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Invasive species have become a pervasive threat on every continent and across a broad array of environments. Several traits predicted to promote invasion success, such as small seed size, rapid vegetative growth and short time to reproduction, are correlated with smaller genome sizes in a number of systems. To understand the influence of genome size on plant invasion dynamics, we compared genome sizes and traits inCentaurea solstitialis(YST) genotypes from the Californian invasion to those from their native source region in Spain. We conducted a common garden experiment and genome size survey to ask: (1) Is the invasion associated with genome size reduction? (2) To what extent can differences in genome size explain previously observed increases in plant size and reproduction in YST invasions? (3) Finally, we tested for expected evolutionary patterns in genome size across populations, including evidence of selection favouring reduced genome sizes at higher elevations, and evidence of stochastic processes leading to increases in genome sizes where effective population sizes are smaller. We found a reduction in corrected genome size in the invaded range, as well as significant interaction effects of range x elevation on genome size, and range x genome size on flowering time variation. Specifically, larger genomes tended to flower later and genome size decreased with increasing elevation in the invasion only. These emergent relationships in invading YST suggest potential selection for smaller genomes following introduction of YST to its invaded range. We also found a significant effect of measurement date on genome size estimation by flow cytometry, and this effect was more pronounced among native range genotypes.

Yellow starthistle (Centaurea solstitialis) is a highly invasive species that has been a model system for the potential contribution of evolution to invader traits. Here, we report the construction of a chromosome-scale reference genome for C. solstitialis using a combination of PacBio HiFi and Dovetail Omni-C technologies, and functional gene annotation with RNAseq. We validate the reference genome using a restriction site-associated DNA (RAD)-based genetic map from an F2 mapping population. We find that syntenic comparisons to other taxa in the Asteraceae reveal a chromosomal fusion in the lineage of C. solstitialis, and widespread fission in globe artichoke (Cynara cardunculus). Using a QTL analysis from the mapping population (derived from a cross between native and invading parents) we identify 13 QTL underpinning size traits that are associated with adaptation in the invaded range, including a putative large-scale chromosomal inversion that has a pleiotropic and overdominant effect on key invader traits.

Plants demonstrate some of the greatest variation in genome size among eukaryotes, and their genome sizes can vary dramatically across individuals and populations within species. This genetic variation can have consequences for traits and fitness, but few studies have been able to attribute genome size differentiation to ecological and evolutionary processes. Biological invasions present particularly useful natural laboratories to infer selective agents that might drive genome size shifts across environments and population histories. Here, we test hypotheses for the evolutionary causes of genome size variation across 14 invading populations of yellow starthistle, Centaurea solstitialis, in California, USA. We use a survey of genome sizes and trait variation to ask: (1) Is variation in genome size associated with developmental trait variation? (2) Are genome sizes smaller toward the leading edge of the expansion, consistent with selection for ‘colonizer’ traits? Or alternatively, does genome size increase toward the leading edge of the expansion, consistent with predicted consequences of founder effects and drift? (3) Finally, are genome sizes smaller at higher elevations, consistent with selection for shorter development times? We found that 2C DNA content varied 1.21-fold among all samples, and was associated with flowering time variation, such that plants with larger genomes reproduced later, with lower lifetime capitula production. Genome sizes increased toward the leading edge of the invasion, but tended to decrease at higher elevations, consistent with genetic drift during range expansion but potentially strong selection for smaller genomes and faster development time at higher elevations.

Competing phylogenetic models have been proposed to explain the success of species introduced to other communities. Here, we present a study predicting the establishment success of birds introduced to Florida, Hawaii, and New Zealand using several alternative models, considering species’ phylogenetic relatedness to source and recipient range taxa, propagule pressure, and traits. We find consistent support for the predictive ability of source region phylogenetic structure. However, we find that the effects of recipient region phylogenetic structure vary in sign and magnitude depending on inclusion of source region phylogenetic structure, delineation of the recipient species pool, and the use of phylogenetic correction in the models. We argue that tests of alternative phylogenetic hypotheses including the both source and recipient community phylogenetic structure, as well as important covariates such as propagule pressure, are likely to be critical for identifying general phylogenetic patterns in introduction success, predicting future invasions, and for stimulating further exploration of the underlying mechanisms of invasibility.

Premise Large-scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from diverse plant communities. Methods We generated >650 Gbp of RNA-seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations. Results Only modest differences in assembly quality were observed across multiple k-mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes. Discussion We provide new RNA-seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high-quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large-scale studies at the intersection of ecology and genomics.

Premise of the studyTagSeq is a cost-effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non-model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range NEON core site.MethodsTissue for TagSeq was sampled from multiple individuals of four species [Bouteloua aristidoidesandEragrostis lehmanniana(Poaceae);Tidestromia lanuginosa(Amaranthaceae), andParkinsonia florida(Fabaceae)] at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA-seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples.ResultsA high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species.DiscussionTagSeq usingde novoreference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non-model plant species.

Premise of the study: Large scale projects such as NEON are collecting ecological data on entire biomes to track and understand plant responses to climate change. NEON provides an opportunity for researchers to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from phylogenetically diverse NEON plant communities, including species with diploid and polyploid genomes.Methods: We used Illumina NextSeq to generate >20 Gb of RNA-seq for each of 24 vascular plant species representing 12 genera and 9 families at the Harvard Forest NEON site. Each species was sampled twice, in July and August 2016. We used Transrate, BUSCO, and GO analyses to assess transcriptome quality and content.Results: We obtained nearly 650 Gb of RNA-seq data that assembled into more than 755,000 translated protein sequences across the 24 species. We observed only modest differences in assembly quality scores across a range of k-mer values. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated genes between diploid and polyploid transcriptomes.Discussion: Our resource provides new RNA-seq datasets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers clear opportunities for large scale studies at the intersection of ecology and genomics.

Background The ability to efficiently characterize microbial communities from host individuals can be limited by co-amplification of host organellar sequences (mitochondrial and/or plastid), which share a common ancestor and thus sequence similarity with extant bacterial lineages. One promising approach is the use of sequence-specific peptide nucleic acid (PNA) clamps, which bind to, and block amplification of, host-derived DNA. Universal PNA clamps have been proposed to block host plant-derived mitochondrial (mPNA) and plastid (pPNA) sequences at the V4 16S rRNA locus, but their efficacy across a wide range of host plant species has not been experimentally tested. Results Using the universal PNA clamps, we amplified and sequenced root microbial communities from replicate individuals of 32 plant species with a most recent common ancestor inferred at 140 MYA. We found the average rate of host plastid contamination across plant species was 23%, however, particular lineages exhibited much higher rates (62–94%), with the highest levels of contamination occurring in the Asteraceae. We investigated chloroplast sequence variation at the V4 locus across 500 land plant species (Embryophyta) and found six lineages with mismatches between plastid and the universal pPNA sequence, including all species within the Asteraceae. Using a modified pPNA for the Asteraceae sequence, we found (1) host contamination in Asteraceae species was reduced from 65 to 23%; and (2) host contamination in non-Asteraceae species was increased from 12 to 69%. These results demonstrate that even single nucleotide mismatches can lead to drastic reductions in pPNA efficacy in blocking host amplification. Importantly, we found that pPNA type (universal or modified) had no effect on the detection of individual bacterial taxa, or estimates of within and between sample bacterial diversity, suggesting that our modification did not introduce bias against particular bacterial lineages. Conclusions When high similarity exists between host organellar DNA and PCR target sequences, PNA clamps are an important molecular tool to reduce host contamination during amplification. Here, we provide a validated framework to modify universal PNA clamps to accommodate host variation in organellar sequences. Electronic supplementary material The online version of this article (10.1186/s40168-018-0534-0) contains supplementary material, which is available to authorized users.

Introduced species are a common feature of modern plant communities and experience environmental challenges alongside native species. Changes to the environment may reveal distinct species-environment relationships for native and introduced components of plant communities. Extreme environmental change, such as drought, is predicted to result in declines in native species and increased opportunities for invasion, but empirical support for these ideas remains mixed. We tested for differences in the response of native and invaded species to environmental changes by analyzing a longterm dataset of species abundance in California grasslands collected during a period of severe drought. Sampling sites included a combination of stressful serpentine soils, which are resilient against invasion and maintain diverse native species assemblages, and more benign nonserpentine soils, which are heavily invaded and harbor low levels of native species cover. We found a significant correlation between sampling year and species composition for nonserpentine sites, but not for serpentine sites. These patterns were repeated when only introduced species were included in the analysis but no pattern of change was found for native species. The species most strongly associated with directional change on nonserpentine soils were three invasive Eurasian grasses, Bromus hordaceus, Taeniatherium caput-medusae, and Avena fatua. Differences in species composition on both serpentine and nonserpentine soils were significantly correlated with specific leaf area, a trait which has been linked to drought tolerance in these communities, although changes in abundance for the three Eurasian grasses most strongly associated with change did not consistently follow this pattern. Our analyses indicate relatively stable native community composition and strong directional change in introduced species composition, contradicting predictions for how native and introduced species will respond to environmental shifts, but supporting the hypothesis that native and invading species groups have important functional differences that shape their relationships to the environment.

The margins of an expanding range are predicted to be challenging environments for adaptation. Marginal populations should often experience low effective population sizes (Ne) where genetic drift is high due to demographic expansion and/or census population size is low due to unfavorable environmental conditions. Nevertheless, invasive species demonstrate increasing evidence of rapid evolution and potential adaptation to novel environments encountered during colonization, calling into question whether significant reductions in Ne are realized during range expansions in nature. Here we report one of the first empirical tests of the joint effects of expansion dynamics and environment on effective population size variation during invasive range expansion. We estimate contemporary values of Ne using rates of linkage disequilibrium among genome-wide markers within introduced populations of the highly invasive plant Centaurea solstitialis (yellow starthistle) in North America (California, USA), as well as in native European populations. As predicted, we find that Ne within the invasion is positively correlated with both expansion history (time since founding) and habitat quality (abiotic climate). History and environment had independent additive effects with similar effect sizes, supporting an important role of both factors in this invasion. These results support theoretical expectations for the population genetics of range expansion, though whether these processes can ultimately arrest the spread of an invasive species remains an open question.

Population genomic analyses can reveal the mechanisms shaping the evolution of colonizing and invasive taxa, as for any species, including the fundamental processes of mutation, genetic drift, gene flow, and selection. Colonization events associated with species introductions, range shifts, and invasions pose a number of unique evolutionary questions, however, for which population genomic approaches are especially well-equipped to answer. These include quantifying the extent of founder effects, genetic bottlenecks, gene flow, and admixture that give rise to successful colonizing populations, identifying the nature and architecture of adaptive variation that resides in these populations (including types of mutations, their effect sizes, and their standing levels of variation), disentangling signatures of adaptation from other mechanisms of evolution, and identifying the ecological traits that have been the targets of natural selection and might be directly involved in the evolution of colonizing ability itself. We address each of these topics in this chapter, highlighting examples of recent research and the potential for population genomics to provide answers to some of the most pressing questions in the biology of colonizing and invasive species.

Plant trait evolution is a topic of interest across disciplines and scales. Phylogenetic studies are powerful for generating hypotheses about the mechanisms that have shaped plant traits and their evolution. Introduced plants are a rich source of data on contemporary trait evolution. Introductions could provide especially useful tests of a variety of evolutionary hypotheses because the environments selecting on evolving traits are still present. We review phylogenetic and contemporary studies of trait evolution and identify areas of overlap and areas for further integration. Emerging tools which can promote integration include broadly focused repositories of trait data, and comparative models of trait evolution that consider both intra and interspecific variation.

Invasive plants may leave enemies behind when they colonize a new habitat, allowing selection to favor increased investment in growth and/or reproduction over defensive traits. Previous studies have identified reduced diversity of potential bacterial pathogens and evolutionary increases in growth and reproduction in invading populations of yellow starthistle (Centaurea solstitialis). This study leverages a recently developed high-throughput assay of immune function to test for evidence of a trade-off between increased growth and defense against bacterial pathogens in yellow starthistle's invasion of California (USA). Seven bacterial strains were cultured from infected leaf tissue in the native range. Healthy leaf tissue from five native European collections and six invading collections were exposed to these native bacterial strains. A standardized assay of peroxidase activity was used measure the oxidative burst immune response to pathogen recognition by the leaf. Immune responses were compared to plant growth within and between ranges to assess evidence for a trade-off. Plant genotypes from the native range demonstrated a higher immune response to bacterial strains than did invading genotypes, consistent with a trade-off with plant growth across regions. The same trade-off was also apparent across genotypes from the native range, but not across genotypes from the invaded range. Our results provide evidence that increased growth in a highly invasive plant species may come at a cost to immune function, consistent with the hypothesis that escape from enemies can provide opportunities for shifts in resource allocation that favor the proliferation of non-native species.

Species introductions often bring together genetically divergent source populations, resulting in genetic admixture. This geographic reshuffling of diversity has the potential to generate favorable new genetic combinations, facilitating the establishment and invasive spread of introduced populations. Observational support for the superior performance of admixed introductions has been mixed, however, and the broad importance of admixture to invasion questioned. Under most underlying mechanisms, admixture’s benefits should be expected to increasewith greater divergence among and lower genetic diversity within source populations. We use a literature survey to quantify the prevalence of admixture and evaluate whether it occurrs under circumstances predicted to be mostbeneficial to introduced species. We find that 39% of species are reported to be admixed when introduced. Admixed introductions come from sources with a wide range of genetic variation, but are disproportionately absent where there is high genetic divergence among native populations. We discuss multiple potential explanations for these patterns, but note that negative epistatic interactions should be expected at high divergence amongpopulations (outbreeding depression). As a case study, we experimentally cross source populations differing in divergence in the invasive plantCentaurea solstitialis. We find many positive (heterotic) interactions, but fitness benefits decline and are ultimately negative at high source divergence, with patterns suggestingcyto-nuclear epistasis. We conclude that admixture is common in species introductions and often happens under conditions expected to be beneficial to invaders, but that these conditions may be constrained by predictable negativegenetic interactions, potentially explaining conflicting evidence for admixture's benefits to invasion.

Species introductions often bring together genetically divergent source populations, resulting in genetic admixture. This geographic reshuffling of diversity has the potential to generate favourable new genetic combinations, facilitating the establishment and invasive spread of introduced populations. Observational support for the superior performance of admixed introductions has been mixed, however, and the broad importance of admixture to invasion questioned. Under most underlying mechanisms, admixture's benefits should be expected to increase with greater divergence among and lower genetic diversity within source populations, though these effects have not been quantified in invaders. We experimentally crossed source populations differing in divergence in the invasive plant Centaurea solstitialis. Crosses resulted in many positive (heterotic) interactions, but fitness benefits declined and were ultimately negative at high source divergence, with patterns suggesting cytonuclear epistasis. We explored the literature to assess whether such negative epistatic interactions might be impeding admixture at high source population divergence. Admixed introductions reported for plants came from sources with a wide range of genetic variation, but were disproportionately absent where there was high genetic divergence among native populations. We conclude that while admixture is common in species introductions and often happens under conditions expected to be beneficial to invaders, these conditions may be constrained by predictable negative genetic interactions, potentially explaining conflicting evidence for admixture's benefits to invasion.

As grassland habitats become degraded, declines in juvenile and adult food resources may limit populations of rare insects. Fender's blue butterfly (Icaricia icarioides fenderi), a species proposed for listing as endangered under the US Endangered Species Act, survives in remnants of upland prairie in western Oregon. We investigated the effects of limited larval hostplants and adult nectar sources on butterfly population size at four sites that encompass a range of resource densities. We used coarse and detailed estimates of resource abundance to test hypotheses relating resource quantity to population size. Coarse estimates of resources (percent cover of hostplant and density of nectar flowers) suggest that butterfly population size is not associated with resource availability. However, more detailed estimates of resources (density of hostplant leaves and quantity of nectar from native nectar sources) suggest that butterfly population size is strongly associated with resource availability. The results of this study suggest that restoring degraded habitat by augmenting adult and larval resources will play an important role in managing populations of this rare butterfly.

Multiple scale-dependent ecological processes infl uence species distributions. Uncovering these drivers of dynamic range boundaries can provide fundamental ecological insights and vital knowledge for species management. We develop a transferable methodology that uses widely available data and tools to determine critical scales in range expansion and to infer dominating scale-dependent forces that infl uence spread. We divide a focal geographic region into diff erent sized square cells, representing diff erent spatial scales. We then used herbarium records to determine the species ’ occupancy of cells at each spatial scale. We calculated the growth in cell occupancy across scales to infer the scale dependent expansion rate. Th is is the fi rst time such a ‘ box-counting ’ method is used to study range expansion. We coupled this multi-scale analysis with species distribution models to determine the range and spatial scales where suitable climate allows the species to spread, and where other factors may be infl uencing the expansion. We demonstrate our methodology by assessing the spread of invasive Sahara mustard in North America. We detect critical scales where its spread is limited (100 – 500 km) or unconstrained (5 – 50 km) by climatic variables. Using climate-based models to assess the similarity of climate envelopes in its native and invaded range, we fi nd that the climate in the invaded range generally predicts the native distribution, suggesting that either there has been little local adaptation to climate occurring since introduction or the biological interaction experienced in the invaded range has not driven the species to occupy climatic conditions much diff erent from its native range. Our novel method can be broadly utilized in other studies to generate critical insights into the scale dependency of diff erent ecological drivers that infl uence the spread and distribution limits, as well as to help parameterizing predictions of future spread, and thus inform management decisions.

Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11−430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios. Fil: Dlugosch, Katrina M.. University of British Columbia; Canadá Fil: Lai, Zhao. Indiana University; Estados Unidos Fil: Bonin, Auélie. Indiana University; Estados Unidos Fil: Hierro, Jose Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; Argentina Fil: Rieseberg, Loren H.. University of British Columbia; Canadá. Indiana University; Estados Unidos

Cultivated plants have been selected by humans for increased yield in a relatively benign environment, where nutrient and water resources are often supplemented, and biotic enemy loads are kept artificially low. Agricultural weeds have adapted to this same benign environment as crops and often have high growth and reproductive rates, even though they have not been specifically selected for yield. Considering the competing demands for resources in any plant, a key question is whether adaptation to agricultural environments has been accompanied by life history trade-offs, in which resistance to (largely absent) stress has been lost in favour of growth and reproduction. The experiments reported here were designed to test for growth-defence trade-offs in agricultural weeds, crops and native varieties of common sunflower (Helianthus annuus L., Asteraceae) by comparing their performance in the presence or absence of abiotic (drought and crowding) or biotic (simulated herbivory, insect herbivory and fungal) stress. We found that growth, as well as viability of crops and weeds, was reduced by abiotic drought stress. The weakened defence in the agricultural genotypes was further evident as increased susceptibility to fungal infection and higher level of insect palatability. To uncover molecular mechanisms underlying these trade-offs, we monitored gene expression kinetics in drought-stressed plants. By correlating phenotypic observations with molecular analyses, we report the identification of several genes, including a protein phosphatase 2C and the HD-Zip transcription factor Athb-8, whose expression is associated with the observed phenotypic variation in common sunflower.

Recent increases in the production of genomic data are yielding new opportunities and challenges for biologists. Among the chief problems posed by next-generation sequencing are assembly and analyses of these large data sets. Here we present an online server, http://EvoPipes.net , that provides access to a wide range of tools for bioinformatic analyses of genomic data oriented for ecological and evolutionary biologists. The EvoPipes.net server includes a basic tool kit for analyses of genomic data including a next-generation sequence cleaning pipeline (SnoWhite), scaffolded assembly software (SCARF), a reciprocal best-blast hit ortholog pipeline (RBH Orthologs), a pipeline for reference protein-based translation and identification of reading frame in transcriptome and genomic DNA (TransPipe), a pipeline to identify gene families and summarize the history of gene duplications (DupPipe), and a tool for developing SSRs or microsatellites from a transcriptome or genomic coding sequence collection (findSSR). EvoPipes.net also provides links to other software developed for evolutionary and ecological genomics, including chromEvol and NU-IN, as well as a forum for discussions of issues relating to genomic analyses and interpretation of results. Overall, these applications provide a basic bioinformatic tool kit that will enable ecologists and evolutionary biologists with relatively little experience and computational resources to take advantage of the opportunities provided by next-generation sequencing in their systems.

The genetic basis of weedy and invasive traits and their evolution remain poorly understood, but genomic approaches offer tremendous promise for elucidating these important features of weed biology. However, the genomic tools and resources available for weed research are currently meager compared with those available for many crops. Because genomic methodologies are becoming increasingly accessible and less expensive, the time is ripe for weed scientists to incorporate these methods into their research programs. One example is next-generation sequencing technology, which has the advantage of enhancing the sequencing output from the transcriptome of a weedy plant at a reduced cost. Successful implementation of these approaches will require collaborative efforts that focus resources on common goals and bring together expertise in weed science, molecular biology, plant physiology, and bioinformatics. We outline how these large-scale genomic programs can aid both our understanding of the biology of weedy and invasive plants and our success at managing these species in agriculture. The judicious selection of species for developing weed genomics programs is needed, and we offer up choices, but noArabidopsis-like model species exists in the world of weeds. We outline the roadmap for creating a powerful synergy of weed science and genomics, given well-placed effort and resources.

The study of sympatric populations of closely related plant species often reveals evidence of hybridization. Mechanisms that reduce outcrossing (e.g., selfing, apomixis) may allow co-occurrence without gene flow. In this study, we describe patterns of genetic variation in two contact zones, each comprising three closely related morphological types, that key to three distinct species in the North American Crepis agamic (apomictic) complex. We used RAPD markers to characterize individuals from two sites: one in northern California (Sardine Lookout) and another in northwestern Oregon (Summit Road). At Sardine Lookout, we discerned a total of four multilocus genotypes, two in one species, and one each in the other two species. Our findings suggest that distinct morphological types are maintained by absolute barriers to gene flow at this site. At Summit Road, we found greater genotypic diversity, with a total of 24 genotypes across 30 individuals. One of the morphological types was clearly genetically differentiated from the other two, with no variable markers shared with other species at this site. The two remaining species showed evidence of gene flow, with no unique markers discerning them. Morphological data tend to support this conclusion, with univariate and multivariate analyses indicating a pattern of variation spanning the two species. Taken together, these patterns suggest that contact zones need not represent hybrid zones, and that apomixis can serve as an effective barrier to gene flow that may allow for stable coexistence of close relatives.

Identifying sources of genetic variation and reconstructing invasion routes for non-native introduced species is central to understanding the circumstances under which they may evolve increased invasiveness. In this study, we used genome-wide single nucleotide polymorphisms to study the colonization history of Centaurea solstitialis in its native range in Eurasia and invasions into the Americas. We leveraged this information to pinpoint key evolutionary shifts in plant size, a focal trait associated with invasiveness in this species. Our analyses revealed clear population genomic structure of potential source populations in Eurasia, including deep differentiation of a lineage found in the southern Apennine and Balkan Peninsulas and divergence among populations in Asia, eastern Europe, and western Europe. We found strongest support for an evolutionary scenario in which western European populations were derived from an ancient admixture event between populations from eastern Europe and Asia, and subsequently served as the main genetic ‘bridgehead’ for introductions to the Americas. Introductions to California appear to be from a single source region, and multiple, independent introductions of divergent genotypes likely occurred into the Pacific Northwest. Plant size has evolved significantly at three points during range expansion, including a large size increase in the lineage responsible for the aggressive invasion of California's interior. These results reveal a long history of colonization, admixture, and trait evolution in C. solstitialis, and suggest routes for improving evidence-based management decisions for one of the most ecologically and economically damaging invasive species in the western United States. This article is protected by copyright. All rights reserved.

Non-native plants are now a pervasive feature of ecosystems across the globe1. One hypothesis for this pattern is that introduced species occupy open niches in recipient communities2,3. If true, then non-native plants should often benefit from low competition for limiting resources that define niches. Many plants have evolved larger size after introduction, consistent with increased access to limiting resources4–9. It has been difficult to test whether larger size reflects adaptation to exploit open resources, however, because vacant niches are generally challenging to identify in plants. Here we take advantage of a situation in which a highly invasive non-native plant, Centaurea solstitialis L. (yellow starthistle, hereafter YST), occupies a well-described environmental niche, wherein water is a known limiting resource10,11. We use a glasshouse common environment and climatic niche modelling to reveal that invading YST has evolved a higher-fitness life history at the expense of increased dependence on water. Critically, historical declines in resident competitors have made water more available for introduced plants11,12, demonstrating how native biodiversity declines can open niches and create opportunities for introduced species to evolve increased resource use, a potentially widespread basis for introduction success and the evolution of invasive life histories. Invasive Centaurea solstitialis (yellow starthistle) is larger than in its native range as declines in native competitors make water more available. Such opening of niches may be a factor in the widespread success of invasives.

The influence of genetic variation on invasion success has captivated researchers since the start of the field of invasion genetics 50 years ago. We review the history of work on this question and conclude that genetic variation-as surveyed with molecular markers-appears to shape invasion rarely. Instead, there is a significant disconnect between marker assays and ecologically relevant genetic variation in introductions. We argue that the potential for adaptation to facilitate invasion will be shaped by the details of genotypes affecting phenotypes, and we highlight three areas in which we see opportunities to make powerful new insights. (i) The genetic architecture of adaptive variation. Traits shaped by large-effect alleles may be strongly impacted by founder events yet more likely to respond to selection when genetic drift is strong. Large-effect loci may be especially relevant for traits involved in biotic interactions. (ii) Cryptic genetic variation exposed during invasion. Introductions have strong potential to uncover masked variation due to alterations in genetic and ecological environments. (iii) Genetic interactions during admixture of multiple source populations. As divergence among sources increases, positive followed by increasingly negative effects of admixture should be expected. Although generally hypothesized to be beneficial during invasion, admixture is most often reported among sources of intermediate divergence, supporting the possibility that incompatibilities among divergent source populations might be limiting their introgression. Finally, we note that these details of invasion genetics can be coupled with comparative demographic analyses to link genetic changes to the evolution of invasiveness itself.

Invasive and endangered species reflect opposite ends of a spectrum of ecological success, yet they experience many similar eco-evolutionary challenges including demographic bottlenecks, hybridization and novel environments. Despite these similarities, important differences exist. Demographic bottlenecks are more transient in invasive species, which (i) maintains ecologically relevant genetic variation, (ii) reduces mutation load, and (iii) increases the efficiency of natural selection relative to genetic drift. Endangered species are less likely to benefit from admixture, which offsets mutation load but also reduces fitness when populations are locally adapted. Invading species generally experience more benign environments with fewer natural enemies, which increases fitness directly and also indirectly by masking inbreeding depression. Adaptive phenotypic plasticity can maintain fitness in novel environments but is more likely to evolve in invasive species encountering variable habitats and to be compromised by demographic factors in endangered species. Placed in an eco-evolutionary context, these differences affect the breadth of the ecological niche, which arises as an emergent property of antagonistic selection and genetic constraints. Comparative studies of invasions and extinctions that apply an eco-evolutionary perspective could provide new insights into the environmental and genetic basis of ecological success in novel environments and improve efforts to preserve global biodiversity. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.

When we set a species loose outside of its historical range, we create opportunities to test fundamental questions about how populations establish, adapt, disperse, and ultimately define range boundaries. A particularly controversial issue here is how genetic variation among and within populations contributes to the dynamics of species distributions. In this issue of Molecular Ecology, Rosenthal and colleagues (2008) seize an opportunity to examine how multiple introductions create genetically distinct establishment events and how these are incorporated into invasive spread. Their findings suggest that a particular recombinant lineage of Brachypodium sylvaticum may be responsible for most of the recent expansion of this invader, highlighting the potential importance of genetic novelty and historical context for colonization success.

Allelic variation within species provides fundamental insights into the evolution and ecology of organisms, and information about this variation is becoming increasingly available in sequence datasets of multiple and/or outbred individuals. Unfortunately, identifying true allelic variants poses a number of challenges, given the presence of both sequencing errors and alleles from other closely related loci. We outline the key considerations involved in this process, including assessing the accuracy of allele resolution in sequence assembly, clustering of alleles within and among individuals, and identifying clusters that are most likely to correspond to true allelic variants of a single locus. Our focus is particularly on the case where alleles must be identified without a fully resolved reference genome, and where sequence depth information cannot be used to infer the putative number of loci sharing a sequence, such as in transcriptome or post-assembly datasets. Throughout, we provide information about publicly available tools to aid allele identification in such cases.

• Premise of study: Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we describe the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic data for evidence of hybridization. • METHODS: We generated 22 expressed sequence tag (EST) libraries for the 11 targeted weeds using Sanger, 454, and Illumina sequencing, compared the coverage and quality of sequence assemblies, and developed NimbleGen microarrays for expression analyses in five taxa. When possible, we also compared the distributions of Ks values between orthologs of congeneric taxa to detect and quantify hybridization and introgression. • RESULTS: Gene discovery was enhanced by sequencing from multiple tissues, normalization of cDNA libraries, and especially greater sequencing depth. However, assemblies from short sequence reads sometimes failed to resolve close paralogs. Substantial introgression was detected in Centaurea and Helianthus, but not in Ambrosia and LACTUCA: • CONCLUSIONS: Transcriptome sequencing using next-generation platforms has greatly reduced the cost of genomic studies of nonmodel organisms, and the ESTs and microarrays reported here will accelerate evolutionary and molecular investigations of Compositae weeds. Our study also shows how ortholog comparisons can be used to approximately estimate the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa.

Cultivated plants have been selected by humans for increased yield in a relatively benign environment, where nutrient and water resources are often supplemented, and biotic enemy loads are kept artificially low. Agricultural weeds have adapted to this same benign environment as crops and often have high growth and reproductive rates, even though they have not been specifically selected for yield. Considering the competing demands for resources in any plant, a key question is whether adaptation to agricultural environments has been accompanied by life history trade-offs, in which resistance to (largely absent) stress has been lost in favour of growth and reproduction. The experiments reported here were designed to test for growth-defence trade-offs in agricultural weeds, crops and native varieties of common sunflower (Helianthus annuus L., Asteraceae) by comparing their performance in the presence or absence of abiotic (drought and crowding) or biotic (simulated herbivory, insect herbivory and fungal) stress. We found that growth, as well as viability of crops and weeds, was reduced by abiotic drought stress. The weakened defence in the agricultural genotypes was further evident as increased susceptibility to fungal infection and higher level of insect palatability. To uncover molecular mechanisms underlying these trade-offs, we monitored gene expression kinetics in drought-stressed plants. By correlating phenotypic observations with molecular analyses, we report the identification of several genes, including a protein phosphatase 2C and the HD-Zip transcription factor Athb-8, whose expression is associated with the observed phenotypic variation in common sunflower.

Human-mediated species introductions offer opportunities to investigate when and how non-native species to adapt to novel environments, and whether evolution has the potential to contribute to colonization success. Many long-established introductions harbour high genetic diversity, raising the possibility that multiple introductions of genetic material catalyze adaptation and/or the evolution of invasiveness. Studies of nascent invasions are rare but crucial for understanding whether genetic diversity facilitates population expansion. We explore variation and evolution in founder populations of the invasive shrub Hypericum canariense. We find that these introductions have experienced large reductions in genetic diversity, but that increased growth and a latitudinal cline in flowering phenology have nevertheless evolved. These life history changes are consistent with predictions for invasive plants. Our results highlight the potential for even genetically depauperate founding populations to adapt and evolve invasive patters of spread.

Whether the potential costs associated with broad-scale use of genetically modified organisms (GMOs) outweigh possible benefits is highly contentious, including within the scientific community. Even among those generally in favour of commercialization of GM crops, there is nonetheless broad recognition that transgene escape into the wild should be minimized. But is it possible to achieve containment of engineered genetic elements in the context of large scale agricultural production? In a previous study, Warwick et al. (2003) documented transgene escape via gene flow from herbicide resistant (HR) canola (Brassica napus) into neighbouring weedy B. rapa populations (Fig. 1) in two agricultural fields in Quebec, Canada. In a follow-up study in this issue of Molecular Ecology, Warwick et al. (2008) show that the transgene has persisted and spread within the weedy population in the absence of selection for herbicide resistance. Certainly a trait like herbicide resistance is expected to spread when selected through the use of the herbicide, despite potentially negative epistatic effects on fitness. However, Warwick et al.'s findings suggest that direct selection favouring the transgene is not required for its persistence. So is there any hope of preventing transgene escape into the wild?

Invasive species are predicted to suffer from reductions in genetic diversity during founding events, reducing adaptive potential. Integrating evidence from two literature reviews and two case studies, we address the following questions: How much genetic diversity is lost in invasions? Do multiple introductions ameliorate this loss? Is there evidence for loss of diversity in quantitative traits? Do invaders that have experienced strong bottlenecks show adaptive evolution? How do multiple introductions influence adaptation on a landscape scale? We reviewed studies of 80 species of animals, plants, and fungi that quantified nuclear molecular diversity within introduced and source populations. Overall, there were significant losses of both allelic richness and heterozygosity in introduced populations, and large gains in diversity were rare. Evidence for multiple introductions was associated with increased diversity, and allelic variation appeared to increase over long timescales (~100 years), suggesting a role for gene flow in augmenting diversity over the long-term. We then reviewed the literature on quantitative trait diversity and found that broad-sense variation rarely declines in introductions, but direct comparisons of additive variance were lacking. Our studies of Hypericum canariense invasions illustrate how populations with diminished diversity may still evolve rapidly. Given the prevalence of genetic bottlenecks in successful invading populations and the potential for adaptive evolution in quantitative traits, we suggest that the disadvantages associated with founding events may have been overstated. However, our work on the successful invader Verbascum thapsus illustrates how multiple introductions may take time to commingle, instead persisting as a 'mosaic of maladaptation' where traits are not distributed in a pattern consistent with adaptation. We conclude that management limiting gene flow among introduced populations may reduce adaptive potential but is unlikely to prevent expansion or the evolution of novel invasive behaviour.

To understand the success of invasive species, it is important to know whether colonization events are facilitated by adaptive evolution or are limited to sites where a species is pre-adapted to thrive. Studies of the ancient colonization patterns of an invader in its native range provide an opportunity to examine its natural history of adaptation and colonization. This study uses molecular (internal transcribed spacer sequence and amplified fragment length polymorphism) and common garden approaches to assess the ancient patterns of establishment and quantitative trait evolution in the invasive shrub Hypericum canariense. This species has an unusually small and discrete native range in the Canary Islands. Our data reveal two genetic varieties with divergent life histories and different colonization patterns across the islands. Although molecular divergence within each variety is large (pairwise FST from 0.18 to 0.32 between islands) and nearly as great as divergence between them, life-history traits show striking uniformity within varieties. The discrepancy between molecular and life-history trait divergence points to the action of stabilizing selection within varieties and the influence of pre-adaptation on patterns of colonization. The colonization history of H. canariense reflects how the relationship between selective environments in founding and source populations can dictate establishment by particular lineages and their subsequent evolutionary stasis or change.