Talk:Fixation index

Untitled

I'm trying to reproduce the FST results from the Hapmap 3 paper (The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861. 2007) and they don't seem to be using the formula provided here. I believe they're using θ as defined by Reynolds, Weir, and Cockerham [Reynolds, John, Weir, B., S., Cockerham, C. Clark, ESTIMATION OF THE COANCESTRY COEFFICIENT: BASIS FOR A SHORT-TERM GENETIC DISTANCE, Genetics 1983 105: 767-779] which is also somewhat complicated. Perhaps this page should just include a simple FST formula, such as would be found in a standard population genetics textbook. —Preceding unsigned comment added by 192.12.88.17 (talk) 00:31, 17 October 2010 (UTC)

This article notes that "Across the autosomes, FST was estimated to be 0.12." but it would be nice to know what this means: Is that large, or small? —Preceding unsigned comment added by Tim bates (talk • contribs) 11:43, 3 June 2008 (UTC)

The 0.12 is a high value and represent populations of high variations (Asian and African origin HapMap populstions). The lowest range in the same HapMAp paper was 0.07. Dr. Rehab Abdel-Rahman —Preceding unsigned comment added by 71.242.172.165 (talk) 03:08, 29 June 2008 (UTC)

I've tried to understand the definition, but I am simply not able to. How do I calculate the variance between different subpopulation? Are the different formulae calculating the same thing (and if so, could the article please explain how?) or does Fst mean differnent things in different contexts? How about an example calculation? 82.134.28.194 (talk) 14:09, 9 April 2013 (UTC)

Don't know if you can read Haskell, but [1] calculates Fst. :-)

Ketil (talk) 12:17, 4 April 2014 (UTC)

And this was useful to me: [2]

Ketil (talk) 12:23, 4 April 2014 (UTC)

Ambiguity

According to Measures of genetic diversity, pp. 22-24, F_ST is different from fixation index (F)!Sylwia Ufnalska (talk) 16:29, 2 August 2013 (UTC)

Fst has been misunderstood for years as an index of differentiation. More and more awareness is developing in this sense. Fst indicates the nearness of fixation of an allele in a subpopulation and should not be used as an indicator of differentiation between (sub)populations. I've never edited a wikipedia page, but I think the current content is equivocal. It needs revision! https://onlinelibrary.wiley.com/doi/full/10.1111/eva.12590 — Preceding unsigned comment added by 192.47.249.244 (talk) 10:03, 25 January 2020 (UTC)

Meaning/relevance/clarification of Harpending's quote on human's FST

"kinship between two individuals of the same human population is equivalent to kinship between grandparent and grandchild or between half siblings" - what does it mean? That "in the same population" (what a "population" is in the level of analysis?) you could get from any random person essentially the same level of compatibility in organ transplantations than you'd get from your grandparent/child or half-sibling? Whereas between populations/mixed/intermediate populations it would be... ? Perhaps it would also deserve a inter-wiki link to the "kinship" article, "In biology, "kinship" typically refers to the degree of genetic relatedness or coefficient of relationship between individual members of a species (e.g. as in kin selection theory). It may also be used in this specific sense when applied to human relationships, in which case its meaning is closer to consanguinity or genealogy." — Preceding unsigned comment added by 201.68.109.57 (talk) 19:33, 9 August 2016 (UTC)

Think of kinship as a measure of gene sharing IN EXCESS of RANDOM gene sharing in a background population. So, kinship between half siblings OVER THE BACKGROUND of a randomly mating population, would be 0.125. Over the background of a subdivided population, unrelated individuals of the same deme (race) have a coefficient of kinship of 0.125, equivalent to kinship between half siblings over the background of a randomly mating population. Over the background of a subdivided population, half siblings of the same deme have a higher coefficient of kinship than 0.125 (the exact formula is in harpending "kinship in a subdivided population" 2002). — Preceding unsigned comment added by 181.49.84.77 (talk) 01:55, 16 April 2019 (UTC)

Figures

I have digitized the The History and Geography of Human Genes (1994) FST data, by Cavalli-Sforza, Menozzi and Piazza for this page. I think the figures would be a good addition to this article. I will put some of them below. All of them display the Cavalli-Sforza as is presented in the book.

The figure on the right is a bit large, so the figures on the left are the same but with fewer populations. Chamaemelum (talk) 22:19, 17 June 2023 (UTC)

Full FST Table

Full Table from Cavalli-Sforza, Menozzi and Piazza:

Extended content

Full Table Bantu E. African Nio-Saharan W. African San Berber Mbuti Indian Iranian Near Eastem Uralic Ainu Japanese Korean Mon Khmer Thai Dravidian Mongol Tungus Tibetan Indonesian Malaysian Filipino N. Turkic S. Chinese Basque Lapp Sardinian Danish English Greek Italian C. Amerind Esiomo Na-Dene N. American S. American Chukchi Melanesian Micronesian Polynesian New Guinean Australian Bantu 0 E. African 0.0658 0 Nio-Saharan 0.0118 0.0828 0 W. African 0.0188 0.0697 0.0196 0 San 0.0084 0.0776 0.1002 0.0865 0 Berber 0.0163 0.0534 0.2321 0.1642 0.0966 0 Mbuti 0.0714 0.1232 0.075 0.0801 0.1495 0.1812 0 Indian 0.2202 0.1076 0.2073 0.1748 0.1246 0.0497 0.2683 0 Iranian 0.2241 0.106 0.2077 0.1796 0.1267 0.0408 0.2588 0.0154 0 Near Eastem 0.1779 0.0709 0.1823 0.1454 0.088 0.0263 0.2138 0.022 0.0158 0 Uralic 0.276 0.169 0.2161 0.1921 0.236 0.1309 0.3283 0.0763 0.0946 0.0905 0 Ainu 0.2769 0.1771 0.2414 0.1942 0.2443 0.1811 0.3228 0.0911 0.0975 0.1044 0.078 0 Japanese 0.2361 0.1345 0.2511 0.2252 0.1905 0.1707 0.3089 0.0718 0.105 0.1056 0.061 0.0222 0 Korean 0.2668 0.1475 0.2368 0.1807 0.185 0.1411 0.2996 0.0681 0.0905 0.0933 0.0505 0.0358 0.0137 0 Mon Khmer 0.2448 0.1538 0.2881 0.1951 0.1077 0.1091 0.2768 0.0866 0.1282 0.0987 0.1708 0.1207 0.0961 0.0946 0 Thai 0.3364 0.1602 0.2976 0.248 0.2064 0.1791 0.3872 0.0652 0.1155 0.1023 0.1445 0.1032 0.0743 0.0614 0.0099 0 Dravidian 0.2112 0.1066 0.2396 0.2055 0.176 0.0849 0.2374 0.027 0.0432 0.0357 0.0914 0.1154 0.096 0.0704 0.1031 0.1136 0 Mongol Tungus 0.2882 0.1423 0.2519 0.1733 0.1398 0.136 0.2568 0.0509 0.0661 0.0827 0.018 0.0338 0.0218 0.017 0.1093 0.0957 0.0417 0 Tibetan 0.232 0.1126 0.2391 0.2243 0.1717 0.1224 0.2354 0.0337 0.0549 0.0535 0.0747 0.06 0.0263 0.0308 0.088 0.0652 0.0303 0.0246 0 Indonesian 0.2008 0.1669 0.2703 0.1709 0.1851 0.1548 0.3125 0.0952 0.1246 0.1009 0.1568 0.115 0.0944 0.0931 0.0358 0.0332 0.1424 0.1046 0.117 0 Malaysian 0.1658 0.1216 0.1714 0.1365 0.1434 0.1625 0.1743 0.113 0.1489 0.1173 0.1796 0.1387 0.1175 0.1001 0.0264 0.0455 0.1305 0.1251 0.1024 0.0411 0 Filipino 0.2913 0.17 0.3033 0.2299 0.1022 0.1268 0.3776 0.0672 0.0908 0.0909 0.1288 0.108 0.102 0.1216 0.0552 0.0625 0.0935 0.0737 0.0724 0.0341 0.0485 0 N. Turkic 0.2486 0.1386 0.2302 0.2163 0.1448 0.1167 0.2089 0.0638 0.0821 0.071 0.0949 0.0704 0.0627 0.0732 0.125 0.1225 0.067 0.0726 0.0503 0.1203 0.1169 0.1044 0 S. Chinese 0.2963 0.1664 0.2863 0.1958 0.2231 0.1703 0.3384 0.0847 0.1092 0.0983 0.1211 0.0626 0.0541 0.0498 0.0254 0.0105 0.1074 0.0705 0.0683 0.0381 0.0635 0.0315 0.1109 0 Basque 0.1474 0.0922 0.157 0.1289 0.1307 0.0392 0.1965 0.0418 0.0285 0.0246 0.1249 0.1153 0.1461 0.1063 0.1831 0.1726 0.0586 0.1049 0.0981 0.158 0.1784 0.1634 0.0903 0.1675 0 Lapp 0.1904 0.0988 0.1697 0.1689 0.1328 0.0738 0.194 0.0459 0.0423 0.0423 0.0857 0.0835 0.0947 0.0769 0.14 0.13 0.0535 0.0682 0.0657 0.1205 0.1463 0.1058 0.0567 0.1064 0.0829 0 Sardinian 0.276 0.16 0.2599 0.2062 0.1442 0.061 0.3275 0.0449 0.0314 0.032 0.1562 0.1483 0.1558 0.1327 0.1214 0.1307 0.0531 0.1287 0.0767 0.1053 0.1486 0.1083 0.1202 0.1192 0.0261 0.0667 0 Danish 0.1708 0.0909 0.1723 0.1459 0.1025 0.0313 0.1462 0.0293 0.0179 0.0238 0.0826 0.1138 0.1176 0.0947 0.1483 0.13 0.0458 0.068 0.0746 0.1425 0.1626 0.127 0.062 0.1306 0.0164 0.0334 0.0348 0 English 0.2288 0.1163 0.1767 0.1487 0.1197 0.0273 0.2373 0.028 0.0197 0.0238 0.1023 0.1219 0.1244 0.0982 0.11 0.1143 0.0556 0.0696 0.0673 0.1098 0.1275 0.1117 0.0668 0.1152 0.0119 0.0404 0.034 0.0021 0 Greek 0.1479 0.0892 0.1534 0.1356 0.1063 0.042 0.1735 0.0272 0.007 0.0129 0.1055 0.0738 0.1175 0.0904 0.1482 0.1355 0.0406 0.0735 0.0648 0.1116 0.1482 0.1109 0.0794 0.1095 0.0231 0.0306 0.019 0.0191 0.0204 0 Italian 0.2292 0.1234 0.2138 0.1794 0.1181 0.0315 0.2931 0.0261 0.0133 0.0208 0.1066 0.1111 0.1145 0.0938 0.1448 0.1382 0.0402 0.0905 0.0737 0.1411 0.1589 0.1136 0.0949 0.1238 0.0141 0.0338 0.0221 0.0072 0.0051 0.0077 0 C. Amerind 0.2237 0.1475 0.2701 0.2253 0.2143 0.1691 0.3499 0.1089 0.119 0.1037 0.1063 0.0888 0.0658 0.079 0.1522 0.1323 0.1012 0.097 0.0648 0.1675 0.1731 0.1527 0.065 0.1182 0.1539 0.1156 0.1513 0.1266 0.1248 0.1271 0.1196 0 Esiomo 0.3251 0.2116 0.2598 0.2853 0.2217 0.1991 0.3329 0.094 0.1234 0.1225 0.0933 0.1089 0.0701 0.0843 0.1595 0.1417 0.1216 0.0545 0.0728 0.1685 0.1617 0.1567 0.0796 0.1304 0.1837 0.0962 0.1881 0.118 0.1185 0.1254 0.1135 0.0903 0 Na-Dene 0.2075 0.2083 0.3124 0.2754 0.2201 0.1888 0.3955 0.1153 0.1286 0.1204 0.1196 0.1146 0.0921 0.091 0.1734 0.1517 0.1245 0.0935 0.0912 0.1656 0.1621 0.1867 0.1115 0.1379 0.1776 0.122 0.1888 0.1305 0.1375 0.1483 0.1373 0.0473 0.0738 0 N. American 0.2589 0.1358 0.2329 0.2011 0.1634 0.1271 0.2905 0.0752 0.0968 0.0733 0.0783 0.1089 0.0721 0.0762 0.1508 0.143 0.0997 0.0774 0.0517 0.1716 0.1726 0.1377 0.0726 0.125 0.1179 0.0897 0.1346 0.0948 0.0947 0.1045 0.0954 0.0291 0.0688 0.0472 0 S. American 0.2793 0.1654 0.2792 0.2502 0.2144 0.1616 0.3822 0.1077 0.1304 0.1119 0.1121 0.1291 0.1045 0.1061 0.1663 0.1713 0.1358 0.1189 0.1076 0.1665 0.1961 0.144 0.0986 0.1284 0.1651 0.1235 0.1628 0.1306 0.13 0.1306 0.1214 0.1508 0.1072 0.0619 0.0304 0 Chukchi 0.1902 0.1374 0.1767 0.1997 0.1648 0.125 0.2547 0.07 0.0916 0.0807 0.1136 0.0751 0.0802 0.0938 0.2232 0.1834 0.0952 0.1058 0.0722 0.2138 0.1776 0.1858 0.0505 0.1854 0.119 0.0848 0.1439 0.0969 0.0904 0.1053 0.0984 0.0698 0.0472 0.0907 0.0627 0.1061 0 Melanesian 0.3375 0.2024 0.3109 0.2722 0.2612 0.1723 0.3956 0.1155 0.1401 0.1262 0.1412 0.1429 0.1124 0.1116 0.1045 0.0789 0.1408 0.1112 0.1173 0.0742 0.0904 0.0535 0.1536 0.0597 0.1834 0.1427 0.147 0.1428 0.155 0.1534 0.1575 0.1724 0.1803 0.21 0.1758 0.2198 0.2025 0 Micronesian 0.2516 0.1722 0.312 0.2295 0.2181 0.1776 0.3403 0.1057 0.1364 0.1107 0.1324 0.1248 0.0867 0.1074 0.1017 0.0682 0.1689 0.108 0.1159 0.0536 0.0762 0.0462 0.1461 0.0605 0.1949 0.1406 0.127 0.1516 0.1174 0.1415 0.1308 0.165 0.1586 0.204 0.1818 0.1738 0.2071 0.0403 0 Polynesian 0.2649 0.1414 0.2491 0.1992 0.194 0.1133 0.3136 0.0927 0.1142 0.0869 0.1063 0.1146 0.0623 0.069 0.086 0.058 0.1416 0.0969 0.0614 0.0742 0.0849 0.065 0.1147 0.0508 0.1408 0.122 0.1083 0.121 0.0991 0.1096 0.1215 0.1312 0.1415 0.1627 0.1268 0.1444 0.1575 0.0584 0.0512 0 New Guinean 0.3372 0.2733 0.3324 0.2752 0.3269 0.2324 0.4573 0.146 0.1751 0.1916 0.1408 0.1539 0.1241 0.142 0.224 0.1803 0.1992 0.1237 0.1493 0.1783 0.1974 0.133 0.1958 0.1503 0.2149 0.1549 0.2214 0.1639 0.1616 0.174 0.1643 0.1924 0.1586 0.2528 0.1958 0.1972 0.2027 0.0711 0.0981 0.1476 0 Australian 0.3272 0.2131 0.3557 0.2694 0.2705 0.1988 0.4267 0.1176 0.1546 0.1408 0.0826 0.1246 0.0621 0.065 0.1699 0.1314 0.1565 0.0781 0.1055 0.1461 0.1665 0.13 0.158 0.1081 0.1049 0.1422 0.1668 0.14 0.1534 0.1498 0.1413 0.136 0.123 0.1977 0.1264 0.1563 0.1738 0.1059 0.093 0.1145 0.0974 0

Chamaemelum (talk) 22:21, 17 June 2023 (UTC)