Inference of population structure using multilocus genotype data: dominant markers and null alleles

AbstractWe describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations (“admixture linkage disequilibium”). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.

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Inference of Population Structure Using Multilocus Genotype Data

Genetics ◽

10.1093/genetics/155.2.945 ◽

2000 ◽

Vol 155 (2) ◽

pp. 945-959 ◽

Cited By ~ 372

Author(s):

Jonathan K Pritchard ◽

Matthew Stephens ◽

Peter Donnelly

Keyword(s):

Population Structure ◽

Genetic Markers ◽

Microsatellite Loci ◽

Bird Species ◽

Multilocus Genotype ◽

Hybrid Zones ◽

Genotype Data ◽

Clustering Method ◽

Mutation Process ◽

Model Based Clustering

Abstract We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.

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Parentage and Sibship Inference From Multilocus Genotype Data Under Polygamy

Genetics ◽

10.1534/genetics.108.100214 ◽

2009 ◽

Vol 181 (4) ◽

pp. 1579-1594 ◽

Cited By ~ 323

Author(s):

J. Wang ◽

A. W. Santure

Keyword(s):

Multilocus Genotype ◽

Genotype Data

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Genetic status of Norway spruce (Picea abies) breeding populations for northern Sweden

Silvae Genetica ◽

10.1515/sg-2013-0017 ◽

2013 ◽

Vol 62 (1-6) ◽

pp. 127-136 ◽

Cited By ~ 15

Author(s):

P. Androsiuk ◽

A. Shimono ◽

J. Westin ◽

D. Lindgren ◽

A. Fries ◽

...

Keyword(s):

Genetic Variation ◽

Norway Spruce ◽

Population Differentiation ◽

Distinct Group ◽

Null Alleles ◽

Multilocus Genotype ◽

Northern Sweden ◽

High Genetic Diversity ◽

Breeding Populations ◽

Ssr Loci

AbstractEfficient use of any breeding resources requires a good understanding of the genetic value of the founder breeding materials for predicting the gain and diversity in future generations. This study evaluates the distribution of genetic variation and level of relatedness among and within nine breeding populations of Norway spruce for Northern Sweden using nuclear microsatellite markers. A sample set of 456 individuals selected from 140 stands were genotyped with 15 SSR loci. Over all loci each individual was identified with unique multilocus genotype. High genetic diversity (average He=0.820) and low population differentiation (FST=0.0087) characterized this material. Although low in FST, the two northernmost populations were clustered as a distinct group diverged from the central populations. The population differentiation pattern corresponds well with the post glacial migration history of Norway spruce and the current gene flow and human activity in the region. The average inbreeding coefficient was 0.084 after removal loci with high frequency of null alleles. The estimated relatedness of the trees gathered in the breeding populations was very low (average kinship coefficient 0.0077) and not structured. The high genetic variation and low and not structured relatedness between individuals found in the breeding populations confirm that the Norway spruce breeding stock for northern Sweden represent valuable genetic resources for both long-term breeding and conservation programs.

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Population structure of the New Zealand whelk, Cominella glandiformis (Gastropoda: Buccinidae), suggests sporadic dispersal of a direct developer

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa033 ◽

2020 ◽

Vol 130 (1) ◽

pp. 49-60

Author(s):

Kirsten M Donald ◽

Graham A McCulloch ◽

Ludovic Dutoit ◽

Hamish G Spencer

Keyword(s):

Population Structure ◽

Gene Flow ◽

New Zealand ◽

Genetic Structure ◽

Geographic Area ◽

Null Alleles ◽

Phylogeographic Structure ◽

Large Geographic Area ◽

Oceanic Currents ◽

Minimal Evidence

Abstract We examined phylogeographic structure in the direct-developing New Zealand endemic intertidal mud whelk, Cominella glandiformis. Two hundred and ninety-six whelks from 12 sites were collected from sheltered shores around New Zealand’s four largest islands (North Island, South Island, Stewart Island and Chatham Island), encompassing the geographical range of this species. Despite being direct developers, gene flow among C. glandiformis populations may occur over short distances by adult floating, and over larger distances by rafting of egg masses. Primers were developed to amplify variable microsatellite regions at six loci. All loci were variable, with 8–34 alleles/loci. Observed and expected heterozygosities were high across all alleles, with minimal evidence of null alleles. The average number of alleles varied from 3.5 (Chatham Island) to 7.5 (Waitemata Harbour). Strong genetic structure was evident, with distinct ‘eastern’ and ‘western’ groups. Each group extended over a large geographic area, including regions of unsuitable habitat, but were linked by oceanic currents. We suggest that the intraspecific geographic genetic structure in C. glandiformis has arisen due a combination of ocean currents (promoting gene flow between geographically distant regions) and upwelling areas (limiting gene flow between certain regions).

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CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data

Bioinformatics ◽

10.1093/bioinformatics/btp499 ◽

2009 ◽

Vol 25 (20) ◽

pp. 2753-2754 ◽

Cited By ~ 7

Author(s):

S. Maenhout ◽

B. De Baets ◽

G. Haesaert

Keyword(s):

Software Tool ◽

Multilocus Genotype ◽

Genotype Data ◽

Coefficient Of Coancestry

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A new set of microsatellite loci for Cattleya walkeriana Gardner, an endangered tropical orchid species and its transferability to Cattleya loddigesii Lindl. and Cattleya nobilior Reichenbach

Plant Genetic Resources ◽

10.1017/s1479262117000193 ◽

2017 ◽

Vol 16 (3) ◽

pp. 284-287

Author(s):

Bruno C. Rossini ◽

Mariá B. Kampa ◽

Celso L. Marino ◽

Fernanda Bortolanza Pereira ◽

Fábio M. Alves ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Loci ◽

Null Alleles ◽

Germplasm Resources ◽

Significant Linkage Disequilibrium ◽

Orchid Species ◽

Expected Heterozygosity ◽

Tropical Orchid ◽

Significant Linkage

AbstractIn this study, we isolate and analyse a new set of microsatellite loci for Cattleya walkeriana. Twenty-two primer pairs were screened for C. walkeriana (n = 32) and assessed for their transferability to Cattleya loddigesii (n = 12) and Cattleya nobilior (n = 06). All loci amplified for C. walkeriana; however, for C. loddigesii and C. nobilior, four and five primers, respectively, did not present amplification. The polymorphic loci presented between 2 and 13 alleles per locus for both C. walkeriana and C. loddigesii, with respective averages of 5.1 and 4.2. For C. nobilior, we found between two and five alleles per locus, with an average of 2.6. For C. walkeriana, observed heterozygosity varied from 0.100 to 0.966, whereas expected heterozygosity ranged from 0.097 to 0.900. The observed and expected heterozygosity for C. loddigesii and C. nobilior were also estimated. We found no significant linkage disequilibrium between any pair of loci, and evidence of null alleles at four loci (Cw16, Cw24, Cw30 and Cw31) for C. walkeriana. The combined power to exclude the first parent and combined non-exclusion probability of identity were 0.999 and 2.3 × 10−20, respectively. These new loci can be used in studies of germplasm resources, and assessments of genotypic and genetic diversity and population structure, thus improving the accuracy of such analyses and their applicability in the conservation and protection of these endangered species.

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Population structure of group B streptococcus from a low-incidence region for invasive neonatal disease

Microbiology ◽

10.1099/mic.0.27826-0 ◽

2005 ◽

Vol 151 (6) ◽

pp. 1875-1881 ◽

Cited By ~ 36

Author(s):

Naiel Bisharat ◽

Nicola Jones ◽

Dror Marchaim ◽

Colin Block ◽

Rosalind M. Harding ◽

...

Keyword(s):

Population Structure ◽

Disease Incidence ◽

Group B Streptococcus ◽

Invasive Disease ◽

Multilocus Genotype ◽

Neonatal Disease ◽

Strain Collection ◽

Low Incidence ◽

Group B ◽

Sequence Types

The population structure of group B streptococcus (GBS) from a low-incidence region for invasive neonatal disease (Israel) was investigated using multilocus genotype data. The strain collection consisted of isolates from maternal carriage (n=104) and invasive neonatal disease (n=50), resolving into 46 sequence types. The most prevalent sequence types were ST-1 (17·5 %), ST-19 (10·4 %), ST-17 (9·7 %), ST-22 (8·4 %) and ST-23 (6·5 %). Serotype III was the most common, accounting for 29·2 % of the isolates. None of the serotypes was significantly associated with invasive neonatal disease. burst analysis resolved the 46 sequence types into seven lineages (clonal complexes), from which only lineage ST-17, expressing serotype III only, was significantly associated with invasive neonatal disease. Lineage ST-22 expressed mainly serotype II, and was significantly associated with carriage. The distribution of the various sequence types and lineages, and the association of lineage ST-17 with invasive disease, are consistent with the results of analyses from a global GBS isolate collection. These findings could imply that the global variation in disease incidence is independent of the circulating GBS populations, and may be more affected by other risk factors for invasive GBS disease, or by different prevention strategies.

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