Tracing the Origin and Evolutionary Fate of Recent Gene Retrocopies in Natural Populations of the House Mouse

Although the contribution of retrogenes to the evolution of genes and genomes has long been recognized, the evolutionary patterns of very recently derived retrocopies that are still polymorphic within natural populations have not been much studied so far. We use here a set of 2,025 such retrocopies in nine house mouse populations from three subspecies (Mus musculus domesticus, M. m. musculus, and M. m. castaneus) to trace their origin and evolutionary fate. We find that ancient house-keeping genes are significantly more likely to generate retrocopies than younger genes and that the propensity to generate a retrocopy depends on its level of expression in the germline. Although most retrocopies are detrimental and quickly purged, we focus here on the subset that appears to be neutral or even adaptive. We show that retrocopies from X-chromosomal parental genes have a higher likelihood to reach elevated frequencies in the populations, confirming the notion of adaptive effects for “out-of-X” retrogenes. Also, retrocopies in intergenic regions are more likely to reach higher population frequencies than those in introns of genes, implying a more detrimental effect when they land within transcribed regions. For a small subset of retrocopies, we find signatures of positive selection, indicating they were involved in a recent adaptation process. We show that the population-specific distribution pattern of retrocopies is phylogenetically informative and can be used to infer population history with a better resolution than with SNP markers.     

Cytology and taxonomy of Coptis teeta Wall.(Ranunculaceae)

Cytological investigations of 13 natural populations of Coptis teeta indicated that the species has a somatic number of 18 chromosomes which form nine homomorphic pairs. The species did not possess any supernumerary chromosomes. The chromosome number, size and morphology were similar in all populationS. Based on the taxonomic studies the 13 natural populations are grouped into two well-defined subspecies, teeta and lohitensis, for which a key is provided.     

Genetic relationships between Amerindian populations of Argentina

A total of 495 individuals from five different Argentinian tribes was examined for variation in 23 blood group and protein genetic systems, and the results were integrated with previous data on some of these systems. These tribes generally present RH * R1, PGM1 * 1, and ACP * A frequencies lower and RH * R2, ESD * 1, and GLO * 1 prevalences higher than those observed in other South American Indian groups. Earlier studies with mitochondrial DNA showed that haplogroup A was present in low frequencies in these tribes, but haplogroup B showed a high prevalence among the Mataco. Average heterozygosities are very similar in the five tribes, while estimates of non-Indian ancestry are generally low. Both the blood group and protein, as well as the mtDNA data sets, divide the five tribes into two groups, and the relationships obtained with the blood group and protein systems are exactly those expected on the basis of geography and language. However, the topology obtained with the mtDNA results was different, possibly due to sampling effects or diverse patterns of exchange between the groups related to sex.     

Origin and evolution of GBV-C/hepatitis G virus and relationships with ancient human migrations

The GB virus C/hepatitis G virus (GBV-C/HGV) is a newly identified human RNA virus, belonging to the Flaviviridae family. Persistent infection by GBV-C/HGV is common in humans, and genetically divergent isolates have been identified in different parts of the world. Due to the absence of a real pathogenic role of GBV-C/HGV in liver disease and its extremely low mutation rate, this virus is a potential marker to trace prehistoric links between human populations. In this study, origin and evolution of GBV-C/HGV were examined using a set of fully sequenced strains of worldwide origin. A first phylogenetic analysis, addressed to the short (255 nucleotides) NS5A overlapping coding region by the neighbor-joining method, suggested an ancient African origin of GBV-C/HGV. This notion was confirmed when the same analysis was applied to the genomic regions showing the lowest rate of synonymous substitutions, covering one-fourth (2184 nucleotides) of the total coding potential of the virus genome. By using a multivariate statistical method and extending the analysis to the complete coding region, fine details of the evolutionary history of GBV-C/HGV were further elucidated. By this approach, isolates from Southeast Asia appeared to be the most closely related to those of African origin, consistent with a major route of ancient human migrations from Africa to southeastern parts of the Asian continent. Received: 26 October 2000 / Accepted: 28 February 2001     

Species pairs of north temperate freshwater fishes: Evolution,taxonomy, and conservation

Many fish species contain morphologically, ecologically and geneticallydistinct populations that are sympatric during at least some portion oftheir life cycle. Such reproductively isolated populations act asdistinct biological species, but are identified by a common Latinbinomial. These species pairs are particularly common in freshwaterfish families such as Salmonidae, Gasterosteidae and Osmeridae and aretypically associated with postglacial lakes in north temperateenvironments. The nature of the divergences between sympatric species,factors contributing to reproductive isolation, and modes of evolutionare reviewed with particular emphasis on benthic and limnetic pairs ofthreespine sticklebacks, Gasterosteus aculeatus, and anadromous(sockeye salmon) and nonanadromous (kokanee) pairs of Oncorhynchusnerka. Phylogenetic analyses typically indicate that divergencesbetween members of replicate pairs have occurred independently and,hence, particular phenotypes are not monophyletic. Consequently,taxonomic resolution of such species complexes is a vexing problem foradherents to our traditional Linnaean classification system. Sympatricspecies pairs represent a significant component of the biodiversity oftemperate freshwater ecosystems which may be underestimated because oursystem of formal taxonomy tends to obscure diversity encompassed byspecies pairs. Conservation of such systems should be recognized as apriority without formal taxonomic designation of members of speciespairs because taxonomic resolution will likely continue to proveextremely difficult when employing traditional hierarchies andprocedures.     

Excitability of an age-structured plankton ecosystem

 We adapt a simple two-component model of a plankton ecosystem to account for the life spans of individual predatory organisms. We investigate the system’s short-term dynamics, in particular its excitability, and its long-term dynamics, and show how both can be highly sensitive to initial conditions. We discover that this effect is enhanced by imposing age structure on the system. Received: 21 June 1996 / Revised version: 19 October 1998     

Differential modulation of murine host immune response by salivary gland extracts from the mosquitoes Aedes aegypti and Culex quinquefasciatus

Mosquitoes (Diptera: Culicidae) are major vectors of numerous infectious agents. Compounds in mosquito saliva not only facilitate blood-feeding, but may also have an impact upon the immune system of vertebrate hosts. Consequently, the exposure to mosquito saliva may influence pathogen transmission, establishment and disease development. Using two medically important vector mosquitoes, Aedes aegypti (L.) and Culex quinquefasciatus Say, we examined the effects of mosquito saliva on immune cells of host mice. After antigen-specific or non-specific stimulation, murine splenocyte proliferation and production of both Th1 and Th2 cytokines were significantly reduced in the presence of salivary gland extract (SGE) from Ae. aegypti, but not SGE from Cx. quinquefasciatus. T cell populations were highly susceptible to this suppression, showing increased mortality and reduced division rates - judged by flow cytometric analyses. Evidently these two culicine mosquitoes differ in their host immunomodulatory activities.     

Neural Population Structures and Consequences for Neural Coding

Researchers studying neural coding have speculated that populations of neurons would more effectively represent the stimulus if the neurons "cooperated:" by interacting through lateral connections, the neurons would process and represent information better than if they functioned independently. We apply our new theory of information processing to determine the fidelity limits of simple population structures to encode stimulus features. We focus on noncooperative populations, which have no lateral connections. We show that they always exhibit positively correlated responses and that as population size increases, they perfectly represent the information conveyed by their inputs regardless of the individual neuron's coding scheme. Cooperative populations, which do have lateral connections, can, depending on the nature of the connections, perform better or worse than their noncooperative counterparts. We further show that common notions of synergy fail to capture the level of cooperation and to reflect the information processing properties of populations.     

Sympatric natural Saccharomyces cerevisiae and S. paradoxus populations have different thermal growth profiles

Saccharomyces cerevisiae and its close congener S. paradoxus are typically indistinguishable by the phenotypic criteria of classical yeast taxonomy, but they are evolutionarily distinct as indicated by hybrid spore inviability and genomic sequence divergence. Previous work has shown that these two species coexist in oak-associated microhabitats at natural woodland sites in North America. Here, we show that sympatric populations of S. cerevisiae and S. paradoxus from a single natural site are phenotypically differentiated in their growth rate responses to temperature. Our main finding is that the S. cerevisiae population exhibits a markedly higher growth rate at 37 degrees C than the S. paradoxus population; we also find possible differences in growth rate between these populations at two lower temperatures. We discuss the implications of our results for the coexistence of these yeasts in natural environments, and we suggest that thermal growth response may be an evolutionarily labile feature of these organisms that could be analyzed using genomic approaches.     

Geographic distribution and recombination of genomic fragments on the short arm of chromosome 2 of Arabidopsis thaliana

Abstract: Range expansion from Pleistocene refugia and anthropogenic influences contribute to the present distribution pattern of Arabidopsis thaliana. We scored a genome-wide set of CAPSs and found two markers with an east-west geographic distribution across the Eurasian range of the species. Regions around the two SNPs were sequenced in 98 accessions, including newly collected plants from Middle Asia and Western Siberia. These regions correspond to a gene (∼ 1500 bp) and a non-coding region (∼ 500 bp) 300 kbp apart on chromosome 2. Nucleotide diversities, π, of the two sequenced fragments were 0.0032 and 0.0130. The haplotypes of both sequences belonged to one of two groups: a rather uniform "Asian" and a more variable "European" haplotype group, on the basis of non-disjunct clusters of SNPs. Recombination between "Asian" and "European" haplotypes occurs where they meet. Especially in the "European" haplotype, many rare SNP variants representing independent mutations are scattered among the shared haplotype-specific SNPs. This agrees with previous suggestions of two large haplotype groups in A. thaliana and the post-glacial colonization of central Europe from the east and the west. A clear correlation between climatic factors and the haplotype distribution may reflect the dispersal history rather than local climate adaptation. The pattern of SNP variation within the contiguous sequences explains why only a minority of SNPs selected across the genome show evidence of this geographic pattern.