Richard A. Nichols

Evaluating loci for use in the genetic analysis of population structure

Loci that show unusually low or high levels of genetic differentiation are often assumed to be subject to natural selection. We propose a method for the identification of loci showing such disparities. The differentiation can be quantified using the statistic FST. For a range of population structures and demographic histories, the distribution of FST is strongly related to the heterozygosity at a locus. Outlying values of FST can be identified in a plot of FST vs. heterozygosity using a null distribution generated by a simple genetic model. We use published data-sets to illustrate the importance of the relationship with heterozygosity. We investigate a number of models of population structure, and demonstrate that the null distribution is robust to a wide range of conditions. In particular, the distribution is robust to differing mutation rates, and therefore different molecular markers, such as allozymes, restriction fragment length polymorphisms (RFLPS) and single strand conformation polymorphisms (SSCPS) can be compared together. We suggest that genetic variation at a discrepant locus, Identified under these conditions, is likely to have been influenced by natural selection, either acting on the locus itself or at a closely linked locus.

Hybridization and speciation

Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow and recombination. It may accelerate speciation via adaptive introgression or cause near‐instantaneous speciation by allopolyploidization. It may have multiple effects at different stages and in different spatial contexts within a single speciation event. We offer a perspective on the context and evolutionary significance of hybridization during speciation, highlighting issues of current interest and debate. In secondary contact zones, it is uncertain if barriers to gene flow will be strengthened or broken down due to recombination and gene flow. Theory and empirical evidence suggest the latter is more likely, except within and around strongly selected genomic regions. Hybridization may contribute to speciation through the formation of new hybrid taxa, whereas introgression of a few loci may promote adaptive divergence and so facilitate speciation. Gene regulatory networks, epigenetic effects and the evolution of selfish genetic material in the genome suggest that the Dobzhansky–Muller model of hybrid incompatibilities requires a broader interpretation. Finally, although the incidence of reinforcement remains uncertain, this and other interactions in areas of sympatry may have knock‐on effects on speciation both within and outside regions of hybridization.

Spatial patterns of genetic variation generated by different forms of dispersal during range expansion

We examined the impact of three forms of dispersal, stepping-stone, normal and leptokurtic, on spatial genetic structure of expanding populations using computer simulations. When dispersal beyond neighbouring demes is allowed, rare long-distance migration leads to the establishment of pocket populations in advance of the main invasion front and results in spatial clustering of genotypes which persists for hundreds of generations. Patchiness is more pronounced when dispersal is leptokurtic as is the case in many animal and plant species. These results are of particular interest because population genetic parameters such as gene flow and effective population size are commonly estimated using gene frequency divergence information assuming equilibrium conditions and island models. We show how the three forms of dispersal during colonization bring about contrasting population genetic structures and how this affects estimates of gene flow. The implications for experimental studies of the spatial dimension of population genetic structure are discussed.

Gene trees and species trees are not the same

The relationship between species is usually represented as a bifurcating tree with the branching points representing speciation events. The ancestry of genes taken from these species can also be represented as a tree, with the branching points representing ancestral genes. The time back to the branching points, and even the branching order, can be different between the two trees. This possibility is widely recognized, but the discrepancies are often thought to be small. A different picture is emerging from new empirical evidence, particularly that based on multiple loci or on surveys with a wide geographical scope. The discrepancies must be taken into account when estimating the timing of speciation events, especially the more recent branches. On the positive side, the different timings at different loci provide information about the ancestral populations.

DNA PROFILE MATCH PROBABILITY CALCULATION - HOW TO ALLOW FOR POPULATION STRATIFICATION, RELATEDNESS, DATABASE SELECTION AND SINGLE BANDS

In DNA profile analysis, uncertainty arises due to a number of factors such as sampling error, single bands and correlations within and between loci. One of the most important of these factors is kinship: criminal and innocent suspect may share one or more bands through identity by descent from a common ancestor. Ignoring this uncertainty is consistently unfair to innocent suspects. The effect is usually small, but may be important in some cases. The report of the US National Research Committee proposed a complicated, ad-hoc and overly-conservative method of dealing with some of these problems. We propose an alternative approach which addresses directly the effect of kinship. Whilst remaining conservative, it is simple, logically coherent and makes efficient use of the data.

Oral immunization with urease and Escherichia coli heat-labile enterotoxin is safe and immunogenic in Helicobacter pylori–infected adults☆☆☆

BACKGROUND & AIMS Oral immunization with Helicobacter pylori urease can cure Helicobacter infection in animals. As a step toward therapeutic immunization in humans, the safety and immunogenicity of oral immunization with recombinant H. pylori urease were tested in H. pylori-infected adults. METHODS Twenty-six H. pylori-infected volunteers were randomized in a double-blind study to four weekly oral doses of 180, 60, or 20 mg of urease with 5 microg heat-labile enterotoxin of Escherichia coli (LT), LT alone, or placebo. Side effects and immune responses were evaluated weekly after immunization, and gastric biopsy specimens were obtained after 1 month and 6 months for histology and quantitative cultures. RESULTS Diarrhea was noted in 16 of 24 (66%) of the volunteers who completed the study. Antiurease serum immunoglobulin A titers increased 1. 58-fold +/- 0.37-fold and 3.66-fold +/- 1.5-fold (mean +/- SEM) after immunization with 60 and 180 mg urease, respectively, whereas no change occurred in the placebo +/- LT groups (P = 0.005). Circulating antiurease immunoglobulin A-producing cells increased in volunteers exposed to urease compared with placebo (38.9 +/- 13. 6/10(6) vs. 5.4 +/- 3.1; P = 0.018). Eradication of H. pylori infection was not observed, but urease immunization induced a significant decrease in gastric H. pylori density. CONCLUSIONS H. pylori urease with LT is well tolerated and immunogenic in H. pylori-infected individuals. An improved vaccine formulation may induce curative immunity.

Y genetic data support the Neolithic demic diffusion model

There still is no general agreement on the origins of the European gene pool, even though Europe has been more thoroughly investigated than any other continent. In particular, there is continuing controversy about the relative contributions of European Palaeolithic hunter-gatherers and of migrant Near Eastern Neolithic farmers, who brought agriculture to Europe. Here, we apply a statistical framework that we have developed to obtain direct estimates of the contribution of these two groups at the time they met. We analyze a large dataset of 22 binary markers from the non-recombining region of the Y chromosome (NRY), by using a genealogical likelihood-based approach. The results reveal a significantly larger genetic contribution from Neolithic farmers than did previous indirect approaches based on the distribution of haplotypes selected by using post hoc criteria. We detect a significant decrease in admixture across the entire range between the Near East and Western Europe. We also argue that local hunter-gatherers contributed less than 30% in the original settlements. This finding leads us to reject a predominantly cultural transmission of agriculture. Instead, we argue that the demic diffusion model introduced by Ammerman and Cavalli-Sforza [Ammerman, A. J. & Cavalli-Sforza, L. L. (1984) The Neolithic Transition and the Genetics of Populations in Europe (Princeton Univ. Press, Princeton)] captures the major features of this dramatic episode in European prehistory.

The genetic consequences of long distance dispersal during colonization

Rare long distance dispersal may have little impact on gene frequencies in established populations but it can dramatically increase gene flow during episodes of range expansion. We model the invasion of new territory by genetically distinct populations of the same species to investigate the dynamics of such episodes. If long distance dispersal is sufficiently frequent, the populations do not spread as a wave of advance but instead found intermingled isolates. We argue that this process can explain many otherwise puzzling patterns in the geographical distribution of alleles.

Chimeric Live, Attenuated Vaccine against Japanese Encephalitis (ChimeriVax-JE): Phase 2 Clinical Trials for Safety and Immunogenicity, Effect of Vaccine Dose and Schedule, and Memory Response to Challenge with Inactivated Japanese Encephalitis Antigen

ChimeriVax-JE is a live, attenuated vaccine against Japanese encephalitis, using yellow fever (YF) 17D vaccine as a vector. In a double-blind phase 2 trial, 99 adults received vaccine, placebo, or YF 17D vaccine (YF-VAX). ChimeriVax-JE was well tolerated, with no differences in adverse events between treatment groups. Viremias resulting from administration of ChimeriVax-JE and YF-VAX were of short duration and low titer; 82 (94%) of 87 subjects administered graded doses (1.8-5.8 log(10)) of ChimeriVax-JE developed neutralizing antibodies. A second dose, administered 30 days later, had no booster effect. Previous inoculation with YF did not interfere with ChimeriVax-JE, but there was a suggestion (not statistically significant) that ChimeriVax-JE interfered with YF-VAX administered 30 days later. A separate study explored immunological memory both in subjects who had received ChimeriVax-JE 9 months before and in ChimeriVax-JE-naive subjects challenged with inactivated mouse-brain vaccine (JE-VAX). Anamnestic responses were observed in preimmune individuals. ChimeriVax-JE appears to be a safe vaccine that provides protective levels of neutralizing antibody after a single dose.

Clinical proof of principle for ChimeriVax™: recombinant live, attenuated vaccines against flavivirus infections

ChimeriVax is a live, attenuated recombinant virus constructed from yellow fever (YF) 17D in which the envelope protein genes of YF 17D are replaced with the corresponding genes of another flavivirus. A ChimeriVax vaccine was developed against Japanese encephalitis (JE). A randomized, double-blind, outpatient study was conducted to compare the safety and immunogenicity of ChimeriVax-JE and YF 17D. Six YF immune and six non-immune adults were randomized to receive a single SC inoculation of ChimeriVax-JE (5log(10)PFU), ChimeriVax-JE (4log(10)PFU) or YF-VAX((R)) (5log(10)PFU). Mild, transient injection site reactions and flu-like symptoms were noted in all treatment groups, with no significant difference between the groups. Nearly all subjects inoculated with ChimeriVax-JE at both dose levels developed a transient, low-level viremia which was similar in magnitude and duration to that following YF-VAX). Neutralizing antibody seroconversion rates to ChimeriVax-JE was 100% in the high and low dose groups in both naïve and YF immune subjects; seroconversion to wild-type JE strains was similar or lower than to the homologous (vaccine) virus. Mean neutralizing antibody responses were higher in the ChimeriVax-JE high dose groups (naïve subjects LNI 1.55, PRNT(50) 254; YF immune subjects LNI 2.23, PRNT(50) 327) than in the low dose groups (naïve subjects 1.38, PRNT(50) 128; YF immune subjects LNI 1.62, PRNT(50) 270). JE antibody levels were higher in YF immune than in naïve subjects, dispelling concerns about anti-vector immunity. The safety and immunogenicity profile of ChimeriVax-JE vaccine appears to be similar to that of YF 17D. The new vaccine holds promise for prevention of JE in travelers and residents of endemic countries. The ChimeriVax technology platform is being exploited for development of new vaccines against dengue and West Nile.