Biology subjects

Lamare, M.

Publications and source records attributed to Lamare, M..

6 recordsLinked to original sources

bioRxiv2025

Recovering historical fish eDNA from museum-preserved Antarctic filter feeders via non-destructive metabarcoding.

O_LIRecent technical advances have significantly enhanced the value of museum specimens for molecular research, with metagenomic and metabarcoding approaches expanding further the utility of museum collections. However, given the finite number of specimens, there is a critical need to move past destructive DNA extraction approaches and to explore non-destructive techniques. C_LIO_LIIn this study, we evaluated the feasibility of extracting historical fish eDNA from the ethanol preservative used to store Antarctic museum specimens. We compared a variety of extraction methods - centrifugation, evaporation, filtration, and precipitation - using ten replicate samples per treatment for statistical analyses. To assess potential differences in preservative-derived eDNA recovery across different filter-feeding taxonomic groups, we included a Bryozoa and two Porifera, i.e., Demospongiae and Hexactinellida. C_LIO_LIComparative analyses with tissue biopsies revealed that the total genomic DNA was significantly reduced for non-destructive approaches. However, 10 ml ethanol filtration performed equal to, or in some instances, outperformed tissue biopsies when investigating the historical eDNA of Antarctic fish using a 16S rRNA metabarcoding approach, both for the number of species detected (-diversity) and community characterisation ({beta}-diversity). C_LIO_LIOur findings demonstrate the potential of ethanol preservative as a valuable, non-destructive source of historical fish eDNA from museum-stored filter-feeding specimens. These results highlight the viability of non-destructive sampling for molecular research on museum collections, preserving specimen integrity while enabling biodiversity assessments. Further refinement of non-destructive eDNA extraction could expand its applicability across taxa, collection types, and preservation methods, ensuring the long-term sustainability of museum-based genomic research. C_LI

ecology↗

bioRxiv2025

The genome of the charismatic sea star Linckia laevigata

Linckia laevigata is a tropical sea star commonly found throughout the Indian and Pacific Oceans, and is one of the top ten-most collected invertebrates, often encountered in the aquarium trade. It has been the subject of investigations into population structure, biodiversity and ecology, particularly regarding gene flow among populations throughout its range, the status of different colour morphs and its relationship with its putative sister species, L. multifora. Here we present and describe a high-quality genome assembly for L. laevigata. Our assembly is 585.97 Mb in length, with a scaffold N50 of 3 Mb. The genome has a typical repeat (36.99%) and GC content (41.33%), when compared with other echinoderm datasets. Our genome annotation recovers 16,178 genes, with high (89.4%) recovery of the metazoan BUSCO set. This novel resource will provide a model organism for studying the biogeography of the tropical Indo-West Pacific region, and more specifically facilitate the investigation of a range of sea star traits at the genomic level. SignificanceSea stars remain poorly characterised at a genomic level. Data from the charismatic tropical sea star Linckia laevigata will enable future studies into the biology, population structure and evolution of these ecologically important species.

genetics↗

bioRxiv2024

tombRaider - improved species and haplotype recovery from metabarcoding data through artefact and pseudogene exclusion.

Environmental DNA metabarcoding has revolutionized ecological surveys of natural systems. By amplifying and sequencing small gene fragments from environmental samples containing complex DNA mixtures, scientists are now capable of exploring biodiversity patterns across the tree of life in a time-efficient and cost-effective manner. However, the accuracy of species and haplotype identification can be compromised by sequence artefacts and pseudogenes. Despite various strategies developed over the years, effective removal of artefacts remains challenging and inconsistent data reporting standards hinder reproducibility in eDNA metabarcoding experiments. To address these issues, we introduce tombRaider, an open-source command line software program (https://github.com/gjeunen/tombRaider) and R package (https://github.com/gjeunen/tombRaider_R) to remove artefacts and pseudogenes from metabarcoding data post clustering and denoising. tombRaider features a modular algorithm capable of evaluating multiple criteria, including sequence similarity, co-occurrence patterns, taxonomic assignment, and the presence of stop codons. We validated tombRaider using various published data sets, including mock invertebrate communities, air eDNA from a zoo, and salmon haplotypes from aquatic eDNA. Our results demonstrate that tombRaider effectively removed a higher proportion of artefacts while retaining authentic sequences, thus enhancing the accuracy and reliability of eDNA-derived diversity metrics. This user-friendly software program not only improves data quality in eDNA metabarcoding studies, but also contributes to standardised reporting practices, an aspect currently lacking in this emerging research field.

bioinformatics↗

bioRxiv2024

Unlocking Antarctic molecular time-capsules - recovering historical environmental DNA from museum-preserved sponges

Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA (heDNA), trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.

molecular biology↗

bioRxiv2021

Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring

Aquatic environmental DNA (eDNA) surveys are transforming how we monitor marine ecosystems. The time-consuming pre-processing step of active filtration, however, remains a bottleneck. Hence, new approaches omitting active filtration are in great demand. One exciting prospect is to use the filtering power of invertebrates to collect eDNA. While proof-of-concept has been achieved, comparative studies between aquatic and filter feeder eDNA signals are lacking. Here, we investigated the differences among four eDNA sources (water; bivalves; sponges; and ethanol in which filter-feeding organisms were stored) along a vertical transect in Doubtful Sound, New Zealand using three metabarcoding primers (fish (16S); MiFish-E/U). While concurrent SCUBA diver observations validated eDNA results, laboratory trials corroborated in-field bivalve eDNA detection results. Combined, eDNA sources detected 59 vertebrates, while divers observed eight fish species. There were no significant differences in alpha and beta diversity between water and sponge eDNA and both sources were highly correlated. Vertebrate eDNA was detected in ethanol, although only a reduced number of species were detected. Bivalves failed to reliably detect eDNA in both field and mesocosm experiments. While additional research into filter feeder eDNA accumulation efficiency is essential, our results provide strong evidence for the potential of incorporating sponges into eDNA surveys.

molecular biology↗

bioRxiv2021

Identification and characterisation of Botrylloides species from Aotearoa New Zealand coasts

Ascidians are marine filter feeder primitive chordates. Botrylloides ascidians possess diverse biological abilities like whole-body regeneration (WBR), hibernation/aestivation, blastogenesis, metamorphosis, and natural chimerism. However, the absence of distinctive morphological features often makes identification problematic. Botrylloides diegensis is an ascidian that has been misidentified in previous studies and is recorded in GenBank as Botrylloides leachii due to the high morphological similarity between the sister species. More available sequences and strategies around identification would help resolve some of the confusion currently surrounding its ambiguous nature. We collected several Botrylloides samples from 7 locations around New Zealand - Dunedin, Christchurch, Picton, Nelson, Whangateau, New Plymouth and Invercargill - and barcoded the species based on Cytochrome Oxidase I, Histone 3, 18S, and 28S ribosomal RNA markers. Network and Bayesian trees confirmed the presence of three Botrylloides species: B. diegensis, B. jacksonianum, and B. aff. anceps. Additionally, morphotypes of three species were investigated regarding zooid size, area, tentacle numbers and colonial arrangement.

genetics↗