Five subspecies of the Dorogostaiskia parasitica complex (Dybowsky) (Crustacea: Amphipoda: Acanthogammaridae), epibionts of sponges in Lake Baikal

A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even in low technology laboratories. The amount of tissue required by this method is approximately 50-100 mg. The quantity and the quality of the DNA extracted by this method is high enough to perform hundreds of PCR-based reactions and also to be used in other DNA manipulation techniques such as restriction digestion, Southern blot and cloning.

With today's technology for production of molecular sequences, DNA taxonomy and barcoding arose as a new tool for evolutionary biology and ecology. However, their validities still need to be empirically evaluated. Of most importance is the strength of the correlation between morphological taxonomy and molecular divergence and the possibility to define some molecular thresholds. Here, we report measurements of this correlation for two mitochondrial genes (COI and 16S rRNA) within the sub-phylum Crustacea. Perl scripts were developed to ensure objectivity, reproducibility, and exhaustiveness of our tests. Our analysis reveals a general correlation between molecular divergence and taxonomy. This correlation is particularly high for shallow taxonomic levels allowing us to propose a COI universal crustacean threshold to help species delimitation. At higher taxonomic levels this correlation decreases, particularly when comparing different families. Those results plead for DNA use in taxonomy and suggest an operational method to help crustacean species delimitation that is linked to the phylogenetic species definition. This pragmatic tool is expected to fine tune the present classification, and not, as some would have believed, to tear it apart.

Water level fluctuations are important modulators of speciation processes in tropical lakes, in that they temporarily form or break down barriers to gene flow among adjacent populations and/or incipient species. Time estimates of the most recent major lowstands of the three African Great Lakes are thus crucial to infer the relative timescales of explosive speciation events in cichlid species flocks. Our approach combines geological evidence with genetic divergence data of cichlid fishes from the three Great East African Lakes derived from the fastest-evolving mtDNA segment. Thereby, we show for each of the three lakes that individuals sampled from several populations which are currently isolated by long geographic distances and/or deep water form clusters of equally closely related haplotypes. The distribution of identical or equally closely related haplotypes in a lake basin allows delineation of the extent of lake level fluctuations. Our data suggest that the same climatic phenomenon synchronized the onset of genetic divergence of lineages in all three species flocks, such that their most recent evolutionary history seems to be linked to the same external modulators of adaptive radiation. A calibration of the molecular clock of the control region was elaborated by gauging the age of the Lake Malawi species flock through the divergence among the utaka-cichlid and the mbuna-cichlid lineages to minimally 570,000 years and maximally 1 Myr. This suggests that the low-lake-level period which established the observed patterns of genetic relatedness dates back less than 57,000 years, probably even to 17,000-12,400 years ago, when Lake Victoria dried up and Lakes Malawi and Tanganyika were also low. A rapid rise of all three lakes about 11,000 years ago established the large-scale population subdivisions observed today. Over that period of time, a multitude of species originated in Lakes Malawi and Victoria with an impressive degree of morphological and ecological differentiation, whereas the Tanganyikan taxa that were exposed to the same habitat changes hardly diverged ecologically and morphologically. Our findings also show that patterns of genetic divergences of stenotopic organisms provide valuable feedback on geological and sedimentological time estimates for lake level changes.