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PMID: 20516497 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Estimating the parameters of selection on nonsynonymous mutations in Drosophila pseudoobscura and D. miranda.

Genetics ·Vol. 185 ·No. 4 ·2010-08-00 ·Pages 1381-96

Haddrill PR, Loewe L, Charlesworth B

Abstract

We present the results of surveys of diversity in sets of >40 X-linked and autosomal loci in samples from natural populations of Drosophila miranda and D. pseudoobscura, together with their sequence divergence from D. affinis. Mean silent site diversity in D. miranda is approximately one-quarter of that in D. pseudoobscura; mean X-linked silent diversity is about three-quarters of that for the autosomes in both species. Estimates of the distribution of selection coefficients against heterozygous, deleterious nonsynonymous mutations from two different methods suggest a wide distribution, with coefficients of variation greater than one, and with the average segregating amino acid mutation being subject to only very weak selection. Only a small fraction of new amino acid mutations behave as effectively neutral, however. A large fraction of amino acid differences between D. pseudoobscura and D. affinis appear to have been fixed by positive natural selection, using three different methods of estimation; estimates between D. miranda and D. affinis are more equivocal. Sources of bias in the estimates, especially those arising from selection on synonymous mutations and from the choice of genes, are discussed and corrections for these applied. Overall, the results show that both purifying selection and positive selection on nonsynonymous mutations are pervasive.

MeSH Terms
Adaptation, Physiological/genetics Algorithms Amino Acids/genetics Animals Drosophila/classification,genetics Drosophila Proteins/genetics Genes, X-Linked/genetics Genetic Variation Models, Genetic Molecular Sequence Data Mutation/genetics Polymorphism, Genetic Selection, Genetic Sequence Analysis, DNA Species Specificity
Chemicals
Amino Acids Drosophila Proteins
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Haddrill Penelope R
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom. [email protected]
Loewe Laurence
Charlesworth Brian
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Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
1943-2631
DOI
10.1534/genetics.110.117614
Email
[email protected]
Published
2010-08-00
Epub
2010-00-01
Pages
1381-96
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC2927764
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BB/D019621/1 · United Kingdom
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HM471340, HM471341, HM471342, HM471343, HM471344, HM471345, HM471346, HM471347, HM471348, HM471349, HM471350, HM471351, HM471352, HM471353, HM471354, HM471355, HM471356, HM471357, HM471358, HM471359, HM471360, HM471361, HM471362, HM471363, HM471364, HM471365, HM471366, HM471367, HM471368, HM471369, HM471370, HM471371, HM471372, HM471373, HM471374, HM471375, HM471376, HM471377, HM471378, HM471379, HM471380, HM471381, HM471382, HM471383, HM471384, HM471385, HM471386, HM471387, HM471388, HM471389, HM471390, HM471391, HM471392, HM471393, HM471394, HM471395, HM471396, HM471397, HM471398, HM471399, HM471400, HM471401, HM471402, HM471403, HM471404, HM471405, HM471406, HM471407, HM471408, HM471409, HM471410, HM471411, HM471412, HM471413, HM471414, HM471415, HM471416, HM471417, HM471418, HM471419, HM471420, HM471421, HM471422, HM471423, HM471424, HM471425, HM471426, HM471427, HM471428, HM471429, HM471430, HM471431, HM471432, HM471433, HM471434, HM471435, HM471436, HM471437, HM471438, HM471439, HM471440, HM471441, HM471442, HM471443, HM471444, HM471445, HM471446, HM471447, HM471448, HM471449, HM471450, HM471451, HM471452, HM471453, HM471454, HM471455, HM471456, HM471457, HM471458, HM471459, HM471460, HM471461, HM471462, HM471463, HM471464, HM471465, HM471466, HM471467, HM471468, HM471469, HM471470, HM471471, HM471472, HM471473, HM471474, HM471475, HM471476, HM471477, HM471478, HM471479, HM471480, HM471481, HM471482, HM471483, HM471484, HM471485, HM471486, HM471487, HM471488, HM471489, HM471490, HM471491, HM471492, HM471493, HM471494, HM471495, HM471496, HM471497, HM471498, HM471499, HM471500, HM471501, HM471502, HM471503, HM471504, HM471505, HM471506, HM471507, HM471508, HM471509, HM471510, HM471511, HM471512, HM471513, HM471514, HM471515, HM471516, HM471517, HM471518, HM471519, HM471520, HM471521, HM471522, HM471523, HM471524, HM471525, HM471526, HM471527, HM471528, HM471529, HM471530, HM471531, HM471532, HM471533, HM471534, HM471535, HM471536, HM471537, HM471538, HM471539, HM471540, HM471541, HM471542, HM471543, HM471544, HM471545, HM471546, HM471547, HM471548, HM471549, HM471550, HM471551, HM471552, HM471553, HM471554, HM471555, HM471556, HM471557, HM471558, HM471559, HM471560, HM471561, HM471562, HM471563, HM471564, HM471565, HM471566, HM471567, HM471568, HM471569, HM471570, HM471571, HM471572, HM471573, HM471574, HM471575, HM471576, HM471577, HM471578, HM471579, HM471580, HM471581, HM471582, HM471583, HM471584, HM471585, HM471586, HM471587, HM471588, HM471589, HM471590, HM471591, HM471592, HM471593, HM471594, HM471595, HM471596, HM471597, HM471598, HM471599, HM471600, HM471601, HM471602, HM471603, HM471604, HM471605, HM471606, HM471607, HM471608, HM471609, HM471610, HM471611, HM471612, HM471613, HM471614, HM471615, HM471616, HM471617, HM471618, HM471619, HM471620, HM471621, HM471622, HM471623, HM471624, HM471625, HM471626, HM471627, HM471628, HM471629, HM471630, HM471631, HM471632, HM471633, HM471634, HM471635, HM471636, HM471637, HM471638, HM471639
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PubMed source DOI: 10.1534/genetics.110.117614 PMC Full Text View journal details
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