Cryptic Diversity in Indo-Australian Rainbowfishes Revealed by DNA Barcoding: Implications for Conservation in a Biodiversity Hotspot Candidate

Abstract

The rainbowfishes of the family Melanotaeniidae represent one of the largest radiations of freshwater fishes from the Indo-Australian archipelago. A total of 75 nominal species have been described, among which several have become very popular among tropical fish hobbyists because of their tendency to form large schools of colourful individuals. Facing habitat loss and competition or predation by introduced species, this group has become a priority in the conservation of ornamental fishes in Indonesia. In this context, several expeditions have been conducted between 2007 and 2010 in Indonesian Papua with the aim to initiate a large-scale survey of the genetic resources in this group. We assessed the diversity of the Papua rainbowfishes with DNA barcoding. We sequenced the mitochondrial COI gene for 350 specimens belonging to 53 nominal species throughout the Indo-Australian archipelago. Unexpected levels of cryptic diversity and endemism were detected since additional cryptic lineages were detected in several watersheds from the Vogelkop and the Lengguru massif. DNA barcoding supports the presence of nearly 30 evolutionary lineages among the 15 nominal species sampled in the Vogelkop and all these lineages are endemic to a single lake or watershed. This result highlights that the diversity of the family has been largely underestimated and urges for the identification of conservation priorities in Papua.

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

“…This cryptic diversity has been further confirmed by the high levels of genetic differentiation based on microsatellite genotyping and the discovery of several diagnostic morphological characters [90]. By doubling the number of known species in the area, Kadarusman and colleagues [13] and Nugraha and colleagues [90] highlighted that the diversity of the family was largely underestimated and pinpointed the urgent need to re-appraise the diversity of this group in other region of Indonesian Papua for national conservation plans.…”

“…The large-scale and standardized sequencing of the COI gene for rainbowfish species from the genus Melanotaenia with the aim to re-estimate the diversity in Indonesian Papua provided an unprecedented level of species discovery in the group [13]. Kadarusman and colleagues [13] have detected 30 mitochondrial lineages among the 13 nominal species of Melanotaenia in the Bird's head, all being distributed in allopatry and restricted to a single watershed.…”

“…Kadarusman and colleagues [13] have detected 30 mitochondrial lineages among the 13 nominal species of Melanotaenia in the Bird's head, all being distributed in allopatry and restricted to a single watershed. This cryptic diversity has been further confirmed by the high levels of genetic differentiation based on microsatellite genotyping and the discovery of several diagnostic morphological characters [90].…”

“…The inventory of Indonesian freshwater fishes has been challenged since its earliest developments by several limitations: (1) the Indonesian archipelago hosts nearly 17,000 islands and most of them are remote islands with limited access, (2) due to a complex political history, tracing the type specimens has been sometimes challenging, particularly for the species described before the 1950's [11], (3) the Indonesian ichthyofauna hosts several large radiation of morphologically similar species that have been subject to either multiple descriptions, recurrent systematic revisions or overlooked diversity [11]. Recently, the use of standardized molecular approaches in some remote rivers in Indonesia emphasized that the sole use of morphology in taxonomy was limiting the estimation of species richness in some cases, as observed in Papuan rainbowfishes, for instance [13].…”

“…Map of Indonesia including the 23 islands considered in the present review (Appendix) with biogeographic provinces and their boundaries. 1, Bali; 2, Bangka; 3, Batam and Bintan; 4, Belitong; 5, Buru; 6, Java; 7, Kalimantan; 8, Madura; 9 Natuna and Riau; 10, Sumatera; 11, Bacan; 12, Celebes; 13 (1) introduced species (i.e. 21 species from 7 families), among which several belong to exotic families for Indonesian waters (e.g.…”