Where is Darwin 200 years later?

The theory of evolution is perceived by many people, particularly but not only in the United States, as a controversial theory not yet fully demonstrated. Yet, that living organisms, including humans, have evolved from ancestors who were very different from them is beyond reasonable doubt, confirmed by at least as much evidence as any other widely accepted scientific theory. I argue that Darwin's contribution to science goes much beyond the theory of evolution in itself. The theory of natural selection explains the adaptations of organisms, their 'design'. The 'Copernican Revolution' brought the phenomena of the physical universe into the realm of science: explanations by natural causes that can be tested by observation and experiment. However, the scientific revolution that occurred in the 16th and 17th centuries had left the living world out of scientific explanations, because organisms seemingly show that they are 'designed,' and thus call for an intentional designer. It was Darwin's greatest contribution to science, to demonstrate that the adaptations of organisms, their apparent 'design', can be explained by natural processes governed by natural laws. At that point, science came into maturity, because all natural phenomena in the universe, living as well as nonliving, could be investigated scientifically, and explained as matter in motion governed by natural laws.

Nucleotide variation at the dopa decarboxylase (Ddc) gene in natural populations of Drosophila melanogaster.

We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in strong positive association, whereas a large number of sites in the Raleigh population are associated nonrandomly but the association is not strong. Linkage disequilibrium analysis shows presence of two groups of haplotypes in the populations, each of which is fairly diverged, suggesting epistasis or inversion polymorphism. There is evidence of two forms of natural selection acting on Ddc. The McDonald-Kreitman test indicates a deficit of fixed amino acid differences between D. melanogaster and D. simulans, which may be due to negative selection. An excess of derived alleles at high frequency, significant according to the H-test, is consistent with the effect of hitchhiking. The hitchhiking may have been caused by directional selection downstream of the locus studied, as suggested by a gradual decrease of the polymorphism-to-divergence ratio. Altogether, the Ddc locus exhibits a complicated pattern of variation apparently due to several evolutionary forces. Such a complex pattern may be a result of an unusually high density of functionally important genes.

Molecular population genetics of the beta-esterase gene cluster of Drosophila melanogaster.

We have investigated nucleotide polymorphism at the beta-esterase gene cluster including the Est-6 gene and psiEst-6 putative pseudogene in four samples of Drosophila melanogaster derived from natural populations of southern Africa (Zimbabwe), Europe (Spain), North America (USA: California), and South America (Venezuela). A complex haplotype structure is revealed in both Est-6 and psiEst-6. Total nucleotide diversity is twice in psiEst-6 as in Est-6; diversity is higher in the African sample than in the non-African ones. Strong linkage disequilibrium occurs within the beta-esterase gene cluster in non-African samples, but not in the African one. Intragenic gene conversion events are detected within Est-6 and, to a much greater extent, within psiEst-6; intergenic gene conversion events are rare. Tests of neutrality with recombination are significant for the beta-esterase gene cluster in the non-African samples but not significant in the African one. We suggest that the demographic history (bottleneck and admixture of genetically differentiated populations) is the major factor shaping the pattern of nucleotide polymorphism in the beta-esterase gene cluster. However there are some 'footprints' of directional and balancing selection shaping specific distribution of nucleotide polymorphism within the cluster. Intergenic epistatic selection between Est-6 and psiEst-6 may play an important role in the evolution of the beta-esterase gene cluster preserving the putative pseudogene from degenerative destruction and reflecting possible functional interaction between the functional gene and the putative pseudogene. Est-6 and psiEst-6 may represent an indivisible intergenic complex ('intergene') in which each single component (Est-6 or psiEst-6) cannot separately carry out the full functional role.

Trypanosoma and Leishmania have clonal population structures of epidemiological significance

This paper presents three results concerning the population structure of Trypanosoma cruzi, the agent of Chagas disease: (1) The mode of propagation of T. cruzi in nature is clonal; sexual reproduction is either totally absent or so rare that it leaves no traces in the population structure of the parasite. (2) The genetic diversity of the clonal lineages is large: extant T. cruzi represent lineages of descent that have evolved independently for long time spans (up to 40 million years). (3) Some genetically identical clonal lineages (®clonets®) are geographically widespread (®ubiquitous®). However, most clonets are endemic, restricted in geographic distribution. These results have each in turn consequences of epidemiological significance: (1) In a sexually-reproducing organism the individual genotype is ephemeral; the entity that persists and evolves is the species (®gene pool®), and a few individuals contain most of the genetic variability of the species. In a clonally-propagating organism, the entity that persists and evolves is the clonal lineage; the genetic diversity of the species can only be captured by extensive sampling of distinct lineages. (2) The extensive genetic divergence among clonal lineages implies proportionally diverse biological characteristics, which are likely to include pathological effects, host propensity, vulnerability to drugs and vaccines, and other medically significant attributes. The extant T. cruzi lineages diverged much before human origins; hence, specific adaptation to human hosts, to whichever extent it exists, has evolved independently in separate lineages, and may not have evolved at all in some T. cruzi. (3) Epidemiological surveys and medical characterization, including search for specific vaccines and drugs, should not proceed randomly; rather, preliminary surveys must identify those clonets that are ubiquitous and target them for investigation. Review of published literature shows that Leishmania (and other parasitic protozoa) also has a clonal population structure. We advance a taxonomic and nomenclatural proposal that is appropriate for clonal organisms, yet simple