, Reef fishes of the East Indies, vol.1260, 2012.
Applications of DNA barcoding to fish landings: Authentication and diversity assessment, ZooKeys, vol.365, pp.49-65, 2013. ,
Molecular Markers, Natural History and Evolution, 1989. ,
Movements and mortality rates of striped mullet in North Carolina, North American Journal of Fisheries Management, vol.25, issue.1, pp.361-373, 2005. ,
A comparative evaluation of sequence classification programs, BMC Bioinformatics, vol.13, issue.1, p.92, 2012. ,
Fish biogeography and molecular clocks: Perspectives from the Panamanian isthmus, Molecular systematics of fishes, pp.113-128, 1997. ,
Untangling taxonomy: A DNA barcode reference library for Canadian spiders, Molecular Ecology Resources, vol.16, issue.1, pp.325-341, 2016. ,
Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma), Molecular Ecology Resources, vol.17, pp.1168-1182, 2017. ,
Error cascades in the biological sciences: The unwanted consequences of using bad taxonomy in ecology, Ambio, vol.37, issue.2, pp.114-118, 2008. ,
BEAST 2: A software platform for Bayesian evolutionary analysis, PLoS Computational Biology, vol.10, 2014. ,
On the unreliability of published DNA sequences, New Phytologist, vol.160, issue.1, pp.43-48, 2003. ,
Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding, Molecular Ecology Resources, vol.12, issue.3, pp.562-565, 2012. ,
A turbo-taxonomic study of Thai Aleiodes (Aleiodes) and Aleiodes (Arcaleiodes) (Hymenoptera: Braconidae: Rogadiniae) based largely on COI barcoded specimens, with rapid descriptions of 179 new species, Zootaxa, vol.3457, pp.1-232, 2012. ,
Indo-Pacific biodiversity of coral reefs: Deviations from a mid-domain model, Ecology, vol.84, issue.8, pp.2178-2190, 2003. ,
Ecology and Culture of Grey Mullets (Mugilidae), Biology, 2016. ,
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities, Molecular Ecology, vol.26, issue.21, pp.5872-5895, 2017. ,
A DNA barcode reference library of French Polynesian shore fishes, Scientific Data, vol.6, issue.1, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02375604
The unholy trinity: Taxonomy, species delimitation and DNA barcoding, Philosophical Transactions of the Royal Society B-Biological Sciences, vol.360, pp.1905-1916, 2005. ,
Geography and life history traits account for the accumulation of cryptic diversity among Indo-West Pacific coral reef fishes, Marine Ecology Progress Series, vol.583, pp.179-193, 2017. ,
URL : https://hal.archives-ouvertes.fr/ird-01710958
Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea, Coral Reefs, vol.36, issue.4, pp.1245-1252, 2017. ,
Mitochondrial phylogeny of grey mullets (Acanthopterygii: Mugilidae) suggests high proportion of cryptic species, Comptes Rendus Biologies, vol.338, pp.266-277, 2015. ,
URL : https://hal.archives-ouvertes.fr/ird-01144054
DNA barcoding grey mullets, Reviews in Fish Biology and Fisheries, vol.27, issue.1, pp.233-243, 2017. ,
URL : https://hal.archives-ouvertes.fr/ird-01469968
Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): Molecular phylogenetic evidence challenges two centuries of morphology-based taxonomy, Molecular Phylogenetics and Evolution, vol.64, issue.1, pp.73-92, 2012. ,
URL : https://hal.archives-ouvertes.fr/ird-00695484
DNA Barcoding is no substitute for taxonomy, Nature, vol.434, 2005. ,
Multi-locus analyses reveal four giraffe species instead of one, Current Biology, vol.26, issue.18, pp.2543-2549, 2016. ,
Cryptic species as a window into the paradigm shift of the species concept, Molecular Ecology, vol.27, issue.3, pp.613-635, 2018. ,
Molecular barcodes for soil nematode identification, Molecular Ecology, vol.11, issue.4, pp.839-850, 2002. ,
, FishBase.www.fishb ase.org, 2019.
Delimiting species using single-locus data and the generalized mixed Yule coalescent approach: A revised method and evaluation on simulated data sets, Systematic Biology, vol.62, issue.5, pp.707-724, 2013. ,
DNA barcoding: How it complements taxonomy, molecular phylogenetics and population genetics, Trends in Genetics, vol.23, issue.4, pp.167-172, 2007. ,
Biological identifications through DNA barcodes, Proceedings of the Royal Society of London Series B, vol.270, pp.313-321, 2003. ,
The promise of DNA barcoding for taxonomy, Systematic Biology, vol.54, issue.5, pp.852-859, 2005. ,
Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator, Proceedings of the National Academy of Sciences of the United States of America, vol.101, pp.14812-14817, 2004. ,
Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species, Proceedings of the Royal Society of London Series B, vol.270, pp.96-99, 2003. ,
Identification of birds through DNA barcodes, PLoS Biology, vol.2, issue.10, pp.1657-1663, 2004. ,
A mirage of cryptic species: Genomics uncover striking mito-nuclear discordance in the butterfly Thymelicus sylvestris, Molecular Ecology, vol.28, pp.3857-3868, 2019. ,
DNA barcoding the ichthyofauna of the Yangtze River: Insights from the molecular inventory of a mega-diverse temperate fauna, Molecular Ecology Resources, vol.19, issue.5, pp.1278-1291, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01959415
Identifying early stages of coral reef fishes through DNA barcoding: A test case with the families Acanthuridae and Holocentridae, Molecular Phylogenetics and Evolution, vol.55, pp.1195-1203, 2010. ,
DNA barcoding, species delineation and taxonomy: A historical perspective, DNA Barcodes, vol.3, pp.44-58, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01958691
Identifying Canadian freshwater fishes through DNA barcodes, PLoS ONE, vol.3, issue.6, 2008. ,
Cryptic diversity in indo-pacific coral-reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis, PLoS ONE, vol.7, issue.3, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00722781
Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs, Ecology Letters, vol.5, issue.6, pp.775-784, 2002. ,
Universal primer cocktails for fish DNA barcoding, Molecular Ecology Notes, vol.7, issue.4, pp.544-548, 2007. ,
Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.360, pp.1835-1845, 1462. ,
Cryptic diversity in Indo-Australian rainbowfishes revealed by DNA barcoding: Implications for conservation in a biodiversity hotspot candidate, PLoS ONE, vol.7, issue.7, 2012. ,
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov Chain Monte Carlo, Bioinformatics, vol.33, pp.1630-1638, 2017. ,
DNA barcode-based delineation of putative species: Efficient start for taxonomic workflows, Molecular Ecology Resources, vol.14, pp.706-715, 2014. ,
Delineating species with DNA barcodes: A case of taxon dependent method performance in moths, PLoS ONE, vol.10, issue.4, 2015. ,
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.16, issue.2, pp.111-120, 1980. ,
The fishes of the inland waters of Southeast Asia: a catalog and core bibliography of the fishes known to occur in freshwaters, mangroves and estuaries. The Raffles Bulletin of Zoology, pp.1-663, 2013. ,
Freshwater fishes of Western Indonesia and Sulawesi, 1993. ,
DNA barcoding: Error rates based on comprehensive sampling, PLoS Biology, vol.3, issue.12, pp.2229-2238, 2005. ,
Patterns and processes in reef fish diversity, Nature, vol.421, pp.933-936, 2003. ,
Defining 'Evolutionary Significant Units' for conservation, Trends in Ecology and Evolution, vol.9, issue.10, pp.373-375, 1994. ,
Statistical assignment of DNA sequences using Bayesian phylogenetics, Systematic Biology, vol.57, issue.5, pp.750-757, 2008. ,
Fast phylogenetic DNA barcoding, Proceedings of the Royal Society of London Series B, vol.363, pp.3997-4002, 1512. ,
Estimating species richness using environmental DNA, Ecology and Evolution, vol.6, issue.12, pp.4214-4226, 2016. ,
APE: Analyses of phylogenetics and evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004. ,
URL : https://hal.archives-ouvertes.fr/ird-01887318
Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation, Proceedings of the Royal Society B: Biological Sciences, vol.286, 1900. ,
Sequence-based species delimitation for the DNA taxonomy of undescribed insects, Systematic Biology, vol.55, issue.4, pp.595-606, 2006. ,
ABGD, automatic barcode gap discovery for primary species delimitation, Molecular Ecology, vol.21, issue.8, pp.1864-1877, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00704914
Large-scale species delimitation method for hyperdiverse groups, R Foundation for Statistical Computing, vol.21, pp.2671-2691, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-02002432
BOLD: The Barcode of Life Data System (www.barcodinglife.org), Molecular Ecology Notes, vol.7, issue.3, pp.355-364, 2007. ,
A DNA-based registry for all animal species: The Barcode Index Number (BIN) system, PLoS ONE, vol.8, issue.7, 2013. ,
Patterns of biodiversity and endemism on Indo-West Pacific coral reefs, Proceedings of the National Academy of Sciences of the United States of America, vol.105, pp.11474-11481, 2008. ,
Integrative taxonomy on the fast track -Towards more sustainability in biodiversity research, Frontiers in Zoology, vol.10, p.15, 2013. ,
The biogeography of Mugilidae in India, Biology, ecology and culture of grey mullets (Mugilidae), 2016. ,
Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections, Proceedings of the National Academy of Sciences of the United States of America, vol.105, pp.12359-12364, 2008. ,
DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists, Proceedings of the National Academy of Sciences of the United States of America, vol.104, pp.4967-4972, 2007. ,
Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate, Molecular Ecology Resources, vol.10, issue.6, pp.1009-1018, 2010. ,
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1313, 2014. ,
DNA barcoding for community ecology -How to tackle a hyperdiverse, mostly undescribed melanesian fauna, PLoS ONE, vol.7, 2012. ,
The Mugilidae of the world, Memoirs of the Queensland Museum, vol.43, pp.457-562, 1997. ,
The biogeography of mitochondrial and nuclear discordance in animals, Molecular Ecology, vol.21, issue.16, pp.3907-3930, 2012. ,
Taxonomic misidentification in public DNA databases, New Phytologist, vol.160, issue.1, pp.4-5, 2003. ,
Diagnosing units of conservation management, Conservation Biology, vol.6, pp.170-178, 1994. ,
The campaign to DNA barcode all fishes, FISH-BOL, Journal of Fish Biology, vol.74, issue.2, pp.329-356, 2009. ,
Market fishes of Indonesia, 2013. ,
A global review of the cosmopolitan flathead mullet Mugil cephalus Linnaeus 1758 (Teleostei: Mugilidae), with emphasis on the biology, genetics, ecology and fisheries aspects of this apparent species complex, Reviews in Fish Biology and Fisheries, vol.22, issue.3, pp.641-681, 2012. ,
The perils of DNA barcoding and the need for integrative taxonomy, Systematic Biology, vol.54, issue.5, pp.844-851, 2005. ,
Fifty thousand years of Arctic vegetation and megafaunal diet, Nature, vol.506, issue.7486, pp.47-51, 2014. ,
A cornucopia of cryptic species -A DNA barcode analysis of the gobiid genus Trimma (Percomorpha, Gobiiformes), ZooKeys, vol.381, pp.79-111, 2014. ,
Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy, Molecular Phylogenetics and Evolution, vol.96, pp.161-177, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01922355
A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods, PLoS ONE, vol.7, issue.2, pp.1-13, 2012. ,
BarcodingR: An integrated r package for species identification using DNA barcodes, Methods in Ecology and Evolution, vol.8, issue.5, pp.627-634, 2017. ,
A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding, Molecular Ecology, vol.21, issue.8, pp.1848-1863, 2012. ,
A general species delimitation method with applications to phylogenetic placements, Bioinformatics, vol.29, issue.22, pp.2869-2876, 2013. ,
Inferring species membership using DNA sequences with back-propagation neural networks, Systematic Biology, vol.57, pp.202-215, 2008. ,
BPSI2.0: a C/C++ interface program for species identification via DNA barcoding with a BP-neural network by calling the Matlab engine, Molecular Ecology Resources, vol.9, pp.104-106, 2009. ,
Additional supporting information may be found online in the Supporting Information section ,
Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods, Evol Appl, vol.00, pp.1-17, 2020. ,
URL : https://hal.archives-ouvertes.fr/hal-02492844
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