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PubMed2006

Comparative analyses of population structure in two subspecies of Nigella degenii: evidence for diversifying selection on pollen-color dimorphisms.

Flower color can be a major determinant of plant fitness, not only because of preferential visitation by pollinators but also because of pleiotropic relationships between the expression of floral pigments and biochemically related compounds that influence vegetative performance variables. Different environments may therefore favor different pigmentation phenotypes. We examined whether spatially varying selection has played a major role in shaping large-scale patterns of differentiation in two subspecies of Nigella degenii (Ranunculaceae), with particular emphasis on pollen color. The two subspecies appear to have been genetically isolated for substantial periods of time and, therefore, provide a "replicated test" for the effect of natural selection. Estimates of population structure based on a suite of floral and vegetative characters were compared with the corresponding data for amplified fragment length polymorphism (AFLP) markers, which were assumed to be selectively neutral. We found low levels of genetic structure within the subspecies using both the AFLP markers (FST < or = 0.05) and quantitative characters (QST < or = 0.15), with no statistically significant differences between the two measures. There is, therefore, no evidence of diversifying selection being important in structuring variation in quantitative characters within each of the two subspecies. In contrast, estimates of differentiation in pollen color (FST > or = 0.10) significantly exceeded the neutral expectations (estimated from AFLP data), suggesting that local adaptation has played a key role in the evolution of this monogenic character.

Analysis of Variance↗
PubMed1988

Clonal population structure of encapsulated Haemophilus influenzae.

Chromosomal genotypes of 2,209 isolates of the six polysaccharide capsule types of Haemophilus influenzae recovered from human hosts worldwide were characterized by an analysis of electrophoretically demonstrable allelic profiles at 17 metabolic enzyme loci. For 222 representative isolates, restriction fragment length polymorphism patterns produced by digestion of cap region DNA were also determined. With few exceptions, isolates belonging to individual phylogenetic lines or groups of allied lineages identified by multilocus enzyme electrophoresis had characteristic cap region restriction fragment length polymorphism patterns and characteristic combinations of cap region patterns and outer membrane protein types. The occurrence of strong associations of characters and the recovery of isolates with identical genetic properties in widely separated geographic regions and over a 40-year period indicated that the population structure of encapsulated H. influenzae is clonal. Recombination of chromosomal genes, including those mediating capsule synthesis, apparently is not a major factor in the short-term evolution of these pathogenic organisms and, therefore, may be of minor clinical significance.

Bacterial Outer Membrane Proteins↗
PubMed2004

Population structure and evolutionary origins of Microsporum canis, M. ferrugineum and M. audouinii.

The recurrent evolutionary emergence of asexual lineages within sexual zoo- and anthropophilic dermatophyte species living in animal-frequented soil is likely to be triggered by changes in ecological niche, i.e., shifts of host animal. Subsequent adaptation to the new host species is noted. Sometimes geographic isolation or intrinsic host factors like human race may also play a role in speciation. In the present study, we elaborate concepts of speciation in dermatophytes using the Microsporum canis complex as an example. The group consists of a cluster of phylogenetically closely related anamorphs: the anthropophilic taxa Microsporum audouinii and M. ferrugineum, and the zoophilic taxon M. canis. The sexually reproducing species underlying this complex is Arthroderma otae. The study is done by an analysis of the population structure of about 200 isolates and using intergenic spacers, non-translated regions of genes as well as hypervariable microsatellite markers that are known to evolve at high mutation rates. The results suggest that sympatric speciation took place already during the period where mating ability was maintained and thus that strictly clonal fungal species emerged in Africa and led to genetically isolated clonal species elsewhere.

Alleles↗
PubMed2006

Evolution in group-structured populations can resolve the tragedy of the commons.

Public goods are the key features of all human societies and are also important in many animal societies. Collaborative hunting and collective defence are but two examples of public goods that have played a crucial role in the development of human societies and still play an important role in many animal societies. Public goods allow societies composed largely of cooperators to outperform societies composed mainly of non-cooperators. However, public goods also provide an incentive for individuals to be selfish by benefiting from the public good without contributing to it. This is the essential paradox of cooperation-known variously as the Tragedy of the Commons, Multi-person Prisoner's Dilemma or Social Dilemma. Here, we show that a new model for evolution in group-structured populations provides a simple and effective mechanism for the emergence and maintenance of cooperation in such a social dilemma. This model does not depend on kin selection, direct or indirect reciprocity, punishment, optional participation or trait-group selection. Since this mechanism depends only on population dynamics and requires no cognitive abilities on the part of the agents concerned, it potentially applies to organisms at all levels of complexity.

Animals↗
PubMed2003

Pulsed field gel electrophoresis of chromosomal DNA reveals a clonal population structure to Bacillus thuringiensis that relates in general to crystal protein gene content.

Seventy strains of Bacillus thuringiensis representing 21 serovars were allocated to 38 genomic groups using pulsed field gel electrophoresis (PFGE) of restriction enzyme-digested DNA. There was a broad correlation between PFGE type and serotype for serovars darmstadiensis, israelensis, kenyae, kumamotoensis, kurstaki, sotto, thuringiensis, and tolworthi, although some serovars included atypical strains. Serovars canadensis and entomocidus were heterogeneous. Detection of crystal protein genes by polymerase chain reaction indicated an approximate correlation between PFGE type and cry gene complement. For example, cry1 products were amplified from DNA from PFGE type 17 strains of serovar aizawai and from PFGE type 23 strains of serovar tolworthi but not from a PFGE 18 strain of aizawai nor from a PFGE type 24 strain of tolworthi. These data suggest a clonal population structure to B. thuringiensis with some consistency of Cry-plasmid composition within PFGE types.

Bacillus thuringiensis↗
PubMed2001

Clonal population structure of Pseudomonas stutzeri, a species with exceptional genetic diversity.

Genetic diversity and genetic relationships among 42 Pseudomonas stutzeri strains belonging to several genomovars and isolated from different sources were investigated in an examination of 20 metabolic enzymes by multilocus enzyme electrophoresis analysis. Forty-two distinct allele profiles were identified, indicating that all multilocus genotypes were represented by a single strain. All 20 loci were exceptionally polymorphic, with an average of 15.9 alleles per locus. To the best of our knowledge, this P. stutzeri sample exhibited the highest mean genetic diversity (H = 0.876) found to date in all bacterial species studied by multilocus enzyme electrophoresis. A high frequency of occurrence of null alleles was identified. The index of association (I(A)) for the P. stutzeri strains analyzed was 1.10. The I(A) values were always significantly different from zero for all subgroups studied, including clinical and environmental isolates and strains classified as genomovar 1. These results suggest that the population structure of P. stutzeri is strongly clonal, indicating that there is no significant level of assortative recombination that might destroy linkage disequilibrium.

Alleles↗
PubMed2006

Population structure and inbreeding in a rare and declining bumblebee, Bombus muscorum (Hymenoptera: Apidae).

Owing to habitat loss populations of many organisms have declined and become fragmented. Vertebrate conservation strategies routinely consider genetic factors, but their importance in invertebrate populations is poorly understood. Bumblebees are important pollinators, and many species have undergone dramatic declines. As monoandrous social hymenopterans they may be particularly susceptible to inbreeding due to low effective population sizes. We study fragmented populations of a bumblebee species, on a model island system, and on mainland Great Britain where it is rare and declining. We use microsatellites to study: population genetic structuring and gene flow; the relationships between genetic diversity, population size and isolation; and frequencies of (sterile) diploid males - an indicator of inbreeding. We find significant genetic structuring (theta = 0.12) and isolation by distance. Populations > 10 km apart are all significantly differentiated, both on oceanic islands and on the mainland. Genetic diversity is reduced relative to closely related common species, and isolated populations exhibit further reductions. Of 16 populations, 10 show recent bottlenecking, and 3 show diploid male production. These results suggest that surviving populations of this rare insect suffer from inbreeding as a result of geographical isolation. Implications for the conservation of social hymenopterans are discussed.

Animals↗
PubMed2000

Nuclear DNA restriction site polymorphisms and the phylogeny and population structure of an intertidal snail species complex (Littorina).

Primers for amplification of four novel, unlinked nuclear DNA loci, the first reported for the rough periwinkles of the genus Littorina, are described. Patterns of restriction site polymorphism for these loci are detailed within the rough periwinkles. RFLPs are not found to be diagnostic for any of the currently accepted species within this group, nor for any of the contentious subspecies, or forms, whose taxonomic status is uncertain. However, there are important differences in allele frequencies between these taxa and certain of these mirror differences detected in a previous study of the mitochondrial DNA. These allele frequency data are used to construct a phylogeny in which groupings of the three recognised species are obvious when either Nei's genetic distances or Reynold's distances are clustered. Contentious forms (L. neglecta, L. saxatilis 'b' and L. tenebrosa) do not cluster as distinct taxa, although populations of L. neglecta have important allele frequency differences from L. saxatilis. These four loci have confirmed the consensus view of Littorina phylogeny and provided important information on population structure-however four loci is insufficient for reaching definitive conclusions. Since analysis of nuclear DNA polymorphisms such as these is invaluable for analysis of phylogeny, population structure and phylogeography, identification of additional loci is considered imperative.

Animals↗
PubMed2002

Population structure and genetic diversity of Actinobacillus actinomycetemcomitans strains isolated from localized juvenile periodontitis patients.

The phylogeny of 20 Actinobacillus actinomycetemcomitans strains isolated from patients with localized juvenile periodontitis (LJP) was investigated by using partial sequence analysis of 16S rRNA genes, arbitrarily primed PCR (AP-PCR), and four additional PCR assays that amplified polymorphic regions in the leukotoxin (lkt), cytolethal distending toxin (cdt), major fimbrial subunit (flp-1), and serotype-specific O polysaccharide gene clusters. Our analysis also included four strains isolated from healthy subjects and nine reference strains. We found that A. actinomycetemcomitans strains comprised three major phylogenetic lineages. One lineage consisted of serotype b strains, a second lineage consisted of serotype c strains, and a third lineage consisted of serotype a, d, e, and f strains. 16S rRNA sequences within each lineage were highly conserved (<1% base substitutions), whereas sequences between lineages were exceptionally divergent (1.9 to 5.0% substitutions). Two strains exhibited 16S rRNA sequences that were even more distantly related to those of the three major lineages (2.7 to 6.7% substitutions), indicating that additional minor lineages or variants exist. The distribution of 16S rRNA sequences and lkt, cdt, flp-1, and AP-PCR genotypes was consistent with a clonal population structure, with little evidence of assortative recombination between strains of different serotypes. Strains from all three major lineages were recovered from LJP patients, suggesting that phylogenetically diverse strains of A. actinomycetemcomitans carry pathogenic potential.

Actinobacillus Infections↗
PubMed2000

Population structure of rat-derived Pneumocystis carinii in Danish wild rats.

The rat model of Pneumocystis carinii pneumonia is frequently used to study human P. carinii infection, but there are many differences between the rat and human infections. We studied naturally acquired P. carinii in wild rats to examine the relevance of the rat model for human infection. P. carinii DNA was detected in 47 of 51 wild rats and in 10 of 12 nonimmunosuppressed laboratory rats. Evidence for three novel formae speciales of rat-derived P. carinii was found, and these were provisionally named Pneumocystis carinii f. sp. rattus-secundi, Pneumocystis carinii f. sp. rattus-tertii, and Pneumocystis carinii f. sp. rattus-quarti. Our data suggest that low-level carriage of P. carinii in wild rats and nonimmunosuppressed laboratory rats is common and that wild rats are frequently coinfected with more than one forma specialis of P. carinii. We also examined the diversity in the internally transcribed spacer (ITS) regions of the nuclear rRNA operon of Pneumocystis carinii f. sp. carinii by using samples from wild rats and laboratory rats and spore trap samples. We report a lack of variation in the ITS1 and ITS2 regions that is consistent with an evolutionary bottleneck in the P. carinii f. sp. carinii population. This study shows that human- and rat-derived P. carinii organisms are very different, not only in genetic composition but also in population structure and natural history.

Animals↗
PubMed1998

Population structure of the relapsing fever spirochete Borrelia hermsii as indicated by polymorphism of two multigene families that encode immunogenic outer surface lipoproteins.

The tick-borne relapsing fever spirochete Borrelia hermsii evades the mammalian immune system by periodically switching expression among members of two multigene families that encode immunogenic, antigenically distinct outer surface proteins. The type strain, B. hermsii HS1, has at least 40 complete genes and pseudogenes that participate in this multiphasic antigenic variation. Originally termed vmp (for variable major protein) genes, they have been reclassified as vsp (for variable small protein) and vlp (for variable large protein) genes, based on size and amino acid sequence similarities. To date, antigenic variation in B. hermsii has been studied only in the type strain, HS1. Nucleotide sequence comparisons of 23 B. hermsii HS1 genes revealed five distinct groups, the vsp gene family and four subfamilies of vlp genes. We used PCR with family- and subfamily-specific primers, followed by restriction fragment length polymorphism analysis, to compare the vsp and vlp repertoires of HS1 and seven other B. hermsii isolates from Washington, Idaho, and California. This analysis, together with pulsed-field gel electrophoresis genome profiles, revealed that the eight isolates formed three distinct groups, which likely represent clonal lineages. Members of the three groups coexisted in the same geographic area, but they could also be isolated across large geographical distances. This population structure may result from immune selection by the host, as has been proposed for other pathogens with polymorphic antigens.

Borrelia↗
PubMed1985

Equilibria in structured populations.

The existence of a stable positive equilibrium state for the density rho of a population which is internally structured by means of a single scalar such as age, size, etc. is studied as a bifurcation problem. Using an inherent birth modulus n as a bifurcation parameter it is shown for very general nonlinear model equations, in which vital birth and growth processes depend on population density, that a global unbounded continuum of of nontrivial equilibrium pairs (n, rho) bifurcates from the unique (normalized) critical point (1, 0). The pairs are locally positive and conditions are given under which the continuum is globally positive. Local stability is shown to depend on the direction of bifurcation. For the important case when density dependence is a nonlinear expression involving a linear functional of density (such as total population size) it is shown how a detailed global bifurcation diagram is easily constructed in applications from the graph of a certain real valued function obtained from an invariant on the continuum. Uniqueness and nonuniqueness of positive equilibrium states are studied. The results are illustrated by several applications to models appearing in the literature.

Animals↗
PubMed2006

Multiple-locus sequence typing analysis of Bacillus cereus and Bacillus thuringiensis reveals separate clustering and a distinct population structure of psychrotrophic strains.

We used multilocus sequence typing (MLST) to characterize phylogenetic relationships for a collection of Bacillus cereus group strains isolated from forest soil in the Paris area during a mild winter. This collection contains multiple strains isolated from the same soil sample and strains isolated from samples from different sites. We characterized 115 strains of this collection and 19 other strains based on the sequences of the clpC, dinB, gdpD, panC, purF, and yhfL loci. The number of alleles ranged from 36 to 53, and a total of 93 allelic profiles or sequence types were distinguished. We identified three major strain clusters-C, T, and W-based on the comparison of individual gene sequences or concatenated sequences. Some less representative clusters and subclusters were also distinguished. Analysis of the MLST data using the concept of clonal complexes led to the identification of two, five, and three such groups in clusters C, T, and W, respectively. Some of the forest isolates were closely related to independently isolated psychrotrophic strains. Systematic testing of the strains of this collection showed that almost all the strains that were able to grow at a low temperature (6 degrees C) belonged to cluster W. Most of these strains, including three independently isolated strains, belong to two clonal complexes and are therefore very closely related genetically. These clonal complexes represent strains corresponding to the previously identified species Bacillus weihenstephanensis. Most of the other strains of our collection, including some from the W cluster, are not psychrotrophic. B. weihenstephanensis (cluster W) strains appear to comprise an effectively sexual population, whereas Bacillus thuringiensis (cluster T) and B. cereus (cluster C) have clonal population structures.

Bacillus cereus↗
PubMed1989

The optimal sex ratio for age-structured populations.

A new nonlinear age-dependent model for age-structured sexual populations is introduced, based on two assumptions: (1) the birth function depends on the ages of the two parents; and (2) the death functions of the two sexes are composed of two types of additive terms depending on age and sex and on time evolution of population densities, respectively. Formal arguments are given that suggest that time-persistent age profiles may exist and that the intrinsic rate of growth for the two sexes is the same. If the ratio between the number of newborn females and the number of newborn males is equal to the square root of the ratio of the corresponding per capita birth rates, then the intrinsic rate of growth has an optimal value. The optimal sex ratio for the whole population is equal to the reciprocal value of the sex ratio at birth.

Age Factors↗
PubMed2004

Mitochondrial DNA variation and population structure of the island endemic Azorean bat (Nyctalus azoreum).

The Azorean bat Nyctalus azoreum is the only endemic mammal native to the remote archipelago of the Azores. It evolved from a continental ancestor related to the Leisler's bat Nyctalus leisleri and is considered threatened because of its restricted and highly fragmented distribution. We studied the genetic variability in 159 individuals from 14 colonies sampled throughout the archipelago. Sequences of the D-loop region revealed moderate but highly structured genetic variability. Half of the 15 distinct haplotypes were restricted to a single island, but the most common was found throughout the archipelago, suggesting a single colonization event followed by limited interisland female gene flow. All N. azoreum haplotypes were closely related and formed a star-like structure typical of expanded populations. The inferred age of demographic expansions was consistent with the arrival of founder animals during the Holocene, well before the first humans inhabited the Azores. Comparisons with a population of N. leisleri from continental Portugal confirmed not only that all N. azoreum lineages were unique to the archipelago, but also that the current levels of genetic diversity were surprisingly high for an insular species. Our data imply that the Azorean bat has a high conservation value. We argue that geographical patterns of genetic structuring indicate the existence of two management units.

Animals↗
PubMed2004

Differential population structuring of two closely related fish species, the mackerel (Scomber scombrus) and the chub mackerel (Scomber japonicus), in the Mediterranean Sea.

Population genetic structures of the mackerel (Scomber scombrus) and chub mackerel (Scomber japonicus) were studied in the Mediterranean Sea. Fragments of 272 bp (S. scomber) and 387 bp (S. japonicus) of the 5'-end of the mitochondrial control region were sequenced from spawning individuals collected off the coasts of Greece, Italy, Spain, and Portugal. High levels of mitochondrial control region haplotypic diversity (> 0.98) were found for both Scomber species. Nucleotide diversity was higher in the mackerel (0.022) than in the chub mackerel (0.017). Global F(ST) values were also higher and significant in the mackerel (0.024, P < 0.0001) as opposed to the chub mackerel (0.003, P > 0.05). Molecular variance analyses showed differential genetic structuring for these two closely related species. There is extensive gene flow between Mediterranean Sea and Atlantic Ocean populations of chub mackerel, which are organized into a larger panmictic unit. In contrast, Mediterranean Sea populations of mackerel show some degree of genetic differentiation and are structured along an east-west axis. The analysed eastern Mediterranean Sea mackerel populations (Greece, Italy) are clearly separated from that of the western Mediterranean Sea (Barcelona), which forms a panmictic unit with eastern Atlantic Ocean populations. The genetic structures of both species showed asymmetric migration patterns and indicated population expansion.

Analysis of Variance↗
PubMed1999

Population structure of the wood decay fungus Fomitopsis pinicola.

Three populations of the wood decay fungus Fomitopsis pinicola, one from each of three countries (Sweden, Russia and Lithuania), were studied by means of arbitrary primed PCR. The genetic structure of the populations was assessed by inferring the genotype of the genets by studying the haplotypes of several single-spore isolates from one sporocarp for each individual. Heterozygotes could therefore be detected with a dominant genetic marker. The amplified band and the null allele of all loci segregated in a way that was in agreement with a 50:50 ratio. Genetic analysis showed that the total population as well as the subpopulations had heterozygote frequencies in agreement with Hardy-Weinberg expectations. No population differentiation was detected in spite of large geographical distances among the populations studied. We also compared the methods of somatic incompatibility and AP-PCR in terms of their value in detecting fungal genets. This was tested for a sample of dikaryotic mycelia from Switzerland. For the tested material the two methods gave congruent results.

Base Sequence↗
PubMed1979

Gene frequency and fitness change in an age-structured population.

Fisher's system of reproductive value weighting, whereby each age group is assigned a weight purported to measure its contribution to the ancestry of future generations, was suggested by him as a way of ironing out irregularities in the change of population numbers when the age structure is not in equilibrium. This has been extended to Mendelian populations for two models. In Model I, the reproductive value of each genotype is computed from a table of age-specific survival and reproduction rates, and the genic values are computed by averaging these genotypic values. The total reproductive value of an allele and of the population always increase at a rate equal to the reproductive value-weighted average fitness regardless of age structure. This has the disadvantage that the total reproductive value is not equal to the census numbers, when age-stability has been reached. In Model II, this difficulty is surmounted, but the formula is no longer exact. The reproductive value of an allele for a specific age x is measured from the average death and reproductive rates of individuals of age x carrying that allele. An expression is given for the rate of change of reproductive value of an allele or of the population. In many circumstances this changes nearly uniformly, regardless of irregularities of age structure, and goes over to the census numbers as age stability is approached. The special difficulties in populations with separate sexes are discussed and a formula for rate of change of mean reproductive value, analogous to Fisher's Fundamental Theorem of Natural Selection, is given.

Age Factors↗