Monitoring of species' genetic diversity in Europe varies greatly and overlooks potential climate change impacts

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species' joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union's Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity.

Re-thinking the environment in landscape genomics

Detecting the extrinsic selective pressures shaping genomic variation is critical for a better understanding of adaptation and for forecasting evolutionary responses of natural populations to changing environmental conditions. With increasing availability of geo-referenced environmental data, landscape genomics provides unprecedented insights into how genomic variation and underlying gene functions affect traits potentially under selection. Yet, the robustness of genotype-environment associations used in landscape genomics remains tempered due to various limitations, including the characteristics of environmental data used, sampling designs employed, and statistical frameworks applied. Here, we argue that using complementary or new environmental data sources and well-informed sampling designs may help improve the detection of selective pressures underlying patterns of local adaptation in various organisms and environments.

The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation

BACKGROUND

Plant mitogenomes vary widely in size and genomic architecture. Although hundreds of plant mitogenomes of angiosperm species have already been sequence-characterized, only a few mitogenomes are available from gymnosperms. Silver fir (Abies alba) is an economically important gymnosperm species that is widely distributed in Europe and occupies a large range of environmental conditions. Reference sequences of the nuclear and chloroplast genome of A. alba are available, however, the mitogenome has not yet been assembled and studied.

RESULTS

Here, we used paired-end Illumina short reads generated from a single haploid megagametophyte in combination with PacBio long reads from high molecular weight DNA of needles to assemble the first mitogenome sequence of A. alba. Assembly and scaffolding resulted in 11 mitogenome scaffolds, with the largest scaffold being 0.25 Mbp long. Two of the scaffolds displayed a potential circular structure supported by PCR. The total size of the A. alba mitogenome was estimated at 1.43 Mbp, similar to the size (1.33 Mbp) of a draft assembly of the Abies firma mitogenome. In total, 53 distinct genes of known function were annotated in the A. alba mitogenome, comprising 41 protein-coding genes, nine tRNA, and three rRNA genes. The proportion of highly repetitive elements (REs) was 0.168. The mitogenome seems to have a complex and dynamic structure featured by high combinatorial variation, which was specifically confirmed by PCR for the contig with the highest mapping coverage. Comparative analysis of all sequenced mitogenomes of gymnosperms revealed a moderate, but significant positive correlation between mitogenome size and proportion of REs.

CONCLUSIONS

The A. alba mitogenome provides a basis for new comparative studies and will allow to answer important structural, phylogenetic and other evolutionary questions. Future long-read sequencing with higher coverage of the A. alba mitogenome will be the key to further resolve its physical structure. The observed positive correlation between mitogenome size and proportion of REs will be further validated once available mitogenomes of gymnosperms would become more numerous. To test whether a higher proportion of REs in a mitogenome leads to an increased recombination and higher structural complexity and variability is a prospective avenue for future research.

The untapped potential of macrofossils in ancient plant DNA research

The rapid development of ancient DNA analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing, and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa are now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of paleogenomic studies still focus on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for paleogenomic analyses: plant remains, such as needles, leaves, wood, seeds, or fruits, that are deposited in natural archives, such as lake sediments, permafrost, or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.

Genomics and adaptation in forest ecosystems

Rapid human-induced environmental changes like climate warming represent a challenge for forest ecosystems. Due to their biological complexity and the long generation time of their keystone tree species, genetic adaptation in these ecosystems might not be fast enough to keep track with conditions changing at such a fast pace. The study of adaptation to environmental change and its genetic mechanisms is therefore key for ensuring a sustainable support and management of forests. The 4-day conference of the European Research Group EvolTree (https://www.evoltree.eu) on the topic of "Genomics and Adaptation in Forest Ecosystems" brought together over 130 scientists to present and discuss the latest developments and findings in forest evolutionary research. Genomic studies in forest trees have long been hampered by the lack of high-quality genomics resources and affordable genotyping methods. This has dramatically changed in the last few years; the conference impressively showed how such tools are now being applied to study past demography, adaptation and interactions with associated organisms. Moreover, genomic studies are now finally also entering the world of conservation and forest management, for example by measuring the value or cost of interspecific hybridization and introgression, assessing the vulnerability of species and populations to future change, or accurately delineating evolutionary significant units. The newly launched conference series of EvolTree will hopefully play a key role in the exchange and synthesis of such important investigations.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11295-022-01542-1.

Arabis alpina: A perennial model plant for ecological genomics and life-history evolution

Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpine Arabis alpina has become a model complementary to Arabidopsis thaliana to study the evolution of life‐history traits, such as perenniality, and ecological genomics in harsh environments. In this review, we provide an overview of the properties that facilitated the rapid emergence of A. alpina as a plant model. We summarize the evolutionary history of A. alpina, including genomic aspects, the diversification of its mating system and demographic properties, and we discuss recent progress in the molecular dissection of developmental traits that are related to its perennial life history and environmental adaptation. From this published knowledge, we derive open questions that might inspire future research in A. alpina, other Brassicaceae species or more distantly related plant families.

The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species

BACKGROUND

Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information.

FINDINGS

The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species' geographic ranges and reflecting local environmental gradients.

CONCLUSION

The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.

Genomic vulnerability to rapid climate warming in a tree species with a long generation time

The ongoing increase in global temperature affects biodiversity, especially in mountain regions where climate change is exacerbated. As sessile, long-lived organisms, trees are especially challenged in terms of adapting to rapid climate change. Here, we show that low rates of allele frequency shifts in Swiss stone pine (Pinus cembra) occurring near the treeline result in high genomic vulnerability to future climate warming, presumably due to the species' long generation time. Using exome sequencing data from adult and juvenile cohorts in the Swiss Alps, we found an average rate of allele frequency shift of 1.23 × 10^-2 /generation (i.e. 40 years) at presumably neutral loci, with similar rates for putatively adaptive loci associated with temperature (0.96 × 10^-2 /generation) and precipitation (0.91 × 10^-2 /generation). These recent shifts were corroborated by forward-in-time simulations at neutral and adaptive loci. Additionally, in juvenile trees at the colonisation front we detected alleles putatively beneficial under a future warmer and drier climate. Notably, the observed past rate of allele frequency shift in temperature-associated loci was decidedly lower than the estimated average rate of 6.29 × 10^-2 /generation needed to match a moderate future climate scenario (RCP4.5). Our findings suggest that species with long generation times may have difficulty keeping up with the rapid climate change occurring in high mountain areas and thus are prone to local extinction in their current main elevation range.

Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species

It has long been discussed to what extent related species develop similar genetic mechanisms to adapt to similar environments. Most studies documenting such convergence have either used different lineages within species or surveyed only a limited portion of the genome. Here, we investigated whether similar or different sets of orthologous genes were involved in genetic adaptation of natural populations of three related plant species to similar environmental gradients in the Alps. We used whole-genome pooled population sequencing to study genome-wide SNP variation in 18 natural populations of three Brassicaceae (Arabis alpina, Arabidopsis halleri, and Cardamine resedifolia) from the Swiss Alps. We first de novo assembled draft reference genomes for all three species. We then ran population and landscape genomic analyses with ~3 million SNPs per species to look for shared genomic signatures of selection and adaptation in response to similar environmental gradients acting on these species. Genes with a signature of convergent adaptation were found at significantly higher numbers than expected by chance. The most closely related species pair showed the highest relative over-representation of shared adaptation signatures. Moreover, the identified genes of convergent adaptation were enriched for nonsynonymous mutations, suggesting functional relevance of these genes, even though many of the identified candidate genes have hitherto unknown or poorly described functions based on comparison with Arabidopsis thaliana. We conclude that adaptation to heterogeneous Alpine environments in related species is partly driven by convergent evolution, but that most of the genomic signatures of adaptation remain species-specific.

Hare's affairs: Lessons learnt from a noninvasive genetic monitoring for tracking mountain hare individuals

Systematic monitoring of individuals and their abundance over time has become an important tool to provide information for conservation. For genetic monitoring studies, noninvasive sampling has emerged as a valuable approach, particularly so for elusive or rare animals. Here, we present the 5-year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in a protected area in the Swiss Alps. We used nuclear microsatellites and a sex marker to identify individuals and assign species to noninvasively collected feces samples. Through including a marker for sex identification, we were able to assess sex ratio changes and sex-specific demographic parameters over time. Male abundance in the area showed high fluctuations and apparent survival for males was lower than for females. Generally, males and females showed only little temporary migration into and out of the study area. Additionally, using genotyped tissue samples from mountain hares, European hares (Lepus europaeus) and their hybrids, we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2,300 m a.s.l. in spring 2016. For future monitoring studies, we suggest to include complementary analysis methods to reliably infer species identities of the individuals analyzed and, thus, not only monitor mountain hare individual abundance, but also assess the potential threats given through competitive exclusion by and hybridization with the European hare.

Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine

It is generally accepted that the spatial distribution of neutral genetic diversity within a species' native range mostly depends on effective population size, demographic history, and geographic position. However, it is unclear how genetic diversity at adaptive loci correlates with geographic peripherality or with habitat suitability within the ecological niche. Using exome-wide genomic data and distribution maps of the Alpine range, we first tested whether geographic peripherality correlates with four measures of population genetic diversity at > 17,000 SNP loci in 24 Alpine populations (480 individuals) of Swiss stone pine (Pinus cembra) from Switzerland. To distinguish between neutral and adaptive SNP sets, we used four approaches (two gene diversity estimates, F_ST outlier test, and environmental association analysis) that search for signatures of selection. Second, we established ecological niche models for P. cembra in the study range and investigated how habitat suitability correlates with genetic diversity at neutral and adaptive loci. All estimates of neutral genetic diversity decreased with geographic peripherality, but were uncorrelated with habitat suitability. However, heterozygosity (H_e ) at adaptive loci based on Tajima's D declined significantly with increasingly suitable conditions. No other diversity estimates at adaptive loci were correlated with habitat suitability. Our findings suggest that populations at the edge of a species' geographic distribution harbour limited neutral genetic diversity due to demographic properties. Moreover, we argue that populations from suitable habitats went through strong selection processes, are thus well adapted to local conditions, and therefore exhibit reduced genetic diversity at adaptive loci compared to populations at niche margins.

A species-discriminatory single-nucleotide polymorphism set reveals maintenance of species integrity in hybridizing European white oaks (Quercus spp.) despite high levels of admixture

BACKGROUND AND AIMS

Hybridization and introgression play an important role in the evolution and diversification of plants. To assess the degree of past and current hybridization, the level of genetic admixture in populations needs to be investigated. Ongoing hybridization and blurred species separation have made it challenging to assign European white oak taxa based on leaf morphology and/or genetic markers and to assess the level of admixture. Therefore, there is a need for powerful markers that differentiate between taxa. Here, we established a condensed set of single-nucleotide polymorphism (SNP) markers to reliably differentiate between the three most common oak species in temperate European forests (Quercus robur, Q. petraea, Q. pubescens) and to assess the degree of admixture in a large set of selected Swiss populations.

METHODS

A training set of 194 presumably pure reference samples from Switzerland and Europe was used to assign 633 test individuals with two different approaches (population genetic-based/Bayesian vs. assumption-free/discriminative classifier) using 58 selected SNPs from coding regions. Admixture was calculated at the individual and population level with the Shannon diversity index based on individual assignment probabilities.

KEY RESULTS

Depending on the approach, 97.5-100 % of training individuals were assigned correctly, and additional analyses showed that the established SNP set could be further reduced while maintaining its discriminatory power. The two assignment approaches showed high overlap (99 %) in assigning training individuals and slightly less overlap in test individuals (84 %). Levels of admixture varied widely among populations. Mixed stands of Q. petraea and Q. pubescens revealed much higher degrees of admixture than mixed stands of the other two taxon pairs, accentuating high levels of gene flow between these two taxa in Switzerland.

CONCLUSIONS

Our set of SNPs warrants reliable taxon discrimination with great potential for further applications. We show that the three European white oak taxa have largely retained their species integrity in Switzerland despite high levels of admixture.

The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.

Conservation genetics: Linking science with practice

Conservation genetics is a well-established scientific field. However, limited information transfer between science and practice continues to hamper successful implementation of scientific knowledge in conservation practice and management. To mitigate this challenge, we have established a conservation genetics community, which entails an international exchange-and-skills platform related to genetic methods and approaches in conservation management. First, it allows for scientific exchange between researchers during annual conferences. Second, personal contact between conservation professionals and scientists is fostered by organising workshops and by popularising knowledge on conservation genetics methods and approaches in professional journals in national languages. Third, basic information on conservation genetics has been made accessible by publishing an easy-to-read handbook on conservation genetics for practitioners. Fourth, joint projects enabled practitioners and scientists to work closely together from the start of a project in order to establish a tight link between applied questions and scientific background. Fifth, standardised workflows simplifying the implementation of genetic tools in conservation management have been developed. By establishing common language and trust between scientists and practitioners, all these measures help conservation genetics to play a more prominent role in future conservation planning and management.

Adaptation to local climate in multi-trait space: evidence from silver fir (Abies alba Mill.) populations across a heterogeneous environment

Heterogeneous environments, such as mountainous landscapes, create spatially varying selection pressure that potentially affects several traits simultaneously across different life stages, yet little is known about the general patterns and drivers of adaptation in such complex settings. We studied silver fir (Abies alba Mill.) populations across Switzerland and characterized its mountainous landscape using downscaled historical climate data. We sampled 387 trees from 19 populations and genotyped them at 374 single-nucleotide polymorphisms (SNPs) to estimate their demographic distances. Seedling morphology, growth and phenology traits were recorded in a common garden, and a proxy for water use efficiency was estimated for adult trees. We tested whether populations have more strongly diverged at quantitative traits than expected based on genetic drift alone in a multi-trait framework, and identified potential environmental drivers of selection. We found two main responses to selection: (i) populations from warmer and more thermally stable locations have evolved towards a taller stature, and (ii) the growth timing of populations evolved towards two extreme strategies, 'start early and grow slowly' or 'start late and grow fast', driven by precipitation seasonality. Populations following the 'start early and grow slowly' strategy had higher water use efficiency and came from inner Alpine valleys characterized by pronounced summer droughts. Our results suggest that contrasting adaptive life-history strategies exist in silver fir across different life stages (seedling to adult), and that some of the characterized populations may provide suitable seed sources for tree growth under future climatic conditions.

Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Advances in high-throughput sequencing have promoted the collection of reference genomes and genome-wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single-nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e., presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population-specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as nonsynonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented data set, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.

Transmembrane transport and stress response genes play an important role in adaptation of Arabidopsis halleri to metalliferous soils

When plants adapt to local environments, strong signatures of selection are expected in the genome, particularly in high-stress environments such as trace metal element enriched (metalliferous) soils. Using Arabidopsis halleri, a model species for metal homeostasis and adaptation to extreme environments, we identifid genes, gene variants, and pathways that are associated with soil properties and may thus contribute to adaptation to high concentrations of trace metal elements. We analysed whole-genome Pool-seq data from two metallicolous (from metalliferous soils) and two non-metallicolous populations (in total 119 individuals) and associated allele frequencies of the identified single-nucleotide polymorphisms (SNPs) with soil variables measured on site. Additionally, we accounted for polygenic adaptation by searching for gene pathways showing enrichment of signatures of selection. Out of >2.5 million SNPs, we identified 57 SNPs in 19 genes that were significantly associated with soil variables and are members of three enriched pathways. At least three of these candidate genes and pathways are involved in transmembrane transport and/or associated with responses to various stresses such as oxidative stress. We conclude that both allocation and detoxification processes play a crucial role in A. halleri for coping with these unfavourable conditions.

Improved recovery of ancient DNA from subfossil wood - application to the world's oldest Late Glacial pine forest

Ancient DNA from historical and subfossil wood has a great potential to provide new insights into the history of tree populations. However, its extraction and analysis have not become routine, mainly because contamination of the wood with modern plant material can complicate the verification of genetic information. Here, we used sapwood tissue from 22 subfossil pines that were growing c. 13 000 yr bp in Zurich, Switzerland. We developed and evaluated protocols to eliminate surface contamination, and we tested ancient DNA authenticity based on plastid DNA metabarcoding and the assessment of post-mortem DNA damage. A novel approach using laser irradiation coupled with bleaching and surface removal was most efficient in eliminating contaminating DNA. DNA metabarcoding confirmed which ancient DNA samples repeatedly amplified pine DNA and were free of exogenous plant taxa. Pine DNA sequences of these samples showed a high degree of cytosine to thymine mismatches, typical of post-mortem damage. Stringent decontamination of wood surfaces combined with DNA metabarcoding and assessment of post-mortem DNA damage allowed us to authenticate ancient DNA retrieved from the oldest Late Glacial pine forest. These techniques can be applied to any subfossil wood and are likely to improve the accessibility of relict wood for genome-scale ancient DNA studies.

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.

Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

BACKGROUND

Microsatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wide patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for Arabidopsis thaliana (cross-species markers) and eight for A. halleri (species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq).

RESULTS

Our analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR-H e) was not significantly correlated with genome-wide SNP diversity estimates (SNP-H e and θ Watterson) in A. halleri. Instead, microsatellite allelic richness (A r) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations (F ST) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high variance in microsatellite-derived estimates. In contrast, genome-wide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation.

CONCLUSIONS

We recommend that future analyses of genetic diversity within and differentiation among populations use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity patterns. In species comparable to A. halleri, a few thousand SNPs are sufficient to achieve this goal.

Repetitive flanking sequences challenge microsatellite marker development: a case study in the lepidopteran Melanargia galathea

Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development. Here, we propose an approach to deal with multiple primer-binding sites by purposefully positioning primers within the detected repetitive element. We developed a new protocol to determine the family type and the primer position in relation to MDFs using the software packages repark and repeatmasker together with an in-house R script. We re-evaluated newly developed nSSR markers for the lepidopteran Marbled White (Melanargia galathea) and explored the implications of our results with regard to published data sets of the butterfly Euphydryas aurinia, the grasshopper Stethophyma grossum, the conifer Pinus cembra and the crucifer Arabis alpina. For M. galathea, we show that it is not only possible to develop reliable nSSR markers for MDF loci, but even to benefit from their presence in some cases: We used one unlabelled primer, successfully binding within an MDF, for two different loci in a multiplex PCR, combining this family primer with uniquely binding and fluorescently labelled primers outside of MDFs, respectively. As MDFs are abundant in many taxa, we propose to consider these during nSSR marker development in taxa concerned. Our new approach might help in reducing the number of tested primers during nSSR marker development.

Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing

The lack of DNA sequence information for most non-model organisms impairs the design of primers that are universally applicable for the study of molecular polymorphisms in nuclear markers. Next-generation sequencing (NGS) techniques nowadays provide a powerful approach to overcome this limitation. We present a flexible and inexpensive method to identify large numbers of nuclear primer pairs that amplify in most Brassicaceae species. We first obtained and mapped NGS transcriptome sequencing reads from two of the distantly related Brassicaceae species, Cardamine hirsuta and Arabis alpina, onto the Arabidopsis thaliana reference genome, and then identified short conserved sequence motifs among the three species bioinformatically. From these, primer pairs to amplify coding regions (nuclear protein coding loci, NPCL) and exon-primed intron-crossing sequences (EPIC) were developed. We identified 2,334 universally applicable primer pairs, targeting 1,164 genes, which provide a large pool of markers as readily usable genomic resource that will help addressing novel questions in the Brassicaceae family. Testing a subset of the newly designed nuclear primer pairs revealed that a great majority yielded a single amplicon in all of the 30 investigated Brassicaceae taxa. Sequence analysis and phylogenetic reconstruction with a subset of these markers on different levels of phylogenetic divergence in the mustard family were compared with previous studies. The results corroborate the usefulness of the newly developed primer pairs, e.g., for phylogenetic analyses or population genetic studies. Thus, our method provides a cost-effective approach for designing nuclear loci across a broad range of taxa and is compatible with current NGS technologies.

Validation of outlier loci through replication in independent data sets: a test on Arabis alpina

Outlier detection and environmental association analysis are common methods to search for loci or genomic regions exhibiting signals of adaptation to environmental factors. However, a validation of outlier loci and corresponding allele distribution models through functional molecular biology or transplant/common garden experiments is rarely carried out. Here, we employ another method for validation, namely testing outlier loci in specifically designed, independent data sets. Previously, an outlier locus associated with three different habitat types had been detected in Arabis alpina. For the independent validation data set, we sampled 30 populations occurring in these three habitat types across five biogeographic regions of the Swiss Alps. The allele distribution model found in the original study could not be validated in the independent test data set: The outlier locus was no longer indicative of habitat-mediated selection. We propose several potential causes of this failure of validation, of which unaccounted genetic structure and technical issues in the original data set used to detect the outlier locus were most probable. Thus, our study shows that validating outlier loci and allele distribution models in independent data sets is a helpful tool in ecological genomics which, in the case of positive validation, adds confidence to outlier loci and their association with environmental factors or, in the case of failure of validation, helps to explain inconsistencies.

High rates of gene flow by pollen and seed in oak populations across Europe

Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea) distributed across Europe.

Adult trees within a given area in each stand were exhaustively sampled (range [239, 754], mean 423), mapped, and acorns were collected ([17,147], 51) from several mother trees ([3], [47], 23). Seedlings ([65,387], 178) were harvested and geo-referenced in six of the eight stands. Genetic information was obtained from screening distinct molecular markers spread across the genome, genotyping each tree, acorn or seedling. All samples were thus genotyped at 5–8 nuclear microsatellite loci. Fathers/parents were assigned to acorns and seedlings using likelihood methods. Mating success of male and female parents, pollen and seed dispersal curves, and also hybridisation rates were estimated in each stand and compared on a continental scale.

On average, the percentage of the wind-borne pollen from outside the stand was 60%, with large variation among stands (21–88%). Mean seed immigration into the stand was 40%, a high value for oaks that are generally considered to have limited seed dispersal. However, this estimate varied greatly among stands (20–66%). Gene flow was mostly intraspecific, with large variation, as some trees and stands showed particularly high rates of hybridisation.

Our results show that mating success was unevenly distributed among trees. The high levels of gene flow suggest that geographically remote oak stands are unlikely to be genetically isolated, questioning the static definition of gene reserves and seed stands.

Validation of SNP allele frequencies determined by pooled next-generation sequencing in natural populations of a non-model plant species

Sequencing of pooled samples (Pool-Seq) using next-generation sequencing technologies has become increasingly popular, because it represents a rapid and cost-effective method to determine allele frequencies for single nucleotide polymorphisms (SNPs) in population pools. Validation of allele frequencies determined by Pool-Seq has been attempted using an individual genotyping approach, but these studies tend to use samples from existing model organism databases or DNA stores, and do not validate a realistic setup for sampling natural populations. Here we used pyrosequencing to validate allele frequencies determined by Pool-Seq in three natural populations of Arabidopsis halleri (Brassicaceae). The allele frequency estimates of the pooled population samples (consisting of 20 individual plant DNA samples) were determined after mapping Illumina reads to (i) the publicly available, high-quality reference genome of a closely related species (Arabidopsis thaliana) and (ii) our own de novo draft genome assembly of A. halleri. We then pyrosequenced nine selected SNPs using the same individuals from each population, resulting in a total of 540 samples. Our results show a highly significant and accurate relationship between pooled and individually determined allele frequencies, irrespective of the reference genome used. Allele frequencies differed on average by less than 4%. There was no tendency that either the Pool-Seq or the individual-based approach resulted in higher or lower estimates of allele frequencies. Moreover, the rather high coverage in the mapping to the two reference genomes, ranging from 55 to 284x, had no significant effect on the accuracy of the Pool-Seq. A resampling analysis showed that only very low coverage values (below 10-20x) would substantially reduce the precision of the method. We therefore conclude that a pooled re-sequencing approach is well suited for analyses of genetic variation in natural populations.

Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps

Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST -based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.

Where do you come from, where do you go? Directional migration rates in landscape genetics

Identifying landscape elements that influence gene flow and migration in wild species is the current main topic of landscape genetics. Most landscape genetic studies infer gene flow and migration from genetic distances among populations or individuals and statistically relate these measurements to landscape composition and configuration. This approach assumes symmetrical gene flow between pairs of populations. Such an assumption, however, will often be violated, especially in source–sink systems. Source populations provide more emigrants than they receive immigrants, and sink populations get many immigrants, but release few emigrants. Source–sink dynamics cannot be explored using common landscape genetic approaches relying on genetic distances. In this issue of Molecular Ecology, Andreasen et al. (2012) apply an alternative approach allowing them to infer asymmetrical migration. They use a Bayesian assignment test among objectively defined populations of mountain lions (Puma concolor) in western USA to estimate recent and directional migration rates. The study shows that an area with a high amount of wildlife refuges and low hunting pressure harbours a source population for mountain lion dispersal, while areas with high hunting pressures form sink populations; a result helpful in making informed decisions in conservation management.

Are adaptive loci transferable across genomes of related species? Outlier and environmental association analyses in Alpine Brassicaceae species

Local adaptation is one possible response of organisms to survive in a changing environment. However, the genetic basis of adaptation is not well understood, especially in nonmodel species. To infer recurrent patterns of local adaptation, we investigated whether the same putative adaptive loci reoccur in related species. We performed genome scans using amplified fragment length polymorphism (AFLP) markers on populations of five Alpine Brassicaceae species sampled across a wide range of environmental conditions. To identify markers potentially under directional selection, we performed outlier and environmental association analyses using a set of topo-climatic variables available as GIS layers. Several AFLP loci showed signatures of adaptation, of which one, found in Cardamine resedifolia (Cre_P1_212.5), was associated with precipitation. We sequence-characterized this candidate locus and genotyped single nucleotide polymorphisms (SNPs) found within this locus for all species. Testing for environmental associations of SNPs revealed the same association of this locus in Arabis alpina but not in other study species. Cumulative statistical evidence indicates that locus Cre_P1_212.5 is environmentally relevant or is linked to a gene under selection in our study range. Furthermore, the locus shows an association to the same potentially selective factor in at least one other related species. These findings help to identify trends in plant adaptation in Alpine ecosystems in response to particular environmental parameters.

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.

Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation

Identifying adaptive genetic variation is a challenging task, in particular in non-model species for which genomic information is still limited or absent. Here, we studied distribution patterns of amplified fragment length polymorphisms (AFLPs) in response to environmental variation, in 13 alpine plant species consistently sampled across the entire European Alps. Multiple linear regressions were performed between AFLP allele frequencies per site as dependent variables and two categories of independent variables, namely Moran's eigenvector map MEM variables (to account for spatial and unaccounted environmental variation, and historical demographic processes) and environmental variables. These associations allowed the identification of 153 loci of ecological relevance. Univariate regressions between allele frequency and each environmental factor further showed that loci of ecological relevance were mainly correlated with MEM variables. We found that precipitation and temperature were the best environmental predictors, whereas topographic factors were rarely involved in environmental associations. Climatic factors, subject to rapid variation as a result of the current global warming, are known to strongly influence the fate of alpine plants. Our study shows, for the first time for a large number of species, that the same environmental variables are drivers of plant adaptation at the scale of a whole biome, here the European Alps.

Tales of the unexpected: phylogeography of the arctic-alpine model plant Saxifraga oppositifolia (Saxifragaceae) revisited

Arctic-alpine biota occupy enormous areas in the Arctic and the northern hemisphere mountain ranges and have undergone major range shifts during their comparatively short history. The origins of individual arctic-alpine species remain largely unknown. In the case of the Purple saxifrage, Saxifraga oppositifolia, an important model for arctic-alpine plants, phylogeographic studies have remained inconclusive about early stages of the species' spatiotemporal diversification but have provided evidence for long-range colonization out of a presumed Beringian origin to cover today's circumpolar range. We re-evaluated the species' large-scale range dynamics based on a geographically extended sampling including crucial areas such as Central Asia and the (south-)eastern European mountain ranges and employing up-to-date phylogeographic analyses of a plastid sequence data set and a more restricted AFLP data set. In accordance with previous studies, we detected two major plastid DNA lineages also reflected in AFLP divergence, suggesting a long and independent vicariant history. Although we were unable to determine the species' area of origin, our results point to Europe (probably the Alps) and Central Asia, respectively, as the likely ancestral areas of the two main lineages. AFLP data suggested that contact areas between the two clades in the Carpathians, Northern Siberia and western Greenland were secondary. In marked contrast to high levels of diversity revealed in previous studies, populations from the major arctic refugium Beringia did not exhibit any plastid sequence polymorphism. Our study shows that adequate sampling of the southern, refugial populations is crucial for understanding the range dynamics of arctic-alpine species.

Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences

Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker’s sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known.

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.

Using the 454 pyrosequencing-based technique in the development of nuclear microsatellite loci in the alpine plant Arabis alpina (Brassicaceae)

PREMISE OF THE STUDY

Polymorphic microsatellite markers were developed for the inbred alpine perennial plant Arabis alpine to infer life-history parameters and measure patterns of contemporary gene fl ow within populations.

METHODS AND RESULTS

Using the 454 pyrosequencing technique, 19 microsatellite primer sets were developed for A. alpina . The primer sets were tested on 60 individuals sampled from three sub-populations in the Swiss Alps. The primers amplifi ed di- and trinucleotide repeats with two to fi ve alleles per locus.

CONCLUSIONS

Previous attempts to isolate microsatellite loci in A. alpina using enrichment libraries and cross-amplifi cation were diffi cult and produced an insufficient number of polymorphic microsatellite loci. In contrast, next-generation sequencing technology was successful in identifying microsatellite repeats in A. alpina. These newly developed microsatellite primers will be useful to further develop A. alpina into a model species for eco-genomic studies.

Effects of floral neighborhood on seed set and degree of outbreeding in a high-alpine cushion plant

Plants flowering together may influence each other's pollination and fecundity over a range of physical distances. Their effects on one another can be competitive, neutral, or facilitative. We manipulated the floral neighborhood of the high-alpine cushion plant Eritrichium nanum in the Swiss Alps and measured the effects of co-flowering neighbors on both the number of seeds produced and the degree of inbreeding and outbreeding in the offspring, as deduced from nuclear microsatellite markers. Seed set of E. nanum did not vary significantly with the presence or absence of two Saxifraga species growing as near neighbors, but it was higher in E. nanum cushions growing at low conspecific density than in those growing at high density. In addition, floral neighborhood had no detectable effect on the degree of selfing of E. nanum, but seeds from cushions growing at low conspecific density were more highly outbred than seeds from cushions at high density. Thus, there was no evidence of either competition or facilitation between E. nanum and Saxifraga spp. as mediated by pollinators at the spatial scale of our experimental manipulation. In contrast, the greater fecundity of E. nanum cushions at low density was consistent with reduced intraspecific competition for pollinators and might also represent a beneficial effect of highly outbred seeds as brought about by more long-distance pollinator flights under low-density conditions.

Landscape genetics of plants

Landscape genetics is the amalgamation of landscape ecology and population genetics to help with understanding microevolutionary processes such as gene flow and adaptation. In this review, we examine why landscape genetics of plants lags behind that of animals, both in number of studies and consideration of landscape elements. The classical landscape distance/resistance approach to study gene flow is challenging in plants, whereas boundary detection and the assessment of contemporary gene flow are more feasible. By contrast, the new field of landscape genetics of adaptive genetic variation, establishing the relationship between adaptive genomic regions and environmental factors in natural populations, is prominent in plant studies. Landscape genetics is ideally suited to study processes such as migration and adaptation under global 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.

Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina

Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.