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Computational detection of natural selection in gene family expansion and contraction

Here we use a model of stochastic birth and death for mapping gene family evolution onto a phylogeny, and show that it can be efficiently applied to multispecies comparisons. The model offers the opportunity for researchers to make stronger inferences regarding the role of natural selection and changing duplication and deletion rates in gene family expansion or contraction. The work is performed as a part of the first author’s MS thesis under the second author’s supervision. | ’ Tap ch´ Tin hoc v` Diˆu khiˆ n hoc, T.23, S.1 (2007), 1—14 ı e e . . a ` . COMPUTATIONAL DETECTION OF NATURAL SELECTION IN GENE FAMILY EXPANSION AND CONTRACTION CHI NGUYEN1 , NELLO CRISTIANINI 2 1 Department of Computer Science, University of California, Davis, USA 2 Department of Statistics, University of California, Davis, USA Abstract. Researchers have generally attributed ostensibly large differences in family size to the effects of natural selection in promoting either the expansion or contraction of families along specific lineages, without a strong statistical basis. Here we use a model of stochastic birth and death for mapping gene family evolution onto a phylogeny, and show that it can be efficiently applied to multispecies comparisons. The model offers the opportunity for researchers to make stronger inferences regarding the role of natural selection and changing duplication and deletion rates in gene family expansion or contraction. The work is performed as a part of the first author’s MS thesis under the second author’s supervision. ´ ´ ’ ` T´m t˘t. Thˆng thu.`.ng c´c nh` nghiˆn c´.u g˘n su. kh´c nhau l´.n theo ve bˆ ngo`i cua k´ c˜. o a o o a a e u a a o e a ’ ıch o . .i su. anh hu.o.ng cua viˆc lu.a chon tu. nhiˆn trong qu´ tr` th´ c dˆ y su. mo. rˆng hay thu ’ ’ ’ e a ınh u a . ’ o e . ınh o gia d` v´ . ’ . . . . ´ ´ ´ ´ . ’ ’ o ınh u hep cua gia d` trong nh˜.ng thˆ hˆ sau m` khˆng du.a trˆn mˆt co. so. thˆng kˆ ch˘c ch˘ n. Trong e a a e e a o e o . . . . dung mˆt mˆ h` thˆng kˆ sinh-tu. dˆ ´nh xa su. tiˆn ho´ cua c´c ho gien ’ ´ ´ ’ ea o o ınh o e a ’ a . b`i b´o n`y, ch´ ng tˆi su . a a a u o ’ . . . e ’ ` ’ t´.i mˆt cˆy phˆn lo`i, v` chı ra r˘ ng mˆ h` n`y c´ thˆ du.o.c ´p dung mˆt c´ch c´ hiˆu qua cho su. o o a a a a ’ a o ınh a o e a o a o e . . . . . . .a ra mˆt co. hˆi cho c´c nh` nghiˆn c´.u thu.c hiˆn nh˜.ng suy diˆn ch´ ˜ o o a a e u e u e ınh a o ınh so s´nh da lo`i. Mˆ h` du a . . . . ´ . x´c ho.n liˆn quan t´.i vai tr` cua su. lu.a chon