Molecular phylogeny and historical biogeography of the Aphanius (Pisces,Cyprinodontiformes) species complex of central Anatolia,Turkey

Phylogenetic relationships of a subset of Aphanius fish comprising central Anatolia, Turkey, are investigated to test the hypothesis of geographic speciation driven by early Pliocene orogenic events in spite of morphological similarity. We use 3434 aligned base pairs of mitochondrial DNA from 42 samples representing 36 populations of three species and six outgroup species to test this hypothesis. Genes analyzed include those encoding the 12S and 16S ribosomal RNAs; transfer RNAs coding for valine, leucine, isoleucine, glutamine, methionine, tryptophan, alanine, asparagine, cysteine, and tyrosine; and complete NADH dehydrogenase subunits I and II. Distance based minimum evolution and maximum-likelihood analyses identify six well-supported clades consisting of Aphanius danfordii, Aphanius sp. aff danfordii, and four clades of Aphanius anatoliae. Parsimony analysis results in 462 equally parsimonious trees, all of which contain the six well supported clades identified in the other analyses. Our phylogenetic results are supported by hybridization studies (Villwock, 1964), and by the geological history of Anatolia. Phylogenetic relationships among the six clades are only weakly supported, however, and differ among analytical methods. We therefore test and subsequently reject the hypothesis of simultaneous diversification among the six central Anatolian clades. However, our analyses do not identify any internodes that are significantly better supported than expected by chance alone. Therefore, although bifurcating branching order is hypothesized to underlie this radiation, the exact branching order is difficult to estimate with confidence.     

The question of uniqueness of ancient bacteria

Microorganisms are associated with a variety of ancient geological materials. However, conclusive proof that these organisms are as old as the geological material and not more recent introductions has generally been lacking. Over the years, numerous reports of the isolation of ancient bacteria from geological materials have appeared. Most of these have suffered from the fact that the protocol for the surface sterilization of the sample was either poorly defined, inadequate or rarely included data to validate the overall effectiveness of the sterilization protocol. With proper sterility validation and isolation protocol, a legitimate claim for the isolation of an ancient microbe can be made. Biochemical, physiological, or morphological data indicate that these ancient microbes are not significantly different from modern isolates. As the role (decomposition) of modern and ancient microbes has not changed over time, it is probably unreasonable to expect these organisms to be vastly different. A discussion on the reasons for the homogeneity of ancient and modern microbes is presented. Journal of Industrial Microbiology & Biotechnology (2002) 28, 32–41 DOI: 10.1038/sj/jim/7000174 Received 20 May 2001/ Accepted in revised form 16 June 2001     

The genetic basis of alcoholism: multiple phenotypes,many genes,complex networks

Alcoholism is a significant public health problem. A picture of the genetic architecture underlying alcohol-related phenotypes is emerging from genome-wide association studies and work on genetically tractable model organisms.     

Predicting the points of interaction of small molecules in the NF-κB pathway

Background  

The similarity property principle has been used extensively in drug discovery to identify small compounds that interact with specific drug targets. Here we show it can be applied to identify the interactions of small molecules within the NF-κB signalling pathway.     

Plate tectonics and biogeographical patterns of the Pseudophoxinus (Pisces: Cypriniformes) species complex of central Anatolia, Turkey

We investigated the phylogenetic relationships of Pseudophoxinus (Cyprinidae: Leuciscinae) species from central Anatolia, Turkey to test the hypothesis of geographic speciation driven by early Pliocene orogenic events. We analyzed 1141 aligned base pairs of the complete cytochrome b mitochondrial gene. Phylogenetic relationships reconstructed by maximum likelihood, Bayesian likelihood, and maximum parsimony methods are identical, and generally well supported. Species and clades are restricted to geologically well-defined units, and are deeply divergent from each other. The basal diversification of central Anatolian Pseudophoxinus is estimated to have occurred approximately 15 million years ago. Our results are in agreement with a previous study of the Anatolian fish genus Aphanius that also shows a diversification pattern driven by the Pliocene orogenic events. The distribution of clades of Aphanius and Pseudophoxinus overlap, and areas of distribution comprise the same geological units. The geological history of Anatolia is likely to have had a major impact on the diversification history of many taxa occupying central Anatolia; many of these taxa are likely to be still unrecognized as distinct.