Identifying coral reef fish larvae through DNA barcoding: A test case with the families Acanthuridae and Holocentridae

Hubert, Nicolas; Delrieu‐Trottin, Erwan; Irisson, Jean‐Olivier; Meyer, Christopher P.; Planes, Serge

doi:10.1016/j.ympev.2010.02.023

Cited by 110 publications

(73 citation statements)

References 34 publications

(39 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A number of papers have used DNA barcoding to identify a range of larvae more or less as a proof of concept (e.g. Zhang et al 2004;Pegg et al 2006;Hubert et al 2010;Ko et al 2013), but, unfortunately, have not taken the next step and provided descriptions or diagnoses of the larvae thus identified and, in some cases, have neglected to deposit their study specimens in an archival collection. Hubert et al (2014) provided digital photographs of the larvae they barcoded as part of their BOLD entries.…”

Section: Ontogeny and Systematicsmentioning

confidence: 99%

Taxonomy and systematics of larval Indo-Pacific fishes: a review of progress since 1981

J.M

2014

Ichthyol Res

View full text Add to dashboard Cite

This paper reviews progress in research on taxonomy and systematics of larval marine and estuarine fishes in the Indo-Pacific since the first Indo-Pacific Fish Conference in 1981. In 1981, the literature on development of fish larvae in the vast Indo-Pacific region was sparse, scattered and of very uneven quality. During the intervening 33 years, taxonomy of adult Indo-Pacific fishes has improved greatly, the proceedings of the landmark Ahlstrom Symposium were published, a large number of larval-fish atlases, or identification guides, have been produced, and the quality of descriptions of larval-fish development in journals has greatly increased. This has resulted in a great improvement in our ability to identify Indo-Pacific fish larvae, particularly oceanic taxa. However, much remains to be done, with the large majority of families having \50 % of species with described larvae, and with only a small proportion of species descriptions based on full developmental series of larvae. DNA technology has helped to establish identities of larvae, but only a small proportion of the larvae so identified have been described, so the potential for DNA to advance larval taxonomy is largely untapped. An integrative approach combining genetics and morphology is required. Online publication of descriptions of larval development and of interactive identification guides to larvae is the most efficient way to make such information available and useful to a variety of users. The great potential for larval-fish ontogeny to contribute to the study of phylogeny of marine fishes has been underrealized. The ageing of current larvalfish taxonomists, and the lack of positions for younger replacement researchers, is a major obstacle to further progress.

show abstract

Section: Ontogeny and Systematicsmentioning

confidence: 99%

Taxonomy and systematics of larval Indo-Pacific fishes: a review of progress since 1981

J.M

2014

Ichthyol Res

View full text Add to dashboard Cite

show abstract

“…The limited number of characters, the multiple developmental stages, and the small size of immatures complicate taxonomic assignments (Busby et al 2000;Baldwin andSmith 2003, Richards 2006), making it unlikely that any comprehensive morphological identification system will be developed (Leis and Hay 2004). Molecular methods have gained increasing recognition as an alternative tool for species identification (Garland and Zimmer 2002), and several studies (e.g., Hubert et al 2010;Ko et al 2013;Valdez-Moreno et al 2010) have confirmed that one of these approaches, DNA barcoding, is a powerful tool for identifying larval fishes.…”

Section: Introductionmentioning

confidence: 99%

Linking adults and immatures of South African marine fishes

Steinke

Connell

Hebert

2016

Genome

View full text Add to dashboard Cite

Abstract:The early life-history stages of fishes are poorly known, impeding acquisition of the identifications needed to monitor larval recruitment and year-class strength. A comprehensive database of COI sequences, linked to authoritatively identified voucher specimens, promises to change this situation, representing a significant advance for fisheries science. Barcode records were obtained from 2526 early larvae and pelagic eggs of fishes collected on the inshore shelf within 5 km of the KwaZulu-Natal coast, about 50 km south of Durban, South Africa. Barcodes were also obtained from 3215 adults, representing 946 South African fish species. Using the COI reference library on BOLD based on adults, 89% of the immature fishes could be identified to a species level; they represented 450 species. Most of the uncertain sequences could be assigned to a genus, family, or order; only 92 specimens (4%) were unassigned. Accumulation curves based on inference of phylogenetic diversity indicate near-completeness of the collecting effort. The entire set of adult and larval fishes included 1006 species, representing 43% of all fish species known from South African waters. However, this total included 189 species not previously recorded from this region. The fact that almost 90% of the immatures gained a species identification demonstrates the power and completeness of the DNA barcode reference library for fishes generated during the 10 years of FishBOL.Key words: DNA barcoding, fish, larval fish, fish eggs.Résumé : Les premiers stades de développement des poissons sont peu connus, ce qui limite l'acquisition des identifications requises pour suivre le recrutement larvaire et l'abondance d'une cohorte annuelle. Une base de données extensives des séquences COI, associée à des spécimens de référence identifiés par des autorités en la matière, promet de changer cette situation et représente une avancée significative pour les sciences aquatiques. Des codes à barres ont été obtenus pour 2526 stades larvaires précoces ou d'oeufs pélagiques d'espèces de poissons échantillonnés sur le plateau continental à l'intérieur d'une zone de 5 km de la côte du KwaZulu-Natal, à environ 50 km au sud de Durban, en Afrique du Sud. Des codes à barres ont également été obtenus pour 3215 adultes représentant 946 espèces de poissons d'Afrique du Sud. À l'aide d'une collection de référence COI sur BOLD, basée sur des poissons adultes, 89 % des poissons immatures ont été identifiés au niveau de l'espèce; ils représentaient au-delà de 450 espèces. La plupart des séquences d'origine incertaine ont été assignées à un genre, une famille ou un ordre et seuls 92 spécimens (4 %) sont demeurés non-assignés. Les courbes d'accumulation basées sur une inférence de la diversité phylogénétique suggèrent que l'effort d'échantillonnage s'est avéré presque complet. La collection entière de poissons adultes et immatures comprenait 1006 espèces, ce que représente 43 % de toutes les espèces connues dans les eaux de l'Afrique du Sud. Cependant, ce total comprend 189 espèces...

show abstract

“…The dominant families, however, varies among biogeographical provinces as Sundaland is dominated by the Cyprinidae (231 species; changes during ontogeny, fish identification is not an easy task. After almost a decade, it has become evident that DNA barcoding presents several advantages compared to morphological characters for species identification including: (1) intraspecific phenotypic variation often overlaps that of sister taxa in nature, which can lead to incorrect identifications or species delineations [21,22], (2) DNA barcodes are effective whatever the life stages under scrutiny [23,24] or available biological materials for identification [25,26], (3) spectacular levels of cryptic diversity have been frequently reported using DNA barcoding [21,[27][28][29][30][31].…”

Section: Introductionmentioning

confidence: 99%

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Hubert¹,

Kadarusman²,

Wibowo³

et al. 2015

DNA Barcodes

Self Cite

View full text Add to dashboard Cite

With 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.

show abstract

Identifying coral reef fish larvae through DNA barcoding: A test case with the families Acanthuridae and Holocentridae

Cited by 110 publications

References 34 publications

Taxonomy and systematics of larval Indo-Pacific fishes: a review of progress since 1981

Taxonomy and systematics of larval Indo-Pacific fishes: a review of progress since 1981

Linking adults and immatures of South African marine fishes

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Contact Info

Product

Resources

About