Variation In Gene Frequencies Research Articles

Global scale phylogeography of functional traits and microdiversity in Prochlorococcus

Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype’s phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.

The Genome Segments of Bluetongue Virus Differ in Copy Number in a Host-Specific Manner.

Genome segmentation is mainly thought to facilitate reassortment. Here, we show that segmentation can also allow differences in segment abundance in populations of bluetongue virus (BTV). BTV has a genome consisting in 10 segments, and its cycle primarily involves periodic alternation between ruminants and Culicoides biting midges. We have developed a reverse transcription-quantitative PCR (RT-qPCR) approach to quantify each segment in wild BTV populations sampled in both ruminants and midges during an epizootic. Segment frequencies deviated from equimolarity in all hosts. Interestingly, segment frequencies were reproducible and distinct between ruminants and biting midges. Beyond a putative regulatory role in virus expression, this phenomenon could lead to different evolution rates between segments.IMPORTANCE The variation in viral gene frequencies remains a largely unexplored aspect of within-host genetics. This phenomenon is often considered to be specific to multipartite viruses. Multipartite viruses have segmented genomes, but in contrast to segmented viruses, their segments are each encapsidated alone in a virion. A main hypothesis explaining the evolution of multipartism is that, compared to segmented viruses, it facilitates the regulation of segment abundancy, and the genes the segments carry, within a host. These differences in gene frequencies could allow for expression regulation. Here, we show that wild populations of a segmented virus, bluetongue virus (BTV), also present unequal segment frequencies. BTV cycles between ruminants and Culicoides biting midges. As expected from a role in expression regulation, segment frequencies tended to show specific values that differed between ruminants and midges. Our results expand previous knowledge on gene frequency variation and call for studies on its role and conservation beyond multipartite viruses.

Edge weight variance: population genetic metrics for social network analysis

We present novel metrics for analysis of weighted social networks that focus explicitly on the distribution of edge weights at hierarchical scales from node to egonet to community and to the network as a whole. The formulae are adapted from existing measures, originally developed in the context of population genetics to analyse variance in gene frequencies at different levels of organization. Our metrics, including ‘effective degree’ (by analogy to effective number of alleles), ‘concentration’ (by analogy to the inbreeding coefficient), ‘observed’ and ‘expected edge weight diversity’ (by analogy to observed and expected gene diversity) and F statistics allow one to partition the variance in edge weights among hierarchical levels of organization within networks. They provide a quantitative method for addressing issues as diverse as disease transmission, social complexity, the spread of learned behaviours and the evolution of cooperation. We illustrate the utility of these new metrics by applying them to three empirical social networks: long-tailed manakins, Chiroxiphia linearis, monk parakeets, Myiopsitta monachus, and mountain goats, Oreamnos americanus.

Ancestry inference of 96 population samples using microhaplotypes

Microhaplotypes have become a new type of forensic marker with a great ability to identify and deconvolute mixtures because massively parallel sequencing (MPS) allows the alleles (haplotypes) of the multi-SNP loci to be determined directly for an individual. As originally defined, a microhaplotype locus is a short segment of DNA with two or more SNPs defining three or more haplotypes. The length is short enough, less than about 300 bp, that the read length of current MPS technology can produce a phase-known sequence of each chromosome of an individual. As part of the discovery phase of our studies, data on 130 microhaplotype loci with estimates of haplotype frequency data on 83 populations have been published. To provide a better picture of global allele frequency variation, we have now tested 13 more populations for 65 of the microhaplotype loci from among those with higher levels of inter-population gene frequency variation, including 8 loci not previously published. These loci provide clear distinctions among 6 biogeographic regions and provide some information distinguishing up to 10 clusters of populations.

Inter-annual maintenance of the fine-scale genetic structure in a biennial plant.

Within plant populations, space-restricted gene movement, together with environmental heterogeneity, can result in a spatial variation in gene frequencies. In biennial plants, inter-annual flowering migrants can homogenize gene frequencies between consecutive cohorts. However, the actual impact of these migrants on spatial genetic variation remains unexplored. Here, we used 10 nuclear microsatellite and one plastid genetic marker to characterize the spatial genetic structure within two consecutive cohorts in a population of the biennial plant Erysimum mediohispanicum (Brassicaceae). We explored the maintenance of this structure between consecutive flowering cohorts at different levels of complexity, and investigated landscape effects on gene flow. We found that cohorts were not genetically differentiated and showed a spatial genetic structure defined by a negative genetic-spatial correlation at fine scale that varied in intensity with compass directions. This spatial genetic structure was maintained when comparing plants from different cohorts. Additionally, genotypes were consistently associated with environmental factors such as light availability and soil composition, but to a lesser extent compared with the spatial autocorrelation. We conclude that inter-annual migrants, in combination with limited seed dispersal and environmental heterogeneity, play a major role in shaping and maintaining the spatial genetic structure among cohorts in this biennial plant.

A Contribution to the Genetic Epidemiology of Structured Populations

A mating system, previously derived, which is more general than random mating is defined by the gene frequency q and a parameter F which measures divergence from Hardy-Weinberg proportions commonly used in genetic analysis. F can be viewed as the average coefficient of inbreeding in a population, the use emphasized here. Also it can characterize the variation in gene frequency in a stratified population. Taking q as fixed, the distribution of F over values admissible under the general mating system is derived by simulation. The mating system may be seen to be based on indifference as to choice of mates. This is the first object of the paper. The second uses the derived distribution of F to make a Bayesian estimate of F from a single sample of genotypic counts. Such an estimate has a number of uses in genetic analysis.

A note on the partitioning of allelic diversity

Gene diversity and allelic diversity are both recognized as useful criteria for establishing priorities of conservation. Similarly to gene diversity partitioning, based on variation of gene frequencies both within and between subpopulations, allelic diversity can be partitioned using variation in allele numbers. Allelic diversity components have to meet a number of desirable properties, among which orthogonality (i.e. independence of the within-subpopulation and between-subpopulation components), and concavity (i.e. no within-subpopulation diversity larger than total diversity). In this note it is shown how the partitioning recommended in species diversity studies should be transposed to allelic diversity. Attention is drawn to some methods of allelic diversity partitioning currently proposed, essentially the widely used rarefaction method of Petit et al. (Conserv Biol 12:844–855, 1998) and a more recently proposed method by Caballero and Rodriguez-Ramilo (Conserv Genet 11:2219–2229, 2010). Their contrasting properties and the potentially contrasting conclusions to be expected from their application in conservation are emphasized. Some simple examples are used to show how an improper measure of allelic diversity may lead to misleading conclusions when defining priorities of conservation.

Genetic Diversity and Selection Regulates Evolution of Infectious Bronchitis Virus

Conventional and molecular epidemiologic studies have confirmed the ability of infectious bronchitis virus (IBV) to rapidly evolve and successfully circumvent extensive vaccination programs implemented since the early 1950s. IBV evolution has often been explained as variation in gene frequencies as if evolution were driven by genetic drift alone. However, the mechanisms regulating the evolution of IBV include both the generation of genetic diversity and the selection process. IBV's generation of genetic diversity has been extensively investigated and ultimately involves mutations and recombination events occurring during viral replication. The relevance of the selection process has been further understood more recently by identifying genetic and phenotypic differences between IBV populations prior to, and during, replication in the natural host. Accumulating evidence suggests that multiple environmental forces within the host, including immune responses (or lack thereof) and affinity for cell receptors, as well as physical and biochemical conditions, are responsible for the selection process. Some scientists have used or adopted the related quasispecies frame to explain IBV evolution. The quasispecies frame, while providing a distinct explanation of the dynamics of populations in which mutation is a frequent event, exhibits relevant limitations which are discussed herein. Instead, it seems that IBV populations evolving by the generation of genetic variability and selection on replicons follow the evolutionary mechanisms originally proposed by Darwin. Understanding the mechanisms underlying the evolution of IBV is of basic relevance and, without doubt, essential to appropriately control and prevent the disease.

Diversity of killer cell immunoglobulin-like receptor genes in Indonesian populations of Sumatra, Sulawesi and Moluccas Islands

Killer immunoglobulin-like receptors (KIRs) regulate the activity of natural killer and T cells through interaction with specific human leukocyte antigen (HLA) molecules on target cells. Like HLA class I genes that are characterised by extreme allelic polymorphism, KIR genes are diverse and vary in both gene content and allelic polymorphism. Population studies conducted over the last several years have showed that KIR gene frequencies (GF) and genotype content vary among different ethnic groups, indicating the extent of KIR diversity. Some studies have also shown the effect of the presence or absence of specific KIR genes in human disease. We have recently reported the distribution of KIR genes in populations from Java (Central Javanese and the Sundanese of West Java), East Timor (Timorese), Kalimantan provinces of Indonesian Borneo (Dayaks) and Irian Jaya (Western half of the island of New Guinea; Melanese). We here extend analysis of the KIR genes in populations from North Sulawesi (Minahasans), West Sumatra (Minangs) and Moluccas Islands. All 16 KIR genes were observed in all three populations. Variation in GF between populations was observed, except for the KIR2DL4, KIR3DL2, KIR3DL3 and KIR3DP1 genes, which were present in every individual tested. When comparing KIR GF between populations, both principal component analysis and phylogenetic tree analyses showed a close relationship between Minahasan and Moluccan populations that are clustered with Timorese in the same clade. The Minang tribe lies between the Javanese/Kalimantan and the Timorese/Minahasan/Moluccan clades, whereas Irianese show the greatest genetic distances from other Indonesian populations. The results correspond well with the history of migration in Indonesia and will contribute to the understanding of the genetic as well as the geographic history of the region.

Diversity of killer cell immunoglobulin‐like receptor genes in Indonesian populations of Java, Kalimantan, Timor and Irian Jaya

Killer cell immunoglobulin-like receptors (KIRs) regulate the activity of natural killer and T cells through interactions with specific human leucocyte antigen class I molecules on target cells. Population studies performed over the last several years have established that KIR gene frequencies (GFs) and genotype content vary considerably among different ethnic groups, indicating the extent of KIR diversity, some of which have also shown the effect of the presence or absence of specific KIR genes in human disease. We have determined the frequencies of 16 KIR genes and pseudogenes and genotypes in 193 Indonesian individuals from Java, East Timor, Irian Jaya (western half of the island of New Guinea) and Kalimantan provinces of Indonesian Borneo. All 16 KIR genes were observed in all four populations. Variation in GFs between populations was observed, except for KIR2DL4, KIR3DL2, KIR3DL3, KIR2DP1 and KIR3DP1 genes, which were present in every individual tested. When comparing KIR GFs between populations, both principal component analysis and a phylogenetic tree showed close clustering of the Kalimantan and Javanese populations, while Irianese populations were clearly separated from the other three populations. Our results indicate a high level of KIR polymorphism in Indonesian populations that probably reflects the large geographical spread of the Indonesian archipelago and the complex evolutionary history and population migration in this region.

The genetic structure of Scandinavian Willow Ptarmigan (Lagopus lagopus lagopus) populations

Temporal (between years) and spatial (between populations) variation in gene frequencies and heterozygosity was studied in 8 polymorphic serum esterase loci in 602 Willow Ptarmigan (Lagopus lagopus lagopus) from Scandinavian localities during four years. Most of the gene diversity (97 %) was found within years from the same population. Of the remaining variation, about twice as much was attributed to temporal as to spatial differences. About the same genetic distance (D, NEI1975) was observed between populations (0.0082) as that between years from the same population (0.0074). The gene frequencies within each population varied significantly between years, average heterozygosity did not. A significantly different heterozygosity was recorded in all but two pairwise comparisons between populations. Since there was little variation in heterozygosity between years compared to the variation between populations, we suggest that average heterozygosity reflects adaption to local environmental conditions in Willow Ptarmigan.

Variation of gene frequencies in ASIP, MC1R and GREY loci in Thoroughbred horses

The objective of the study has been to verify the hypothesis that the coat colour is regarded in the selection of Polish Thoroughbred horse population. Formally, the colour is not a selection criterion in this breed selected mainly for speed. The material consisted of twelve groups of foals registered in successive volumes of the Stud Book (11,688 foals, in total) and their parents selected to the breeding stud. The frequency of alleles in ASIP, MC1R and GREY loci controlling the coat colours was estimated from the recessive phenotype frequency square in the groups of foals. The inflow of foreign genes was limited and the population great, hence the migration effect was very low. The drift and Wahlund effect hardly influenced the genetic structure in the groups which enabled to analyze the population not divided. The total offspring frequency of recessive a, e and g alleles amounted to 0.1552, 0.4877 and 0.9773, respectively. Accuracy of the assessment of the a and e frequency was confirmed on the basis of test matings. The a, e and g alleles were more frequent in dams than in sires and the a alleles occurred more often in fillies than in colts. The frequency of a and e alleles was higher in the offspring than in the parents. The genotype distribution in the offspring differed from the expected one, assessed from the gamete frequency in sires and in dams. Fewer bay foals were born than anticipated. All the results show that the coat colour is not entirely disregarded in the breeding of Thoroughbred horses. The dominant A and E alleles producing the colour are preferred in the selection, particularly in the sires. This leads to some alterations in the phenotypic structure of the population. On the other hand, the horses are mated randomly, irrespective of the coat colour.

Variation of sugary1 and shrunken2 gene frequency in different maize genetic backgrounds

AbstractGenotypes affect the survival of mutant genes in segregating populations. This study elucidates the effect of different maize genetic backgrounds on variation in gene frequency in sweet corn, sugary1 (su1) and sugary enhancer1 (se1), and supersweet corn, shrunken2 (sh2). Four sweet corn inbred lines and a supersweet synthetic were crossed to six field corn inbreds from diverse heterotic groups. The crosses were self‐pollinated and the F2 population was recombined twice. Gene frequencies were calculated from grain frequencies. Variation of su1 frequency differed significantly from random drift and a significant linear reduction was observed for half of the su1su1Se1Se1Sh2Sh2 × Su1Su1Se1Se1Sh2Sh2 crosses. The su1 and sh2 frequencies suffered a significant linear reduction for most su1su1se1se1Sh2Sh2 × Su1Su1Se1Se1Sh2Sh2 and Su1Su1Se1Se1sh2sh2 × Su1Su1Se1Se1Sh2Sh2 crosses, respectively. Also, the residual sums of squares, due to deviations from the linear trend, were significant for some crosses due to frequency‐dependent selection and genotypic interactions. Viability of su1 and sh2 depended on the specific sweet × field corn genotype combination but was not related to field corn heterotic groups. The se1 gene could have a detrimental effect on su1 viability.

Natural selection and climate change: temperature‐linked spatial and temporal trends in gene frequency in Fagus sylvatica

Rapid increases in global temperature are likely to impose strong directional selection on many plant populations, which must therefore adapt if they are to survive. Within populations, microgeographic genetic differentiation of individuals with respect to climate suggests that some populations may adapt to changing temperatures in the short-term through rapid changes in gene frequency. We used a genome scan to identify temperature-related adaptive differentiation of individuals of the tree species Fagus sylvatica. By combining molecular marker and dendrochronological data we assessed spatial and temporal variation in gene frequency at the locus identified as being under selection. We show that gene frequency at this locus varies predictably with temperature. The probability of the presence of the dominant marker allele shows a declining trend over the latter half of the 20th century, in parallel with rising temperatures in the region. Our results show that F. sylvatica populations may show some capacity for an in situ adaptive response to climate change. However as reported ongoing distributional changes demonstrate, this response is not enough to allow all populations of this species to persist in all of their current locations.

Population structure in Ascaris suum (Nematoda) among domestic swine in Denmark as measured by whole genome DNA fingerprinting

We here analyze the population structure in the pig roundworm, Ascaris suum, among domestic pigs in Denmark using a whole-genome DNA fingerprinting technique, "amplified fragment length polymorphism" (AFLP) analysis. With these data, we can extract absolute gene frequency variance components and G-statistics for 135 independent nucleotide polymorphisms. The average proportion of total variance partitioned between Jutland and Zealand is less than 3% of the total variance, implying no restriction in gene flow between worms from different regions in Denmark. The average gene frequency difference between two farms widely separated in Jutland represents 5% of the total genetic variance of these two farms combined. Conversely, worms from different hosts within these two farms are more subdivided, with an average of 12% of the total variance in gene frequencies within farms being distributed between hosts. This result implies substantial single generation inbreeding due to founder effects in the establishment of adult worms in single hosts. Absolute variance components extracted from the gene diversities also showed significant differences, with the among-host variance being greater that the between-farm and between-region values. This little geographical variation is discussed in relation to the hierarchic structure of the Danish swine production system. Comparison of our results with other studies on parasitic roundworms, suggests that patterns of host dispersal effectively control patterns of worm gene flow. Furthermore, the potential spread of anthelminth resistance among A. suum may thus be rapid, due to the flow of infected hosts within the domestic swine stocks in Denmark.

Assigning individuals to ethnic groups based on 13 STR loci

Inferring the ethnic origin of individuals by means of short tandem repeat (STR) profiles has received considerable attention recently. Gene frequency variation among human populations has been extensively documented, and it has been suggested that the differences in allele proportions between ethnic groups could form the basis of an inferential system. We report the use of DNA profiles from 13 STR loci for inferring the ethnic origin of samples of unknown provenance using five populations of immigrants. This preliminary work shows that a population assignment test can be already used in real casework studies.

Temporal genetic variation in Aedes aegypti populations in Ho Chi Minh City (Vietnam).

Aedes aegypti, the main vector of dengue viruses in Asia, displays variation in population density over time. The larval habitats of this species being unevenly distributed and transient (depending on cycles of drought and flood), the forces generating temporal variation in gene frequencies in populations are studied. We sampled seven mosquito populations from Ho Chi Minh City (Vietnam) and its suburbs on five occasions between April 1999 and August 2000. We investigated genetic variation by studying isoenzyme and microsatellite polymorphism and susceptibility to a dengue 2 virus strain. Ae. aegypti populations collected during the dry season (January-April) showed genetic differentiation (F(ST) = 0.016, P < 10(-6) for isoenzymes) and showed more differentiated infection rates of the dengue 2 virus. The genetic structure of the population is less marked during the rainy season (F(ST) = 0.081, P < 10(-6)). Thus, environmental factors, such as rainfall and factors related to human activity, such as breeding site density and insecticide treatment, control the genetic structure of Ae. aegypti populations in the short term. The implications of studies of this kind for the design of future control programmes are discussed.

&lt;I&gt;Coleomegilla maculata&lt;/I&gt; (Coleoptera: Coccinellidae) is a Species Complex

Abstract Coleomegilla maculata De Geer is an abundant, widely distributed, New World polyphagous lady beetle. High levels of variation at 14 polymorphic allozyme loci were used to examine breeding structure of populations from New England, Iowa, south Texas, and Honduras. Analysis of variance of gene frequencies and F-statistics showed high levels of gene flow within each region and between the Texan and northern United States populations, but negligible rates of gene flow between these and the Honduran populations. Thus, gene flow was largely unrestricted in North American C. maculata. Honduras populations were highly differentiated genetically from the North American populations and shared with North American beetles only 41 of 70 alleles at 14 allozyme loci. Nei’s genetic distances within Honduran, Texas, and Iowa–New England samples did not differ significantly from zero, but the intergroup distances were large. Reciprocal crosses within and between Texas and Iowan populations were fertile, but recipr...

Molecular markers to study genetic drift and selection in wheat populations

Studying the heterogeneity in variation of gene frequency among populations or between generations may be a possible way to detect genomic regions experiencing selection. In order to evaluate this approach, RFLP markers were used to compare the allelic frequencies in wheat populations that had been submitted to natural selection. In 1984, samples of two composite cross populations were distributed in the French network for dynamic management of genetic resources. Since then, all the sub-populations have been cultivated in the same sites with no human selection. The strong differentiation between populations found for agro-morphological traits (earliness, resistance to pathogens, …) provided evidence of their adaptation to local conditions. The two initial populations and six derived sub-populations cultivated for 10 years in four contrasted sites were studied with RFLP markers. Differentiation between sub-populations based on RFLP diversity was highly significant. Variations of allelic frequencies of the 30 loci scored were found to be much greater than expected under genetic drift only. This led us to conclude that selection greatly influenced the evolution of the populations. Some of the loci clearly presented a higher differentiation than the others. This might indicate that they were genetically linked to other loci polymorphic in the populations and involved in adaptation. However, the effect of one selected gene on a marker, even located very close to the gene, could not be predicted with certainty. Hence, though the populations were predominantly selfing, it seems that initial linkage disequilibriums between markers and selected genes were not strong enough to control closely the evolution of allelic fequencies at the markers.

GENETIC STRUCTURE AND LOCAL ADAPTATION IN NATURAL INSECT POPULATIONS. Edited by Susan Mopper and Sharon Y. Strauss. Chapman and Hall, New York. 1998. Hardback, £65.00. ISBN 0–412–08031–1.

GENETIC STRUCTURE AND LOCAL ADAPTATION IN NATURAL INSECT POPULATIONS. Edited by Susan Mopper and Sharon Y. Strauss. Chapman and Hall, New York. 1998. Hardback, £65.00. ISBN 0–412–08031–1.