The role of selection in the evolution of human mitochondrial genomes
High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (P < 0.01) excess of rRNA and nonsynonymous base su...
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Genetics Society of America
2006
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Online Access: | http://hdl.handle.net/11573/237098 https://doi.org/10.1534/genetics.105.043901 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000235197700033&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-33244457956&partnerID=65&md5=83850af8827de8169476734020793b13 |
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ftunivromairis:oai:iris.uniroma1.it:11573/237098 2024-02-27T08:38:16+00:00 The role of selection in the evolution of human mitochondrial genomes T. Kivisild P. d. Shen D. p. Wall B. Do R. Sung K. Davis G. Passarino P. a. Underhill C. Scharfe A. Torroni P. De Knijff M. Feldman L. l. Cavalli Sforza P. j. Oefner SCOZZARI, Rosaria MODIANO, David COPPA, Alfredo T., Kivisild P. d., Shen D. p., Wall B., Do R., Sung K., Davi G., Passarino P. a., Underhill C., Scharfe A., Torroni Scozzari, Rosaria Modiano, David Coppa, Alfredo P., De Knijff M., Feldman L. l., Cavalli Sforza P. j., Oefner 2006 http://hdl.handle.net/11573/237098 https://doi.org/10.1534/genetics.105.043901 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000235197700033&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-33244457956&partnerID=65&md5=83850af8827de8169476734020793b13 eng eng Genetics Society of America info:eu-repo/semantics/altIdentifier/pmid/16172508 info:eu-repo/semantics/altIdentifier/wos/WOS:000235197700033 volume:172 issue:1 firstpage:373 lastpage:387 numberofpages:15 journal:GENETICS http://hdl.handle.net/11573/237098 doi:10.1534/genetics.105.043901 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-33244457956 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000235197700033&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-33244457956&partnerID=65&md5=83850af8827de8169476734020793b13 mitochondrial dna human population genetic natural selection molecular clock evolution info:eu-repo/semantics/article 2006 ftunivromairis https://doi.org/10.1534/genetics.105.043901 2024-01-31T17:46:27Z High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (P < 0.01) excess of rRNA and nonsynonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, with thymine-to-cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNA Thr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of nonsynonymous changes from and to threonine and valine differed significantly (P = 0.003) between populations with neutral (22/58) and populations with significantly negative Tajima's D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of nonsilent mutations is characteristic of Arctic populations, implying their role in cold adaptation, we demonstrate that the surplus of nonsynonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups. Article in Journal/Newspaper Arctic Sapienza Università di Roma: CINECA IRIS Arctic Genetics 172 1 373 387 |
institution |
Open Polar |
collection |
Sapienza Università di Roma: CINECA IRIS |
op_collection_id |
ftunivromairis |
language |
English |
topic |
mitochondrial dna human population genetic natural selection molecular clock evolution |
spellingShingle |
mitochondrial dna human population genetic natural selection molecular clock evolution T. Kivisild P. d. Shen D. p. Wall B. Do R. Sung K. Davis G. Passarino P. a. Underhill C. Scharfe A. Torroni P. De Knijff M. Feldman L. l. Cavalli Sforza P. j. Oefner SCOZZARI, Rosaria MODIANO, David COPPA, Alfredo The role of selection in the evolution of human mitochondrial genomes |
topic_facet |
mitochondrial dna human population genetic natural selection molecular clock evolution |
description |
High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (P < 0.01) excess of rRNA and nonsynonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, with thymine-to-cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNA Thr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of nonsynonymous changes from and to threonine and valine differed significantly (P = 0.003) between populations with neutral (22/58) and populations with significantly negative Tajima's D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of nonsilent mutations is characteristic of Arctic populations, implying their role in cold adaptation, we demonstrate that the surplus of nonsynonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups. |
author2 |
T., Kivisild P. d., Shen D. p., Wall B., Do R., Sung K., Davi G., Passarino P. a., Underhill C., Scharfe A., Torroni Scozzari, Rosaria Modiano, David Coppa, Alfredo P., De Knijff M., Feldman L. l., Cavalli Sforza P. j., Oefner |
format |
Article in Journal/Newspaper |
author |
T. Kivisild P. d. Shen D. p. Wall B. Do R. Sung K. Davis G. Passarino P. a. Underhill C. Scharfe A. Torroni P. De Knijff M. Feldman L. l. Cavalli Sforza P. j. Oefner SCOZZARI, Rosaria MODIANO, David COPPA, Alfredo |
author_facet |
T. Kivisild P. d. Shen D. p. Wall B. Do R. Sung K. Davis G. Passarino P. a. Underhill C. Scharfe A. Torroni P. De Knijff M. Feldman L. l. Cavalli Sforza P. j. Oefner SCOZZARI, Rosaria MODIANO, David COPPA, Alfredo |
author_sort |
T. Kivisild |
title |
The role of selection in the evolution of human mitochondrial genomes |
title_short |
The role of selection in the evolution of human mitochondrial genomes |
title_full |
The role of selection in the evolution of human mitochondrial genomes |
title_fullStr |
The role of selection in the evolution of human mitochondrial genomes |
title_full_unstemmed |
The role of selection in the evolution of human mitochondrial genomes |
title_sort |
role of selection in the evolution of human mitochondrial genomes |
publisher |
Genetics Society of America |
publishDate |
2006 |
url |
http://hdl.handle.net/11573/237098 https://doi.org/10.1534/genetics.105.043901 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000235197700033&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-33244457956&partnerID=65&md5=83850af8827de8169476734020793b13 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/16172508 info:eu-repo/semantics/altIdentifier/wos/WOS:000235197700033 volume:172 issue:1 firstpage:373 lastpage:387 numberofpages:15 journal:GENETICS http://hdl.handle.net/11573/237098 doi:10.1534/genetics.105.043901 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-33244457956 http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000235197700033&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=0c7ff228ccbaaa74236f48834a34396a http://www.scopus.com/inward/record.url?eid=2-s2.0-33244457956&partnerID=65&md5=83850af8827de8169476734020793b13 |
op_doi |
https://doi.org/10.1534/genetics.105.043901 |
container_title |
Genetics |
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172 |
container_issue |
1 |
container_start_page |
373 |
op_container_end_page |
387 |
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