Between-population Variation Research Articles

Wings ofCoenagrion puellavary in shape at the northern range margin (Odonata: Coenagrionidae)

A previous study has shown that wing size in Coenagrion puella varied considerably along a latitudinal gradient in the UK. Using landmark data from wing images, patterns of shape variation were also determined along the same transect by geometric morphometric analysis of wing shape. Wing shape was uniform at all sites other than those closest to the range margin, which differed significantly. The potential mechanisms that might have generated such between-population variation are discussed.

Maternal nutritional condition and genetic differentiation affect brood size and offspring body size in Nicrophorus

In most animal species, brood size and body size exhibit some variation within and between populations. This is also true for burying beetles (genus Nicrophorus), a group in which the body size of offspring depends critically on the number of offspring competing for food due to the discrete nature of resource used for larval nutrition (vertebrate carcasses). In one species, brood size and body size are correlated with population density, and appear to be phenotypically plastic. We investigated potential proximate causes of between-population variation in brood size and body size in two species, Nicrophorus vespilloides and Nicrophorus defodiens. Our first experiment supported the notion that brood size is phenotypically plastic, because it was affected by environmental variation in adult nutritional condition. We found that the pre-breeding nutritional status of female N. vespilloides affected the number of eggs they laid, the number of surviving larvae in their broods, and the body size of their offspring. We do not know whether this plasticity is adaptive because greater offspring body size confers an advantage in contests over breeding resources, or whether starved females are constrained to produce smaller clutches because they cannot fully compensate for their poor pre-breeding nutritional status by feeding from the carcass. Our second experiment documents that brood size, specifically the infanticidal brood-size adjustment behavior, has undergone genetic differentiation between two populations of N. defodiens. Even under identical breeding conditions with identical numbers of first-instar larvae, females descended from the two populations produced broods of different size with corresponding differences in offspring body size.

Variation in estimated recombination rates across human populations

Recently it has been reported that recombination hotspots appear to be highly variable between humans and chimpanzees, and there is evidence for between-person variability in hotspots, and evolutionary transience. To understand the nature of variation in human recombination rates, it is important to describe patterns of variability across populations. Direct measurement of recombination rates remains infeasible on a large scale, and population-genetic approaches can be imprecise, and are affected by demographic history. Reports to date have suggested broad similarity in recombination rates at large genomic scales and across human populations. Here, we examine recombination rate estimates at a finer population and genomic scale: 28 worldwide populations and 107 SNPs in a 1 Mb stretch of chromosome 22q. We employ analysis of variance of recombination rate estimates, corrected for differences in effective population size using genome-wide microsatellite mutation rate estimates. We find substantial variation in fine-scale rates between populations, but reduced variation within continental groups. All effects examined (SNP-pair, region, population and interactions) were highly significant. Adjustment for effective population size made little difference to the conclusions. Observed hotspots tended to be conserved across populations, albeit at varying intensities. This holds particularly for populations from the same region, and also to a considerable degree across geographical regions. However, some hotspots appear to be population-specific. Several results from studies on the population history of humans are in accordance with our analysis. Our results suggest that between-population variation in DNA sequences may underly recombination rate variation.

Thriving in an arid environment: High prevalence of avian lice in low humidity conditions

Abiotic factors have been reported to cause variation in parasite pressure among host populations, but such relationships have not been studied in detail, and conflicting evidence exists about the nature of these relationships. Here we study within- and between-population variation in chewing lice parasitization in an arid bird species, the Trumpeter finch (Bucanetes githagineus), and the influence of ambient humidity on parasite load. We found a high prevalence of 2 chewing lice even in particularly dry years and a positive effect of humidity on prevalence at a monthly scale. Nonetheless, our results clearly reveal that lice can become abundant at low ambient humidity conditions and that birds in arid environments are not necessarily under lower ectoparasitic pressure than birds in humid regions. We suggest that lice may adapt their life cycle to overcome the most critical period by synchronizing the more resistant phase (eggs) to the period when relative humidity is lowest (i.e., summertime). We stress that studies on the effect of ecological factors on host-parasite relationships should consider detailed aspects of the life cycle of the latter and the main biological traits of the different stages of the parasites.

Identification of a candidate genetic variant for the high prevalence of type II diabetes in Polynesians

The prevalence of non-insulin-dependent diabetes mellitus (type II diabetes) in Polynesia is among the highest recorded worldwide and is substantially higher than in neighboring human populations. Such large differences in the frequency of a phenotype between populations may be explained by large allele frequency differences between populations in genes associated with the phenotype. To identify genes that may explain the high between-population variation in type II diabetes prevalence in the Pacific, we determined the frequency of 10 type II diabetes-associated alleles in 23 Polynesians, 23 highland New Guineans and 19 Han Chinese, calculated population-pairwise Fst values for each allele and compared these values to the distribution of Fst values from approximately 100,000 SNPs from the same populations. The susceptibility allele in the PPARGC1A gene is at a frequency of 0.717 in Polynesians, 0.368 in Chinese but is absent in the New Guineans. The striking frequency difference between Polynesians and New Guineans is highly unusual (Fst=0.703, P=0.007) and we therefore suggest that this allele may play a role in the large difference in type II diabetes prevalence between Polynesians and neighboring populations.

An Integrated Analysis of Individual and Aggregated Health Data Using Estimating Equations

Analyses of individual disease-exposure data within a population are useful when exposure of interest varies sufficiently within the population. When the within-population variance of exposure is limited, however, power of the individual-data analysis is reduced. In such situations, aggregated-data analyses of disease data across populations, with a sample of individual exposure data from each population, can be powerful in estimating the exposure effect if between population variation of exposure is large. In this paper, we consider a new analytical framework that is a combination of the individual- and aggregated-data analyses, based on an estimating equation approach. The proposed analysis utilizes strengths from individual data and aggregated data in the estimation of the exposure effect of interest, depending on which of the exposure variations (within- versus between-population) dominates. Simulation studies under various different scenarios were performed to show the strengths of the proposed approach in the estimation of the exposure effects of interest.

Genetic Determinants of Prepubertal and Pubertal Growth and Development

This article surveys the current general understanding of genetic influences on within- and between-population variation in growth and development in the context of establishing an International Growth Standard for Preadolescent and Adolescent Children. Traditional genetic epidemiologic analysis methods are reviewed, and evidence from family studies for genetic effects on different measures of growth and development is then presented. Findings from linkage and association studies seeking to identify specific genomic locations and allelic variants of genes influencing variation in growth and maturation are then summarized. Special mention is made of the need to study the interactions between genes and environments. At present, specific genes and polymorphisms contributing to variation in growth and maturation are only beginning to be identified. Larger genetic epidemiologic studies are needed in different parts of the world to better explore population differences in gene frequencies and gene-environment interactions. As advances continue to be made in molecular and statistical genetic methods, the genetic architecture of complex processes, including those of growth and development, will become better elucidated. For now, it can only be concluded that although the fundamental genetic underpinnings of the growth and development of children worldwide are likely to be essentially the same, there are also likely to be differences between populations in the frequencies of allelic gene variants that influence growth and maturation and in the nature of gene-environment interactions. This does not necessarily preclude an international growth reference, but it does have important implications for the form that such a reference might ultimately take.

Three single-nucleotide polymorphisms in LPA account for most of the increase in lipoprotein(a) level elevation in African Americans compared with European Americans

Background: The extent which universally common or population-specific alleles can explain between-population variations in phenotypes is unknown. The heritable coronary heart disease risk factor lipoprotein(a) (Lp(a)) level provides a useful...

Pollination Ecology of Silene acutifolia (Caryophyllaceae): Floral Traits Variation and Pollinator Attraction

The floral display influences the composition of pollinators interacting with a plant species. Geographic and temporal variation in pollinator composition complicates the understanding of the evolutionary consequences of floral display variation. This paper analyses the relationships between Silene acutifolia, a hermaphroditic perennial herb, and its pollinators, based on field studies in the north-west of Spain. Studies were conducted over three years (1997-1999). Firstly, the main pollinators of this species were determined for two years in one population. Secondly, pollen limitation in fruit and seed production was analysed by supplementary hand pollinations, and counting the pollen grains and tubes growing in styles for two different-sized populations. Finally, the effect of flower size and number on the rate of visitation and total seed number was examined for 15 marked plants. The primary pollinators were long-tongued insects, including Hymenoptera, Lepidoptera and Diptera, but the composition and visitation frequencies differed between years. Pollen limitation occurred in one of the years of study. There was between-population variation in the number of pollen grains and pollen tubes found in styles, suggesting pollen limitation in one population. Overall, pollinators visited plants with more open flowers more frequently, and pollinated more flowers within these plants. Conversely, petal and calyx sizes had no effect on insect visitation. Plants with higher rates of visits produced higher number of seeds, suggesting that pollinator-mediated limitation of seed and fruit production may be important in some years.

PATTERNS OF GENETIC DIFFERENTIATION AND CONSERVATION OF THE SLABSIDE PEARLYMUSSEL, LEXINGTONIA DOLABELLOIDES (LEA, 1840) IN THE TENNESSEE RIVER DRAINAGE

The restoration and recovery of imperiled mussel species will require the re-establishment of populations into historically occupied habitats. The possible existence of genetic differentiation among populations should be considered before inter-basin transfers are made. Eighty individuals of the federal candidate species Lexingtonia dolabelloides were sampled from populations in the North Fork Holston, Middle Fork Holston, Clinch, Paint Rock and Duck rivers of the Tennessee River basin in the southeastern United States. We sequenced 603 base-pairs of a mitochondrial DNA gene (ND-1 ) and 512 base-pairs of a nuclear DNA gene (ITS-1 ). Analyses of molecular variation (AMOVA) values for both genes indicated that the majority of variation in L. dolabelloides resided within populations (82.9 –88.3%), with 11.7 – 17.1% of variation among populations. Haplotype frequencies differed significantly among populations for both genes sequenced. Clustering of haplotypes in minimum-spanning networks did not conform stringently to population boundaries, reflecting high within-population and low between-population variability. Maximum parsimony analysis did not identify any population as a monophyletic lineage. A Mantel test showed no significant correlation between geographical stream distance and genetic distance, thus not supporting a pattern of isolationby-distance. Overall, results provided support to manage fragmented populations of L. dolabelloides in the Tennessee River drainage as two management units (MUs), but did not provide evidence for the existence of ESUs following published molecular criteria.

Differences in egg thermotolerance between tropical and temperate populations of the migratory locust Locusta migratoria (Orthoptera: Acridiidae)

The migratory locust Locusta migratoria L., which is widely distributed throughout the world, exhibits within- and between-population variation in cold tolerance. To understand physiological adaptation in populations, we studied the genetic basis of thermotolerance in Hainan (tropical) and Liaoning (temperate) populations and measured expression of Hsp70 and Hsp90 mRNA in both populations at low (0 °C) and high temperatures (40 °C). Phenotypic variation of thermotolerance is heritable. Heritable characteristics differed among different stages of locust egg development, as well as among different measures of thermotolerance. Nuclear genetic factors, rather than cytoplasmic factors, contribute to differences in cold tolerance between the tropical and temperate populations of the migratory locust; for heat tolerance, maternal effects were involved in three stages of egg development. Expression of Hsp90 mRNA was induced in temperate population after heat shock (40 °C×12 h), whereas expression of Hsp70 and 90 was induced in tropical population after cold shock (0 °C×12 h). We suggest that thermotolerance of locust eggs has a complex genetic basis and heat shock proteins may be involved in differences of thermotolerance between locust populations.

Spatial genetic structure in populations of the terrestrial orchid Orchis cyclochila (Orchidaceae)

Orchid seeds are minute, dust-like, wind-borne and, thus, would seem to have the potential for long-distance dispersal. Based on this perception, one may predict near-random spatial genetic structure within orchid populations. In reality we do not know much about seed dispersal in orchids and the few empirical studies of fine-scale genetic structure have revealed significant genetic structure at short distances (< 5m), suggesting that most seeds of orchids fall close to the maternal plant. To obtain more empirical data on dispersal, Ripley’s L(d)-statistics, spatial autocorrelation analyses (coancestry, fij analyses) and Wright’s F statistics were used to examine the distribution of individuals and the genetic structure within two populations of the terrestrial orchid Orchis cyclochila in southern Korea. High levels of genetic diversity (He = 0.210) and low between-population variation were found (FST = 0.030). Ripley’s L(d)-statistics indicated significant aggregation of individuals, and patterns varied depending on populations. Spatial autocorrelation analysis revealed significant positive genetic correlations among individuals located <1 m, with mean fij values expected for half sibs. This genetic structure suggests that many seeds fall in the immediate vicinity of the maternal plant. The finding of significant fine-scale genetic structure, however, does not have to preclude the potential for the long distance dispersal of seeds. Both the existence of fine-scale genetic structure and low FST are consistent with a leptokurtic distribution of seed dispersal distances with a very flat tail.

Characterization and conservation of genetic diversity in subdivided populations

We review the available tools for analysing genetic diversity in conservation programmes of subdivided populations. Ways for establishing conservation priorities have been developed in the context of livestock populations, both from the classical population genetic analysis and from the more recent Weitzman's approach. We discuss different reasons to emphasize either within or between-population variation in conservation decisions and the methodology to establish some compromise. The comparison between neutral and quantitative variation is reviewed from both theoretical and empirical points of view, and the different procedures for the dynamic management of conserved subdivided populations are discussed.

Pathogen-Driven Selection and Worldwide HLA Class I Diversity

The human leukocyte antigen (HLA; known as MHC in other vertebrates) plays a central role in the recognition and presentation of antigens to the immune system and represents the most polymorphic gene cluster in the human genome [1]. Pathogen-driven balancing selection (PDBS) has been previously hypothesized to explain the remarkable polymorphism in the HLA complex, but there is, as yet, no direct support for this hypothesis [2 and 3]. A straightforward prediction coming out of the PDBS hypothesis is that populations from areas with high pathogen diversity should have increased HLA diversity in relation to their average genomic diversity. We tested this prediction by using HLA class I genetic diversity from 61 human populations. Our results show that human colonization history explains a substantial proportion of HLA genetic diversity worldwide. However, between-population variation at the HLA class I genes is also positively correlated with local pathogen richness (notably for the HLA B gene), thus providing support for the PDBS hypothesis. The proportion of variations explained by pathogen richness is higher for the HLA B gene than for the HLA A and HLA C genes. This is in good agreement with both previous immunological and genetic data suggesting that HLA B could be under a higher selective pressure from pathogens.

Population Variation in Femur Subtrochanteric Shape

Use of proximal femur shape to determine ancestry has appeal, but its validity is problematic because of unaddressed issues associated with skeletal plasticity, within- and between-population variation, sample selection, and interobserver error. In this paper, I inspect within- and between-group variation in proximal femur shape using five groups (American Blacks, American Whites, Hispanics, Native Americans, and Polynesians), and examine the affect of three environmental variables (subsistence strategy, physical terrain, and geographical region). Finally. I consider the validity of using the proximal femur to assess ancestry. The results show that there is significant within-group variation in proximal femur shape. Among Native Americans, both geographical location and subsistence strategy have a significant affect on proximal femur shape. Nevertheless, this study generally verifies the assertion that the proximal femur can be used reliably to distinguish Native Americans from American Blacks and Whites, but its precision may be reduced in some geographical regions.

Genetic Variation of the Y Chromosome in Chibcha-Speaking Amerindians of Costa Rica and Panama

Genetic variation of the Y chromosome in five Chibchan tribes (Bribri, Cabecar, Guaymi, Huetar, and Teribe) of Costa Rica and Panama was analyzed using six microsatellite loci (DYS19, DYS389A, DYS389B, DYS390, DYS391, and DYS393), the Y-chromosome-specific alphoid system (alphah), the Y-chromosome Alu polymorphism (YAP), and a specific pre-Columbian transition (C-->T) (M3 marker) in the DYS 199 locus that defines the Q-M3 haplogroup. Thirty-nine haplotypes were found, resulting in a haplotype diversity of 0.937. The Huetar were the most diverse tribe, probably because of their high levels of interethnic admixture. A candidate founder Y-chromosome haplotype was identified (15.1% of Chibchan chromosomes), with the following constitution: YAP-, DYS199*T, alphah-II, DYS19*13, DYS389A*17, DYS389B*10, DYS390*24, DYS391*10, and DYS393*13. This haplotype is the same as the one described previously as one of the most frequent founder paternal lineages in native American populations. Analysis of molecular variance indicated that the between-population variation was smaller than the within-population variation, and the comparison with mtDNA restriction data showed no evidence of differential structuring between maternally and paternally inherited genes in the Chibchan populations. The mismatch-distribution approach indicated estimated coalescence times of the Y chromosomes of the Q-M3 haplogroup of 3,113 and 13,243 years before present; for the mtDNA-restriction haplotypes the estimated coalescence time was between 7,452 and 9,834 years before present. These results are compatible with the suggested time for the origin of the Chibchan group based on archeological, linguistic, and genetic evidence.

DNA Sequence Variation and Haplotype Structure of the ICAM1 and TNF Genes in 12 Ethnic Groups of India Reveal Patterns of Importance in Designing Association Studies

We have examined the patterns of DNA sequence variation in and around the genes coding for ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India. We aimed to (a) quantify the nature and extent of the variation, and (b) analyse the observed patterns of variation in relation to population history and ethnic background. At the ICAM1 and TNF loci, respectively, the total numbers of SNPs that were detected were 28 and 12. Many of these SNPs are not shared across ethnic groups and are unreported in the dbSNP or TSC databases, including two fairly common non-synonymous SNPs at positions 13487 and 13542 in the ICAM1 gene. Conversely, the TNF-376A SNP that is reported to be associated with susceptibility to malaria was not found in our study populations, even though some of the populations inhabit malaria endemic areas. Wide between-population variation in the frequencies of shared SNPs and coefficients of linkage disequilibrium have been observed. These findings have profound implications in case-control association studies.

Blood Ionized Calcium Is Associated with Clustered Polymorphisms in the Carboxyl-Terminal Tail of the Calcium-Sensing Receptor

Blood ionized calcium (iCa) is a quantitative trait subject to genetic influence. iCa is maintained in a narrow range through the action of the calcium-sensing receptor (CASR) controlling PTH secretion and calcium excretion. A CASR single nucleotide polymorphism (SNP) prevalent in Caucasian populations (A986S) has shown significant association with iCa in a cohort of young women, but association with the neighboring SNPs, R990G and Q1011E, has not been examined. We studied 377 unrelated adults (184 men and 193 women) recruited as healthy adults from a blood donor clinic. The subjects were not taking any medications, nor did they have disorders of calcium metabolism. Relative frequencies for the CASR 986S, 990G, and 1011E minor alleles were 24%, 4%, and 3% respectively. At the A986S locus, subjects with the AA genotype had significantly lower iCa (P = 0.0001) than subjects with one or two S alleles (mean +/- se, 1.221 +/- 0.003 vs. 1.239 +/- 0.003 mmol/liter). For the R990G site, subjects with the RR genotype had higher iCa than those with one copy of the 990G allele (1.230 +/- 0.002 vs. 1.213 +/- 0.007 mmol/liter; P = 0.032). With respect to the 1011 locus, iCa was lower in QQ genotype subjects than in the QE group (1.227 +/- 0.002 vs. 1.255 +/- 0.008 mmol/liter; P = 0.002). After resolution of phase for the doubly heterozygous subjects, analysis was conducted on haplotypes across all three loci. As expected, subjects with SRQ and ARE haplotypes are relatively hypercalcemic, and those with AGQ are hypocalcemic, relative to subjects with the common ARQ haplotype. Multiple regression analysis with clinical covariates (age, sex and menopausal status, creatinine, and PTH) showed that 16.5% of the total variance in iCa may be explained, and the seven CASR haplotypes contribute significantly (P < 0.0001) and substantially (49.1% of the explained variance) to the model, with the following corrected iCa means: ARQ/AGQ, 1.21 +/- 0.01; ARQ/ARQ, 1.22 +/- 0.01; ARQ/SRQ, 1.24 +/- 0.01; SRQ/AGQ, 1.24 +/- 0.03; SRQ/SRQ, 1.25 +/- 0.01; ARQ/ARE, 1.25 +/- 0.01; and SRQ/ARE, 1.27 +/- 0.01. Our data confirm the association between iCa and the A986S locus and suggest that R990G and Q1011E are also predictive. Given the significant between-population variations in frequency of variant alleles in this CASR SNP cluster, tri-locus haplotyping may prove to be more informative in studies of association between variation in CASR and disease.

Genetic Differences Between Two Wild and One Farmed Population of Atlantic Salmon (Salmo salar) Revealed by Three Classes of Genetic Markers

Mjelnerad, I. B., Refseth, U. H., Karlsen, E., Balstad, T., Jakobsen, K. S. and Hindar, K. 1997. Genetic differences between two wild and one farmed population of Atlantic salmon (Salmo salar) revealed by three classes of genetic markers. Hereditas 127: 239-248. Lund, Sweden. ISSN 0018-0661. Received April 7, 1997. Accepted August 21, 1997 Genetic diversity within and between two wild and one farmed population of Atlantic salmon was estimated by 12 variable enzyme loci, three single locus- and one multilocus DNA minisatellite probe. The farmed salmon were fifth-generation fish from one of the principal commercial strains in Norway and the wild salmon were from the rivers Numedalslagen and Tana, Norway. All three classes of markers detected significant differentiation between the populations, with the farmed population being genetically most divergent. The farmed fish showed less genetic variability than the wild populations, as all techniques revealed a lower (14 %-45 %) number of variable bands/alleles in this group. However, only multilocus DNA fingerprinting detected a significantly lower level of heterozygosity within the farmed population. Estimates of average heterozygosity within populations were almost identical for single locus and multilocus minisatellites (0.558 and 0.548, respectively), which were more than three times higher than for polymorphic allozymes (0.162). Estimates of interpopulation genetic differentiation, however, gave highly concordant results between the allozymes and minisatellites (Fst range: 0.106-0.135). Our results show that fifth generation farmed Atlantic salmon differ significantly from wild salmon in loci others than those chosen for selection in the breeding program. The study also suggests that the choice of genetic markers for studies of Atlantic salmon depends on the aim of the study (within- versus between-population variability).

Sperm size evolution in Drosophila: inter- and intraspecific analysis.

Numerous reports were devoted to the variation of sperm length in relation to sperm competition amongst species. However, studies on intraspecific variations of sperm size are very scarce and the number of sperm measured, very limited. This paper investigates within-individual, between-individual and between-population variation of sperm length in the two cosmopolitan species, D. simulans and D. melanogaster. Sperm length distributions are completely discriminated against with these two species, with the mean values equal to 1.121 +/- 0.002 and 1.989 +/- 0.008 mm, respectively. Results of intraspecific variation show a contrasting pattern between the two species. The mode of sperm length distributions is much less variable in D. simulans than in D. melanogaster. The sperm size divergence is unaffected whenever the two species are in sympatry (tested at 'Evolution Canyon', Mount Carmel, Israel) or in allopatry, but the two species react differentially to abiotic local factors. D. melanogaster, in contrast to D. simulans, shows a clinal pattern in sperm size associated with drought. We discussed this pattern in relation to the potential role of sperm length in the ongoing process of non-random mating and incipient sympatric speciation observed in this locality in D. melanogaster.