Conference Agenda

Genetic diversity assessments are routine for many conservation programmes. Single nucleotide polymorphisms (SNPs) are often used to measure genome-wide diversity. However, structural variants (SVs, chromosomal rearrangements ≥ 50bp) represent a higher proportion of genomic variation, intersect more often with genes and gene regions and, like SNPs, can be associated with both adaptive and maladaptive traits. Despite this, SVs are rarely included in holistic assessments of genome-wide diversity due to the significant resources required to characterise them with confidence. However, emerging sequencing technologies and bioinformatic approaches are putting SVs within reach for highly threatened populations. We combine a long-read reference genome and short-read whole-genome sequencing with an emerging variant graph approach to measure the relative levels of SNP and SV diversity within–and the extent of population genomic structure between– New Zealand’s rarest breeding bird, the New Zealand fairy tern | tara iti and the Western Australia (WA) population of Australian fairy tern. These combined data are being used to develop a position statement regarding the efficacy of genetic rescue for tara iti. We argue that the routine characterisation of both SNPs and SVs will ultimately lead to more accurate assessments of genetic risks of inbreeding and outbreeding depression in imperiled populations.

Effective population size (Ne) is a fundamental parameter used to predict genetic diversity loss in populations. The ability to infer Ne from census size (Nc) data, especially when genetic data are unavailable, has favoured the inclusion of an Ne-based indicator in the Kunming-Montreal Global Biodiversity Framework, for monitoring infraspecific genetic diversity. In some species, particularly those with complex life-history traits, inferring Ne from Nc is hindered by the lack of knowledge of Ne/Nc ratios, which are often population-specific. In this study, we used SNPs derived from ddRAD sequencing to estimate contemporary Ne in British populations of three terrestrial orchids: Cephalanthera longifolia, C. damasonium and C. rubra. These orchids exhibit different reproductive strategies, and their populations are isolated to varying extents. We discuss the Ne estimates obtained in the context of specific reproductive strategies (selfing in C. damasonium vs. outcrossing in C. longifolia), extent of gene flow, and degree of isolation (from little in C. longifolia to extreme in C. rubra). We consider potential biases and analytical constraints associated with the methods used. Our findings advance the knowledge of Ne/Nc ratios and contribute to informing conservation practices for declining terrestrial orchids and other species with similar life-history traits.

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning. Until recently genetic diversity had been largely neglected in biodiversity monitoring, and if addressed, was treated separately and detached from other conservation issues, such as effects of climate change. We describe an accounting of efforts in Europe to monitor population genetic diversity (GME), the evaluation of which can guide capacity building and collaboration towards the areas most in need of expanded monitoring. We identify where GME likely coincides with anticipated climate change effects on biodiversity. Our analyses suggest that area, financial resources and conservation policy influence country GME, high values of which only partially match species’ joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Thus, our results highlight the need in Europe to expand investment in genetic monitoring across the climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. The European Union’s Birds and Habitats Directives should be expanded to fully address the conservation and monitoring of genetic diversity.

Increasing the extent of protected areas (PA) through 30x30 and other area-based conservation initiatives can help to achieve global biodiversity conservation goals across all biodiversity levels. However, intraspecific genetic variation, the foundational level of biodiversity, is rarely explicitly considered in PA design or quality performance assessments. Repurposing existing genetic data could rapidly inform area-based conservation planning and improve the preservation of genetic variation. Through a global compilation of population-level nuclear genetic data (>2 million individuals; 36,356 populations; 2,809 species), we identified both data-rich areas, and substantial geographic and taxonomic gaps. These gaps are within many protected areas and hotspots of species biodiversity, and may preclude robust protection of genetic diversity. Addressing data unevenness through efforts to collect, gather, harmonize and share genetic data globally could help support integration of genetic information into PA design, PA performance assessments, and genetically-oriented global conservation policies.

Recent advancements in genomics technology present a diverse range of opportunities and challenges for conservation practitioners and decision-makers.

Some of these technologies are discussed to be applied to the most pressing conservation challenges, such as small population management, or controlling invasive species. However, choosing the right tools from the genomic toolbox can be a challenging task for the conservation community. We thus here highlight the advancement of the field and for which applications, new technologies might be helpful not only for researchers, but also to managers. In each case, ethical, and political considerations must be considered to ensure responsible and informed implementation.

In addition, we here present results from a survey during a webinar where we presented several case studies to the audience of more than 50 professionals from the field of applied conservation. Our aim was to increase the understanding and application of genomic and biotechnological advancements. While the community is highly interested in topics such as gene drive and editing, or application of eDNA, many participants identified these topics as challenging, underscoring the need for more targeted information and training. This feedback highlights the critical role of continuous education and dialogue about the implementation of new genomic tools.

The relative effects of intra- and interspecific diversity on ecosystem functions are poorly understood, especially under natural and multi-trophic conditions. Here, we assessed the relationships between species diversity, genetic diversity and ecosystem functioning across three trophic levels (trees, shredders and fishes) in natural aquatic ecosystems. We estimated species diversity and genetic diversity within each trophic level, as well as seven ecosystem functions, and we assessed the strength of each possible relationship between biodiversity and ecosystem functions (BEF). Although BEFs effect sizes were similar at both the genetic and species levels, we found that genetic diversity was positively and consistently associated with ecosystem functions, whereas species diversity was negatively associated. However, these antagonist effects of species and genetic diversity were only observed when BEFs were measured within trophic levels, not across trophic levels. This demonstrates the importance of considering both species and genetic diversity loss to predict ecosystem dynamics. This further calls for developing novel integrative estimates of biodiversity allowing to jointly reveal functional genomic diversity at both the intra- and interspecific levels within community, which can be achievable using phylogenetically-conserved candidate genes.