This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the spatial scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance are restricted, microclimatic variation over distances of only a few kilometres can maintain strong geographic isolation extending back several millions of years. Further to this, we demonstrate congruent diversification with gene flow across species, mediated by Quaternary climate oscillations that have facilitated a dynamic of isolation and secondary contact. The unprecedented scale of parallel species responses to a common environmental driver for evolutionary change has profound consequences for understanding past and future species responses to climate variation.

Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully ac-

Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA-based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome-db.org) provides an intuitive solution for maintaining links between genetic data sets stored by the International Nucleotide Sequence Database Collaboration (INSDC) and their associated ecological metadata. GEOME facilitates the deposition of raw genetic data to INSDCs sequence read archive (SRA) while maintaining persistent links to standardscompliant ecological metadata held in the GEOME database. This approach facilitates findable, accessible, interoperable and reusable data archival practices. Moreover, | 1459 RIGINOS et al. How to cite this article: Riginos C, Crandall ED, Liggins L, et al. Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research.

1. Metabarcoding of Metazoa using mitochondrial genes is confounded by the co-amplification of mitochondrial pseudogenes (NUMTs). Current denoising protocols have been designed to remove PCR and sequencing artefacts, but pseudogenes are not usually recognised by these procedures.Authentic mitochondrial amplicon sequence variants (ASVs), which represent the majority of reads, can be distinguished from PCR-derived errors, sequencing errors and NUMTs (non-authentic ASVs) due to their lower abundances. However, the use of simple read abundance thresholds is complicated by the highly variable DNA contribution of individuals in a metabarcoding sample.2. We show how ASVs that survive standard denoising, but are identified as non-authentic, are consistent with expectations for NUMTs with regard to patterns of phylogenetic relatedness, readabundance, and library co-occurrence. We then propose and demonstrate a new self-validating framework, named NUMT dumping, which allows NUMT filtering strategies to be evaluated by quantifying (i) the prevalence of non-authentic ASVs (NUMT and erroneous sequences) and (ii) the collateral effects on the removal of authentic ASVs (mtDNA haplotypes) in filtered data. We propose several filtering strategies within the NUMT dumping framework, based on the application of read-abundance thresholds, structured with regard to sequence library and phylogeny.3. The framework was validated using mock and natural communities, both of which showed opposing trends for the removal of authentic and non-authentic ASVs, when threshold values for minimum abundance to filter out sequences were increased. Filtering can be optimized to retain less than 5% of non-authentic ASVs while retaining more than 89% of authentic mitochondrial ASVs, or complete removal of non-authentic ASV with 77% of authentic mitochondrial ASVs retained. 4. We provide a program, NUMTdumper, that can be used to evaluate and decide upon the most adequate metabarcoding filtering strategy for specific research objectives, providing a measure of expected prevalence of non-authentic ASVs in metabarcoding datasets. In addition, this evaluation allows the user to quantify effects of taxonomic inflation when ASVs are clustered into OTUs. It improves the reliability of intraspecific genetic information derived from metabarcode data, opening the door for community-level genetic analyses requiring haplotype-level resolution.

15Soil mesofauna communities are hyperdiverse and critical for ecosystem functioning. 16 However, our knowledge on spatial structure and underlying processes of community 17 assembly for soil arthropods is scarce, hampered by limited empirical data on species 18 diversity and turnover. We implement a high-throughput-sequencing approach to 19 generate comparative data for thousands of arthropods at three hierarchical levels: 20 genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement 21 across these levels can reveal the predominant processes driving the variation in 22 biological assemblages at the local scale. This multi-hierarchical approach was performed 23 using haplotype-level-COI metabarcoding of entire communities of mites, springtails and 24 beetles from three Iberian mountain regions. Tens of thousands of specimens were 25 2 extracted from deep and superficial soil layers and produced comparative 26 phylogeographic data for >1000 co-distributed species and nearly 3000 haplotypes. Local 27 assemblages were highly distinctive between grasslands and forests, and within each of 28 them showed strong spatial structures and high endemicity at the scale of a few kilometres 29 or less. The local distance-decay patterns were self-similar for the haplotypes and higher 30 hierarchical entities, and this fractal structure was very similar in all three regions, 31 pointing to a significant role of dispersal limitation driving the local-scale community 32 assembly. Our results from whole-community metabarcoding provide unprecedented 33 insight into how dispersal limitations constrain mesofauna community structure within 34 local spatial settings over evolutionary timescales. If generalized across wider areas, the 35 high turnover and endemicity in the soil locally may indicate extremely high richness 36 globally, challenging our current estimations of total arthropod-diversity on Earth. 37 38 39

Dispersal limitation has been recurrently suggested to shape both macroecological patterns and microevolutionary processes within invertebrates. However, because of potential interactions among biological, environmental, temporal, and spatial variables, causal links among flight-related traits, diversification and spatial patterns of community assembly remain elusive. Integrating genetic variation within species across whole insect assemblages, within a simplified spatial and environmental framework, can be used to reduce the impact of these potentially confounding variables. Here, we used standardized sampling and mitochondrial DNA sequencing for a whole-community characterization of the beetle fauna inhabiting a singular forested habitat (laurel forest) within an oceanic archipelago setting (Canary Islands). The spatial structure of species assemblages together with species-level genetic diversity was compared at the archipelago and island scales for 104 winged and 110 wingless beetle lineages. We found that wingless beetle lineages have: (i) smaller range sizes at the archipelago scale, (ii) lower representation in younger island communities, (iii) stronger population genetic structure, and (iv) greater spatial structuring of species assemblages between and within islands. Our results reveal that dispersal limitation is a fundamental trait driving diversity patterns at multiple hierarchical levels by promoting spatial diversification and affecting the spatial configuration of entire assemblages at both island and archipelago scales.

Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change.