Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)

Yang, Lei; Arunachalam, M.; Sadõ, Tetsuya; Левин, Б. А.; Голубцов, А. С.; Freyhof, Joerg; Friel, John; Chen, Wei‐Jen; Hirt, M. Vincent; Raja, Manickam; Agnew, Mary K.; Simons, Andrew M.; Saitoh, Kenji; Miya, Masaki; Mayden, Richard L.; He, Shunping

doi:10.1016/j.ympev.2012.06.007

Cited by 70 publications

(99 citation statements)

References 39 publications

(54 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The most spectacular and diverse of these radiations occurs in the ancient lakes of Central Sulawesi, namely the Malili Lakes system, and Lake Poso. Besides of lacustrine radiations of gastropods, crabs, shrimps, and other invertebrates, the ecosystems of these isolated, deep, and long-term stable freshwater lakes are [43,[56][57][58][59][60][61][62]. The Cyprinidae subfamily Danioninae, a large group composed predominantly of South and Southeast Asian minnows, is among the best known subfamily and harbors several genera that are very popular in the ornamental fish trade (e.g.…”

Section: The Wallacea Ichthyofaunamentioning

confidence: 99%

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Hubert¹,

Kadarusman²,

Wibowo³

et al. 2015

DNA Barcodes

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

Section: The Wallacea Ichthyofaunamentioning

confidence: 99%

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Hubert¹,

Kadarusman²,

Wibowo³

et al. 2015

DNA Barcodes

View full text Add to dashboard Cite

show abstract

“…Thus, as in Geiger et al [10], Zheng et al [29], Yang et al [30], and Hamidan et al [31] species lacking a mental disc (Hemigrammocapoeta, Crossocheilus, Tylognathus) are nested within groups presenting this diagnostic character state. With both markers, the two species G. rossica and G. variabilis with small and partly reduced mental disc group together with G. klatti (formerly Crossocheilus) and G. kemali (formerly Hemigrammocapoeta) lacking this diagnostic character.…”

Section: Mtcoi Vs Nuclear Rhodopsin In the Labeonine Cyprinidsmentioning

confidence: 67%

“…This new hypothesis was supported by phylogenetic analyses of nuclear and mitochondrial genes in labeonines by Yang et al [30]. Likewise, mtCOI-based findings in Hamidan et al [31] and Geiger et al [10] showed the same pattern with different labeonine genera (defined by the mental disc apparatus) to be nested within Garra, which could be explained by past hybridization events.…”

mentioning

confidence: 70%

“…We compared the divergence levels present based on sequences of the mitochondrial mtCOI and the nuclear rhodopsin marker. Given the nonmonophyletic clustering of Garra in our data based on mtCOI and the previous findings [10,29,30], we analysed two different versions of our data: a) with traditional Garra taxonomy -using five different genera; b) a taxonomy placing the species included herein from Crossocheilus, Hemigrammocapoeta, Tylognathus and Typhlogarra to Garra (for more detailed information see Table 1). …”

Section: Resultsmentioning

confidence: 99%

“…The nuclear rhodopsin gene (ncRHO) is an intronless gene [36], which has been recommended for teleost fishes by Sevilla et al [37], and been applied in different phylogenetic analyses [30,38,39]. A first comparison of mtCOI to ncRHO for species identification in billfishes revealed a discrepancy between both markers in the species-complex of white and striped marlin [40].…”

mentioning

confidence: 99%

See 2 more Smart Citations

Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids?

Behrens-Chapuis¹,

Herder²,

Esmaeili³

et al. 2015

DNA Barcodes

View full text Add to dashboard Cite

or haplotype sharing (12 species pairs) with presumed introgression based on mtCOI data. We aimed to test the utility of the nuclear rhodopsin marker to uncover reasons for the high similarity and haplotype sharing in these different groups. The included labeonine species belonging to Crossocheilus, Hemigrammocapoeta, Tylognathus and Typhlogarra were found to be nested within the genus Garra based on mtCOI. This specific taxonomic uncertainty was also addressed by the use of the additional nuclear marker. As a measure of the delineation success we computed barcode gaps, which were present in 75% of the species based on mtCOI, but in only 39% based on nuclear rhodopsin sequences. Most cases where standard barcodes failed to offer unambiguous species identifications could not be resolved by adding the nuclear marker. However, in the labeonine cyprinids included, nuclear rhodopsin data generally supported the lineages as defined by the mitochondrial marker. This suggests that mitochondrial patterns were not mislead by introgression, but are caused by an inadequate taxonomy. Our findings support the transfer of the studied species of Crossocheilus, Hemigrammocapoeta, Tylognathus and Typhlogarra to Garra.Keywords: Barcode gap, mtCOI, nuclear rhodopsin (ncRHO), Cyprinidae, labeonine cyprinids, introgression IntroductionThe idea of being able to distinguish species and identify whole or even only parts of specimens accurately across any life stage using a short gene sequence received substantial interest in the fields of taxonomy, protection and conservation of biodiversity, observation and management of fisheries, as well as fish trade [1][2][3][4]. DNA Abstract: DNA barcoding is a fast and reliable tool for species identification, and has been successfully applied to a wide range of freshwater fishes. The limitations reported were mainly attributed to effects of geographic scale, taxon-sampling, incomplete lineage sorting, or mitochondrial introgression. However, the metrics for the success of assigning unknown samples to species or genera also depend on a suited taxonomic framework. A simultaneous use of the mitochondrial COI and the nuclear RHO gene turned out to be advantageous for the barcode efficiency in a few previous studies. Here, we examine 14 cyprinid fish genera, with a total of 74 species, where standard DNA barcoding failed to identify closely related species unambiguously. Eight of the genera (Acanthobrama, Alburnus, Chondrostoma, Gobio, Mirogrex, Phoxinus, Scardinius, and Squalius) contain species that exhibit very low interspecific divergence,

show abstract