Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula

TY - JOUR

T1 - Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula

AU - Paape, Timothy

AU - Bataillon, Thomas

AU - Zhou, Peng

AU - J Y Kono, Tom

AU - Briskine, Roman

AU - Young, Nevin D

AU - Tiffin, Peter

N1 - © 2013 Blackwell Publishing Ltd.

PY - 2013

Y1 - 2013

N2 - Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50-75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism with expression data, we estimated the distribution of fitness effects and found that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (nonexpressed) in a previous RNA-seq experiment and greater for broadly expressed genes than those expressed in only a single tissue. Expression level is the strongest correlate of evolutionary rates at nonsynonymous sites, and despite multiple genomic features being significantly correlated with evolutionary rates, they explain less than 20% of the variation in nonsynonymous rates (dN) and

AB - Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50-75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism with expression data, we estimated the distribution of fitness effects and found that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (nonexpressed) in a previous RNA-seq experiment and greater for broadly expressed genes than those expressed in only a single tissue. Expression level is the strongest correlate of evolutionary rates at nonsynonymous sites, and despite multiple genomic features being significantly correlated with evolutionary rates, they explain less than 20% of the variation in nonsynonymous rates (dN) and

U2 - 10.1111/mec.12329

DO - 10.1111/mec.12329

M3 - Journal article

C2 - 23773281

SN - 0962-1083

VL - 22

SP - 3525

EP - 3538

JO - Molecular Ecology

JF - Molecular Ecology

IS - 13

ER -