Biodiversity resilience relies on genetic diversity, which sustains the persistence and evolutionary potential of organisms in dynamic ecosystems. Genomics is a powerful tool for estimating genome-wide genetic diversity, offering precise and accurate estimates of the status and trajectory of genetic diversity within species and populations. However, the widespread integration of genomic information into biodiversity conservation and management efforts faces challenges due to a lack of standardised genome-wide data generation methods and applications. The heterogeneity of approaches can make it difficult to consistently interpret the results and clearly communicate key information to stakeholders such as practitioners and decision-makers. To begin to address these challenges, the European Reference Genome Atlas (ERGA) promotes the standardisation of methodologies for high-quality reference genome sequencing and analysis as part of the global network of the Earth BioGenome Project. ERGA is also proactively developing best practices to engage stakeholders in biodiversity genomics research, starting with examining case studies and conducting mapping efforts to familiarise researchers with pathways to effective engagement. An emerging theme is the researchers’ experience of variable perceptions amongst stakeholders of the value and utility of reference genomes and genomics data in biodiversity conservation and management. Addressing this issue calls for consensus on standardised genome-wide data generation methods and applications that will help to deliver the highest standards for accuracy, interpretability, and comparability. We believe converging on consensus methods standardisation is essential for fostering the stakeholder trust and confidence required to successfully promote widespread adoption of genome-wide genetic diversity assessments in biodiversity conservation and management.

Although species radiations on island archipelagos are broadly studied, the geographic and ecological modes of speciation that underlie diversification are often not fully understood. Both allopatry and sympatry play a role during radiations, particularly on islands with profound habitat diversity. Here, we use the most diverse Canary Island plant radiation, Aeonium (Crassulaceae), to phylogenetically test two hypotheses: (1) allopatric speciation, which predicts that closely related taxa are ecologically similar but do not co-occur, and (2) sympatric speciation, whereby closely related taxa co-occur geographically but are ecologically distinct. We fitted niche and spatial distribution models based on extensive field surveys to quantify geographic and ecological divergence among taxa integrated in a phylogenetic context. While allopatry seems to be the main driver in speciation among islands, within-island speciation occurs in sympatry. Contrary to our expectation, phylogenetically closely related species tend to occupy similar ecological niches, suggesting that ecological niche divergence among species accumulates slowly, even in sympatry. This suggests that evolutionary young taxa, may be partially reproductively isolated due to subtle phenotypic differences, such as reproductive morphology and phenology rather than by ecology and may putatively exacerbate divergence among populations. Thus, allopatry and sympatry are complementary speciation mechanisms on oceanic islands, jointly spurring this enigmatic radiation.

Holocentric organisms, unlike typical monocentric organisms, have kinetochore activity distributed along almost the whole length of the chromosome. Because of this, chromosomal rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for their extraordinary rates of chromosome evolution. Genome synteny has been reported to be conserved in animals with holocentric chromosomes despite high rates of chromosome rearrangements. Comparing genomes of Carex species and a genome of a distantly related Cyperaceae we have characterised conserved vs. rearranged genome regions across pairs of species that range in time since divergence between 2 and 50 million years. We have compared a C. scoparia genome with a linkage map of the same species to study rearrangements at a population level and suppression of recombination patterns. We found a surprisingly conserved genome synteny even between very distantly related species and extraordinarily high rates of chromosome evolution in genus Carex. Comparing the distribution of repetitive DNA and gene density between conserved and rearranged genomic regions, we found repetitive DNA to be related to holocentromeres and as well as rearranged regions of the genome. This evidence of extremely conserved synteny in sedges and the massive events of chromosome fission and fusion found across the evolution of genus Carex suggests the presence of common genomic hotspots of chromosome evolution related to repetitive DNA.