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Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single‐species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost‐effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems. [ABSTRACT FROM AUTHOR]

Pollen dispersal regulates the formation of the invasive, wind-pollinated hybrid cattail Typha × glauca Godron, the F1 offspring of the broadleaf (Typha latifolia L.) and narrowleaf (Typha angustifolia L.) cattail. An earlier study suggested that pollen dispersal by T. latifolia might be spatially restricted, with most dispersal occurring over distances less than 2 m. Restricted pollen dispersal would imply that hybrid formation primarily occurs within mixed stands of cattails. Hybrid formation might also be affected by preferential receipt of conspecific pollen, but this has not been investigated for cattails. We compared patterns of pollen dispersal for T. latifolia and T. angustifolia using a wind tunnel. We then tested whether patterns of pollen receipt were biased toward the capture of conspecific versus heterospecific pollen using monospecific cattail stands with a single local pollen source. Results from the wind tunnel partially supported the previous finding of spatially restricted pollen dispersal for T. latifolia, the paternal parent of F1 hybrids. Pollen receipt by T. angustifolia was biased toward the capture of conspecific pollen. Localized pollen dispersal by T. latifolia and preferential conspecific pollen capture by T. angustifolia should reduce rates of hybrid formation below that expected under random mating. [ABSTRACT FROM AUTHOR]

Cattails (Typha species) comprise a genus of emergent wetland plants with a global distribution. Typha latifolia and Typha angustifolia are two of the most widespread species, and in areas of sympatry can interbreed to produce the hybrid Typha ) glauca. In some regions, the relatively high fitness of Typha ) glauca allows it to outcompete and displace both parent species, while simultaneously reducing plant and invertebrate biodiversity, and modifying nutrient and water cycling. We generated a high-quality whole-genome assembly of T. latifolia using PacBio long-read and high coverage Illumina sequences that will facilitate evolutionary and ecological studies in this hybrid zone. Genome size was 287Mb and consisted of 1158 scaffolds, with an N50 of 8.71Mb; 43.84% of the genome were identified as repetitive elements. The assembly has a BUSCO score of 96.03%, and 27,432 genes and 2700 RNA sequences were putatively identified. Comparative analysis detected over 9000 shared orthologs with related taxa and phylogenomic analysis supporting T. latifolia as a divergent lineage within Poales. This high-quality scaffold-level reference genome will provide a useful resource for future population genomic analyses and improve our understanding of Typha hybrid dynamics. [ABSTRACT FROM AUTHOR]

Hybrids of a single pair of parent species can be much more common in some geographical regions than in others. The reasons for this are not well understood, but could help explain processes such as species diversification or the range expansion of invasive hybrids. The widespread cattails Typha latifolia and T. angustifolia seldom hybridize in some parts of their range, but in other areas produce the dominant hybrid T. × glauca. We used a combination of field and greenhouse experiments to investigate why T. × glauca has invaded wetlands in the Laurentian Great Lakes region of southern Ontario, Canada, but is much less common in the coastal wetlands of Nova Scotia (NS) in eastern Canada. One potentially important environmental difference between these two regions is salinity. We therefore tested three hypotheses: (1) T. latifolia and T. angustifolia in NS are genetically incompatible; (2) the germination or growth of T. × glauca is reduced by salinity; and (3) T. latifolia, a main competitor of T. × glauca, is locally adapted to saline conditions in NS. Our experiments showed that NS T. latifolia and T. angustifolia are genetically compatible, and that saline conditions do not impede growth of hybrid plants. However, we also found that under conditions of high salinity, germination rates of hybrid seeds were substantially lower than those of NS T. latifolia. In addition, germination rates of NS T. latifolia were higher than those of Ontario T. latifolia, suggesting local adaptation to salinity in coastal wetlands. This study adds to the growing body of literature which identifies the important roles that local habitat and adaptation can play in the distributions and characteristics of hybrid zones. [ABSTRACT FROM AUTHOR]

Invasive species affect native vegetation through combinations of direct interactions (e.g. competition) and indirect interactions (e.g. altered pollination regimes) mediated through the occupation of shared environments. Hybrid cattails ( Typha × glauca ) are rapidly displacing their parental species, the native broadleaf cattail ( T.latifolia ) and the introduced narrow-leaf cattail ( T. angustifolia ), but the mechanisms involved are poorly understood. We evaluated the potential for direct and indirect interactions among cattails using a series of experiments. First, we evaluated whether seed germination was affected by hybrid leaf litter using a factorial experiment in which we tested for indirect effects of leaf-litter leachate and shading. Second we tested whether these indirect effects of hybrid leaf litter affected seedling performance using a factorial common-garden experiment. Finally, we tested for direct competitive interactions between hybrid and native cattail seedlings. One or more components of hybrid leaf-litter leachate strongly reduced the germination of the parental cattail species, but not that of the hybrid. There was no evidence that direct competitive interactions affected seedling performance. Because regular recruitment by seeds appears to be important in shaping patterns of genetic diversity in natural populations, our findings provide a mechanism for explaining the dominance of hybrid cattails in eastern North America. [ABSTRACT FROM AUTHOR]

Spatial separation between hybridizing taxa can limit hybridization and introgression when mating occurs between near neighbours. Water depth can be an important factor structuring wetland plant communities, which often include cattails ( Typha spp., Typhaceae). In eastern North America, native Typha latifolia regularly hybridizes with introduced T. angustifolia to produce the invasive F 1 hybrid T. × glauca, which can backcross to parental species. Hybridization in this wind-pollinated species complex may be facilitated by overlapping niches among taxa, but previous studies have yielded contradictory results, possibly because these studies were limited to shallow sites or single locations. We investigated patterns of depth occupancy in ditches (mean depth 3.4 cm) and permanent wetlands (mean depth 25.0 cm) with various mixtures of T. latifolia, T. angustifolia, and T. × glauca across a 1700 km transect from Michigan, USA, to Nova Scotia, Canada. Overall, we found that water depth cannot on its own explain patterns of cattail occupancy. We therefore conclude that niche partitioning by water depth does not promote mating isolation in Typha . Previous findings of habitat segregation by depth may be attributable to a combination of idiosyncratic features of individual sites, multi-dimensional niches, and phenotypic plasticity, which could prevent consistent niche segregation among Typha taxa. A lack of spatial segregation between Typha taxa should promote hybridization and introgression. This, coupled with the competitive superiority of hybrids, appears to be facilitating the displacement of native T. latifolia across a wide geographical range. [ABSTRACT FROM AUTHOR]

Phragmites australis subsp. australis is an invasive and ecologically detrimental plant in multiple regions of North America. Its co-occurrence with the native subspecies, and multiple instances of hybridization, has created the need to differentiate Phragmites subspecies or haplotypes so that management can be appropriately targeted to the invader. We compiled a review of current genetic discrimination methods among the three Phragmites subspecies inhabiting the United States and Canada, and discussed how each method can contribute to control of the introduced subspecies while preserving the two endemic subspecies. We also discussed various control tools and the implications of Phragmites genetics for implementation. The Phragmites subspecies endemic to North America have environmental or infrastructure significance (e.g., habitat sustainability, biodiversity, storm surge and erosion protection). Thus, faster and more accurate differentiation among the endemic and introduced subspecies is needed. Additionally, more in-depth genetic information on Phragmites subspecies could support better management decisions, as well as the development of improved control treatments. This review highlights technologies and approaches currently available for genetic identification, recently collected genomic, transcriptomic and proteomic information, and implications for biological control and herbicide treatments. • Review of genetic discrimination methods among Phragmites australis lineages. • Development of a new nDNA PCR-RFLP method to differentiate P. australis hybrids. • Development of novel qPCR assays to differentiate three P. australis subspecies. • Information to support better management decisions and improved control treatments. • Discussion of future needs in the P. australis research and development community. [ABSTRACT FROM AUTHOR]

Cattails ( Typha spp.) are common and abundant in wetlands around the world, and can be invasive. Typha latifolia and T. angustifolia are two widely distributed species that in North America produce the invasive hybrid T. × glauca, of which T. angustifolia is the maternal parent. A recent study identified polyphyly in T. angustifolia resulting from core and divergent chloroplast DNA (cpDNA) lineages. We used a combination of chloroplast and nuclear genetic data to test two hypotheses: (1) T. angustifolia with the divergent cpDNA lineage represents a cryptic species and (2) divergent cpDNA T. angustifolia haplotypes predominate in areas where T. × glauca is invasive. Our data reject the hypothesis of a cryptic species, and we suggest that the divergent lineage arose in T. angustifolia following historical hybridization and introgression . Typha × glauca may therefore be a three-way hybrid involving T. latifolia, T. angustifolia, and an introgressed cpDNA lineage from an unidentified congener. The divergent cpDNA T. angustifolia haplotype is widespread across areas where T. × glauca is invasive, but is also found in areas where T. × glauca is maintained at very low frequencies; therefore, cpDNA lineages cannot be the sole explanation for T. × glauca invasiveness. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) comprises DNA fragments that have been shed into the environment by organisms, and which can be extracted from environmental samples such as water or soil. Characterization of eDNA can allow researchers to infer the presence or absence of species from a particular site without the need to locate and identify individuals, and therefore may provide an extremely valuable tool for quantifying biodiversity. However, as is often the case with relatively new protocols, methodological challenges remain. A number of earlier reviews have discussed these challenges, but none have provided extensive treatment of the critical decisions surrounding molecular markers and primer development for use in eDNA assays. This review discusses a number of options and approaches that can be used when determining which primers and gene regions are most appropriate for either targeted species detection or metabarcoding macro-organisms from eDNA. The latter represents a new field that is growing rapidly, and which has the potential to revolutionize future assessments of community and ecosystem diversity. [ABSTRACT FROM AUTHOR]

Although cattails ( Typha spp.) are important components of wetlands around the world, the three most widespread species ( T. angustifolia, T. domingensis, T. latifolia) are becoming increasingly dominant. We used global phylogenetic and phylogeographic assessments to test the hypotheses that each species has experienced multiple introductions of divergent lineages into North America and that commercial retailers are aiding long-distance dispersal. Our analyses identified T. angustifolia as a paraphyletic species with a highly divergent lineage. We found evidence for at least one introduced T. angustifolia lineage in wild populations and garden centres of North America. Although potentially complicated by incomplete lineage sorting, our data suggest dispersal of T. domingensis between Europe and Australia, and further investigation should assess a possible introduction of a non-native T. domingensis lineage into North America. T. latifolia has experienced bidirectional dispersal between North America and Europe, and a sample of T. latifolia purchased in a Canadian garden centre was an Asian lineage. Interspecific hybridization and novel intraspecific admixture have been repeatedly implicated in biological invasions, including invasions by the hybrid cattail Typha × glauca, and future work should focus on the potential contributions of non-native lineages to regional patterns of invasion by Typha spp. in North America. [ABSTRACT FROM AUTHOR]

Rapid evolution following interspecific hybridization can facilitate biological invasions. Around the Great Lakes in North America, the hybrid cattail Typha  ×  glauca is dominating wetlands and displacing both parental species. We measured water depth and height of T.  ×  glauca and its parental species ( Typha angustifolia and Typha latifolia ) throughout the growing season at a site near Lake Ontario that harbors both parental species plus hybrids. We found no evidence of niche partitioning by water depth, nor was there evidence that water depth was influencing plant height. At the beginning of the growing season, T. latifolia comprised the tallest plants, but this potential advantage was short-lived, and for most of the growing season, F 1 hybrids were taller than all or most other taxa ( T. angustifolia, T. latifolia, and advanced-generation/backcrossed hybrids). Heterosis, inferred from height, is therefore evident in F 1 hybrids, but not in advanced-generation/backcrossed hybrids. Typha stands often achieve high densities, and the competitive advantage of superior height is likely contributing to the invasive success of T . ×  glauca F 1 hybrids in the Great Lakes region . [ABSTRACT FROM AUTHOR]

Abstract: Cattails (Typha spp.) in northeastern North American wetlands are increasingly dominant, partly because of hybridization between Typha latifolia and Typha angustifolia which results in the widespread and successful hybrid T. × glauca. Both parental species are protogynous, and previous studies have shown that T. angustifolia flowers earlier than T. latifolia. Nevertheless, experimental studies have shown that hybridization is overwhelmingly asymmetric, involving T. angustifolia female flowers and T. latifolia pollen which should have minimal overlap in the times at which they are produced. In this study we surveyed two Typha stands in eastern North America, and at both sites found substantial overlap in the times at which the parental species and the hybrids shed pollen and presumably are receptive to fertilization; this means that flowering time is not a prezygotic barrier to either the formation of hybrids or their subsequent backcrossing to parental species. Consistent with experimental studies, all hybrids had T. angustifolia as their maternal parent. Our results suggest that reproductive barriers between Typha spp. are evolving. [Copyright &y& Elsevier]

In 2011, Vachon and Freeland presented the results of a study that illustrated the importance of considering mutation patterns, including the potential for homoplasy, when deciding whether to include or exclude repetitive sequences from phylogeographic inferences. Saltonstall and Lambertini (2012) criticized this study by suggesting that some of the analyses and interpretations were flawed. In this reply, we explain why we disagree with most of their criticisms and identify some inconsistencies in their analyses. Most importantly, we reiterate the need to examine underlying assumptions, particularly with respect to mutation patterns, when using molecular genetic data to untangle evolutionary relationships. [ABSTRACT FROM AUTHOR]

The spatial genetic structure of plant populations is determined by a combination of gene flow, genetic drift, and natural selection. Gene flow in most plants can result from either seed or pollen dispersal, but detailed investigations of pollen and seed flow among populations that have diverged following local adaptation are lacking. In this study, we compared pollen and seed flow among 10 populations of sweet vernal grass (Anthoxanthum odoratum) on the Park Grass Experiment. Overall, estimates of genetic differentiation that were based on chloroplast DNA (cpDNA) and, which therefore resulted primarily from seed flow, were lower (average FST = 0.058) than previously published estimates that were based on nuclear DNA (average FST = 0.095). Unlike nuclear DNA, cpDNA showed no pattern of isolation by adaptation; cpDNA differentiation was, however, inversely correlated with the number of additions (nutrients and lime) that each plot had received. We suggest that natural selection is restricting pollen flow among plots, whereas nutrient additions are increasing seed flow and genetic diversity by facilitating the successful germination and growth of immigrant seeds. This study highlights the importance of considering all potential gene flow mechanisms when investigating determinants of spatial genetic structure, and cautions against the widespread assumption that pollen flow is more important than seed flow for population connectivity in wind-pollinated species. [ABSTRACT FROM PUBLISHER]

The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection. [ABSTRACT FROM AUTHOR]

Phylogeographic inference can be a powerful tool in reconstructing species' evolutionary histories; however, although inferred phylogeographic patterns should depend in part on the underlying types and rates of mutations, the effects of different types of mutations have seldom been quantified. In this study we identified two chloroplast minisatellites in the common reed Phragmites australis, and showed that these are more variable than chloroplast microsatellites. We then recreated parsimony networks of the global phylogeography of P. australis based on data that either included or excluded repetitive sequences (minisatellites and microsatellites), thereby illustrating the influence that these repetitive sequences can have on large-scale phylogeographic inference. The resulting networks differed in the numbers of mutational steps, degrees of uncertainty, and total numbers of haplotypes. In addition, the suggested ancestor-descendant relationships among lineages changed substantially depending on whether repetitive sequences were included. We therefore caution against the inclusion of repetitive sequences in large-scale networks because of their high potential for homoplasy. Nevertheless, we advocate the inclusion of repetitive sequences in other analyses: specifically, we show that the ratio of mutations in repetitive vs. non-repetitive regions can provide insight into the relative ages of lineages. [ABSTRACT FROM AUTHOR]

Populations at the edges of their geographical ranges are often characterized by reduced genetic diversity and increased genetic differentiation. These patterns may be exacerbated by specialized associations between plants and uncommon habitats. Together, reduced diversity and increased subdivision may increase the risk of population extirpation, an issue that is particularly important for plants classified as rare or threatened. Hill's thistle (Cirsium hillii (Canby) Fernald), is a perennial herb endemic to the Great Lakes region and is considered threatened in Canada where its northernmost distribution occurs. We used microsatellite markers to genotype plants from 11 populations of Hill's thistle that span the range of the species distribution within Canada. These data were used to investigate levels of genetic diversity within populations and genetic differentiation between populations, and to evaluate associations between patterns of genetic variation and those expected under ongoing habitat loss. Genetic differentiation among populations was low, although significant pairwise FST values, along with the presence of private alleles in most populations, was consistent with moderate to low gene flow. Nevertheless, in comparison with a congeneric rare species (Cirsium pitcheri) that occurs in the same geographical region in Canada, genetic diversity within most populations was high, and we suggest that this is at least partially attributable to this species' combination of sexual and clonal reproduction. Despite high levels of genetic diversity, Hill's thistle should probably remain a designated species at risk because of ongoing habitat loss; however, our data suggest that Hill's thistle is unlikely to suffer from reduced genetic diversity in the foreseeable future. [ABSTRACT FROM AUTHOR]

In the northern hemisphere, glacial periods have had profound and lasting effects on the population genetics of numerous species, with founder effects often persisting for many generations in formerly glaciated regions. We found an unusual example of this in the freshwater bryozoan Cristatella mucedo, which showed regional differences in haplotype diversity with relatively low levels of haplotype diversity in northern Europe compared to central/southern Europe despite previous evidence for frequent dispersal between C. mucedo populations. Such contradictions between high dispersal and low gene flow have now been reported in several other freshwater taxa and may be attributed to persistent founder effects following colonization of sites by a few individuals whose efficient reproduction leads to rapid population growth. Alternatively, selection may determine which genotypes can thrive in northerly locations, or it may be that C. mucedo has undergone cryptic speciation. Future work on adaptive genomic regions is required before we can understand how gene flow, local adaptation, and speciation influence the current distribution patterns of bryozoans and other freshwater invertebrates. [ABSTRACT FROM AUTHOR]

We report the successful amplification of microsatellite markers for the chloroplast genome from century-old samples of 2 grasses growing in the Park Grass Experiment (PGE): Anthoxanthum ordoratum and Festuca rubra. This opens the possibility of establishing a long-term genetic time series for the PGE, which began in 1856 and is believed to be the oldest ecological experiment in existence. Although the plant samples used were not originally prepared or stored with molecular analysis in mind, the hexadecyltrimethylammonium bromide (CTAB) method of DNA extraction was successfully used. Obtained DNA was degraded but could be amplified by means of PCR. It produced bands around the expected size for chloroplast microsatellite primers derived from rice. When sequenced, bands showed good homology with sequences from rice chloroplast genomes listed in GenBank (accession No X15901). [ABSTRACT FROM AUTHOR]

Abstract. 1. Species that undertake regular two-way migration may be expected, through population connectivity, to exhibit some level of genetic similarity over broad spatial scales. Although seldom following two-way migration, highly mobile insect species tend to exhibit either low haplotype diversity and no phylogeographic structuring, or relatively high haplotype diversity and pronounced phylogeographic structuring. 2. This study reveals the first wide-scale genetic characterisation of a migratory dragonfly, the common green darner Anax junius Drury. Unusually for insects, north-south two-way migration is common in this species, although not obligatory. In at least part of its range, some individuals follow an extended developmental period and overwinter in a state of diapause. 3. Mitochondrial sequence data were obtained from 92 A. junius individuals collected from 35 sites across Canada, U.S.A., and Mexico. These revealed 38 haplotypes, some of which were extremely widespread, although the majority (27 haplotypes) was found in only one individual. In contrast to previous studies on mobile insects, the overall pattern was of relatively high haplotype diversity in the absence of phylogeographic structuring. 4. Migrants and non-migrants, which sometimes shared haplotypes, were distributed across multiple genetic lineages. This suggests that, contrary to some earlier assertions, developmental pathways in this species may be plastic. Such plasticity would allow highly mobile species to adapt to a range of environmental conditions, and may be key to the widespread distribution of multiple haplotypes. [ABSTRACT FROM AUTHOR]

SUMMARY 1. The freshwater bryozoan Cristatella mucedo , in common with other sessile, benthic freshwater taxa, has an unusual life history: sex occurs during a relatively brief period near the start of the growing season, and overwintering occurs in the form of asexually produced dormant propagules (statoblasts). Consistent observed heterozygosity (Ho) deficits in C. mucedo populations have previously suggested that inbreeding is common, although a possible contribution of a Wahlund effect to low Ho could not be discounted. 2. We have used microsatellite data in the first study based on codominant markers to genetically characterise maternal colonies and larval offspring of C. mucedo . The ‘population’ represented by the larvae was in Hardy–Weinberg equilibrium, which has previously been found in only one of 39 populations of C. mucedo . At least 64% of larvae were the products of outcrossing. We suggest that the unusual early timing of sex may be a strategy to maximise rates of outcrossing within populations of sessile freshwater invertebrates. [ABSTRACT FROM AUTHOR]

Movement between discrete habitat patches can present significant challenges to organisms. Freshwater invertebrates achieve dispersal using a variety of mechanisms that can be broadly categorized as active or passive, and which have important consequences for processes of colonization, gene flow, and evolutionary divergence. Apart from flight in adult freshwater insects, active dispersal appears relatively uncommon. Passive dispersal may occur through transport by animal vectors or wind, often involving a specific desiccation-resistant stage in the life cycle. Dispersal in freshwater taxa is difficult to study directly, and rare but biologically significant dispersal events may remain undetected. Increased use of molecular markers has provided considerable insight into the frequency of dispersal in freshwater invertebrates, particularly for groups such as crustaceans and bryozoans that disperse passively through the transport of desiccation-resistant propagules. The establishment of propagule banks in sediment promotes dispersal in time and may be particularly important for passive dispersers by allowing temporal escape from unfavorable conditions. Patterns that apply to dispersal in freshwater invertebrates can be readily extended to other freshwater taxa, since common challenges arise from the colonization of isolated aquatic systems. [ABSTRACT FROM AUTHOR]

We have used microsatellite and mitochondrial sequence data to gain insight into patterns of gene flow and genetic diversity among North American and European populations of the freshwater bryozoan Cristatella mucedo. Mitochondrial sequence data reveal numerous, widely distributed, divergent genetic lineages in North America that can be broadly categorized into two groups, one of which is genetically homogenous and relatively similar to the European haplotypes, the other of which is more diverse. The maximum North American sequence differentiation translates into a divergence time of approximately 1.5 Myr BP. In contrast, European populations contained only three haplotypes that are all closely related. Microsatellite data reveal higher overall levels of genetic diversity in North America than Europe, although levels of within-population genetic variation are similar on the two continents. In North America, two of the three microsatellite loci show bimodal distributions of allele sizes which are significantly associated between the two loci. As a result, two microsatellite lineages are evident, and these are assortatively distributed between the mitochondrial haplotype groupings. The combined mitochondrial and microsatellite data suggest two distinct genetic lineages in North America that may represent cryptic species. Hybridization between the two presumptive species or subspecies may have contributed to the high levels of genetic diversity in North America. The overall lower levels of genetic diversity in Europe can be attributed to postglacial derivation of extant populations from a single mitochondrial lineage, and conformation to a metapopulation structure. [ABSTRACT FROM AUTHOR]

Abstract Research over the past 20 years has shown, with the help of molecular markers, that the population genetics and distribution patterns of freshwater invertebrates in North America are often more complex than was previously believed. Here we extend this research to an, as yet, unstudied but widespread and common group, the freshwater bryozoans. Colonies of the bryozoan Cristatella mucedo were collected from a number of lakes across central North America, and were characterized genetically by analysis of microsatellite loci and mitochondrial DNA (mtDNA) cytochrome b sequences. The microsatellites illustrate a pattern of generally diverse and highly differentiated populations that contain little evidence of recent gene flow. The mtDNA sequences yielded highly variable levels of divergence, ranging from 0.0 to 8.8% within populations, and 0.0 to 9.8% among populations. The multiple divergent mtDNA lineages within populations provide evidence for repeated colonization events. The lack of clustering of haplotypes by site suggests that there has been widespread dispersal of multiple genetic lineages since the last ice age. While some of the haplotype lineages may have evolved in disjunct glacial refugia, the maximum levels of divergence predate the time since the last glacial-interglacial cycles. It is likely that multiple factors including vicariance events, patterns of dispersal, localized extinction, and an unusual life history, explain the unique phylogeographic patterns evident today in populations of C. mucedo. [ABSTRACT FROM AUTHOR]

Presents a study on the phylogeny of Darwin's finches. Classification of Darwin's finches; Methods of the study; Relationship of three groups of finches.

Deals with a study which investigated the evolutionary history and genetic relationships of the phenotypically diverse Darwin's ground finches. Research methodology; Results and discussion.

A critical knowledge gap in freshwater plant research is the lack of genetic tools necessary to answer fundamental questions about their demographic histories, adaptation and phylogenetic relationships. One example of this is Typha, a global genus of freshwater plants foundational to wetlands that also is becoming an increasingly problematic biological invader in numerous regions worldwide; although important insights have been discovered for this genus, existing markers are insufficient to answer fundamental questions about their demographic histories, adaptation and phylogenetic relationships; to identify introduced and hybrid lineages; and to examine patterns of hybridisation and introgression.We optimised a library preparation and data processing protocol to develop genome–wide nuclear and plastid resources for studying the evolutionary history, genetic structure and diversity, hybridisation, local adaptation, invasiveness, and geographical expansion dynamics of Typha.We sequenced 140 Typha samples and identified ~120 K nuclear single nucleotide polymorphisms (SNPs) that differentiate T. angustifolia, T. domingensis and T. latifolia, and retrieved their plastome sequences. We observed genetic introgression among the three species.Following a fast, straightforward and cost‐efficient genomic library preparation protocol, we produced a suite of genome‐wide resources to facilitate investigations into the taxonomy and population genetics of Typha and to advance the genomic understanding of wetland plants.The protocol described, the updated chromosome‐level genome assembly of T. latifolia, the catalogue of species‐specific SNPs, and the chloroplast sequences produced in this study comprise permanent resources that can be applied to study the genetic composition of multiple populations and hybrid zones, and will be incorporated into future studies of Typha, an ecologically important and globally invasive macrophyte. [ABSTRACT FROM AUTHOR]

Background: Alliaria petiolata (garlic mustard) is a widespread allelopathic invasive species in North America, but despite extensive research we do not fully understand how it impacts plant communities. Aims: We tested the hypothesis that A. petiolata facilitates the introduction of additional alien species as predicted by the invasional meltdown hypothesis. Methods: We conducted co-occurrence surveys to compare the numbers of alien and native species in communities surrounding A. petiolata plants with those surrounding an allelopathic native species. We also conducted an experiment to compare recruitment of native and alien species in pots dominated by either A. petiolata or a native species. Results: A. petiolata plots in the co-occurrence surveys had relatively high proportions of bare ground, suggesting habitat modification, plus lower species richness and disproportionately fewer alien species. There was a greater tendency for native species than alien species to establish in A. petiolata pots. Conclusions: A. petiolata does not promote additional alien species, and in fact may be a more effective competitor against alien than native species in North America. This could help explain its invasive success in disturbed habitats, and illustrates the need to consider separately alien and native species when assessing the outcomes of competition. [ABSTRACT FROM AUTHOR]

Forest fragmentation and introduced pathogens are negatively impacting trees and forests globally, including the Carolinian forest of southern Ontario, Canada. Multiple species at risk live in this threatened but biodiverse forest, including the endangered Cornus florida (eastern flowering dogwood), which is now limited to fragmented woodlots, and has been decimated by the introduced fungal pathogen Discula destructiva (dogwood anthracnose). Ongoing management of C. florida in Canada is challenged by multiple knowledge gaps, two of which we aimed to address in this study. We first evaluated the association between anthracnose disease prevalence and a suite of ecological and environmental variables across 21 sites. Across our sites, larger trees tended to have the highest disease incidence, and trees on shallow slopes had the most crown dieback. We then quantified genetic diversity and gene flow, and found that genetic structure has not been substantially impacted by habitat fragmentation, although dispersal typically covers short distances. However, genetic diversity is relatively low in smaller populations and in younger trees. Localized dispersal and eroding genetic diversity may limit future adaptation and hence exacerbate population declines. We recommend that managers prioritize plantings in small populations, avoid shallow slopes, and track younger trees to evaluate age-related mortality. [ABSTRACT FROM AUTHOR]

Presents a study identifying polymorphic microsatellite loci in freshwater bryozoan Cristatella mucedo in England, Scotland, France, Netherlands, Denmark, Sweden, andFinland. Description of the breed and its reproductive and population habits; Screening for polymorphic microsatellites; Description of the methods used in the study; Results, conclusions and discussion.

Cattails (Typha spp.) have become an increasingly dominant component of wetlands in eastern North America and this dominance is largely attributable to the high frequency of Typha × glauca, the hybrid of native Typha latifolia and putatively introduced Typha angustifolia. Hybridization in this group is asymmetric, with T. angustifolia nearly always the maternal parent of F1 hybrids. However, the magnitude of hybrid infertility and whether mating asymmetries extend to the formation of advanced-generation hybrids have not been examined. We used hand-crosses to measure seed set and germination success. We found that mating asymmetries extend to the formation of backcrosses, with ~0 seeds set when T. latifolia was pollinated by hybrid cattails. Seed set was unaffected by pollen source for T. × glauca or T. angustifolia. However, seed production by T. angustifolia was consistently high while that of T. × glauca was variable and when pollinated by other T. × glauca more than 75% lower than for any other intraspecific cross indicating reduced hybrid fertility. We used these results to parameterize a model of hybrid zone evolution in which mating patterns and fertility were governed by interactions between alleles at nuclear and cytoplasmic loci. The model revealed that asymmetric mating and reduced hybrid fertility should favor the maintenance of T. latifolia over T. angustifolia compared to null expectations. However, the model also indicated restrictive conditions for the long-term maintenance of T. latifolia within populations, indicating that asymmetric mating might only stall rather than prevent the displacement of native cattails by hybrids. [ABSTRACT FROM AUTHOR]

Cattails ( Typha spp.) are essential components of wetland around the world, although they can also be problematic invaders. In some regions of North America, T. latifolia and T. angustifolia hybridize to produce T. x glauca, which is invading and dominating wetlands around the Laurentian Great Lakes. However, in other regions such as China and the maritime provinces of Canada, hybrids are either non-existent or maintained at very low frequencies, and cattails are not considered invasive. Little is known about cattail hybrids in Europe. We used microsatellite markers to characterize T. latifolia, T. angustifolia, T. laxmannii, and T. domingensis sampled from 63 sites across nine European countries. Hybrids were very uncommon (<2% of all sampled plants), and resulted from crosses involving two of T. latifolia, T. angustifolia and T. domingensis . Infrequent hybridization may partly explain why Typha does not dominate European wetlands. However, we identified two distinct genetic clusters within T. angustifolia , broadly corresponding to eastern and western Europe. In addition, our T. laxmannii samples were from countries where it is considered alien, and populations show a high degree of genetic differentiation that is consistent with independent introductions. Managers should continue to monitor range expansions of Typha spp. in Europe, partly because novel interactions among species and lineages may increase the likelihood of future hybridization. [ABSTRACT FROM AUTHOR]

Background: Sparganium (Typhaceae) is a widespread temperate genus of ecologically important aquatic plants. Previous reconstructions of the phylogenetic relationships among Sparganium species are incompletely resolved partly because they were based on molecular markers comprising < 7,000 bp. Here, we sequenced and assembled the complete chloroplast genomes from 19 Sparganium samples representing 15 putative species and three putative subspecies in order to explore chloroplast genome evolution in this genus, clarify taxonomic lineages, estimate the divergence times of Sparganium species, and reconstruct aspects of the biogeographic history of the genus. Results: The 19 chloroplast genomes shared a conserved genome structure, gene content, and gene order. Our phylogenomic analysis presented a well-resolved phylogeny with robust support for most clades. Non-monophyly was revealed in three species: S. erectum, S. eurycarpum, and S. stoloniferum. Divergence time estimates suggest that the two subgenera of Sparganium split from each other ca. 30.67 Ma in the middle Oligocene. The subgenus Xanthosparganium diversified in the late Oligocene and Miocene, while the subgenus Sparganium diversified in the late Pliocene and Pleistocene. Ancestral area reconstruction suggested that the two subgenera may have originated in East Eurasia and North America. Conclusion: The non-monophyletic nature of three putative species underscores the necessity of taxonomic revision for Sparganium: S. stoloniferum subsp. choui may be more appropriately identified as S. choui, and subspecies of S. erectum may be in fact distinct species. The estimated diversification times of the two subgenera correspond to their species and nucleotide diversities. The likely ancestral area for most of subgenus Xanthosparganium was East Eurasia and North America from where it dispersed into West Eurasia and Australia. Most of subgenus Sparganium likely originated in North America and then dispersed into Eurasia. Our study demonstrates some of the ways in which complete chloroplast genome sequences can provide new insights into the evolution, phylogeny, and biogeography of the genus Sparganium. [ABSTRACT FROM AUTHOR]

Understanding the spatial distribution of genetic diversity and its evolutionary history is an essential part of developing effective biodiversity management plans. This may be particularly true when considering the value of peripheral or disjunct populations. Although conservation decisions are often made with reference to geopolitical boundaries, many policy-makers also consider global distributions, and therefore a species' global status may temper its regional status. Many disjunct populations can be found in the Great Lakes region of North America, including those of Bartonia paniculata subsp. paniculata, a species that has been designated as threatened in Canada but globally secure. We compared chloroplast sequences between disjunct (Canada) and core (USA) populations of B. paniculata subsp. paniculata separated by 600 km, which is the minimum distance between disjunct and core populations in this subspecies. We found that although lineages within the disjunct populations shared a relatively recent common ancestor, the genetic divergence between plants from Ontario and New Jersey was substantially greater than expected for a consubspecific comparison. A coalescence-based analysis dated the most recent common ancestor of the Canadian and US populations at approximately 534 000 years ago with the lower confidence estimate at 226 000 years ago. This substantially predates the Last Glacial Maximum and suggests that disjunct and core populations have followed independent evolutionary trajectories throughout multiple glacial-interglacial cycles. Our findings provide important insight into the diverse processes that have resulted in numerous disjunct species in the Great Lakes region and highlight a need for additional work on Canadian B. paniculata subsp. paniculata taxonomy prior to a reevaluation of its conservation value. [ABSTRACT FROM AUTHOR]

Abstract: A recent increase in the abundance of cattails (Typha spp.) in North American wetlands has been anecdotally linked with hybridization between Typha latifolia and Typha angustifolia. In this study, we used molecular genetic markers (microsatellites) to investigate whether the hybrid lineage (Typha × glauca) is restricted to The Great Lakes region, or exists across a much broader spatial scale. We also investigated the possibility of backcrossing and genetic introgression in natural populations. Parental species could be distinguished from one another based on the distribution of alleles at six microsatellite loci. Species identification based on genetic data corresponded well with species identifications based on leaf width, a key morphological trait that can distinguish the two parental species. We found that hybrids occur in Ontario, Quebec, New Brunswick, and Nova Scotia, but we did not detect hybrids in Maine. F1s are more abundant than backcrossed or intercrossed hybrids, although we also found evidence of backcrossing, particularly in Ontario. This indicates that hybrids are fertile, and are therefore potential conduits of gene flow between the parental species. Further work is needed to determine whether T. × glauca is particularly successful in the Great Lakes region relative to other areas in which the two parental species co-exist, and to assess whether introgression may lead to increased invasiveness in the species complex. [Copyright &y& Elsevier]

Reedbeds, which are dominated by the common reed Phragmites australis, provide one of the most important aquatic habitats in the United Kingdom, and have been identified as a priority habitat under the UK Biodiversity Action Plan. Ongoing conservation and management of reedbeds is necessary because past eradication and fragmentation have been extensive. However, there has been little consideration of the potential long-term effects that may arise if processes such as founder effects during restoration projects, or genetic bottlenecks following harvesting, are leading to reductions in genetic diversity. In this study, we used microsatellite data to compare the genetic diversity of 19 P. australis stands in the UK, and found that neither size, management, nor habitat disturbance were affecting genetic diversity. Mixed reproduction (clonal and sexual), possibly combined with gene flow across relatively small spatial scales, appears to be maintaining genetic diversity within most stands. However, most stands were highly genetically differentiated from one another, which implies low gene flow. Long-term genetic diversity in managed stands may therefore require periodic bolstering from other populations, combined with the simultaneous cultivation of multiple generations. In addition, low gene flow suggests that managers should actively introduce plants into all areas in which reedbeds are desired. In conclusion, our study shows that reedbed restoration and maintenance do not seem to be adversely affecting the population genetics of P. australis, but the importance of genetic diversity should be factored into long-term projects. [ABSTRACT FROM AUTHOR]

Abstract: Interspecific hybridization is widespread in plants and is an important evolutionary process. Hybrids may be fitter than their parental species, at least under some environmental conditions, and this may lead to partitioning of taxa by habitat. In eastern Canada, two cattail species (Typha latifolia and Typha angustifolia) and their hybrid (Typha x glauca) are known to have become increasingly widespread in recent decades, although their habitat preferences and patterns of co-existence at the local scale are not well known. We quantified the occurrence of these three taxa in three different habitat types (high traffic, low traffic, and ‘natural’) at 40 different sites along a sampling route of approximately 2000km in eastern Canada. There were no significant overall associations between habitat type and taxon, although intraspecific comparisons among sites showed that the hybrid was most likely to grow in high traffic (highly disturbed) sites. In addition, pairwise comparisons revealed significant independence of T. latifolia and T. angustifolia, although the hybrid was equally likely to co-exist with either of its parental species. The presence of the three taxa in several habitats, including highly disturbed roadside areas, is consistent with their increasingly invasive tendencies. [Copyright &y& Elsevier]

We used the Park Grass Experiment, begun in 1856, to test alternative hypotheses about the relationship between genetic diversity and plant species diversity. The niche variation hypothesis predicts that populations with few interspecific competitors and hence broader niches are expected to contain greater genetic diversity. The coexistence hypothesis predicts that genetic diversity within species favours coexistence among species and therefore species and genetic diversity should be positively correlated. Amplified Fragment Length Polymorphism (AFLP) markers were used to measure the genetic diversity of populations of Anthoxanthum odoratum growing in 10 plots of differing species richness that lie along resource and soil pH gradients. Genetic diversity in A. odoratum was positively correlated with the number of resources added to a plot, but not correlated with species richness. However, separate analyses have shown a negative correlation between resource addition and species richness at Park Grass and elsewhere, so genetic and species diversity appear to respond in opposite directions. [ABSTRACT FROM AUTHOR]

Invasive aquatic plants can disrupt native biodiversity with considerable ecological impacts. Glyphosate-based herbicides provide one effective option to manage invasive macrophytes, but the variation in glyphosate sensitivity and accumulation in both target and non-target macrophytes is unclear. We performed an outdoor microcosm concentration-response study in which we applied seven glyphosate concentrations (0.1-8% of the Roundup WeatherMAX® formulation, corresponding to 0.5-43.2 g L-1 glyphosate) in order to compare sensitivities and accumulation amounts of glyphosate and aminomethylphosphonic acid (AMPA; one degradation product) within and among two invasive emergent plants in North America (Phragmites australis and Typha × glauca), plus a native co-occurring plant (Typha latifolia) over a period of 27 days. Phragmites australis (dose lethal to 50% of the plant population, LC50 = 0.34 ± 0.03%) exhibited four to five times higher glyphosate sensitivity than T. latifolia (LC50 = 1.37 ± 0.13%) and T. × glauca (LC50 = 1.70 ± 0.17%). Invasive T. × glauca and native T. latifolia exhibited a similar glyphosate response, although individual variation was high within both taxa. 27 days after treatment with 5% glyphosate, a concentration that mimics many real-world applications, P. australis retained more glyphosate (348 ± 27 mg kg-1 dw) than either T. latifolia (102 ± 20 mg kg-1 dw; P < 0.001) or T. × glauca (92 ± 12 mg kg-1 dw; P < 0.0001). Our results suggest that glyphosate response varies among and within emergent aquatic macrophyte taxa, independent of taxon invasiveness. When the goal is to minimize glyphosate exposure of the environment, managers could consider variation in glyphosate response at both individual and taxonomic levels. Moreover, managers should be aware that glyphosate accumulates in macrophytes. [ABSTRACT FROM AUTHOR]

Although microsatellite markers have become exceedingly popular in molecular studies of wild organisms, their development in some taxonomic groups is challenging. This is partly because of repetitive flanking sequences, which lead to the simultaneous amplification of alleles from multiple loci. Until now, these microsatellite DNA families have been considered unsuitable for population genetics studies, but here we describe our development of these repetitive flanking sequences (ReFS) as novel molecular markers. We illustrate the utility of these markers by using them to address an outstanding taxonomic question in the moth genus Schrankia. [ABSTRACT FROM AUTHOR]

A set of microsatellite markers was isolated from Arctia caja, a species that has been declining in UK for several decades. As has been found with other Lepidoptera species, this proved to be a difficult task. Eight enriched libraries identified 103 positive clones, and these yielded only seven polymorphic microsatellites. Allelic diversity ranged from 10 to 23 alleles per locus in a population of 30 individuals. Significant heterozygosity deficits were shown by three of these loci, presumably due to null alleles. The remaining four loci were in Hardy–Weinberg equilibrium and will be used to investigate the population genetic structure of A. caja. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) is emerging as a potentially powerful tool for inferring species' presence, and hence occupancy, from DNA that is shed into environmental samples such as water. Although eDNA screening has been used to detect DNA from a variety of taxonomic groups, it has not yet been used to identify DNA from species with numerous potentially sympatric confamilial species, a situation that may preclude the development of species-specific markers. There are 41 native freshwater mussel species (Unionidae) in Ontario, Canada. Many of these are potentially sympatric, and 14 species have been formally assessed as endangered, threatened, or special concern. We investigated whether there was sufficient variation within the cytochrome oxidase region (COI) to develop species-specific eDNA markers for at-risk unionids. We developed 32 COI markers for eight unionid species, and tested each of these on the target species plus 29 potentially sympatric unionid taxa. Six of these markers amplified DNA only from the intended target species. We then extracted and amplified mussel eDNA from rearing-tank water samples. We conclude that despite high species diversity, it should be possible to develop eDNA COI markers and screen water samples for habitat occupancy by unionid mussels. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) has recently been employed as a surveillance tool for invasive species, although its use has so far been limited to animals. We investigated the possibility of using eDNA to monitor aquatic invasive plants by assessing the potential utility of three regions of the chloroplast genome- matK, rbcL, and trnH–psbA- in ten aquatic invasive plant species. Of the three regions, matK was most likely to harbor putatively species-specific nucleotides in candidate primer-binding sites, and the potentially diagnostic primers that we designed for this region were least likely to amplify DNA from non-target species. A lack of species-specific nucleotides precluded the design of appropriate rbcL primers in most of our species, and amplification of non-target DNA often precluded the use of trnH–psbA markers. We, therefore, suggest that of the three regions, matK is the most useful starting point for designing eDNA markers for aquatic plants. We also demonstrated that these markers can identify species from eDNA that has been extracted from water samples. Our results should be useful to the ongoing development of eDNA as a tool for the early detection and ongoing surveillance of aquatic invasive plants. [ABSTRACT FROM AUTHOR]

Premise of the study : The Eurasian subspecies of the common reed ( Phragmites australis subsp. australis , hereafter abbreviated as P. a. australis ) was introduced to North America in the late 18 th century and rapidly expanded its range, posing an ecological threat to wetlands. In this study, we aimed to determine whether admixture among multiple lineages, dispersal mechanisms, and high genetic diversity have contributed to the invasion of P. a. australis in the northeastern part of its range. Understanding mechanisms of the P. a. australis invasion will 1) contribute to a broader understanding of the factors that facilitate plant invasion, and 2) help us to develop effective management strategies for wetlands threatened by P. a . australis invasion. Methods : We used a population genetics approach incorporating nine microsatellite loci to study genetic diversity and population structure in relation to biogeography of introduced North American Phragmites a . australis stands in the northeastern continental region. Key Results : Phragmites a . australis is genetically diverse in the region studied here. Significant population structure exists, and population structure is likely influenced by both long-distance dispersal via major waterways, and short-distance dispersal overland. Different lineages sometimes colonize geographically proximate locations leading to opportunities for admixture. Clonal reproduction likely exaggerates geographical structure among some stands, although high genetic and clonal diversity within some stands implies that sexual reproduction occurs frequently in P. a . australis . Conclusions : A variety of factors, including admixture among multiple lineages, multiple modes of dispersal, and plasticity in reproductive strategy promote the invasion success of Phragmites a . australis . Wetland managers in the St. Lawrence River/ Great Lakes region should focus monitoring efforts on the shores of conservation lands to prevent the establishment of propagules from novel lineages. [ABSTRACT FROM AUTHOR]

High rates of mutation and homoplasy mean that microsatellites generally are not considered to be useful molecular markers for inferring systematic relationships between species. However, an earlier pilot study suggested that conserved flanking microsatellite sequences, also known as repetitive flanking sequences (ReFS), may form a basis for a dominant marker that can differentiate between species of Lepidoptera. We present data that demonstrate that ReFS are quick and easy to use, and generate highly repeatable banding patterns from a range of Lepidoptera species. Sequence data from a subset of ReFS-amplified bands revealed microsatellite families with flanking sequences that are more conserved within than among species: this is probably attributable to recombination-mediated events, transposition of mobile elements or a combination of the two. Our data support the use of ReFS as dominant interspecific molecular markers, and add to the growing literature on the evolution of microsatellites in Lepidoptera. [ABSTRACT FROM AUTHOR]

Pitcher's thistle (Cirsium pitcheri Torr. ex Eaton (Torr. & Gray)) is a Great Lakes endemic that in Canada is designated as threatened at both the provincial (Ontario) and national levels. Management plans will benefit from conservation genetic data, which can provide insight into population genetic diversity and differentiation. We obtained genetic data from nuclear and chloroplast microsatellite markers from 17 populations of C. pitcheri around the Great Lakes. The nuclear data revealed overall low levels of diversity, high levels of inbreeding, and low levels of population connectivity. The chloroplast data identified a single haplotype, which is consistent with reduced genetic diversity following postglacial colonization. The high levels of inbreeding within populations will likely pose a serious threat to populations in the short term; these have resulted from a combination of low connectivity between populations, and small and fluctuating population sizes. Future management of C. pitcheri populations should consider human-mediated dispersal of plants or seeds among sites. [ABSTRACT FROM AUTHOR]