Conserving the genetic diversity of condemned populations: Optimizing collections and translocation

Ex situ conservation of two rare oak species using microsatellite and SNP markers

Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.

Molecular insights into the dynamics of species invasion by hybridisation in Tasmanian eucalypts

In plants where seed dispersal is limited compared with pollen dispersal, hybridisation may enhance gene exchange and species dispersal. We provide genetic evidence of hybridisation contributing to the expansion of the rare Eucalyptus risdonii into the range of the widespread Eucalyptus amygdalina. These closely related tree species are morphologically distinct, and observations suggest that natural hybrids occur along their distribution boundaries and as isolated trees or in small patches within the range of E. amygdalina. Hybrid phenotypes occur outside the range of normal dispersal for E. risdonii seed, yet in some hybrid patches small individuals resembling E. risdonii occur and are hypothesised to be a result of backcrossing. Using 3362 genome-wide SNPs assessed from 97 individuals of E. risdonii and E. amygdalina and 171 hybrid trees, we show that (i) isolated hybrids match the genotypes expected of F₁ /F₂ hybrids, (ii) there is a continuum in the genetic composition among the isolated hybrid patches from patches dominated by F₁ /F₂ -like genotypes to those dominated by E. risdonii-backcross genotypes, and (iii) the E. risdonii-like phenotypes in the isolated hybrid patches are most-closely related to proximal larger hybrids. These results suggest that the E. risdonii phenotype has been resurrected in isolated hybrid patches established from pollen dispersal, providing the first steps in its invasion of suitable habitat by long-distance pollen dispersal and complete introgressive displacement of E. amygdalina. Such expansion accords with the population demographics, common garden performance data, and climate modelling which favours E. risdonii and highlights a role of interspecific hybridisation in climate change adaptation and species expansion.

Evolutionary processes in an undescribed eucalypt: implications for the translocation of a critically endangered species

BACKGROUND AND AIMS

Knowledge of the evolutionary processes responsible for the distribution of threatened and highly localized species is important for their conservation. Population genomics can provide insights into evolutionary processes to inform management practices, including the translocation of threatened plant species. In this study, we focus on a critically endangered eucalypt, Eucalyptus sp. Cattai, which is restricted to a 40-km2 area of Sydney, Australia, and is threatened by increased urbanization. Eucalyptus sp. Cattai has yet to be formally described in part due to its suspected hybrid origin. Here, we examined evolutionary processes and species boundaries in E. sp. Cattai to determine whether translocation was warranted.

METHODS

We used genome-wide scans to investigate the evolutionary relationships of E. sp. Cattai with related species, and to assess levels of genetic health and admixture. Morphological trait and genomic data were obtained from seedlings of E. sp. Cattai propagated in a common garden to assess their genetic provenance and hybrid status.

KEY RESULTS

All analyses revealed that E. sp. Cattai was strongly supported as a distinct species. Genetic diversity varied across populations, and clonality was unexpectedly high. Interspecific hybridization was detected, and was more prevalent in seedlings compared to in situ adult plants, indicating that post-zygotic barriers may restrict the establishment of hybrids.

CONCLUSIONS

Multiple evolutionary processes (e.g. hybridization and clonality) can operate within one rare and restricted species. Insights regarding evolutionary processes from our study were used to assist with the translocation of genetically 'pure' and healthy ex situ seedlings to nearby suitable habitat. Our findings demonstrate that it is vital to provide an understanding of evolutionary relationships and processes with an examination of population genomics in the design and implementation of an effective translocation strategy.

Plant collections for conservation and restoration: can they be adapted and adaptable?

Plant collections are important for the conservation of threatened species, and can provide material for ecological restoration. Typically we want collections to have high genetic diversity so populations founded from it are adaptable to future challenges. Sometimes, we have additional objectives for collections, such as enrichment for desirable traits controlled by adaptive alleles. We used landscape genomic datasets for two plants, Westringia fruticosa and Wilkiea huegeliana, to design collections that are genetically diverse, and that are adapted to warming climates. We characterized temperature adaptation by: (i) using the mean annual temperature of the sites of origin of the plants, and (ii) using the representation of alleles that are associated with warm temperatures. In Westringia fruticosa, there was a negative correlation, or tradeoff, between designing a collection that was both genetically diverse and adapted to warm temperatures. This tradeoff was weaker in Wilkiea huegeliana. We hypothesized this was because neutral genetic variation was strongly correlated with temperature in Westringia fruticosa, and not in Wilkiea huegeliana. Accordingly, when we shuffled the temperature data, breaking up the covariance between Westringia fruticosa genetic variation and temperature, there was a relaxation of the observed tradeoff. In sum, we explore tradeoffs between promoting genetic diversity and selecting for a specific trait in plant collections, and show that the strength of this tradeoff varies between two species. This represents a useful step towards understanding when selection will have a large cost in genetic diversity, and when it will be possible to design a collection that is both adapted and adaptable.