PMC:1271393 / 28851-30937
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1271393","sourcedb":"PMC","sourceid":"1271393","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1271393","text":"Neutrality Tests\nThe identification of a strong decay in LD between CD209 and CD209L facilitated the interpretation of neutrality tests, because the noise introduced by hitchhiking effects between the genes is reduced. We applied Tajima's D and Fay and Wu's H tests to determine whether these statistics significantly deviated from expectations under neutrality, using both coalescent simulations and the empirical distribution obtained from Akey et al. (2004). Globally, Tajima's D test indicated different tendencies for the two genes (table 2). CD209 always yielded negative values for Tajima's D but never achieved significance to reject the hypothesis of neutrality, whereas CD209L yielded significantly positive values for non-African populations, with use of both coalescent simulations and the empirical distribution. For Fay and Wu's H test, the hypothesis of neutrality was rejected for CD209 in the African and East Asian samples (table 2).\nTo evaluate the selective pressures at the protein level, we performed two interspecies tests: K A/K S, which gives the ratio of nonsynonymous and synonymous changes between species, and the McDonald-Kreitman test, which tests the null hypothesis that the ratio of the number of fixed differences to polymorphisms is the same for both nonsynonymous and synonymous mutations. For the K A/K S test, CD209 and CD209L showed similar values, 0.34 and 0.37, respectively. For the McDonald-Kreitman test, the hypothesis of neutrality was rejected for only CD209, because of a clear lack of nonsynonymous polymorphic sites (table 3 ).\nTable 3 McDonald-Kreitman Test Results\nNo. of Substitutions andPValue for\nExonic Region Only Entire Sequencea\nGene and Type of Site Synonymous Nonsynonymous P Synonymous Nonsynonymous P\nCD209: .04 .009\n Fixed 4 5 51 5\n Polymorphic 6 0 86 0\nCD209L: .23 1\n Fixed 5 6 78 6\n Polymorphic 0 4 65 4\nNote.—\nThe highly variable exon 4 has been excluded from this analysis, because no ancestral state could be inferred. Significant P values are shown in bold italics.\na Mutations in introns are considered synonymous.","divisions":[{"label":"title","span":{"begin":0,"end":16}},{"label":"p","span":{"begin":17,"end":951}},{"label":"label","span":{"begin":1579,"end":1586}},{"label":"caption","span":{"begin":1587,"end":1617}},{"label":"p","span":{"begin":1587,"end":1617}},{"label":"table","span":{"begin":1618,"end":1870}},{"label":"tr","span":{"begin":1618,"end":1652}},{"label":"th","span":{"begin":1618,"end":1652}},{"label":"tr","span":{"begin":1653,"end":1688}},{"label":"th","span":{"begin":1653,"end":1671}},{"label":"th","span":{"begin":1672,"end":1688}},{"label":"tr","span":{"begin":1689,"end":1764}},{"label":"th","span":{"begin":1689,"end":1710}},{"label":"th","span":{"begin":1711,"end":1721}},{"label":"th","span":{"begin":1722,"end":1735}},{"label":"th","span":{"begin":1736,"end":1737}},{"label":"th","span":{"begin":1738,"end":1748}},{"label":"th","span":{"begin":1749,"end":1762}},{"label":"th","span":{"begin":1763,"end":1764}},{"label":"tr","span":{"begin":1765,"end":1780}},{"label":"td","span":{"begin":1765,"end":1771}},{"label":"td","span":{"begin":1772,"end":1775}},{"label":"td","span":{"begin":1776,"end":1780}},{"label":"tr","span":{"begin":1781,"end":1796}},{"label":"td","span":{"begin":1781,"end":1787}},{"label":"td","span":{"begin":1788,"end":1789}},{"label":"td","span":{"begin":1790,"end":1791}},{"label":"td","span":{"begin":1792,"end":1794}},{"label":"td","span":{"begin":1795,"end":1796}},{"label":"tr","span":{"begin":1797,"end":1818}},{"label":"td","span":{"begin":1797,"end":1809}},{"label":"td","span":{"begin":1810,"end":1811}},{"label":"td","span":{"begin":1812,"end":1813}},{"label":"td","span":{"begin":1814,"end":1816}},{"label":"td","span":{"begin":1817,"end":1818}},{"label":"tr","span":{"begin":1819,"end":1832}},{"label":"td","span":{"begin":1819,"end":1826}},{"label":"td","span":{"begin":1827,"end":1830}},{"label":"td","span":{"begin":1831,"end":1832}},{"label":"tr","span":{"begin":1833,"end":1848}},{"label":"td","span":{"begin":1833,"end":1839}},{"label":"td","span":{"begin":1840,"end":1841}},{"label":"td","span":{"begin":1842,"end":1843}},{"label":"td","span":{"begin":1844,"end":1846}},{"label":"td","span":{"begin":1847,"end":1848}},{"label":"tr","span":{"begin":1849,"end":1870}},{"label":"td","span":{"begin":1849,"end":1861}},{"label":"td","span":{"begin":1862,"end":1863}},{"label":"td","span":{"begin":1864,"end":1865}},{"label":"td","span":{"begin":1866,"end":1868}},{"label":"td","span":{"begin":1869,"end":1870}},{"label":"table-wrap-foot","span":{"begin":1871,"end":2036}},{"label":"footnote","span":{"begin":1871,"end":1877}},{"label":"p","span":{"begin":1871,"end":1877}},{"label":"footnote","span":{"begin":1878,"end":2036}},{"label":"p","span":{"begin":1878,"end":2036}},{"label":"label","span":{"begin":2037,"end":2038}}],"tracks":[{"project":"2_test","denotations":[{"id":"16252244-15361935-2049632","span":{"begin":455,"end":459},"obj":"15361935"}],"attributes":[{"subj":"16252244-15361935-2049632","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93ecb6","default":true}]}]}}