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PubMed1997

Population structure and seasonal movements of narwhals, Monodon monoceros, determined from mtDNA analysis.

We determined the nucleotide sequence of the first 287 base pairs in the mitochondrial control region from 74 narwhals, Monodon monoceros, collected in the North-west Atlantic. We detected four polymorphic sites that defined five haplotypes, two of which were found in single specimens. The same DNA sequence was characterized in an additional 353 specimens by digestion with two restriction endonucleases. In this manner each specimen could be assigned to one of the three most common haplotypes. The nucleotide diversity for the total sample (as well as the sequenced subset) was estimated as 0.0017 and pairwise genetic distances between haplotypes ranged from 0.0035-0.0070. The low nucleotide diversity and the low average pairwise genetic distance between haplotypes suggest a recent expansion in abundance from a small founding population. Despite the low degree of variation, frequencies of the common haplotypes differed markedly between areas. The results indicate isolation, even between geographically close areas, as well as fidelity to specific summer and autumn feeding grounds. Heterogeneity within a presumed single breeding ground suggests mixing of pods with different haplotypic composition.

Animals↗
PubMed2002

Population structure and antibiotic resistance of Acinetobacter DNA group 2 and 13TU isolates from hospitals in the UK.

A total of 287 Acinetobacter isolates belonging to DNA groups 2 (A. baumannii) and 13TU was collected consecutively from 46 hospitals and typed by randomly amplified polymorphic DNA fingerprinting with primers DAF-4 and ERIC-2. With a similarity coefficient of >/=72% as a cut-off value, 37 clusters of genotypically similar isolates (genotypes) were recognised. Four major clusters, found in 15, 12, 12 and 8 hospitals respectively, accounted for 42% of isolates, but only three of these predominant clusters were associated with outbreaks of infection in individual hospitals. Many of the isolates were resistant to multiple antibiotics, including expanded-spectrum beta-lactam agents, aminoglycosides, tetracyclines and fluoroquinolones, but >98% remained susceptible to carbapenems and colistin. Overall, the study demonstrated that a heterogeneous population of Acinetobacter DNA group 2 and 13TU isolates, frequently showing multiple resistance to antibiotics, was causing infections in UK hospitals, and that four predominant genotypes appeared to have disseminated among geographically distinct locations.

Acinetobacter↗
PubMed2003

Phylogeography and population structure of the common warthog (Phacochoerus africanus) inferred from variation in mitochondrial DNA sequences and microsatellite loci.

Global climate fluctuated considerably throughout the Pliocene and Pleistocene, influencing the evolutionary history of a wide range of species. Using both mitochondrial sequences and microsatellites, we have investigated the evolutionary consequences of such environmental fluctuation for the patterns of genetic variation in the common warthog, sampled from 24 localities in Africa. In the sample of 181 individuals, 70 mitochondrial DNA haplotypes were identified and an overall nucleotide diversity of 4.0% was observed. The haplotypes cluster in three well-differentiated clades (estimated net sequence divergence of 3.1-6.6%) corresponding to the geographical origins of individuals (i.e. eastern, western and southern African clades). At the microsatellite loci, high polymorphism was observed both in the number of alleles per locus (6-21), and in the gene diversity (in each population 0.59-0.80). Analysis of population differentiation indicates greater subdivision at the mitochondrial loci (FST=0.85) than at nuclear loci (FST=0.20), but both mitochondrial and nuclear loci support the existence of the three warthog lineages. We interpret our results in terms of the large-scale climatic fluctuations of the Pleistocene.

Animals↗
PubMed2006

Nitrite concentration influences the population structure of Nitrospira-like bacteria.

Chemolithoautotrophic nitrite oxidizers of the genus Nitrospira are a monophyletic but diverse group of organisms, are widely distributed in many natural habitats, and play a key role in nitrogen elimination during biological wastewater treatment. Phylogenetic analyses of cloned 16S rRNA genes and fluorescence in situ hybridization with newly developed rRNA-targeted oligonucleotide probes revealed coexistence of uncultured members of sublineages I and II of the genus Nitrospira in biofilm and activated sludge samples taken from nitrifying wastewater treatment plants. Quantitative microscopic analyses of their spatial arrangement relative to ammonia oxidizers in the biofilm and activated sludge flocs showed that members of the Nitrospira sublineage I occurred significantly more often in immediate vicinity to ammonia oxidizers than would be expected from random community assembly while such a relationship was not observed for Nitrospira sublineage II. This spatial distribution suggested a niche differentiation of these coexisting Nitrospira populations with respect to their preferred concentrations of nitrite. This hypothesis was tested by mathematical modelling of nitrite consumption and resulting nitrite gradients in nitrifying biofilms and by quantifying the abundance of sublineage I and II Nitrospira in activated sludge during incubations with nitrite in different concentrations. Consistent with the observed localization patterns, a higher nitrite concentration selected for sublineage I but suppressed sublineage II Nitrospira.

Ammonia↗
PubMed2004

Global population structure and taxonomy of the wandering albatross species complex.

A recent taxonomic revision of wandering albatross elevated each of the four subspecies to species. We used mitochondrial DNA and nine microsatellite markers to study the phylogenetic relationships of three species (Diomedea antipodensis, D. exulans and D. gibsoni) in the wandering albatross complex. A small number of samples from a fourth species, D. dabbenena, were analysed using mitochondrial DNA only. Mitochondrial DNA sequence analyses indicated the presence of three distinct groups within the wandering albatross complex: D. exulans, D. dabbenena and D. antipodensis/D. gibsoni. Although no fixed differences were found between D. antipodensis and D. gibsoni, a significant difference in the frequency of a single restriction site was detected using random fragment length polymorphism. Microsatellite analyses using nine variable loci, showed that D. exulans, D. antipodensis and D. gibsoni were genetically differentiated. Despite the widespread distribution of D. exulans, we did not detect any genetic differentiation among populations breeding on different island groups. The lower level of genetic differentiation between D. antipodensis and D. gibsoni should be reclassified as D. antipodensis. Within the context of the current taxonomy, these combined data support three species: D. dabbenena, D. exulans and D. antipodensis.

Animals↗
PubMed2001

Inheritance and population structure of the white-phased "Kermode" black bear.

We report that a single nucleotide replacement in the melanocortin 1 receptor gene [1] (mc1r) is responsible for the white coat color of the "Kermode" bear [2], a color phase of the black bear (Ursus americanus Pallus) found in the rainforests along the north coast of British Columbia. In a sample of 220 bears, of which 22 were white, there was complete association of a recessive Tyr-to-Cys replacement at codon 298 with the white phase. This variant has not been yet been reported in other mammals, and it also is the lightest-colored variant yet found at mc1r. Also, we found that heterozygotes, which act as a hidden reservoir for the allele among black bears, were infrequent outside of the three islands where Kermodes are common and that, within these three islands, heterozygotes were less frequent than expected under random mating. Immigration of black bears into Kermode populations can depress the occurrence of the white phase, and management practices should be designed to avoid facilitating higher immigration rates.

Animals↗
PubMed1978

Population structure in the Western Pyrenees: social class, migration and the frequency of consanguineous marriage, 1850 to 1910.

The effects of social class on migration distances and on the frequency of consanguineous marriages in Errazu, a Pyrenean village in Navarre, Spain, have been studied using data from parish records of baptisms and marriages, 1850-1910, and the census data for the year 1897. Migration distances are greater for tenants than for land-owners. Mean marital distances are not significantly different for the two social classes, but the movement of tenant families during married life results in significantly different parent-offspring distances for the two classes, at the 0.001 level for fathers and at the 0.002 level for mothers, by a t-test. Consanguineous marriages, up to and including third cousin marriages, are more frequent among land-owners (16.3 per cent) than among tenants (3.7 per cent). These frequencies are consistent with estimates based on the demographic characteristics of the population. Some implications of these results are discussed with reference to the findings of communities elsewhere in Europe and studies of communities in Japan. The implications of variation in the social class composition of populations with population density, for pedigree inbreeding values, are also considered.

Consanguinity↗
PubMed2002

Population structure and mating-type genes of Colletotrichum graminicola from Agrostis palustris.

Eighty-seven isolates of Colletotrichum graminicola, mostly from Agrostis palustris, were collected in grass fields, most of which were in Ontario, Canada. Specific primers were designed to amplify the mating-type (MAT) genes and, among 35 isolates tested, all yielded a band of the expected size for MAT2. For six isolates, the MAT2 PCR products were sequenced and found to be similar to that reported for MAT2 of C. graminicola from maize. Based on 119 polymorphic bands from 10 random amplified polymorphic DNA primers, analyses of genetic distances were found to generally cluster isolates by host and geographic origin. Among 42 isolates from a grass field in Ontario, significant spatial autocorrelation was found to occur within a 20-m distance, implying that this is the effective propagule dispersal distance. Although clonal propagation was observed in the 87 isolates with 67 unique genotypes, the extent of genetic variation in local populations implies some occurrence of sexual or asexual recombination.

Agrostis↗
PubMed2003

Activity and population structure of nitrifying bacteria in an activated-sludge reactor containing polymer beads.

Photo-crosslinked polymer beads were introduced into a laboratory activated-sludge unit containing municipal sewage sludge and the effect on nitrifying capacity was examined. The ammonia load started at a nitrogen-loading rate of 0.02 kg m(-3) day(-1) and was increased stepwise. It was found that the bead-containing unit could almost completely oxidize ammonia (over 95%) up to a nitrogen-loading rate of 0.216 kg m(-3) day(-1), whereas the maximum loading rate of the control unit (without polymer beads) was 0.096 kg m(-3) day(-1). The nitrifying potential of suspended and bead-associated organisms in the bead-containing unit was measured under different loading conditions. It was found that the bead-associated organisms exhibited high specific activities under high loading conditions and that the contribution of the bead-associated organisms to nitrification was greater than that of the suspended solids under these conditions. The bacterial population dynamics in the suspended solids and bead-associated organisms were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments and by fluorescence in situ hybridization with group-specific probes. Among the known nitrifying organisms, ammonia-oxidizing beta-proteobacteria and Nitrospira-related organisms were detected by these approaches. A comparison of the activity dynamics and population dynamics, however, suggested a possibility that other organisms may also have been involved in the nitrification process under high loading conditions.

Ammonia↗
PubMed1987

Genetic relationships and clonal population structure of serotype 2 strains of Neisseria meningitidis.

Two hundred and thirty-four strains of Neisseria meningitidis, including 94 serotype 2a, 111 serotype 2b, and 19 serotype 2c isolates, together with 10 isolates that were serotyped as 2 with polyvalent antiserum but did not react with monoclonal antibodies, were characterized by the electrophoretic mobilities of 15 metabolic enzymes. Of these enzymes, 14 were polymorphic, and 56 distinctive combinations of alleles at the enzyme loci (electrophoretic types) were identified, among which the mean genetic diversity per locus was 0.413, or about 75% of that recorded for the species N. meningitidis as a whole. Mean genetic diversity among electrophoretic types of the same serotype (2a, 2b, or 2c) was, however, on average, less than half the total species diversity, and no multilocus genotypes were shared between isolates of the different serotypes, which belong to distinctive clonal lineages. Recent temporal changes in the frequencies of recovery of pathogenic strains of serotypes 2a and 2b in South Africa and North America resulted from clone replacement in these populations rather than evolutionary modification of the serotype protein of the initially dominant clones.

Genetic Variation↗
PubMed2005

Investigation of the methanogen population structure and activity in a brackish lake sediment.

The methanogen community in sediment from the edge of a small brackish lake connected to the Beaulieu Estuary (Hampshire, UK) was investigated by analysis of 16S rRNA gene diversity using new methanogen-specific primers plus Archaea-specific primers. 16S rRNA gene primers previously used for polymerase chain reaction (PCR) detection of methanogenic Archaea from a variety of environments were evaluated by in silico testing. The primers displayed variable coverage of the four main orders of methanogens, highlighting the importance of this type of primer evaluation. Three PCR primer sets were designed using novel reverse primers to facilitate specific amplification of the orders Methanomicrobiales/Methanosarcinales, Methanobacteriales and Methanococcales. Diversity of the methanogen functional gene, methyl coenzyme M reductase (mcrA), was also studied. All gene libraries constructed from this sediment indicated that Methanomicrobiales and Methanosarcinales were the only methanogens detected. There was good agreement between the relative sequence abundances in the methanogen-specific 16S rRNA gene library and terminal restriction fragment length polymorphism (T-RFLP) profiling, suggesting that the population was dominated by putative H2 CO2 utilizing Methanomicrobiales, although acetate-utilizing methanogens were also present. The methanogen population analyses were in agreement with methanogenic activity measurements, which indicated that bicarbonate methanogenesis was higher than acetate methanogenesis at all depths measured and overall there was a significant difference (P = 0.001) between the rates of the two pathways. This study demonstrates the utility of new 16S rRNA gene PCR primers targeting specific methanogenic orders, and the combined results suggest that the CO2 reduction pathway dominates methanogenesis in the brackish sediment investigated.

Acetates↗
PubMed1992

Genetic heterogeneity and population structure of Gond-related tribes in the Vidarbha region of Maharashtra.

Genetic heterogeneity in nine polymorphic loci is observed among Gond-related tribes in the Vidarbha region of Maharashtra. Pardhans, with their high ABO*A2 gene frequency (4.01%), low m gene frequency (57%), high P*1 gene frequency (42.7%), and high HbS trait (31.58%), differ significantly from other tribes. Per locus average heterozygosity among the studied tribes ranged from 36.24% to 40.37%, with Pardhans being more heterozygous. Analysis by FST and the empirical relationship between average allele frequencies and the ratio of within-gene to total gene diversity show that the tribes are isolated and that differentiation among them is at an early stage and approximately in conformity with expected differentiation under genetic drift. However, distances and principal components analysis reveal that Pardhans are far removed from the other tribes and from other central Dravidian tribes. Furthermore, of the various demographic parameters estimated, the high average heterozygosity in Pardhans is significantly correlated with mean marital distance (MMD), regression of MMD on wife's age, and effective population size. There is congruence between genetic and demographic data, showing that Pardhans are distinct. This conforms with Haimendorf's (1979) contention based on cultural traits that Pardhans are Gonds by historical accident and are later migrants to the Gond area from the north. The most significant and practical observation of the present study is that migration from an originally nontribal (Pardhan) to a tribal (Gond) area and admixture lead to severe disease course, differential selection pressure, and hence highly elevated HbS trait frequency.

Blood Group Antigens↗
PubMed1996

Genetic differentiation and population structure of some occupational caste groups in Uttar Pradesh, India.

Phenotypes and gene frequencies of 24 genetic markers (9 blood groups, 11 red cell enzymes, and 4 serum proteins) were investigated in 5 occupational caste groups (Brahmin, Khatri, Vaish, Kayastha, and scheduled castes) and 1 religious group of Muslims in Uttar Pradesh, India. This is the first extensive genetic study in Uttar Pradesh that establishes the range of genetic variation in different endogamous groups. The extent of genetic variation among different occupational caste groups is low, and only two genetic systems (C3 and ACP) showed heterogeneity. The genetic affinity analysis showed an unexpected close affinity of scheduled castes with the Khatri. This observation warrants further analysis of these groups, but the present results may be a chance finding resulting from the nature of the samples, which represent individuals from vastly different regions of Uttar Pradesh. The affinity of the Muslim group with other caste groups suggests that the samples may include descendants of converts from the seventeenth century who are still at an early stage of differentiation. The FST estimate for the populations is 0.009, which is close to other estimates reported from north and northwest India. The overall mean FIS value is 0.066, and for each locus the FIS estimate is considerably higher than the FST estimate, suggesting that the infrastructure of the populations is influenced by nonrandom mating (inbreeding). There is no evidence of any disruptive selection, but the allele frequency of each caste group of Uttar Pradesh must be affected by its large population size, which, because of chance migration of individuals with different gene frequencies, would accentuate genetic differences.

Ethnicity↗
PubMed2006

Long term effects of salt on activity, population structure and floc characteristics in enriched bacterial cultures of nitrifiers.

The effect of salinity on the activity, the composition of nitrifiers and floc characteristics of nitrifying sludge was studied. Non-adapted and adapted (to 10g NaCl-Cl(-)/L for one year) enriched cultures of nitrifiers were tested in three sequencing batch reactors. Salt was increased gradually with 5 up to 40 g Cl(-)/L. No difference in steady state activity was observed between the adapted and non-adapted sludge. The activities of ammonia and nitrite oxidizers dropped 36% and 11%, respectively, at salt concentrations of 10 g Cl(-)/L. At 40 g Cl(-)/L inhibition reached 95% of salt free activity for ammonia and nitrite oxidizers in both adapted and non-adapted reactors. Nitrosomonas europaea and Nitrobacter sp. (fluorescent in situ hybridization) were the only nitrifiers present at high salt levels. Increased salt concentrations resulted in better settling characteristics of the nitrifying sludge. After 118 days the sludge was brought back to the initial conditions (0 g Cl(-)/L for non-adapted and 10 g Cl(-)/L for adapted). Despite the change in population composition similar kinetics as before the salt stress were observed.

Ammonia↗
PubMed2000

Microsatellite Polymorphism and the Population Structure of the Black Tiger Shrimp (Penaeus monodon) in Thailand.

Genetic variation and differentiation of Thai Penaeus monodon from five geographic locations (Chumphon, Trad, Phangnga, Satun, and Trang) were investigated using five microsatellite loci (CUPmo18, Di25, Di27, CSCUPmo1, and CSCUPmo2). The number of alleles across the five loci ranged from 19 to 30, and heterozygosities ranged from 0.49 to 0.95. The mean number of alleles and effective number of alleles per locus were 21.0 to 26.6 and 13.1 to 20.4, respectively. The average heterozygosity across all investigated samples was 0.78, indicating high genetic diversity in this species. Geographic heterogeneity analysis of the results from two of the loci, CUPmo18 and Di25, showed significant differences among the Gulf of Thailand (Trad and Chumphon) but not the Andaman samples. Comparison between regions revealed significant heterogeneity of the Andaman and Trad P. monodon (P <.001), whereas those from Chumphon and the Andaman were genetically similar (P >.05). Significant genetic differentiation was consistently observed between the Andaman-Trad samples (F(ST) = 0.0101, P <.0001) and the Chumphon-Trad samples (F(ST) = 0.0101, P <.0001). On the basis of our analyses, the investigated samples from five geographic locations were allocated to three distinct populations composed of the Andaman Sea (A), Chumphon (B), and Trad (C).

Journal Article↗
PubMed1997

Analysis of population structure of cactophilic yeast from the genus Pichia: P. cactophila and P. norvegensis.

DNAs from 40 strains of Pichia cactophila and Pichia norvegensis, yeasts characteristic of cactus necroses, were compared using randomly amplified polymorphic DNA (RAPD) banding patterns and killer/sensitive phenotypes. Both species belong to the same species complex within the genus. The levels of between-strain RAPD variation were high in both species (higher in the automictic P. cactophila than in the heterothallic P. norvegensis), although there is little variation in physiological abilities within either species. Although each species was a separate lineage, RAPD analysis confirms that the species are related. Within each species, RAPD variation was related to the geographic origin of the strains. Pichia cactophila strains from southern Florida were more related to those from Antigua than to those from northern Florida. These results correlated well with the differences among killer/sensitive phenotypes of strains. Principal component analysis indicated that the phenotypes of each species differ. Here too, strains from southern Florida were more similar to those from Antigua than to those from northern Florida. Previous work had identified differences in the cactophilic yeast communities from southern and northern Florida, and these results indicate that the differences are detectable at the population levels as well.

DNA, Fungal↗
PubMed1995

The forensic debut of the NRC's DNA report: population structure, ceiling frequencies and the need for numbers.

This paper reviews judicial opinions that have discussed the April 1992 recommendations of a committee of the U.S. National Research Council concerning the statistics of forensic DNA profiles obtained with single-locus VNTR probes. It observes that a few courts have held 'ceiling frequencies' (as opposed to less 'conservative' estimates) admissible, but that the implications of the scientific criticisms of the ceiling procedures have yet to be addressed adequately in court opinions. It urges courts to distinguish between policy judgments and scientific assessments in both the NRC report and the scientific literature, and to defer less to the former than to the latter.

Alleles↗
PubMedDate not supplied

Genetic variation of southern hemisphere fur seals (Arctocephalus spp.): investigation of population structure and species identity.

We have examined phylogenetic and geographic patterns of variation in the mitochondrial cytochrome b gene of Southern Hemisphere fur seals (Arctocephalus spp.). Our survey of 106 individuals from four putative species reveals three distinct patterns of variation reflecting ancient, recent historic, and contemporary gene flow. For the combined samples of Subantarctic (Arctocephalus tropicalis) and Antarctic (Arctocephalus gazella) fur seals, we find low levels of sequence diversity and reciprocal paraphyly of hapiotypes (where representative haplotypes of a species are found to occur infrequently in another species and vice versa). For the Australian and Cape fur seal subspecies (Arctocephalus pusillus doriferus and A. p. pusillus, respectively), we find low levels of sequence diversity but significant differences in the regional distribution of haplotypes that are consistent with, but not conclusive of, the current subspecies definition based on nonmolecular data. For the New Zealand fur seal (Arctocephalus forsteri), we find high levels of average sequence diversity because of the survival of two divergent lineages of mitochondrial hapiotypes with differences approaching that found in interspecific comparisons of other mammals. The two divergent clades are distributed sympatrically in some regions, but the overall geographic structure of the variation is significant across the range of this species. These new molecular data are inconsistent with current taxonomic definitions of species within the Southern Hemisphere fur seals and argue for reevaluation of these "species" definitions. For management purposes, the definition of evolutionarily significant units (Ryder 1986) and genetic management units (Moritz 1994) in relation to these species may also be evaluated in light of this molecular genetic information.

Animals↗