Using environmental and geographic data to optimize ex situ collections and preserve evolutionary potential

Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation

Understanding the contribution of neutral and adaptive evolutionary processes to population differentiation is often necessary for better informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world's rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species' evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to identify loci possibly under selection, and evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation within both Torrey pine populations, reflecting consistently low effective population sizes across time, and limited genetic differentiation, suggesting maintenance of gene flow between populations following divergence. However, genome scans identified more than 2000 candidate SNPs potentially under divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates natural selection has likely contributed to the evolution of population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effects of rarity, evidence for adaptive differentiation suggests genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.

Seed morphological traits as a tool to quantify variation maintained in ex situ collections: a case study in Pinus torreyana

Understanding the within- and among-population distribution of trait variation within seed collections may provide a means to approximate standing genetic variation and inform plant conservation. This study aimed to estimate population- and family-level seed trait variability for existing seed collections of Torrey pine (Pinus torreyana), and to use these data to guide sampling of future collections. We quantified variation in 14 seed morphological traits and seedling emergence within and among Torrey pine populations. Using a simulation-based approach, we used estimates of within-population variance to assess the number of maternal families required to capture 95 % of trait variation within each existing seed collection. Substantial structure was observed both within and among Torrey pine populations, with island and mainland seeds varying in seed size and seed coat thickness. Despite morphological differences, seedling emergence was similar across populations. Simulations revealed that 83 % and 71 % of all maternal families within island and mainland seed collections respectively needed to be resampled to capture 95 % of seed trait variation within existing collections. From a conservation perspective, our results indicate that to optimize genetic diversity captured in Torrey pine seed collections, maximizing the number of maternal families sampled within each population will be necessary.

The relevance of pedigrees in the conservation genomics era

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.

Maximizing genetic representation in seed collections from populations of self and cross-pollinated banana wild relatives

BACKGROUND

Conservation of plant genetic resources, including the wild relatives of crops, plays an important and well recognised role in addressing some of the key challenges faced by humanity and the planet including ending hunger and biodiversity loss. However, the genetic diversity and representativeness of ex situ collections, especially that contained in seed collections, is often unknown. This limits meaningful assessments against conservation targets, impairs targeting of future collecting and limits their use. We assessed genetic representation of seed collections compared to source populations for three wild relatives of bananas and plantains. Focal species and sampling regions were M. acuminata subsp. banksii (Papua New Guinea), M. balbisiana (Viet Nam) and M. maclayi s.l. (Bougainville, Papua New Guinea). We sequenced 445 samples using suites of 16-20 existing and newly developed taxon-specific polymorphic microsatellite markers. Samples of each species were from five populations in a region; 15 leaf samples from different individuals and 16 seed samples from one infructescence ('bunch') were analysed for each population.

RESULTS

Allelic richness of seeds compared to populations was 51, 81 and 93% (M. acuminata, M. balbisiana and M. maclayi respectively). Seed samples represented all common alleles in populations but omitted some rarer alleles. The number of collections required to achieve the 70% target of the Global Strategy for Plant Conservation was species dependent, relating to mating systems. Musa acuminata populations had low heterozygosity and diversity, indicating self-fertilization; many bunches were needed (> 15) to represent regional alleles to 70%; over 90% of the alleles from a bunch are included in only two seeds. Musa maclayi was characteristically cross-fertilizing; only three bunches were needed to represent regional alleles; within a bunch, 16 seeds represent alleles. Musa balbisiana, considered cross-fertilized, had low genetic diversity; seeds of four bunches are needed to represent regional alleles; only two seeds represent alleles in a bunch.

CONCLUSIONS

We demonstrate empirical measurement of representation of genetic material in seeds collections in ex situ conservation towards conservation targets. Species mating systems profoundly affected genetic representation in seed collections and therefore should be a primary consideration to maximize genetic representation. Results are applicable to sampling strategies for other wild species.

Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

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.

Local Adaptation in Marine Foundation Species at Microgeographic Scales

AbstractNearshore foundation species in coastal and estuarine systems (e.g., salt marsh grasses, mangroves, seagrasses, corals) drive the ecological functions of ecosystems and entire biomes by creating physical structure that alters local abiotic conditions and influences species interactions and composition. The resilience of foundation species and the ecosystem functions they provide depends on their phenotypic and genetic responses to spatial and temporal shifts in environmental conditions. In this review, we explore what is known about the causes and consequences of adaptive genetic differentiation in marine foundation species over spatial scales shorter than dispersal capabilities (i.e., microgeographic scales). We describe the strength of coupling field and laboratory experiments with population genetic techniques to illuminate patterns of local adaptation, and we illustrate this approach by using several foundation species. Among the major themes that emerge from our review include (1) adaptive differentiation of marine foundation species repeatedly evolves along vertical (i.e., elevation or depth) gradients, and (2) mating system and phenology may facilitate this differentiation. Microgeographic adaptation is an understudied mechanism potentially underpinning the resilience of many sessile marine species, and this evolutionary mechanism likely has particularly important consequences for the ecosystem functions provided by foundation species.

Genetic relationships and low diversity among the tea-oil Camellia species in Sect. Oleifera, a bulk woody oil crop in China

Tea-oil Camellia is one of the four woody oil crops in the world and has high ecological, economic and medicinal values. However, there are great differences in the classification and merging of tea-oil Camellia Sect. Oleifera species, which brings difficulties to the innovative utilization and production of tea-oil Camellia resources. Here, ISSR, SRAP and chloroplast sequence markers were analyzed in 18 populations of tea-oil Camellia Sect. Oleifera species to explore their phylogenetic relationships and genetic diversity. The results showed that their genetic diversity were low, with mean H and π values of 0.16 and 0.00140, respectively. There was high among-population genetic differentiation, with ISSR and SRAP markers showing an Fst of 0.38 and a high Nm of 1.77 and cpDNA markers showing an Fst of 0.65 and a low Nm of 0.27. The C. gauchowensis, C. vietnamensis and Hainan Island populations formed a single group, showing the closest relationships, and supported being the same species for them with the unifying name C. drupifera and classifying the resources on Hainan Island as C. drupifera. The tea-oil Camellia resources of Hainan Island should be classified as a special ecological type or variety of C. drupifera. However, cpDNA marker-based STRUCTURE analysis showed that the genetic components of the C. osmantha population formed an independent, homozygous cluster; hence, C. osmantha should be a new species in Sect. Oleifera. The C. oleifera var. monosperma and C. oleifera populations clustered into two distinct clades, and the C. oleifera var. monosperma populations formed an independent cluster, accounting for more than 99.00% of its genetic composition; however, the C. oleifera populations contained multiple different cluster components, indicating that C. oleifera var. monosperma significantly differs from C. oleifera and should be considered the independent species C. meiocarpa. Haplotype analysis revealed no rapid expansion in the tested populations, and the haplotypes of C. oleifera, C. meiocarpa and C. osmantha evolved from those of C. drupifera. Our results support the phylogenetic classification of Camellia subgenera, which is highly significant for breeding and production in tea-oil Camellia.