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The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage,Canis coreanus. To investigate the Korean wolf genetic affiliations and their taxonomic implications, we sequenced and analysed the genomes of a historical Korean wolf dated to the beginning of the 20th century, and a captive wolf originally located at the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find the Korean wolf has similar diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is more genetically similar to wolves from the Tibetan Plateau, hence, Korean wolf conservation programs might not benefit from the inclusion of this specimen.

Bryophytes generally have broad geographical ranges that suggest high dispersal ability. The aim of this study was to test hypotheses about dispersal limitation, as indicated by isolation by distance, in four spore-producing species of the moss genus Sphagnum (Sphagnum carolinianum, Sphagnum missouricum, Sphagnum macrophyllum and Sphagnum pylaesii) and to assess whether plants in the southern USA harbour high levels of unique alleles and/or other indicators of exceptional genetic diversity. Isolation by distance was detected in all four species, but regional patterns of genetic structure were very species specific. Northern and southern genotype groups were detected in S. carolinianum and S. missouricum, but in S. pylaesii plants from the Adirondack Mountains of New York were genetically distinct from others to the north and south. One species, S. macrophyllum, exhibited differentiation between northern and southern genetic groups that appeared to reflect more ancient phylogenetic diversification.

Unraveling the origin and colonization history of invasive plants is a long-standing challenge in evolutionary and conservation biology. The knowledge of the origin of the invasive plants in Europe is often confounded by limited sampling in the source region. We determined the extent of genetic structuring in the native range and reconstructed the origin and the invasion history of Persian hogweed, Heracleum persicum, into Europe. We used allelic polymorphism of microsatellite markers obtained from 36 Iranian populations from Middle East combined with data from 38 European populations representing the major native and introduced ranges, respectively. Comprehensive sampling in the native range covered 97% of allelic diversity found in the introduced range, and showed that allelic variation, heterozygosity and population differentiation are significantly reduced in the introduced populations. Results from Bayesian structure, neighbor-net, and ordination analyses showed that populations in the native range consist of three distinct genetic clusters: Eastern, Central, and Western. Although we observed high genetic differentiation among these groups, the Western cluster was genetically closer to the Central cluster. Approximate Bayesian Computation (ABC) analysis supports at least three independent origins for European populations. No European population originated from the Eastern cluster within the native range. Danish populations originated from the Central cluster, whereas the UK and Finland populations originated independently from the Western cluster. Norwegian populations originated from UK, and subsequently established the FI-Kar population in Finland. Our results shed light on the complex origin and history of an aggressive invasive plant species in Europe, supporting contribution from multiple genetic lineages in recent ancestry of introduced populations, thus suggesting the potential for ecological diversification within the introduced range.

The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade. Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ILS), and identification and quantification of gene flow in the presence of ILS is challenging and requires knowledge about the true phylogenetic relationship among the species. We use whole nuclear, plastid, and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods. We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ILS following the rapid radiation of the genus rather than by postspeciation introgression. Our analyses support the idea of ancient introgression among the ancestral lineages followed by ILS, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group. Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ILS and introgression.

Sphagnum magellanicum is one of two Sphagnum species for which a reference-quality genome exists to facilitate research in ecological genomics. Phylogenetic and comparative genomic analyses were conducted based on resequencing data from 48 samples and RADseq analyses based on 187 samples. We report herein that there are four clades/species within the S. magellanicum complex in eastern North America and that the reference genome belongs to Sphagnum divinum. The species exhibit tens of thousands (RADseq) to millions (resequencing) of fixed nucleotide differences. Two species, however, referred to informally as S. diabolicum and S. magni because they have not been formally described, are differentiated by only 100 (RADseq) to 1000 (resequencing) of differences. Introgression among species in the complex is demonstrated using D-statistics and f

SummaryThe Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s) 1–7. Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM) 8,9, until human persecutions led them to extinction 1–7.There are only seven known Sicilian wolf specimens from the 19th and 20th century preserved in museums in Italy and recent morphometric analyses assigned them to the new subspecies Canis lupus cristaldii10. To better understand the origins of the Sicilian wolf, and its relationship to other wolf populations, we sequenced four whole genomes (3.8×-11.6×) and five mitogenomes. We investigated the relationship between Sicilian wolves and other modern breeds to identify potential admixture. Furthermore, considering that the last land-bridge between Sicily and Italy disappeared after the LGM 11, around 17 kya, we explored the possibility that the Sicilian wolf retained ancestry from ancient wolf and dog lineages. Additionally, we explored whether the long-term isolation might have affected the genomic diversity, inbreeding levels and genetic load of the Sicilian wolf.Our findings show that the Sicilian wolves shared most ancestry with the modern Italian wolf population but are better modelled as admixed with European dog breeds, and shared traces of Eneolithic and Bronze age European dogs. We also find signatures of severe inbreeding and low genomic diversity at population and individual levels due to long-term isolation and drift, suggesting also low effective population size.

Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th–19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics., We acknowledge the following for funding our research: Carlsbergfondet grants CF14-0995 and Marie Skłodowska-Curie Actions grant 655732 (to S.G.), Danish National Research Foundation grant DNRF94, Lundbeckfonden grant R52-5062, Carlsbergfondet grant CF18-1109 and ERC Consolidator grant (681396-ExtinctionGenomics) (to M.T.P.G.), and MEDHEAL600 funded by the Research Council of Norway (FRIHUMSAM) project number is 262424. G.L.C. is supported by the Science Foundation Ireland under grant number 16/RC/3948. T.M.B. is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 864203).

The Quaternary climatic oscillations caused pronounced changes in the distribution of the genetic variation among populations as well as phenotypic diversification worldwide. However, how important these processes have been in plants with high gene flow potential has been less studied. Sphagnum warnstorfii is a peatmoss species with a wide circumpolar distribution range exhibiting considerable morphological variation. In particular, many Arctic plants differ morphologically from plants in the rest of its distribution range. We used single nucleotide polymorphism (SNP) genotyping to investigate the patterns of genetic diversity in 112 plants from 105 localities sampled throughout the species distribution range and explored how this was correlated with phenotypic variation. Genetic cluster analysis identified two main genetic lineages with an average FST of 0.21 between them. The first cluster is restricted to the Arctic region, whereas the second has a wider distribution range covering the Arctic, boreal and boreo-nemoral regions of Eurasia and North America. We show that morphological variation is mostly concordant with patterns of genetic differentiation, and possibly representing adaptation to local environments. Based on approximate Bayesian computation simulations, we find that the two lineages probably diverged from each other before the Last Glacial Maximum (LGM). Our results show that vicariance due to glacial oscillations probably played a role for current patterns of diversification in a common peatmoss exhibiting a high gene flow potential.

1. The relative importance of global versus local environmental factors for growth and thus carbon uptake of the bryophyte genus Sphagnum—the main peat‐former and ecosystem engineer in northern peatlands—remains unclear. 2. We measured length growth and net primary production (NPP) of two abundant Sphagnum species across 99 Holarctic peatlands. We tested the importance of previously proposed abiotic and biotic drivers for peatland carbon uptake (climate, N deposition, water table depth and vascular plant cover) on these two responses. Employing structural equation models (SEMs), we explored both indirect and direct effects of drivers on Sphagnum growth. 3. Variation in growth was large, but similar within and between peatlands. Length growth showed a stronger response to predictors than NPP. Moreover, the smaller and denser Sphagnum fuscum growing on hummocks had weaker responses to climatic variation than the larger and looser Sphagnum magellanicum growing in the wetter conditions. Growth decreased with increasing vascular plant cover within a site. Between sites, precipitation and temperature increased growth for S. magellanicum. The SEMs indicate that indirect effects are important. For example, vascular plant cover increased with a deeper water table, increased nitrogen deposition, precipitation and temperature. These factors also influenced Sphagnum growth indirectly by affecting moss shoot density. 4. Synthesis. Our results imply that in a warmer climate, S. magellanicum will increase length growth as long as precipitation is not reduced, while S. fuscum is more resistant to decreased precipitation, but also less able to take advantage of increased precipitation and temperature. Such species‐specific sensitivity to climate may affect competitive outcomes in a changing environment, and potentially the future carbon sink function of peatlands.

Many studies on Heracleum have shown poor correspondence between observed molecular clusters and established taxonomic classification amongst closely related species. This might reflect both unresolved taxonomy but perhaps also a lack of good genetic markers. This lack of appropriate and cost effective species-specific genetic markers hinders a resolved relationship for the species complex, and this in turn causes profound management challenges for a genus that contains both endemic species, with important ecological roles, and species with an invasive potential. Microsatellites are traditionally considered markers of choice for comprehensive, yet inexpensive, analyses of genetic variation, including examination of population structure, species identity, linkage map construction and cryptic speciation. In this study, we have used double digest restriction site associated DNA sequencing (ddRADseq) to develop microsatellite markers in Heracleum rechingeri. Genomic DNA from three individuals were digested with Sbf1 and Nde1 and size selected for library construction. The size-selected fragments were sequenced on an Ion Torrent sequencer and a total of 54 microsatellite sequences were bioinformatically confirmed. Twenty five loci were then tested for amplification, resulting in 19 of these being successfully amplified across eight species, comprising both the so-called thick-stemmed species (H. persicum, H. rechingeri, H. gorganicum and H. lasiopetalum), and thin-stemmed species (H. anisactis, H. pastinasifolium and H. transcaucasicum). Both Bayesian and distance-based clustering, and principal coordinate analyses clearly separated these into two groups. Surprisingly, three H. pastinacifolium populations were not separated from populations of the morphologically similar endemic species, H. anisactis, suggesting lack of genetic differentiation. Likewise, high genetic similarity was found between H. persicum and H. rechingeri populations, questioning taxonomic separation at the species level between these taxa. Further analyses are needed to re-evaluate the taxonomic significance of observed morphological variability currently applied to distinguish these sister taxa. Nevertheless, our results represent progress in the effort to develop cost-efficient molecular tools for species discrimination in this genus. Copyright: © 2020 Daemi-Saeidabad et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Sphagnum magellanicum has been viewed as being a predominantly circumpolar species in the northern hemisphere, but it occurs in the southern hemisphere and was originally described from the souther...

A long-term reduction in effective population size will lead to major shift in genome evolution. In particular, when effective population size is small, genetic drift becomes dominant over natural selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size of populations. Theory predicts that this reduction should be more dramatic in organisms capable for haploid than for diploid selfing. Although theoretically well-grounded, this assertion received mixed experimental support. Here, we test this hypothesis by analyzing synonymous codon usage bias of genes in the model moss Physcomitrella patensfrequently undergoing haploid selfing. In line with population genetic theory, we found that the effect of natural selection on synonymous codon usage bias is very weak. Our conclusion is supported by four independent lines of evidence: 1) Very weak or nonsignificant correlation between gene expression and codon usage bias, 2) no increased codon usage bias in more broadly expressed genes, 3) no evidence that codon usage bias would constrain synonymous and nonsynonymous divergence, and 4) predominant role of genetic drift on synonymous codon usage predicted by a model-based analysis. These findings show striking similarity to those observed in AT-rich genomes with weak selection for optimal codon usage and GC content overall. Our finding is in contrast to a previous study reporting adaptive codon usage bias in the moss P. patens. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

Quaternary glaciations have played a major role in shaping the genetic diversity and distribution of plant species. Strong palaeoecological and genetic evidence supports a postglacial recolonization of most plant species to northern Europe from southern, eastern and even western glacial refugia. Although highly controversial, the existence of small in situ glacial refugia in northern Europe has recently gained molecular support. We used genomic analyses to examine the phylogeography of a species that is critical in this debate. Carex scirpoidea Michx subsp. scirpoidea is a dioecious, amphi‐ Atlantic arctic–alpine sedge that is widely distributed in North America, but absent from most of Eurasia, apart from three extremely disjunct populations in Norway, all well within the limits of the Weichselian ice sheet. Range‐wide population sampling and variation at 5,307 single nucleotide polymorphisms show that the three Norwegian populations comprise unique evolutionary lineages divergent from Greenland with high between‐population divergence. The Norwegian populations have low within‐population genetic diversity consistent with having experienced genetic bottlenecks in glacial refugia, and host private alleles that probably accumulated in long‐term isolated populations. Demographic analyses support a single, pre‐Weichselian colonization into Norway from East Greenland, and subsequent divergence of the three populations in separate refugia. Other refugial areas are identified in North‐east Greenland, Minnesota/Michigan, Colorado and Alaska. Admixed populations in British Columbia and West Greenland indicate postglacial contact. Taken together, evidence from this study strongly indicates in situ glacial survival in Scandinavia. arctic–alpine phylogeography, Carex scirpoidea, ddRAD‐seq, demographic inference, glacial survival, Pleistocene refugia

Rain-fed peatlands are dominated by peat mosses (Sphagnum sp.), which for their growth depend on elements from the atmosphere. As the isotopic composition of carbon (12,13C) and oxygen (16,18O) of these Sphagnum mosses are affected by environmental conditions, the dead Sphagnum tissue accumulated in peat constitutes a potential long-term archive that can be used for climate reconstruction. However, there is a lack of adequate understanding of how isotope values are influenced by environmental conditions, which restricts their current use as environmental and palaeoenvironmental indicators. Here we tested (i) to what extent C and O isotopic variation in living tissue of Sphagnum is species-specific and associated with local hydrological gradients, climatic gradients (evapotranspiration, temperature, precipitation), and elevation; (ii) if the C isotopic signature can be a proxy for net primary productivity (NPP) of Sphagnum; and (iii) to what extent Sphagnum tissue δ18O tracks the δ18O isotope signature of precipitation. In total, we analysed 337 samples from 93 sites across North America and Eurasia using two important peat-forming Sphagnum species (S. magellanicum, S. fuscum) common to the Holartic realm. There were differences in δ13C values between species. For S. magellanicum δ13C decreased with increasing height above the water table (HWT, R2 = 17 %) and was positively correlated to productivity (R2 = 7 %). Together these two variables explained 46 % of the between-site variation in δ13C values. For S. fuscum, productivity was the only significant predictor of δ13C (total R2 = 6 %). For δ18O values, ca. 90 % of the variation was found between sites. Globally-modelled annual δ18O values in precipitation explained 69% of the between-site variation in tissue δ18O. S. magellanicum showed lower δ18O enrichment than S. fuscum (−0.83 ‰ lower) . Elevation and climatic variables were weak predictors of tissue δ18O values after controlling for δ18O values of the precipitation. To summarise, our study provides evidence for (a) good predictability of tissue δ18O values from modelled annual δ18O values in precipitation, and (b) the possibility to relate tissue δ13C values to HWT and NPP, but this appears to be species-dependent. These results suggest that isotope composition can be used at a large scale for climatic reconstructions but that such models should be species-specific.

Salmonella enterica serovar Paratyphi C causes enteric (paratyphoid) fever in humans. Its presentation can range from asymptomatic infections of the blood stream to gastrointestinal or urinary tract infection or even a fatal septicemia. Paratyphi C is very rare in Europe and North America, except for occasional travelers from South and East Asia or Africa where the disease is more common. However, early 20th century observations in Eastern Europe suggest that Paratyphi C enteric fever may once have had a wide-ranging impact on human societies. Here we describe a draft Paratyphi C genome (Ragna) recovered from the 800- year-old skeleton (SK152) of a young woman in Trondheim, Norway. Paratyphi C sequences were recovered from her teeth and bones, suggesting that she died of enteric fever, and demonstrating that these bacteria have long caused invasive salmonellosis in Europeans. Comparative analyses against modern Salmonella genome sequences revealed that Paratyphi C is a clade within the Para C Lineage, which also includes serovars Choleraesuis, Typhisuis and Lomita. Although Paratyphi C only infects humans, Choleraesuis causes septicemia in pigs and boar (and occasionally humans), and Typhisuis causes epidemic, chronic paratyphoid/caseous lymphadenitis in domestic pigs. These different host specificities likely evolved in Europe over the last ~4,000 years, since the time of their most recent common ancestor (tMRCA), and are possibly associated with the differential acquisitions of two genomic islands, SPI-6 and SPI-7. The tMRCAs of these bacterial clades coincide with the timing of pig domestication in Europe.

Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.

Peatmosses are interesting for studies of speciation processes not only because of their frequent hybridization and recent diversification, but also their phenotypic diversity, ecological importance and ancient history. Diverse and widespread hybridization has been widely documented in the genus, but little is known about what factors underlie this phenomenon. We hypothesize that these factors include phylogenetic distance and variation in life-history traits of parental species. We summarize current knowledge about the occurrence of hybridization in peatmosses and explore how it is associated with phylogenetic distance and life-history trait variation of parental species. Possibly as much as one out of five (or more) peatmoss species hybridize, mostly producing allopolyploid hybrids. Parents of admixed haploids are more closely related to each other than parents of allopolyploids. Hybridization seems to be most frequent in 1) monoicous and polyoicous species exhibiting 2) relatively high sporulation frequency, 3) producing relatively small spores, as well as 4) growing in poor habitats. Surprisingly, neither phylogenetic proximity nor life-history trait variation explain patterns of hybridization in peatmosses, and other likely explanations for patterns observed are discussed. © 2018 The Authors. This work is licensed under the terms of a Creative Commons Attribution 4.0 International License (CC-BY)

Summary Salmonella enterica serovar Paratyphi C causes enteric (paratyphoid) fever in humans. Its presentation can range from asymptomatic infections of the blood stream to gastrointestinal or urinary tract infection or even a fatal septicemia [1]. Paratyphi C is very rare in Europe and North America except for occasional travelers from South and East Asia or Africa, where the disease is more common [2, 3]. However, early 20th-century observations in Eastern Europe [3, 4] suggest that Paratyphi C enteric fever may once have had a wide-ranging impact on human societies. Here, we describe a draft Paratyphi C genome (Ragna) recovered from the 800-year-old skeleton (SK152) of a young woman in Trondheim, Norway. Paratyphi C sequences were recovered from her teeth and bones, suggesting that she died of enteric fever and demonstrating that these bacteria have long caused invasive salmonellosis in Europeans. Comparative analyses against modern Salmonella genome sequences revealed that Paratyphi C is a clade within the Para C lineage, which also includes serovars Choleraesuis, Typhisuis, and Lomita. Although Paratyphi C only infects humans, Choleraesuis causes septicemia in pigs and boar [5] (and occasionally humans), and Typhisuis causes epidemic swine salmonellosis (chronic paratyphoid) in domestic pigs [2, 3]. These different host specificities likely evolved in Europe over the last ∼4,000 years since the time of their most recent common ancestor (tMRCA) and are possibly associated with the differential acquisitions of two genomic islands, SPI-6 and SPI-7. The tMRCAs of these bacterial clades coincide with the timing of pig domestication in Europe [6]., Highlights • Salmonella enterica aDNA sequences were found within 800-year-old teeth and bone • The invasive Para C lineage was defined from 50,000 modern S. enterica genomes • The Para C lineage includes Ragna, the aDNA genome, and human and swine pathogens • Only few genomic changes occurred in the Para C lineage over its 3,000-year history, Zhou et al. reshape our understandings of the origins of an invasive bacterial pathogen, Salmonella enterica Paratyphi C, by combining a reconstructed pan-genome from an 800-year-old skeleton in Norway with 221 genomes from modern bacteria.

Although it is an uncommon distribution in seed plants, many bryophytes occur around the Pacific Rim of north-western North America and eastern Asia. This work focuses on a clade of peatmosses (Sphagnum) that is distributed around the Pacific Rim region, with some individual species found across the total range. The goals were to infer divergent phylogenetic relationships among haploid species in the clade, assess parentage of allopolyploid taxa, and evaluate alternative hypotheses about inter- and intraspecific geographical range evolution. Multiple data sets and analyses resolved an ‘Alaska’ clade, distributed across western North America, eastern China and Japan, and an ‘Asia’ clade that includes western Chinese, Thai, Korean, eastern Chinese and Japanese lineages. Allopolyploids have arisen at least four times in the Pacific Rim clade of Sphagnum subgen. Subsecunda; it appears that all allopolyploid origins involved closely related haploid parental taxa. Biogeographical inferences were impacted by topological uncertainty and especially by the biogeographical model utilized to reconstruct ancestral areas. Most analyses converge on the conclusion that the ancestor to this clade of Pacific Rim Sphagnum species was widespread from Alaska south to eastern Asia, but a northern origin for the Alaska subclade was supported by one of the two biogeographical models we employed, under which it was robust to phylogenetic uncertainty.

High Arctic environments are particularly sensitive to climate changes, but retrieval of paleoecological data is challenging due to low productivity and biomass. At the same time, Arctic soils and sediments have proven exceptional for long-term DNA presentation due to their constantly low temperatures. Lake sediments contain DNA paleorecords of the surrounding ecosystems and can be used to retrieve a variety of organismal groups from a single sample. In this study, we analyzed vascular plant, bryophyte, algal (in particular diatom) and copepod DNA retrieved from a sediment core spanning the Holocene, taken from Bliss Lake on the northernmost coast of Greenland. A previous multi-proxy study including microscopic diatom analyses showed that this lake experienced changes between marine and lacustrine conditions. We inferred the same environmental changes from algal DNA preserved in the sediment core. Our DNA record was stratigraphically coherent, with no indication of leaching between layers, and our cross-taxon comparisons were in accordance with previously inferred local ecosystem changes. Authentic ancient plant DNA was retrieved from nearly all layers, both from the marine and the limnic phases, and distinct temporal changes in plant presence were recovered. The plant DNA was mostly in agreement with expected vegetation history, but very early occurrences of vascular plants, including the woody Empetrum nigrum, document terrestrial vegetation very shortly after glacial retreat. Our study shows that multi-taxon metabarcoding of sedimentary ancient DNA from lake cores is a valuable tool both for terrestrial and aquatic paleoecology, even in low-productivity ecosystems such as the High Arctic. (C) 2015 Elsevier Ltd. All rights reserved.

Peat mosses (Sphagnum) are ecosystem engineers-species in boreal peatlands simultaneously create and inhabit narrow habitat preferences along two microhabitat gradients: an ionic gradient and a hydrological hummock-hollow gradient. In this article, we demonstrate the connections between microhabitat preference and phylogeny in Sphagnum. Using a dataset of 39 species of Sphagnum, with an 18-locus DNA alignment and an ecological dataset encompassing three large published studies, we tested for phylogenetic signal and within-genus changes in evolutionary rate of eight niche descriptors and two multivariate niche gradients. We find little to no evidence for phylogenetic signal in most component descriptors of the ionic gradient, but interspecific variation along the hummock-hollow gradient shows considerable phylogenetic signal. We find support for a change in the rate of niche evolution within the genus-the hummock-forming subgenus Acutifolia has evolved along the multivariate hummock-hollow gradient faster than the hollow-inhabiting subgenus Cuspidata. Because peat mosses themselves create some of the ecological gradients constituting their own habitats, the classic microtopography of Sphagnum-dominated peatlands is maintained by evolutionary constraints and the biological properties of related Sphagnum species. The patterns of phylogenetic signal observed here will instruct future study on the role of functional traits in peatland growth and reconstruction.

Summary 1. Euglossine bees (Apidae: Euglossini) have long been hypothesized to act as long-distance pollinators of many low-density tropical plants. We tested this hypothesis by analyzing gene flow and genetic structure within and among populations of the euglossine bee-pollinated vine Dalechampia scandens.2. Using microsatellite markers, we assessed historical gene flow by quantifying regional-scale genetic structure and isolation by distance among 18 populations, and contemporary gene flow by estimating recent migration rates among populations. To assess bee-mediated pollen dispersal on a smaller scale, we conducted paternity analyses within a focal population, and quantified within-population spatial genetic structure in four populations.3. Gene flow was limited to certain nearby populations within continuous forest blocks, while drift appeared to dominate on larger scales. Limited long-distance gene flow was supported by within-population patterns; gene flow was biased towards nearby plants, and significant small-scale spatial genetic structure was detected within populations.4. These findings suggest that, although female euglossine bees might be effective at moving pollen within populations, and perhaps within forest blocks, their contribution to gene flow on the regional scale seems too limited to counteract genetic drift in patchily distributed tropical plants. Among-population gene flow might have been reduced following habitat fragmentation.

Premise of the study Populations with phenotypic polymorphism in discrete characters may be good models for investigating genome evolution and speciation. Sphagnum magellanicum Brid. is found throughout the northern hemisphere, and despite considerable variation in morphological characters, it is considered one of the least taxonomically controversial peatmoss species. We have observed two main morphs of the species associated with different microhabitats. Here we investigated the genomic and environmental basis of this intraspecific morphological variation. Methods We conducted transplant and common garden experiments to test whether the two morphs are genetically differentiated. We then used RAD-sequencing to quantify the genomic divergence between the morphs and approximate Bayesian computation (ABC) to infer the most likely demographic scenario explaining the genome-wide differentiation of the two morphs. Key results We found that genomic differentiation between the two morphs is unexpectedly high and that several of the differentiated morphological characters have a genetic basis. Using simulation approaches, we found support for a scenario of ancient divergence followed by recent secondary contact. Conclusions We show that the two morphs represent the two main genetic clusters previously found worldwide. Our results demonstrate that relatively minor morphological differentiation in a presumed phenotypically plastic peatmoss may be associated with massive divergence across the genome.

Aim Arctic plant species are often characterized by a complex genetic structure because of changes in their population size, the fragmentation of metapopulation systems, extensive hybridization and allopolyploidization, and survival in disjunct refugia, historical features associated with Pleistocene glaciation. We assessed the biogeographical and genetic patterns in three closely related northern species of peat-moss (Sphagnum inexspectatum, S. orientale and S. miyabeanum), especially interspecific hybridization, infraspecific geographical differentiation and Pleistocene survival in one or more refugial areas. We tested alternative hypotheses of refugial survival in three widely disjunct regions: eastern Asia, Alaska and Greenland. Location North America (Canada, western USA and Greenland), China, Japan and Russia. Methods Four hundred and forty-three plants were genotyped at 12 microsatellite loci. Nucleotide sequences from 130 accessions for two plastid and two nuclear loci were used to reconstruct haplotype relationships. Population genetic analyses produced estimates of genetic diversity, levels of interspecific gene flow and rates of infraspecific intercontinental migration. Approximate Bayesian computation was used to test alternative biogeographical scenarios. Results We found evidence of hybridization between two of the three species, but phylogenetic patterns are predominantly divergent rather than reticulate. Disjunct populations of one species, S. orientale, in Greenland, Alaska and China are genetically differentiated, but migration has occurred among all three metapopulation systems. Divergence-time analyses strongly support the hypothesis that S. orientale survived the Last Glacial Maximum in Beringia and also in Greenland. Main conclusions Our results indicate that Beringia served as a refugium for peat-mosses, and therefore peatlands, which are currently extensive at high latitudes of the Northern Hemisphere. Sphagnum orientale also appears to have survived the Last Glacial Maximum in Greenland, indicating that the species persisted in multiple Pleistocene refugia. Phylogenetic patterns are relatively simple in these mosses compared with those commonly encountered in Arctic angiosperms.

Most species are assumed to have survived south or east of the ice sheet covering northern Europe during the last glacial maximum. Molecular and macrofossil evidence suggests, however, that some species may have survived in ice-free areas in Scandinavia. In plants, inbreeding and vegetative growth are associated with low genetic load and enhanced survival in small, isolated populations. These characteristics are often found in bryophytes, possibly allowing them to survive extreme conditions in isolated refugia and also within ice sheets. Here, we review the Holocene bryophyte history in Europe highlighting main glacial refugia and post-glacial colonization routes. Also, meta-analyses are performed to investigate if distribution ranges and genetic structure are associated with life-history traits. Bryophytes survived the last glaciation in several refugia, but there is no unequivocal evidence of survival within the Scandinavian ice sheet. Northern Europe was colonized from southern, eastern and western Europe, as well as North America. Species with small spores have broader distribution ranges than species with large spores, and high frequency of sporophyte production is associated with limited genetic differentiation between populations. © 2014 The Authors. This is an Open Access article.

In plants, hybridization between interspecific taxa leading to chromosome doubling seems to happen regularly and may be an important driver of speciation. Allopolyploid species often have morphological traits from both parents, broader ecological niches, and are hypothesized to be more common going northwards. About 20% of all Sphagnum species have been inferred to be allopolyploids. Here we describe the first allotriploid Sphagnum species in the northern hemisphere, using molecular data, Feulgen densitometry, and morphological examination. Our molecular data also supports the finding of the first polyploid species with inter-subgeneric origin between Acutifolia and Subsecunda. Morphological examination further supports this finding. The Acutifolia progenitor is likely the maternal parent of the new species, named S. ×lydiae, and it is probably S. incundum, S. ×arcticum or S. ×olafii. The Subsecunda parent could not be identified based on molecular and morphological characters. The currently known distribution of S. ×lydiae is confined to regions with arctic and subarctic climate and tundra vegetation in northern Russia.

Unlike seed plants where global biogeographical patterns typically involve interspecific phylogenetic history, spore-producing bryophyte species often have intercontinental distributions that are best understood from a population genetic perspective. We sought to understand how reproductive processes, especially dispersal, have contributed to the intercontinental ‘Pacific Rim’ distribution of Sphagnum miyabeanum. In total, 295 gametophyte plants from western North America (California, Oregon, British Columbia, Alaska), Russia, Japan, and China were genotyped at 12 microsatellite loci. Nucleotide sequences were obtained for seven anonymous nuclear loci plus two plastid regions from 21 plants of S. miyabeanum and two outgroup species. We detected weak but significant genetic differentiation among plants from China, Japan, Alaska, British Columbia, and the western USA. Alaskan plants are genetically most similar to Asian plants, and British Columbian plants are most similar to those in the western USA. There is detectable migration between regions, with especially high levels between Alaska and Asia (China and Japan). Migration appears to be recent and/or ongoing, and more or less equivalent in both directions. There is weak (but significant) isolation-by-distance within geographical regions, and the slope of the regression of genetic on geographical distance differs for Asian versus North American plants. A distinctive Vancouver Island morphotype is very weakly differentiated, and does not appear to be reproductively isolated from plants of the normal morphotype. The intercontinental geographical range of S. miyabeanum reflects recent and probably ongoing migration, facilitated by the production of tiny spores capable of effective long distance dispersal. The results of the present study are consistent with Pleistocene survival of S. miyabeanum in unglaciated Beringia, although we cannot eliminate the possibility that the species recolonized Alaska from Asia more recently. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 17–37.

We developed novel microsatellite markers for D alechampia scandens L. (Euphorbiaceae). The target plants belong to a distinct, but undescribed, species in the D . scandens species complex, characterized by small resin-producing glands. In total, 110 alleles over 36 novel markers were identified across 39 individuals from three populations. The number of alleles varied from one to seven, with an average of 3.06 ± 0.26 alleles per locus. The developed markers, along with previously developed ones for a large-glanded D . scandens species, were tested for amplification in 11 additional species of the genus D alechampia. Four markers did not produce any detectable allele in 37 individuals from two populations of the large-glanded species. Average expected heterozygosity across all small- and large-glanded specific loci was 0.36 and 0.15, for the small and large glanded populations, respectively. Cross-species amplification showed that 89% of all markers were successfully amplified in at least one of the 11 other D alechampia species. These microsatellite markers may be useful for detecting undescribed species in the D . scandens species complex, and can be used for comparative analyses of genetic structure, mating system and phylogeography of other D alechampia species. This is the peer reviewed version of the following article: [FULL CITE], which has been published in final form at doi:10.1111/1442-1984.12142. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."

Aim Disjunctly distributed peatmosses (Sphagnum) have been found to exhibit little genetic structure over regional and intercontinental scales, mainly caused by high ability for transoceanic long-distance dispersal. Although, most Northern Hemisphere peatmoss species have wide circumboreal/nemoral ranges, little is known about the magnitude and effects of long-distance dispersal and barriers in shaping the genetic structure of such species. We investigate whether high dispersal capacity has caused genetic homogeneity across broad areas of the Northern Hemisphere, or whether barriers act to shape genetic structure across different species with similar distributional ranges. Location Northern Hemisphere. Methods We studied genetic variation and structure in six Sphagnum species using 19 microsatellite loci. Results Four out of six species were genetically structured in similar ways; with mainly one Beringian and one Atlantic group. Overall, both the North American and Eurasian continents seemed to act as a barrier to gene flow in several species. However, the most abrupt breakpoint between genetic groups was found in south-east Alaska. Main conclusions We found evidence for extensive gene flow between regions across the Northern Hemisphere among peatmosses, with oceans seemingly acting as weaker barriers to gene flow than landmasses. Plants from the amphi-Atlantic and amphi-Beringian regions of several species were genetically differentiated. Similar genetic structuring across several species, indicate that spore-producing species do not disperse freely across their entire distributional range, but are likely limited by wind directions, landmass barriers and/or habitat availability. This is the peer reviewed version of the following article: [Long-distance dispersal and barriers shape genetic structure of peatmosses (Sphagnum) across the Northern Hemisphere], which has been published in final form at [http://onlinelibrary.wiley.com/doi/10.1111/jbi.12716/abstract]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.

Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum. © 2016 Kyrkjeeide et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Aim Arctic plant phylogeography has largely focused on seed plants, and studies on other plant groups are necessary for comparison. Bryophytes have a unique life cycle and can be resistant to extreme conditions, suggesting that their phylogeographic patterns may differ from those of vascular plants. We address the history of the bryophyte genus Cinclidium in order to assess: (1) interspecific relationships, (2) whether its current broad circumarctic distribution results from recent dispersal or has been maintained by long-term local survival under severe glacial conditions, and (3) the origin of its bipolar disjunction. Location Arctic/boreal and bipolar. Methods We sequenced three plastid regions (atpH–atpI, rpl32–trnL and clpP1.1–clpP1.2) in 129 accessions covering the entire geographical range of all four described species, and inferred phylogenetic relationships and phylogeographical patterns using maximum parsimony, statistical parsimony and Bayesian inference. Results Cinclidium subrotundum was inferred to be monophyletic, in agreement with its distinct morphology and ecology. The three remaining known species (the haploids C. latifolium and C. arcticum, and the diploid C. stygium) shared a number of closely related or identical haplotypes despite their clear morphological differentiation. In all species, identical haplotypes occurred across the entire circumpolar region, including North Atlantic islands. In the bipolar species C. stygium, the haplotype observed in South America (Tierra del Fuego) was identical to one found in Iceland. Three populations originally referred to C. latifolium harboured highly divergent haplotypes and may represent a new species. Main conclusions The extensive haplotype sharing suggests a polyploid origin of C. stygium from C. arcticum, as well as incomplete lineage sorting and/or hybridization between the two haploids C. arcticum and C. latifolium. We interpret the finding of identical haplotypes over vast areas, including isolated islands, as a result of recent dispersal causing the circumpolar distribution of all species in the Northern Hemisphere and the extreme bipolar disjunction in C. stygium. The patterns in the bryophyte genus Cinclidium resemble those previously documented in arctic–alpine and bipolar vascular plants, suggesting that similar mechanisms have shaped species distributions in bryophytes and higher plants.

An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. To test this hypothesis, we assessed genetic diversity and structure in the populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances

Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (~16,000-50,000 years bp) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a palaeoecological tool.

The application of genetic tools for studying species delimitation and relationships in Sphagnum (peatmosses) has demonstrated that evolutionary patterns are complex and include homoploid hybridization and multiple taxa of allopolyploid origin. We investigated evolutionary relationships in the so-called S. fimbriatum complex and tested hypotheses of species delimitation derived from patterns of morphological variation, and determined the origin of one species with diploid gametophytes. Plastid DNA sequences resolve a single haplotype shared by one described species, S. concinnum, and a morphotype that we had hypothesized to be another species (referred to informally as S. “diskoense”). All samples of the polyploid, S. tescorum, share an identical haplotype with most samples of S. girgensohnii. Sphagnum fimbriatum and S. girgensohnii share several plastid DNA haplotypes, and also share haplotypes with two other morphotypes that we had hypothesized to be distinct species (S. “obscurum” and S. “uber...

Seed banks may increase the effective population size (N(e)) of plants as a result of elevated coalescence times for alleles residing in the populations. This has been empirically demonstrated in populations of the annual Arabidopsis thaliana, whereas comparable data for perennial species are currently lacking. We studied the contribution of seed banks to effective sizes of natural populations of the self-incompatible, perennial Arabidopsis lyrata subsp. petraea, a close relative of A. thaliana. •Fourteen populations of A. lyrata collected throughout the Norwegian distribution range were analyzed using microsatellite markers. •The genetic composition of seed-bank and aboveground cohorts was found to be highly similar, with little genetic differentiation between cohorts in most populations. However, the proportion of private alleles was higher in aboveground than in seed-bank cohorts. The presence of seed banks significantly increased total N(e), but the contribution from seed banks to overall N(e) were lower than the contribution from aboveground cohorts in most populations. Estimated historical N(e) values, reflecting the effective sizes of populations throughout the history of the species, were considerably higher than estimates of contemporary N(e), reflecting number of reproducing individuals within the past few generations. •The results show that the seed bank contributes to total N(e) in the perennial herb A. lyrata. However, the contribution is similar to or lower than that of the above-ground fraction of the population and markedly weaker than that previously documented in the annual A. thaliana.

Genetic and morphological similarity between populations separated by large distances may be caused by frequent long-distance dispersal or retained ancestral polymorphism. The frequent lack of differentiation between disjunct conspecific moss populations on different continents has traditionally been explained by the latter model, and has been cited as evidence that many or most moss species are extremely ancient and slowly diverging. We have studied intercontinental differentiation in the amphi-Atlantic peat moss Sphagnum angermanicum using 23 microsatellite markers. Two major genetic clusters are found, both of which occur throughout the distributional range. Patterns of genetic structuring and overall migration patterns suggest that the species probably originated in North America, and seems to have been established twice in Northern Europe during the past 40,000 years. We conclude that similarity between S. angermanicum populations on different continents is not the result of ancient vicariance and subsequent stasis. Rather, the observed pattern can be explained by multiple long-distance dispersal over limited evolutionary time. The genetic similarity can also partly be explained by incomplete lineage sorting, but this appears to be caused by the short time since separation. Our study adds to a growing body of evidence suggesting that Sphagnum, constituting a significant part of northern hemisphere biodiversity, may be more evolutionary dynamic than previously assumed.

Biodiversity of threatened species can be preserved in cryopreservation repositories, allowing storage of biological information and future re-introduction to the wild. The success of ex situ programs for species conservation relies on using simple and efficient cryopreservation techniques. Bryophytes may be classified as stress-tolerant plants, but a large fraction worldwide is nevertheless threatened by extinction to various degrees. The aims of this study were to investigate how to exploit natural stress tolerance of bryophytes in the development of simple cryopreservation protocols without the use of cryoprotectants or pretreatment. We studied regeneration capacity of bryophytes found at different moisture and light conditions in vivo (reflecting varying levels of plant desiccation tolerance), both sampled from herbarium specimens of varying ages and also collected in situ during winter season and thus naturally cold acclimated. Furthermore, to identify optimal samples for direct cryopreserva...

It is commonly found that individual hybrid, polyploid species originate recurrently and that many polyploid species originated relatively recently. It has been previously hypothesized that the extremely rare allopolyploid peat moss Sphagnum troendelagicum has originated multiple times, possibly after the last glacial maximum in Scandinavia. This conclusion was based on low linkage disequilibrium in anonymous genetic markers within natural populations, in which sexual reproduction has never been observed. Here we employ microsatellite markers and chloroplast DNA (cpDNA)-encoded trnG sequence data to test hypotheses concerning the origin and evolution of this species. We find that S. tenellum is the maternal progenitor and S. balticum is the paternal progenitor of S. troendelagicum. Using various Bayesian approaches, we estimate that S. troendelagicum originated before the Holocene but not before c. 80 000 years ago (median expected time since speciation 40 000 years before present). The observed lack of complete linkage disequilibrium in the genome of this species suggests cryptic sexual reproduction and recombination. Several lines of evidence suggest multiple origins for S. troendelagicum, but a single origin is supported by approximate Bayesian computation analyses. We hypothesize that S. troendelagicum originated in a peat-dominated refugium before last glacial maximum, and subsequently immigrated to central Norway by means of spore flow during the last thousands of years.

† Background and Aims The gene flow through pollen or seeds governs the extent of spatial genetic structure in plant populations. Another factor that can contribute to this pattern is clonal growth. The perennial species Arabidopsis lyrata ssp. petraea (Brassicaceae) is a self-incompatible, clonal species found in disjunctive populations in central and northern Europe. † Methods Fourteen microsatellite markers were employed to study the level of kinship and clonality in a highaltitude mountain valley at Spiterstulen, Norway. The population has a continuous distribution along the banks of the River Visa for about 1.5 km. A total of 17 (10 m × 10 m) squares were laid out in a north‐ south transect following the river on both sides. † Key Results It is shown that clonal growth is far more common than previously shown in this species, although the overall size of the genets is small (mean diameter ¼ 6.4 cm). Across the whole population there is no indication of isolation by distance, and spatial genetic structure is only visible on fine spatial scales. In addition, no effect of the river on the spatial distribution of genotypes was found. † Conclusions Unexpectedly, the data show that populations of small perennials like A. lyrata can behave like panmictic units across relatively large areas at local sites, as opposed to earlier findings in central Europe.

In most plant species, seeds after dispersing from the mother plant (primary dispersal) may undergo secondary dispersal, either in time by remaining dormant in the soil and forming a seed bank, or in space by movement to other locations. Seed bank and dispersal in space are bet-hedging strategies that minimize the extinction risk and aid to population stability and persistence in temporally variable environments. The ability to establish seed bank via depositing a fraction of seeds into the soil may also increase the potential of early stage adaptation into new habitats. A persistent seed bank preserves genetic diversity and buffers populations from the loss of genetic variants due to random drift. Although theoretical studies have highlighted the role of seed banks in elevating effective population size, little information exists regarding the evolutionary potential of seed banks in natural populations. In this thesis I studied inter- and intraspecific variation in genetic composition of seed banks and its significance in natural populations of two closely related species in the genus Arabidopsis. A. thaliana is an annual self-compatible plant whereas A. lyrata is perennial and self-incompatible. The potential contribution of seed banks to effective population size (Ne), generation time, genetic variation, and population dynamics has been addressed. The pattern of dispersal over time and space was investigated by monitoring of natural populations over five consecutive years in A. thaliana. In addition, regional differences in seed bank, genetic composition and structure in A. lyrata were investigated between three contrasting regions in northern Europe. The results showed that both species form persistent seed banks throughout their Norwegian distribution range. Seedling density was lower in A. lyrata than A. thaliana, as would be expected from a perennial. Moreover, the seed bank contributes to total effective population size in perennial A. lyrata, though not to the same extent as in A. thaliana. In A. lyrata both seed bank and above-ground individuals seemingly have a similar contribution to the total Ne. Monitoring A. thaliana populations over multiple years revealed that in most populations two or more distinct multilocus genotypes were present, which often varied in frequency between years, leading to variation in within-population diversity. Although most of the distinct multilocus genotypes within each population were genetically similar, probably due to historical mutation and recombination events, in some cases multiple colonization events due to migration from other populations were evident. Many geographically closely situated populations shared common multilocus genotypes and expressed low differentiation compared to distant ones. The results show evidence dispersal in time, i.e., persistence of dormant or ungerminated seeds in ten populations in which 29% of seeds descended two or three years before present, on average. Additionally there are signs of seed and pollen immigration from other populations in almost one fifth of the studied cohorts, reflecting an effective migration rate of 1.8% per generation. Migration through pollen and seeds in A. thaliana is therefore common, and the seed bank plays, at the same time a substantial role in overall population dynamics. Comparing natural populations of A. lyrata in different regions revealed that soil seed banks are either absent or small in Icelandic populations and average density of seed bank is 2.5 fold smaller than what was observed among Norwegian populations, though the overall differences between regions was not statistically significant. The level of genetic variation in Icelandic was similar to Swedish and significantly higher than what found in Norwegian populations. In addition population differentiation on Icelandic was significantly lower than what found in Swedish and Norwegian populations. When comparing similar distribution areas in the regions, the effect of habitat structure was found to be less important to explain the differences in genetic structuring. Immigration rate over time was similar between regions that show variable population differentiations. The results suggest that relatively low differentiation among Icelandic populations is more likely due to large historical effective population sizes compared to Scandinavian populations, rather than immigration per se.

Sympatric species are expected to minimize competition by partitioning resources, especially when these are limited. Herbivores inhabiting the High Arctic in winter are a prime example of a situation where food availability is anticipated to be low, and thus reduced diet overlap is expected. We present here the first assessment of diet overlap of high arctic lemmings during winter based on DNA metabarcoding of feces. In contrast to previous analyses based on microhistology, we found that the diets of both collared (Dicrostonyx groenlandicus) and brown lemmings (Lemmus trimucronatus) on Bylot Island were dominated by Salix while mosses, which were significantly consumed only by the brown lemming, were a relatively minor food item. The most abundant plant taxon, Cassiope tetragona, which alone composes more than 50% of the available plant biomass, was not detected in feces and can thus be considered to be non-food. Most plant taxa that were identified as food items were consumed in proportion to their availability and none were clearly selected for. The resulting high diet overlap, together with a lack of habitat segregation, indicates a high potential for resource competition between the two lemming species. However, Salix is abundant in the winter habitats of lemmings on Bylot Island and the non-Salix portion of the diets differed between the two species. Also, lemming grazing impact on vegetation during winter in the study area is negligible. Hence, it seems likely that the high potential for resource competition predicted between these two species did not translate into actual competition. This illustrates that even in environments with low primary productivity food resources do not necessarily generate strong competition among herbivores. © 2015 Soininen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

This is the submitted manuscript version. Published version can be found at http://doi.org/10.1111/mec.13411. Sparse, incomplete and inappropriate historical records of invasive species often hamper invasive species management interventions. Population genetic analyses of invaders might provide a suitable context for the identification of their source populations and possible introduction routes. Here, we describe the population genetics of Heracleum persicum Desf. ex Fisch and trace its route of introduction into Europe. Microsatellite markers revealed a significantly higher genetic diversity of H. persicum in its native range, and the loss of diversity in the introduced range may be attributed to a recent genetic bottleneck. Bayesian cluster analysis on regional levels identified three and two genetic clusters in the native and the introduced ranges, respectively. A global structure analysis revealed two worldwide distinct genetic groups: one primarily in Iran and Denmark, the other primarily in Norway. There were also varying degrees of admixture in England, Sweden, Finland and Latvia. Approximate Bayesian computation indicated two independent introductions of H. persicum from Iran to Europe: the first one in Denmark and the second one in England. Finland was subsequently colonized by English populations. In contrast to the contemporary hypothesis of English origin of Norwegian populations, we found Finland to be a more likely source for Norwegian populations, a scenario supported by higher estimated histor-ical migration from Finland to Norway. Genetic diversity per se is not a primary determinant of invasiveness in H. persicum. Our results indicate that, due to either pre-adaptations or rapid local adaptations, introduced populations may have acqu-ired invasiveness after subsequent introductions, once a suitable environment was encountered.