Cryptic Diversity in Indo-Pacific Coral-Reef Fishes Revealed by DNA-Barcoding Provides New Support to the Centre-of-Overlap Hypothesis

Abstract

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.

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

“…While contributing by only the settlement of this gradient including the existence of a center of overlap among distinct biogeographic domains [29,107,108], the highest connectivity of the Pleistocene coral reef refuges in the Indo-Australian archipelago [109] and geometric constraints on the distribution of species richness [110,111].…”

“…Compared to morphological characters, DNA barcodes presents several advantages: (1) intraspecific phenotypic variation often These detailed specimens and barcode records ensure the reproducibility of the PCR and sequencing protocols by providing contact of the peoples involved in generating DNA barcodes. In addition, it enables the continuous updating of the identification of specimens by the community of users and facilitates the use of DNA barcodes for further taxonomic studies [21,[27][28][29][30][31]183]. To further improve the quality of DNA barcode data, the BARCODE data standard as been implemented in GenBank for the records that are compliant with the following requirements: 1.…”

“…Recent large-scale DNA barcoding campaigns have demonstrated that DNA barcoding will have to face the undescribed diversity of earth biotas [e.g. [27][28][29] and that DNA barcodes might help to speed up the pace of species discovery through automated delineation of mitochondrial lineages. This approach is particularly relevant when applied to areas of exceptional diversity facing massive anthropogenic threats and as such, urgently awaiting more comprehensive assessments [1][2][3]185].…”

“…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].…”

Redescription and Geographic Variations of <i>Pterois antennata</i> and First Record of <i>Pterois paucispinula</i> from French Polynesia (Scorpaenidae: Pteroinae)

“…and Scorpaenodes parvipinnis (Garrett, 1864) (as an out group) were taken from DDBJ/EMBL/GenBank which includes sequences analyzed by Hubert et al (2012). Identifications of the following sequences were determined by our examination of voucher specimens: P. antennata: DDBJ/EMBL/GenBank accession number: JQ432077 (voucher specimen: USNM 392525) and KU943359 (ASIZP 72229); P. paucispinula: JQ432074 (USNM 392530).…”