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"Hubert, Nicolas"
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Identifying Canadian Freshwater Fishes through DNA Barcodes
DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5' region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons.
We bi-directionally sequenced the standard 652 bp \"barcode\" region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species.
The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.
Journal Article
Cryptic Diversity in Indo-Pacific Coral-Reef Fishes Revealed by DNA-Barcoding Provides New Support to the Centre-of-Overlap Hypothesis
Diversity in coral reef fishes is not evenly distributed and tends to accumulate in the Indo-Malay-Philippines Archipelago (IMPA). The comprehension of the mechanisms that initiated this pattern is in its infancy despite its importance for the conservation of coral reefs. Considering the IMPA either as an area of overlap or a cradle of marine biodiversity, the hypotheses proposed to account for this pattern rely on extant knowledge about taxonomy and species range distribution. The recent large-scale use of standard molecular data (DNA barcoding), however, has revealed the importance of taking into account cryptic diversity when assessing tropical biodiversity. We DNA barcoded 2276 specimens belonging to 668 coral reef fish species through a collaborative effort conducted concomitantly in both Indian and Pacific oceans to appraise the importance of cryptic diversity in species with an Indo-Pacific distribution range. Of the 141 species sampled on each side of the IMPA, 62 presented no spatial structure whereas 67 exhibited divergent lineages on each side of the IMPA with K2P distances ranging between 1% and 12%, and 12 presented several lineages with K2P distances ranging between 3% and 22%. Thus, from this initial pool of 141 nominal species with Indo-Pacific distribution, 79 dissolved into 165 biological units among which 162 were found in a single ocean. This result is consistent with the view that the IMPA accumulates diversity as a consequence of its geological history, its location on the junction between the two main tropical oceans and the presence of a land bridge during glacial times in the IMPA that fostered allopatric divergence and secondary contacts between the Indian and Pacific oceans.
Journal Article
Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia)
The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass‐based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass‐based approaches. Recent meta‐analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
The Coral Triangle is home of the highest marine biodiversity. Artisanal fisheries are extremely important in the Coral Triangle. Fish species are poorly known and hardly identifiable. We propose a DNA barcode reference library for the fish harvested by the artisanal fisheries in Ambon Island.
Journal Article
Post-2000 milestones in freshwater fish taxonomy: a comprehensive review of newly described species in Türkiye
The 2000s are the revolutionary decade for the taxonomy of freshwater fishes of Türkiye in terms of the most significant ever rate of increase in species descriptions. Among the approximately 390 freshwater fish species reported from Türkiye, a remarkable 136 have been described since 2000, reflecting an accelerated pace of taxonomic and morphological activity. This surge has been prompted by the influx of new researchers and the widespread adoption of molecular sequencing techniques, currently at the center of taxonomic work since the 2010s. This synthesis gives a complete view of these 136 new species named, examining predominant parameters such as genera, descriptors, contributing countries, and the chronological order of discoveries. The results are presented through visual data, which help illustrate the progress in taxonomic research and the contributions of international collaboration. The study also highlights the rapid development of freshwater biodiversity research in Türkiye and emphasizes the value of using integrated methods and global partnerships to better understand less-studied aquatic species. The bibliometric analysis indicates that a substantial proportion of new species descriptions is ascribed to a limited cohort of prolific researchers, with the majority of contributions made by a core group of the top 10 authors. These discoveries not only augment our comprehension of Türkiye’s freshwater fish fauna but also illuminate broader trends influencing taxonomic study in the 21 st century.
Journal Article
“Alarm-corrected” ergonomic armrest use could improve learning curves of novices on robotic simulator
Background
In robotic surgery, the professional ergonomic habit of using an armrest reduces operator fatigue and increases the precision of motion. We designed and validated a pressure surveillance system (PSS) based on force sensors to investigate armrest use. The objective was to evaluate whether adding an alarm to the PSS system could shorten ergonomic training and improve performance.
Study design
Twenty robot and simulator-naïve participants were recruited and randomized in two groups (A and B). The PSS was installed on a robotic simulator, the dV-Trainer, to detect contact with the armrest. The Group A members completed three tasks on the dV-Trainer without the alarm, making 15 attempts at each task. The Group B members practiced the first two tasks with the alarm and then completed the final tasks without the alarm. The simulator provided an overall score reflecting the trainees’ performance. We used the new concept of an “armrest load” score to describe the ergonomic habit of using the armrest.
Results
Group B had a significantly higher performance score (
p
< 0.001) and armrest load score (
p
< 0.001) than Group A from the fifth attempt of the first task to the end of the experiment.
Conclusions
Based on the conditioned reflex effect, the alarm associated with the PSS rectified ergonomic errors and accelerated professional ergonomic habit acquisition. The combination of the PSS and alarm is effective in significantly shortening the learning curve in the robotic training process.
Journal Article
Aquatic Organisms Research with DNA Barcodes
Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.
Journal Article
Revised diagnoses of the gudgeons Belobranchus belobranchus and B. segura (Actinopterygii, Gobiiformes, Eleotridae)
Diagnostic characters distinguishing the gudgeons Belobranchus belobranchus and Belobranchus segura were reassessed and found to be inconsistent, making it difficult to accurately identify them. Numerous specimens of both species were examined combining genetic (mitochondrial COI gene) and morpho-meristic analyses. Our findings demonstrate that B. belobranchus and B. segura can be reliably distinguished from each other based on revised diagnostic characters, including several morphometric features (interorbital width, jaw length, and caudal-peduncle depth) as well as distinct head, body, and fin coloration.
Journal Article
DNA barcode reference library of the fish larvae and eggs of the South China Sea: taxonomic effectiveness and geographic structure
Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.
Journal Article
DNA barcoding the ichthyofauna of the Beibu Gulf: Implications for fisheries management in a seafood market hub
The Beibu Gulf in China is situated in the tropics, in the western Pacific Ocean. It is an emblematic region combining proximity to a marine biodiversity hotspot and a major seafood hub. Intensification of marine fishing and ocean warming led to a drastic decline in fish populations in the Beibu Gulf during the last decades. This situation urges the development of molecular resources of the Beibu Gulf fish fauna in order to enable automated molecular identifications at the species level for next‐generation monitoring. With this objective, we present the results of a large‐scale campaign to DNA barcode fishes of the Beibu Gulf. We successfully generated 789 new DNA barcodes corresponding to 263 species which, together with 291 sequences mined from Genbank and BOLD, resulted in a reference library of 1080 sequences from 285 species. Based on the use of four DNA‐based species delimitation methods (BIN, ASAP, mPTP, mGMYC), a total of 285 Molecular Operational Taxonomical Units (MOTUs). A single case of cryptic diversity was detected in Scomberomorus guttatus and a single species pair was not captured by delimitation methods. Intraspecific K2P genetic distances averaged 0.36% among sequences within species, whereas K2P genetic distances among species within genera averaged 6.96%. The most speciose families in open water trawling differ from those at fish market, and discrepancies with historical data are discussed in the light of recently documented stock collapses.
The fish fauna of the beibu gulf, one of the largest sea food hubs in Southeast Asia, is characterized here by DNA barcoding. The 1080 DNA barcodes analyzed show concordance between morphological identifications and DNA‐based species delimitation. Lower level of diversity detected here compared to historical observations is concordant with the stock collapses previously described in the literature for the area. This study opens new perspectives by enabling next‐generation monitoring of the 285 species DNA barcoded here.
Journal Article