Micro- and Macro-Geographic Scale Effect on the Molecular Imprint of Selection and Adaptation in Norway Spruce

Forest tree species of temperate and boreal regions have undergone a long history of demographic changes and evolutionary adaptations. The main objective of this study was to detect signals of selection in Norway spruce (Picea abies [L.] Karst), at different sampling-scales and to investigate, accounting for population structure, the effect of environment on species genetic diversity. A total of 384 single nucleotide polymorphisms (SNPs) representing 290 genes were genotyped at two geographic scales: across 12 populations distributed along two altitudinal-transects in the Alps (micro-geographic scale), and across 27 populations belonging to the range of Norway spruce in central and south-east Europe (macro-geographic scale). At the macrogeographic scale, principal component analysis combined with Bayesian clustering revealed three major clusters, corresponding to the main areas of southern spruce occurrence, i.e. the Alps, Carpathians, and Hercynia. The populations along the altitudinal transects were not differentiated. To assess the role of selection in structuring genetic variation, we applied a Bayesian and coalescent-based F _ST-outlier method and tested for correlations between allele frequencies and climatic variables using regression analyses. At the macro-geographic scale, the F _ST-outlier methods detected together 11 F _ST-outliers. Six outliers were detected when the same analyses were carried out taking into account the genetic structure. Regression analyses with population structure correction resulted in the identification of two (micro-geographic scale) and 38 SNPs (macro-geographic scale) significantly correlated with temperature and/or precipitation. Six of these loci overlapped with F _ST-outliers, among them two loci encoding an enzyme involved in riboflavin biosynthesis and a sucrose synthase. The results of this study indicate a strong relationship between genetic and environmental variation at both geographic scales. It also suggests that an integrative approach combining different outlier detection methods and population sampling at different geographic scales is useful to identify loci potentially involved in adaptation.     

Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

Background

Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.

Results

We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (R_ST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu R_ST = 0.96%, Andhra Pradesh R_ST = 0.77%) exceeds the estimate of variation between these geographically separated groups (R_ST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.

Conclusion

Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.     

Microsatellites reveal a high population structure in Triatoma infestans from Chuquisaca, Bolivia

Background

For Chagas disease, the most serious infectious disease in the Americas, effective disease control depends on elimination of vectors through spraying with insecticides. Molecular genetic research can help vector control programs by identifying and characterizing vector populations and then developing effective intervention strategies.

Methods and Findings

The population genetic structure of Triatoma infestans (Hemiptera: Reduviidae), the main vector of Chagas disease in Bolivia, was investigated using a hierarchical sampling strategy. A total of 230 adults and nymphs from 23 localities throughout the department of Chuquisaca in Southern Bolivia were analyzed at ten microsatellite loci. Population structure, estimated using analysis of molecular variance (AMOVA) to estimate F_ST (infinite alleles model) and R_ST (stepwise mutation model), was significant between western and eastern regions within Chuquisaca and between insects collected in domestic and peri-domestic habitats. Genetic differentiation at three different hierarchical geographic levels was significant, even in the case of adjacent households within a single locality (R _ST = 0.14, F _ST = 0.07). On the largest geographic scale, among five communities up to 100 km apart, R _ST = 0.12 and F _ST = 0.06. Cluster analysis combined with assignment tests identified five clusters within the five communities.

Conclusions

Some houses are colonized by insects from several genetic clusters after spraying, whereas other households are colonized predominately by insects from a single cluster. Significant population structure, measured by both R _ST and F _ST, supports the hypothesis of poor dispersal ability and/or reduced migration of T. infestans. The high degree of genetic structure at small geographic scales, inferences from cluster analysis and assignment tests, and demographic data suggest reinfesting vectors are coming from nearby and from recrudescence (hatching of eggs that were laid before insecticide spraying). Suggestions for using these results in vector control strategies are made.     

Molecular and quantitative trait variation within and among small fragmented populations of the endangered plant species Psilopeganum sinense

Background and Aims

Natural selection and genetic drift are important evolutionary forces in determining genetic and phenotypic differentiation in plant populations. The extent to which these two distinct evolutionary forces affect locally adaptive quantitative traits has been well studied in common plant and animal species. However, we know less about how quantitative traits respond to selection pressures and drift in endangered species that have small population sizes and fragmented distributions. To address this question, this study assessed the relative strengths of selection and genetic drift in shaping population differentiation of phenotypic traits in Psilopeganum sinense, a naturally rare and recently endangered plant species.

Methods

Population differentiation at five quantitative traits (Q_ST) obtained from a common garden experiment was compared with differentiation at putatively neutral microsatellite markers (F_ST) in seven populations of P. sinense. Q_ST estimates were derived using a Bayesian hierarchical variance component method.

Key Results

Trait-specific Q_ST values were equal to or lower than F_ST. Neutral genetic diversity was not correlated with quantitative genetic variation within the populations of P. sinense.

Conclusions

Despite the prevalent empirical evidence for Q_ST > F_ST, the results instead suggest a definitive role of stabilizing selection and drift leading to phenotypic differentiation among small populations. Three traits exhibited a significantly lower Q_ST relative to F_ST, suggesting that populations of P. sinense might have experienced stabilizing selection for the same optimal phenotypes despite large geographical distances between populations and habitat fragmentation. For the other two traits, Q_ST estimates were of the same magnitude as F_ST, indicating that divergence in these traits could have been achieved by genetic drift alone. The lack of correlation between molecular marker and quantitative genetic variation suggests that sophisticated considerations are required for the inference of conservation measures of P. sinense from neutral genetic markers.     

Molecular characterization of Nicaraguan Pinus tecunumanii Schw. ex Eguiluz et Perry populations for in situ conservation

Key message

We conducted molecular characterization of Nicaraguan Pinus tecunumanii populations using microsatellite markers. Populations possess considerable genetic variation but there are risks associated with inbreeding and population fragmentation.

Abstract

We carried out a molecular characterization of three natural populations of Pinus tecunumanii using nine microsatellite markers. All studied populations occur in Nicaragua, where the species has declined primarily due to human-influenced factors. The results showed that there is a high amount of genetic variation in populations (expected heterozygosities 0.775–0.841), populations do not show significant differentiation (mean F _ST 0.0073), apparently due to frequent gene flow or a more continuous distribution and homogenous genetic composition in the past, and inbreeding is common in all populations (F _IS 0.705–0.780). The Structure analysis revealed that there is no evident clustering pattern among P. tecunumanii individuals. Although all studied populations possess a considerable amount of genetic variation, risks associated with inbreeding and population fragmentation should be acknowledged and a conservation strategy developed to safeguard the genetic resources of P. tecunumanii.     

Morphological and genetic divergence in Swedish postglacial stickleback (Pungitius pungitius) populations

Background

An important objective of evolutionary biology is to understand the processes that govern phenotypic variation in natural populations. We assessed patterns of morphological and genetic divergence among coastal and inland lake populations of nine-spined stickleback in northern Sweden. Coastal populations are either from the Baltic coast (n = 5) or from nearby coastal lakes (n = 3) that became isolated from the Baltic Sea (< 100 years before present, ybp). Inland populations are from freshwater lakes that became isolated from the Baltic approximately 10,000 ybp; either single species lakes without predators (n = 5), or lakes with a recent history of predation (n = 5) from stocking of salmonid predators (~50 ybp).

Results

Coastal populations showed little variation in 11 morphological traits and had longer spines per unit of body length than inland populations. Inland populations were larger, on average, and showed greater morphological variation than coastal populations. A principal component analysis (PCA) across all populations revealed two major morphological axes related to spine length (PC1, 47.7% variation) and body size (PC2, 32.9% variation). Analysis of PCA scores showed marked similarity in coastal (Baltic coast and coastal lake) populations. PCA scores indicate that inland populations with predators have higher within-group variance in spine length and lower within-group variance in body size than inland populations without predators. Estimates of within-group P _ST (a proxy for Q _ST) from PCA scores are similar to estimates of F _ST for coastal lake populations but P _ST > F _ST for Baltic coast populations. P _ST > F _ST for PC1 and PC2 for inland predator and inland no predator populations, with the exception that P _ST < F _ST for body size in inland populations lacking predators.

Conclusions

Baltic coast and coastal lake populations show little morphological and genetic variation within and between groups suggesting that these populations experience similar ecological conditions and that time since isolation of coastal lakes has been insufficient to demonstrate divergent morphology in coastal lake populations. Inland populations, on the other hand, showed much greater morphological and genetic variation characteristic of long periods of isolation. Inland populations from lakes without predators generally have larger body size, and smaller spine length relative to body size, suggesting systematic reduction in spine length. In contrast, inland populations with predators exhibit a wider range of spine lengths relative to body size suggesting that this trait is responding to local predation pressure differently among these populations. Taken together the results suggest that predation plays a role in shaping morphological variation among isolated inland populations. However, we cannot rule out that a causal relationship between predation versus other genetic and environmental influences on phenotypic variation not measured in this study exists, and this warrants further investigation.     

Tertiary Origin and Pleistocene Diversification of Dragon Blood Tree (Dracaena cambodiana-Asparagaceae) Populations in the Asian Tropical Forests

Background

The origin of extraordinarily rich biodiversity in tropical forests is often attributed to evolution under stable climatic conditions over a long period or to climatic fluctuations during the recent Quaternary period. Here, we test these two hypotheses using Dracaena cambodiana, a plant species distributed in paleotropical forests.

Methods

We analyzed nucleotide sequence data of two chloroplast DNA (cpDNA: atpB-rbcL and trnD-trnT) regions and genotype data of six nuclear microsatellites from 15 populations (140 and 363 individuals, respectively) distributed in Indochina Peninsular and Hainan Island to infer the patterns of genetic diversity and phylogeographic structure. The population bottleneck and genetic drift were estimated based upon nuclear microsatellites data using the software programs BOTTLENECK and 2MOD. The lineage divergence times and past population dynamics based on cpDNA data were estimated using coalescent-based isolation-with-migration (IMa) and BEAST software programs.

Results

A significant phylogeographic structure (N _ST = 0.876, G _ST = 0.796, F _ST-SSR =0.329, R _ST =0.449; N _ST>G _ST, R _ST>F _ST-SSR, P<0.05) and genetic differentiation among populations were detected. Bottleneck analyses and Bayesian skyline plot suggested recent population reduction. The cpDNA haplotype network revealed the ancestral populations from the southern Indochina region expanded to northward. The most recent ancestor divergence time of D. cambodiana dated back to the Tertiary era and rapid diversification of terminal lineages corresponded to the Quaternary period.

Conclusions

The results indicated that the present distribution of genetic diversity in D. cambodiana was an outcome of Tertiary dispersal and rapid divergence during the Quaternary period under limited gene flow influenced by the uplift of Himalayan-Tibetan Plateau and Quaternary climatic fluctuations respectively. Evolutionary processes, such as extinction-recolonization during the Pleistocene may have contributed to the fast diversification in D. cambodiana.     

Population genetics of an ecosystem-defining reef coral Pocillopora damicornis in the Tropical Eastern Pacific

Background

Coral reefs in the Tropical Eastern Pacific (TEP) are amongst the most peripheral and geographically isolated in the world. This isolation has shaped the biology of TEP organisms and lead to the formation of numerous endemic species. For example, the coral Pocillopora damicornis is a minor reef-builder elsewhere in the Indo-West Pacific, but is the dominant reef-building coral in the TEP, where it forms large, mono-specific stands, covering many hectares of reef. Moreover, TEP P. damicornis reproduces by broadcast spawning, while it broods mostly parthenogenetic larvae throughout the rest of the Indo-West Pacific. Population genetic surveys for P. damicornis from across its Indo-Pacific range indicate that gene flow (i.e. larval dispersal) is generally limited over hundreds of kilometers or less. Little is known about the population genetic structure and the dispersal potential of P. damicornis in the TEP.

Methodology

Using multilocus microsatellite data, we analyzed the population structure of TEP P. damicornis among and within nine reefs and test for significant genetic structure across three geographically and ecologically distinct regions in Panama.

Principal Findings/Conclusions

We detected significant levels of population genetic structure (global R_ST = 0.162), indicating restricted gene flow (i.e. larvae dispersal), both among the three regions (R_RT = 0.081) as well as within regions (R_SR = 0.089). Limited gene flow across a distinct environmental cline, like the regional upwelling gradient in Panama, indicates a significant potential for differential adaptation and population differentiation. Individual reefs were characterized by unexpectedly high genet diversity (avg. 94%), relatively high inbreeding coefficients (global F_IS = 0.183), and localized spatial genetic structure among individuals (i.e. unique genets) over 10 m intervals. These findings suggest that gene flow is limited in TEP P. damicornis populations, particularly among regions, but even over meter scales within populations.     

Population structure of the malaria vector Anopheles sinensis (Diptera: Culicidae) in China: two gene pools inferred by microsatellites

Background

Anopheles sinensis is a competent malaria vector in China. An understanding of vector population structure is important to the vector-based malaria control programs. However, there is no adequate data of A. sinensis population genetics available yet.

Methodology/Principal Findings

This study used 5 microsatellite loci to estimate population genetic diversity, genetic differentiation and demographic history of A. sinensis from 14 representative localities in China. All 5 microsatellite loci were highly polymorphic across populations, with high allelic richness and heterozygosity. Hardy–Weinberg disequilibrium was found in 12 populations associated with heterozygote deficits, which was likely caused by the presence of null allele and the Wahlund effect. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes six and the other includes eight populations. Out of 14 samples, six samples were mixed with individuals from both gene pools, indicating the coexistence of two genetic units in the areas sampled. The overall differentiation between two genetic pools was moderate (F _ST = 0.156). Pairwise differentiation between populations were lower within clusters (F _ST = 0.008–0.028 in cluster I and F _ST = 0.004–0.048 in cluster II) than between clusters (F _ST = 0.120–0.201). A reduced gene flow (Nm = 1–1.7) was detected between clusters. No evidence of isolation by distance was detected among populations neither within nor between the two clusters. There are differences in effective population size (Ne = 14.3-infinite) across sampled populations.

Conclusions/Significance

Two genetic pools with moderate genetic differentiation were identified in the A. sinensis populations in China. The population divergence was not correlated with geographic distance or barrier in the range. Variable effective population size and other demographic effects of historical population perturbations could be the factors affecting the population differentiation. The structured populations may limit the migration of genes under pressures/selections, such as insecticides and immune genes against malaria.     

Geographic Influence on Genetic Structure in the Widespread Neotropical Tree Simarouba amara (Simaroubaceae)

This study aimed to assess the population genetic structure of a widespread Neotropical tree species, Simarouba amara, at local, regional and continental spatial scales. We used five microsatellite loci to examine genetic variation in 14 natural populations (N?=?478 individuals) of this vertebrate-dispersed rain forest tree species in Panama, Ecuador, and French Guiana. Estimates of genetic differentiation (F _st and R _st) were significant among all but one population pair and global differentiation was moderate (F _st?=?0.25, R _st?=?0.33) with 94% of genetic variation ascribed to differences among three main geographic regions (Central America, Western Ecuador, Amazon basin). There was no evidence of isolation by distance within regions. Allele-size mutations contributed significantly (R _ST > F _ST) to the divergences between cis- and trans-Andean populations, highlighting the role of the northern Andean cordilleras as an important geographic barrier for this species.     

Smells like home: Desert ants, Cataglyphis fortis, use olfactory landmarks to pinpoint the nest

Background

Although some mechanisms of habitat adaptation of conspecific populations have been recently elucidated, the evolution of female preference has rarely been addressed as a force driving habitat adaptation in natural settings. Habitat adaptation of fire salamanders (Salamandra salamandra), as found in Middle Europe (Germany), can be framed in an explicit phylogeographic framework that allows for the evolution of habitat adaptation between distinct populations to be traced. Typically, females of S. salamandra only deposit their larvae in small permanent streams. However, some populations of the western post-glacial recolonization lineage use small temporary ponds as larval habitats. Pond larvae display several habitat-specific adaptations that are absent in stream-adapted larvae. We conducted mate preference tests with females from three distinct German populations in order to determine the influence of habitat adaptation versus neutral genetic distance on female mate choice. Two populations that we tested belong to the western post-glacial recolonization group, but are adapted to either stream or pond habitats. The third population is adapted to streams but represents the eastern recolonization lineage.

Results

Despite large genetic distances with F_ST values around 0.5, the stream-adapted females preferred males from the same habitat type regardless of genetic distance. Conversely, pond-adapted females did not prefer males from their own population when compared to stream-adapted individuals of either lineage.

Conclusion

A comparative analysis of our data showed that habitat adaptation rather than neutral genetic distance correlates with female preference in these salamanders, and that habitat-dependent female preference of a specific pond-reproducing population may have been lost during adaptation to the novel environmental conditions of ponds.     

<Emphasis Type="Italic">Geropogon hybridus</Emphasis> (L.) Sch.Bip. (Asteraceae) exhibits micro-geographic genetic divergence at ecological range limits along a steep precipitation gradient

We analyzed the population genetic pattern of 12 fragmented Geropogon hybridus ecological range edge populations in Israel along a steep precipitation gradient. In the investigation area (45 × 20 km²), the annual mean precipitation changes rapidly from 450 mm in the north (Mediterranean-influenced climate zone) to 300 mm in the south (semiarid climate zone) without significant temperature changes. Our analysis (91 individuals, 12 populations, 123 polymorphic loci) revealed strongly structured populations (AMOVA Φ_ST = 0.35; P < 0.001); however, differentiation did not change gradually toward range edge. IBD was significant (Mantel test r = 0.81; P = 0.001) and derived from sharply divided groups between the northernmost populations and the others further south, due to dispersal or environmental limitations. This was corroborated by the PCA and STRUCTURE analyses. IBD and IBE were significant despite the micro-geographic scale of the study area, which indicates that reduced precipitation toward range edge leads to population genetic divergence. However, this pattern diminished when the hypothesized gene flow barrier was taken into account. Applying the spatial analysis method revealed 11 outlier loci that were correlated to annual precipitation and, moreover, were indicative for putative precipitation-related adaptation (BAYESCAN, MCHEZA). The results suggest that even on micro-geographic scales, environmental factors play prominent roles in population divergence, genetic drift, and directional selection. The pattern is typical for strong environmental gradients, e.g., at species range edges and ecological limits, and if gene flow barriers and mosaic-like structures of fragmented habitats hamper dispersal.     

Clear genetic structure of Pinus kwangtungensis (Pinaceae) revealed by a plastid DNA fragment with a novel minisatellite

Background and Aims

Pinus kwangtungensis is a five-needled pine, inhabiting isolated mountain tops, cliffs or slopes in the montane areas of southern China and northern Vietnam. Global warming and long-term deforestation in southern China threaten its existence and genetic integrity, and this species is listed as vulnerable in the China Species Red List. However, the level and distribution of genetic diversity in this vulnerable species are completely unknown. In this paper, the genetic diversity and structure are examined using paternally inherited plastid markers to shed light on its evolutionary history and to provide a genetic perspective for its conservation.

Methods

By means of direct sequencing, a new polymorphic fragment containing a minisatellite site was identified within the plastid genome of P. kwangtungensis. Using the minisatellite site along with five SNPs (one indel and four substitutions) within the same fragment, the population genetic structure and pollen flow were analysed in 17 populations of P. kwangtungensis in southern China.

Key Results

Analysis of 227 individuals from 17 populations revealed ten haplotypes at the minisatellite site. The haplotype diversity at species level was relatively high (0·629). Genetic diversity of each population ranged from 0 to 0·779, and the western populations harboured more genetic variation than the eastern and Hainan populations, although the former appeared to have experienced a bottleneck in recent history. Population subdivision based on this site was high (F_ST = 0·540 under IAM; R_ST = 0·677 under SMM). Three major clusters (eastern, western and Hainan) were identified based on a neighbor-joining dendrogram generated from genetic distances among the populations. The genetic structures inferred from all the polymorphic sites and the SNPs were in concordance with that from the minisatellite site.

Conclusions

The results suggest that there are at least three refugia for P. kwangtungensis and that populations in these refugia should be treated as separate evolutionarily significant units or conservation units. The high diversities in the western populations suggest that these were much larger in the past (e.g. glacial stages) and that the shrinking population size might have been caused by recent events (e.g. deforestation, global warming, etc.). The western populations should be given priority for conservation due to their higher genetic diversity and limited population sizes. It is concluded that the newly found minisatellite may serve as a novel and applicable molecular marker for unravelling evolutionary processes in P. kwangtungensis.Key words: Pinus kwangtungensis, minisatellite, population genetics, conservation     

Genome-wide investigation of genetic changes during modern breeding of Brassica napus

Key message

Considerable genome variation had been incorporated within rapeseed breeding programs over past decades.

Abstract

In past decades, there have been substantial changes in phenotypic properties of rapeseed as a result of extensive breeding effort. Uncovering the underlying patterns of allelic variation in the context of genome organisation would provide knowledge to guide future genetic improvement. We assessed genome-wide genetic changes, including population structure, genetic relatedness, the extent of linkage disequilibrium, nucleotide diversity and genetic differentiation based on F _ST outlier detection, for a panel of 472 Brassica napus inbred accessions using a 60 k Brassica Infinium^® SNP array. We found genetic diversity varied in different sub-groups. Moreover, the genetic diversity increased from 1950 to 1980 and then remained at a similar level in China and Europe. We also found ~6–10 % genomic regions revealed high F _ST values. Some QTLs previously associated with important agronomic traits overlapped with these regions. Overall, the B. napus C genome was found to have more high F _ST signals than the A genome, and we concluded that the C genome may contribute more valuable alleles to generate elite traits. The results of this study indicate that considerable genome variation had been incorporated within rapeseed breeding programs over past decades. These results also contribute to understanding the impact of rapeseed improvement on available genome variation and the potential for dissecting complex agronomic traits.     

Uniform selection as a primary force reducing population genetic differentiation of cavitation resistance across a species range

Background

Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs.

Methodology

We assessed cavitation resistance (P ₅₀), growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (F _ST) and quantitative genetic differentiation (Q _ST), for retrospective identification of the evolutionary forces acting on these traits.

Results/Discussion

In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h² _ns = 0.43±0.18, CV_A = 4.4%). Q _ST was significantly lower than F _ST, indicating uniform selection for P ₅₀, rather than genetic drift. Putative mechanisms underlying Q_STST are discussed.     

A review of data needed to parameterize a dynamic model of measles in developing countries

Background

Dynamic models of infection transmission can project future disease burden within a population. Few dynamic measles models have been developed for low-income countries, where measles disease burden is highest. Our objective was to review the literature on measles epidemiology in low-income countries, with a particular focus on data that are needed to parameterize dynamic models.

Methods

We included age-stratified case reporting and seroprevalence studies with fair to good sample sizes for mostly urban African and Indian populations. We emphasized studies conducted before widespread immunization. We summarized age-stratified attack rates and seroprevalence profiles across these populations. Using the study data, we fitted a "representative" seroprevalence profile for African and Indian settings. We also used a catalytic model to estimate the age-dependent force of infection for individual African and Indian studies where seroprevalence was surveyed. We used these data to quantify the effects of population density on the basic reproductive number R ₀.

Results

The peak attack rate usually occurred at age 1 year in Africa, and 1 to 2 years in India, which is earlier than in developed countries before mass vaccination. Approximately 60% of children were seropositive for measles antibody by age 2 in Africa and India, according to the representative seroprevalence profiles. A statistically significant decline in the force of infection with age was found in 4 of 6 Indian seroprevalence studies, but not in 2 African studies. This implies that the classic threshold result describing the critical proportion immune (p _c) required to eradicate an infectious disease, p _c = 1-1/R ₀, may overestimate the required proportion immune to eradicate measles in some developing country populations. A possible, though not statistically significant, positive relation between population density and R ₀ for various Indian and African populations was also found. These populations also showed a similar pattern of waning of maternal antibodies. Attack rates in rural Indian populations show little dependence on vaccine coverage or population density compared to urban Indian populations. Estimated R ₀ values varied widely across populations which has further implications for measles elimination.

Conclusions

It is possible to develop a broadly informative dynamic model of measles transmission in low-income country settings based on existing literature, though it may be difficult to develop a model that is closely tailored to any given country. Greater efforts to collect data specific to low-income countries would aid in control efforts by allowing highly population-specific models to be developed.     

Genetic structure and seed-mediated dispersal rates of an endangered shrub in a fragmented landscape: a case study for Juniperus communis in northwestern Europe

Background

Population extinction risk in a fragmented landscape is related to the differential ability of the species to spread its genes across the landscape. The impact of landscape fragmentation on plant population dynamics will therefore vary across different spatial scales. We quantified successful seed-mediated dispersal of the dioecious shrub Juniperus communis in a fragmented landscape across northwestern Europe by using amplified fragment length polymorphism (AFLP) markers. Furthermore we investigated the genetic diversity and structure on two spatial scales: across northwestern Europe and across Flanders (northern Belgium). We also studied whether seed viability and populations size were correlated with genetic diversity.

Results

Unexpectedly, estimated seed-mediated dispersal rates were quite high and ranged between 3% and 14%. No population differentiation and no spatial genetic structure were detected on the local, Flemish scale. A significant low to moderate genetic differentiation between populations was detected at the regional, northwest European scale (PhiPT = 0.10). In general, geographically nearby populations were also genetically related. High levels of within-population genetic diversity were detected but no correlation was found between any genetic diversity parameter and population size or seed viability.

Conclusions

In northwestern Europe, landscape fragmentation has lead to a weak isolation-by-distance pattern but not to genetic impoverishment of common juniper. Substantial rates of successful migration by seed-mediated gene flow indicate a high dispersal ability which could enable Juniperus communis to naturally colonize suitable habitats. However, it is not clear whether the observed levels of migration will suffice to counterbalance the effects of genetic drift in small populations on the long run.     

Population genetic structure of the Korean threadsail filefish (Stephanolepis cirrhifer) based on microsatellite marker analysis

The threadsail filefish Stephanolepis cirrhifer is one of the most important commercial fish resources in Korea. However, its natural populations have declined drastically over the last several decades. To investigate the genetic characteristics of the threadsail filefish for conservation and management purposes, its genetic variation was analyzed in Korean fishing grounds using 11 microsatellite loci. All populations showed moderate genetic diversity (mean number of alleles (N_A) = 8.6, expected heterozygosity (He) = 0.73), representing a slightly lower level of genetic variability than other congeneric species. The presence of a weak genetic population substructure was detected (F_ST = 0.023, R_ST = 0.030, P < 0.001), but this substructure did not feature significant isolation based on the distance between populations. This differentiation may be primarily attributable to genetic differences between populations from Geomundo and other localities, based on relative low level of gene flow, a high level of pairwise F_ST and R_ST or the position of this population in a phylogenetic tree. An analysis of molecular variance (AMOVA) also revealed a greater part of the variation within the population and genetic differentiation among the samples analyzed and identified two genetic clusters. The possibility of a recent genetic bottleneck was observed in some populations of S. cirrhifer. Given the prevailing ocean currents and the intensity of threadsail filefish harvesting activities in Korea, the possibility that human harvest and stock enhancement activities may have partially contributed to our detected genetic pattern cannot be excluded. Management strategies that take these findings into account might lower the risk of harmful genetic change in the species.     

Quantitative trait loci that control the oil content variation of rapeseed (Brassica napus L.)

Key message

This report describes an integrative analysis of seed-oil-content quantitative trait loci (QTL) in Brassica napus , using a high-density genetic map to align QTL among different populations.

Abstract

Rapeseed (Brassica napus) is an important source of edible oil and sustainable energy. Given the challenge involved in using only a few genes to substantially increase the oil content of rapeseed without affecting the fatty acid composition, exploitation of a greater number of genetic loci that regulate the oil content variation among rapeseed germplasm is of fundamental importance. In this study, we investigated variation in the seed-oil content among two related genetic populations of Brassica napus, the TN double-haploid population and its derivative reconstructed-F₂ population. Each population was grown in multiple experiments under different environmental conditions. Mapping of quantitative trait loci (QTL) identified 41 QTL in the TN populations. Furthermore, of the 20 pairs of epistatic interaction loci detected, approximately one-third were located within the QTL intervals. The use of common markers on different genetic maps and the TN genetic map as a reference enabled us to project QTL from an additional three genetic populations onto the TN genetic map. In summary, we used the TN genetic map of the B. napus genome to identify 46 distinct QTL regions that control seed-oil content on 16 of the 19 linkage groups of B. napus. Of these, 18 were each detected in multiple populations. The present results are of value for ongoing efforts to breed rapeseed with high oil content, and alignment of the QTL makes an important contribution to the development of an integrative system for genetic studies of rapeseed.