Bassos-Hull, K. | Search bioRxiv

bioRxiv2026

Manta and devil ray genome assemblies uncover signatures of pelagic adaptation

Manta and devil rays (Mobulidae) are iconic marine megafauna highly adapted to life in the open ocean, with forward-facing mouths, enlarged pectoral fins and specialised filter-feeding apparatus. These innovations have enabled mobulids to occupy vast pelagic habitats, yet the genetic changes underlying them remain poorly understood. Here we use a combination of chromatin conformation capture, PacBio HiFi and Nanopore long-reads to generate highly contiguous annotated chromosome-level reference genomes for two mobulid species: the Atlantic pygmy devil ray (Mobula hypostoma) and the Atlantic manta ray (Mobula yarae). The assemblies span 3.5 and 4.0 Gb, with contig N50s of 23.3 and 7.3 Mb, respectively. We combine these into a Progressive Cactus whole genome alignment with benthic batoid outgroups to characterise the landscape of structural variation and identify candidate molecular regions associated with pelagic adaptation. This approach revealed that over 1.5 million structural rearrangements occurred along the ancestral mobulid lineage, with deletions encompassing three times more sequence compared to the benthic sister lineage. Genes affected by mobulid specific deletions were significantly enriched for neurogenesis pathways linked to craniofacial patterning, with several deletions overlapping the putative promoter sequences of craniofacial and roof of mouth development genes. Our findings highlight candidate developmental pathways through which ancestral deletions may have driven mobulid adaptations, while the high-quality genome resources provide a foundation for comparative and functional studies in Chondrichthyes.

evolutionary biology↗

bioRxiv2018

Phylogenomics and species delimitation of mobulid rays reveals cryptic diversity and a new species of manta ray

Practical biodiversity conservation relies on delineation of biologically meaningful units, particularly with respect to global conventions and regulatory frameworks. Traditional approaches have typically relied on morphological observation, resulting in artificially broad delineations and non-optimal species units for conservation. More recently, species delimitation methods have been revolutionised with High-Throughput Sequencing approaches, allowing study of diversity within species radiations using genome-wide data. The highly mobile elasmobranchs, manta and devil rays (Mobula spp.), are threatened globally by targeted and bycatch fishing pressures resulting in recent protection under several global conventions. However, a lack of global data, morphological similarities, a succession of recent taxonomic changes and ineffectual traceability measures combine to impede development and implementation of a coherent and enforceable conservation strategy. Here, we generate genome-wide Single Nucleotide Polymorphism (SNP) data from among the most globally and taxonomically representative set of mobulid tissues. The resulting phylogeny and delimitation of species units represents the most comprehensive assessment of mobulid diversity with molecular data to date. We find a mismatch between current species classifications, and optimal species units for effective conservation. Specifically, we find robust evidence for an undescribed species of manta ray in the Gulf of Mexico and show that species recently synonymised are reproductively isolated. Further resolution is achieved at the population level, where cryptic diversity is detected in geographically distinct populations, and indicates potential for future traceability work determining regional location of catch. We estimate the optimal species tree and uncover substantial incomplete lineage sorting, where standing variation in extinct ancestral populations is identified as a driver of phylogenetic uncertainty, with further conservation implications. Our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.

genomics↗