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.

Inter- and intra-specific variability in isoprene production and photosynthesis of Central European oak species

European deciduous oaks are closely related and are known for their strong emission of volatile isoprenoids. They are chemo-taxonomically diverse, but hybridise frequently. Four-year-old oak seedlings growing together in a model ecosystem facility under near-natural conditions were studied. The leaves were morphologically classified in the three oak species Quercus robur, Q. pubescens and Q. petraea (with four provenances each) and further investigated by a molecular-genetic approach. Q. robur was morphologically and genetically clearly different from Q. pubescens and Q. petraea, whereas Q. pubescens and Q. petraea individuals used in this study were morphologically and genetically more similar. There was a minor impact of among and within species variability on isoprene synthesis, isoprene emission and photosynthesis. Isoprene emission rates normalised to 25 °C leaf temperature ranged from 5.78 to 10.66 nmol m(-2)  s(-1) , whereas photosynthesis ranged from 12.8 to 17.6 μmol m(-2)  s(-1) . On cloudy days, among the provenances of each species, only net photosynthesis of the Q. robur provenance Hünenberg was reduced and isoprene synthase activity of the Q. pubescens provenance Promotogno increased. On sunny days, photosynthesis did not differ among the provenances. Over all provenances, gas exchange on cloudy days did not differ significantly from sunny days. In the combined data of cloudy and sunny days, no differences between the studied provenances and oak species were detected in isoprene emission and photosynthesis. Thus, isoprene emission and photosynthesis rates were remarkably stable among oak species and provenances. The results indicate that taxonomic differences in the studied oak species are not reflected in isoprene emission and photosynthesis, probably because of the high plasticity of gene expression resulting in high phenotypic flexibility.

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.

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.

Isolation and characterization of polymorphic nuclear microsatellite loci in Pinus cembra L

We developed eight polymorphic nuclear microsatellite markers for the Swiss stone pine (Pinus cembra L.), of which seven may be amplified in a multiplex polymerase chain reaction. Allelic polymorphism across all loci and 40 individuals representing two populations in the Swiss Alps was high (mean = 7.6 alleles). No significant linkage disequlibrium was displayed between pairs of loci. Significant deviation from Hardy-Weinberg equilibrium was revealed at three loci in one population. Cross-amplification was achieved in two related species within the genus (P. sibirica and P. pumila). Thus, the markers may be useful for population genetic studies in these three pine species. They will be applied in ongoing projects on genetic diversity and patterns of gene flow in P. cembra.

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.

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.

Recombination and clonal propagation in different populations of the lichen Lobaria pulmonaria

Propagation, dispersal, and establishment are fundamental population processes, and are critical stages in the life cycle of an organism. In symbiotic organisms such as lichens, consisting of a fungus and a population of photobionts, reproduction is a complex process. Although many lichens are able to reproduce both sexually and asexually, the extent of vegetative propagation within local populations is unknown. We used six polymorphic microsatellite loci to investigate whether recombination is common in natural populations, and to assess if and how clonal reproduction influences the spatial genetic structure within populations of the epiphytic lichen species Lobaria pulmonaria. High genetic diversity within all 12 investigated populations and evidence of recombination, from various tests, indicated that L. pulmonaria is a predominantly outcrossing species. Nevertheless, clonality occurred in all populations, but the presence of recurring multilocus genotypes influenced the spatial genetic structure only within low-density populations. This could be interpreted as indicative of genetic bottlenecks owing to increased habitat loss and disturbance. Consequently, for a predominantly outcrossing lichen species, exogenous factors might be substantially altering population processes and hence genetic structure.

The evolutionary split of Pinaceae from other conifers: evidence from an intron loss and a multigene phylogeny

The second intron in the mitochondrial gene nad1 was surveyed using PCR, DNA sequencing, or Southern hybridization in 323 species (313 genera, 212 families) of seed plants. The intron was absent in all 22 species (22 genera, 8 families) of non-Pinaceae conifers studied, in Welwitschia mirabilis, and in seven angiosperms. Whereas absence of the intron in seven angiosperms and Welwitschia is likely due to seven independent losses when evaluated against the recently published multigene phylogenies, the lack of the intron in all non-Pinaceae conifers can be best explained by a single loss. These data suggest that the non-Pinaceae conifers represent a monophyletic group. We also conducted a phylogenetic analysis of seed plants using a combined data set of the partial exon and intron sequences of nad1 generated from this study and published sequences of mitochondrial cox1 and small subunit (SSU) rDNA, chloroplast rbcL, and nuclear 18S rDNA. The results supported the split of conifers into two groups: Pinaceae and non-Pinaceae conifers. The Gnetales were sister to Pinaceae, in agreement with the conclusion from other recent molecular phylogenetic studies that refute the anthophyte hypothesis.

Chloroplast microsatellites and mitochondrial nad1 intron 2 sequences indicate congruent phylogenetic relationships among Swiss stone pine (Pinus cembra), Siberian stone pine (Pinus sibirica), and Siberian dwarf pine (Pinus pumila)

We studied the phylogenetic relationships among the three stone pine species, Pinus cembra, P. sibirica, and P. pumila, using chloroplast microsatellites and mitochondrial nad1 intron 2 sequences. The three chloroplast microsatellite loci combined into a total of 18 haplotypes. Fourteen haplotypes were detected in 15 populations of P. cembra and one population of P. sibirica, five of which were shared between the two species, and the two populations of P. pumila comprised four species-specific haplotypes. Mitochondrial intron sequences confirmed this grouping of species. Sequences of P. cembra and P. sibirica were identical, but P. pumila differed by several nucleotide substitutions and insertions/deletions. A repeat region found in the former two species showed no intraspecific variation. These results indicate a relatively recent evolutionary separation of P. cembra and P. sibirica, despite their currently disjunct distributions. The species-specific chloroplast and mitochondrial markers of P. sibirica and P. pumila should help to trace the hybridization in their overlapping distribution area and to identify fossil remains with respect to the still unresolved postglacial re-colonization history of these two species.

Haplotype variation in a mitochondrial tandem repeat of Norway spruce (Picea abies) populations suggests a serious founder effect during postglacial re-colonization of the western Alps

Populations from 13 elevational transects of Norway spruce [Picea abies (L.) Karst] across the Alpine range were sampled to elucidate the geographical pattern of genetic variation in relation to postglacial re-colonization and to study elevational effects on haplotypic diversity. We assessed fragment length variation in a tandem repeat region of the mitochondrial (mt) nad1 intron 2. This maternally inherited genetic marker is suited to infer migration as it is dispersed by seed only. A total of 10 haplotypes was found, most of which were due to repeat copy number variation. An analysis of molecular variance (amova) showed that overall population differentiation was high (F(ST)=0.41), and it revealed a significant differentiation between monomorphic western and moderately to highly variable eastern Alpine populations. This phylogeographic pattern may be explained by a founder effect during postglacial re-colonization. An early arriving haplotype, assumed to originate from a western Carpathian refugium, could expand into suitable habitats, reducing the chances for establishment of subsequently arriving haplotypes. On the other hand, the high variation in populations within an Italian transect of the south-eastern Alps may be the consequence of merging migration pathways from and close distance to putative glacial refugia, most likely those assumed in the Carpathian mountains and on the Balkan peninsula or possibly in the central plains of Italy. An effect of elevation on haplotypic diversity was not evident, though a low, but significant, partition of total genetic variation was attributed to among-population variation in one Italian transect. Various factors, such as vertical seed dispersal and forest management, may account for blurring an otherwise established pattern of genetic variation on a small geographical scale.

Tandem repeats in plant mitochondrial genomes: application to the analysis of population differentiation in the conifer Norway spruce

Mitochondrial DNA, widely applied in studies of population differentiation in animals, is rarely used in plants because of its slow rate of sequence evolution and its complex genomic organization. We demonstrate the utility of two polymorphic mitochondrial tandem repeats located in the second intron of the nad1 gene of Norway spruce. Most of the size variants showed pronounced population differentiation and a distinct geographical distribution. A GenBank search revealed that mitochondrial tandem repeats occur in a broad range of plant species and may serve as a novel molecular marker for unravelling population processes in plants.

Patterns of genetic variation detected by RAPDs suggest a single origin with subsequent mutations and long-distance dispersal in the apomictic fern Dryopteris remota (Dryopteridaceae)

Debates on speciation processes in pteridophytes have revived. In order to study the evolutionary origin of an apomictic fern species, we investigated the genetic variation in the strictly agamosporous Dryopteris remota. We determined the genotypes of 22 individuals from many different locations within the species' European distribution and of 20 individuals from a Swiss population. A previous study on isozyme variation showed no intraspecific genetic variation in a similar sample set (Schneller and Holderegger, 1994, American Fern Journal 84: 94-98). In contrast to this, four out of 12 random amplified polymorphic DNA (RAPD) primers tested revealed low genetic diversity among individuals of D. remota from different locations. Intrapopulational genetic variation was also very low, but in the single population studied, a unique multiband genotype could be detected. The geographic distribution of genetic variation found in D. remota was best explained by the assumption of a single origin, the accumulation of somatic mutations during spread, and occasional, but effective, events of dispersal over large distances. The present study thus stresses the importance of long-distance dispersal in evolutionary processes and biogeography of ferns.