Pinder, A. | Search bioRxiv

bioRxiv2024

What are the best practices for curating eDNA custom barcode reference libraries? A case study using Australian subterranean fauna.

Identification of species for environmental assessment and monitoring is essential for understanding anthropogenic impacts on biodiversity, but for subterranean fauna this task is frequently difficult and time consuming. The implementation of environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improving the rate, accuracy and efficiency of species detection in ecosystems both above and below the ground. Importantly, for a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata--i.e., a barcode reference library (BRL)--is required. Yet, minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, that permits metadata and has a unified nomenclature) and accurate (i.e. verified) custom BRL can be achieved. Here, we present a detailed roadmap for curation of a BRL for subterranean fauna. To do this, we (1) curated a custom sequence database of subterranean fauna at an environmentally sensitive location, Bungaroo Creek in the Pilbara region of Western Australia, for four gene loci useful for eDNA metabarcoding (COI, 18S rRNA, 12S rRNA and 16S rRNA); (2) addressed major gaps in taxonomy and disparate nomenclature of subterranean fauna by estimating 17-29 putative new species with standard delimitation methods, including 34 Barcode Index Numbers (BINs) in BOLD, and (3) summarised a best practice workflow for curation of a custom BRL that has broad applicability and can be applied to any taxa. Scientific Significance StatementIn threatened ecosystems, environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers considerable promise for improvement in the rate, efficiency and accuracy of species detection. For a better understanding of the biodiversity and ecology of organisms detected using eDNA, a custom library of known reference sequences with associated correct taxonomic metadata is required. Minimal guidance is currently available on how an effective (i.e. shareable, multi-sequence, permits metadata and provides a unified nomenclature) custom barcode reference library (BRL) can be achieved for subterranean fauna. Here, we present a road map for sound and reliable curation of a BRL using subterranean fauna from Australia as a case study.

evolutionary biology↗

bioRxiv2022

Seascape genomics reveals limited dispersal and suggest spatially varying selection among European populations of sea lamprey (Petromyzon marinus)

Sea lamprey Petromyzon marinus is an anadromous and semelparous fish without homing behaviours. Despite being a freshwater, free-living organism for large part of their life cycle, its adulthood is spent as a parasite of marine vertebrates. In their native European range, while it is well-established that sea lampreys comprise a single nearly-panmictic population, few studies have further explored the evolutionary history of natural populations. Here, we performed the first genome-wide characterization of sea lampreys genetic diversity in their European natural range. The objectives were to investigate the connectivity among river basins and explore evolutionary processes mediating dispersal during the marine phase, with the sequencing 186 individuals from 8 locations spanning the North Eastern Atlantic coast and the North Sea with double-digest RAD-sequencing, obtaining a total of 30910 bi-allelic SNPs. Population genetic analyses reinforced the existence of a single metapopulation encompassing freshwater spawning sites within the north eastern Atlantic and the North Sea, though the prevalence of private alleles at northern latitudes suggested some limits to the species dispersal. Seascape genomics suggested a scenario where oxygen concentration and river runoffs impose spatially varying selection across their distribution range. Exploring associations with abundance of potential hosts further suggested that hake and cod could also impose selective pressures, although the nature of such putative biotic interactions was unresolved. Overall, the identification of adaptive seascapes in a panmictic anadromous species could contribute to conservation practices by providing information for restoration activities to mitigate local extinctions on freshwater sites. Sea lamprey Petromyzon marinus is an anadromous and semelparous fish without homing behaviours. Despite being a freshwater, free-living organism for large part of its life cycle, its adulthood is spent as a parasite of marine vertebrates. Here, we performed the first genome-wide characterization of sea lampreys genetic diversity in their European natural range. The objectives were to investigate the connectivity among river basins and explore evolutionary processes mediating dispersal during the marine phase. For that, we sequenced 186 individuals from 8 locations spanning the North-eastern Atlantic coast and the North Sea with double-digest RAD-sequencing, obtaining a total of 30910 bi-allelic SNPs. Population genomic analyses reinforced the existence of a single metapopulation encompassing freshwater spawning sites within the north-eastern Atlantic and the North Sea, though the prevalence of private alleles at northern latitudes suggested some limits to the species dispersal. Seascape analyses revealed candidate loci associated with the abundance of some host species and were located in a genomic region coding for variable lymphocyte receptors, an adaptive immunity tool unique to jawless vertebrates, and to MARCH proteins, a family of E3 ubiquitin ligases also involved in the regulation of immune responses. Abiotic factors (e.g., maximum phosphate, dissolved oxygen and water temperature) were significantly correlated with candidate loci associated with the myo-inositol synthesis, a pathway linked to osmoregulation, and to other genomic regions involved in organismal homeostasis. The identification of adaptive seascapes in this ancient species, especially if linked to primitive adaptive immune responses, could be relevant to understand the evolutionary pathways early in vertebrate evolution.

evolutionary biology↗