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PubMed2004

Population structure and conservation genetics of wild rice Oryza rufipogon (Poaceae): a region-wide perspective from microsatellite variation.

Oryza rufipogon Griff. is the most agriculturally important but seriously endangered wild rice species. To better estimate how genetic structure can be used to obtained a conservation perspective of the species, genetic variability at six polymorphic microsatellite DNA loci was examined. High levels of genetic variability were detected at six loci in 1245 individuals of 47 natural populations covering most of the species' range in China (overall RS = 3.0740, HO = 0.2290, HS = 0.6700). Partitioning of genetic variability (FST = 0.246) showed that most microsatellite variation was distributed within populations. Significant departures from Hardy-Weinberg expectations and very strong linkage disequilibrium indicate a high degree of inbreeding in the species and severe subdivision within populations. A mean Nm value of 0.7662 suggested a limited gene flow among the assayed populations. Our study suggests that conservation and restoration genetics should focus in particular on the maintenance of historically significant processes such as high levels of outbreeding and gene flow and large effective population size in the species.

China↗
PubMed2006

Host species-dependent population structure of a pollen-borne plant virus, Cherry leaf roll virus.

Cherry leaf roll virus (CLRV) belongs to the Nepovirus genus within the family Comoviridae. It has a host range which includes a number of wild tree and shrub species. The serological and molecular diversity of CLRV was assessed using a collection of isolates and samples recovered from woody and herbaceous host plants from different geographical origins. Molecular diversity was assessed by sequencing a short (375-bp) region of the 3' noncoding region (NCR) of the genomic RNAs while serological diversity was assessed using a panel of seven monoclonal antibodies raised initially against a walnut isolate of CLRV. The genomic region analyzed was shown to exhibit a significant degree of molecular variability with an average pairwise divergence of 8.5% (nucleotide identity). Similarly, serological variability proved to be high, with no single monoclonal antibody being able to recognize all isolates analyzed. Serological and molecular phylogenetic reconstructions showed a strong correlation. Remarkably, the diversity of CLRV populations is to a large extent defined by the host plant from which the viral samples are originally obtained. There are relatively few reports of plant viruses for which the genetic diversity is structured by the host plant. In the case of CLRV, we hypothesize that this situation may reflect the exclusive mode of transmission in natural plant populations by pollen and by seeds. These modes of transmission are likely to impose barriers to host change by the virus, leading to rapid biological and genetic separation of CLRV variants coevolving with different plant host species.

3' Untranslated Regions↗
PubMed2005

On human STR sub-population structure.

This study is an investigation of genetic variation among the CODIS (combined DNA index system) STR (short tandem repeat) reference collections. The analysis was conducted in two parts. The first is an overall comparison (G-test) of allelic frequency distributions for 12 STR loci among 19 forensic databases representing various major groups and ethnic populations. In the second phase of the study, the impact of database replacement on DNA profile frequencies and inclusion probabilities is examined. The G-test results reveal clear allelic frequency differences among the major divisions, and, in some cases, among ethnically distinct subdivisions of the same major group affiliation. Other results indicate that database substitution may sometimes lead to substantial alterations in individual inclusion probabilities. Furthermore, there are numerous instances in which an allele present in some databases is missing in others. Fortunately, in most cases, these effects may not be forensically significant due to the increased discriminatory power of the STR markers employed in the CODIS system. However, differences in inclusion probabilities may become critical in situations in which DNA quantity is severely limited and/or compromised by degradation since, in these cases, the power of forensic STR analysis may be mitigated by reducing the number of informative loci.

DNA Fingerprinting↗
PubMed2003

Population structure of the Southeast Asian river catfish Mystus nemurus.

A total of 143 microsatellites were isolated from Mystus nemurus using a 5' anchored polymerase chain reaction technique or the random amplified hybridization microsatellite method, the first set of microsatellite markers developed for the Southeast Asian river catfish. Twenty polymorphic microsatellite loci were used as markers for population characterization of M. nemurus from six different geographical locations in Malaysia (Perak, Kedah, Johor, UPM, Sarawak and Terengganu). The number of alleles per locus ranged from 2 to 11 with 6.3 as the average number of alleles per locus. Characterization of the populations showed relatively high levels of genetic variation compared with previous studies using allozyme markers. The highest genetic similarity was found between Perak and Kedah, while the highest genetic distance was found between Terengganu and Kedah. The majority of clustering was in accordance with geographical locations and the histories of the populations. Microsatellite analysis indicated that the Sarawak population might be genetically closer to the Peninsular Malaysian populations than has been previously shown by other molecular marker studies.

Animals↗
PubMed1991

Approximation for age-structured population models using projection methods.

"In this paper we present a class of rapidly convergent numerical schemes to solve the Sharpe-Lotka model equation from age-dependent population dynamics. This work is based on spline approximation techniques described by Banks and Kappel for functional differential equations. We provide a motivation for and description of a generalized problem which under suitable conditions is equivalent to the Sharpe-Lotka problem, we describe approximation in general which exploits the Hilbert space structure in which the generalized problem is set, and for a particular space of approximating functions we obtain estimates on the rates of convergence."

Age Factors↗
PubMed1973

Self-fertilization and genetic population structure in a colonizing land snail.

The pulmonate land snail Rumina decollata in its native Mediterranean range is a complex of monogenic or weakly polygenic strains generated by a breeding system of facultative self-fertilization. One strain colonized North America and now occupies much of the southern United States and northern Mexico. No genetic variation within or among populations in the United States was detected in an electrophoretic analysis of proteins encoded by 25 loci. These findings emphasize the potential for adaptive convergence in the genetic systems of hermaphroditic animals and plants.

Journal Article↗
PubMed1979

Influence of genetic population structure on the results of chronic toxicity studies.

The importance of the genetic makeup of animals used for toxicological testing has been recognized, although there are few data regarding this. In the study discussed here offspring from a BALB/cStCrlfC3Hf/Nctr male and C57BL/6jfC3Hf/Nctr female cross were used to produce a homogeneous (F1) strain, and brother-sister mating of the F1 population was used to produce a heterogeneous (F2) strain of mice, both having essentially the same gene pool but with different distributions. The end points of mortality and body weights were used to demonstrate relative variability about a mean resulting from genetic constitution when the mice were exposed to benzidine dihydrochloride. This life-span study demonstrated that genetic constitution in research animals should be an important consideration in toxicological research. There were significant differences in body weight and mortality between the two populations, with the F2 mice exhibiting wider body weight ranges and greater susceptibility to the test chemical.

Animals↗
PubMed1986

Private production, collective consumption, and regional population structure: the interactions between public and private good provision as determinants of community composition.

"Theories of trade and migration explain the distribution of individuals among regions based on private good productivities. The theory of local public goods (LPG's) uses collective good consumption economies to explain the size and composition of communities. This essay combines the two theories, to explore regional population heterogeneity and stability. Assuming that individuals must consume and produce in the same jurisdiction, the paper examines the nature of efficient allocations, the tensions between the private and public incentives, the nature of the equilibrium (if any) which migration among jurisdictions will generate, and how such equilibrium will depend on tax rules for sharing the costs of the LPG."

Commerce↗
PubMed2005

Population structure of Enterococcus faecium causing bacteremia in a Spanish university hospital: setting the scene for a future increase in vancomycin resistance?

Over an 8-year period (1995 to 2002), 86 Enterococcus faecium blood isolates from 84 patients, of which 54 were ampicillin resistant (AREF) and 32 were ampicillin susceptible (ASEF), were studied in a university hospital (1,200 beds; serving a population of 600,000) in Spain, a country characterized by a near-absence of resistance to vancomycin and very high rates of ampicillin resistance among enterococci. Clonal relatedness by pulsed-field gel electrophoresis (PFGE), antibiotic susceptibility, presence of the virulence/epidemicity genes esp(Efm) and hyl(Efm), and identification of purK alleles were studied. A group of isolates was also analyzed by amplified fragment length polymorphism (AFLP) and multilocus sequence typing. Medical charts (30 variables collected) were reviewed for 60/84 patients. ASEF showed high clonal diversity (32 PFGE types, 11 purK alleles, 4 AFLP genogroups), did not harbor putative virulence genes, and had no specific association with hospital acquisition. AREF isolates belonged to a clonal complex (CC) of genetically related strains (purK-1, AFLP genogroup C), occasionally harboring putative virulence traits, and were from patients with particular risk factors. Within this CC, previously associated with vancomycin-resistant E. faecium isolates causing outbreaks worldwide (W. L. Homan et al., J. Clin. Microbiol. 40:1963-1971, 2002), a great genetic diversity of antibiotic resistance and virulence/epidemicity profiles was found. Associations between esp and a >7-day hospital stay and between purK-1, hospital location, and nosocomial acquisition were noted (P < 0.001). These findings reflect the importance of local environmental differences in the evolution of this CC, suggesting that the emergence of vancomycin resistance among AREF strains in Spain may be a question of time.

Ampicillin↗
PubMed1986

Primate population structure: evaluation of models.

Genetic markers among macaques on Cayo Santiago island were analyzed in an attempt to infer aspects of mating structure. Several models that included high levels of gene flow among groups could not be distinguished, but the data are clearly incompatible with group endogamy and with high variance in male fitness. Drift effective size is approximately one half census size in this population.

Animals↗