Search

This special issue of the journal Alpine Botany brings together syntheses, macroecological and taxon-specific studies of patterns and processes of plant evolution in major mountain ranges across Europe, Africa, the Americas and Asia. Apart from reflecting current conceptual and methodological perspectives in the field, it contributes to our understanding of the interplay between factors determining the evolution and distribution of plant variation across topographically complex areas, and will help to identify the components necessary for building an integrative model of the origin and distribution of diversity in mountain areas.

Although there exist over 7000 crop species, only a few are commercially valuable and grown on a large scale in monocultures worldwide. However, underutilised crops (also called orphan crops) have significant potential for food security and Telfairia occidentalis Hook. F. (Cucurbitaceae) is one such orphan crop grown in West Africa for its nutritious leaves, oil and protein-rich seeds. In this dioecious crop, farmers like to eliminate male plants and keep mostly females to increase their yield. However, they face the challenge of determining sex due to limited morphological differences between females and males before flowering. This study used double digested restriction site-associated DNA sequencing data (ddRADseq) to examine the genetic diversity within and among landraces of T. occidentalis, identify common sex-determining loci, and establish reliable assays to characterize the sex of immature plants in the vegetative state. To differentiate males from females of T. occidentalis, two molecular assays were thereupon developed based on polymerase chain reaction (PCR) to genotype sex-specific sequence variation either through restriction by Mfe1 or the direct use of sex-specific primers. Both assays require standard laboratory conditions to reach a certainty of 94.3% for females and 95.7% for males from the studied samples. With the inclusion of additional landraces, medium to largescale farms growing T. occidentalis as a crop can readily benefit from an early determination of the sex of plants.

SummaryKnowledge about the molecular underpinnings of phenotypic plasticity is still scarce and quantifying gene expression in response to abiotic and biotic factors enables to investigate transcriptional plasticity. RNAseq data on clones of the alpine plantBiscutella laevigata(Brassicaceae) subjected to control, cold, heat, drought and herbivory treatments assessed differentially expressed genes (DEGs) and transposable elements (DE-TEs) in comparison to similar experiments inArabidopsis thaliana. Synergistic and trade-off DEGs presenting parallel and antagonistic regulation among treatments were further identified and used with networks of co-expressed DEGs to characterize transcriptional plasticity in response to environmental changes. Compared toA. thaliana,B. laevigatapresented fewer DEGs that were mostly up-regulated by stronger expression shifts in response to environmental treatments.Biscutella laevigatashowed constitutive expression of half of theA. thalianaDEGs. It further presented a higher proportion of synergistic DEGs, a lower number of trade-off DEGs and a transcriptome organized in environment-specific subnetworks. Several DE-TEs were identified as activated by heat and herbivory. The stress-tolerant perennialB. laevigatapresents a highly modular transcriptional plasticity in response to environmental changes, contrasting with the more integrated transcriptome ofA. thaliana.Significance statementLittle is known about the molecular underpinnings of phenotypic plasticity. Here, focusing on expression shifts during changes in abiotic and biotic conditions, we highlight environment-responsive genes acting synergistically or antagonistically among treatments and underlying modular transcriptional plasticity in two Brassicacea species.

Species range expansions are a common demographic history presenting populations with multiple evolutionary challenges. It is not yet fully understood if self-fertilization, which is often observed at species range edges, may create an evolutionary advantage against these challenges. Selfing provides reproductive reassurance to counter Allee effects and selfing may purge accumulated mutational burden due to founder events (expansion load) by further increasing homozygosity. We study how selfing impacts the accumulation of genetic load during range expansion via purging and/or speed of colonization. Using simulations, we disentangle inbreeding effects due to demography versus due to selfing and find that selfers expand faster, but still accumulate load, regardless of mating system. The severity of variants contributing to this load, however, differs across mating system: higher selfing rates purge large-effect recessive variants leaving a burden of smaller-effect alleles. We compare these predictions to the mixedmating plantArabis alpina, using whole-genome sequences from refugial outcrossing populations versus expanded selfing populations. Empirical results indicate accumulation of expansion load along with evidence of purging in selfing populations, concordant with our simulations, and suggesting that while purging is a benefit of selfing evolving during range expansions, it is not sufficient to prevent load accumulation due to range expansion.Author SummaryThe geographic space that species occupy, i.e. the species range, is known to fluctuate over time due to changing environmental conditions. Since the most recent glaciation, many species have recolonized available habitat as the ice sheets melted, expanding their range. When populations at species range margins expand into newly available space, they suffer from an accumulation of deleterious alleles due to repeated founder effects. We study whether self-fertilization, which is considered an evolutionary deadend, can be favored under these expanding edge conditions. Selfing has two important effects: allowing for faster expansion due to reproductive assurance and purging recessive deleterious alleles by exposing them to selection as homozygotes. We use simulations to identify the impact of selfing on expanded populations and then compare these results to an empirical dataset to assess whether our predictions are met. We use the mixed-mating plant alpine rock-cress (Arabis alpina) since it has both expanded since the last glaciation and undergone a mating shift to selfing. We find that selfing does not prevent the accumulation of deleterious load, however purging does still act to remove the most severe variants, indicating that selfing provides this benefit during range expansions.

Lateral gene transfer (LGT) has been reported in multiple eukaryotes. This process seems particularly widespread in the grass family, although we know very little about the underlying dynamics and how it impacts gene content variation within a species.Alloteropsis semialatais a tropical grass, and multiple LGT were detected in a reference genome assembled from an Australian individual. As part of this study we assemble three additionalde novogenomes forA. semialataand one for its sister speciesAlloteropsis angusta. In total we detect 168 LGT across the five reference genomes. Using whole-genome resequencing data for a further 40 individuals we establish the distribution of these transfers and map their origin along the species phylogeny. This shows that many LGTs were acquired relatively recently, with numerous secondary losses. Exponential decay models indicate that the rate of LGT acquisitions varied significantly among lineages [6-28 per Ma], with a high rate of subsequent LGT losses [11-24% per Ma] that largely exceeds that of native loci [0.02-0.8% per Ma]. This high turnover creates large intraspecific structural variants, with a preponderance of LGT occurring as accessory genes in theAlloteropsispangenome. The acquired genes represent unparalleled genetic novelties, having independently evolved for tens of millions of years before they were transferred. Ultimately, the rapid LGT turnover generates standing variation that can fuel local adaptation.

Although there exist over 7’000 crop species, only a few are commercially valuable and grown on a large scale in monocultures worldwide. However, underutilised crops (also called orphan crops) have great potential for food security and Telfairia occidentalis (Cucurbitaceae) is one such orphan crop grown in West Africa for its nutritious leaves and oil and protein-rich seeds. In this dioecious crop, farmers like to eliminate male plants and mostly keep females to increase their yield but face the challenge of determining sex with limited morphological differences between females and males before flowering. This study used double digested restriction site-associated DNA sequencing data (ddRADseq) to examine the genetic diversity within and among landraces of T. occidentalis, identify common sex-determining loci, and establish reliable assays to characterize the sex of immature plants in the vegetative state. Two molecular assays for distinguishing males from females of T. occidentalis were thereupon developed based on polymerase chain reaction (PCR) to genotype sex-specific sequence variation either through restriction by Mfe1 or the direct use of sex-specific primers. Both assays require standard laboratory conditions to reach a certainty of 94.3% for females and 95.7% for males from studied samples. With the inclusion of additional landraces, medium to large scale farms growing T. occidentalis as a crop can readily benefit from an early determination of the sex of plants.

The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome‐scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short‐reads, single‐molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non‐Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g., related to the maintenance of oxidation‐reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant., see also the Perspective by Tanja Pyhäjärvi and Tiina M. Mattila

Background and AimsHybridization is known to drive plant speciation through the establishment of homoploid or allopolyploid hybrid species. Here we investigate the origin of Pulmonaria helvetica, a narrow endemic species described across a restricted area of Switzerland that was entirely covered by ice during the last glacial maximum. This species presents an original number of chromosomes (2n = 24) and morphological traits suggestive of a hybrid origin.MethodsWe sequenced a plastid locus and 1077 double-digest restriction-site-associated DNA (ddRAD) loci in 67 individuals from across the distribution range of P. helvetica and candidate progenitor species growing in the same area. Assignment of genotypes to main genetic clusters within and among taxa using STRUCTURE tested whether P. helvetica represents a genetically differentiated lineage and addressed the hypothesis of its hybrid origin. Comparative ecological modelling further addressed possible niche differentiation among taxa.Key ResultsPulmonaria helvetica was highlighted as a genetically homogeneous species distinct from co-occurring taxa. Consistent with a scenario of hybrid speciation, it presented clear evidence of balanced admixture between Pulmonaria officinalis (2n = 16) and Pulmonaria mollis s.l. (2n = 18, 22), which was also highlighted as a maternal progenitor based on plastid sequences. Limited genetic structure within the maternal progenitor is consistent with an origin of P. helvetica through either homoploid hybridization with considerable karyotype changes or via complex scenarios of allopolyploidy involving a dysploid taxon of P. mollis s.l. Comparative niche modelling indicated non-significant ecological differences between P. helvetica and its progenitors, supporting intrinsic factors resulting from hybridization as main drivers of speciation.ConclusionsHybridization appears as a major process having promoted the postglacial origin of the narrow endemic P. helvetica, suggesting hybrid speciation as an effective process that rapidly produces new species under climate changes.

Underpinnings of the distribution of allopolyploid species (hybrids with duplicated genome) along spatial and ecological gradients are elusive. As allopolyploid speciation combines the range of genetic and ecological characteristics of divergent diploids, allopolyploids initially show their additivity and are predicted to evolve differentiated ecological niches to establish in face of their competition. Here, we use four diploid wild wheats that differentially combined into four independent allopolyploid species to test for such additivity and assess the impact of ecological constraints on species ranges. Divergent genetic variation from diploids being fixed in heterozygote allopolyploids supports their genetic additivity. Spatial integration of comparative phylogeography and modelling of climatic niches supports ecological additivity of locally adapted diploid progenitors into allopolyploid species which subsequently colonised wide ranges. Allopolyploids fill suitable range to a larger extent than diploids and conservative evolution following the combination of divergent species appears to support their expansion under environmental changes.

Background and Aims Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness, which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management. Methods We studied the population genetic signatures of the local extinction of Biscutella laevigata subsp. gracilis populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as a surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations. Key Results Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both the spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as a powerful predictor of functional connectivity which may promote decision-making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination. Conclusions Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex situ population and a germination trial underlines the need for genetic rescue measures to prevent extinction of B. laevigata in Central Germany.

The vulnerability of alpine environments to climate change presses an urgent need to accurately model and understand these ecosystems. Popularity in the use of digital elevation models (DEMs) to derive proxy environmental variables has increased over the past decade, particularly as DEMs are relatively cheaply acquired at very high resolutions (VHR

Climatic oscillations of the Quaternary rapidly compelled plant species to shift their geographical range. How alpine plant species responded to climate change, however, remains elusive and remnants of the cold-adapted flora that currently strive in restricted ranges as small, isolated populations have been particularly overlooked. To address the evolutionary history of such a ‘glacial relict’, we here sampled and genotyped all known native populations of a narrow endemic species from the northwestern Alps, Papaver occidentale, as well as closely related taxa with double digest restriction-site Associated DNA (ddRAD) sequencing. Spatial patterns of genetic variation across populations coupled with insights from climatic niche modelling through time address underpinings of the long-term persistence of the species in face of climate changes. Evidence from population genetics and ecological modelling indicates that P. occidentale likely persisted through the last glacial maximum outside of the Western Prealps and that a major lineage recolonized the area from lower elevation, external regions. Differentiated lineages at the Northern margins of the species distribution range highlight highly divergent and geographically restricted populations that include considerable share of private markers and may indicate local glacial survival in isolated conditions. Our data thus imply that processes having shaped intraspecific spatial genetic structure within the Alps can be complex and lead to mosaic of populations with a mixed-history of local survival and immigration. A better understanding of spatio-temporal aspects of range contraction–expansion is crucial to shed light on processes underlying the evolution of remnant populations of such endemic species and set conservation priorities considering current climate changes.

Botrychium s.s. is a cosmopolitan fern genus comprising about 35 currently recognized species. Despite unexpected high genetic diversity recently highlighted within Botrychium lunaria in the circumboreal region, few studies have included representative samples from Central Europe. Therefore, the aim of this work was to study the phylogeography of B. lunaria in the Central-European Mountain System and to compare it with that of flowering plants. Two noncoding chloroplast regions (psbA-trnH and trnL-F) were sequenced (918 bp) from 87 individuals from 34 populations in the major European mountain chains (Sierra Nevada, Pyrenees, Massif Central, Jura, Vosges, Black Forest, Alps, Apennines, and Carpathians). Among the 24 haplotypes found in the B. lunaria aggregate in Europe, bayesian phylogeny and median-joining network support four main clades (LUN1, LUN2, LUN3, and TUN). NST and GST comparison as well as homogeneous groups indicated by SAMOVA indicate a clear phylogeographical pattern. However, unlinked to geographical distance, genetic diversity is greatest in the Prealps and highlights three main barriers to gene flow: S–N of Central Alps (Aosta-Lepontic Alps), and two separating E–W Alps (Lago di Como-Rhaetian Alps and Dolomites-Noric-Julian Alps). Our results indicate that alpine populations of the B. lunaria aggregate survived the Quaternary glaciations in situ in two main refugia, in the southern and eastern periphery of the Alps. Not only areas with higher values of genetic diversity, but also refugia and sites of geographical boundaries to gene flow, appear similar in both ferns and flowering plants.

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 non-synonymous 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 dataset, 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. This article is protected by copyright. All rights reserved.

SummaryEvolutionary relationships among theAegilops-Triticumrelatives of cultivated wheats have been difficult to resolve owing to incomplete lineage sorting and reticulate evolution. Recent studies have suggested that the wheat D-genome lineage (progenitor ofAe. tauschii) originated through homoploid hybridization between the A-genome lineage (progenitor ofTriticums.str.) and the B-genome lineage (progenitor ofAe. speltoides). Scenarios of reticulation have been debated, calling for adequate phylogenetic analyses based on comprehensive sampling. To reconstruct the evolution ofAegilops-Triticumdiploids, we here combined high-throughput sequencing of 38 nuclear low-copy loci of multiple accessions of all 13 species with inferences of the species phylogeny using the full-parameterized MCMC_SEQ method. Phylogenies recovered a monophyleticAegilops-Triticumlineage that began diversifying ~6.5 Ma ago and gave rise to four sublineages, i.e. the A- (2 species), B- (1 species), D- (9 species) and T- (Ae. mutica) genome lineage. Full-parameterized phylogenies as well as patterns of tree dilation and tree compression supported a hybrid origin of the D-genome lineage from A and B ~4.1 Ma ago, and did not indicate additional hybridization events. This comprehensive and dated phylogeny of wheat relatives indicates that the origin of the hybrid D-genome was followed by intense diversification into almost all diploid as well as allopolyploid wild wheats.

Significance Certain adapted insect herbivores utilize plant toxins for self-defense against their own enemies. These adaptations structure ecosystems and limit our capacity to use biological control agents to manage specialized agricultural pests. We show that entomopathogenic nematodes that are exposed to the western corn rootworm, an important agricultural pest that sequesters defense metabolites from maize, can evolve resistance to these defenses. Resisting the plant defense metabolites likely allows the nematodes to infect and kill the western corn rootworm more efficiently. These findings illustrate how predators can counter the plant-based resistance strategies of specialized insect herbivores. Breeding or engineering biological control agents that resist plant defense metabolites may improve their capacity to kill important agricultural pests such as the western corn rootworm., Plants defend themselves against herbivores through the production of toxic and deterrent metabolites. Adapted herbivores can tolerate and sometimes sequester these metabolites, allowing them to feed on defended plants and become toxic to their own enemies. Can herbivore natural enemies overcome sequestered plant defense metabolites to prey on adapted herbivores? To address this question, we studied how entomopathogenic nematodes cope with benzoxazinoid defense metabolites that are produced by grasses and sequestered by a specialist maize herbivore, the western corn rootworm. We find that nematodes from US maize fields in regions in which the western corn rootworm was present over the last 50 y are behaviorally and metabolically resistant to sequestered benzoxazinoids and more infective toward the western corn rootworm than nematodes from other parts of the world. Exposure of a benzoxazinoid-susceptible nematode strain to the western corn rootworm for 5 generations results in higher behavioral and metabolic resistance and benzoxazinoid-dependent infectivity toward the western corn rootworm. Thus, herbivores that are exposed to a plant defense sequestering herbivore can evolve both behavioral and metabolic resistance to plant defense metabolites, and these traits are associated with higher infectivity toward a defense sequestering herbivore. We conclude that plant defense metabolites that are transferred through adapted herbivores may result in the evolution of resistance in herbivore natural enemies. Our study also identifies plant defense resistance as a potential target for the improvement of biological control agents.

Recombination and selection drive the extent of linkage disequilibrium (LD) among loci and therefore affect the reshuffling of adaptive genetic variation. However, it is poorly known to what extent the enrichment of transposable elements (TEs) in recombinationally-inert regions reflects their inefficient removal by purifying selection and whether the presence of polymorphic TEs can modify the local recombination rate. In this study, we investigate how TEs and recombination interact at fine scale along chromosomes and possibly support linked selection in natural populations. Whole-genome sequencing data of 304 individuals from nearby alpine populations of Arabis alpina were used to show that the density of polymorphic TEs is specifically correlated with local LD along chromosomes. Consistent with TEs modifying recombination, the characterization of 28 such LD blocks of up to 5.5Mb in length revealed strong evidence of selective sweeps at a few loci through either site frequency spectrum or haplotype structure. A majority of these blocks were enriched in genes related to ecologically relevant functions such as responses to cold, salt stress or photoperiodism. In particular, the S-locus (i.e. supergene responsible for strict outcrossing) was identified in a LD block with high levels of polymorphic TEs and evidence of selection. Another such LD block was enriched in cold-responding genes and presented evidence of adaptive loci related to photoperiodism and flowering being increasingly linked by polymorphic TEs. These results are consistent with the hypothesis that TEs modify recombination landscapes and thus interact with selection in driving blocks of linked adaptive loci in natural populations. This article is protected by copyright. All rights reserved.

Glacial relicts, especially those with very narrow habitat requirements, are particularly affected by global warming. We considered Papaver occidentale, a glacial relict endemic to the Western Prealps, belonging to the alpine poppy complex (P. alpinum aggr.), as a model taxon to study the actual status and potential future distribution of species restricted to particular microrefugia. For this study, all known localities were visited, each population was georeferenced and the number of individuals was estimated. Species Distribution Modelling (SDM) was used to evaluate the present and future potential distribution range and habitat suitability, taking into account the specificity of its habitat (calcareous screes). According to our study, there are globally 19 natural populations of P. occidentale, and a total of about 30,000 individuals. The taxon is a highly specialized alpine plant growing in the majority of natural sites between 1900 and 2100 m a.s.l. on north-facing screes. Predictions for the end of the 21st century indicate that a suitable area will significantly decrease (0&ndash, 30% remaining). Under the most severe climatic scenarios (RCP 8.5), the species risks complete extinction. The long-term in situ conservation of P. occidentale, and all other taxa of the P. alpinum complex, is unlikely to be achieved without slowing global climate change. More generally, our fine-scale study shows that local environmental buffering of large-scale climate change in high-mountain flora may be very limited in specialised taxa of patchy environments such as screes.

At the beginning of the twentieth century, Marie Brockmann-Jerosch wrote, partly in collaboration with her husband Heinrich Brockmann-Jerosch, three influential overview articles on the origin and history of the Swiss alpine flora. Of special interest to her were the types and locations of Pleistocene glacial refugia of alpine plants. She summarised that there had been glacial refugia in the southern and northern peripheral European Alps and also supported glacial survival of high-alpine specialist plants in central Alpine nunatak regions within glaciated areas of the Alps. In contrast, Marie Brockmann-Jerosch dismissed the occurrence of glacial relicts in the lowlands and foothills north of the Alps: she rather saw the conspicuous stations of alpine plants in the lowlands as the result of post-glacial long-distance dispersal of seed out of the Alps. In this article, we first give a brief description of Marie Brockmann-Jerosch’s life and then show that modern phylogeographic research has largely proven her views of the glacial history of the alpine flora and that her writings are still intellectually stimulating and worthwhile reading.

Plant species are known to adapt locally to their environment, particularly in mountainous areas where conditions can vary drastically over short distances. The climate of such landscapes being largely influenced by topography, using fine-scale models to evaluate environmental heterogeneity may help detecting adaptation to micro-habitats. Here, we applied a multiscale landscape genomic approach to detect evidence of local adaptation in the alpine plant Biscutella laevigata. The two gene pools identified, experiencing limited gene flow along a 1-km ridge, were different in regard to several habitat features derived from a very high resolution (VHR) digital elevation model (DEM). A correlative approach detected signatures of selection along environmental gradients such as altitude, wind exposure, and solar radiation, indicating adaptive pressures likely driven by fine-scale topography. Using a large panel of DEM-derived variables as ecologically relevant proxies, our results highlighted the critical role of spatial resolution. These high-resolution multiscale variables indeed indicate that the robustness of associations between genetic loci and environmental features depends on spatial parameters that are poorly documented. We argue that the scale issue is critical in landscape genomics and that multiscale ecological variables are key to improve our understanding of local adaptation in highly heterogeneous landscapes.

Glaciation during the Pleistocene confined alpine species to refugial areas. These range contractions had major impacts on the spatial genetic structure of alpine species. Consequently, one should take into account the often complex phylogeographic structure of species when performing genomic research, e.g. on signatures of local adaptation. Understanding the phylogeography of the widespread arctic and alpine Arabis alpina is particularly important, as this species is developing into a model species for ecological genetics. The first objective of this study was to assess the genetic variation of A. alpina across the Alps and to compare the spatial genetic patterns resulting from two different types of molecular markers, namely nuclear microsatellites and amplified fragment length polymorphisms (AFLPs). A second objective was to infer the distribution of genetic variation at the regional scale to understand the genetic structure of populations in the area of a previously suggested contact zone between genetic clusters that presumably recolonised their current range from different glacial refugia. We characterized the phylogeographic structure of 372 individuals from 127 populations across the entire Alpine range, complemented by 364 individuals from 22 populations in the western Swiss Alps. Nuclear microsatellite and AFLP markers described consistent population clustering, coherent with previous phylogeographic analyses. Furthermore, regional population structure in the western Alps of Switzerland highlighted a contact zone of genetic clusters associated with different presumed refugia. Again, this finding was in accordance with recolonisation routes formerly inferred for other plant taxa of the western Swiss Alps. Our results highlight the coincidence of large-scale patterns of genetic structure among alternative types of molecular markers and set a valuable basis for further studies on ecological genomics in A. alpina.

First paragraph: Explaining what species are and how they arise has been at the center of biological research since the first evolutionary concepts were developed by Buffon, Lamarck, and Darwin (Tirard,2010). With the widespread acceptance of the biological species concept, according to which ‘species are a group of interbreeding natural populations that are reproductively isolated from other such groups’ (Mayr,1996), much recent speciation research has focused on the processes and mechanisms involved in the evolution of reproductive isolation barriers (Coyne & Orr,2004). The molecular basis of these isolating barriers was known in only a few instances at the time of the Plant Speciation New Phytologist Symposium held in 2003 (Rieseberg & Wendel,2004). However, the last decade has witnessed major advances to current knowledge on this and other aspects of plant speciation research as was made clear at the recent European Molecular Biology Organization (EMBO) workshop ‘Mechanisms of plant speciation’ held in 2015 at Åkersberga, Sweden.

Plant species are known to adapt locally to their environment, particularly in mountainous areas where conditions can vary drastically over short distances. The climate of such landscapes being largely influenced by topography, using fine‐scale models to evaluate environmental heterogeneity may help detecting adaptation to micro‐habitats. Here, we applied a multiscale landscape genomic approach to detect evidence of local adaptation in the alpine plant Biscutella laevigata. The two gene pools identified, experiencing limited gene flow along a 1‐km ridge, were different in regard to several habitat features derived from a very high resolution (VHR) digital elevation model (DEM). A correlative approach detected signatures of selection along environmental gradients such as altitude, wind exposure, and solar radiation, indicating adaptive pressures likely driven by fine‐scale topography. Using a large panel of DEM‐derived variables as ecologically relevant proxies, our results highlighted the critical role of spatial resolution. These high‐resolution multiscale variables indeed indicate that the robustness of associations between genetic loci and environmental features depends on spatial parameters that are poorly documented. We argue that the scale issue is critical in landscape genomics and that multiscale ecological variables are key to improve our understanding of local adaptation in highly heterogeneous landscapes.

• Background and Aims The long-lived and mainly outcrossing species Sarracenia purpurea has been introduced into Switzerland and become invasive. This creates the opportunity to study reactions to founder effect and how a species can circumvent deleterious effects of bottlenecks such as reduced genetic diversity, inbreeding and extinction through mutational meltdown, to emerge as a highly invasive plant. • Methods A population genetic survey by random amplified polymorphism DNA markers (RAPD) together with historical insights and a field pollination experiment were carried out. • Key Results At the regional scale, S. purpurea shows low structure (θst = 0·072) due to a recent founder event and important subsequent growth. Nevertheless, multivariate statistical analyses reveal that, because of a bottleneck that shifted allele frequencies, most of the variability is independent among populations. In one population (Tenasses) the species has become invasive and genetic analysis reveals restricted gene flow and family structure (θst = 0·287). Although inbreeding appears to be high (Fis > 0·410 from a Bayesian estimation), a field pollination experiment failed to detect significant inbreeding depression upon F1 seed number and seed weight fitness-traits. Furthermore, crosses between unrelated individuals produced F1 seeds with significantly reduced fitness, thus showing local outbreeding depression. • Conclusions The results suggest that, under restricted gene flow among families, the species may not only have rapidly purged deleterious alleles, but also have undergone some form of selection for inbreeding due to co-adaptation between loci.

Background and Aims: Knowledge on how climate-induced range shifts might affect natural selection is crucial to understand the evolution of species range. Methods: Using historical demographic perspectives gathered from regional-scale phylogeography on the alpine herb Biscutella laevigata, indirect interferences on gene flow and signature of selection based on AFLP genotyping were compared between local populations persisting at the trailing edge and expanding at the leading edge. Key results: Spatial autocorrelation revealed that gene flow was two times more restricted at the trailing edge and genome scans indicated divergent selection in this persisting population. In contrast, no pattern of selection emerged in the expanding population at the leading edge. Conclusions: Historical effects may determine different architecture of genetic variation and selective patterns within local populations, what is arguably important to understand evolutionary processes acting across the species ranges.

SPE IPM UB; International audience; Contents 66 I. 67 II. 68 III. 69 IV. 70 V. 73 VI. 75 VII. 77 78 References 78 SUMMARY: Recent decades have seen declines of entire plant clades while other clades persist despite changing environments. We suggest that one reason why some clades persist is that species within these clades use similar habitats, because such similarity may increase the degree of co-occurrence of species within clades. Traditionally, co-occurrence among clade members has been suggested to be disadvantageous because of increased competition and enemy pressure. Here, we hypothesize that increased co-occurrence among clade members promotes mutualist exchange, niche expansion or hybridization, thereby helping species avoid population decline from environmental change. We review the literature and analyse published data for hundreds of plant clades (genera) within a well-studied region and find major differences in the degree to which species within clades occupy similar habitats. We tentatively show that, in clades for which species occupy similar habitats, species tend to exhibit increased co-occurrence, mutualism, niche expansion, and hybridization - and rarely decline. Consistently, throughout the geological past, clades whose species occupied similar habitats often persisted through long time-spans. Overall, for many plant species, the occupation of similar habitats among fellow clade members apparently reduced their vulnerability to environmental change. Future research should identify when and how this previously unrecognized eco-evolutionary feedback operates.

Studying hybridization has the potential to elucidate challenging questions in evolutionary biology such as the nature of adaptive genetic variation and reproductive isolation. A growing body of work highlights that the merging of divergent genomes goes beyond the reshuffling of standing variation from related species and promotes mutations (Abbott et al., 2013). However, to what extent such genome instability generates evolutionary significant variation remains largely elusive. In this issue of Molecular Ecology, Dennenmoser et al. (2017) report considerable dynamics of transposable elements (TEs) in a recent invasive fish species of hybrid origin (Cottus; Figure 1). It adds to the recent examples from plants to support TE-specific genome variation following hybridization. Insights from early, as well as established, hybrids are largely coherent with increased TE activity, and this fish system thus represents an inspiring opportunity to further address the possible association between genome dynamics and “rapid evolution of hybrid species.” This work based on genome (re)sequencing contrasts with prior transcriptomics or PCR-based studies of TEs and illustrates how unprecedented amount of information promises a better understanding of the multiple patterns of variation across eukaryotic genomes; provided that we get the better of methodological advances. As discussed here, unbiased assessment of TE variation from genome surveys indeed remains a challenge precluding firm conclusions to be reached about the evolutionary significance of TEs. Despite methodological and conceptual developments that appear necessary to unambiguously uncover the unexplored iceberg below the known tip, the role of coding genes vs. TEs in promoting adaptation and speciation might be clarified in a not so remote future.

Transposable elements (TEs) are expectedly central to genome evolution. To assess the impact of TEs in driving genome turnover, we used allopolyploid genomes, showing considerable deviation from the predicted additivity of their diploid progenitors and thus having undergone major restructuring. Genome survey sequencing was used to select 17 putatively active families of long terminal repeat retrotransposons. Genome-wide TE insertions were genotyped with sequence-specific amplified polymorphism (SSAP) in diploid progenitors and their derived polyploids, and compared with changes in random sequences to assess restructuring of four independent Aegilops allotetraploid genomes. Generally, TEs with different evolutionary trajectories from those of random sequences were identified. Thus, TEs presented family-specific and species-specific dynamics following polyploidy, as illustrated by Sabine showing proliferation in particular polyploids, but massive elimination in others. Contrasting with that, only a few families (BARE1 and Romani) showed proliferation in all polyploids. Overall, TE divergence between progenitors was strongly correlated with the degree of restructuring in polyploid TE fractions. TE families present evolutionary trajectories that are decoupled from genome-wide changes after allopolyploidy and have a pervasive impact on their restructuring.

Transposable elements (TE) represent a major fraction of eukaryotic genomes and play many roles in plant epigenetics. In this chapter, we describe the use of Sequence-Specific Amplified Polymorphism (SSAP) as a reliable Transposon Display technique applicable for use in many plant species. We also discuss the interpretation of SSAP data and associated risks. This technique has potential to allow rapid screening of plant populations, especially in nonmodel or wild species.

Extensive gene flow between wheat (Triticum sp.) and several wild relatives of the genus Aegilops has recently been detected despite notoriously high levels of selfing in these species. Here, we assess and model the spread of wheat alleles into natural populations of the barbed goatgrass (Aegilops triuncialis), a wild wheat relative prevailing in the Mediterranean flora. Our sampling, based on an extensive survey of 31 Ae. triuncialis populations collected along a 60 km × 20 km area in southern Spain (Grazalema Mountain chain, Andalousia, totalling 458 specimens), is completed with 33 wheat cultivars representative of the European domesticated pool. All specimens were genotyped with amplified fragment length polymorphism with the aim of estimating wheat admixture levels in Ae. triuncialis populations. This survey first confirmed extensive hybridization and backcrossing of wheat into the wild species. We then used explicit modelling of populations and approximate Bayesian computation to estimate the selfing rate of Ae. triuncialis along with the magnitude, the tempo and the geographical distance over which wheat alleles introgress into Ae. triuncialis populations. These simulations confirmed that extensive introgression of wheat alleles (2.7 × 10(-4) wheat immigrants for each Ae. triuncialis resident, at each generation) into Ae. triuncialis occurs despite a high selfing rate (Fis ≈ 1 and selfing rate = 97%). These results are discussed in the light of risks associated with the release of genetically modified wheat cultivars in Mediterranean agrosystems.

The last decade highlighted polyploidy as a rampant evolutionary process that triggers drastic genome reorganization, but much remains to be understood about their causes and consequences in both autopolyploids and allopolyploids. Here, we provide an overview of the current knowledge on the pathways leading to different types of polyploids and patterns of polyploidy-induced genome restructuring and functional changes in plants. Available evidence leads to a tentative ‘diverge, merge and diverge' model supporting polyploid speciation and stressing patterns of divergence between diploid progenitors as a suitable predictor of polyploid genome reorganization. The merging of genomes at the origin of a polyploid lineage may indeed reveal different kinds of incompatibilities (chromosomal, genic and transposable elements) that have accumulated in diverging progenitors and reduce the fitness of nascent polyploids. Accordingly, successful polyploids have to overcome these incompatibilities through non-Mendelian mechanisms, fostering polyploid genome reorganization in association with the establishment of new lineages. See also sister article focusing on animals by Collares-Pereira et al., in this themed issue.

Taking transposable elements into consideration in surveys of genetic and epigenetic variation remains challenging in species lacking a high-quality reference genome. Here, molecular techniques reducing genome complexity and specifically targeting restructuring and methylation changes in TE genome fractions are described. In particular, methyl-sensitive transposon display (MSTD) uses isoschizomers and PCR amplifications to assess the methylation environment of TE insertions. MSTD offers reliable insights into genome-wide epigenetic changes associated with TEs, especially when used together with similar techniques tracking random sequences.

Taking transposable elements into consideration in surveys of genetic and epigenetic variation remains challenging in species lacking a high-quality reference genome. Here, molecular techniques reducing genome complexity and specifically targeting restructuring and methylation changes in TE genome fractions are described. In particular, methyl-sensitive transposon display (MSTD) uses isoschizomers and PCR amplifications to assess the methylation environment of TE insertions. MSTD offers reliable insights into genome-wide epigenetic changes associated with TEs, especially when used together with similar techniques tracking random sequences.

Summary Transposable elements support genome diversification, but comparison of their proliferation and genomic distribution within and among species is necessary to characterize their role in evolution. Such inferences are challenging because of potential bias with incomplete sampling of repetitive genome regions. Here, using the assembled genome as well as genome skimming datasets in Arabis alpina, we assessed the limits of current approaches inferring the biology of transposable elements. Long terminal repeat-retrotransposons (LTR-RTs) identified in the assembled genome were classified into monophyletic lineages (here called tribes), including families of similar copies in Arabis along with elements from related Brassicaceae. Inference of their dynamics using divergence of LTRs in full-length copies and mismatch distribution of genetic variation among all copies congruently highlighted recent transposition bursts, although ancient proliferation events were apparent only with mismatch distribution. Similar inferences of LTR-RT dynamics based on random sequences from genome skimming were highly correlated with assembly-based estimates, supporting accurate analyses from shallow sequencing. Proportions of LTR-RT copies next to genes from both assembled genomes and genome skimming were congruent, pointing to tribes being over- or under-represented in the vicinity of genes. Finally, genome skimming at low coverage revealed accurate inferences of LTR-RT dynamics and distribution, although only the most abundant families appeared robustly analyzed at 0.1X. Examining the pitfalls and benefits of approaches relying on different genomic resources, we highlight that random sequencing reads represent adequate data suitably complementing biased samples of LTR-RT copies retrieved from assembled genomes towards comprehensive surveys of the biology of transposable elements. This article is protected by copyright. All rights reserved.

Introgression of sequences from crop species in wild relatives is of fundamental and practical concern. Here, we address gene flow between cultivated wheat and its widespread polyploid relative, Aegilops triuncialis, using 12 EST-SSR markers mapped on wheat chromosomes. The presence of wheat diagnostic alleles in natural populations of the barbed goatgrass growing in proximity to cultivated fields highlights that substantial gene flow occurred when both species coexisted. Furthermore, loci from the A subgenome of wheat were significantly less introgressed than sequences from other subgenomes, indicating differential introgression into Ae. triuncialis. Gene flow between such species sharing nonhomeologous chromosomes addresses the evolutionary outcomes of hybridization and may be important for efficient gene containment.