Genetic analysis of an interspecific hybrid swarm of Populus: occurrence of unidirectional introgression

Does Asymmetric Reproductive Isolation Predict the Direction of Introgression in Plants?

The evolution of reproductive isolation (RI) results in the reduction of interspecific hybridization and the maintenance of species boundaries. Asymmetries in RI, where one species more frequently serves as the maternal or paternal parent in initial F1 hybrid formation, are commonly observed in plants. Asymmetric introgression, the predominantly unidirectional transfer of genetic material through hybridization and backcrossing, has also been frequently documented in hybridizing plant taxa as well. This study investigates whether asymmetries in total RI measured between species can predict the direction of introgression in naturally hybridizing plant taxa. A meta-analysis was conducted on 19 plant species pairs with published data on both asymmetric total RI, and asymmetric introgression. Species pairs that met these criteria were identified through a comprehensive literature review. A two-tailed binomial test was performed to evaluate whether asymmetric RI was associated with asymmetries in introgression. No significant relationship was found between asymmetries in total RI and the direction of introgression (p = 0.3593). Asymmetric RI largely does not predict the direction of introgression. Rather, introgression patterns may be better understood by examining F1 and later-generation hybrids in natural settings, focusing on their fitness, mating behaviors, and the ecological and demographic factors that shape hybrid zones.

Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles

Most tree species underwent cycles of contraction and expansion during the Quaternary. These cycles led to an ancient and complex genetic structure that has since been affected by extensive gene flow and by strong local adaptation. The extent to which hybridization played a role in this multi-layered genetic structure is important to be investigated. To study the effect of hybridization on the joint population genetic structure of two dominant species of the Eurasian boreal forest, Picea abies and P. obovata, we used targeted resequencing and obtained around 480 K nuclear SNPs and 87 chloroplast SNPs in 542 individuals sampled across most of their distribution ranges. Despite extensive gene flow and a clear pattern of Isolation-by-Distance, distinct genetic clusters emerged, indicating the presence of barriers and corridors to migration. Two cryptic refugia located in the large hybrid zone between the two species played a critical role in shaping their current distributions. The two species repeatedly hybridized during the Pleistocene and the direction of introgression depended on latitude. Our study suggests that hybridization helped both species to overcome main shifts in their distribution ranges during glacial cycles and highlights the importance of considering whole species complex instead of separate entities to retrieve complex demographic histories.

Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idiosyncratic biological features of the eucalypts, including widespread plastome introgression. Here we present phylogenetic analyses of Eucalyptus subgenus Eudesmia (22 species from western, northern, central and eastern Australia), in the first study to apply a target-capture sequencing approach using custom, eucalypt-specific baits (of 568 genes) to a lineage of Eucalyptus. Multiple accessions of all species were included, and target-capture data were supplemented by separate analyses of plastome genes (average of 63 genes per sample). Analyses revealed a complex evolutionary history likely shaped by incomplete lineage sorting and hybridization. Gene tree discordance generally increased with phylogenetic depth. Species, or groups of species, toward the tips of the tree are mostly supported, and three major clades are identified, but the branching order of these clades cannot be confirmed with confidence. Multiple approaches to filtering the nuclear dataset, by removing genes or samples, could not reduce gene tree conflict or resolve these relationships. Despite inherent complexities in eucalypt evolution, the custom bait kit devised for this research will be a powerful tool for investigating the evolutionary history of eucalypts more broadly.

Heterozygous Trees Rebound the Fastest after Felling by Beavers to Positively Affect Arthropod Community Diversity

Although genetic diversity within stands of trees is known to have community-level consequences, whether such effects are present at an even finer genetic scale is unknown. We examined the hypothesis that genetic variability (heterozygosity) within an individual plant would affect its dependent community, which adds a new dimension to the importance of genetic diversity. Our study contrasted foliar arthropod community diversity and microsatellite marker-derived measures of genetic diversity of cottonwood (Populus fremontii) trees that had been felled by beavers (Castor canadensis) and were resprouting, relative to adjacent standing, unfelled trees. Three patterns emerged: 1. Productivity (specific leaf area), phytochemical defenses (salicortin), and arthropod community richness, abundance, and diversity were positively correlated with the heterozygosity of individual felled trees, but not with that of unfelled trees; 2. These relationships were not explained by population substructure, genetic relatedness of the trees, or hybridization; 3. The underlying mechanism appears to be that beaver herbivory stimulates increased productivity (i.e., 2× increase from the most homozygous to the most heterozygous tree) that is the greatest in more heterozygous trees. Salicortin defenses in twigs were also expressed at higher concentrations in more heterozygous trees (i.e., 3× increase from the most homozygous to the most heterozygous tree), which suggests that this compound may dissuade further herbivory by beavers, as has been found for other mammalian herbivores. We suggest that high stress to trees as a consequence of felling reveals a heterozygosity–productivity linkage, which in turn is attractive to arthropods. Although experiments are required to demonstrate causality, these results link the genetic diversity of individual trees to community diversity, supporting the hypothesis that interactions among foundation species (beavers and trees) have community-level effects, and underscores the importance of genetic diversity for biodiversity, conservation, and restoration.

Efficient Cryopreservation of Populus tremula by In Vitro-Grown Axillary Buds and Genetic Stability of Recovered Plants

Axillary buds of in vitro microshoots were successfully frozen at -196 °C by the one-step freezing method using the protective vitrification solution 2 (PVS2). Microshoots were taken from 11 transgenic lines and three wild type lines. Influence of different explant pretreatments were analyzed from the point of their influence towards recovery after cryopreservation. It was found out that the use of axillary buds as explants after removal of the apical one increases recovery on average by 8%. The cultivation on growth medium of higher density insignificantly raises the regenerants survival rate. Pretreatment of the osmotic fluid (OF) shows the greatest influence on the survival rate. It leads to the increase in survival rate by 20%. The cryopreservation technology providing regenerants average survival rate of 83% was developed. It was based on the experimental results obtained with explant pretreatment. Incubation time in liquid nitrogen did not affect the explants survival rate after thawing. After six months cryostorage of samples their genetic variability was analyzed. Six variable simple sequence repeat (SSR) loci were used to analyze genotype variability after the freezing-thawing procedure. The microsatellite analysis showed the genetic status identity of plants after cryopreservation and of the original genotypes. The presence of the recombinant gene in the transgenic lines after cryostorage were confirmed so as the interclonal variation in the growth rate under greenhouse conditions. The developed technique is recommended for long-term storage of various breeding and genetically modified lines of aspen plants, as it provides a high percentage of explants survival with no changes in genotype.

Intraspecific trait variation across elevation predicts a widespread tree species' climate niche and range limits

Global change is widely altering environmental conditions which makes accurately predicting species range limits across natural landscapes critical for conservation and management decisions. If climate pressures along elevation gradients influence the distribution of phenotypic and genetic variation of plant functional traits, then such trait variation may be informative of the selective mechanisms and adaptations that help define climatic niche limits. Using extensive field surveys along 16 elevation transects and a large common garden experiment, we tested whether functional trait variation could predict the climatic niche of a widespread tree species (Populus angustifolia) with a double quantile regression approach. We show that intraspecific variation in plant size, growth, and leaf morphology corresponds with the species' total climate range and certain climatic limits related to temperature and moisture extremes. Moreover, we find evidence of genetic clines and phenotypic plasticity at environmental boundaries, which we use to create geographic predictions of trait variation and maximum values due to climatic constraints across the western US. Overall, our findings show the utility of double quantile regressions for connecting species distributions and climate gradients through trait-based mechanisms. We highlight how new approaches like ours that incorporate genetic variation in functional traits and their response to climate gradients will lead to a better understanding of plant distributions as well as identifying populations anticipated to be maladapted to future environments.

Genetic analysis of admixture and hybrid patterns of Populus hopeiensis and P. tomentosa

Hybridization and introgression have resulted in reticulate evolution within the genus Populus. Consequently, the origin and evolutionary history of some hybrids has become blurred. P. hopeiensis and P. tomentosa are endemic to China, and there is still controversy about their origin. We employ phylogeny, Bayesian estimation of admixture, and approximate Bayesian computation to investigate their origin with 10 nuclear DNA and 6 cpDNA regions. The combined evidences firmly support the hypothesis that they are hybrids and dominated by F1s. P. hopeiensis was generated via hybridization between the paternal species P. alba and maternal species P. davidiana. Surprisingly, P. tomentosa was divided into two genetic types with different maternal parents. P. adenopoda hybridized with P. alba directly to generate the first genetic type (mb1) and hybridized with P. davidiana followed by P. alba to generate the second (mb2). In both genetic types, P. alba acted as the male parent. The maternal parent was P. adenopoda and P. davidiana for mb1 and mb2, respectively. Hybridization not only generated these hybrids but also resulted in a unidirectional gene flow from P. davidiana to P. adenopoda. The Populus species have maintained a delicate balance between their genetic integrity and gene exchange.

Heterosis in poplar involves phenotypic stability: cottonwood hybrids outperform their parental species at suboptimal temperatures

Heterosis or hybrid vigor is common in hybrid poplars, and to investigate its occurrence and physiological basis we compared narrowleaf cottonwoods, Populus angustifolia James, prairie cottonwoods, Populus deltoides Bartr. ex Marsh, and their native intersectional hybrids, P. × acuminata Rydb., from Alberta, Canada. Clonal replicates from 10 separate trees from each taxon were raised in growth chambers at different temperatures (T). Growth was similarly vigorous across the taxa at 20 and 24 °C, and morphological and physiological traits of the hybrids were generally intermediate between the parental species, or similar to the larger parent, demonstrating additive inheritance or dominance, respectively. Growth declined at 18 and 15 °C particularly in the parental species, and consequently hybrid vigor was displayed for root and especially leaf growth. Stomatal distributions and chlorophyll indices were intermediate in the hybrids and unaffected by T. Foliar nitrogen (N), net assimilation (Asat), stomatal conductance (gs) and transpiration (E) per unit of leaf area were lower in the hybrids, but the hybrids generally had larger leaf areas. Water-use efficiencies (Asat/gs) were similar across the taxa and reduced with warming, while nitrogen-use efficiencies (Asat/N) increased. δ13C was correlated with leaf mass per area, which varied across the taxa. Photosynthesis (Asat) was correlated with chlorophyll content index, N and/or gs in P. deltoides and the hybrids, but not in P. angustifolia, indicating different physiological limitations. We conclude that heterosis in P. × acuminata results from the compound benefits from multiple dominant traits, and superior growth particularly at suboptimal conditions. This indicates phenotypic stability or environmental adaptability, whereby heterozygosity provides metabolic diversity that allows hybrids to thrive across a broader environmental range.

Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: Implications for gene discovery

Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full‐sib population of hybrid cottonwoods (Populus spp.) to search for quantitative trait loci (QTL) for the SPGs salicortin and HCH‐salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH‐salicortin (R² = .52) that colocated with a QTL for salicortin on chr12. Using the V3.0 Populus genome sequence, we identified 2,983 annotated genes and 1,480 genes of unknown function within our QTL intervals. We note ten candidate genes of interest, including a BAHD‐type acyltransferase that has been potentially linked to PopulusSPGs. Our results complement other recent studies in Populus with implications for gene discovery and the evolution of defensive chemistry in a model genus. To our knowledge, this is the first study to use a full‐sib mapping population to identify QTL intervals and gene lists associated with SPGs.

Discovery and genomic analyses of hybridization between divergent lineages of Trypanosoma congolense, causative agent of Animal African Trypanosomiasis

Hybrid populations and introgressive hybridization remain poorly documented in pathogenic micro-organisms, as such that genetic exchange has been argued to play a minor role in their evolution. Recent work demonstrated the existence of hybrid microsatellite profiles in Trypanosoma congolense, a parasitic protozoan with detrimental effects on livestock productivity in sub-Saharan Africa. Here, we present the first population genomic study of T. congolense, revealing a remarkable number of single nucleotide polymorphisms (SNPs), small insertions/deletions (indels) and gene deletions among 56 parasite genomes from ten African countries. One group of parasites from Zambia was particularly diverse, displaying a substantial number of heterozygous SNP and indel sites compared to T. congolense parasites from the nine other sub-Saharan countries. Genomewide 5-kb phylogenetic analyses based on phased SNP data revealed that these parasites were the product of hybridization between phylogenetically distinct T. congolense lineages. Other parasites within the same region in Zambia presented a mosaic of haplotypic ancestry and genetic variability, indicating that hybrid parasites persisted and recombined beyond the initial hybridization event. Our observations challenge traditional views of trypanosome population biology and encourage future research on the role of hybridization in spreading genes for drug resistance, pathogenicity and virulence.

Arthropod communities on hybrid and parental cottonwoods are phylogenetically structured by tree type: Implications for conservation of biodiversity in plant hybrid zones

Although hybridization in plants has been recognized as an important pathway in plant speciation, it may also affect the ecology and evolution of associated communities. Cottonwood species (Populus angustifolia and P. fremontii) and their naturally occurring hybrids are known to support different plant, animal, and microbial communities, but no studies have examined community structure within the context of phylogenetic history. Using a community composed of 199 arthropod species, we tested for differences in arthropod phylogenetic patterns within and among hybrid and parental tree types in a common garden. Three major patterns emerged. (1) Phylogenetic diversity (PD) was significantly different between arthropod communities on hybrids and Fremont cottonwood when pooled by tree type. (2) Mean phylogenetic distance (MPD) and net relatedness index (NRI) indicated that communities on hybrid trees were significantly more phylogenetically overdispersed than communities on either parental tree type. (3) Community distance (D_pw) indicated that communities on hybrids were significantly different than parental species. Our results show that arthropod communities on parental and hybrid cottonwoods exhibit significantly different patterns of phylogenetic structure. This suggests that arthropod community assembly is driven, in part, by plant-arthropod interactions at the level of cottonwood tree type. We discuss potential hypotheses to explain the effect of plant genetic dissimilarity on arthropod phylogenetic community structure, including the role of competition and environmental filtering. Our findings suggest that cottonwood species and their hybrids function as evolutionarily significant units (ESUs) that affect the assembly and composition of associated arthropod communities and deserve high priority for conservation.

Asymmetry matters: A genomic assessment of directional biases in gene flow between hybridizing spruces

Assessing directional bias in interspecific gene flow might be important in determining the evolutionary trajectory of closely related species pairs. Using a set of 300 single nucleotide polymorphisms (SNPs) having variable propensity to cross species boundary, we evaluated the genomic extent and direction of interspecific gene flow in a progenitor‐derivative spruce species pair (black spruce and red spruce). A higher rate of gene flow was found from black spruce toward red spruce purebreds than vice versa. This asymmetry could reflect the historical gene flow between the two taxa at the time of species inception and during postglacial colonization. A clear asymmetry in introgression was depicted by a greater gene flow between red spruce and hybrids than between black spruce and hybrids. While backcrossing toward red spruce was invariably high across the genome, the actual species boundary is between hybrids and black spruce where gene flow is impeded at those genomic regions impermeable to introgression. Associations between hybrid index and climatic variables (total annual precipitation and mean annual temperature) were tested, as these might indicate a role for exogenous selection in maintaining the species boundary. While an apparent association was found between the hybrid index and precipitation, it collapsed when considered in light of the directional bias in interspecific gene flow. Hence, considering asymmetrical patterns of introgression allowed us to falsify an apparent role for exogenous selection. Although this was not formerly tested here, we suggest that this pattern could result from asymmetrical endogenous selection, a contention that deserves further investigations.

Introgression Threatens the Genetic Diversity of Quercus austrocochinchinensis (Fagaceae), an Endangered Oak: A Case Inferred by Molecular Markers

Natural introgression can cause negative effects where rare species experience genetic assimilation and invade by their abundant congeners. Quercus austrocochinchinensis and Q. kerrii (subgenus Cyclobalanopsis) are a pair of closely related species in the Indo-China area. Morphological intermediates of the two species have been reported in this region. In this study, we used AFLP, SSR and two key leaf morphological diagnostic traits to study the two Q. austrocochinchinensis populations, two pure Q. kerrii and two putative hybrid populations in China. Rates of individual admixture were examined using the Bayesian clustering programs STRUCTURE and NewHybrids, with no a priori species assignment. In total, we obtained 151 SSR alleles and 781 polymorphic loci of AFLP markers. Population differentiation inferred by SSR and AFLP was incoherent with recognized species boundaries. Bayesian admixture analyses and principal coordinate analysis identified more hybrids and backcrossed individuals than morphological intermediates in the populations. SSR inferred a wide genetic assimilation in Q. austrocochinchinensis, except for subpopulation D2 in the core area of Xi-Shuang-Ban-Na Nature Reserve (XSBN). However, AFLP recognized more Q. austrocochinchinensis purebreds than SSR. Analysis using NewHybrids on AFLP data indicated that these hybridized individuals were few F2 and predominantly backcrosses with both parental species. All these evidences indicate the formation of a hybrid swarm at XSBN where the two species co-exist. Both AFLP and SSR recognized that the core protected area of XSBN (D2) has a high percentage of Q. austrocochinchinensis purebreds and a unique germplasm. The Hainan population and the other subpopulations of XSBN of the species might have lost their genetic integrity. Our results revealed a clear genetic differentiation in the populations and subpopulations of Q. austrocochinchinensis and ongoing introgression between Q. austrocochinchinensis and Q. kerrii at the disturbed contact areas. Combining the results from genetic and morphological analyses, the conservation of subpopulation D2 should be prioritized. Conservation and restoration of the integrity of tropical ravine rainforest is an important long-term goal for the successful conservation of Q. austrocochinchinensis. The fine-scale landscape might play an essential role in shaping the spatial patterns of hybridization. Further studies are needed to evaluate these patterns and dynamics.

The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem

Foliar chemistry influences leaf decomposition, but little is known about how litter chemistry affects the assemblage of bacterial communities during decomposition. Here we examined relationships between initial litter chemistry and the composition of the bacterial community in a stream ecosystem. We incubated replicated genotypes of Populus fremontii and P. angustifolia leaf litter that differ in percent tannin and lignin, then followed changes in bacterial community composition during 28 days of decomposition using 16S rRNA gene-based pyrosequencing. Using a nested experimental design, the majority of variation in bacterial community composition was explained by time (i.e., harvest day) (R(2) = 0.50). Plant species, nested within harvest date, explained a significant but smaller proportion of the variation (R(2) = 0.03). Significant differences in community composition between leaf species were apparent at day 14, but no significant differences existed among genotypes. Foliar chemistry correlated significantly with community composition at day 14 (r = 0.46) indicating that leaf litter with more similar phytochemistry harbor bacterial communities that are alike. Bacteroidetes and β-proteobacteria dominated the bacterial assemblage on decomposing leaves, and Verrucomicrobia and α- and δ-proteobacteria became more abundant over time. After 14 days, bacterial diversity diverged significantly between leaf litter types with fast-decomposing P. fremontii hosting greater richness than slowly decomposing P. angustifolia; however, differences were no longer present after 28 days in the stream. Leaf litter tannin, lignin, and lignin: N ratios all correlated negatively with diversity. This work shows that the bacterial community on decomposing leaves in streams changes rapidly over time, influenced by leaf species via differences in genotype-level foliar chemistry.

Genetic origin and composition of a natural hybrid poplar Populus × jrtyschensis from two distantly related species

BACKGROUND

The factors that contribute to and maintain hybrid zones between distinct species are highly variable, depending on hybrid origins, frequencies and fitness. In this study, we aimed to examine genetic origins, compositions and possible maintenance of Populus × jrtyschensis, an assumed natural hybrid between two distantly related species. This hybrid poplar occurs mainly on the floodplains along the river valleys between the overlapping distributions of the two putative parents.

RESULTS

We collected 566 individuals from 45 typical populations of P. × jrtyschensis, P. nigra and P. laurifolia. We genotyped them based on the sequence variations of one maternally inherited chloroplast DNA (cpDNA) fragment and genetic polymorphisms at 20 SSR loci. We further sequenced eight nuclear genes for 168 individuals from 31 populations. Two groups of cpDNA haplotypes characteristic of P. nigra and P. laurifolia respectively were both recovered for P. × jrtyschensis. Genetic structures and coalescent tests of two sets of nuclear population genetic data suggested that P. × jrtyschensis originated from hybridizations between the two assumed parental species. All examined populations of P. × jrtyschensis comprise mainly F1 hybrids from interspecific hybridizations between P. nigra and P. laurifolia. In the habitats of P. × jrtyschensis, there are lower concentrations of soil nitrogen than in the habitats occupied by the other two species.

CONCLUSIONS

Our extensive examination of the genetic composition of P. × jrtyschensis suggested that it is typical of F1-dominated hybrid zones. This finding plus the low concentration of soil nitrogen in the floodplain soils support the F1-dominated bounded hybrid superiority hypothesis of hybrid zone maintenance for this particular hybrid poplar.

Phylogenetic and Taxonomic Status Analyses of the Abaso Section from Multiple Nuclear Genes and Plastid Fragments Reveal New Insights into the North America Origin of Populus (Salicaceae)

Although, the Abaso section is widely accepted as an independent section, the taxonomic status of Populus mexicana (section Abaso) has not yet been resolved due to the limited availability markers and/or the lack of P. mexicana specimens in previous studies. Thirty-one poplar species that represent six sections of the Populus genus were sampled, and 23 single-copy nuclear DNA and 34 chloroplast fragments were sequenced. The present study obtained two updated phylogenies of Populus. We found that monophyly of the genus Populus is strongly supported by nuclear and plastid gene, which is consistent with previous studies. P. mexicana, diverged first in the nuclear DNA tree, which occupied the basal position, implying that the section Abaso may be the most ancestral lineage in extant populous species. Given that the short branches and low statistical support for the divergence of sections Abaso and Turanga, this observation probably indicated that a rapid radiation evolution following the early split of the genus Populus. In the plastid tree, P. mexicana clustered with modern-day species of section Tacamahaca in the plastid tree. Based on cytoplasmic and single-copy nuclear marker sequences, we hypothesized that chloroplast capture resulted in the inconsistent position of P. mexicana between the phylogenetic trees. Given the first unequivocal records of poplar fossils from the Eocene with similar leaf morphology to the extant P. mexicana and the phylogenetic positions of P. mexicana in our study, we support the hypothesis that the Populus genus originated in North America, which will provide new insights to the development of the origin of Populus species.

The extent of hybridization and its impact on the genetic diversity and population structure of an invasive tree, Ulmus pumila (Ulmaceae)

Ulmus pumila is considered an invasive tree in 41 of the United States. In this study, we examined the extent of hybridization in naturalized populations of U. pumila, its impact on genetic diversity and genetic structure and its potential role in explaining the invasion process of U. pumila. Genetic analyses indicated widespread hybridization with native Ulmus rubra in naturalized U. pumila populations. Hybridization increased the genetic diversity of U. pumila populations and affected their genetic structure. The level of genetic diversity in 'mature' accessions, many of which may represent original plantings throughout the USA, was high and similar to the diversity of East Asian accessions. Hybridization with the native red elm may play an important role in the success of Siberian elm as an invader in temperate regions of the USA.

Fitness dynamics within a poplar hybrid zone: I. Prezygotic and postzygotic barriers impacting a native poplar hybrid stand

Hybridization and introgression are pervasive evolutionary phenomena that provide insight into the selective forces that maintain species boundaries, permit gene flow, and control the direction of evolutionary change. Poplar trees (Populus L.) are well known for their ability to form viable hybrids and maintain their distinct species boundaries despite this interspecific gene flow. We sought to quantify the hybridization dynamics and postzygotic fitness within a hybrid stand of balsam poplar (Populus balsamifera L.), eastern cottonwood (P. deltoides Marsh.), and their natural hybrids to gain insight into the barriers maintaining this stable hybrid zone. We observed asymmetrical hybrid formation with P. deltoides acting as the seed parent, but with subsequent introgression biased toward P. balsamifera. Native hybrids expressed fitness traits intermediate to the parental species and were not universally unfit. That said, native hybrid seedlings were absent from the seedling population, which may indicate additional selective pressures controlling their recruitment. It is imperative that we understand the selective forces maintaining this native hybrid zone in order to quantify the impact of exotic poplar hybrids on this native system.

Fitness dynamics within a poplar hybrid zone: II. Impact of exotic sex on native poplars in an urban jungle

Trees bearing novel or exotic gene components are poised to contribute to the bioeconomy for a variety of purposes such as bioenergy production, phytoremediation, and carbon sequestration within the forestry sector, but sustainable release of trees with novel traits in large-scale plantations requires the quantification of risks posed to native tree populations. Over the last century, exotic hybrid poplars produced through artificial crosses were planted throughout eastern Canada as ornamentals or windbreaks and these exotics provide a proxy by which to examine the fitness of exotic poplar traits within the natural environment to assess risk of exotic gene escape, establishment, and spread into native gene pools. We assessed postzygotic fitness traits of native and exotic poplars within a naturally regenerated stand in eastern Canada (Quebec City, QC). Pure natives (P. balsamifera and P. deltoides spp. deltoides), native hybrids (P. deltoides × P. balsamifera), and exotic hybrids (trees bearing Populus nigra and P. maximowiczii genetic components) were screened for reproductive biomass, yield, seed germination, and fungal disease susceptibility. Exotic hybrids expressed fitness traits intermediate to pure species and were not significantly different from native hybrids. They formed fully viable seed and backcrossed predominantly with P. balsamifera. These data show that exotic hybrids were not unfit and were capable of establishing and competing within the native stand. Future research will seek to examine the impact of exotic gene regions on associated biotic communities to fully quantify the risk exotic poplars pose to native poplar forests.

Genetic by environment interactions affect plant-soil linkages

The role of plant intraspecific variation in plant–soil linkages is poorly understood, especially in the context of natural environmental variation, but has important implications in evolutionary ecology. We utilized three 18- to 21-year-old common gardens across an elevational gradient, planted with replicates of five Populus angustifolia genotypes each, to address the hypothesis that tree genotype (G), environment (E), and G × E interactions would affect soil carbon and nitrogen dynamics beneath individual trees. We found that soil nitrogen and carbon varied by over 50% and 62%, respectively, across all common garden environments. We found that plant leaf litter (but not root) traits vary by genotype and environment while soil nutrient pools demonstrated genotype, environment, and sometimes G × E interactions, while process rates (net N mineralization and net nitrification) demonstrated G × E interactions. Plasticity in tree growth and litter chemistry was significantly related to the variation in soil nutrient pools and processes across environments, reflecting tight plant–soil linkages. These data overall suggest that plant genetic variation can have differential affects on carbon storage and nitrogen cycling, with implications for understanding the role of genetic variation in plant–soil feedback as well as management plans for conservation and restoration of forest habitats with a changing climate.

Genetic components to belowground carbon fluxes in a riparian forest ecosystem: a common garden approach

Soil carbon dioxide (CO(2)) efflux is a major component of terrestrial carbon (C) cycles; yet, the demonstration of covariation between overstory tree genetic-based traits and soil C flux remains a major frontier in understanding biological controls over soil C. Here, we used a common garden with two native tree species, Populus fremontii and P. angustifolia, and their naturally occurring hybrids to test the predictability of belowground C fluxes on the basis of taxonomic identity and genetic marker composition of replicated clones of individual genotypes. Three patterns emerged: soil CO(2) efflux and ratios of belowground flux to aboveground productivity differ by as much as 50-150% as a result of differences in clone identity and cross type; on the basis of Mantel tests of molecular marker matrices, we found that c. 30% of this variation was genetically based, in which genetically similar trees support more similar soil CO(2) efflux under their canopies than do genetically dissimilar trees; and the patterns detected in an experimental garden match observations in the wild, and seem to be unrelated to measured abiotic factors. Our findings suggest that the genetic makeup of the plants growing on soil has a significant influence on the release of C from soils to the atmosphere.

Relative importance of genetic, ontogenetic, induction, and seasonal variation in producing a multivariate defense phenotype in a foundation tree species

Plant adaptations for defense against herbivory vary both among species and among genotypes. Moreover, numerous forms of within-plant variation in defense, including ontogeny, induction, and seasonal gradients, allow plants to avoid expending resources on defense when herbivores are absent. We used an 18-year-old cottonwood common garden composed of Populus fremontii, Populus angustifolia, and their naturally occurring F(1) hybrids (collectively referred to as "cross types") to quantify and compare the relative influences of three hierarchical levels of variation (between cross types, among genotypes, and within individual genotypes) on univariate and multivariate phytochemical defense traits. Within genotypes, we evaluated ontogeny, induction (following cottonwood leaf beetle herbivory), and seasonal variation. We compared the effect sizes of each of these sources of variation on the plant defense phenotype. Three major patterns emerged. First, we observed significant differences in concentrations of defense phytochemicals among cross types, and/or among genotypes within cross types. Second, we found significant genetic variation for within-plant differences in phytochemical defenses: (a) based on ontogeny, levels of constitutive phenolic glycosides were nearly three times greater in the mature zone than in the juvenile zone within one cottonwood cross type, but did not significantly differ within another cross type; (b) induced levels of condensed tannins increased up to 65 % following herbivore damage within one cottonwood cross type, but were not significantly altered in another cross type; and (c) concentrations of condensed tannins tended to increase across the season, but did not do so across all cross types. Third, our estimates of effect size demonstrate that the magnitude of within-plant variation in a phytochemical defense can rival the magnitude of differences in defense among genotypes and/or cross types. We conclude that, in cottonwood and likely other plant species, multiple forms of within-individual variation have the potential to substantially influence ecological and evolutionary processes.

Weak prezygotic isolating mechanisms in threatened Caribbean Acropora corals

The Caribbean corals, Acropora palmata and A. cervicornis, recently have undergone drastic declines primarily as a result of disease. Previous molecular studies have demonstrated that these species form a hybrid (A. prolifera) that varies in abundance throughout the range of the parental distribution. There is variable unidirectional introgression across loci and sites of A. palmata genes flowing into A. cervicornis. Here we examine the efficacy of prezygotic reproductive isolating mechanisms within these corals including spawning times and choice and no-choice fertilization crosses. We show that these species have subtly different mean but overlapping spawning times, suggesting that temporal isolation is likely not an effective barrier to hybridization. We found species-specific differences in gametic incompatibilities. Acropora palmata eggs were relatively resistant to hybridization, especially when conspecific sperm are available to outcompete heterospecific sperm. Acropora cervicornis eggs demonstrated no evidence for gametic incompatibility and no evidence of reduced viability after aging four hours. This asymmetry in compatibility matches previous genetic data on unidirectional introgression.

Hybrid swarm between divergent lineages of mule deer (Odocoileus hemionus)

Studies of hybrid zones have revealed an array of evolutionary outcomes, yet the underlying structure is typically characterized as one of three types: a hybrid zone, a hybrid swarm or a hybrid taxon. Our primary objective was to determine which of these three structures best characterizes a zone of hybridization between two divergent lineages of mule deer (Odocoileus hemionus), mule deer and black-tailed deer. These lineages are morphologically, ecologically and genetically distinct, yet hybridize readily along a zone of secondary contact between the east and west slopes of the Cascade Mountains (Washington and Oregon, USA). Using microsatellite and mitochondrial DNA, we found clear evidence for extensive hybridization and introgression between lineages, with varying degrees of admixture across the zone of contact. The pattern of hybridization in this region closely resembles a hybrid swarm; based on data from 10 microsatellite loci, we detected hybrids that extend well beyond the F1 generation, did not detect linkage disequilibrium at the centre of the zone and found that genotypes were associated randomly within the zone of contact. Introgression was characterized as bidirectional and symmetric, which is surprising given that the zone of contact occurs along a sharp ecotone and that lineages are characterized by large differences in body size (a key component of mating success). Regardless of the underlying mechanisms promoting hybrid swarm maintenance, it is clear that the persistence of a hybrid swarm presents unique challenges for management in this region.

Amplified fragment length polymorphism and sequence analyses reveal massive gene introgression from the European fungal pathogen Heterobasidion annosum into its introduced congener H. irregulare

The paucity of fungal species known to be currently hybridizing has significantly hindered our understanding of the mechanisms driving gene introgression in these eukaryotic microbes. Here, we describe an area of hybridization and gene introgression between the invasive plant pathogen Heterobasidion irregulare (introduced from North America) and the native H. annosum in Italy. A STRUCTURE analysis of amplified fragment length polymorphism data for 267 individuals identified gene introgression in 8-42% of genotypes in the invasion area, depending on site. Data indicate that introgression is mostly occurring unilaterally from the native to the invasive species and is responsible for 5-45% of genomes in admixed individuals. Sequence analysis of 11 randomly selected and unlinked loci for 30 individuals identified introgression at every locus, thus confirming interspecific gene flow involves a large number of loci. In 37 cases, we documented movement of entire alleles between the two species, but in 7 cases, we also documented the creation of new alleles through intralocus recombination. Sequence analysis did not identify enrichment of either transcriptionally different nonsynonymous alleles or of transcriptionally identical synonymous alleles. These findings may suggest introgression is occurring randomly for extant alleles without an obvious enrichment process driven by selection. However, further studies are needed to ensure selection is not at work elsewhere in the genome.

Pollen-mediated gene flow in isolated and continuous stands of bur oak, Quercus macrocarpa (Fagaceae)

PREMISE OF THE STUDY

Pollination patterns determine the reproductive neighborhood size of plants, the connectivity of populations, and the impacts of habitat fragmentation. We characterized pollination in three populations of Quercus macrocarpa occurring in a highly altered landscape in northeastern Illinois to determine whether isolated remnant stands were reproductively isolated. •

METHODS

We used microsatellites to genotype all adults and 787 acorns from two isolated savanna remnants and a stand in an old-growth forest. One isolated remnant occurred in a highly urbanized/industrialized landscape, and one occurred in an agricultural landscape. Parentage assignment was used to assess pollen-mediated gene flow. •

KEY RESULTS

Pollen donors from outside the study sites accounted for between 46% and 53% of paternities and did not differ significantly among sites, indicating that similar high levels of gene flow occurred at all three sites. Within stands, the mean pollination distance ranged from 42 to 70 meters, and when accounting for outside pollinations, mean pollination distances were well over 100 meters. Genetic diversity of incoming pollen was extremely high in all three stands. The number of effective pollen donors, N(ep), calculated from paternity assignment was higher than that estimated by an indirect correlated paternity approach. •

CONCLUSIONS

Our findings indicate that extremely isolated stands of oaks are unlikely to be genetically and reproductively isolated, and remnant stands may contribute to maintaining genetic connectivity in highly modified landscapes.

Genetic basis of aboveground productivity in two native Populus species and their hybrids

Demonstration of genetic control over riparian tree productivity has major implications for responses of riparian systems to shifting environmental conditions and effects of genetics on ecosystems in general. We used field studies and common gardens, applying both molecular and quantitative techniques, to compare plot-level tree aboveground net primary productivity (ANPP(tree)) and individual tree growth rate constants in relation to plant genetic identity in two naturally occurring Populus tree species and their hybrids. In field comparisons of four cross types (Populus fremontii S. Wats., Populus angustifolia James, F(1) hybrids and backcross hybrids) across 11 natural stands, productivity was greatest for P. fremontii trees, followed by hybrids and lowest in P. angustifolia. A similar pattern was observed in four common gardens across a 290 m elevation and 100 km environmental gradient. Despite a doubling in productivity across the common gardens, the relative differences among the cross types remained constant. Using clonal replicates in a common garden, we found ANPP(tree) to be a heritable plant trait (i.e., broad-sense heritability), such that plant genetic factors explained between 38% and 82% of the variation in ANPP(tree). Furthermore, analysis of the genetic composition among individual tree genotypes using restriction fragment length polymorphism molecular markers showed that genetically similar trees also exhibited similar ANPP(tree). These findings indicate strong genetic contributions to natural variation in ANPP with important ecological implications.

From genes to ecosystems: a synthesis of the effects of plant genetic factors across levels of organization

Using two genetic approaches and seven different plant systems, we present findings from a meta-analysis examining the strength of the effects of plant genetic introgression and genotypic diversity across individual, community and ecosystem levels with the goal of synthesizing the patterns to date. We found that (i) the strength of plant genetic effects can be quite high; however, the overall strength of genetic effects on most response variables declined as the levels of organization increased. (ii) Plant genetic effects varied such that introgression had a greater impact on individual phenotypes than extended effects on arthropods or microbes/fungi. By contrast, the greatest effects of genotypic diversity were on arthropods. (iii) Plant genetic effects were greater on above-ground versus below-ground processes, but there was no difference between terrestrial and aquatic environments. (iv) The strength of the effects of intraspecific genotypic diversity tended to be weaker than interspecific genetic introgression. (v) Although genetic effects generally decline across levels of organization, in some cases they do not, suggesting that specific organisms and/or processes may respond more than others to underlying genetic variation. Because patterns in the overall impacts of introgression and genotypic diversity were generally consistent across diverse study systems and consistent with theoretical expectations, these results provide generality for understanding the extended consequences of plant genetic variation across levels of organization, with evolutionary implications.

Florivory increases selfing: an experimental study in the wild strawberry, Fragaria virginiana

Florivores are antagonists that damage flowers, and have direct negative effects on flowering and pollination of the attacked plants. While florivory has mainly been studied for its consequences on seed production or siring success, little is known about its impact on mating systems. Damage to flowers can alter pollinator attraction to the plant and may therefore modify patterns of pollen transfer. However, the consequences of damage for mating systems can take two forms: a decrease in flower number reduces opportunities for intra-inflorescence pollen deposition (geitonogamy), which, in turn, may lead to a decrease in selfing; whereas a decrease in floral display may also reduce overall visitation and thus increase the chances of self-pollination via facilitated or autonomous autogamy. We investigated the effects of damage by a bud-clipping weevil (Anthonomus signatus) in Fragaria virginiana in an experimental setting mimicking natural conditions. We found that increased damage led to an increase in selfing, a result consistent with the increased autogamy pathway. We discuss the implications of this finding and evaluate the generality of florivore-mediated mating system expression.

Review. The genic view of plant speciation: recent progress and emerging questions

The genic view of the process of speciation is based on the notion that species isolation may be achieved by a modest number of genes. Although great strides have been made to characterize 'speciation genes' in some groups of animals, little is known about the nature of genic barriers to gene flow in plants. We review recent progress in the characterization of genic species barriers in plants with a focus on five 'model' genera: Mimulus (monkey flowers); Iris (irises); Helianthus (sunflowers); Silene (campions); and Populus (poplars, aspens, cottonwoods). The study species in all five genera are diploid in terms of meiotic behaviour, and chromosomal rearrangements are assumed to play a minor role in species isolation, with the exception of Helianthus for which data on the relative roles of chromosomal and genic isolation factors are available. Our review identifies the following key topics as being of special interest for future research: the role of intraspecific variation in speciation; the detection of balancing versus directional selection in speciation genetic studies; the timing of fixation of alleles of major versus minor effects during plant speciation; the likelihood of adaptive trait introgression; and the identification and characterization of speciation genes and speciation gene networks.

Tree hybridization and genotypic variation drive cryptic speciation of a specialist mite herbivore

Few studies have investigated the roles that plant hybridization and individual plant genotype play in promoting population divergence within arthropod species. Using nrDNA sequence information and reciprocal transfer experiments, we examined how tree cross type (i.e., pure Populus angustifolia and P. angustifolia x P. fremontii F(1) type hybrids) and individual tree genotype influence host race formation in the bud-galling mite Aceria parapopuli. Three main findings emerged: (1) Strong genetic differentiation of mite populations found on pure P. angustifolia and F(1) type hybrids indicates that these mites represent morphologically cryptic species. (2) Within the F(1) type hybrids, population genetic analyses indicate migration among individual trees; however, (3) transfer experiments show that the mites found on heavily infested F(1) type trees perform best on their natal host genotype, suggesting that genetic interactions between mites and their host trees drive population structure, local adaptation, and host race formation. These findings argue that hybridization and genotypic differences in foundation tree species may drive herbivore population structure, and have evolutionary consequences for dependent arthropod species.