Abstract
Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.
Highlights
IntroductionOver the past two decades, the spectacular aggregation of species in biodiversity hotspots has attracted attention by scientists and stakeholders alike[1,2,3,4]
The sequences ranged from 459 bp to 651 bp long, with 99 percent of the sequences being above 500 bp length, and no stop codons were detected, suggesting that all the sequences correspond to functional mitochondrial Cytochrome Oxidase 1 (COI) sequences
Several of the detected misidentifications involve species from different Rasbora species groups[24] such as Rasbora dusonensis, from the R. argyrotaenia group, that has been previously mistaken for R. sumatrana from the sumatrana group and R. myersi, from the R. sumatrana group, that has been confounded with R. dusonensis from the argyrotaenia group
Summary
Over the past two decades, the spectacular aggregation of species in biodiversity hotspots has attracted attention by scientists and stakeholders alike[1,2,3,4] This exceptional concentration of often-endemic species at small spatial scales is threatened by the rise of anthropogenic disturbances. The inventory of Sundaland’s freshwater fishes started more than two centuries ago and despite the acceleration of species discovery over the last three decades, it is still a work in progress[15]. The family Cyprinidae sensu lato is a good example for the complexity of Sundaland freshwater fishes taxonomy and systematics. The systematics of this large family of Cypriniformes, with over 3,000 species, has been controversial for more than a century[18]. We generated a DNA barcode reference library to (1) explore biological species boundaries with DNA-based species delimitation methods, (2) validate species identity, taxonomy and precise range distribution by producing DNA barcodes from type localities or neighboring watersheds, (3) validate or revise of the previously published DNA barcodes records for the subfamily Rasborinae available on GenBank
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