Amphioxus (Cephalochordata) are small marine chordates that have broad ecological ranges, yet as adults form local settlements and exhibit limited mobility. Genomic surveys of two amphioxus species have suggested that they rank among the most genetically diverse metazoans. Here, we present the first accurate assessment of genomic diversity in the European amphioxus (Branchiostoma lanceolatum) and investigate the processes underlying this diversity. We leverage whole-genome sequencing data from multiple individuals sampled at two geographically distant Atlantic and Mediterranean locations. Consistent with previous estimates in other amphioxus species, we measure exceptionally high genomic diversity, with an average heterozygosity of 2.73% in B. lanceolatum. Despite the large geographic separation between sampling sites, population differentiation is minimal, indicating extensive gene flow among distant adult settlements. Phylogenetic analyses combined with population genetic simulations confirm that this elevated genomic diversity is primarily driven by a large effective population size. Although adult amphioxus have limited mobility, our results indicate that long-distance larval dispersal mediated by ocean currents is sufficient to generate a near-panmictic population structure across their broad ecological range. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, 207853 Agence Nationale de la Recherche, ANR-21-CE13-0034

Arthropod developmental modes are highly diverse, ranging from direct development with little morphological change between moults to metamorphic life-stage progressions characterised by profound transformations. Metamorphosis can be defined as a post-embryonic life-stage progression event leading to adulthood that is characterised by major morphological changes and modifications of the adaptive landscape. Within this framework, we compare four independent evolutionary life history transitions to metamorphic development across Pancrustacea. Using a phylogenomic dataset of 54 species spanning 26 orders, we investigated gene family evolutionary dynamics associated with the inferred origins of metamorphosis in Insecta, Copepoda, Eucarida, and Thecostraca. Compared with non-metamorphic sister lineages as well as descendent and ancestral nodes, transitions to metamorphic development were consistently associated with elevated gene family births and expansions. Although these expansions predominantly involved different gene families in each lineage, they repeatedly converged on shared biological functions, particularly those related to embryonic and post-embryonic development, morphogenesis, nervous system differentiation, and other processes relevant to the biology and evolution of metamorphosis. Evolutionary modelling further identified a subset of gene families exhibiting adaptive, lineage-specific expansions, including genes implicated in neural and sensory development, segmentation, and moulting. Together, these findings support a model in which independent transitions to metamorphic development repeatedly recruited different components of a shared developmental toolkit, achieving functional convergence through distinct genetic trajectories. This reframes the arthropod moulting programme as an evolutionarily flexible developmental substrate whose repeated modification has facilitated the emergence of complex multi-phasic life histories and contributed to the extraordinary diversification of Pancrustacea. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, 198691

METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining this method with transgenic models, the authors ...

Amphioxus are small marine chordates that have broad ecological ranges, yet as adults form local settlements and exhibit limited mobility. Genomic surveys of two amphioxus species have suggested that they rank among the most genetically diverse metazoans. Here, we present the first accurate assessment of genomic diversity in the European amphioxus ( Branchiostoma lanceolatum ) and investigate the processes underlying this diversity. We leverage high-coverage whole-genome sequencing data from multiple individuals sampled at two geographically distant Atlantic and Mediterranean locations. Consistent with previous estimates in other amphioxus species, we measure exceptionally high genomic diversity, with an average heterozygosity of 2.73% in B. lanceolatum . Despite the large geographic separation between sampling sites, population differentiation is minimal, indicating extensive gene flow among distant adult settlements. Phylogenetic analyses combined with population genetic simulations confirm that this elevated genomic diversity is primarily driven by a large effective population size. Although adult amphioxus have limited mobility, our results indicate that long-distance larval dispersal mediated by ocean currents is sufficient to generate a near-panmictic population structure across their broad ecological range. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, 207853 Agence Nationale de la Recherche, ANR-21-CE13-0034

Abstract. Genomic diversity within species encompasses a range of sequence-related, structural, and regulatory features. To illustrate their complexity, we