Outcrossing between an agroforestry plantation and remnant native populations of Eucalyptus loxophleba

Gene flow from Fraxinus cultivars into natural stands of Fraxinus pennsylvanica occurs range-wide, is regionally extensive, and is associated with a loss of allele richness

In North America, a comparatively small number of Fraxinus (ash) cultivars were planted in large numbers in both urban and rural environments across the entire range of Fraxinus pennsylvanica Marsh (green ash) over the last 80 years. Undetected cultivar gene flow, if extensive, could significantly lower genetic diversity within populations, suppress differentiation between populations, generate interspecific admixture not driven by long-standing natural processes, and affect the impact of abiotic and biotic threats. In this investigation we generated the first range-wide genetic assessment of F. pennsylvanica to detect the extent of cultivar gene flow into natural stands. We used 16 EST-SSR markers to genotype 48 naturally regenerated populations of F. pennsylvanica distributed across the native range (1291 trees), 19 F. pennsylvanica cultivars, and one F. americana L. (white ash) cultivar to detect cultivar propagule dispersal into these populations. We detected first generation cultivar parentage with high confidence in 171 individuals in 34 of the 48 populations and extensive cultivar parentage (23-50%) in eight populations. The incidence of cultivar parentage was negatively associated with allele richness (R2 = 0.151, p = 0.006). The evidence for a locally high frequency of cultivar propagule dispersal and the interspecific admixture in eastern populations will inform Fraxinus gene pool conservation strategies and guide the selection of individuals for breeding programs focused on increasing resistance to the emerald ash borer (Agrilus planipennis Fairmaire), an existential threat to the Fraxinus species of North America.

Genetic assessment of the value of restoration planting within an endangered eucalypt woodland

Assessment of woodland restoration often focusses on stand demographics, but genetic factors likely influence long-term stand viability. We examined the genetic composition of Yellow Box (Eucalyptus melliodora) trees in endangered Box-Gum Grassy Woodland in SE Australia, some 30 years after planting with seeds of reportedly local provenance. Using DArT sequencing for 1406 SNPs, we compared genetic diversity and population structure of planted E. melliodora trees with remnant bushland trees, paddock trees and natural recruits. Genetic patterns imply that natural stands and paddock trees had historically high gene flow (among group pairwise F_ST = 0.04-0.10). Genetic diversity was highest among relictual paddock trees (H_e = 0.17), while diversity of revegetated trees was identical to natural bushland trees (H_e = 0.14). Bayesian clustering placed the revegetated trees into six genetic groups with four corresponding to genotypes from paddock trees, indicating that revegetated stands are mainly of genetically diverse, local provenance. Natural recruits were largely derived from paddock trees with some contribution from planted trees. A few trees have likely hybridised with other local eucalypt species which are unlikely to compromise stand integrity. We show that paddock trees have high genetic diversity and capture historic genetic variety and provide important foci for natural recruitment of genetically diverse and outcrossed seedlings.

The Genetics and Ecology of Post-Fire Eucalyptus globulus Recruitment in an Isolated Stand in Central Portugal

Eucalyptus globulus Labill. is a widespread forest tree species, reported as naturalized across the introduced range, often showing abundant natural regeneration after wildfires. This paper studies a post-fire cohort of seedlings derived from a small, isolated E. globulus stand in central Portugal. The aim is to better understand the genetic dynamics and dispersal mechanisms of naturally established E. globulus populations in the introduced range. The seedling density at 55 m from adult trees was 12,000 ha−1, the farthest seedling being registered at 101 m. Post-fire expansion occurred in a southward direction, in accordance with predominant wind. Seedlings had significantly lower levels of genetic diversity (Ae = 5.8.; He = 0.8) than adult trees (Ae = 6.5; He = 0.8). Crossings were strongly unbalanced, with only eight trees contributing to the sampled seedlings, and one single tree contributing to 52% of these seedlings. Moreover, the co-ancestry amongst seedlings more than doubled (from θ = 0.03 to 0.076), and the population status number was around one third of the value registered for the adult population (from Ns = 16.2 to 6.6). Despite its isolation, external pollen was detected in the stand, and appears to have travelled at least 700 m, contributing to 22% of the offspring. Overall, the seedling cohort is much less diverse than the parent trees, with expected lower resilience and persistence to environmental stresses.

Out of the OCBILs: new hypotheses for the evolution, ecology and conservation of the eucalypts

OCBIL theory is a multi-hypothesis formulation aimed towards an understanding of the evolution, ecology and conservation of biological and cultural diversity on old, climatically buffered, infertile landscapes (OCBILs). OCBILs have been in existence contemporaneously with rainforest since Gondwanan times. Such landscapes are common in areas of eucalypt species richness embraced by Australia’s two Global Biodiversity Hotspots, the Southwest Australian Floristic Region and the Forests of East Australia. Here, I summarize evidence pertaining to the eucalypts in the context of a recent reformulation of OCBIL theory into 12 evolutionary, ecological and cultural hypotheses and ten conservation management hypotheses. A compelling argument emerges for a new interpretation of the eucalypts evolving out of the OCBILs, rather than out of the rainforests as traditionally interpreted. This calls for a significant reinterpretation of best conservation management of the eucalypts. For example, traditional ideas on application of fire in eucalypt communities regarded as well adapted to this disturbance need to give way to a more nuanced and cautious view. This review of eucalypts seen as evolving out of the OCBILs helps in understanding the group from several new perspectives. Interpretation of other sedentary plant and animal groups as out of the OCBILs is commended for further study.

Differential exposure and susceptibility to threats based on evolutionary history: how OCBIL theory informs flora conservation

Optimal conservation approaches have been proposed to differ for biota with contrasting evolutionary histories. Natural selection filters the distribution of plant traits over evolutionary time, with the current expression of traits mediating susceptibility to contemporary and often novel threats. We use old, climatically buffered, infertile landscape (OCBIL) theory to compile predictions regarding differences in exposure and susceptibility to key threats between OCBIL and young, often disturbed, fertile landscape (YODFEL) flora. Based on literature and existing data from the Southwest Australian Floristic Region (SWAFR), we evaluate evidence in support of our predictions, finding strong theoretical and empirical support for the proposition that exposure and/or impact of many threats differs between OCBILs and YODFELs. OCBILs have more exposure to land clearance from mining, whereas many YODFELs have greater exposure to land clearance from agriculture, and urban and industrial land uses, and greater overall levels of habitat loss and fragmentation. OCBIL flora are more susceptible to pathogens and extremes of fire interval than YODFEL flora, but conversely may have a greater capacity to persist in smaller populations if small populations featured in the evolutionary history of the species prior to anthropogenic fragmentation, and have substantial resistance to weed invasion. We argue that consideration of evolutionary history has an important role in informing conservation management.

Flowering phenology in a Eucalyptus loxophleba seed orchard, heritability and genetic correlation with biomass production and cineole: breeding strategy implications

Reproductive synchronicity within a seed orchard facilitates gene exchange and reduces self-fertilisation. Here we assessed key flowering traits, biomass and foliar 1,8-cineole concentrations of Eucalyptus loxophleba (subsp. lissophloia and gratiae) in an open-pollinated seed orchard. Monthly flowering observations were made on 1142 trees from 60 families and nine provenances across 2 years. The percentage of trees flowering in both years was similar at 87%. There were differences between provenances and families within provenances for flowering traits, biomass and 1,8-cineole and interactions between provenances and year for flowering traits. Heritability of start and end flowering, and 1,8-cineole were high to moderate (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hat{h}^{2}$$\end{document}h^2 = 0.75–0.45) and duration of flowering, propensity to flower and biomass estimates were moderate to low (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hat{h}^{2}$$\end{document}h^2 = 0.31–0.10). Genetic and phenotypic correlations between flowering traits were high (r_g = 0.96–0.63 and r_p = 0.93–0.34) except between duration and end of flowering. The correlations were weaker between flowering traits and biomass or 1,8-cineole. ‘Dual flowering’, when trees underwent two reproductive cycles in a year, was responsible for out-of-phase flowering and those with low biomass and 1,8-cineole concentration should be removed from the breeding programme to hasten selection for desirable traits.

Mating system and early viability resistance to habitat fragmentation in a bird-pollinated eucalypt

Habitat fragmentation has been shown to disrupt ecosystem processes such as plant-pollinator mutualisms. Consequently, mating patterns in remnant tree populations are expected to shift towards increased inbreeding and reduced pollen diversity, with fitness consequences for future generations. However, mating patterns and phenotypic assessments of open-pollinated progeny have rarely been combined in a single study. Here, we collected seeds from 37 Eucalyptus incrassata trees from contrasting stand densities following recent clearance in a single South Australian population (intact woodland=12.6 trees ha(-1); isolated pasture=1.7 trees ha(-1); population area=10 km(2)). 649 progeny from these trees were genotyped at eight microsatellite loci. We estimated genetic diversity, spatial genetic structure, indirect contemporary pollen flow and mating patterns for adults older than the clearance events and open-pollinated progeny sired post-clearance. A proxy of early stage progeny viability was assessed in a common garden experiment. Density had no impact on mating patterns, adult and progeny genetic diversity or progeny growth, but was associated with increased mean pollen dispersal. Weak spatial genetic structure among adults suggests high historical gene flow. We observed preliminary evidence for inbreeding depression related to stress caused by fungal infection, but which was not associated with density. Higher observed heterozygosities in adults compared with progeny may relate to weak selection on progeny and lifetime-accumulated mortality of inbred adults. E. incrassata appears to be resistant to the negative mating pattern and fitness changes expected within fragmented landscapes. This pattern is likely explained by strong outcrossing and regular long-distance pollen flow.

Biological invasions, climate change and genomics

The rate of biological invasions is expected to increase as the effects of climate change on biological communities become widespread. Climate change enhances habitat disturbance which facilitates the establishment of invasive species, which in turn provides opportunities for hybridization and introgression. These effects influence local biodiversity that can be tracked through genetic and genomic approaches. Metabarcoding and metagenomic approaches provide a way of monitoring some types of communities under climate change for the appearance of invasives. Introgression and hybridization can be followed by the analysis of entire genomes so that rapidly changing areas of the genome are identified and instances of genetic pollution monitored. Genomic markers enable accurate tracking of invasive species' geographic origin well beyond what was previously possible. New genomic tools are promoting fresh insights into classic questions about invading organisms under climate change, such as the role of genetic variation, local adaptation and climate pre-adaptation in successful invasions. These tools are providing managers with often more effective means to identify potential threats, improve surveillance and assess impacts on communities. We provide a framework for the application of genomic techniques within a management context and also indicate some important limitations in what can be achieved.

Microsatellite resources of Eucalyptus: current status and future perspectives

Eucalyptus is the premier paper pulp, short rotation plantation species grown all over the world. Genetic improvement programs integrating molecular marker tools are in progress in many parts of the globe to increase the productivity. Whole genome sequence and expressed sequence tags (ESTs) of the eucalypts paved way for introduction of molecular genetics and breeding in this genus. Different molecular characterization approaches have been used simultaneously in eucalypts, however, microsatellites or simple sequence repeats (SSRs) with their prolific characteristics could occupy a special niche in Eucalyptus genetic improvement. Further, highly informative SSRs were used for the clonal identity, genetic fidelity and in certification of breeder's rights. Eucalyptus genetic linkage maps generated with microsatellite loci were used successfully to identify quantitative trait loci (QTLs) for various economically important traits. Progressively more numbers of microsatellites are being linked to genes associated with adaptive and functional variations, therefore making their utility broader in genetic applications. Availability of common SSR markers across the species provides an opportunity to validate the expression of QTLs across variable genetic backgrounds and accurately compare the position of QTLs in other species. Recent evidences suggest that the presence of SSRs in micro RNAs of plant species play a role in the quantitative trait expression. Similar studies in eucalypts may provide new insights into the genetic architecture of transcript-level variations and post transcriptional gene regulation. This review on eucalypts microsatellites, highlights the availability and characteristics of genomic and eSSRs and their potential in genetic analysis of natural and breeding populations and also discusses the future prospects in population genetics and marker assisted selection.

Adaptive consequences of human-mediated introgression for indigenous tree species: the case of a relict Pinus pinaster population

Human-induced gene movement via afforestation and restoration programs is a widespread phenomenon throughout the world. However, its effects on the genetic composition of native populations have received relatively little attention, particularly in forest trees. Here, we examine to what extent gene flow from allochthonous plantations of Pinus pinaster Aiton impacts offspring performance in a neighboring relict natural population and discuss the potential consequences for the long-term genetic composition of the latter. Specifically, we conducted a greenhouse experiment involving two contrasting watering treatments to test for differences in a set of functional traits and mortality rates between P. pinaster progenies from three different parental origins: (i) local native parents, (ii) exotic parents and (iii) intercrosses between local mothers and exotic fathers (intraspecific hybrids). Our results showed differences among crosses in cumulative mortality over time: seedlings of exotic parents exhibited the lowest mortality rates and seedlings of local origin the highest, while intraspecific hybrids exhibited an intermediate response. Linear regressions showed that seedlings with higher water-use efficiency (WUE, δ(13)C) were more likely to survive under drought stress, consistent with previous findings suggesting that WUE has an important role under dry conditions in this species. However, differences in mortality among crosses were only partially explained by WUE. Other non-measured traits and factors such as inbreeding depression in the relict population are more likely to explain the lower performance of native progenies. Overall, our results indicated that intraspecific hybrids and exotic individuals are more likely to survive under stressful conditions than local native individuals, at least during the first year of development. Since summer drought is the most important demographic and selective filter affecting tree establishment in Mediterranean ecosystems, a potential early selective advantage of exotic and hybrid genotypes would enhance initial steps of introgression of non-native genes into the study relict population of P. pinaster.

Signatures of diversifying selection at EST-SSR loci and association with climate in natural Eucalyptus populations

Understanding the environmental parameters that drive adaptation among populations is important in predicting how species may respond to global climatic changes and how gene pools might be managed to conserve adaptive genetic diversity. Here, we used Bayesian FST outlier tests and allele-climate association analyses to reveal two Eucalyptus EST-SSR loci as strong candidates for diversifying selection in natural populations of a southwestern Australian forest tree, Eucalyptus gomphocephala (Myrtaceae). The Eucalyptus homolog of a CONSTANS-like gene was an FST outlier, and allelic variation showed significant latitudinal clinal associations with annual and winter solar radiation, potential evaporation, summer precipitation and aridity. A second FST outlier locus, homologous to quinone oxidoreductase, was significantly associated with measures of temperature range, high summer temperature and summer solar radiation, with important implications for predicting the effect of temperature on natural populations in the context of climate change. We complemented these data with investigations into neutral population genetic structure and diversity throughout the species range. This study provides an investigation into selection signatures at gene-homologous EST-SSRs in natural Eucalyptus populations, and contributes to our understanding of the relationship between climate and adaptive genetic variation, informing the conservation of both putatively neutral and adaptive components of genetic diversity.

Thank you for not flowering: conservation genetics and gene flow analysis of native and non-native populations of Fraxinus (Oleaceae) in Ireland

The risks of gene flow between interfertile native and introduced plant populations are greatest when there is no spatial isolation of pollen clouds and phenological patterns overlap completely. Moreover, invasion probabilities are further increased if introduced populations are capable of producing seeds by selfing. Here we investigated the mating system and patterns of pollen-mediated gene flow among populations of native ash (Fraxinus excelsior) and mixed plantations of non-native ash (F. angustifolia and F. excelsior) as well as hybrid ash (F. excelsior × F. angustifolia) in Ireland. We analysed the flowering phenology of the mother trees and genotyped with six microsatellite loci in progeny arrays from 132 native and plantation trees (1493 seeds) and 444 potential parents. Paternity analyses suggested that plantation and native trees were pollinated by both native and introduced trees. No signs of significant selfing in the introduced trees were observed and no evidence of higher male reproductive success was found for introduced trees compared with native ones either. A small but significant genetic structure was found (φft=0.05) and did not correspond to an isolation-by-distance pattern. However, we observed a significant temporal genetic structure related to the different phenological groups, especially with early and late flowering native trees; each phenological group was pollinated with distinctive pollen sources. Implications of these results are discussed in relation to the conservation and invasiveness of ash and the spread of resistance genes against pathogens such as the fungus Chalara fraxinea that is destroying common ash forests in Europe.

Human-impacted landscapes facilitate hybridization between a native and an introduced tree

Spatial and temporal dynamics of hybridization, in particular the influence of local environmental conditions, are well studied for sympatric species but less is known for native-introduced systems, especially for long-lived species. We used microsatellite and chloroplast DNA markers to characterize the influence of anthropogenic landscapes on the extent, direction, and spatial distribution of hybridization between a native North American tree Juglans cinerea (butternut) and an introduced tree Juglans ailantifolia (Japanese walnut) for 1363 trees at 48 locations across the native range of butternut. Remarkably, admixture in anthropogenic sites reached nearly 70%, while fragmented and continuous forests showed minimal admixture (<8%). Furthermore, more hybrids in anthropogenic sites had J. ailantifolia seed parents (95%) than hybrids in fragmented and continuous forests (69% and 59%, respectively). Our results show a strong influence of landscape type on rate and direction of realized gene flow. While hybrids are common in anthropogenic landscapes, our results suggest that even small forested landscapes serve as substantial barriers to hybrid establishment, a key consideration for butternut conservation planning, a species already exhibiting severe decline, and for other North American forest trees that hybridize with introduced congeners.

Native bees mediate long-distance pollen dispersal in a shade coffee landscape mosaic

Coffee farms are often embedded within a mosaic of agriculture and forest fragments in the world's most biologically diverse tropical regions. Although shade coffee farms can potentially support native pollinator communities, the degree to which these pollinators facilitate gene flow for native trees is unknown. We examined the role of native bees as vectors of gene flow for a reproductively specialized native tree, Miconia affinis, in a shade coffee and remnant forest landscape mosaic. We demonstrate extensive cross-habitat gene flow by native bees, with pollination events spanning more than 1,800 m. Pollen was carried twice as far within shade coffee habitat as in nearby forest, and trees growing within shade coffee farms received pollen from a far greater number of sires than trees within remnant forest. The study shows that shade coffee habitats support specialized native pollinators that enhance the fecundity and genetic diversity of remnant native trees.

Populations of weedy crop-wild hybrid beets show contrasting variation in mating system and population genetic structure

Reproductive traits are key parameters for the evolution of invasiveness in weedy crop–wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop–wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop–wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management.

Comparison of contemporary mating patterns in continuous and fragmented Eucalyptus globulus native forests

While habitat fragmentation is a central issue in forest conservation studies in the face of broad-scale anthropogenic changes to the environment, its effects on contemporary mating patterns remain controversial. This is partly because of the inherent variation in mating patterns which may exist within species and the fact that few studies have replication at the landscape level. To study the effect of forest fragmentation on contemporary mating patterns, including effective pollen dispersal, we compared four native populations of the Australian forest tree, Eucalyptus globulus. We used six microsatellite markers to genotype 1289 open-pollinated offspring from paired fragmented and continuous populations on the island of Tasmania and in Victoria on mainland Australia. The mating patterns in the two continuous populations were similar, despite large differences in population density. In contrast, the two fragmented populations were variable and idiosyncratic in their mating patterns, particularly in their pollen dispersal kernels. The continuous populations showed relatively high outcrossing rates (86-89%) and low correlated paternity (0.03-0.06) compared with the fragmented populations (65-79% and 0.12-0.20 respectively). A greater proportion of trees contributed to reproduction in the fragmented (de/d>or= 0.5) compared with the continuous populations (de/d = 0.03-0.04). Despite significant inbreeding in the offspring of the fragmented populations, there was little evidence of loss of genetic diversity. It is argued that enhanced medium- and long-distance dispersal in fragmented landscapes may act to partly buffer the remnant populations from the negative effects of inbreeding and drift.

Estimation of outcrossing rates at hierarchical levels of fruits, individuals, populations and species in Magnolia stellata

In plant species with mixed mating systems, differences in diverse factors-including their pollination system, flowering phenology, life form and susceptibility to inbreeding depression-cause variation in outcrossing rates among fruits within individuals, among individuals within populations and among populations within species. To quantify this hierarchical variation, we examined outcrossing rates at the seed stage in five populations of Magnolia stellata, a self-compatible, insect-pollinated and protogynous tree species. For this purpose, we sampled 1498 seeds within 204 fruits obtained from 56 individuals of the five populations, determined genotypes of the sampled seeds and maternal individuals at six polymorphic microsatellite loci, then estimated outcrossing rates and their variance components at four hierarchical levels (fruits, individuals, populations and species) using a nested analysis of variance-type linear model with a Bayesian approach. The species-level outcrossing rate was 0.730 (95% credible interval, 0.595-0.842), indicating that this species has a mixed mating system. Outcrossing rates were not significantly different among populations, but were significantly different among individuals within populations. Variance components at the levels of individual and fruit were statistically supported and were highest for the former. Thus, factors influencing outcrossing rates at the individual level, such as differences in flowering phenology and early-stage inbreeding depression, appear to have important effects within these M. stellata populations, but not among them. The method of hierarchically estimating outcrossing rates using a Bayesian approach, as applied in this study, is compared with conventional methods for estimating outcrossing rates, and the statistical properties of the Bayesian approach are discussed.