Population structures

Du Preez, L.H., Solomon, K.R., and Carr, J. A. et al. (2005). Population structure of the African Clawed Frog (Xenopus laevis) in maize-growing areas with atrazine application versus non-maize-growing areas in South Africa. African Journal of Herpetology 54, 61-68. 

Carter, D.A., Burt, A., Taylor, J.W., Koenig, G.L. and White, T.J. (1996) Clinical isolates of Histoplasma capsulatum from Indianapolis have a recombining population structure. Journal of Clinical Microbiology 34, 2577-2584. 

Representatives of this phylum have been used extensively as indicators of stressed environments. Population structure and species diversity of free-living nematodes inhabiting sediments in the New York Bight were moderately influenced by the heavy-metal content of sands. In medium-grained sands, species diversity was inversely correlated with increased concentrations of chromium and other metals. Sands containing 3.0 to 21.5 mg Cr/kg were also marked by high relative abundances of one or two nematode species the tolerance of these species to chromium stress probably exceeded that of the normal nematode inhabitants of such sediments (Tietjen 1980). 

Tietjen, J.H. 1980. Population structure and species composition of the free-living nematodes inhabiting sands of the New York Bight Apex. Estuar. Coast. Mar. Sci. 10 61-73. 

Lee, C.J., M.C. Newman, and M. Mulvey. 1992. Time to death of mosquitofish (Gambusia holbrooki) during acute inorganic mercury exposure population structure effects. Arch. Environ. Contam. Toxicol. 22 284-287. 

Widespread use of mirex may lead to altered population structure in terrestrial systems, with resurgence or escalation of nontarget pests due to selective mirex-induced mortality of predators (NAS 1978). For example, populations of immature horn flies and rove beetles, two species of arthropods normally preyed upon by fire ants, were higher in mirex-treated areas than in control areas (Howard and Oliver 1978). Conversely, other species, such as crickets, ground beetles, and various species of oil-loving ants, were directly affected and populations were still depressed or eliminated 14 months posttreatment (NAS 1978), whereas fire ants recovered to higher than pretreatment levels, as judged by mound numbers and mound size (Summerlin et al. 1977). 

Pritchard, J.K., et al., "Inference of Population Structure Using Multilocus Genotype Data," Genetics, 155, 945-959 (2000). 

Populations, gene flow between, 55-56 Population structure, 55-56 Positional cloning, 35, 36 Positive drug response, 262 Positive predictive value (PPV), 169-171 Postmarketing surveillance, 94—95, 324-325... 

Zizumbo D, Colunga P, Payro de la Crus E, Delgado P, Gepts P (2005) Population structure and evolutionary dynamics of wild-weedy-domesticated complexes of common bean in a Mesoamerican region. Crop Sci 45 1073-1083... 

Phospholipid fatty acid (PLFA) Methanol-KOH extraction Indicates bacterial population structure time-consuming determined in nonstandard laboratory with specialized equipment expensive equipment Dick et al. (1996)... 

Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E (2001) Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67 4215-4224... 

Some effects have been observed in fauna living close to paper mill discharges, such as skin and physiological diseases in fish and a decrease in the number of juveniles, changes in communities and population structure, changes in growth rates, and delayed sexual maturation and reproduction, among others [2,58,59]. 

Van der Strate H, Van de Zande L, Stam WT, Olsen JL (2002) The contribution of haploids, diploids and clones to fine-scale population structure in the seaweed Cladophoropsis membranacea (Chlorophyta). Mol Ecol 11 329-345 Verlaque M, Boudouresque CF, Meinesz A, Gravez V (2000) The Caulerpa racemosa complex (Caulerpales, Ulvophyceae) in the Mediterranean sea. Bot Mar 43 49-68 Vinueza LR, Branch GM, Branch ML, Bustamante RH (2006) Top-down herbivory and bottom-up El Nino effects on Galapagos rocky-shore communities. Ecol Monogr 76 111-131 Wahl M and Hay ME (1995) Associational resistance and shared doom effects of epibiosis on herbivory. Oecologia 102 329-340... 

Studying variation in human genomic sequences may serve two general purposes to characterize genetic population structure and its history and to elucidate the genotype/phenotype relationship in individuals or families. Both aspects are strongly interdependent, and it is only with the advent of new methods of individual sequencing on a mass scale that they become technically feasible. 

Keywords Admixture association study confounding human genetics population structure. 

One major concern of the association study is that spurious associations may occur if the genetic background in cases is different from that in controls. Genetic heterogeneity in a population can be a result of population structure and recent admixture. In this chapter, we review the problem of population structure, demonstrate how that structure affects association study, and discuss solutions to this problem. 

A thorough study by Rosenberg et al. (4) examined human population structure using 377 markers in 1056 individuals from 52 populations around the world. Without prior information about the origins of individuals, these authors used a Bayesian algorithm to identify six major genetic clusters (1) sub-Saharan Africans ... 

Confounding is not a concern in TDT because the allelic transmission within families is unaffected by population structure and admixture. Information on hap-lotypes is available in family-based design and may help increase the test power. There are two major drawbacks in family-based design. First, if the disease occurs... 

Because of the difficulties in family-based design, an association study with a case-control design is more and more commonly used by investigators. Because of the concern of confounding caused by population structure and recent admixture, appropriate adjustment of stratification should be used in association studies. A number of approaches have been developed for this purpose. 

Marchini et al. examined the consequences of population structure on association studies and evaluated the effectiveness of GC in correcting for population structure (17). In simulated scenarios that involved two or three populations, GC did not remove the effects of population structure in association studies when a small number of loci were used. When a large number of loci were used, the correction by GC became conservative. This problem of GC became severe with small p values and large sample sizes. 

In summary, GC adjusts for population stratification without the assumption or estimation of parameters such as the number of subpopulations involved in the study. It provides control of false-positive results caused by population structure as well as by multiple testing. One possible drawback of this method is that the correction of the test statistic is constant across the genome. As a result, GC may have less power in certain situations. 

In addition to these three major methods mentioned, several other computational approaches can also be used to deal with population stratification. For example, ADMIXMAP (22-26) is a model-based method that estimates the individual history of admixture. It can be applied to an admixed population with two or more ancestral populations. It also tests the association of a trait with ancestry at a marker locus with control for population structure. Wu et al. developed a software package in R (PSMIX) for the inference of population stratification and admixture (27). PSMIX is based on the maximum likelihood method. It performs as well as model-based methods such as STRUCTURE and is more computationally efficient. 

M. W. (2005) Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genet. 1, e70. 

Ziv, E., and Burchard, E.G. (2003) Human population structure and genetic association studies. Pharmacogenomics. 4, 431-441. 

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