Mixing source populations increases genetic diversity of restored rare plant populations

Species-specific effects of production practices on genetic diversity in plant reintroduction programs

Plant production practices can influence the genetic diversity of cultivated plant materials and, ultimately, their potential to adapt to a reintroduction site. A common step in the plant production process is the application of seed pretreatment to alleviate physiological seed dormancy and successfully germinate seeds. In production settings, the seeds that germinate more rapidly may be favored in order to fill plant quotas. In this study, we investigated how the application of cold-moist stratification treatments with different durations can lead to differences in the genetic diversity of the propagated plant materials. Specifically, we exposed seeds of three Viola species to two different cold stratification durations, and then we analyzed the genetic diversity of the resulting subpopulations through double-digestion restriction site-associated sequencing (ddRADseq). Our results show that, in two out of three species, utilizing a short stratification period will decrease the genetic diversity of neutral and expressed loci, likely due to the imposition of a genetic bottleneck and artificial selection. We conclude that, in some species, the use of minimal stratification practices in production may jeopardize the adaptive potential and long-term persistence of reintroduced populations and suggest that practitioners carefully consider the evolutionary implications of their production protocols. We highlight the need to consider the germination ecology of target species when selecting the length of dormancy-breaking pretreatments.

Host genetic identity determines parasite community structure across time and space in oyster restoration

Intraspecific variation in host susceptibility to individual parasite species is common, yet how these effects scale to mediate the structure of diverse parasite communities in nature is less well understood. To address this knowledge gap, we tested how host genetic identity affects parasite communities on restored reefs seeded with juvenile oysters from different sources-a regional commercial hatchery or one of two wild progenitor lines. We assessed prevalence and intensity of three micro- and two macroparasite species for 4 years following restoration. Despite the spatial proximity of restored reefs, oyster source identity strongly predicted parasite community prevalence across all years, with sources varying in their relative susceptibility to different parasites. Oyster seed source also predicted reef-level parasite intensities across space and through time. Our results highlight that host intraspecific variation can shape parasite community structure in natural systems, and reinforce the importance of considering source identity and diversity in restoration design.

High Prevalence of Clonal Reproduction and Low Genetic Diversity in Scutellaria floridana, a Federally Threatened Florida-Endemic Mint

The threatened mint Florida skullcap (Scutellaria floridana) is endemic to four counties in the Florida panhandle. Because development and habitat modification extirpated several historical occurrences, only 19 remain to date. To inform conservation management and delisting decisions, a comprehensive investigation of the genetic diversity and relatedness, population structure, and clonal diversity was conducted using SNP data generated by ddRAD. Compared with other Lamiaceae, we detected low genetic diversity (H_E = 0.125-0.145), low to moderate evidence of inbreeding (F_IS = -0.02-0.555), and moderate divergence (F_ST = 0.05-0.15). We identified eight populations with most of the genetic diversity, which should be protected in situ, and four populations with low genetic diversity and high clonality. Clonal reproduction in our circular plots and in 92% of the sites examined was substantial, with average clonal richness of 0.07 and 0.59, respectively. Scutellaria floridana appears to have experienced a continued decline in the number of extant populations since its listing under the Endangered Species Act; still, the combination of sexual and asexual reproduction may be advantageous for maintaining the viability of extant populations. However, the species will likely require ongoing monitoring, management, and increased public awareness to ensure its survival and effectively conserve its genetic diversity.

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.

Supporting long-term sustainability of ex situ collections using a pedigree-based population management approach

PREMISE

Living collections maintained for generations are at risk of diversity loss, inbreeding, and adaptation to cultivation. To address these concerns, the zoo community uses pedigrees to track individuals and implement crosses that maximize founder contributions and minimize inbreeding. Using a pedigree management approach, we demonstrate how conducting strategic crosses can minimize genetic issues that have arisen under current practices.

METHODS

We performed crosses between collections and compared progeny fitness, including plant performance and reproductive health. We genotyped the progeny and parental accessions to measure changes in diversity and relatedness within and between accessions.

RESULTS

The mean relatedness values among individuals within each accession suggest they are full siblings, demonstrating that there was high inbreeding and low diversity within accessions, although less so among accessions. Progeny from the wider crosses had increased genetic diversity and were larger and more fertile, while self-pollinated accessions were smaller and less fertile.

DISCUSSION

Institutions that hold exceptional species should consider how diversity is maintained within their collections. Implementing a pedigree-based approach to managing plant reproduction ex situ will slow the inevitable loss of genetic diversity and, in turn, result in healthier collections.

Overcoming biotic homogenization in ecological restoration

Extensive evidence shows that regional (gamma) diversity is often lower across restored landscapes than in reference landscapes, in part due to common restoration practices that favor widespread species through selection of easily-grown species with high survival and propagation practices that reduce genetic diversity. We discuss approaches to counteract biotic homogenization, such as reintroducing species that are adapted to localized habitat conditions and are unlikely to colonize naturally; periodically reintroducing propagules from remnant populations to increase genetic diversity; and reintroducing higher trophic level fauna to restore interaction networks and processes that promote habitat heterogeneity. Several policy changes would also increase regional diversity; these include regional coordination amongst restoration groups, financial incentives to organizations producing conservation-valued species, and experimental designations for rare species introductions.

Assessing Population Genetic Status for Designing Plant Translocations

Assisted gene flow interventions such as plant translocations are valuable complementary techniques to habitat restoration. Bringing new genetic variants can contribute to increasing genetic diversity and evolutionary resilience, counteract inbreeding depression and improve plant fitness through heterosis. Large, highly genetically variable populations are usually recommended as sources for translocation. Unfortunately, many critically endangered species only occur as small populations, which are expected to show low genetic variation, high inbreeding level, paucity of compatible mates in self-incompatible species, and increased genetic divergence. Therefore, assessment of population genetic status is required for an appropriate choice of the source populations. In this paper, we exemplify the different analyses relevant for genetic evaluation of populations combining both molecular (plastid and nuclear) markers and fitness-related quantitative traits. We assessed the genetic status of the adult generation and their seed progeny (the potential translocation founders) of small populations of Campanula glomerata (Campanulaceae), a self-incompatible insect-pollinated herbaceous species critically endangered in Belgium. Only a few small populations remain, so that the species has been part of a restoration project of calcareous grasslands implementing plant translocations. In particular, we estimated genetic diversity, inbreeding levels, genetic structure in adults and their seed progeny, recent bottlenecks, clonal extent in adults, contemporary gene flow, effective population size (Ne), and parentage, sibship and seed progeny fitness variation. Small populations of C. glomerata presented high genetic diversity, and extensive contemporary pollen flow within populations, with multiple parentage among seed progenies, and so could be good seed source candidates for translocations. As populations are differentiated from each other, mixing the sources will not only optimize the number of variants and of compatible mates in translocated populations, but also representativeness of species regional genetic diversity. Genetic diversity is no immediate threat to population persistence, but small Ne, restricted among-population gene flow, and evidence of processes leading to genetic erosion, inbreeding and inbreeding depression in the seed progeny require management measures to counteract these trends and stochastic vulnerability. Habitat restoration facilitating recruitment, flowering and pollination, reconnecting populations by biological corridors or stepping stones, and creating new populations through translocations in protected areas are particularly recommended.

Guidelines for genetic monitoring of translocated plant populations

Plant translocation is a useful tool for implementing assisted gene flow in recovery plans of critically endangered plant species. Although it helps to restore genetically viable populations, it is not devoid of genetic risks, such as poor adaptation of transplants and outbreeding depression in the hybrid progeny, which may have negative consequences in terms of demographic growth and plant fitness. Hence, a follow-up genetic monitoring should evaluate whether the translocated populations are genetically viable and self-sustaining in the short and long term. The causes of failure to adjust management responses also need to be identified. Molecular markers and fitness-related quantitative traits can be used to determine whether a plant translocation enhanced genetic diversity, increased fitness, and improved the probability of long-term survival. We devised guidelines and illustrated them with studies from the literature to help practitioners determine the appropriate genetic survey methods so that management practices can better integrate evolutionary processes. These guidelines include methods for sampling and for assessing changes in genetic diversity and differentiation, contemporary gene flow, mode of local recruitment, admixture level, the effects of genetic rescue, inbreeding or outbreeding depression and local adaptation on plant fitness, and long-term genetic changes.

Mixing gene pools to prevent inbreeding issues in translocated populations of clonal species

Assisted gene flow by plant translocations is increasingly implemented for restoring populations of critically endangered species. The success in restoring genetically healthy populations may depend on translocation design, in particular the choice of the source populations. Highly clonal populations may show low genetic diversity despite large census sizes, and disrupted and geitonogamous pollination may result in selfing and inbreeding issues in the offspring intended for translocation. We carried out a genetic monitoring of translocated populations of the clonal Dianthus deltoides using 14 microsatellite markers and quantified fitness traits over two generations (transplants, F1 seed progeny and newly established individuals). Inbreeding levels were higher in the offspring used as transplants than in the adult generation of the source populations, as a result of high clonality and pollination disruption leading to self-pollination. The F1 generation in translocated populations showed high genetic diversity maintained across generations, diminished inbreeding levels, low genetic differentiation, pollen flow and genetic mixing between the four sources. New individuals were established from seed germination. Fitness patterns were a combination of inbreeding depression in inbred transplants and F1 progeny, heterosis in admixed F1 progeny, source population adaptive capacities, phenotypic plasticity, maternal effects and site environmental specificities. The strategy in the translocation design to mix several local sources, combined with large founding population sizes and ecological management has proved success in initiating the processes leading to the establishment of genetically healthy populations, even when source populations are highly clonal with low genetic diversity leading to inbreeding issues in the transplants.

Perceptions of Similarity Can Mislead Provenancing Strategies—An Example from Five Co-Distributed Acacia Species

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts.