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PubMed2005

Phenotypic plasticity in Carlina vulgaris: effects of geographical origin, population size, and population isolation.

If phenotypic plasticity is under genetic control, it may vary in amount and pattern on a geographical scale, e.g. among different regions of a species' distribution. It may also differ between large and small or between less and more isolated populations, due to differences in genetic diversity. In a 2-year common garden study, the responses of several traits to drought and fertilizer treatments were studied in the grassland herb Carlina vulgaris. Individuals originating from populations of different size and degree of isolation in six European countries, representing "central" and "marginal" regions, were compared. Fertilizing had a negative effect on early plant survival, as well as on flowering probability in surviving plants. However, in those plants that flowered, fertilizing strongly increased mean number of flowerheads, flowerhead area (a correlate of seed number), and seed mass. Drought had generally weaker effects but enhanced survivorship, indicating that this treatment was closer to optimal conditions than were non-drought conditions. For some traits there were significant interactions of region x fertilizer, but the geographical pattern of reaction norms was inconsistent and lent no support to the hypothesis that central and marginal populations differ in overall plasticity. Population size and isolation had hardly any influence on treatment responses, but populations within regions differed in their mean response to fertilizing with regard to survival and flowering probabilities, as well as in their response to drought with regard to survival and total flowerhead area. It is concluded that response to raised nutrient levels is highly variable within populations, ranging from death to strongly increased reproductive output, but also among populations irrespective of size or isolation. This also goes for the response to water supply, though this variation shows a more unclear pattern. There is no evidence that small or isolated/marginal populations are less plastic than large or non-isolated/central populations, and the explanation for differences in treatment responses among plant populations should be sought in other population characteristics.

Analysis of Variance↗
PubMed2001

Population bottleneck and effective size in Bonamia ostreae-resistant populations of Ostrea edulis as inferred by microsatellite markers.

Genetic variability at five microsatellite loci was analysed in three hatchery-propagated populations of the flat oyster, Ostrea edulis. These populations were part of a selection programme for resistance to the protozoan parasite Bonamia ostreae and were produced by mass spawns, without control of the genealogy. Evidence for population bottlenecks and inbreeding was sought. A reduction in the number of alleles, mainly due to the loss of rare alleles, was observed in all selected populations, relative to the natural population from which they were derived. Heterozygote excesses were observed in two populations, and were attributed to substructuring of the population into a small number of families. Pedigree reconstruction showed that these two populations were produced by at most two spawning events involving a limited number of parents. Most individuals within these populations are half or full-sib, as shown by relatedness coefficients. The occurrence of population bottlenecks was supported by estimates of effective number of breeders derived by three methods: temporal variance in allelic frequencies, heterozygote excess, and a new method based on reduction in the number of alleles. The estimates from the different methods were consistent. The evidence for bottleneck and small effective number of breeders are expected to lead to increasing inbreeding, and have important consequences for the future management of the three O. edulis selected populations.

Animals↗
PubMed2004

Evaluating habitat as a surrogate for population viability using a spatially explicit population model.

Because data for conservation planning are always limited, surrogates are often substituted for intractable measurements such as species richness or population viability. We examined the ability of habitat quality to act as a surrogate for population performance for both Red-shouldered Hawks (Buteo lineatus) and Northern Goshawks (Accipiter gentilis). We compared simple measures of habitat quality to estimates of population growth rates obtained from a spatially explicit model of population dynamics. We found that habitat quality was a relatively poor predictor of simulated population growth rates for several reasons. First, a relatively small proportion of the potential habitat for each species served as population sources in our simulations--15% for Red-shouldered Hawks and 2% for Goshawks. Second, when habitat quality correctly predicted demographic sources on the landscape, it consistently underestimated the contribution of these areas to the population. In areas where habitat quality correctly anticipated the presence of demographic sinks, we found no useful quantitative relationship between the two measures. Our simulation model captured the influence of habitat quality on the hawk populations, but it also incorporated interactions between dispersing individuals and landscape patterns. Thus, the discrepancies we observed likely reflected the influence of forest fragmentation and the spatial arrangement of forest patches on the populations. We conclude that simple measures of habitat quality will often be poor surrogates for population persistence, but that spatially explicit population models can help inform the development of better indices.

Animals↗
PubMed2005

Population differentiation within and among Asian elephant (Elephas maximus) populations in southern India.

Southern India, one of the last strongholds of the endangered Asian elephant (Elephas maximus), harbours about one-fifth of the global population. We present here the first population genetic study of free-ranging Asian elephants, examining within- and among-population differentiation by analysing mitochondrial DNA (mtDNA) and nuclear microsatellite DNA differentiation across the Nilgiris-Eastern Ghats, Anamalai, and Periyar elephant reserves of southern India. Low mtDNA diversity and 'normal' microsatellite diversity were observed. Surprisingly, the Nilgiri population, which is the world's single largest Asian elephant population, had only one mtDNA haplotype and lower microsatellite diversity than the two other smaller populations examined. There was almost no mtDNA or microsatellite differentiation among localities within the Nilgiris, an area of about 15,000 km2. This suggests extensive gene flow in the past, which is compatible with the home ranges of several hundred square kilometres of elephants in southern India. Conversely, the Nilgiri population is genetically distinct at both mitochondrial and microsatellite markers from the two more southerly populations, Anamalai and Periyar, which in turn are not genetically differentiated from each other. The more southerly populations are separated from the Nilgiris by only a 40-km-wide stretch across a gap in the Western Ghats mountain range. These results variably indicate the importance of population bottlenecks, social organization, and biogeographic barriers in shaping the distribution of genetic variation among Asian elephant populations in southern India.

Animals↗
PubMed2006

Population structure in a critically endangered arctic fox population: does genetics matter?

The arctic fox (Alopex lagopus) in Scandinavia is classified as critically endangered after having gone through a severe decline in population size in the beginning of the 20th century, from which it has failed to recover despite more than 65 years of protection. Arctic foxes have a high dispersal rate and often disperse over long distances, suggesting that there was probably little population differentiation within Scandinavia prior to the bottleneck. It is, however, possible that the recent decline in population size has led to a decrease in dispersal and an increase in population fragmentation. To examine this, we used 10 microsatellite loci to analyse genetic variation in 150 arctic foxes from Scandinavia and Russia. The results showed that the arctic fox in Scandinavia presently is subdivided into four populations, and that the Kola Peninsula and northwest Russia together form a large fifth population. Current dispersal between the populations seemed to be very low, but genetic variation within them was relatively high. This and the relative F(ST) values among the populations are consistent with a model of recent fragmentation within Scandinavia. Since the amount of genetic variation is high within the populations, but the populations are small and isolated, demographic stochasticity seems to pose a higher threat to the populations' persistence than inbreeding depression and low genetic variation.

Alleles↗
PubMed2005

Original birthplace of cultivated common buckwheat inferred from genetic relationships among cultivated populations and natural populations of wild common buckwheat revealed by AFLP analysis.

The genetic relationships among seven cultivated populations and eight natural populations of wild common buckwheat were analyzed using amplified fragment length polymorphism (AFLP). The genetic distance was estimated for each pair of the 15 populations based on the AFLP data, and a phylogenetic tree was constructed using the neighbor-joining (NJ) method based on the genetic distance. All the cultivated populations were grouped in a cluster. The natural populations were grouped into two clusters composed of (1) the Sanjiang group (three populations from eastern Tibet and one population from Adong village of Yunnan province) and (2) two populations from Yunnan province and two populations from Sichuan province. The Sanjiang group is more closely related to cultivated populations. These results indicate that the direct ancestor of common buckwheat was natural populations of wild common buckwheat from the Sanjiang area.

Agriculture↗
PubMed2006

Development of a near-isogenic line population of Arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population.

In Arabidopsis recombinant inbred line (RIL) populations are widely used for quantitative trait locus (QTL) analyses. However, mapping analyses with this type of population can be limited because of the masking effects of major QTL and epistatic interactions of multiple QTL. An alternative type of immortal experimental population commonly used in plant species are sets of introgression lines. Here we introduce the development of a genomewide coverage near-isogenic line (NIL) population of Arabidopsis thaliana, by introgressing genomic regions from the Cape Verde Islands (Cvi) accession into the Landsberg erecta (Ler) genetic background. We have empirically compared the QTL mapping power of this new population with an already existing RIL population derived from the same parents. For that, we analyzed and mapped QTL affecting six developmental traits with different heritability. Overall, in the NIL population smaller-effect QTL than in the RIL population could be detected although the localization resolution was lower. Furthermore, we estimated the effect of population size and of the number of replicates on the detection power of QTL affecting the developmental traits. In general, population size is more important than the number of replicates to increase the mapping power of RILs, whereas for NILs several replicates are absolutely required. These analyses are expected to facilitate experimental design for QTL mapping using these two common types of segregating populations.

Arabidopsis↗
PubMed2001

Population mixing and the adaptive divergence of quantitative traits in discrete populations: a theoretical framework for empirical tests.

Empirical tests for the importance of population mixing in constraining adaptive divergence have not been well grounded in theory for quantitative traits in spatially discrete populations. We develop quantitative-genetic models to examine the equilibrium difference between two populations that are experiencing different selective regimes and exchanging individuals. These models demonstrate that adaptive divergence is negatively correlated with the rate of population mixing (m, most strongly so when m is low), positively correlated with the difference in phenotypic optima between populations, and positively correlated with the amount of additive genetic variance (G, most strongly so when G is low). The approach to equilibrium is quite rapid (fewer than 50 generations for two populations to evolve 90% of the distance to equilibrium) when either heritability or mixing are not too low (h2 > 0.2 or m > 0.05). The theory can be used to aid empirical tests that: (1) compare observed divergence to that predicted using estimates of population mixing, additive genetic variance/covariance, and selection; (2) test for a negative correlation between population mixing and adaptive divergence across multiple independent population pairs; and (3) experimentally manipulate the rate of mixing. Application of the first two of these approaches to data from two well-studied natural systems suggests that population mixing has constrained adaptive divergence for color patterns in Lake Erie water snakes (Nerodia sipedon), but not for trophic traits in sympatric pairs of benthic and limnetic stickleback (Gasterosteus aculeatus). The theoretical framework we outline should provide an improved basis for future empirical tests of the role of population mixing in adaptive divergence.

Adaptation, Physiological↗
PubMed1988

Population amalgamation and genetic variation: observations on artificially agglomerated tribal populations of Central and South America.

The interpretation of data on genetic variation with regard to the relative roles of different evolutionary factors that produce and maintain genetic variation depends critically on our assumptions concerning effective population size and the level of migration between neighboring populations. In humans, recent population growth and movements of specific ethnic groups across wide geographic areas mean that any theory based on assumptions of constant population size and absence of substructure is generally untenable. We examine the effects of population subdivision on the pattern of protein genetic variation in a total sample drawn from an artificial agglomerate of 12 tribal populations of Central and South America, analyzing the pooled sample as though it were a single population. Several striking findings emerge. (1) Mean heterozygosity is not sensitive to agglomeration, but the number of different alleles (allele count) is inflated, relative to neutral mutation/drift/equilibrium expectation. (2) The inflation is most serious for rare alleles, especially those which originally occurred as tribally restricted "private" polymorphisms. (3) The degree of inflation is an increasing function of both the number of populations encompassed by the sample and of the genetic divergence among them. (4) Treating an agglomerated population as though it were a panmictic unit of long standing can lead to serious biases in estimates of mutation rates, selection pressures, and effective population sizes. Current DNA studies indicate the presence of numerous genetic variants in human populations. The findings and conclusions of this paper are all fully applicable to the study of genetic variation at the DNA level as well.

Alleles↗
PubMed1995

Intra- and inter-population diversity at short tandem repeat loci in diverse populations of the world.

To study the level of intra- and inter-population variation at hypervariable DNA loci, we have characterized 15 human populations of diverse ethnic and geographic origins at six short tandem repeat loci by using the polymerase chain reaction. Even though the spectrum of allelic variation is quite broad and there are substantial differences in allele frequency distributions among populations, in general, population within a major racial group show a greater degree of similarity. This observation is reflected in the analysis of gene diversity. When the total diversity is apportioned, the maximum variation becomes attributable to inter-individual differences within a population; of the variation that is attributed to differences between populations within a racial group and differences between racial groups, namely, African, Caucasian, and Mongoloid, than the American Indians and the Pacific Islanders. As expected, a reciprocal relationship between gene diversity and FST levels is observed. Higher values of FST in the American Indian and the Pacific Islanders may reflect smaller population size and a higher level of isolation. An analysis of genetic distance encompassing the populations belonging to the three major racial groups recognizes three distinct clusters - all the populations of African affiliation cluster together, as do the Caucasian affiliated and the Mongoloid groups, in two distinct clusters. Interestingly, three broadly classified cosmopolitan US populations, namely, US White, US Black and US Asian, cluster with their ancestrally related populations. This study dispels some of the concerns regarding the applicability of DNA typing data for forensic use.

Alleles↗
PubMed1991

Sick population--treated population: the need for a better definition. The VALIDATA Group.

There are many questions concerned with therapy and its application. Depending on the perspective of the study there can be several "populations" which, when considered individually, may give different, or even inconsistent conclusions. These populations are: the sick population, the therapist's target population, the eligible population for a study, the study population, the treatment target population, and the treatment distribution population. Semantic precision, giving a better definition of the populations, is an essential prerequirement in order to tackle scientifically all the facets of assessment of therapy. Accurate definition will help in the study of areas as varied as the methodology, the therapeutic studies, the validity of the recommendations made, the impact of these recommendations on prescription, and finally, the consequences of the prescription in terms of public health (clinical and economical). Several examples are given to show the relationship between these populations and the importance of an accurate definition for each. Guidelines for the identification of these populations are provided. In this overall approach to therapy, epidemiology is an essential, complementary tool to clinical trials.

Adrenergic beta-Antagonists↗
PubMed2003

Parental selection, number of breeding populations, and size of each population in inbred development.

Some breeders select inbreds from many F(2) or backcross breeding populations, each with relatively few progenies. Other breeders select inbreds from only a few breeding populations, each with many progenies. My objectives were to: (1) determine the relative importance of parental selection, number of breeding populations, and size of each population, and (2) find optimum combinations between number and size of breeding populations. I assumed that a breeder has resources to test a total of 2,000 recombinant inbreds for a quantitative trait that was controlled by 100 additive loci and had a heritability of 0.20, 0.60, or 1.0. The parental inbreds had an inherent pedigree structure due to advanced cycle breeding. The parental inbreds were ranked according to their mean performance, and breeding populations were made among all parents, the top 25% of parents, and the top 10% of parents. I found that the issue of number versus size of breeding populations was only secondary compared with the ability to identify, prior to making the crosses, the breeding populations with the highest mean performance. For a given level of effectiveness of parental selection, the selection response was largest when the maximum number of breeding populations was used. The effect of the number of breeding populations was minor, however, when selection was practiced among the parents or when heritability was less than 1.0. The results suggested that, in practice, large selection responses could be obtained with a wide range of combinations between number and size of breeding populations.

Computer Simulation↗
PubMed1986

The ecological genetics of introduced populations of the giant toad, Bufo marinus. IV. Gene flow estimated from admixture in Australian populations.

Allele frequency variation is described at nine polymorphic enzyme loci in 21 samples from populations of the introduced Giant Toad, Bufo marinus, in the region of Townsville in north Queensland, Australia. Some of these populations appear to have been established through the introgression of other populations that previously had been isolated. Comparisons of allele frequencies at three polymorphic loci between the introgressed populations and the original populations are used to obtain admixture estimates. These are used to estimate a rate of gene flow among the populations of approximately 2 km/year. This is consistent with an estimate based on the rate at which Bufo marinus has colonised new areas in Australia when discontinuities in the pattern of this colonisation are taken into account. The estimate of gene flow is combined with published data on population density to estimate neighbourhood size. The estimate obtained is substantially greater than the effective population size estimate determined previously from data on allele frequency variances in other populations. This discrepancy is most likely due to inaccuracies in the population density estimates, to underestimates of the extent of offspring number variance and perhaps to occasional departures from sex ratio parity. It has important implications for the study of the genetic structure of populations which are discussed.

Alleles↗
PubMed1998

Population genetic characteristics of the STR Loci D21S11 and FGA in eight diverse human populations.

A highly polymorphic multiplex short tandem repeat (STR) system composed of D21S11, FGA, and the sex-typing system amelogenin (AMG) has been used to investigate allele frequency distributions in two Canadian Caucasian samples (British Columbia and Alberta), three Canadian aboriginal populations (Coastal Salishans from British Columbia, Ojibwa from northern Ontario, and Cree from Saskatchewan), and three ethnic groups from Singapore (Chinese, Malays, and Asian Indians). Using the automated fluorescence detection approach on an ABD 373A DNA Sequencer, we distinguished 20 D21S11 and 22 FGA alleles with a nearly equal representation of two- and four-base variants. An overlap in allele sizes for both STR loci across populations was observed, but frequency differences were noted. Statistical analysis revealed that (1) both D21S11 and FGA loci conform to Hardy-Weinberg equilibrium in all eight surveyed populations based on five different tests and (2) both STR loci are in linkage equilibrium. Results from the 2 x N contingency table exact tests for population differentiation demonstrated that the Canadian samples from two different provinces were not distinguishable from one another at either STR locus and therefore could be combined to form one Caucasian group. Likewise, Chinese and Malays from Singapore did not show significant differences at either STR locus. In contrast, all other examined populations exhibited differences deemed statistically significant. As a complement to our study, we compared D21S11 allele frequency distributions in 21 worldwide populations and FGA allele frequency distributions in 14 populations. Many alleles never previously reported in worldwide populations were identified in Canadian aboriginal and Asian samples from this study. Twenty-four D21S11 and 29 FGA alleles were distinguished in worldwide groups. Interesting similarities in allele frequency distribution patterns across populations suggest that the STR polymorphism at these loci predates the geographic dispersal of ancestral human populations. This study further demonstrates the utility of highly informative STR loci such as D21S11 and FGA in human population evolutionary history and in forensic medicine.

Canada↗
PubMed2004

Consequences of unequal population size, asymmetric gene flow and sex-biased dispersal on population structure in brook charr (Salvelinus fontinalis).

Unravelling relationships between dispersal and population structure requires considering the impacts of assumption violations of indirect gene flow models in a given system. We combined temporal, individual and coalescent-based analyses of microsatellite DNA variation to explore the general hypothesis that unequal effective population size (Ne), asymmetric gene flow (m) and nonrandom (sex-biased) individual dispersal had an important effect on spatiotemporal population structuring in lake-dwelling brook charr (Salvelinus fontinalis). This integrative examination shed light on the dichotomous structuring observed between an outlet and three tributary-spawning populations and their potential for adaptive divergence. It revealed further that finer tributary population structuring incongruent with drainage structure has been shaped by asymmetric m from one population with a large Ne towards two populations of smaller Ne. Gene flow among the tributaries was also mediated mainly by male-biased dispersal. However, longer distance dispersal from tributaries to the outflow was female-biased. Spatially dependent sex-biased dispersal may have contributed therefore to gene flow at different levels of population structuring. Our results demonstrate how dispersal and population structure may interrelate to produce spatial variation in intraspecific diversity, and are therefore relevant for conservation programmes seeking to define conservation units or predict recolonization rates of extirpated populations.

Animals↗
PubMed1998

The effective population size of Anopheles gambiae in Kenya: implications for population structure.

We estimated current and long-term effective population size (Ne) of two Anopheles gambiae (savanna cytotype) populations in Kenya. Temporal variation at nine microsatellite loci in each population sampled 7 and 9 years apart and genetic diversity in each sample were analyzed to answer the following questions. (1) Do bottlenecks occur in Kenyan populations of A. gambiae? (2) How variable are different populations with respect to their current and long-term Ne values? (3) What are the implications of these results on population structure and history? The estimates of Ne of Asembo and Jego were 6,359 and 4,258, respectively, and the lower 95% limits were 2,455 and 1,669, respectively. Thus, despite the typical observation of low density at the village level during the dry season, large populations are maintained annually. Large current Ne is consistent with previous studies showing low differentiation across the continent, especially under Wright's isolation-by-distance model. Current Ne in Asembo was 1.5-fold higher than in Jego, but this difference was not significant. Long-term Ne in Asembo (22,667) was 2.9-fold higher than that in Jego (7,855) based on the stepwise mutation model. The difference between populations was significant at both time points regardless of whether long-term Ne values were calculated based on the stepwise mutation model or the infinite-alleles model. Heterozygosity in Jego declined significantly between 1987 (59%) and 1996 (54%), whereas heterozygosity in Asembo was stable (66%-65%). Despite the relatively high and significant differentiation between Asembo and Jego (FST = 0.072-0.10, RST = 0.037-0.038), all alleles in Jego were found in Asembo but not vice versa. All of these findings suggest that lower Ne in Jego magnifies differentiation between the two populations. The long-term Ne was biased downward, because its calculation was based on an upper bound estimate of microsatellite mutation rate. Ne values based on mtDNA and allozymes were an order of magnitude higher. Long-term Ne therefore, is probably measured in hundreds of thousands and hence does not support a recent expansion of this species from a small population.

Animals↗
PubMed1993

Population data of the HLA DQ alpha locus in Dutch Caucasians. Comparison with other population studies.

The HLA DQ alpha amplification and typing kit has been designed to be used by the forensic community for purposes of identity testing. The introduction of any new DNA marker in forensic identity testing requires the establishment of a population database for the relevant population(s). To this end allele and genotype frequencies for the HLA DQ alpha locus were determined in a Dutch Caucasian population sample and compared with 7 other population genetic studies. In our population sample the HLA DQ alpha genotype frequencies did not deviate from Hardy-Weinberg expectations and for this locus the power of discrimination is 0.94. A test for homogeneity of the HLA DQ alpha population data based on the allele frequency counts for 8 Caucasian population samples was performed and significant differences were found (P = 0.007). The differences in the frequency of the HLA DQ alpha 2 and 3 alleles are the major cause of this deviation. No deviation from population homogeneity was observed when we compared the genotype frequency distributions among the 8 Caucasian population samples. Combined with the extensive validation studies from Comey and Budowle and Helmuth et al. this population genetic study will allow HLA DQ alpha typing to be used in forensic identity testing in the Netherlands.

Female↗
PubMed2004

Population resistance to climate change: modelling the effects of low recruitment in open populations.

Isolated populations or those at the edge of their distribution are usually more sensitive to changes in the environment, such as climate change. For the barnacle Semibalanus balanoides (L.), one possible effect of climate change is that unpredictable spring weather could lead to the mismatching of larval release with spring phytoplankton bloom, hence reducing the recruitment. In this paper, model simulations of a variable open population with space limited recruitment were used to investigate the effects of low and zero recruitment on population abundance in S. balanoides. Data for model parameters was taken from an isolated population in the Isle of Man, British Isles. Model simulations with observed frequencies of years with low recruitment showed only small changes in population dynamics. Increased frequencies of low recruitment had large effects on the variation in population growth rate and free space and on population structure. Furthermore, populations with intermediate to high frequencies of low recruitment appeared more sensitive to additional changes in recruitment. Exchanging low recruitment with zero recruitment severely increased the risk of local extinctions. Simulations with consecutive years of low recruitment showed a substantial increase in free space and an increase in the time taken to recover to normal densities. In conclusion, model simulations indicate that variable populations can be well buffered to changes in the demography caused by introduced environmental noise, but also, that intermediate to high frequencies of disturbance can lead to a swift change in population dynamics, which in turn, may affect the dynamics of whole communities.

Animals↗