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PubMed2002

Fitness versus longevity in age-structured population dynamics.

We examine the dynamics of an age-structured population model in which the life expectancy of an offspring may be mutated with respect to that of the parent. While the total population of the system always reaches a steady state, the fitness and age characteristics exhibit counter-intuitive behavior as a function of the mutational bias. By analytical and numerical study of the underlying rate equations, we show that if deleterious mutations are favored, the average fitness of the population reaches a steady state, while the average population age is a decreasing function of the average fitness. When advantageous mutations are favored, the average population fitness grows linearly with time t, while the average age is independent of the average fitness. For no mutational bias, the average fitness grows as t2/3.

Life Expectancy↗
PubMed2002

Population structure of an endangered species living in contrasted habitats: Parnassia palustris (Saxifragaceae).

In endangered species, it is critical to analyse the level at which populations interact (i.e. dispersal) as well as the levels of inbreeding and local adaptation to set up conservation policies. These parameters were investigated in the endangered species Parnassia palustris living in contrasted habitats. We analysed population structure in 14 populations of northern France for isozymes, cpDNA markers and phenotypic traits related to fitness. Within population genetic diversity and inbreeding coefficients were not correlated to population size. Populations seem not to have undergone severe recent bottleneck. Conversely to pollen migration, seed migration seems limited at a regional scale, which could prevent colonization of new sites even if suitable habitats appear. Finally, the habitat type affects neither within-population genetic diversity nor genetic and phenotypic differentiation among populations. Thus, even if unnoticed local adaptation to habitats exists, it does not influence gene flow between populations.

DNA, Chloroplast↗
PubMed2006

Genetic population structure of three Armillaria species at the landscape scale: a case study from Swiss Pinus mugo forests.

Armillaria species are plant pathogens that cause Armillaria root rot and are known to cause mortality of mountain pines (Pinus mugo) in the Swiss National Park in the Central Alps. The identity of isolates and the spatially explicit population structure of the Armillaria species were investigated in a 3.3km(2) study area in the Swiss National Park. In total, 242 Armillaria isolates, 205 from wood samples and 37 from epiphytic rhizomorphs, were collected. Species were identified using haploid-diploid pairings and genets were determined using intraspecific somatic incompatibility tests. The population structure differed markedly among the Armillaria species. A. cepistipes and A. borealis mainly occurred as genets of small spatial extent (mean 0.2ha, and 0.6ha), whereas A. ostoyae formed significantly larger genets (mean 6.8ha). The largest A. ostoyae genet extended over approx. 37ha. Several disease centres associated with Heterobasidion annosum were found to be embedded within large Armillaria genets. The extension of large A. ostoyae genets suggests that forests that occupy the study area have developed in the presence of these Armillaria genets. The finding of large Armillaria genets supports the assumption that large genets occur in areas with cold climate and little precipitation.

Agaricales↗
PubMed2005

Sampling from natural populations with RNAI reveals high outcrossing and population structure in Caenorhabditis elegans.

Despite a nearly worldwide distribution in nature, Caenorhabditis elegans exhibits low levels of genetic polymorphism, possibly as an indirect consequence of low levels of outcrossing. In the laboratory, Caenorhabditis elegans males are produced at low rates and are steadily eliminated from cultures, so that reproduction happens largely through self-fertilization in hermaphrodites. C. elegans is increasingly the focus of evolutionary research; however, natural outcrossing rates are difficult to measure because mating tests with laboratory strains are usually required to identify C. elegans. We sampled natural populations of C. elegans with an RNA interference (RNAi) assay. Heterozygosities and polymorphism patterns revealed surprisingly high levels of population structure and outcrossing (approximately 22% of individuals are estimated to be the result of outcrossing and not self-fertilization). The finding of strong local population structure, together with low levels of diversity on local and global scales, suggests a metapopulation model of frequent extinction and recolonization of local populations. The occurrence of substantial outcrossing suggests that the extinction of local populations is probably not driven by the accumulation of harmful mutations.

Adenosine Triphosphatases↗
PubMed1993

Natural selection on multivariate traits in age-structured populations.

The theory of selection on multivariate traits in age-structured populations has important implications for empirical and theoretical studies of life-history evolution. A model of natural selection on a set of correlated quantitative traits with age structure is derived here, using an extension of previous work on selection at a single locus. This formulation provides an equation for the change of the mean of a vector of traits that is accurate is selection is weak, and does not require the population always to be in demographic equilibrium as selection proceeds. The treatment is extended to density-dependent populations, and to equilibrium populations under frequency-dependent selection. In addition, further approximations are derived that produce evolutionary equilibria equivalent to those predicted by optimization and evolutionarily stable strategy (ESS) theory. It is shown that the conditions for equilibrium are valid even if selection is strong.

Aging↗
PubMed2003

Number of SNPS loci needed to detect population structure.

The study of the association of polymorphic genetic markers with common diseases is one of the most powerful tools in modern genetics. Interest in single nucleotide polymorphisms (SNPs) has steadily grown over the last decade. SNPs are currently the most developed markers in the human genome because they have a number of advantages over other marker types. One of the critical problems responsible for 'spurious' association findings in case-control studies is population stratification. There are many statistical approaches developed for detecting population heterogeneity. However the power to detect population structure by known methods is highly dependent on the number of loci utilised. We performed an analysis of SNPs data available in the public domain from The Single Nucleotide Consortia Ltd. (TSCL). Three populations, Afro-American, Asian and Caucasian, were compared. Estimation of the minimum number of SNPs loci necessary for detection of the population structure was performed. Two clustering approaches, distance-based and model-based, were compared. The model-based approach was superior when compared with the distance-based method. We found more than 65 random SNPs loci are required for identifying distinct geographically separated populations. Increasing the number of markers to over 100 raises the probability of correct assignment of a particular individual to an origin group to over 90%, even with conventional clustering methods.

Genetic Markers↗
PubMed2004

Mating system and population structure of the primitively eusocial wasp Ropalidia revolutionalis: a model system for the evolution of complex societies.

Mating systems are important determinants of genetic structure in cooperative groups, and their effects can influence profoundly the interactions of group members. The primitively eusocial wasp, Ropalidia revolutionalis, has an interesting genetic and social structure that makes it an excellent model system for examining the evolution of more complex societies. In particular, its colonies sometimes have multiple queens, a key characteristic of more advanced wasp societies. In this study, we have characterized the mating system of the social wasp Ropalidia revolutionalis to understand better its colony genetic structure. R. revolutionalis females nearly always mate singly and they are unrelated to their mates. However, different females in the same colony do mate with males, on average, who are related as cousins. Single mating will help to maintain high relatedness, which should be important for continued cooperation in multiple queen societies, but it creates potential conflicts in single queen colonies over the production of males as well as over the timing of male production. We have also characterized the population structure of R. revolutionalis from Townsville, in tropical north Queensland, to Brisbane in the subtropics. Even at such a large scale, the population is remarkably unstructured with an average F(ST) of 0.0546. There is weak isolation by distance, and evidence for subtle differentiation between a southern region with no dry season, which extends as far north as Rockhampton, and a northern region with a severe to moderate dry season. This may reflect historical effects of extreme aridity on the population structure.

Analysis of Variance↗
PubMed2003

Competition in size-structured populations: mechanisms inducing cohort formation and population cycles.

In this paper we investigate the consequences of size-dependent competition among the individuals of a consumer population by analyzing the dynamic properties of a physiologically structured population model. Only 2 size-classes of individuals are distinguished: juveniles and adults. Juveniles and adults both feed on one and the same resource and hence interact by means of exploitative competition. Juvenile individuals allocate all assimilated energy into development and mature on reaching a fixed developmental threshold. The combination of this fixed threshold and the resource-dependent developmental rate, implies that the juvenile delay between birth and the onset of reproduction may vary in time. Adult individuals allocate all assimilated energy to reproduction. Mortality of both juveniles and adults is assumed to be inversely proportional to the amount of energy assimilated. In this setting we study how the dynamics of the population are influenced by the relative foraging capabilities of juveniles and adults. In line with results that we previously obtained in size-structured consumer-resource models with pulsed reproduction, population cycles primarily occur when either juveniles or adults have a distinct competitive advantage. When adults have a larger per capita feeding rate and are hence competitively superior to juveniles, population oscillations occur that are primarily induced by the fact that the duration of the juvenile period changes with changing food conditions. These cycles do not occur when the juvenile delay is a fixed parameter. When juveniles are competitively superior, two different types of population fluctuations can occur: (1) rapid, low-amplitude fluctuations having a period of half the juvenile delay and (2) slow, large-amplitude fluctuations characterized by a period, which is roughly equal to the juvenile delay. The analysis of simplified versions of the structured model indicates that these two types of oscillations also occur if mortality and/or development is independent of food density, i.e. in a situation with a constant juvenile developmental delay and a constant, food-independent background mortality. Thus, the oscillations that occur when juveniles are more competitive are induced by the juvenile delay per se. When juveniles exert a larger foraging pressure on the shared resource, maturation implies an increase not only in adult density, but also in food density and consequently fecundity. Our analysis suggests that this correlation in time between adult density and fecundity is crucial for the occurrence of population cycles when juveniles are competitively superior.

Animals↗
PubMed2004

[Population structure and distribution pattern of rare plant communities in Houhe Nature Reserve].

An investigation on the size structure and spatial pattern of 26 major tree species with a diameter at breast height (DBH) > or = 5 cm was made on a 1 hm2 fixed plot in the mixed evergreen and deciduous broad-leaved forest in Houhe National Nature Reserve of Central China. The results showed that 7 populations of the 26 species, i.e., Dipteronia sinensi, Aesculus wilsonii, Pterostyrax psilophyllus, Davidia involucrate, Euptelea pleiosperma, Tetracentron sinense and Cercidiphyllum japonicum, were rare endangered, species, and two of the 7 populations, T. sinense and C. japonicum, were very limited in numbers. The population structure of P. psilophyllus was in declining, and that of the rest was in growing. The spatial distribution pattern of P. psilophyllus, A. wilsonii and T. sinense was in random, and that of the others was clumped. Among the other 19 non-rare populations, the population structure of P. wilsonii was in declining, that of D. lotus, A. palmatum, A. wilsonii, A. franchetii, M. cuneifolia and H. dulcis was stable, and the rest was in growing. The spatial distribution pattern of D. lotus and H. dulcis was in random, and that of the others was clumped. On the whole, the growing populations were dominant, amounting to 61.54%, and the stable and declining populations accounted for 6.92% and 11.54%, respectively. The results of the two judging methods were consistent, showing that the distribution pattern of clumping (80.77%) was dominant, while the random and even distribution patterns were infrequent.

Aesculus↗
PubMedDate not supplied

Neural population structures and consequences for neural coding.

Researchers studying neural coding have speculated that populations of neurons would more effectively represent the stimulus if the neurons "cooperated:" by interacting through lateral connections, the neurons would process and represent information better than if they functioned independently. We apply our new theory of information processing to determine the fidelity limits of simple population structures to encode stimulus features. We focus on noncooperative populations, which have no lateral connections. We show that they always exhibit positively correlated responses and that as population size increases, they perfectly represent the information conveyed by their inputs regardless of the individual neuron's coding scheme. Cooperative populations, which do have lateral connections, can, depending on the nature of the connections, perform better or worse than their noncooperative counterparts. We further show that common notions of synergy fail to capture the level of cooperation and to reflect the information processing properties of populations.

Algorithms↗
PubMed1983

Population structure of the Indian people: some microevolutionary aspects.

Some aspects of population structure, namely village endogamy, marital distance and consanguinity in India are discussed. These parameters show social and geographic variation. The role of culture is of great importance in determining the mating pattern of a population. In the Indian situation, group endogamy in general does not cause inbreeding. Consanguinity is a cultural phenomenon of long-standing tradition, and so far there is no strong indication of a temporal change.

Biological Evolution↗
PubMed2002

Combined ribotyping and random multiprimer DNA analysis to probe the population structure of Listeria monocytogenes.

To improve our understanding of the genetic links between strains originating from food and strains responsible for human diseases, we studied the genetic diversity and population structure of 130 epidemiologically unrelated Listeria monocytogenes strains. Strains were isolated from different sources and ecosystems in which the bacterium is commonly found. We used rRNA gene restriction fragment length polymorphism analysis with two endonucleases and random multiprimer DNA analysis with seven oligonucleotide primers to study multiple genetic features of each strain. We used three clustering methods to identify genetic links between individual strains and to determine the precise genetic structure of the population. The combined results confirmed that L. monocytogenes strains can be divided into two major phylogenetic divisions. The method used allowed us to demonstrate that the genetic structure and diversity of the two phylogenetic divisions differ. Division I is the most homogeneous and can easily be divided into subgroups with dissimilarity distances of less than 0.30. Each of these subgroups mainly, or exclusively, contains a single serotype (1/2b, 4b, 3b, or 4a). The serotype 4a lineage appears to form a branch that is highly divergent from the phylogenetic group containing serotypes 1/2b, 4b, and 3b. Division II contains strains of serotypes 1/2a, 1/2c, and 3a. It exhibits more genetic diversity with no peculiar clustering. The fact that division II is more heterogeneous than division I suggests that division II evolved from a common ancestor earlier than division I. A significant association was found between division I and human strains, suggesting that strains from division I are better adapted to human hosts.

DNA Primers↗
PubMed2002

Comparative population structure and genetic diversity of Arceuthobium americanum (Viscaceae) and its Pinus host species: insight into host-parasite evolution in parasitic angiosperms.

In a recent study we revealed that the parasitic angiosperm Arceuthobium americanum is comprised of three distinct genetic races, each associated with a different host in regions of allopatry. In order to assess the role of host identity and geographical isolation on race formation in A. americanum, we compared the genetic population structure of this parasite with that of its three principal hosts, Pinus banksiana, Pinus contorta var. latifolia and Pinus contorta var. murrayana. Despite the fact that A. americanum was divided into three genetic races, hosts were divided into only two genetic groups: (i) Pinus banksiana and hybrids, and (ii) P. contorta var. latifolia and var. murrayana. These findings suggest that factors such as geographical isolation and adaptation to different environmental conditions are important for race formation in the absence of host-driven selection pressures. To assess factors impacting population structure at the fine-scale, genetic and geographical distance matrices of host and parasite were compared within A. americanum races. The lack of a relationship between genetic and geographical distance matrices suggests that isolation-by-distance plays a negligible role at this level. The effect of geographical isolation may have been diminished because of the influence of factors such as random seed dispersal by animal vectors or adaptation to nongeographically patterned environmental conditions. Host-parasite interactions might also have impacted the fine-scale structure of A. americanum because the parasite and host were found to have similar patterns of gene flow.

Genetic Variation↗
PubMed2001

Periodic and quasi-periodic behavior in resource-dependent age structured population models.

To describe the dynamics of a resource-dependent age structured population, a general non-linear Leslie type model is derived. The dependence on the resources is introduced through the death rates of the reproductive age classes. The conditions assumed in the derivation of the model are regularity and plausible limiting behaviors of the functions in the model. It is shown that the model dynamics restricted to its omega-limit sets is a diffeomorphism of a compact set, and the period-1 fixed points of the model are structurally stable. The loss of stability of the non-zero steady state occurs by a discrete Hopf bifurcation. Under general conditions, and after the loss of stability of the structurally stable steady states, the time evolution of population numbers is periodic or quasi-periodic. Numerical analysis with prototype functions has been performed, and the conditions leading to chaotic behavior in time are discussed.

Age Distribution↗
PubMed1997

A combined DNA-microsatellite and isozyme analysis of the population structure of the harbour porpoise in Danish waters and west Greenland.

One hundred and twenty-four specimens of the harbour porpoise, Phocoena phocoena, occurring in inner Danish waters (IDW), the North Sea and West Greenland were analysed to study subdivision into genetically differentiated subpopulations using PCR-amplified DNA-microsatellites and isozyme markers. Three polymorphic microsatellites, 415/416, 417/418 and Igf-I (insulin-like growth factor I) were detected with nine, eight and 15 alleles, respectively, and from a former study two polymorphic isozymes, Mpi-1 and Pgm, with three and two alleles, respectively, were used in the analysis. Overall deviations from the expected Hardy-Weinberg distribution were only observed in the total sample and at a single locus in the North Sea-summer sample and at two loci in the West Greenland sample. Whenever this occurred a surplus of homozygotes was observed, suggesting a Wahlund effect, a null allele or nonrandom mating. The analysis of the genetical population structure showed that harbour porpoises from West Greenland, the North Sea and IDW were three geographically, genetically differentiated populations even though connected through some degree of gene flow. A tendency for females to be more stationary than males was suggested. Furthermore, the population structure suggested a closer relationship between IDW and the North Sea.

Animals↗
PubMed1978

Population structure and genetic heterogeneity in the Upper Markham Valley of New Guinea.

An analysis is presented of the standardized Wahlund's variances (f) in gene frequencies of the ABO, Rh and MNS blood group systems among 19 villages of the Atsera isolate of the upper Markham Valley, Papua New Guinea. In the past, there has been some disagreement over the relative importance of population structure and natural selection in the determination of these variances. The Lewontin-Krakauer test is presented as a means of resolving this disagreement. According to this test, selectively neutral variation in gene frequencies should generate essentially homogeneous values of f for all loci, a homogeneity which can be tested by comparing the value of (formula: see text) to a theoretical (formula: see text) expected when variations in (formula: see text) are due solely to sampling error. The observed value of (formula: see text) for the Atsera isolate is 2.9 x 10(-5), which is not significantly different from the expected values that range from 1.23 x 10(-5) to 2.46 x 10(-5) depending on the constant used in calculating (formula: see text). Therefore it appears that nonselective aspects of population structure such as genetic drift and intervillage migration are responsible for the recorded genetic variation in this isolate.

ABO Blood-Group System↗
PubMed2005

Pedigree information reveals moderate to high levels of inbreeding and a weak population structure in the endangered Catalonian donkey breed.

The Catalonian donkey is one of the most endangered donkey breeds in the world. At present, five main subpopulations exist: AFRAC, which consists of many genetically connected Catalonian localities; Berga, which consists of a single herd located also in Catalunya but under private management; and three minor non-Catalonian subpopulations (Huesca, Sevilla and Toledo). In this study, we analysed the pedigree information of the Catalonian donkey herdbook to assess the genetic diversity and population structure of the breed. We found that the Catalonian donkey has suffered an important loss of genetic diversity and moderate to high increases of inbreeding because of the abuse of a few individuals in matings. This scenario is mainly characterized by the fact that both the effective number of founders and ancestors for the whole population was 70.6 and 27, respectively, while the equivalent number of founders was 146.5 and the number of ancestors explaining overall genetic variability was 93. In addition, only 14% of animals born between the 1960s and 1970s were significantly represented in the pedigree. Our results also show that subpopulations where breeders exchanged reproductive individuals had low levels of inbreeding and average relatedness. One subpopulation, Berga, was reproductively isolated and showed high levels of inbreeding (F = 7.22%), with average relatedness (AR = 6.61%) playing an important role in increasing the values of these coefficients in the whole pedigree. Using genealogical F-statistics we have found little evidence of population structuring (F(ST) = 0.0083) with major genetic differences among non-Catalonian subpopulations.

Animals↗
PubMed1988

Diversity of some gene frequencies in European and Asian populations. IV. Genetic population structure assessed by the variogram.

Isolation-by-distance models of population structure predict an exponential decrease of genetic relatedness with distance. Under the Kimura-Weiss (1964) model the plots of gene frequency variance versus distance (variograms), computed at various loci, are expected to have equal slope and reach a common asymptote. The gene frequency distributions at eight loci in 192 European and Asian populations have been summarized by variograms. On the average, the Kimura-Weiss model seems to describe adequately allele frequency change up to 900 km, but gradients are apparent at greater distances for most markers studied. These patterns may result form either differential selection or long-range gene flow; however, the extensive clinal variation observed for glyoxalase, esterase D and 6-PGD cannot be entirely accounted for by the Neolithic radiation of early farmers in the Middle East and Europe.

Alleles↗