DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts

Abstract

Despite ongoing efforts to protect species and ecosystems in Cuba, habitat degradation, overuse and introduction of alien species have posed serious challenges to native freshwater fish species. In spite of the accumulated knowledge on the systematics of this freshwater ichthyofauna, recent results suggested that we are far from having a complete picture of the Cuban freshwater fish diversity. It is estimated that 40% of freshwater Cuban fish are endemic; however, this number may be even higher. Partial sequences (652 bp) of the mitochondrial gene COI (cytochrome c oxidase subunit I) were used to barcode 126 individuals, representing 27 taxonomically recognized species in 17 genera and 10 families. Analysis was based on Kimura 2-parameter genetic distances, and for four genera a character-based analysis (population aggregation analysis) was also used. The mean conspecific, congeneric and confamiliar genetic distances were 0.6%, 9.1% and 20.2% respectively. Molecular species identification was in concordance with current taxonomical classification in 96.4% of cases, and based on the neighbour-joining trees, in all but one instance, members of a given genera clustered within the same clade. Within the genus Gambusia, genetic divergence analysis suggests that there may be at least four cryptic species. In contrast, low genetic divergence and a lack of diagnostic sites suggest that Rivulus insulaepinorum may be conspecific with Rivulus cylindraceus. Distance and character-based analysis were completely concordant, suggesting that they complement species identification. Overall, the results evidenced the usefulness of the DNA barcodes for cataloguing Cuban freshwater fish species and for identifying those groups that deserve further taxonomic attention.

DNA Barcoding of Freshwater Fishes from Lake Laut Tawar, Aceh Province, Indonesia

“…Ward et al (2005) reported that phylogenetic COX1 sequences could effectively cluster most congeneric and confamilial species. This was observed in previous studies for example in Australian fishes (Ward et al 2005), Canadian freshwater fishes (Hubert et al 2008), Indian carangid fishes (Persis et al 2009), freshwater fishes from Mexico and Guatemala (Valdez-Moreno et al 2009), and Cuban freshwater fishes (Lara et al 2009).…”

The genus Basilichthys (Teleostei: Atherinopsidae) revisited along its Chilean distribution range (21° to 40° S) using variation in morphologyand mtDNA

“…mtDNA analysis in fi sh biodiversity has been increasing in the last years (Ward et al 2005, Hubert et al 2008, Lara et al 2010, showing that this technique concurs with previous morphological analyses. Ward & Holmes (2007) showed in a study performed in 338 fi sh species that this region gave conclusive results except for one pair of species that may hybridize (Ward & Holmes 2007).…”

“…In the case of freshwater fi shes, molecular markers have proved ver y useful because they tend to show clear phylogenetic patterns and their relation to the histor y of each watershed (Ber natchez & Wilson 1998, Bermingham & Martin 1998, Avise 2000. In recent years, sequencing of the cytochrome c oxidase I gene (COI) has been used in the taxonomy of freshwater fi sh; this gene has proved to be useful in identifying species in accordance with morphology (e.g., Ward et al 2005, Hubert et al 2008, Lara et al 2010.…”

Genetic calibration of species diversity among North America's freshwater fishes

“…With a correct species identification rate of 90%, freshwater fishes are among the groups of animals harboring the most frequent cases of interspecific haplotype sharing (Table S1): 8% in Canadian freshwater fishes, 4% in Cuban freshwater fishes, 2% in Australian marine fishes, 6% in North American birds, and 1% in Lepidoptera (23)(24)(25)(26)(27). The relatively elevated proportion of species sharing haplotypes in this study (10%) has four possible nonexclusive explanations: hybridization, incomplete lineage sorting, inadequate taxonomy, and erroneous identification (15).…”