Biodiversity Genomics Europe 2023
Last October 2, Biodiversity Genomics Europe has its day at the Biodiversity Genomics Conference 2023, the most important and global event related to the world of biodiversity genomics, attracting and connecting thousands of scientists of all ages from around the world. An entire day of sessions about our project that provided the perfect opportunity to draw attention to BGE’s goals and gain a great deal of knowledge on everything relevant to European biodiversity genomics today.
Videos from the BGE day at BG23
Session 3 of the BGE Day at the BG23 Conference: Increasing utilisation of genomics data in biodiversity characterisation and conservation, covering such topics as pollinator biomonitoring; dark-taxon barcoding; and monitoring from airborne DNA.
Session 1 of the BGE Day at the BG23 provided an opportunity to talk about the biodiversity policy landscape post-COP15 and introduce the BGE project, as well as the iBOL Europe (formerly known as BIOSCAN) and ERGA communities.
Session 2a of the BGE Day at the BG23 Conference: Applications: using DNA sequencing to understand and conserve biodiversity (Whole Genome Sequencing), including butterflies, frogs, otters, octocorals, Hymenoptera and others.
Session 2a of the BGE Day at the BG23 Conference: Applications: using DNA sequencing to understand and conserve biodiversity (DNA Barcoding), including seagrass, heteroptera, pollinators and others.
The last session of the BGE Day at the BG23 Conference discusses a crucial question: What do we need to do – to make meaningful progress – to maximise the impact of major biodiversity genomic projects in meeting stakeholder needs?
Summaries of session 3
Increasing utilisation of genomics data in biodiversity characterisation and conservation
DNA Barcoding for long term pollinator biomonitoring
Monitoring biodiversity from airborne DNA
Monitoring genetic diversity: a genomics-based pilot study
Dark-taxon barcoding
Genomics for the conservation and recovery of threatened species
Selection of abstracts from BGE Day at BG23
Gilles Doignon is team leader, Biodiversity & Nature-Based Solutions, DG Research & Innovation, EC.
At a time when one million species are at risk of extinction within decades, as a result of human activities fueling the intertwined nature and climate crises, the adoption of the Global Biodiversity Framework in December 2022 was a milestone. The GBF defined the goals and targets for all countries in order to protect, restore and sustainably use biodiversity. With the EU Green Deal and its Biodiversity Strategy, the EU is working to put Europe’s biodiversity on a path to recovery by 2030. Taxonomy is key to describe, identify, monitor species and the EU research programmes have funded several important projects in this area. Yet biodiversity loss is not only observed at the species level; it is parts of the genetic diversity we are losing, from specimens to populations. Thanks to genomic science, in particular the Biodiversity Genomics Europe (BGE) project, we are opening a new chapter in our understanding of nature, including new tools for its conservation. These developments are crucial for the implementation of the Global Biodiversity Framework, in particular its Target 13 (Fair and equitable sharing of benefits from genetic resources, digital sequence information and associated traditional knowledge) but also Targets 1 to 6. There are several other EU funded research projects focusing on or using genomic science, and the European Commission is rationalising the very complex biodiversity knowledge landscape. It is also preparing the next research and innovation work programmes and the EU long term strategic research agenda on biodiversity, to identify knowledge gaps and define priorities.
The Biodiversity Genomics Europe (BGE) consortium spans the remit of two major global biodiversity genomics programmes: (1) the International Barcode of Life (iBOL)– focusing on the use of short standardised DNA barcode sequences for large-scale species characterisation, and (2) the Earth Biogenome Project (EBP) focusing on the large-scale production of reference genomes to understand genomic and genetic diversity. In this talk I will focus on the DNA barcoding component of BGE. I will firstly provide background to the International Barcode of Life programme, and outline the development of BIOSCAN Europe as a European node for iBOL. I will then outline the objectives of the DNA barcoding ‘stream’ of the BGE project, describing plans to (a) develop and expand the activities of BIOSCAN Europe, and (b) establish workflows, data infra-structures, and data production pipelines ranging from sampling, barcode sequence generation, data processing and analyses, and ultimately linking the resulting data through to practical applications. Building on these objectives I will then provide a brief summary of the progress to-date for DNA barcoding in the first year of the BGE project.
Camila Mazzoni, Leibniz Institute for Zoo and Wildlife Research. Berlin Center for Genomics in Biodiversity Research, Berlin, Germany.
The Biodiversity Genomics Europe (BGE) project, funded by Horizon Europe, brings together two major European networks: the European Reference Genome Atlas (ERGA) and BIOSCAN-Europe ERGA is dedicated to creating high-quality genomes for all of Europe’s biodiversity, while BIOSCAN-Europe focuses on characterizing species on a large-scale using DNA barcoding. Within BGE, the Genome stream is a collaborative pan-European initiative aimed at establishing standardized procedures for generating reference genomes that comprehensively represent Europe’s biodiversity In this presentation, I will illustrate how BGE is supporting ERGA’s consolidation as the European branch of the Earth BioGenome Project (EBP). Additionally, I will highlight key accomplishments from BGE’s first year, including the development of essential standardized protocols that can be adopted across Europe. These protocols ensure that the produced genomes meet the minimum quality standards set by EBP. The creation of these resources aligns with calls launched by BGE to involve the European scientific community more extensively in the application of genomes for biodiversity research and conservation. The next main steps of the Genome stream involve the large-scale production of ~500 Gb worth of reference genomes across a distributed sequencing and computational infrastructure.
Kay Lucek (University of Nuchátel)
Taxonomic entities below the species level often pose difficulties for conservation practice, especially when they are ecologically distinct from the nominal species. Reference genomes and genomic tools provide the opportunity to study and potentially resolve such cryptic diversity. Here I present a showcase on how genomic insights can help to resolve taxonomic problems for conservation and uncover novel evolutionary insights into the processes that promote the emergence of biodiversity. We studied the Alcon blue butterfly Phengaris alcon species complex comprising different ecotypes or even subspecies, one of them is the high elevation taxon P. rebeli from the European Alps. We sequenced a first reference genome assembly for Phengaris alcon from a caterpillar and generated whole genome resequence data for individuals of three Swiss ecotypes. At a European scale, our results suggest that biogeography and the evolutionary context of diversification of the P. alcon complex is more multifaceted than previously suggested, falling in the range of more recent ecological speciation. In Switzerland, the three ecotypes were genetically isolated with only limited current gene flow between them. Past gene flow, however, could have given rise to the mid elevation ecotype. Our findings emphasise that high elevation P. rebeli should be treated as a distinct species allowing proper conservation actions. Our study highlights how the availability of reference genome assemblies allows to address so far open taxonomic questions in conservation research and that broadscale studies are needed to understand the biogeographic history of apparent diversification.
Jacob Höglund, Uppsala University
Twelve populations of the green toad Bufotes viridis, six from Sweden, one from Denmark and two from Poland as well as three populations held in captivity, were investigated with ddRAD protocol and whole genome resequencing. Furthermore we assembled a reference genome with long read sequencing and scaffolding (PacBio and Hi-C). The populations were sampled partly just after the year 2000 (early) and 2021 (late). In some cases, therefore, the same population is examined with approx. 15 year gap. The Scandinavian populations showed lower genetic variation than the continental populations (Poland). All natural populations were genetically differentiated. The differentiation can be explained by a historically limited or almost non-existent gene flow due to limited migration. The breeding population at the zoo Nordens Ark was established with animals from a natural population in Limhamn, Sweden, which explains why these populations are not differentiated. The survey shows that a recently established population in Norra Hamnen, Malmö-Sweden, is of mixed origin and probably established by individuals from different stocks. This had the highest genetic variation of the Scandinavian populations and the lowest degree of inbreeding. The significance of the results for the practical conservation work with the species is discussed.
Sarah J. du Plessis (1), Mark Blaxter (2), Klaus-Peter Koepfli (3,4), Elizabeth A. Chadwick (1), Frank Hailer (1)
1 School of Biosciences, Sir Martin Evans Building, Cardiff University, Wales, UK.
2 Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
3 Smithsonian-Mason School of Conservation, George Mason University, USA.
4 Centre for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Washington DC, USA.
Conservation genetic studies of many endangered species have typically been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. With more recently available genomic approaches, it is unclear to what extent increased power and resolution might alter insights from previous genetic approaches. For example, previous genetic work on Eurasian otters in the UK identified four genetically differentiated ‘strongholds’, derived from regional sub-populations that survived the anthropogenic, contaminant induced population crash in the 1950-80s. Here we provide a matched comparison of whole genome resequencing versus microsatellite genotyping and control region sequencing for 45 samples from all UK stronghold populations. We found that genomic analyses (autosomal and mitogenome data) confirmed some aspects of population structure shown previously, but also revealed significant shortcomings of the genetic markers: (i) identification of two strongly divergent mitochondrial lineages not previously identified using control region fragments, and (ii) otters in the east of England are genetically distinct and highly variable. Both the origin of this unexpected variation, and the impact on otter conservation in the UK, are currently unclear, but may be related to releases of non-native Eurasian otters in England in the late 20th century. Our work highlights that even reasonably well studied species may harbour genetic surprises when genomic tools are applied.
Ana I. Tavares (1), Xenia Sarropoulou (2), Tereza Manousaki (2), Costas Tsigenopoulos (2), Didier Aurelle (3), Márcio Coelho (4), Gareth Pearson (4), Jamie Stevens (5), Kirsty McLeod (5), Joana R. Xavier (1,6), Joaquim Garrabou (7), Stephane Sartoretto (8), Marta Gut (9), Jessica Gomes-Garrido (9), Fernando Cruz (9), Tyler Alioto (9), Frédérique Viard (10), Jean-Baptiste Ledoux (1)
1 CIIMAR – Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Matosinhos, Portugal
2 Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
3 OSU Institut Pythéas, CNRS, IRD, Aix Marseille University, Université de Toulon, Marseille, France
4 Center of Marine Sciences (CCMAR-CIMAR), Universidade do Algarve, Faro, Portugal
5 Department of Biosciences, Faculty of Health and Life Sciences, University of Exeter, UK
6 Department of Biological Sciences, University of Bergen, Bergen, Norway
7 Institut de Ciències del Mar CSIC, Barcelona, Spain.
8 Ifremer, LITTORAL, F-83500 La Seyne-sur-Mer, France
9 Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
10 ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France.
Our knowledge of the patterns of genetic diversity within and between species remains limited despite their implications for biodiversity conservation. Current advances in sequencing technologies offer new perspectives to conservation biology, making reference genomes and resequencing data essential resources to support conservation efforts. Yet, assembling reference genomes, mapping of resequencing data, SNP calling remain challenging steps. In this context, alignment-free methods are gaining momentum, providing insights into genome wide patterns of diversity and structure.
Habitat-forming octocorals play crucial ecological roles in benthic communities. They are however under strong anthropogenic pressures (e.g., marine heat-waves). Current knowledge gaps regarding their genome structure and genetic diversity prevent to support conservation policies.
Focusing on six octocoral species from the North-east Atlantic and Mediterranean (Eunicella singularis, E. cavolini and E. verrucosa and Alcyonium acaule, A. coralloides and A. digitatum), we analyzed whole genome resequencing datasets (4 to 8 individuals per species) using k-mers based approach. We generated genome-wide diversity estimates and determined population structure at a large geographic scale (Atlantic vs Mediterranean). We found that Eunicella spp. has higher genetic diversity than Alcyonium spp.. Our results supported contrasting divergence in the two genera, with fuzzy species boundaries between E. cavolini and E. singularis but strong genetic differentiation among Atlantic vs. Mediterranean populations of A. coralloides. We discuss the conservation implications of our results and how they should guide future studies.
This case study supports that alignment-free methods are an effective approach to gain insights into population genomics parameters with valuable implications in conservation.
Will Nash (1), Adam Ciezarek (1), Vanessa Huml (2), Angela Man (1), Seanna McTaggart (1), Noel Vella (3), Bjoren Von-Reumont (4), Jon Ellis (2), Andrew Bourke (5), Mairi Knight (2), Adriana Vella (3), Wilfried Haerty (1).
1.The Earlham Institute
2.The University of Plymouth
3.The University of Malta
4.The University of Giessen
5.The University of East Anglia
Earth BioGenome Project initiatives provide unique opportunities to investigate ecologically and economically important species with ongoing large-scale range shifts. Globally, many Hymenopteran species are in decline, yet some species thrive and are expanding their ranges. What makes these species successful? What are the impacts of such rapid expansions? Are newly established populations viable? Population genomic analyses allow us to answer these pressing questions, but such analyses rely on high-quality reference genomes and annotations. Here we provide examples of this process using two Hymenopterans with rapidly expanding ranges across Europe. Firstly, we have generated an ERGA chromosome level assembly for The Violet Carpenter Bee (Xylocopa violacea). This ERGA pilot represents a collaboration between sample ambassadors in Malta and sequencing centres in the UK and is an exemplar on the required processes to ensure compliance with international regulatory frameworks. We found Violet Carpenter Bee genome to be highly repetitive, with around 80% of the contig assembly being repetitive sequence. As an example of the potential of high-quality genomic resources, we use a DToL reference genome, in conjunction with population data, to characterise the genomic implications of rapid population expansion in the Tree Bumblebee (Bombus hypnorum). We show that rapid range expansion can cause the spread of large runs of homozygosity in the population, with potentially deleterious fitness implications.
Michal Rendoš (1), Andrea Parimuchová (2), Dana Klímová Hřívová (3), Maciej Karpowicz (4), Vladimír Papáč (5), Aleksandra Jabłońska (6), Mateusz Płóciennik (6) Dagmar Haviarová (5), Michał Grabowski (6)
(1) Department of Ecology, University of Prešov, Prešov, Slovakia.
(2) Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Košice, Slovakia.
(3) Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
(4) Department of Hydrobiology, Faculty of Biology, University of Białystok, Białystok, Poland.
(5) State Nature Conservancy of the Slovak Republic, Slovak Caves Administration, Liptovský Mikuláš, Slovakia.
(6) Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.
Based on the case study in the Western Carpathians, which belong to the Carpathian biodiversity hotspot, we have compiled the first DNA barcode reference library for molecular identification of invertebrates associated with epikarst, a unique, yet understudied, shallow subterranean aquatic habitat that extends at the interface between the soil and carbonate rocks. We analysed invertebrates collected between 2019 and 2020 from epikarst water that continuously seeps into four caves of the Demänovský Cave System in northern Slovakia. The standard barcode marker of the mitochondrial COI gene was amplified in more than 920 individuals of aquatic, semi-aquatic, and terrestrial invertebrates. The final data set consisted of 784 barcode sequences representing 36 morphospecies, the majority (98.3%) belonged to Arthropoda. Automated cluster delineation using the Barcode of Life Data System (BOLD) revealed 60 Barcode Index Numbers (BINs), of which 43 BINs were new to BOLD, representing mostly typical subterranean species. Almost 20% of the morphospecies displayed high intraspecific variation (>2.2%), suggesting the need for further investigation to assess potential taxonomic problems or cryptic diversity. Our results also indicated the existence of several yet undescribed invertebrate species and possible heteroplasmy or COI numts in the collembolan Megalothorax sp. (incertus species group). The resulting DNA barcode library represents a significant advance not only in the characterisation of epikarst biodiversity but also in the understanding of subterranean biodiversity in general, paving the way for future complex evolutionary and biogeographical studies.
Vanessa A. Mata(1,2), Sónia Ferreira (1,2), Rebeca M. Campos (1,2), Luís P. da Silva (1,2), Joana Verissimo (1,2,3), Martin F.V. Corley (1,2), Pedro Beja (1,2,4)
1 CIBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Portugal.
2 BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Portugal.
3 Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Portugal.
4 CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Instituto de Agronomia, Universidade de Lisboa, Lisboa, Portugal
Evidence worldwide indicates a concerning decline in insect populations, posing significant risks to numerous species and crucial ecosystem services. Yet, apart from a few groups like pollinators, our understanding of how human-induced factors impact insect communities remains limited. DNA metabarcoding offers a potential solution to this knowledge gap, serving as a relatively simple method for assessing entire insect communities. Here we present a case study evaluating the conservation significance of both natural (cork oak woodlands and riparian galleries) and man-made (olive groves and vineyards) habitats for nocturnal flying insects within a Mediterranean mosaic landscape. To analyse insect communities, bulk samples were collected in July and September 2017 using UV light traps. The goal was to measure variations in community diversity, composition, and functional traits. The results identified 1081 operational taxonomic units, predominantly Lepidoptera, Diptera, and Coleoptera, though species accumulation curves indicated the likely presence of many undetected species. Richness was consistently lower in vineyards, whereas olive groves exhibited comparable richness to cork oak and riparian habitats. A functional trait analysis focusing on moths revealed that oak and riparian habitats harboured larger species, with oak habitats hosting species with more specialized diets. This study underscores the conservation value of natural habitats within agricultural landscapes and emphasizes the pivotal role of extensive land uses like traditional olive groves. Overall, it demonstrates the power of DNA metabarcoding in enabling comprehensive assessments encompassing hundreds to thousands of species, providing essential insights to integrate insects into conservation strategies and practices.
Ethan Ross, University of Aberdeen
Seagrass beds provide us with important ecosystem services such as carbon sequestration, coastal protection and supporting fisheries but have recently faced global declines. This project is generating DNA barcodes for marine macroinvertebrates inhabiting Scottish seagrass beds for biomonitoring purposes. The project began by generating DNA barcodes with traditional Sanger sequencing but with the need to generate hundreds of reference sequences, the project is now using Oxford Nanopore Flongles instead. Our comparison between the two sequencing methods reiterates the use of Flongles as rapid, medium output sequencing devices well suited for larger scale DNA barcoding projects. We also reflect on some of the drawbacks and limitations of the method, including cost and failure rate as well as a list of considerations for others seeking to use these methods for their own projects.
Thomas A. Wilding, Scottish Association for Marine Science
Aquaculture has replaced fisheries in terms of fish supply and continues to grow rapidly across the globe. The Scottish aquaculture sector which is focussed around marine-based salmon production, aspires to double production value to ~£2 bn by 2030 and this needs to be demonstrably sustainable.
In Europe, under the Water Framework Directive and the Marine Strategy Framework Directive, any marine activity, including aquaculture, must ensure that impacts, including on the seabed, are spatially limited. Salmonid culture impacts stem primarily from the localised seabed accumulation of faecal material (organic enrichment) occurring around the fish cages.
A central metric by which seabed-impacts are assessed is the infaunal quality index (IQI), which is derived from macrobenthic analysis, an expensive, laborious, and time-consuming process. We have demonstrated, using a trained and optimised random forest algorithm, that patterns in bacterial assemblage, as determined using metabarcoding, can be used predict the IQI with a high degree of accuracy. Our approach offers much faster (near-real time) assessments of the seabed, allowing active site management and is already more cost-effective than traditional methods. We have developed an ‘eDNA2IQI’ R-package which enables users to upload sequence data and, from these, predict IQI values (following standard operating sampling and library preparation procedures). We have linked eDNA-bacterial patterns with individual members of the macrobenthic community.
Our archived DNA extracts offer a unique opportunity to collaborate to investigate other members of the benthic assemblage including eucaryotes/multicellular taxa, and their response to organic enrichment, via targeting other DNA markers.
Lake Skadar with its surrounding springs, wetlands and larger affluents is among the most diverse freshwater ecosystems in the Mediterranean region and a key biodiversity/endemism hotspot in Europe. It is also highly endangered due to climate change and rapid tourism development in the area. Being abundant, diverse and mostly predatory, true aquatic bugs play an important role in the functioning of freshwater ecosystems and are used as indicators of aquatic habitat quality. Nevertheless, this taxonomic group has been scarcely studied in the area. Our survey provides the first comprehensive DNA barcode library for 24 out of 25 species of aquatic Heteroptera collected in the Skadar Lake basin and adjacent regions. By this, we extend the list of species known from the area by 60%. In the case of three species, Notonecta maculata, Hydrometra stagnorum and Nepa cinerea, we detected multiple highly divergent, and also new BINs indicating possible taxonomic inconsistencies, the potential for (pseudo)cryptic diversity and intricate phylogeographic patterns. We show that presumably well-known hotspots, such as Lake Skadar region, are heavily understudied regarding even the prominent insect taxa and, thus, particularly vulnerable to undocumented biodiversity loss. Finally, we underline the value of simple DNA-barcoding-based surveys for providing reference barcode libraries for effective biomonitoring and signaling taxonomic and biogeographic issues.
Natasha de Vere (1), Laura Jones (2) and Abigail Lowe (3)
- Natural History Museum Denmark, University of Copenhagen, Denmark
- National Botanic Garden of Wales, UK
- Natural History Museum London, UK
Decreasing floral resources, as a result of habitat loss, is a key driver in the decline of pollinating insects worldwide. Understanding which plants pollinators use is vital to inform the provision of appropriate floral resources to help prevent pollinator loss. Pollen DNA metabarcoding provides a powerful tool to rapidly characterise the plants used by pollinators, by identifying pollen from the bodies of insects or found within honey. Here, I present case studies that use pollen DNA metabarcoding to understand plant-use and plant-pollinator networks, at different spatial and temporal scales. In Case Study 1 we analysed honey samples from throughout the UK in 2017 and compared these to a survey from 1952. We show how changes in agricultural intensification, crop use and the spread of invasive species, have altered the nectar and pollen sources available in the UK. In Case Study 2 we investigated changes in the diet of honeybee colonies through the flowering season. We found that honeybees visit a wide range of plants, but there is monthly variation in their degree of diet specialization that relates to periods of floral resource limitation. We conclude that it is important to track floral resource use through the year to fully understand species and network stability in the face of ecological change. In Case Study 3 we tracked the foraging preferences of bumblebees, honeybees, non-corbiculate bees and hoverflies through the flowering season. We use these results to provide recommendations to gardeners on the best plants for pollinators through the year.
We currently lack long-term monitoring data for diverse pollinator taxa. The UK Pollinator Monitoring Scheme (PoMS) is setting out to change this through various activities including systematic 1km square surveys across the UK using pan traps. We will present an overview on the first five years of UK PoMS and opportunities for using these samples to better understand insect species diversity and abundance through a new project. This new project, iBOL Europe, is aiming to generate spatiotemporal barcodes for 1M individual insects caught across the country. An overview of BIOSCAN status and future plans as well as opportunities under this new partnership with PoMS will be presented.
Speakers
Claire Carvell, UK Centre for Ecology & Hydrology (UKCEH)
Mara Lawniczak, Wellcome Sanger Institute
Co-authors
Alfried Vogler and Huaxi Liu, Natural History Museum (NHM)
Daniel Read, UK Centre for Ecology & Hydrology (UKCEH)
Paul Woodcock, Joint Nature Conservation Committee (JNCC)
Lyndall Pereira da Conceicoa, Wellcome Sanger Institute
Jemma Salmon, Wellcome Sanger Institute
Alex Makunin, Wellcome Sanger Institute
Priyanka Surana, Wellcome Sanger Institute
Biodiversity science neglects hyperdiverse arthropod clades despite their importance with regard to terrestrial biomass, species diversity, and ecosystem services. In the talk, I will first document that more than half of the flying insect diversity in Malaise trap samples is concentrated in 20 family-level clades regardless of where the samples were collected. I then demonstrate how little we know about most of these arthropods clades by comparing the species richness in quantitative samples with the number of described species. This leads to the conclusion that we need new techniques for these taxa. At the Center for Integrative Biodiversity Discovery of the Natural History Museum in Berlin we have collaborated with colleagues from the Karlsruhe Institute of Technology to develop a robot (“DiversityScanner”) for tackling abundance and efficient DNA barcoding techniques for tackling species richness. The DiversityScanner detects, images, and measures individual specimens before they are placed into microplates for barcoding with rapid and cost-effective techniques involving Nanopore sequencers. After assigning images to species based on DNA barcodes, we can start to train Convolutional neural networks (CNNs) for all taxa with more than 50 images. The goal is delivering AI tools for large numbers of common species so that they become identifiable for everyone based on images. The power of the approach will be discussed for a few examples from tropical and non-tropical environments. One goal is to dramatically increase the number of species that can be described and make all the new species identifiable via a range of different techniques.
Elizabeth Clare, York University, Canada.
The accelerating loss of biodiversity is threatening the functioning of ecosystems on a global scale. Estimates suggest a 69% decline in wild populations since 1970. International agreements ask countries to quantify their biodiversity and monitor shifts in community composition to try and gauge species decline and the effect of interventions to mitigate loss. However, quantifying biodiversity anywhere is a challenge and monitoring continual change is impossible at almost any scale. We rely mainly on taxon, specific targets and local studies and try to extrapolate to larger trends. A commonly stated problem is that infrastructure for global monitoring of biodiversity does not exist. However, we analysed DNA captured along with particulate matter by two air quality samplers used at routine air quality monitoring stations in the UK and identified more than 180 vertebrate, arthropod, plant and fungal taxa representative of local ecology. Our pilot data suggests that air monitoring networks are gathering standardised, local biodiversity measures on a global scale, as a result of their routine functioning, but the ecological significance of these samples has gone unnoticed. These samples are collected using highly standardised approaches and are sometimes stored for decades, presenting the potential for high resolution ecological time series data. With minimal modification of current protocols, this material provides the best opportunity to date for detailed monitoring of terrestrial biodiversity using an existing, replicated transnational design and it’s already operating around the world.
Martin C. Fischer (1), Oliver Reutimann (1), Gabriel Ulrich (1), Karim Clivaz (1), Jasmine N. Tschan (1), Nik Zemp (2), Felix Gugerli (3), Rolf Holderegger (1,3), Alex Widmer (1)
1 Institute of Integrative Biology (IBZ), ETH Zurich, Switzerland
2 Genetic Diversity Centre (GDC), ETH Zurich, Switzerland
3 Biodiversity and Conservation Biology, WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
Genetic diversity is the raw material of evolution and is essential for species and populations to adapt to and persist in a changing environment. Systematic monitoring of genetic diversity on a national scale has rarely been undertaken, and relevant experiences first had to be established. We have initiated a pilot study on genetic diversity monitoring in Switzerland, with the aim of assessing genetic diversity indicators for five animal and plant species, thereby gaining the practical experience necessary for setting up a monitoring programme using genomic approaches. Each of the five species occurs in a specific habitat type of national importance and/or in anthropogenically modified landscapes. We sampled >1,200 individuals from >150 populations across all biogeographic regions in Switzerland. For each of the five species, we de novo assembled a reference genome and re-sequenced the genomes of all individuals using short-read technology at approximately 10x coverage. Together, these data allow detailed conservation-relevant analyses, such as, e.g., the identification of runs of homozygosity (ROH), or estimates of contemporary effective population size (Ne). These analyses provide unprecedented insights into temporal changes in genetic diversity or levels of inbreeding in natural populations. With this information obtained from the pilot study, it is now technically possible to carry out national monitoring of genetic diversity using genomics. An ongoing challenge is to develop scientifically sound but intuitive indicators of the state of genetic diversity and the extent of possible change that can be effectively communicated to relevant authorities and practitioners for subsequent implementation in conservation management.
Cock van Oosterhout, School of Environmental Sciences, University of East Anglia (UEA), UK.
The Red List of Species by the International Union for Conservation of Nature (IUCN) uses external threats to species to assess their conservation status, but it does not fully incorporate genetic or genomic information. A rich population genetic theory has been developed over the past 100 years, and the extinction risk assessment of threatened species would benefit from including this analytical framework. Perhaps surprisingly, the relationship between genetic diversity and the Red List status is weak and variable across taxa. Many conservation biologists therefore argue that genetic data has little value for saving species from extinction. Rather, I argue it shows that genetic data can provide additional information about extinction risk that is not captured by the Red List. Furthermore, I believe that the Red List likely underestimates the extinct risk of many species since it does not evaluate the long-term effects of genomic erosion. In this talk, I will discuss genomics data I can be used to help in the assessment and conservation of biodiversity, particularly focusing on the long-term threats posed by the genetic load of deleterious mutations. I show the value of genomic techniques to reduce inbreeding depression and improve the long-term viability of populations. In addition, I show how genomic data can be used to inform genetic rescue programs, identifying the optimal individuals for reintroduction, and thereby helping species recovery.
