Canchaya, C. | Search bioRxiv

bioRxiv2021

The spatial network structure of intertidal meiofaunal communities derived from environmental DNA metabarcoding surveys in Northwest Iberia

The identification of the patterns and mechanisms behind species distribution is one of the major challenges in ecology, having also important outcomes for the conservation and management of ecosystems. This is especially true for those components of biodiversity providing essential ecosystem functions and for which standard surveys may underestimate their real taxonomic diversity due to their high degree of cryptic diversity and inherent diagnosis difficulties, such as meiofaunal communities. Environmental DNA (eDNA) metabarcoding may provide a fast and reliable way to refine and scale-up the characterization of biological diversity in complex environmental samples, allowing to bypass such drawbacks and increase the resolution of biodiversity estimates. Moreover, the possibility of integrating eDNA metabarcoding-derived data with tools and methods rooted in network theory would deepen the knowledge of the structuring processes of ecological communities in ways that cannot be predicted from studying individual species/communities in isolation. Here, a sediment eDNA metabarcoding of mitochondrial cytochrome c oxidase I (COI) and the nuclear hypervariable V4 region of the 18S rDNA (18S) was used to reconstruct the spatial networks of intertidal meiofaunal OTUs from three estuaries of North-Western Iberian Peninsula. Null models were used to identify the role of environmental and spatial constraints on the structure of COI- and 18S-derived spatial networks and to characterize the macroecological features of surveyed phyla. Our results show the feasibility of eDNA metabarcoding, not only to capture a fair amount of diversity hard to detect with standard surveys procedures, but also to identify hierarchical spatial structures in intertidal meiofaunal assemblages. This suggests that exclusivity of occurrence rather than pervasiveness appears to be the norm in meiofaunal organisms and that niche-based processes predominantly drive the spatial aggregation and contemporary distribution of meiofaunal phyla within the system.

ecology↗

bioRxiv2019

Massive gene presence/absence variation in the mussel genome as an adaptive strategy: first evidence of a pan-genome in Metazoa

Mussels are ecologically and economically relevant edible marine bivalves, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other species. Here we show that the Mediterranean mussel Mytilus galloprovincialis has a complex pan-genomic architecture, which includes a core set of 45,000 genes shared by all individuals plus a surprisingly high number of dispensable genes ([~]15,000). The latter are subject to presence/absence variation (PAV), i.e., they may be entirely missing in a given individual and, when present, they are frequently found as a single copy. The enrichment of dispensable genes in survival functions suggests an adaptive value for PAV, which might be the key to explain the extraordinary capabilities of adaptation and invasiveness of this species. Our study underpins a unique metazoan pan-genome architecture only previously described in prokaryotes and in a few non-metazoan eukaryotes, but that might also characterize other marine invertebrates.\n\nSignificance statementIn animals, intraspecific genomic diversity is generally thought to derive from relatively small-scale variants, such as single nucleotide polymorphisms, small indels, duplications, inversions and translocations. On the other hand, large-scale structural variations which involve the loss of genomic regions encoding protein-coding genes in some individuals (i.e. presence/absence variation, PAV) have been so far only described in bacteria and, occasionally, in plants and fungi. Here we report the first evidence of a pan-genome in the animal kingdom, revealing that 25% of the genes of the Mediterranean mussel are subject to PAV. We show that this unique feature might have an adaptive value, due to the involvement of dispensable genes in functions related with defense and survival.

genetics↗