Estimating the extended and hidden species diversity from environmental DNA in hyper-diverse regions

Species inventories are the building blocks of our assessment of biodiversity patterns and human impact. Yet, historical inventories based on visual observations are often incomplete, impairing subsequent analyses of ecological mechanisms, extinction risk and management success. Environmental DNA (eDNA) metabarcoding is an emerging tool that can provide wider biodiversity assessments than classical visual-based surveys. However, eDNA-based inventories remain limited by sampling effort and reference database incompleteness. In this study, we propose a new framework coupling eDNA surveys and sampling-theory methods to estimate species richness in under-sampled and hyper-diverse regions where some species remain absent from the checklist or undetected by visual surveys. We applied this framework to the coastal fish diversity in the heart of the coral triangle, the richest marine biodiversity hotspot worldwide. Combining data from 279 underwater visual censuses, 92 eDNA samples and an extensive custom genetic reference database, we show that eDNA metabarcoding recorded 196 putative species not detected by underwater visual census including 37 species absent from the regional checklist. We provide an updated checklist of marine fishes in the ‘Raja Ampat Bird's Head Peninsula' ecoregion with 2534 species including 1761 confirmed and 773 highly probable presences. The Chao lower-bound diversity estimator, based on the incidence of rare species, shows that the region potentially hosts an additional 123 fish species, including pelagic, cryptobenthic and vulnerable species. The extended and hidden biodiversity along with their asymptotic estimates highlight the ability of eDNA to expand regional inventories and species distributions to better guide conservation strategies

Phylogeography of long-spined sea urchin Diadema setosum across the Indo-Malay archipelago

Widely distributed, broadcast-spawning Diadema sea urchins have been used as model in-vertebrate species for studying the zoogeography of the tropical Indo-Pacific. So far, the Indo-Malay archipelago, a wide and geographically complex maritime region extending from the eastern Indian Ocean to the western Pacific Ocean, has been under-sampled. This study aims to fill this sampling gap and uncover the phylogeographic structure of the long-spined sea-urchin D. setosum in the central Indo-West pacific region. D. setosum samples (total N = 718) were collected in 13 sites throughout the Indo-Malay archipelago. We se-quenced 1157 base pairs of the COI gene. The phylogeographic structure was derived from pairwise Фst estimates using multidimensional scaling and hierarchical clustering analysis; biogeographic hypotheses were tested by AMOVA; genetic relationships between haplo-types were summarised in the form of a minimum-spanning network; pairwise mismatch distributions were compared to the expectations from demographic and spatial expansion models. All samples from the Indo-West Pacific were of the previously uncovered D. se-tosum-a lineage. Phylogeographic structure was evident: the Andaman Sea population and the northern New Guinea population were genetically distinct. Subtler but significant hap-lotype-frequency differences distinguished two populations within the Indonesian seas, distributed in a parapatric-like fashion. The phylogeographic partition observed was insuffi-ciently explained by previous biogeographic hypotheses. The haplotype network showed a series of closely related star-shaped haplogroups with a high proportion of singletons. Nu-cleotide-pairwise mismatch patterns in the two populations from the Indonesian seas were consistent with both demographic and spatial expansion models. While geographic barriers to gene flow were inferred at the western and eastern extremities of the Indo-Malay archi-pelago, the subtler parapatric pattern observed within the Indonesian seas indicated re-striction in gene flow, in a fashion that can hardly be explained by geographic isolation giv-en the dynamic current systems that cross this region. Our results thus raise the hypothesis of subtle reproductive isolation between ecologically incompatible populations. While the coalescence pattern of the Andaman-Sea population suggested demographic stability over evolutionary timescales, that of the two populations from the Indonesian seas indicated recent population expansion, possibly linked to the rapid changes in available D. setosum habitat caused by sea-level oscillations in the late Pleistocene. The phylogeographic pat-terns observed in this study point to likely allopatric differentiation in the central Indo-West Pacific region. Genetic differences between populations were likely reinforced during inter-glacials by some form of reproductive isolation

At the heart of the coral triangle in West Papua: an Indonesian-French scientific exploration of a white area with closed-circuit rebreathers (eCCR) : [poster]

International audienceThe Bird’s Head Isthmus connecting the Bird’s Head Peninsula with the rest of New Guinea is one of the last pristine areas remaining in Southeast Asia. Dominantly covered by limestone karsts, this vast region of West Papua (Indonesia) is still a terra incognita. At the heart of the coral triangle, the Kumawa and Lengguru limestone karsts and reef slopes are today a major biodiversity reservoir with high levels of endemism.The French-Indonesian ‘Lengguru 2014’ expedition was headed by IRD and P2O-LIPI, RCB-LIPI and POLTEK. Exploration and sampling effort were concentrated on several reef slopes from -100 m to the surface using closed-circuit rebreathers (eCCR) and open circuits. ‘Lengguru 2014’ expedition was the first French oceanographic campaign organized by a national and academic research organization to use the rebreather.The scientific diving operations were made under the responsibility of the French research institute IRD. Nevertheless, the French regulation presently only allows the use of rebreather for recreational uses. The main author participates as an expert for the Ministry of Labor to reform the law with specific applications to scientific purposes. This scientific expedition was therefore permitted in phase advance.The Lengguru 2014 expedition was organized in complete autonomy for 6 weeks. It required extensive preparation and logistics, as well as some strengthened safety procedures for scientific dives.Forty vertical transects have been performed from -100 meters depth to the surface, silently with great autonomy and optimized decompression. The exploration of flooded karsts by cave diving has been also possible with rebreather. It does not bubble and offers such autonomy. The use of eCCR offers together scientific benefits and enhanced diving safety.The ‘Lengguru 2014’ Expedition provided a science-based assessment of functional, genetic and morphological diversity for several marine biotas (echinoderms, hard corals, gorgonians, mollusks) with prime importance for biodiversity conservation

Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle

International audienceEnvironmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict (R² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation

Estimating the extended and hidden species diversity from environmental DNA in hyper‐diverse regions

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