheritance were verified in artificial pollination experiments and investigations of pollen tube growth. The smallest population (N = 8) harbored 9 different S-alleles and showed a mate availability of 92.9%, whereas the 2 larger populations harbored 18 and 25 S-alleles and exhibited mate availabilities of 98.4% and 99.2%, respectively. Therefore, we conclude that even small populations of gametophytic self-incompatible plants may exhibit high diversity at the S-locus and are not immediately threatened owing to reduced mate availability.

Common factors drive adaptive genetic variation at different spatial scales in Arabis alpina.

A major challenges facing landscape geneticists studying adaptive variation is to include all the environmental variables that might be correlated with allele frequencies across the genome. One way of identifying loci that are possibly under selection is to see which ones are associated with environmental gradient or heterogeneity. Since it is difficult to measure all environmental variables, one may take advantage of the spatial nature of environmental filters to incorporate the effect of unaccounted environmental variables in the analysis. Assuming that the spatial signature of these variables is broad-scaled, broad-scale Moran's eigenvector maps (MEM) can be included as explanatory variables in the analysis as proxies for unmeasured environmental variables. We applied this approach to two data sets of the alpine plant Arabis alpina. The first consisted of 140 AFLP loci sampled at 130 sites across the European Alps (large scale). The second one consisted of 712 AFLP loci sampled at 93 sites (regional scale) in three mountain massifs (local scale) of the French Alps. For each scale, we regressed the frequencies of each AFLP allele on a set of eco-climatic and MEM variables as predictors. Twelve (large scale) and 11% (regional scale) of all loci were detected as significantly correlated to at least one of the predictors ( > 0.5), and, except for one massif, 17% at the local scale. After accounting for spatial effects, temperature and precipitation were the two major determinants of allele distributions. Our study shows how MEM models can account for unmeasured environmental variation in landscape genetics models.

Frequent long-distance gene flow in a rare temperate forest tree (Sorbus domestica) at the landscape scale.

Precise empirical data on current gene flow by pollen, both with respect to distance and abundance, is crucial to understand whether habitat fragments are functionally connected. Based on a large-scale inventory ( approximately 100 km(2)) in which all individuals of a naturally scattered forest tree (Sorbus domestica) were mapped, we inferred current gene flow by pollen using genetic paternity analysis. We detected an extensive network of effective pollen transfer. Although short pollen flow distances were most abundant, 10% of the assigned pollen donors were more than 2 km away from their female mating partners, and 1.8% were even at a distance of 12-16 km. This latter pollen flow shows that current long-distance gene flow over a fragmented landscape clearly occurs. Pollen dispersal was well described by a fat-tailed inverse curve. Using parentage analysis of established trees, maternally inherited chloroplast markers and diameter at breast height measurements as an indicator of individual tree age, we were able to infer regular seed dispersal distances over several hundred metres up to more than 10 km. We conclude that in temperate, insect-pollinated and animal-dispersed tree species such as S. domestica, fragmented subpopulations are functionally connected by gene flow through both pollen and seed.

Patterns in genetic diversity of Trifolium pallescens populations do not reflect chronosequence on alpine glacier forelands.

How does genetic diversity within populations of plants develop during primary succession on alpine glacier forelands? Theory predicts that pioneer populations are characterized by low genetic diversity due to founder effects and that genetic diversity increases within populations as they mature and recurrent gene flow occurs. However, few genetic studies have so far been carried out on plants on glacier forelands. In this study, we analysed the development of genetic diversity with time for populations of Trifolium pallescens along successional series (chronosequences) on three parallel glacier forelands in the European Alps, using neutral amplified fragment length polymorphism. No general trend in the development of genetic diversity was observed with increasing population age: even pioneer populations harboured substantial genetic diversity. Assignment tests showed that the latter consist of a genetic sub-sample from several source areas, and not just from other populations on the glacier forelands. We also detected some long distances-that is, inter-valley gene flow events. However, gene flow was not spatially unrestricted, as shown by a weak isolation by distance pattern within glacier valleys. The actual patterns of genetic diversity along the chronosequences are a result of the combination of factors, such as gene flow and growth rate, influenced by site- and species-specific attributes.

Fully informative microsatellite markers for the tetraploid plant Eritrichium nanum (Boraginaceae).

We characterized eight polymorphic, codominant nuclear microsatellite loci in the tetraploid plant Eritrichium nanum. The different allelic configurations occurring under tetrasomic inheritance were fully resolved at all loci. Two natural populations showed high observed heterozygosities, which were in agreement with Hardy-Weinberg expectations. There was no evidence of genetic linkage disequilibrium for any pair of loci. The results suggest that these microsatellite markers are useful for mating system and population genetic analyses in high-alpine E. nanum.

Phylogeography of the high alpine plant Senecio halleri (Asteraceae) in the European Alps: in situ glacial survival with postglacial stepwise dispersal into peripheral areas.

Whether alpine plant species survived Pleistocene glaciations in situ on high alpine nunatak mountains is still under debate. To test this hypothesis, Senecio halleri, a high alpine and endemic species with a narrow distribution range in the European Alps, was chosen as a model organism. Polymerase chain reaction-restriction fragment length polymorphisms of chloroplast DNA (cpDNA PCR-RFLPs) were used in a phylogeographic analysis of 14 populations of S. halleri, covering its total distribution area. The results of haplotype diversity and distribution gave evidence of in situ glacial survival on siliceous central-alpine nunatak mountains in two areas, southwest and northeast of the Aosta valley. According to the absence of genetic differentiation between these two nunatak areas (based on amova), nested clade analysis implied a history of preglacial gene flow, in situ survival and extinction of intermediate populations during glaciation and postglacial stepwise recolonization of peripheral and intermediate areas.

Coincidence of small-scale spatial discontinuities in leaf morphology and nuclear microsatellite variation of Quercus petraea and Q. robur in a mixed forest.

BACKGROUND AND AIMS: The taxon complex comprising Quercus petraea and Q. robur shows distinct morphologies and ecological preferences, but mostly low differentiation in various types of molecular markers at a broad spatial range. Local, spatially explicit analyses may reveal patterns induced by microevolutionary processes operating mainly over short distances. However, no attempts have been made to date to explore the potential of spatial analyses combining morphological and genetic data of these oaks. METHODS: A mixed oak stand was studied to elucidate the small-scale population genetic structure. All adult individuals were classified and putative hybrids were identified using multivariate discrimination analysis of leaf morphological characters. Likewise, all trees were genotyped with five nuclear microsatellites, and a Bayesian assignment method was applied based on maximum likelihood of multilocus genotypes for taxon and putative hybrid classification. KEY RESULTS: Multivariate analyses of leaf morphological data recognized two groups with few individuals as putative hybrids. These groups were significantly differentiated at the five microsatellites, and genetic taxon assignment coincided well with morphological classification. Furthermore, most putative hybrids were assigned to the taxon found in their spatial neighbourhood. When grouping trees into clusters according to their spatial positions, these clusters were clearly dominated by one taxon. Discontinuities in morphological and genetic distance matrices among these clusters showed high congruence. CONCLUSIONS: The spatial-genetic analyses and the available literature led to the assumption that reproductive barriers, assortative mating, limited seed dispersal and microsite-induced selection in favour of the locally adapted taxon at the juvenile stage may reinforce taxon-specific spatial aggregation that fosters species separation. Thus, the results tend to support the hypothesis that Q. petraea and Q. robur are distinct taxa which share a recent common ancestry. Occasional hybrids are rarely found in adults owing to selection during establishment of juveniles.

Regional population dynamics define the local genetic structure in Sorbus torminalis.

Recent changes in sylvicultural practices in Central Europe have created forests with closed canopies, and tree species preferring open and sunny forests have declined in area and abundance. This led to increased isolation of populations of many rare insect-pollinated, fleshy-fruited species with a naturally scattered distribution. To gain insight into the regional population dynamics of such species, we investigated the consequences of spatial isolation, population size and density on the genetic structure of Sorbus torminalis and simultaneously considered the relationship between fecundity and habitat quality. Genotype data for biparentally (ISSRs) and maternally inherited (cpDNA PCR-RFLPs) molecular markers were generated for 26 Swiss populations of S. torminalis. We applied analyses of molecular variance (amova) to both marker types and separated the relative contributions of pollen and seed dispersal to historical gene flow. amova detected significant differentiation among populations (Phi(ST ISSR) = 0.107; Phi(ST cpDNA) = 0.370) in both marker types. The relative rate of pollen to seed gene flow was low (r = 2.919) and significantly different from equality. Isolation by distance was weak within Eastern and Western Switzerland, although populations were substantially differentiated. Within-population molecular variance was not explained by population size, whereas habitat quality (openness) positively influenced the percentage of fruiting trees and the degree of fruiting per tree, indicating that more open forests enhance sexual reproduction. Our findings of significant genetic differentiation in the absence of clear geographical structuring can be explained by the distinct ecology of S. torminalis and nondirectional colonization events in metapopulation-like dynamics.

Mating patterns and contemporary gene flow by pollen in a large continuous and a small isolated population of the scattered forest tree Sorbus torminalis.

The influence of population size and spatial isolation on contemporary gene flow by pollen and mating patterns in temperate forest trees are not well documented, although they are crucial factors in the life history of plant species. We analysed a small, isolated population and a large, continuous population of the insect-pollinated tree species Sorbus torminalis in two consecutive years. The species recently experienced increased habitat fragmentation due to altered forest management leading to forests with closed canopies. We estimated individual plant size, percentage of flowering trees, intensity of flowering, degree of fruiting and seed set per fruit, and we determined mating patterns, pollen flow distances and external gene flow in a genetic paternity analysis based on microsatellite markers. We found clear effects of small population size and spatial isolation in S. torminalis. Compared with the large, continuous population, the small and isolated population harboured a lower percentage of flowering trees, showed less intense flowering, lower fruiting, less developed seeds per fruit, increased selfing and received less immigrant pollen. However, the negative inbreeding coefficients (F(IS)) of offspring indicated that this did not result in inbred seed at the population level. We also show that flowering, fruiting and pollen flow patterns varied among years, the latter being affected by the size of individuals. Though our study was unreplicated at the factor level (i.e. isolated vs non-isolated populations), it shows that small and spatially isolated populations of S. torminalis may also be genetically isolated, but that their progeny is not necessarily more inbred.

Molecular evidence for glacial refugia of mountain plants in the European Alps.

Many mountain ranges have been strongly glaciated during the Quaternary ice ages, and the locations of glacial refugia of mountain plants have been debated for a long time. A series of detailed molecular studies, investigating intraspecific genetic variation of mountain plants in the European Alps, now allows for a first synopsis. A comparison of the phylogeographic patterns with geological and palaeoenvironmental data demonstrates that glacial refugia were located along the southwestern, southern, eastern and northern border of the Alps. Additional glacial refugia were present in central Alpine areas, where high-elevation plants survived the last glaciation on ice-free mountain tops. The observed intraspecific phylogeographies suggest general patterns of glacial survival, which conform to well-known centres of Alpine species diversity and endemism. This implies that evolutionary or biogeographic processes induced by climatic fluctuations act on gene and species diversity in a similar way.

Understanding population history for conservation purposes: population genetics of Saxifraga aizoides (Saxifragaceae) in the lowlands and lower mountains north of the Alps.

Several alpine species have outlying populations in the lowlands and lower mountains north of the Alps. These small, isolated populations are usually described as either (1) glacial relics, (2) descendants from populations living on forelands and moraines during the ice ages, or (3) populations founded by long-distance dispersal after glaciation. A floristic survey of the historic and present distributions and an allozyme investigation were performed on one of these relic species, Saxifraga aizoides. The species was historically more abundant and had more stations in more regions of northeastern Switzerland. The former population structures within regions, nowadays destroyed, were still reflected in distinct and high regional genetic diversity and variation. There was weak evidence of increased inbreeding in outlying populations, but populations did not deviate from Hardy-Weinberg equilibrium. No geographic pattern of genetic variation above the regional scale (>10 km) was found. Based on the spatial and genetic structures found, it was not possible to discriminate between the abovementioned hypotheses. Nevertheless, the study shows how a thorough evaluation of distribution and abundance data aids the interpretation of genetic data with respect to population history, biogeography, and conservation biology.

Historical bottlenecks decrease genetic diversity in natural populations of Dryopteris cristata.

The reconstruction of recent historical population sizes allowed us to investigate the influence of random evolutionary processes on present-day genetic diversity in populations of Dryopteris cristata. This long-lived, allotetraploid fern is rare and endangered in the study area at the southwestern border of its European distribution. Random amplified polymorphic DNA (RAPD) diversity of 280 individuals from 14 populations of D. cristata was extraordinarily low, suggesting an ancient bottleneck in the species' history. Analysis of molecular variance (AMOVA) of 25 different RAPD multiband phenotypes revealed significant genetic variation among three geographical regions (15%) and among populations within regions (34%); 51% of total variance was attributed to variation within populations. High population differentiation indicated limited gene flow among populations, and genetic divergence was not correlated with geographical distance. There was no relationship between genetic variation within population, estimated as molecular variance, and present-day population size. Populations with recent historical bottlenecks of fewer than 25 individuals showed a substantial and significant reduction in genetic variation, compared with populations without bottlenecks. Comparatively high levels of genetic variation were still maintained in small remnants (60-110 individuals) of formerly large populations. Average deviations of frequencies of widespread polymorphic markers within populations from their frequencies in the whole dataset were significantly higher in small or recently bottlenecked populations than in constantly large populations, thus providing evidence for random sampling effects during genetic bottlenecks and drift in small populations. The present investigation demonstrates the importance of population history for understanding present-day genetic diversity within natural populations, as well as for conservation biology.