Revisiting the Diversity of Barbonymus (Cypriniformes, Cyprinidae) in Sundaland Using DNA-Based Species Delimitation Methods

Hadi Dahruddin,Dirk Steinke,Sopian Sauri,Arni Sholihah,Tedjo Sukmono,Ujang Nurhaman,Daisy Wowor,Nicolas Hubert

doi:10.3390/d13070283

Abstract

Biodiversity hotspots often suffer from a lack of taxonomic knowledge, particularly those in tropical regions. However, accurate taxonomic knowledge is needed to support sustainable management of biodiversity, especially when it is harvested for human sustenance. Sundaland, the biodiversity hotspot encompassing the islands of Java, Sumatra, Borneo, and Peninsular Malaysia, is one of those. With more than 900 species, its freshwater ichthyofauna includes a large number of medium- to large-size species, which are targeted by inland fisheries. Stock assessment requires accurate taxonomy; however, several species groups targeted by inland fisheries are still poorly known. One of those cases is the cyprinid genus Barbonymus. For this study, we assembled a consolidated DNA barcode reference library for Barbonymus spp. of Sundaland, consisting of mined sequences from BOLD, as well as newly generated sequences for hitherto under-sampled islands such as Borneo. A total of 173 sequences were analyzed using several DNA-based species delimitation methods. We unambiguously detected a total of 6 Molecular Operational Taxonomic Units (MOTUs) and were able to resolve several conflicting assignments to the species level. Furthermore, we clarified the identity of MOTUs occurring in Java.

Highlights

Sundaland, comprising the islands of Java, Bali, Sumatra, Borneo, and peninsularMalaysia, constitutes one of the world’s largest biodiversity hotspots [1,2]
The total of 173 DNA barcodes used for this study comprised 154 sequences mined from BOLD and 19 sequences generated for Barbonymus specimens originating from Sumatra and Borneo
DNA-based species delimitation methods resulted in congruent delimitation schemes with 6 Molecular Operational Taxonomic Units (MOTUs) for mPTP, sPTP, Automatic Barcode Gap Discovery (ABGD), Refined Single Linkage (RESL), and sGMYC (Figure 2; Table S1)

Summary

Introduction

Sundaland, comprising the islands of Java, Bali, Sumatra, Borneo, and peninsularMalaysia, constitutes one of the world’s largest biodiversity hotspots [1,2]. With circa 900 freshwater fish species, half of which are endemic, the ichthyofauna of this biogeographical region is rich, with a density of 0.8 species per km, a value twice as large as that observed in Brazil and the Democratic Republic of Congo [3]. This large diversity is critically threatened, mostly due to the alarming rate of deforestation over the past few decades [4,5,6], in conjunction with pollution [7] and watershed fragmentation through the development of dams for irrigation and hydroelectric power [8]. The diversity for a number of genera has likely been underestimated [15,16,17]

Objectives

Results

Discussion

Conclusion