Molecular phylogeny, biogeography, population structure and taxonomy of large barbine minnows (Labeobarbus: Cyprinidae)

Abstract

The phylogeny, biogeography, population genetics and taxonomy of Labeobarbus (Cyprinidae), a genus of large hexaploid minnows, was estimated by a variety of phylogenetic and population genetics methods. In Chapter 2 relationships among species of large barbine minnows was examined based on analysis of variation in complete mitochondrial (mt) cytochrome b (cyt b) gene sequences. In all analyses hexaploid minnows from Saharan and Sub-Saharan Africa and the Middle East were recovered as a monophyletic group. This clade diverged from European tetraploid and African diploid and tetraploid lineages approximately 13 MYA. The earliest cladogenetic event within this clade occurred ca 5.0 MYA giving rise to Sub-Saharn African and Saharan African-Levant clades. Subsequent cladodenesis within the clade took place during the Plio-Pleistocene. Chapter 3 investigated the phylogeography of Labeobarbus intermedius across its geographic distribution in Ethiopia based on analysis of complete cyt b gene sequences. Phylogenetic analysis recovered two distinct geographic lineages (northern and southern) within L. intermedius, which diverged from each other ca Late Pleistocene consistent with the timing of Pleistocene volcanic activities in East Africa. Chapter 4 developed microsatellite DNA markers for use in Chapter 5. Seventy-two microsatellite primers were developed based on a genomic library of Labeobarbus intermedius employing next generation 454 sequencing. Six polymorphic loci were examined over 35 L. intermedius specimens and tested for cross-species amplification in other Labeobarbus taxa. Genetic diversity was high with 99 alleles identified in L. intemedius with an average of 16.5 alleles per locus. Observed heterozygosity ranged from 0.8-1.0 across all loci. These loci also amplified successfully across all taxa. In Chapter 5, ten microsatllite DNA loci and mitochondrial cytochrome oxidase I (COI) and cyt b gene sequences were analyzed to investigate population structure and evolutionary relationships within the Labeobarbus species flock of Lake Tana. Phylogenetic analyses based on COI and cyt b gene sequences consistently rejected the monophyly of Lake Tana Labeobarbus haplotypes and recovered all haplotypes as part of a larger clade that contained haplotypes from independent drainages throughout Ethiopia. Bayesian clustering analysis of ten microsatellite markers employing STRUCTURE revealed little genetic differentiation within the Lake Tana Labeobarbus suggesting that alleles were shared among individuals and putative species in the species flock. The resolved phylogeny and lack of population differentiation in Lake Tana Labeobarbus may suggest either these evolutionary lineages are at an early stage of an ongoing adaptive radiation in Lake Tana or lack of signal in molecular markers examined.