Ken A. Thompson

The Biodiversity Genomics Europe plus (BGE+) Project builds on a pan-European collaboration to scale up the production and uptake of genomic evidence for taxonomy, monitoring, and policy. It widens participation, standardises methods, and prepares a distributed European system for biodiversity genomics that links molecules to ecosystems. The BGE+ consortium unites the International Barcode of Life in Europe (iBOL Europe, barcoding), the European Reference Genome Atlas (ERGA, reference genomes) and the Consortium of European Taxonomic Facilities (CETAF, taxonomic research and natural history collections) to align end-to-end workflows from field sampling to application. This publication is an abridged version of the successful grant proposal developed jointly by iBOL Europe, ERGA, and CETAF in response to the Horizon Europe call HORIZON-CL6-2025-01-BIODIV-03. BGE+ has four overarching objectives: (1) broaden participation and capacity; (2) make distributed genomic data production interoperable and FAIR (Findable, Accessible, Interoperable, and Reusable) by design; (3) translate evidence into practice through co-designed use-case roadmaps; and (4) define the service portfolio and assess the financial and technical feasibility of a future European research infrastructure in biodiversity genomics. Through targeted cascade grants (Financial Support to Third Parties) and hands-on training, BGE+ enlarges community capacity while converging on shared protocols and standard practices, improving data interoperability and consolidating community efforts. Building on previous work, BGE+ carries forward the communities’ long-term vision: turning fragmented efforts into a coherent, scalable system that delivers reliable genomic evidence for taxonomy and policy.

DNA barcoding involves the recovery of a DNA sequence for a target gene region from its source specimen. This process gains complexity when multiple sequences are recovered from a specimen, as is often the case when data are generated by high-throughput sequencers. This diversity can reflect both methodological artifacts (e.g., chimeras, PCR errors, sequencing errors, tag jumps) and real template diversity in the DNA extract (e.g., contamination, endosymbionts, NUMTs, parasites). To support analysis of the sequence data from three million specimens annually, the Centre for Biodiversity Genomics (CBG) has developed BIP, the Barcode Inference Pipeline. Compatible with all sequencing platforms, BIP processes .fastq files and returns both target DNA barcodes and non-target sequences. To generate results, BIP implements quality and size filtration, demultiplexing, primer trimming, chimera scanning, sequence error correction, OTU delineation, and sequence identification. When analysis targets the cytochrome c oxidase 1 (COI) barcode region, BIP also assigns each OTU to a known BIN or identifies its nearest neighbour BIN. As final output, BIP returns summary files ready for upload to BOLD or for other downstream analyses. They include a taxonomic assignment for each OTU, generated by comparison with a DNA barcode reference library. We describe BIP’s flexibility and structure, then demonstrate its functionality by analyzing COI sequence data from 100K specimens. Because of its capacity to disentangle target and non-target sequences, BIP outperforms an alternative software package, ONTbarcoder, in several important ways. To ease access, installation, and functionality, BIP is provided as a Docker container (github.com/cbg-innov/BIP).

Current metabarcoding pipelines are inflexible with respect to study design and are poorly suited to long-read sequence data. To address these limitations, we developed MAP, the Metabarcoding Analysis Pipeline, which is a sequence-to-answer workflow supporting the analysis of amplicons from highly multiplexed and replicated study designs. Although MAP can analyze amplicons of any length from any genetic marker, it includes several features tailored to long-read COI metabarcoding. MAP installs from a Docker container and requires only sequence data, a parameters file, and a reference library. It produces intuitive reports, enabling users to evaluate their data immediately after analysis. We validate MAP by showing that it generates biodiversity estimates that correspond closely to a ground-truth dataset of single-specimen DNA barcode data and by demonstrating that it outperforms alternative platforms for COI metabarcoding. MAP is free, open-source, and available from: https://github.com/cbg-innov/MAP .

Nanopore sequencers have the potential to liberate DNA sequencing from centralized core facilities to distributed analytical nodes. Until now, Oxford Nanopore Technologies (ONT) has been the sole manufacturer of a portable nanopore sequencer, but analogous platforms are in production. Nanopore sequencers from Qitan Technology (QT) are widely used in China but have been unavailable outside that nation and lack independent performance testing. Enabled by early access to QT’s least expensive sequencer and flow cell, the QNome-3841 and QCell-384, we tested whether they could generate accurate DNA barcodes cost-effectively. In several tests involving amplicon pools from 95 to 9,120 specimens, QT recovered valid DNA barcodes from nearly as many specimens (98%) as ONT. QT sequences had slightly lower fidelity than their ONT counterparts and QT frequently failed to resolve the correct length of G/C homopolymers. However, barcode sequences from the two platforms were nearly indistinguishable after bioinformatic treatment. QT’s wash kit performed well, enabling a QCell to sequence eight amplicon pools with zero carryover between runs and minimal degradation of the flow cell. Its ultra-fast protocol allowed library preparation in a single step that could be completed in 15 minutes, but this came at the cost of lower quality data. Once widely available, QT devices will be well-suited for supporting DNA barcode analysis.

Rates of mitogenome evolution differ among animal lineages, and this variation has been linked to life history, to ecological traits and—potentially—to the sex-determination system. Insects are a compelling model for examining the latter factor because haplodiploid (HD) has evolved on multiple occasions from a diplodiploid (DD) ancestral state. We tested for rate differences between DD and HD taxa by examining sequence change in a sentinel segment of the mitogenome, the 658 bp barcode region of the cytochrome c oxidase subunit I (COI) gene. Specifically, we investigated if amino acid substitutions and indels are more frequent in HD than DD lineages by inspecting COI sequences from over 86 000 BINs (a species proxy) representing 783 insect families and 26 orders. Among them, 10 lineages, varying in rank from tribe to order, are HD. Our analysis, which accounts for phylogeny, indicates that HD lineages have higher rates (1.7×) of amino acid substitution, higher K _a / K _s (3.5×) and far more indels than DD taxa. While our results demonstrate that HD accelerates mitogenome evolution, future work is needed to clarify its mechanistic basis. We hypothesize that HD facilitates positive selection for mitochondrial mutations which encode proteins that interact with nuclear gene products. Such coevolutionary interactions should be facilitated because recessive mutations in the nuclear genome are fully exposed to selection in males of the HD but not the DD lineages.

A biodiversity monitoring program in south-central British Columbia, Canada, at sites on traditional nłeʔképmx territory near the Highland Valley Copper mine, collected many specimens of an unknown moth. DNA barcode analysis revealed its affinity but deep divergence (14.3%) from Tridentaforma fuscoleuca (Braun, 1923), the only species in the family Tridentaformidae. The new species was assigned to the BIN (Barcode Index Number) BOLD:AFK8960. Morphological study confirmed its placement in this family but revealed marked genitalic differences from T. fuscoleuca . Given its genetic and morphological divergence, we describe Tridentaforma browncopper Monckton & Levesque-Beaudin, sp. nov. The scientific name is a translation of the name, skʷúnkʷl̓itkax̣n̓I, chosen by nłeʔképmx Elders and Knowledge Keepers, which means “brown copper moth”. Its discovery and naming reflect an effective collaboration among biodiversity scientists, industry representatives, and Indigenous communities. It also demonstrates how DNA barcoding can facilitate species descriptions without requiring taxonomists with specialist expertise in the group under investigation.

Ecologically mediated selection against hybrids, caused by hybrid phenotypes fitting poorly into available niches, is typically viewed as distinct from selection caused by epistatic Dobzhansky–Muller hybrid incompatibilities. Here, we show how selection against transgressive phenotypes in hybrids manifests as incompatibility. After outlining our logic, we summarize current approaches for studying ecology-based selection on hybrids. We then quantitatively review QTL-mapping studies and find traits differing between parent taxa are typically polygenic. Next, we describe how verbal models of selection on hybrids translate to phenotypic and genetic fitness landscapes, highlighting emerging approaches for detecting polygenic incompatibilities. Finally, in a synthesis of published data, we report that trait transgression—and thus possibly extrinsic hybrid incompatibility in hybrids—escalates with the phenotypic divergence between parents. We discuss conceptual implications and conclude that studying the ecological basis of hybrid incompatibility will facilitate new discoveries about mechanisms of speciation.

The vertebrate gut microbiota is a critical determinant of organismal function, yet it remains unclear if and how gut microbial communities affect host fitness under natural conditions. Here, we investigate associations between growth rate (a fitness proxy) and gut microbiota diversity and composition in a field experiment with threespine stickleback fish ( Gasterosteus aculeatus ). We detected on average 63% more bacterial taxa in the guts of high-fitness fish compared to low-fitness fish (i.e., higher α-diversity), suggesting that higher diversity promotes host growth. The microbial communities of high-fitness fish had higher similarity (i.e., lower β-diversity) than low-fitness fish, supporting the Anna Karenina principle— that there are fewer ways to have a functional microbiota than a dysfunctional microbiota. Our findings provide a basis for functional tests of the fitness consequences of host-microbiota interactions. Significance statement: The vertebrate gut microbiota is important for many aspects of their hosts’ biology—such as nutrient metabolism and defense against pathogens—that could ultimately affect host fitness. However, studies investigating the effects of gut microbiota composition on vertebrate host fitness under natural conditions remain exceedingly rare. We tested for associations between gut microbiota diversity and growth rate (a fitness proxy) in threespine stickleback fish reared in large outdoor ponds. We found evidence that a more diverse gut microbiota was predictive of higher growth rate and therefore increased host fitness. Notably, high-fitness fish had higher gut microbiota similarity to one another than did low-fitness fish, providing experimental evidence for the Anna Karenina principle—that there are fewer ways to have a functional microbiota than a dysfunctional microbiota—as it relates to host fitness.

When divergent populations interbreed, their alleles are brought together in hybrids. In the initial F1 cross, most divergent loci are heterozygous. Therefore, F1 fitness can be influenced by dominance effects that could not have been selected to function well together. We present a systematic study of these F1 dominance effects by introducing variable phenotypic dominance into Fisher's geometric model. We show that dominance often reduces hybrid fitness, which can generate optimal outbreeding followed by a steady decline in F1 fitness, as is often observed. We also show that “lucky” beneficial effects sometimes arise by chance, which might be important when hybrids can access novel environments. We then show that dominance can lead to violations of Haldane's Rule (reduced fitness of the heterogametic F1) but strengthens Darwin's Corollary (F1 fitness differences between cross directions). Taken together, results show that the effects of dominance on hybrid fitness can be surprisingly difficult to isolate, because they often resemble the effects of uniparental inheritance or expression. Nevertheless, we identify a pattern of environment‐dependent heterosis that only dominance can explain, and for which there is some suggestive evidence. Our results also show how existing data set upper bounds on the size of dominance effects. These bounds could explain why additive models often provide good predictions for later‐generation recombinant hybrids, even when dominance qualitatively changes outcomes for the F1.