Genetic Structure of Threatened Native Populations and Propagules Used for Restoration in a Clonal Species, American Beachgrass (Ammophila breviligulataFern.)

Why are some plant species missing from restorations? A diagnostic tool for temperate grassland ecosystems

The U.N. Decade on Ecosystem Restoration aims to accelerate actions to prevent, halt, and reverse the degradation of ecosystems, and re-establish ecosystem functioning and species diversity. The practice of ecological restoration has made great progress in recent decades, as has recognition of the importance of species diversity to maintaining the long-term stability and functioning of restored ecosystems. Restorations may also focus on specific species to fulfill needed functions, such as supporting dependent wildlife or mitigating extinction risk. Yet even in the most carefully planned and managed restoration, target species may fail to germinate, establish, or persist. To support the successful reintroduction of ecologically and culturally important plant species with an emphasis on temperate grasslands, we developed a tool to diagnose common causes of missing species, focusing on four major categories of filters, or factors: genetic, biotic, abiotic, and planning & land management. Through a review of the scientific literature, we propose a series of diagnostic tests to identify potential causes of failure to restore target species, and treatments that could improve future outcomes. This practical diagnostic tool is meant to strengthen collaboration between restoration practitioners and researchers on diagnosing and treating causes of missing species in order to effectively restore them.

Testing for evolutionary change in restoration: A genomic comparison between ex situ, native, and commercial seed sources of Helianthus maximiliani

Globally imperiled ecosystems often depend upon collection, propagation, and storage of seed material for use in restoration. However, during the restoration process demographic changes, population bottlenecks, and selection can alter the genetic composition of seed material, with potential impacts for restoration success. The evolutionary outcomes associated with these processes have been demonstrated using theoretical and experimental frameworks, but no study to date has examined their impact on the seed material maintained for conservation and restoration. In this study, we compare genomic variation across seed sources used in conservation and restoration for the perennial prairie plant Helianthus maximiliani, a key component of restorations across North American grasslands. We compare individuals sourced from contemporary wild populations, ex situ conservation collections, commercially produced restoration material, and two populations selected for agronomic traits. Overall, we observed that ex situ and contemporary wild populations exhibited similar genomic composition, while four of five commercial populations and selected lines were differentiated from each other and other seed source populations. Genomic differences across seed sources could not be explained solely by isolation by distance nor directional selection. We did find evidence of sampling effects for ex situ collections, which exhibited significantly increased coancestry relative to commercial populations, suggesting increased relatedness. Interestingly, commercially sourced seed appeared to maintain an increased number of rare alleles relative to ex situ and wild contemporary seed sources. However, while commercial seed populations were not genetically depauperate, the genomic distance between wild and commercially produced seed suggests differentiation in the genomic composition could impact restoration success. Our results point toward the importance of genetic monitoring of seed sources used for conservation and restoration as they are expected to be influenced by the evolutionary processes that contribute to divergence during the restoration process.

Managing Genetic Diversity and Representation in Banksia marginata (Proteaceae) Seed Production Areas Used for Conservation and Restoration

Landscape degradation is a major threat to global biodiversity that is being further exacerbated by climate change. Halting or reversing biodiversity decline using seed-based restoration requires tons of seed, most of which is sourced from wild populations. However, in regions where restoration is most urgent, wild seed sources are often fragmented, declining and producing seed with low genetic diversity. Seed production areas (SPAs) can help to reduce the burden of collecting native seed from remnant vegetation, improve genetic diversity in managed seed crops and contribute to species conservation. Banksia marginata (Proteaceae) is a key restoration species in south-eastern Australia but is highly fragmented and declining across much of its range. We evaluated genetic diversity, population genetic structure and relatedness in two B. marginata SPAs and the wild populations from which the SPA germplasm was sourced. We found high levels of relatedness within most remnants and that the population genetic structure was best described by three groups of trees. We suggest that SPAs are likely to be important to meet future native seed demand but that best practice protocols are required to assist land managers design and manage these resources including genetic analyses to guide the selection of germplasm.

How well do revegetation plantings capture genetic diversity?

Revegetation plantings are a key management tool for ecological restoration. Revegetation success is usually measured using ecological traits, however, genetic diversity should also be considered as it can influence fitness, adaptive capacity and long-term viability of revegetation plantings and ecosystem functioning. Here we review the global literature comparing genetic diversity in revegetation plantings to natural stands. Findings from 48 studies suggest variable genetic outcomes of revegetation, with 46% demonstrating higher genetic diversity in revegetation than natural stands and 52% demonstrating lower diversity. Levels of genetic diversity were most strongly associated with the number of source sites used-where information was available, 69% of studies showing higher genetic diversity in revegetation reported using multiple provenances, compared with only 33% for those with lower diversity. However, with a few exceptions, it was unclear whether differences in genetic diversity between revegetation and natural stands were statistically significant. This reflected insufficient reporting of statistical error and metadata within the published studies, which limited conclusions about factors contributing to patterns. Nonetheless, our findings indicate that mixed seed sourcing can contribute to higher genetic diversity in revegetation. Finally, we emphasize the type of metadata needed to determine factors influencing genetic diversity in revegetation and inform restoration efforts.

Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species

Achieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long-term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay transfer between 1997 and 2014. RAD-seq genotyping revealed that the stenoecious floodplain species Arabis nemorensis is co-occurring with individuals that, based on ploidy, ITS-sequencing and morphology, probably belong to the close relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay transfer maintains genetic diversity for both species. Additionally, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay transfer on genetic diversity also depend on the genetic make-up of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay transfer for habitat restoration and emphasize the importance of prerestoration characterization of microgeographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, that is maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo- and reference-based RAD-seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.

Can local adaptation research in plants inform selection of native plant materials? An analysis of experimental methodologies

Local adaptation is used as a criterion to select plant materials that will display high fitness in new environments. A large body of research has explored local adaptation in plants, however, to what extent findings can inform management decisions has not been formally evaluated. We assessed local adaptation literature for six key experimental methodologies that have the greatest effect on the application of research to selecting plant materials for natural resource management: experimental environment, response variables, maternal effects, intraspecific variation, selective agents, and spatial and temporal variability. We found that less than half of experiments used reciprocal transplants or natural field conditions, which are both informative for revegetation and restoration. Population growth rate was rarely (5%) assessed, and most studies measured only single generations (96%) and ran for less than a year. Emergence and establishment are limiting factors in successful revegetation and restoration, but the majority of studies measured later life‐history stages (66%). Additionally, most studies included limited replication at the population and habitat levels and tested response to single abiotic selective factors (66%). Local adaptation research should be cautiously applied to management; future research could use alternative methodologies to allow managers to directly apply findings.

Fungal symbiosis and precipitation alter traits and dune building by the ecosystem engineer, Ammophila breviligulata

Ecosystem engineer species influence their community and ecosystem by creating or altering the physical structure of habitats. The function of ecosystem engineers is variable and can depend on both abiotic and biotic factors. Here we make use of a primary successional system to evaluate the direct and interactive effects of climate change (precipitation) and fungal endophyte symbiosis on population traits and ecosystem function of the ecosystem engineering grass species, Ammophila breviligulata. We manipulated endophyte presence in A. breviligulata in combination with rain-out shelters and rainfall additions in a factorial field experiment established in 2010 on Lake Michigan sand dunes. We monitored plant traits, survival, growth, and sexual reproduction of A. breviligulata from 2010-2013, and quantified ecosystem engineering as the sand accumulation rate. Presence of the endophyte in A. breviligulata increased vegetative growth by up to 19%, and reduced sexual reproduction by up to 46% across all precipitation treatments. Precipitation was a less significant factor than endophyte colonization for A. breviligulata growth. Reduced precipitation increased average leaf number per tiller but had no other effects on plant traits. Changes in A. breviligulata traits corresponded to increases in sand accumulation in plots with the endophyte as well as in plots with reduced precipitation. Sand accumulation is a key ecosystem function in these primary successional habitats, and so microbial symbiosis in this ecosystem engineer could lead to direct effects on the value of these dune habitats for humans.

Next generation restoration genetics: applications and opportunities

Restoration ecology is a young scientific discipline underpinning improvements in the rapid global expansion of ecological restoration. The application of molecular tools over the past 20 years has made an important contribution to understanding genetic factors influencing ecological restoration success. Here we illustrate how recent advances in next generation sequencing (NGS) methods are revolutionising the practical contribution of genetics to restoration. Novel applications include a dramatically enhanced capacity to measure adaptive variation for optimal seed sourcing, high-throughput assessment and monitoring of natural and restored biological communities aboveground and belowground, and gene expression analysis as a measure of genetic resilience of restored populations. Challenges remain in data generation, handling and analysis, and how best to apply NGS for practical outcomes in restoration.

No effect of seed source on multiple aspects of ecosystem functioning during ecological restoration: cultivars compared to local ecotypes of dominant grasses

Genetic principles underlie recommendations to use local seed, but a paucity of information exists on the genetic distinction and ecological consequences of using different seed sources in restorations. We established a field experiment to test whether cultivars and local ecotypes of dominant prairie grasses were genetically distinct and differentially influenced ecosystem functioning. Whole plots were assigned to cultivar and local ecotype grass sources. Three subplots within each whole plot were seeded to unique pools of subordinate species. The cultivar of the increasingly dominant grass, Sorghastrum nutans, was genetically different than the local ecotype, but genetic diversity was similar between the two sources. There were no differences in aboveground net primary production, soil carbon accrual, and net nitrogen mineralization rate in soil between the grass sources. Comparable productivity of the grass sources among the species pools for four years shows functional equivalence in terms of biomass production. Subordinate species comprised over half the aboveground productivity, which may have diluted the potential for documented trait differences between the grass sources to influence ecosystem processes. Regionally developed cultivars may be a suitable alternative to local ecotypes for restoration in fragmented landscapes with limited gene flow between natural and restored prairie and negligible recruitment by seed.

Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community

Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species diversity and genetic diversity interact to influence community structure may be critically important for predicting the consequences of biodiversity loss.

Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape

Connecting broad-scale patterns of genetic variation and population structure to genetic diversity on a landscape is a key step towards understanding historical processes of migration and adaptation. New genomic approaches can be used to increase the resolution of phylogeographic studies while reducing locus sampling effects and circumventing ascertainment bias. Here, we use a novel approach based on high-throughput sequencing to characterize genetic diversity in complete chloroplast genomes and >10,000 nuclear loci in switchgrass, at continental and landscape scales. Switchgrass is a North American tallgrass species, which is widely used in conservation and perennial biomass production, and shows strong ecotypic adaptation and population structure across the continental range. We sequenced 40.9 billion base pairs from 24 individuals from across the species' range and 20 individuals from the Indiana Dunes. Analysis of plastome sequence revealed 203 variable SNP sites that define eight haplogroups, which are differentiated by 4-127 SNPs and confirmed by patterns of indel variation. These include three deeply divergent haplogroups, which correspond to the previously described lowland-upland ecotypic split and a novel upland haplogroup split that dates to the mid-Pleistocene. Most of the plastome haplogroup diversity present in the northern switchgrass range, including in the Indiana Dunes, originated in the mid- or upper Pleistocene prior to the most recent postglacial recolonization. Furthermore, a recently colonized landscape feature (approximately 150 ya) in the Indiana Dunes contains several deeply divergent upland haplogroups. Nuclear markers also support a deep lowland-upland split, followed by limited gene flow, and show extensive gene flow in the local population of the Indiana Dunes.

Restoration of coral populations in light of genetic diversity estimates

Due to the importance of preserving the genetic integrity of populations, strategies to restore damaged coral reefs should attempt to retain the allelic diversity of the disturbed population; however, genetic diversity estimates are not available for most coral populations. To provide a generalized estimate of genetic diversity (in terms of allelic richness) of scleractinian coral populations, the literature was surveyed for studies describing the genetic structure of coral populations using microsatellites. The mean number of alleles per locus across 72 surveyed scleractinian coral populations was 8.27 (±0.75 SE). In addition, population genetic datasets from four species (Acropora palmata, Montastraea cavernosa, Montastraea faveolata and Pocillopora damicornis) were analyzed to assess the minimum number of donor colonies required to retain specific proportions of the genetic diversity of the population. Rarefaction analysis of the population genetic datasets indicated that using 10 donor colonies randomly sampled from the original population would retain >50% of the allelic diversity, while 35 colonies would retain >90% of the original diversity. In general, scleractinian coral populations are genetically diverse and restoration methods utilizing few clonal genotypes to re-populate a reef will diminish the genetic integrity of the population. Coral restoration strategies using 10-35 randomly selected local donor colonies will retain at least 50-90% of the genetic diversity of the original population.