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Multi-population GWAS lead to identification of common and population-specific QTLs for leaf rust resistance in barley. Genome-wide association studies (GWAS) are a powerful tool for detecting genetic markers associated with traits of interest. However, these studies are typically restricted to a single population, and transferability of identified marker effects across populations is challenged by population differences in linkage, allele frequencies, epistatic effects, and environmental context. When comparing GWAS results between populations, a lack of overlapping signals is often interpreted as a lack of common quantitative trait loci (QTLs), although such discrepancies may result from differences in statistical power to detect signals. In barley (Hordeum vulgare L.), where genetic leaf rust resistance is rapidly overcome by evolving pathogens, identification of cross-population robust and potentially transferable resistance loci is a key task. Here, we present a mixed model approach for multi-population GWAS that estimates correlated marker effects in multiple populations and use this to test for significant effects across and within populations. Applying this model to four barley breeding populations revealed both common and population-specific QTL effects for leaf rust resistance, including loci colocalizing with known Rph genes and novel regions with plausible candidate genes. Multi-population GWAS increased power, revealing signals not detected by GWAS within populations. We categorized the reported QTLs into three groups based on marker-associated allele effects: (1) consistent effect direction across populations, (2) differing effect direction across populations, and (3) present in a single population. The study highlights the transferability and limitations of leaf rust resistance QTLs across different barley populations and provides a general statistical framework to support robust marker-assisted selection across populations.
We compared demography of populations along gradients of population density in two medium-sized herbivorous marsupials, the common brushtail possum Trichosurus vulpecula and the rufous bettong Aepyprymnus rufescens, to test for net dispersal from high density populations (acting as sources) to low density populations (sinks). In both species, population density was positively related to soil fertility, and variation in soil fertility produced large differences in population density of contiguous populations. We predicted that if source-sink dynamics were operating over this density gradient, we should find higher immigration rates in low-density populations, and positive relationships of measures of individual fitness--body condition, reproductive output, juvenile growth rates and survivorship--to population density. This was predicted because under source-sink dynamics, immigration from high-density sites would hold population density above carrying capacity in low-density sites. The study included 13 populations of these two species, representing a more than 50-fold range of density for each species, but we found that individual fitness, immigration rates and population turnover were similar in all populations. We conclude that net dispersal from high to low density populations had little influence on population dynamics in these species; rather, all populations appeared to be independently regulated at carrying capacity, with a balanced exchange of dispersers among populations. These two species have suffered recent reductions in range, and they are ecologically similar to other species that have declined to extinction in inland Australia. It has been argued that part of the cause of the vulnerability of species like these is that they exhibit source-sink dynamics, and disturbance to source habitats can therefore cause large-scale population collapses. The results of our study argue against this interpretation.
Populations of the temperate seagrass, Zostera marina L. (eelgrass), often exist as discontinuous beds in estuaries, harbors, and bays where they can reproduce sexually or vegetatively through clonal propagation. We examined the genetic structure of three geographically and morphologically distinct populations from central California (Elkhorn Slough, Tomales Bay, and Del Monte Beach), using multilocus restriction fragment length polymorphisms (DNA fingerprints). Within-population genetic similarity (Sw) values for the three eelgrass populations ranged from 0.44 to 0.68. The Tomales Bay population located in an undisturbed, littoral site possessed a within-population genetic similarity (Sw = 0.44) that was significantly lower than those of the other two populations. Cluster analysis identified genetic substructure in only the undisturbed subtidal population (Del Monte Beach). Between-population similarity values (Sb) for all pairwise comparisons ranged from 0.47 to 0.51. The three eelgrass populations show significantly less between locale genetic similarity than found within populations, indicating that gene flow is restricted between locales even though two of the populations are separated by only 30 km. The study demonstrates that (i) natural populations of Z. marina from both disturbed and undisturbed habitats possess high genetic diversity and are not primarily clonal, (ii) gene flow is restricted even between populations in close proximity, (iii) an intertidal population from a highly disturbed habital shows much lower genetic diversity than an intertidal population from an undisturbed site, and (iv) DNA fingerprinting techniques can be exploited to understand gene flow and population genetic structure in Z. marina, a widespread and ecologically important species, and as such are relevant to the management of this coastal resource.
In order to examine the operation of diversifying selection as the maintenance mechanism of excessive additive genetic variance for viability in southern populations in comparison with northern populations of Drosophila melanogaster, two sets of experiments were conducted using second chromosomes extracted from the Ogasawara population (a southern population in Japan) and from the Aomori population (a northern population in Japan). Chromosomal homozygote and heterozygote viabilities were estimated in eight kinds of artificially produced breeding environments. The main findings in the present investigation are as follows: (1) Significant genotype-environment interaction was observed using chromosomes extracted from the Ogasawara population. Indeed, the estimate of the genotype-environment interaction variance for heterozygotes was significantly larger than that of the genotypic variance. On the other hand, when chromosomes sampled from the Aomori population were examined, that interaction variance was significant only for homozygotes and its value was no more than one quarter of that for the chromosomes from the Ogasawara population. (2) The average genetic correlation between any two viabilities of the same lines estimated in the eight kinds of breeding environments for the chromosomes sampled from the Ogasawara population was smaller than that for the chromosomes from the Aomori population both in homozygotes and in heterozygotes, especially in the latter. (3) The stability of heterozygotes over homozygotes against fluctuations of environmental conditions was seen in the chromosomes from the Ogasawara population, but not from the Aomori population. (4) From the excessive genotype-environment interaction variance compared with the genotypic variance in heterozygotes, it was suggested for the chromosomes from the Ogasawara population that the reversal of viability order between homozygotes took place in some environments at the locus level. On the basis of these findings, it is strongly suggested that diversifying selection is operating in a southern population of D. melanogaster on some of the viability polygenes which are probably located outside the structural loci, and the excessive additive genetic variance of viability in southern populations is maintained by this type of selection.
To prevent a population irretrievably depleting its resources, mammals have evolved a behavioural and physiological response to population crisis. When a mammalian population becomes dangerously dense, there is a reversal of behaviour. Co-operation and parental behaviour are replaced by competition, dominance and aggressive violence, leading to high mortality, especially of females and young, and a reduced population. The stress of overpopulation and the resulting violence impairs both the immune and the reproductive systems. Hence epidemics complete the crash of the population, and reproduction is slowed for three or four generations, giving the resources ample time to recover. In some mammal species, crisis and crisis response recur regularly, leading to cycles of population growth and relapse, oscillating about a fixed mean. Population crisis response and population cycles have been equally prominent in the history of human societies. But in man successive advances in food production have made possible growing populations, though with every such advance population soon outgrew resources again. Hence human cycles have been superimposed on a rising curve, producing a saw-tooth graph. Because advances in food production amounted to sudden disturbances in the relations between human populations and their environments, the crisis response in man has failed to avert famine and resource damage. In the large human societies evolved since the coming of settled agriculture and cities, the basic effects of violence, epidemics, famine and resource damage have been mediated by such specifically human disasters as inflation, unemployment, and political tyranny. An account of past crises, periods of relative relief from population pressure, and resulting cycles, is given for a number of regions: China, North Africa and Western Asia, the northern Mediterranean, and north-western Europe. The paper ends with an account of the present world-wide population crisis, and the solution made possible by Malthus's discovery that, unlike animals, we can choose to check population growth by reducing the birth-rate, instead of raising the death-rate, as in other mammals, by the population crisis response.
To determine whether human immunodeficiency virus type 1 (HIV-1) in faeces is representative of the HIV-1 population in intestinal tissue, we studied HIV-1 V3 variation in faeces, intestinal biopsies and serum from two individuals. Phylogenic analysis of HIV-1 V3-coding RNA in faeces from one individual showed three distinct genotypes. Viruses belonging to all three genotypes were also present in sigmoidal tissue and in serum. Jejunal tissue contained two of these three genotypes. Analysis of the V3-coding RNA in faeces of the other individual showed five distinct genotypes. One of these genotypes was present in all specimens from this individual. Besides this shared genotype, jejunal tissue and serum contained sequences belonging to one other genotype. In addition, one of the other three V3 variants was detected in sigmoidal tissue. For both persons the shared HIV-1 RNA genotypes in faeces and serum displayed a distinctly different frequency distribution. In one individual, the genotype which was detected in a majority of the clones in faeces (59%) and as a minority in serum (11%), was the most abundant genotype in jejunal and sigmoidal tissue (61% and 80%, respectively). For the other individual the genotype that was present in faeces in a significant number of clones (43%) was detected in serum as a minority (8%), whereas this genotype composed 47% of the clones isolated from jejunal tissue. Taken together these data suggest that faeces contain HIV-1 sequences that are derived from local HIV-1 replication in intestinal tissue.
Results of the maximum-likelihood estimation of heterozygous beta-thalassemia frequency in the Crimean Tartar ancestral population obtained by evaluating the gametic contribution of Uzbeks to the Crimean Tartar ethnic group are presented. The computing algorithm is given, and reliability of the obtained results is discussed.
The Deng-Lynch method was developed to estimate the rate and effects of deleterious genomic mutations (DGM) in natural populations under the assumption that populations are either completely outcrossing or completely selfing and that populations are at mutation-selection (M-S) balance. However, in many plant and animal populations, selfing or outcrossing is often incomplete in that a proportion of populations undergo inbreeding while the rest are outcrossing. In addition, the degrees of deviation of populations from M-S balance are often not known. Through computer simulations, we investigated the robustness and the applicability of the Deng-Lynch method under different degrees of partial selfing or partial outcrossing and for nonequilibrium populations approaching M-S balance at different stages. The investigation was implemented under constant, variable, and epistatic mutation effects. We found that, generally, the estimation by the Deng-Lynch method is fairly robust if the selfing rate (S) is <0.10 in outcrossing populations and if S > 0.8 in selfing populations. The estimation may be unbiased under partial selfing with variable and epistatic mutation effects in predominantly outcrossing populations. The estimation is fairly robust in nonequilibrium populations at different stages approaching M-S balance. The dynamics of populations approaching M-S balance under various parameters are also studied. Under mutation and selection, populations approach balance at a rapid pace. Generally, it takes 400-2000 generations to reach M-S balance even when starting from homogeneous individuals free of DGM. Our investigation here provides a basis for characterizing DGM in partial selfing or outcrossing populations and for nonequilibrium populations.
The Argentine ant (Linepithema humile) is a damaging invasive species that has become established in many Mediterranean-type ecosystems worldwide. To identify likely sources of introduced populations we examined the relationships among native Linepithema populations from Argentina and Brazil and introduced populations of L. humile using mitochondrial cytochrome b sequence data and nuclear microsatellite allele frequencies. The mitochondrial phylogeny revealed that the populations in Brazil were only distantly related to both the introduced populations and the native populations in Argentina, and confirmed that populations in Brazil, previously identified as L. humile, are likely a different species. The microsatellite-based analysis provided resolution among native and introduced populations of L. humile that could not be resolved using the mitochondrial sequences. In the native range, colonies that were geographically close to one another tended to be genetically similar, whereas more distant colonies were genetically different. Most samples from the introduced range were genetically similar, although some exceptions were noted. Most introduced populations were similar to native populations from the southern Rio Parana and were particularly similar to a population from Rosario, Argentina. These findings implicate populations from the southern Rio Parana as the most likely source of introduced populations. Moreover, these data suggest that current efforts to identify natural enemies of the Argentine ant for biological control should focus on native populations in the southern Rio Parana watershed.
Divergence of biological performance of a laboratory-reared population of Moniliformis moniliformis (Acanthocephala) was investigated after 31 yr, or approximately 60 generations, of genetic isolation. An isolate of the laboratory-reared population and isolates of 2 wild populations were used to begin 3 independent life cycles that were maintained for 1 generation for interbreeding and life history trait comparison. Both wild population isolates represented populations with open gene flow. One wild population isolate represented a present-day sample of descendants of the parent population of the laboratory isolate. All 3 populations hybridized, and egg production occurred in all mixed-sex pairs of different populations. The 3 populations did not differ significantly in prepatent period, mean daily egg production, or establishment within the definitive host Rattus norvegicus. The 3 populations varied in patent period, but the laboratory-isolated worms differed from the 2 wild population isolates no more than they did from each other. A positive correlation between mean daily egg production and duration of patent period resulted in different cumulative egg productions. A 31-yr period of isolation did not produce greater divergence in a laboratory population of M. moniliformis than occurs between wild populations with respect to the biological parameters measured.
The black muntjac (Muntiacus crinifrons) is a rare species endemic to China and its current distribution is confined to partial mountain ranges in eastern China. To assess the population structure and gene flow among the extant populations, we sequenced a portion of the mitochondrial control region (424 bp) for 47 samples collected from its current three large populations (Huangshan, Tiammushan and Suichang). A total of 18 unique haplotypes were defined based on 22 polymorphic sites. Of these haplotypes, 15 ones were population-specific and only one haplotype was shared among the three populations. Significant genetic differentiation was detected between Suichang and Huangshan populations (ø(ST)=0.1677, P<0.001) or between Suichang and Tianmushan populations (ø(ST)=0.2002, P<0.001), indicating that the Suichang population may be spatially structured from other two populations along matriline. The Mantel test revealed that this significant differentiation was not driven by geographic distance (P=0.14), implying that genetic divergence of Suichang population might result from recent human disturbances. Phylogenetic analyses suggested the mitochondrial control region haplotypes were split into two well divergent clades (Clade I and Clade II). Interestingly, the two distinct haplotype clades were found to coexist in Suichang area. The nested clade analysis revealed a significant phylogeographic structure among the black muntjac populations (total cladogram: chi2=18.68; P<0.001), which was inferred to result from past fragmentation followed by range expansion. The population expansion was supported by the analysis of mismatch distribution and the tests of neutrality. Therefore, we suggest that the coexistence of distinct haplotypes in Suichang population was induced by historical population expansion after fragmentation and that the current genetic differentiation should be attributed to the reduction of female-mediated gene flow due to recent habitat fragmentation and subsequent loss.
Inter-population variability in long-bone and pelvic-bone growth during the Early Medieval period is examined. The materials comprise four archaeological populations: two Slavonic (Gars-Thunau, Zwentendorf, Austria, 10th-century AD), one Avar (Zwölfaxing, Austria, 8th-century AD), and one Anglo-Saxon (Raunds, England, 10th-century AD). Bone measurements are analyzed against dental age estimates in order to assess inter-population differences in growth rates for long-bone and os coxae bone dimensions. Growth curves of the upper and lower extremities of additional archaeological populations and a modern North-American population are also assessed. The expectation was that the greatest differences in growth patterns would be found between the Anglo-Saxon and the Austrian samples, due to their distinct genetic and biocultural background. Minimal differences were expected between the two Slavonic populations, as these were approximately contemporaneous, recovered from geographically close locations, and shared relatively similar archaeological contexts. Growth curves were estimated for each bone dimension by fitting least-squares fourth-order polynomials (which allowed testing of population differences by analysis of covariance), and iteratively estimating Gompertz growth curves. The results showed differences between bones in the extent of inter-population variability, with diaphyseal long-bone growth showing equivalent patterns across the four populations, but significant differences between populations in the growth patterns of distal diaphyseal dimensions of the femur and humerus and the dimensions of the ilium. Varying growth patterns are therefore associated with inter-population differences in absolute dimensions in relation to age as well as variations in growth velocities. Inter-population variability in growth curves in the case of femoral and humeral dimensions were most pronounced during infancy (0-2 years). The most consistent differences in bone growth and related dimensions are between Zwölfaxing and the other samples. No significant differences in growth were detected between the Anglo-Saxon and the Austrian populations.
The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation among populations of marine animals. We investigated the genetic characteristics of perennial and annual populations of the marine angiosperm, Zostera marina, along the Pacific coast of Baja California and in the Gulf of California, respectively. Populations of Z. marina from five coastal lagoons along the Pacific coast and four sites in the Gulf of California were studied using nine microsatellite loci. Analyses of variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using theta(ST) values, was observed among all populations within the two regions. Z. marina populations along the Pacific coast are separated by more than 220 km and had the greatest theta(ST) (0.13-0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among populations within the Gulf of California (theta(ST) = 0.04-0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among Gulf of California populations relative to Pacific coast populations. Direction of gene flow was predominantly southward among Pacific coast populations, whereas no dominant polarity in the Gulf of California populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Niño Southern Oscillation (ENSO) events along the Pacific coast.
BACKGROUND: We have examined genetic diversity at fifteen autosomal microsatellite loci in seven predominant populations of Orissa to decipher whether populations inhabiting the same geographic region can be differentiated on the basis of language or ancestry. The studied populations have diverse historical accounts of their origin, belong to two major ethnic groups and different linguistic families. Caucasoid caste populations are speakers of Indo-European language and comprise Brahmins, Khandayat, Karan and Gope, while the three Australoid tribal populations include two Austric speakers: Juang and Saora and a Dravidian speaking population, Paroja. These divergent groups provide a varied substratum for understanding variation of genetic patterns in a geographical area resulting from differential admixture between migrants groups and aboriginals, and the influence of this admixture on population stratification. RESULTS: The allele distribution pattern showed uniformity in the studied groups with approximately 81% genetic variability within populations. The coefficient of gene differentiation was found to be significantly higher in tribes (0.014) than caste groups (0.004). Genetic variance between the groups was 0.34% in both ethnic and linguistic clusters and statistically significant only in the ethnic apportionment. Although the populations were genetically close (FST = 0.010), the contemporary caste and tribal groups formed distinct clusters in both Principal-Component plot and Neighbor-Joining tree. In the phylogenetic tree, the Orissa Brahmins showed close affinity to populations of North India, while Khandayat and Gope clustered with the tribal groups, suggesting a possibility of their origin from indigenous people. CONCLUSIONS: The extent of genetic differentiation in the contemporary caste and tribal groups of Orissa is highly significant and constitutes two distinct genetic clusters. Based on our observations, we suggest that since genetic distances and coefficient of gene differentiation were fairly small, the studied populations are indeed genetically similar and that the genetic structure of populations in a geographical region is primarily influenced by their ancestry and not by socio-cultural hierarchy or language. The scenario of genetic structure, however, might be different for other regions of the subcontinent where populations have more similar ethnic and linguistic backgrounds and there might be variations in the patterns of genomic and socio-cultural affinities in different geographical regions.