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Population structure (genetics)

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1023: 983: 146: 982: 1482:, which seek to isolate and estimate the contribution of genetics to a trait by summing the effects of many individual genetic variants. To construct a score, researchers first enroll participants in an association study to estimate the contribution of each genetic variant. Then, they can use the estimated contributions of each genetic variant to calculate a score for the trait for an individual who was not in the original association study. If structure in the study population is correlated with environmental variation, then the polygenic score is no longer measuring the genetic component alone. 137:, or homogeneity in an ancestral population. Misspecification of such models, for instance by not taking into account the existence of structure in an ancestral population, can give rise to heavily biased parameter estimates. Simulation studies show that historical population structure can even have genetic effects that can easily be misinterpreted as historical changes in population size, or the existence of admixture events, even when no such events occurred. 4086: 1411:(UMAP) can visualize continental and subcontinental structure in human data. With larger datasets, UMAP better captures multiple scales of population structure; fine-scale patterns can be hidden or split with other methods, and these are of interest when the range of populations is diverse, when there are admixed populations, or when examining relationships between genotypes, phenotypes, and/or geography. 1532:. If environmental effects are related to a variant that exists in only one specific region (for example, a pollutant is found in only one city), it may not be possible to correct for this population structure effect at all. For many traits, the role of structure is complex and not fully understood, and incorporating it into genetic studies remains a challenge and is an active area of research. 976:, but rather an approximation considered useful for a given question. They are sensitive to sampling strategies, sample size, and close relatives in data sets; there may be no discrete populations at all; and there may be hierarchical structure where subpopulations are nested. Clusters may be admixed themselves, and may not have a useful interpretation as source populations. 60:) population, allele frequencies are expected to be roughly similar between groups. However, mating tends to be non-random to some degree, causing structure to arise. For example, a barrier like a river can separate two groups of the same species and make it difficult for potential mates to cross; if a 1026:
A map of the locations of genetic samples of several African populations (left) and principal components 1 and 2 of the data superimposed on the map (right). The principal coordinate plane has been rotated 16.11° to align with the map. It corresponds to the east–west and north–south distributions of
1435:. By exploiting this fact and matching shared haplotype chunks from individuals within a genetic dataset, researchers may trace and date the origins of population admixture and reconstruct historic events such as the rise and fall of empires, slave trades, colonialism, and population expansions. 1463:
as the genetic variant is simply more common in Asians than in Europeans. Also, actual genetic findings may be overlooked if the locus is less prevalent in the population where the case subjects are chosen. For this reason, it was common in the 1990s to use family-based data where the effect of
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Population structure is a complex phenomenon and no single measure captures it entirely. Understanding a population's structure requires a combination of methods and measures. Many statistical methods rely on simple population models in order to infer historical demographic changes, such as the
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Genetic variants do not necessarily cause observable changes in organisms, but can be correlated by coincidence because of population structure—a variant that is common in a population that has a high rate of disease may erroneously be thought to cause the disease. For this reason, population
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PCA and LMMs have become the most common methods to control for confounding from population structure. Though they are likely sufficient for avoiding false positives in association studies, they are still vulnerable to overestimating effect sizes of marginally associated variants and can
173:. The scale is important — an individual with both parents born in the United Kingdom is not inbred relative to that country's population, but is more inbred than two humans selected from the entire world. This motivates the derivation of Wright's 1375:
PCA transforms data to maximize variance; given enough data, when each individual is visualized as point on a plot, discrete clusters can form. Individuals with admixed ancestries will tend to fall between clusters, and when there is homogenous
124:, random chance, and (in humans) cultural factors. Even in lieu of these factors, individuals tend to stay close to where they were born, which means that alleles will not be distributed at random with respect to the full range of the species. 989: 900:
is 0, then the allele frequencies between populations are identical, suggesting no structure. The theoretical maximum value of 1 is attained when an allele reaches total fixation, but most observed maximum values are far lower.
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Sakaue S, Hirata J, Kanai M, Suzuki K, Akiyama M, Lai Too C, Arayssi T, Hammoudeh M, Al Emadi S, Masri BK, Halabi H, Badsha H, Uthman IW, Saxena R, Padyukov L, Hirata M, Matsuda K, Murakami Y, Kamatani Y, Okada Y (March 2020).
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for pairs of individuals, making PCA useful for inference about the population histories of groups in a given sample. PCA cannot, however, distinguish between different processes that lead to the same mean coalescent times.
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is one of the most common measures of population structure and there are several different formulations depending on the number of populations and the alleles of interest. Although it is sometimes used as a
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Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, et al. (February 2006). "A unified mixed-model method for association mapping that accounts for multiple levels of relatedness".
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A study of population structure of humans in Northern Africa and neighboring populations modelled using ADMIXTURE and assuming K=2,4,6,8 populations (Figure B, top to bottom). Varying
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will partition populations into finer subgroups. Though clustering methods are popular, they are open to misinterpretation: for non-simulated data, there is never a "true" value of
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Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (August 2006). "Principal components analysis corrects for stratification in genome-wide association studies".
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discrete clusters of populations. Each cluster is defined by the frequencies of its genotypes, and the contribution of a cluster to an individual's genotypes is measured via an
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within subpopulations, especially if the subpopulations are small or have been isolated for long periods. This reduction in heterozygosity can be thought of as an extension of
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Henn BM, Botigué LR, Gravel S, Wang W, Brisbin A, Byrnes JK, Fadhlaoui-Zid K, Zalloua PA, Moreno-Estrada A, Bertranpetit J, Bustamante CD, Comas D (January 2012).
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should be similar between groups. Population structure commonly arises from physical separation by distance or barriers, like mountains and rivers, followed by
1000:=2, 80% of the inferred ancestry for most North Africans is assigned to cluster that is common to Basque, Tuscan, and Qatari Arab individuals (in purple). At 3924: 3455: 770: 153:
can result in a loss of heterozygosity. In this hypothetical population, an allele has become fixed after the population repeatedly dropped from 10 to 3.
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Sohail M, Maier RM, Ganna A, Bloemendal A, Martin AR, Turchin MC, et al. (March 2019). Nordborg M, McCarthy MI, Barton NH, Hermisson J (eds.).
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can generate artificial genotypes with structure representative of the input data, though they do not recreate linkage disequilibrium patterns.
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Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR, Stephens M, Bustamante CD (2008).
3949: 1283: 1807:"The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure" 17: 133:
presence of population bottlenecks, admixture events or population divergence times. Often these methods rely on the assumption of
2706:"Dimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction" 4071: 3705: 3563: 1427:. Events like migrations and interactions between groups leave a genetic imprint on populations. Admixed populations will have 64:
occurs, over many generations it can spread and become common in one subpopulation while being completely absent in the other.
3460: 145: 3929: 1460: 563: 1595: 3773: 180:(also called "fixation indices"), which measure inbreeding through observed versus expected heterozygosity. For example, 3944: 3738: 469: 3297:"Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies" 3405: 1868: 256: 2145:
Novembre J, Ramachandran S (2011). "Perspectives on human population structure at the cusp of the sequencing era".
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could be incorrect. As an example, in a study population of Europeans and East Asians, an association study of
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for populations, though later it was found that by coding SNPs as integers (for example, as the number of
3480: 1517: 1032: 2290:"A quantitative comparison of the similarity between genes and geography in worldwide human populations" 3778: 2339:
Menozzi P, Piazza A, Cavalli-Sforza L (1978). "Synthetic maps of human gene frequencies in Europeans".
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usage may "discover" a gene in the Asian individuals that leads to chopstick use. However, this is a
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Cardon LR, Palmer LJ (February 2003). "Population stratification and spurious allelic association".
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have been used to study differentiation, population assignment, and to analyze genetic distances.
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for the entire human population will subdivide people roughly by continent, while using large
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RodrĂ­guez W, Mazet O, Grusea S, Arredondo A, Corujo JM, Boitard S, Chikhi L (December 2018).
1432: 1396: 1377: 1142: 942: 150: 121: 113: 2912:"Use of unlinked genetic markers to detect population stratification in association studies" 2614:
Li W, Cerise JE, Yang Y, Han H (August 2017). "Application of t-SNE to human genetic data".
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Lawson DJ, Davies NM, Haworth S, Ashraf B, Howe L, Crawford A, et al. (January 2020).
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Hellenthal G, Busby GB, Band G, Wilson JF, Capelli C, Falush D, Myers S (February 2014).
1758:"Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?" 1756:
Scerri EM, Thomas MG, Manica A, Gunz P, Stock JT, Stringer C, et al. (August 2018).
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subpopulations, which are assumed to be unstructured. More recent approaches make use of
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Several methods can at least partially control for this confounding effect. The
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chunks from their ancestral groups, which gradually shrink over time because of
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Devlin B, Roeder K (December 1999). "Genomic control for association studies".
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between groups: if all individuals within a population mate randomly, then the
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Zaidi AA, Mathieson I (November 2020). Perry GH, Turchin MC, Martin P (eds.).
2627: 1982: 1822: 80:(GWAS). By tracing the origins of structure, it is also possible to study the 4104: 3627: 3617: 3573: 2533: 2474: 2368: 2205: 2106: 2049: 1990: 1913: 1726: 1664: 1452: 105: 97: 2835: 2652:
Diaz-Papkovich A, Anderson-Trocmé L, Ben-Eghan C, Gravel S (November 2019).
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population structure can easily be controlled for using methods such as the
1008:=6, opposite clines of Near Eastern (Qatari) ancestry appear (in green). At 3990: 3870: 3643: 3495: 3381: 3332: 3281: 3230: 3169: 3126: 3091: 3034: 2999: 2945: 2888: 2853: 2796: 2747: 2689: 2635: 2592: 2551: 2492: 2427: 2360: 2325: 2274: 2223: 2166: 2124: 2067: 2008: 1921: 1840: 1791: 1734: 1682: 1633:"A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots" 1569: 1529: 174: 2880: 2098: 3970: 2583: 2566: 2376: 1858: 1521: 1513: 1381: 3313: 3262: 2980: 2466: 210:
measures the inbreeding coefficient at a single locus for an individual
3975: 3844: 3824: 3799: 2239:"Genomic ancestry of North Africans supports back-to-Africa migrations" 1591: 1380:
in the data, the top PC vectors will reflect geographic variation. The
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can illustrate different scales of population structure; using a small
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studies, and accounting for and controlling its effect is important in
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introduced the STRUCTURE algorithm to estimate these proportions via
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allowing us to compute the expected heterozygosity of subpopulation
4015: 3985: 3829: 3819: 3747: 3190: 3161: 3118: 3073: 2927: 161:. When populations split, alleles have a higher chance of reaching 134: 61: 53: 3055: 2083:"Fast model-based estimation of ancestry in unrelated individuals" 2024:"Inference of Population Structure Using Multilocus Genotype Data" 169:, with individuals in subpopulations being more likely to share a 27:
Stratification of a genetic population based on allele frequencies
1365:{\displaystyle {\frac {g_{i,l}-2p_{l}}{\sqrt {2p_{l}(1-p_{l})}}}} 3056:
Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (July 2000).
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Hamer D, Sirota L (January 2000). "Beware the chopsticks gene".
2763:"Visualizing population structure with variational autoencoders" 2508:"A Genealogical Interpretation of Principal Components Analysis" 1423:
Population structure is an important aspect of evolutionary and
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generated by PCA can be explicitly written in terms of the mean
1004:=4, clines of North African ancestry appear (in light blue). At 3839: 3814: 42: 3104: 1804: 1504:
to estimate each individual's ancestry proportions from some
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One of the results of population structure is a reduction in
2567:"Genetic markers in the playground of multivariate analysis" 1520:(also called a kinship matrix) and including it in a linear 446:, it is expected that under random mating the subpopulation 3716: 2338: 2182:"Pritchard, Stephens, and Donnelly on Population Structure" 2140: 2138: 2136: 2134: 1892:
Wright S (1949). "The Genetical Structure of Populations".
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substantially bias estimates of polygenic scores and trait
3294: 2440: 1451:, where the association between the trait of interest and 1043:(PCA) was first applied in population genetics in 1978 by 3809: 3804: 3345: 2964:"How well can we separate genetics from the environment?" 2809: 2021: 1701:"Assessing population structure:FST and related measures" 2131: 1051:. Initially PCA was used on allele frequencies at known 1012:=8, Tunisian Berbers appear as a cluster (in dark blue). 3147: 2702: 1967:"FST and the triangle inequality for biallelic markers" 366:
that are heterozygous. Assuming there are two alleles,
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Loh PR, Tucker G, Bulik-Sullivan BK, Vilhjálmsson BJ,
2080: 1755: 2236: 2074: 2015: 1958: 1694: 1692: 1286: 1257: 1230: 1210: 1178: 1145: 1125: 1105: 1085: 1065: 773: 740: 720: 667: 647: 631:{\displaystyle F_{IS}=1-{\frac {H_{I}}{2p_{S}q_{S}}}} 566: 472: 452: 412: 372: 352: 325: 259: 236: 216: 186: 2647: 2645: 2564: 2287: 2144: 1630: 1626: 1624: 1622: 949:, modelling allele frequencies at each locus with a 913:
between populations, it does not always satisfy the
2434: 2389: 2909: 1689: 1489:method was introduced in 1999 and is a relatively 1364: 1269: 1243: 1216: 1196: 1164: 1131: 1111: 1091: 1071: 885: 756: 726: 706: 653: 630: 549: 458: 438: 398: 358: 338: 308: 242: 222: 202: 3006: 2760: 2642: 2332: 1964: 1619: 550:{\displaystyle H_{S}=2p_{S}(1-p_{S})=2p_{S}q_{S}} 4102: 2390:Patterson N, Price AL, Reich D (December 2006). 346:is the fraction of individuals in subpopulation 41:) is the presence of a systematic difference in 3058:"Association mapping in structured populations" 2761:Battey CJ, Coffing GC, Kern AD (January 2021). 2613: 2288:Wang C, Zöllner S, Rosenberg NA (August 2012). 1698: 1438: 1172:is the number of non-reference alleles (one of 929:An individual's genotype can be modelled as an 309:{\displaystyle F_{IS}=1-{\frac {H_{I}}{H_{S}}}} 3243: 2803: 2565:Jombart T, Pontier D, Dufour AB (April 2009). 3732: 3406: 2022:Pritchard JK, Stephens M, Donnelly P (2000). 1409:uniform manifold approximation and projection 1039:techniques can capture population structure. 3012: 2957: 2955: 2812:"A genetic atlas of human admixture history" 2607: 2173: 1852: 1850: 1547: 1277:matrix of normalized genotypes has entries: 2866: 2558: 1405:t-distributed stochastic neighbor embedding 1017: 92:The basic cause of population structure in 3739: 3725: 3413: 3399: 3339: 3288: 2754: 2696: 2499: 2081:Alexander DH, Novembre J, Lange K (2009). 1945: 1943: 1941: 1939: 1937: 1935: 1933: 1931: 1856: 1443:Population structure can be a problem for 3371: 3322: 3312: 3271: 3261: 3237: 3220: 3081: 2989: 2979: 2961: 2952: 2935: 2843: 2786: 2737: 2679: 2669: 2582: 2541: 2523: 2482: 2417: 2407: 2315: 2305: 2264: 2254: 2213: 2114: 2057: 2039: 1998: 1885: 1847: 1830: 1781: 1716: 1672: 2910:Pritchard JK, Rosenberg NA (July 1999). 2392:"Population structure and eigenanalysis" 2281: 2230: 2179: 1631:Lawson DJ, van Dorp L, Falush D (2018). 1493:method for controlling the inflation of 1418: 1021: 144: 4072:List of genetics research organizations 3420: 1928: 14: 4103: 3706:Index of evolutionary biology articles 3195:, Salem RM, et al. (March 2015). 2505: 2443:"Genes mirror geography within Europe" 1891: 1590: 1478:. These traits can be predicted using 924: 3720: 3394: 1099:bi-allelic SNPs. For each individual 406:that occur at respective frequencies 1952:Population and Quantitative Genetics 1949: 996:changes the scale of clustering. At 641:Similarly, for the total population 2159:10.1146/annurev-genom-090810-183123 466:will have a heterozygosity rate of 24: 3062:American Journal of Human Genetics 2962:Blanc J, Berg JJ (December 2020). 2916:American Journal of Human Genetics 1965:Arbisser IM, Rosenberg NA (2020). 1906:10.1111/j.1469-1809.1949.tb02451.x 25: 4132: 1860:Principles of population genetics 1762:Trends in Ecology & Evolution 1516:and colleagues, or by deriving a 1047:and colleagues and resurged with 707:{\displaystyle H_{T}=2p_{T}q_{T}} 140: 4085: 4084: 3027:10.1111/j.0006-341X.1999.00997.x 1718:10.1111/j.1755-0998.2010.02927.x 1699:Meirmans PG, Hedrick PW (2010). 1466:transmission disequilibrium test 981: 3184: 3141: 3098: 3049: 2903: 2860: 2383: 230:relative to some subpopulation 78:genome wide association studies 3506:Constructive neutral evolution 1971:Theoretical Population Biology 1798: 1749: 1584: 1541: 1356: 1337: 1204:). If the allele frequency at 518: 499: 87: 13: 1: 1562:10.1016/S0140-6736(03)12520-2 1535: 1497:. It is also possible to use 4031:Missing heritability problem 3746: 3456:Fisher's fundamental theorem 2671:10.1371/journal.pgen.1008432 2525:10.1371/journal.pgen.1000686 2409:10.1371/journal.pgen.0020190 2307:10.1371/journal.pgen.1002886 2256:10.1371/journal.pgen.1002397 1510:principal component analysis 1439:Role in genetic epidemiology 1041:Principal component analysis 7: 3481:Coefficient of relationship 2198:10.1534/genetics.116.195164 2147:Annu Rev Genomics Hum Genet 1857:Hartl DL, Clark AG (1997). 1705:Molecular Ecology Resources 1518:genetic relationship matrix 439:{\displaystyle p_{S},q_{S}} 399:{\displaystyle A_{1},A_{2}} 127: 84:of groups and individuals. 10: 4137: 3364:10.1007/s00439-019-02014-8 2730:10.1038/s41467-020-15194-z 2041:10.1093/genetics/155.2.945 1774:10.1016/j.tree.2018.05.005 1657:10.1038/s41467-018-05257-7 1512:(PCA), as demonstrated by 1049:high-throughput sequencing 4080: 4059: 3958: 3909: 3853: 3792: 3754: 3701: 3636: 3610: 3572: 3547: 3514: 3476:Coefficient of inbreeding 3428: 2779:10.1093/g3journal/jkaa036 2628:10.1142/S0219720017500172 1983:10.1016/j.tpb.2019.05.003 1823:10.1038/s41437-018-0148-0 1270:{\displaystyle N\times S} 39:population stratification 18:Population stratification 3654:Evolutionary game theory 3436:Hardy–Weinberg principle 1413:Variational autoencoders 1393:Multidimensional scaling 1037:dimensionality reduction 1018:Dimensionality reduction 947:Markov chain Monte Carlo 3466:Shifting balance theory 2836:10.1126/science.1243518 2616:J Bioinform Comput Biol 1165:{\displaystyle g_{i,l}} 108:. Other causes include 3451:Linkage disequilibrium 2361:10.1126/science.356262 1596:"Population Structure" 1366: 1271: 1245: 1218: 1198: 1166: 1133: 1113: 1093: 1073: 1028: 951:Dirichlet distribution 887: 758: 757:{\displaystyle F_{ST}} 728: 708: 655: 632: 551: 460: 440: 400: 360: 340: 310: 244: 224: 204: 203:{\displaystyle F_{IS}} 171:recent common ancestor 154: 114:population bottlenecks 68:structure is a common 4067:List of genetic codes 3693:Quantitative genetics 3602:Balding–Nichols model 3587:Population bottleneck 3582:Small population size 3486:Selection coefficient 2881:10.1038/sj.mp.4000662 2099:10.1101/gr.094052.109 1637:Nature Communications 1476:genes and environment 1461:spurious relationship 1419:Demographic inference 1397:discriminant analysis 1378:isolation by distance 1367: 1272: 1251:, then the resulting 1246: 1244:{\displaystyle p_{l}} 1219: 1199: 1197:{\displaystyle 0,1,2} 1167: 1134: 1119:, the value at locus 1114: 1094: 1074: 1057:non-reference alleles 1025: 943:Jonathan K. Pritchard 888: 759: 729: 709: 656: 633: 552: 461: 441: 401: 361: 341: 339:{\displaystyle H_{I}} 311: 245: 225: 205: 151:population bottleneck 148: 122:evolutionary pressure 4111:Genetic epidemiology 3966:Behavioural genetics 3564:Background selection 3551:on genomic variation 3549:Effects of selection 3501:Population structure 2869:Molecular Psychiatry 2584:10.1038/hdy.2008.130 1449:case-control studies 1284: 1255: 1228: 1208: 1176: 1143: 1123: 1103: 1083: 1063: 771: 738: 718: 665: 645: 564: 470: 450: 410: 370: 350: 323: 257: 234: 214: 184: 94:sexually reproducing 70:confounding variable 31:Population structure 4121:Population genetics 4046:Population genomics 4036:Molecular evolution 3996:Genetic engineering 3683:Population genomics 3559:Genetic hitchhiking 3446:Identity by descent 3422:Population genetics 3314:10.7554/eLife.39702 3263:10.7554/eLife.61548 2981:10.7554/eLife.64948 2828:2014Sci...343..747H 2722:2020NatCo..11.1569S 2467:10.1038/nature07331 2459:2008Natur.456...98N 2353:1978Sci...201..786M 2180:Novembre J (2016). 1649:2018NatCo...9.3258L 1445:association studies 1425:population genetics 925:Admixture inference 915:triangle inequality 4006:Genetic monitoring 3669:Landscape genetics 1894:Annals of Eugenics 1401:Neighborhood graph 1362: 1267: 1241: 1214: 1194: 1162: 1129: 1109: 1089: 1069: 1029: 917:and thus is not a 883: 754: 724: 704: 651: 628: 547: 456: 436: 396: 356: 336: 306: 240: 220: 200: 155: 102:allele frequencies 4098: 4097: 4021:He Jiankui affair 4011:Genetic genealogy 4001:Genetic diversity 3930:the British Isles 3835:Genetic variation 3714: 3713: 3664:Genetic genealogy 3659:Fitness landscape 2822:(6172): 747–751. 2506:McVean G (2009). 2347:(4358): 786–792. 1954:. pp. 22–44. 1556:(9357): 598–604. 1360: 1359: 1217:{\displaystyle l} 1132:{\displaystyle l} 1112:{\displaystyle i} 1092:{\displaystyle S} 1072:{\displaystyle N} 1031:Genetic data are 881: 818: 727:{\displaystyle S} 654:{\displaystyle T} 626: 459:{\displaystyle S} 359:{\displaystyle S} 304: 243:{\displaystyle S} 223:{\displaystyle I} 112:from migrations, 98:non-random mating 35:genetic structure 16:(Redirected from 4128: 4116:Medical genetics 4088: 4087: 4051:Reverse genetics 4026:Medical genetics 3741: 3734: 3727: 3718: 3717: 3623:J. B. S. Haldane 3415: 3408: 3401: 3392: 3391: 3386: 3385: 3375: 3343: 3337: 3336: 3326: 3316: 3292: 3286: 3285: 3275: 3265: 3241: 3235: 3234: 3224: 3188: 3182: 3181: 3145: 3139: 3138: 3102: 3096: 3095: 3085: 3053: 3047: 3046: 3010: 3004: 3003: 2993: 2983: 2959: 2950: 2949: 2939: 2907: 2901: 2900: 2864: 2858: 2857: 2847: 2807: 2801: 2800: 2790: 2758: 2752: 2751: 2741: 2700: 2694: 2693: 2683: 2673: 2664:(11): e1008432. 2649: 2640: 2639: 2611: 2605: 2604: 2586: 2571:Heredity (Edinb) 2562: 2556: 2555: 2545: 2527: 2518:(10): e1000686. 2503: 2497: 2496: 2486: 2453:(7218): 98–101. 2438: 2432: 2431: 2421: 2411: 2387: 2381: 2380: 2336: 2330: 2329: 2319: 2309: 2285: 2279: 2278: 2268: 2258: 2234: 2228: 2227: 2217: 2177: 2171: 2170: 2142: 2129: 2128: 2118: 2093:(9): 1655–1664. 2078: 2072: 2071: 2061: 2043: 2019: 2013: 2012: 2002: 1962: 1956: 1955: 1947: 1926: 1925: 1889: 1883: 1882: 1854: 1845: 1844: 1834: 1802: 1796: 1795: 1785: 1753: 1747: 1746: 1720: 1696: 1687: 1686: 1676: 1628: 1617: 1616: 1614: 1613: 1607: 1601:. Archived from 1600: 1588: 1582: 1581: 1545: 1480:polygenic scores 1403:approaches like 1386:coalescent times 1371: 1369: 1368: 1363: 1361: 1355: 1354: 1336: 1335: 1323: 1322: 1321: 1320: 1305: 1304: 1288: 1276: 1274: 1273: 1268: 1250: 1248: 1247: 1242: 1240: 1239: 1223: 1221: 1220: 1215: 1203: 1201: 1200: 1195: 1171: 1169: 1168: 1163: 1161: 1160: 1138: 1136: 1135: 1130: 1118: 1116: 1115: 1110: 1098: 1096: 1095: 1090: 1079:individuals and 1078: 1076: 1075: 1070: 1033:high dimensional 1027:the populations. 985: 911:genetic distance 892: 890: 889: 884: 882: 880: 879: 878: 869: 868: 855: 854: 853: 844: 843: 830: 819: 817: 816: 807: 806: 797: 786: 785: 763: 761: 760: 755: 753: 752: 733: 731: 730: 725: 713: 711: 710: 705: 703: 702: 693: 692: 677: 676: 661:, we can define 660: 658: 657: 652: 637: 635: 634: 629: 627: 625: 624: 623: 614: 613: 600: 599: 590: 579: 578: 556: 554: 553: 548: 546: 545: 536: 535: 517: 516: 498: 497: 482: 481: 465: 463: 462: 457: 445: 443: 442: 437: 435: 434: 422: 421: 405: 403: 402: 397: 395: 394: 382: 381: 365: 363: 362: 357: 345: 343: 342: 337: 335: 334: 315: 313: 312: 307: 305: 303: 302: 293: 292: 283: 272: 271: 249: 247: 246: 241: 229: 227: 226: 221: 209: 207: 206: 201: 199: 198: 116:and expansions, 82:genetic ancestry 74:medical genetics 21: 4136: 4135: 4131: 4130: 4129: 4127: 4126: 4125: 4101: 4100: 4099: 4094: 4076: 4055: 3954: 3945:the Middle East 3911:Archaeogenetics 3905: 3849: 3788: 3750: 3745: 3715: 3710: 3697: 3632: 3606: 3568: 3552: 3550: 3543: 3510: 3441:Genetic linkage 3424: 3419: 3389: 3344: 3340: 3293: 3289: 3242: 3238: 3213:10.1038/ng.3190 3201:Nature Genetics 3189: 3185: 3150:Nature Genetics 3146: 3142: 3107:Nature Genetics 3103: 3099: 3054: 3050: 3021:(4): 997–1004. 3011: 3007: 2960: 2953: 2908: 2904: 2865: 2861: 2808: 2804: 2759: 2755: 2701: 2697: 2650: 2643: 2612: 2608: 2563: 2559: 2504: 2500: 2439: 2435: 2388: 2384: 2337: 2333: 2300:(8): e1002886. 2286: 2282: 2249:(1): e1002397. 2235: 2231: 2178: 2174: 2143: 2132: 2087:Genome Research 2079: 2075: 2020: 2016: 1963: 1959: 1950:Coop G (2019). 1948: 1929: 1890: 1886: 1871: 1855: 1848: 1803: 1799: 1754: 1750: 1697: 1690: 1629: 1620: 1611: 1609: 1605: 1598: 1589: 1585: 1546: 1542: 1538: 1502:genetic markers 1495:test statistics 1487:genomic control 1441: 1421: 1350: 1346: 1331: 1327: 1316: 1312: 1294: 1290: 1289: 1287: 1285: 1282: 1281: 1256: 1253: 1252: 1235: 1231: 1229: 1226: 1225: 1209: 1206: 1205: 1177: 1174: 1173: 1150: 1146: 1144: 1141: 1140: 1124: 1121: 1120: 1104: 1101: 1100: 1084: 1081: 1080: 1064: 1061: 1060: 1053:genetic markers 1020: 1015: 1014: 1013: 991: 986: 927: 906: 874: 870: 864: 860: 856: 849: 845: 839: 835: 831: 829: 812: 808: 802: 798: 796: 778: 774: 772: 769: 768: 745: 741: 739: 736: 735: 719: 716: 715: 698: 694: 688: 684: 672: 668: 666: 663: 662: 646: 643: 642: 619: 615: 609: 605: 601: 595: 591: 589: 571: 567: 565: 562: 561: 541: 537: 531: 527: 512: 508: 493: 489: 477: 473: 471: 468: 467: 451: 448: 447: 430: 426: 417: 413: 411: 408: 407: 390: 386: 377: 373: 371: 368: 367: 351: 348: 347: 330: 326: 324: 321: 320: 298: 294: 288: 284: 282: 264: 260: 258: 255: 254: 235: 232: 231: 215: 212: 211: 191: 187: 185: 182: 181: 143: 130: 118:founder effects 90: 54:randomly mating 28: 23: 22: 15: 12: 11: 5: 4134: 4124: 4123: 4118: 4113: 4096: 4095: 4093: 4092: 4081: 4078: 4077: 4075: 4074: 4069: 4063: 4061: 4057: 4056: 4054: 4053: 4048: 4043: 4041:Plant genetics 4038: 4033: 4028: 4023: 4018: 4013: 4008: 4003: 3998: 3993: 3988: 3983: 3981:Genome editing 3978: 3973: 3968: 3962: 3960: 3959:Related topics 3956: 3955: 3953: 3952: 3947: 3942: 3937: 3932: 3927: 3922: 3916: 3914: 3907: 3906: 3904: 3903: 3898: 3893: 3888: 3883: 3881:Immunogenetics 3878: 3873: 3868: 3863: 3857: 3855: 3851: 3850: 3848: 3847: 3842: 3837: 3832: 3827: 3822: 3817: 3812: 3807: 3802: 3796: 3794: 3793:Key components 3790: 3789: 3787: 3786: 3781: 3776: 3771: 3766: 3761: 3755: 3752: 3751: 3744: 3743: 3736: 3729: 3721: 3712: 3711: 3709: 3708: 3702: 3699: 3698: 3696: 3695: 3690: 3688:Phylogeography 3685: 3680: 3678:Microevolution 3675: 3666: 3661: 3656: 3651: 3646: 3640: 3638: 3637:Related topics 3634: 3633: 3631: 3630: 3625: 3620: 3614: 3612: 3608: 3607: 3605: 3604: 3599: 3594: 3592:Founder effect 3589: 3584: 3578: 3576: 3570: 3569: 3567: 3566: 3561: 3555: 3553: 3548: 3545: 3544: 3542: 3541: 3536: 3531: 3526: 3520: 3518: 3512: 3511: 3509: 3508: 3503: 3498: 3493: 3488: 3483: 3478: 3473: 3471:Price equation 3468: 3463: 3461:Neutral theory 3458: 3453: 3448: 3443: 3438: 3432: 3430: 3426: 3425: 3418: 3417: 3410: 3403: 3395: 3388: 3387: 3352:Human Genetics 3338: 3287: 3236: 3183: 3162:10.1038/ng1702 3140: 3119:10.1038/ng1847 3097: 3074:10.1086/302959 3048: 3005: 2951: 2928:10.1086/302449 2902: 2859: 2802: 2753: 2695: 2641: 2622:(4): 1750017. 2606: 2557: 2498: 2433: 2382: 2331: 2280: 2229: 2192:(2): 391–393. 2172: 2130: 2073: 2034:(2): 945–959. 2014: 1957: 1927: 1900:(1): 323–354. 1884: 1869: 1846: 1817:(6): 663–678. 1797: 1768:(8): 582–594. 1748: 1688: 1618: 1583: 1539: 1537: 1534: 1440: 1437: 1420: 1417: 1373: 1372: 1358: 1353: 1349: 1345: 1342: 1339: 1334: 1330: 1326: 1319: 1315: 1311: 1308: 1303: 1300: 1297: 1293: 1266: 1263: 1260: 1238: 1234: 1213: 1193: 1190: 1187: 1184: 1181: 1159: 1156: 1153: 1149: 1128: 1108: 1088: 1068: 1045:Cavalli-Sforza 1019: 1016: 988: 987: 980: 979: 978: 926: 923: 904: 894: 893: 877: 873: 867: 863: 859: 852: 848: 842: 838: 834: 828: 825: 822: 815: 811: 805: 801: 795: 792: 789: 784: 781: 777: 751: 748: 744: 734:and the value 723: 701: 697: 691: 687: 683: 680: 675: 671: 650: 639: 638: 622: 618: 612: 608: 604: 598: 594: 588: 585: 582: 577: 574: 570: 544: 540: 534: 530: 526: 523: 520: 515: 511: 507: 504: 501: 496: 492: 488: 485: 480: 476: 455: 433: 429: 425: 420: 416: 393: 389: 385: 380: 376: 355: 333: 329: 317: 316: 301: 297: 291: 287: 281: 278: 275: 270: 267: 263: 239: 219: 197: 194: 190: 159:heterozygosity 142: 141:Heterozygosity 139: 129: 126: 89: 86: 50:subpopulations 26: 9: 6: 4: 3: 2: 4133: 4122: 4119: 4117: 4114: 4112: 4109: 4108: 4106: 4091: 4083: 4082: 4079: 4073: 4070: 4068: 4065: 4064: 4062: 4058: 4052: 4049: 4047: 4044: 4042: 4039: 4037: 4034: 4032: 4029: 4027: 4024: 4022: 4019: 4017: 4014: 4012: 4009: 4007: 4004: 4002: 3999: 3997: 3994: 3992: 3989: 3987: 3984: 3982: 3979: 3977: 3974: 3972: 3969: 3967: 3964: 3963: 3961: 3957: 3951: 3948: 3946: 3943: 3941: 3938: 3936: 3933: 3931: 3928: 3926: 3923: 3921: 3918: 3917: 3915: 3912: 3908: 3902: 3899: 3897: 3894: 3892: 3889: 3887: 3884: 3882: 3879: 3877: 3874: 3872: 3869: 3867: 3864: 3862: 3859: 3858: 3856: 3852: 3846: 3843: 3841: 3838: 3836: 3833: 3831: 3828: 3826: 3823: 3821: 3818: 3816: 3813: 3811: 3808: 3806: 3803: 3801: 3798: 3797: 3795: 3791: 3785: 3782: 3780: 3777: 3775: 3772: 3770: 3767: 3765: 3762: 3760: 3757: 3756: 3753: 3749: 3742: 3737: 3735: 3730: 3728: 3723: 3722: 3719: 3707: 3704: 3703: 3700: 3694: 3691: 3689: 3686: 3684: 3681: 3679: 3676: 3674: 3670: 3667: 3665: 3662: 3660: 3657: 3655: 3652: 3650: 3647: 3645: 3642: 3641: 3639: 3635: 3629: 3628:Sewall Wright 3626: 3624: 3621: 3619: 3616: 3615: 3613: 3609: 3603: 3600: 3598: 3595: 3593: 3590: 3588: 3585: 3583: 3580: 3579: 3577: 3575: 3574:Genetic drift 3571: 3565: 3562: 3560: 3557: 3556: 3554: 3546: 3540: 3537: 3535: 3532: 3530: 3527: 3525: 3522: 3521: 3519: 3517: 3513: 3507: 3504: 3502: 3499: 3497: 3494: 3492: 3489: 3487: 3484: 3482: 3479: 3477: 3474: 3472: 3469: 3467: 3464: 3462: 3459: 3457: 3454: 3452: 3449: 3447: 3444: 3442: 3439: 3437: 3434: 3433: 3431: 3427: 3423: 3416: 3411: 3409: 3404: 3402: 3397: 3396: 3393: 3383: 3379: 3374: 3369: 3365: 3361: 3357: 3353: 3349: 3342: 3334: 3330: 3325: 3320: 3315: 3310: 3306: 3302: 3298: 3291: 3283: 3279: 3274: 3269: 3264: 3259: 3255: 3251: 3247: 3240: 3232: 3228: 3223: 3218: 3214: 3210: 3207:(3): 284–90. 3206: 3202: 3198: 3194: 3187: 3179: 3175: 3171: 3167: 3163: 3159: 3155: 3151: 3144: 3136: 3132: 3128: 3124: 3120: 3116: 3112: 3108: 3101: 3093: 3089: 3084: 3079: 3075: 3071: 3068:(1): 170–81. 3067: 3063: 3059: 3052: 3044: 3040: 3036: 3032: 3028: 3024: 3020: 3016: 3009: 3001: 2997: 2992: 2987: 2982: 2977: 2973: 2969: 2965: 2958: 2956: 2947: 2943: 2938: 2933: 2929: 2925: 2921: 2917: 2913: 2906: 2898: 2894: 2890: 2886: 2882: 2878: 2874: 2870: 2863: 2855: 2851: 2846: 2841: 2837: 2833: 2829: 2825: 2821: 2817: 2813: 2806: 2798: 2794: 2789: 2784: 2780: 2776: 2772: 2768: 2767:G3 (Bethesda) 2764: 2757: 2749: 2745: 2740: 2735: 2731: 2727: 2723: 2719: 2715: 2711: 2707: 2699: 2691: 2687: 2682: 2677: 2672: 2667: 2663: 2659: 2655: 2648: 2646: 2637: 2633: 2629: 2625: 2621: 2617: 2610: 2602: 2598: 2594: 2590: 2585: 2580: 2577:(4): 330–41. 2576: 2572: 2568: 2561: 2553: 2549: 2544: 2539: 2535: 2531: 2526: 2521: 2517: 2513: 2512:PLOS Genetics 2509: 2502: 2494: 2490: 2485: 2480: 2476: 2472: 2468: 2464: 2460: 2456: 2452: 2448: 2444: 2437: 2429: 2425: 2420: 2415: 2410: 2405: 2401: 2397: 2396:PLOS Genetics 2393: 2386: 2378: 2374: 2370: 2366: 2362: 2358: 2354: 2350: 2346: 2342: 2335: 2327: 2323: 2318: 2313: 2308: 2303: 2299: 2295: 2291: 2284: 2276: 2272: 2267: 2262: 2257: 2252: 2248: 2244: 2240: 2233: 2225: 2221: 2216: 2211: 2207: 2203: 2199: 2195: 2191: 2187: 2183: 2176: 2168: 2164: 2160: 2156: 2153:(1): 245–74. 2152: 2148: 2141: 2139: 2137: 2135: 2126: 2122: 2117: 2112: 2108: 2104: 2100: 2096: 2092: 2088: 2084: 2077: 2069: 2065: 2060: 2055: 2051: 2047: 2042: 2037: 2033: 2029: 2025: 2018: 2010: 2006: 2001: 1996: 1992: 1988: 1984: 1980: 1976: 1972: 1968: 1961: 1953: 1946: 1944: 1942: 1940: 1938: 1936: 1934: 1932: 1923: 1919: 1915: 1911: 1907: 1903: 1899: 1895: 1888: 1880: 1876: 1872: 1870:0-87893-306-9 1866: 1862: 1861: 1853: 1851: 1842: 1838: 1833: 1828: 1824: 1820: 1816: 1812: 1808: 1801: 1793: 1789: 1784: 1779: 1775: 1771: 1767: 1763: 1759: 1752: 1744: 1740: 1736: 1732: 1728: 1724: 1719: 1714: 1710: 1706: 1702: 1695: 1693: 1684: 1680: 1675: 1670: 1666: 1662: 1658: 1654: 1650: 1646: 1642: 1638: 1634: 1627: 1625: 1623: 1608:on 2018-11-23 1604: 1597: 1593: 1587: 1579: 1575: 1571: 1567: 1563: 1559: 1555: 1551: 1544: 1540: 1533: 1531: 1525: 1523: 1519: 1515: 1511: 1507: 1503: 1500: 1496: 1492: 1491:nonparametric 1488: 1483: 1481: 1477: 1473: 1469: 1467: 1462: 1458: 1454: 1450: 1446: 1436: 1434: 1433:recombination 1430: 1426: 1416: 1414: 1410: 1406: 1402: 1398: 1394: 1390: 1387: 1383: 1379: 1351: 1347: 1343: 1340: 1332: 1328: 1324: 1317: 1313: 1309: 1306: 1301: 1298: 1295: 1291: 1280: 1279: 1278: 1264: 1261: 1258: 1236: 1232: 1211: 1191: 1188: 1185: 1182: 1179: 1157: 1154: 1151: 1147: 1126: 1106: 1086: 1066: 1058: 1054: 1050: 1046: 1042: 1038: 1034: 1024: 1011: 1007: 1003: 999: 995: 990: 984: 977: 975: 971: 967: 963: 958: 957:populations. 956: 952: 948: 944: 940: 936: 932: 922: 920: 916: 912: 907: 899: 875: 871: 865: 861: 857: 850: 846: 840: 836: 832: 826: 823: 820: 813: 809: 803: 799: 793: 790: 787: 782: 779: 775: 767: 766: 765: 749: 746: 742: 721: 699: 695: 689: 685: 681: 678: 673: 669: 648: 620: 616: 610: 606: 602: 596: 592: 586: 583: 580: 575: 572: 568: 560: 559: 558: 542: 538: 532: 528: 524: 521: 513: 509: 505: 502: 494: 490: 486: 483: 478: 474: 453: 431: 427: 423: 418: 414: 391: 387: 383: 378: 374: 353: 331: 327: 299: 295: 289: 285: 279: 276: 273: 268: 265: 261: 253: 252: 251: 237: 217: 195: 192: 188: 179: 177: 172: 168: 164: 160: 152: 147: 138: 136: 125: 123: 119: 115: 111: 107: 106:genetic drift 103: 99: 95: 85: 83: 79: 75: 71: 65: 63: 59: 55: 51: 47: 44: 40: 36: 33:(also called 32: 19: 3991:Genetic code 3925:the Americas 3901:Quantitative 3871:Cytogenetics 3866:Conservation 3759:Introduction 3644:Biogeography 3618:R. A. Fisher 3500: 3496:Heritability 3429:Key concepts 3358:(1): 23–41. 3355: 3351: 3341: 3304: 3300: 3290: 3253: 3249: 3239: 3204: 3200: 3186: 3156:(2): 203–8. 3153: 3149: 3143: 3113:(8): 904–9. 3110: 3106: 3100: 3065: 3061: 3051: 3018: 3014: 3008: 2971: 2967: 2922:(1): 220–8. 2919: 2915: 2905: 2872: 2868: 2862: 2819: 2815: 2805: 2770: 2766: 2756: 2713: 2709: 2698: 2661: 2657: 2619: 2615: 2609: 2574: 2570: 2560: 2515: 2511: 2501: 2450: 2446: 2436: 2402:(12): e190. 2399: 2395: 2385: 2344: 2340: 2334: 2297: 2293: 2283: 2246: 2242: 2232: 2189: 2185: 2175: 2150: 2146: 2090: 2086: 2076: 2031: 2027: 2017: 1974: 1970: 1960: 1951: 1897: 1893: 1887: 1859: 1814: 1810: 1800: 1765: 1761: 1751: 1708: 1704: 1640: 1636: 1610:. Retrieved 1603:the original 1586: 1553: 1549: 1543: 1530:heritability 1526: 1505: 1484: 1470: 1442: 1422: 1407:(t-SNE) and 1391: 1382:eigenvectors 1374: 1030: 1009: 1005: 1001: 997: 993: 973: 969: 965: 961: 959: 954: 934: 928: 902: 897: 895: 640: 318: 175: 156: 131: 91: 66: 57: 38: 34: 30: 29: 3971:Epigenetics 3597:Coalescence 3193:Finucane HK 2875:(1): 11–3. 2716:(1): 1569. 1977:: 117–129. 1711:(1): 5–18. 1643:(1): 3258. 1522:mixed model 1514:Alkes Price 941:. In 2000, 178:-statistics 96:species is 88:Description 46:frequencies 4105:Categories 3976:Geneticist 3950:South Asia 3896:Population 3876:Ecological 3845:Amino acid 3825:Nucleotide 3800:Chromosome 3539:Ecological 3529:Artificial 3307:: e39702. 3256:: e61548. 3015:Biometrics 2974:: e64948. 2710:Nat Commun 2658:PLOS Genet 2294:PLOS Genet 2243:PLOS Genet 1612:2020-11-14 1536:References 1472:Phenotypes 1447:, such as 167:inbreeding 3891:Molecular 3886:Microbial 3861:Classical 3649:Evolution 3516:Selection 2534:1553-7404 2475:0028-0836 2369:0036-8075 2206:1943-2631 2107:1088-9051 2050:1943-2631 1991:0040-5809 1914:2050-1420 1727:1755-098X 1665:2041-1723 1457:chopstick 1429:haplotype 1344:− 1307:− 1262:× 939:estimator 931:admixture 827:− 794:− 587:− 506:− 280:− 135:panmictia 110:gene flow 58:panmictic 4090:Category 4016:Heredity 3986:Genomics 3830:Mutation 3820:Heredity 3784:Glossary 3774:Timeline 3748:Genetics 3673:genomics 3611:Founders 3382:31030318 3333:30895926 3282:33200985 3231:25642633 3170:16380716 3127:16862161 3092:10827107 3035:11315092 3000:33355092 2946:10364535 2889:10673763 2854:24531965 2797:33561250 2748:32218440 2690:31675358 2636:28718343 2601:10739417 2593:19156164 2552:19834557 2493:18758442 2428:17194218 2326:22927824 2275:22253600 2224:27729489 2186:Genetics 2167:21801023 2125:19648217 2068:10835412 2028:Genetics 2009:31132375 1922:24540312 1879:37481398 1841:30293985 1811:Heredity 1792:30007846 1743:24403040 1735:21429096 1683:30108219 1594:(2001). 1592:McVean G 1578:14255234 1570:12598158 1499:unlinked 960:Varying 933:between 557:. Then: 163:fixation 128:Measures 62:mutation 48:between 3769:History 3764:Outline 3524:Natural 3491:Fitness 3373:6942007 3324:6428571 3273:7758063 3222:4342297 3178:8507433 3135:8127858 3083:1287075 3043:6297807 2991:7758058 2937:1378093 2897:9760182 2845:4209567 2824:Bibcode 2816:Science 2788:8022710 2739:7099015 2718:Bibcode 2681:6853336 2543:2757795 2484:2735096 2455:Bibcode 2419:1713260 2349:Bibcode 2341:Science 2317:3426559 2266:3257290 2215:5068833 2116:2752134 2059:1461096 2000:8448291 1832:6221895 1783:6092560 1674:6092366 1645:Bibcode 1524:(LMM). 1468:(TDT). 52:. 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Index

Population stratification
allele
frequencies
subpopulations
randomly mating
mutation
confounding variable
medical genetics
genome wide association studies
genetic ancestry
sexually reproducing
non-random mating
allele frequencies
genetic drift
gene flow
population bottlenecks
founder effects
evolutionary pressure
panmictia

population bottleneck
heterozygosity
fixation
inbreeding
recent common ancestor
F-statistics
genetic distance
triangle inequality
metric
admixture

Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.

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