Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula.

Genetics
Pär K Ingvarsson

Abstract

I have studied nucleotide polymorphism and linkage disequilibrium using multilocus data from 77 fragments, with an average length of fragments of 550 bp, in the deciduous tree Populus tremula (Salicaceae). The frequency spectrum across loci showed a modest excess of mutations segregating at low frequency and a marked excess of high-frequency derived mutations at silent sites, relative to neutral expectations. These excesses were also seen at replacement sites, but were not so pronounced for high-frequency derived mutations. There was a marked excess of low-frequency mutations at replacement sites, likely indicating deleterious amino acid-changing mutations that segregate at low frequencies in P. tremula. I used approximate Bayesian computation (ABC) to evaluate a number of different demographic scenarios and to estimate parameters for the best-fitting model. The data were found to be consistent with a historical reduction in the effective population size of P. tremula through a bottleneck. The timing inferred for this bottleneck is largely consistent with geological data and with data from several other long-lived plant species. The results show that P. tremula harbors substantial levels of nucleotide polymorphism with the post...Continue Reading

References

Apr 1, 1975·Theoretical Population Biology·G A Watterson
May 16, 1998·Genome Research·D GordonP Green
May 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·A Eyre-WalkerB S Gaut
Jun 6, 1998·Theoretical Population Biology·J Wakeley
Nov 5, 1999·Methods in Molecular Biology·S Rozen, H Skaletsky
Dec 22, 1999·Molecular Biology and Evolution·J K PritchardM W Feldman
Jun 3, 2000·Genetics·J K PritchardP Donnelly
Jul 6, 2000·Genetics·J C Fay, C I Wu
Sep 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·D L RemingtonE S Buckler
Jan 10, 2002·Nature Genetics·Magnus NordborgDetlef Weigel
Mar 20, 2002·Genetics·Molly Przeworski
Apr 5, 2002·Genome Research·W James Kent
Jun 7, 2003·Science·Rémy J PetitGiovanni G Vendramin
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Aug 22, 2003·Genetics·Tomoyuki KadoHidenori Tachida
Nov 25, 2003·Bioinformatics·Kevin Thornton
Dec 12, 2003·Genetics·Emmanuelle Baudry, Frantz Depaulis
Feb 6, 2004·Genome Research·Daniel L HalliganPeter D Keightley
Mar 12, 2004·Molecular Biology and Evolution·Maud I TenaillonBrandon S Gaut
Apr 23, 2004·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·G M Hewitt
Jul 3, 2004·Trends in Plant Science·David B Neale, Outi Savolainen
Sep 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Fredrik SterkyStefan Jansson
Oct 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Garth R BrownDavid B Neale
May 24, 2005·PLoS Biology·Magnus NordborgJoy Bergelson
May 28, 2005·Science·Stephen I WrightBrandon S Gaut
Dec 3, 2005·Genetics·Aizhong Liu, John M Burke
Jun 7, 2006·Journal of Molecular Evolution·Nina M Talyzina, Pär K Ingvarsson

❮ Previous
Next ❯

Citations

Apr 23, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jérémy ClotaultDidier Peltier
May 9, 2012·Journal of Molecular Evolution·Mohamed IsmailYousry A El-Kassaby
Jun 26, 2010·Molecular Genetics and Genomics : MGG·Deqiang ZhangBailian Li
May 6, 2009·Journal of Experimental Botany·Ulf Lagercrantz
Mar 20, 2010·Molecular Biology and Evolution·Toni I GossmannAdam Eyre-Walker
Oct 19, 2010·Molecular Biology and Evolution·Jared L StrasburgLoren H Rieseberg
Nov 25, 2011·Molecular Biology and Evolution·Jonathan C ThomasD Ashley Robinson
Nov 6, 2008·BMC Evolutionary Biology·Pär K Ingvarsson
Aug 9, 2013·Biotechnology for Biofuels·Aude C PerdereauColin T Kelleher
Sep 25, 2014·International Journal of Molecular Sciences·Bowen Wang, Deqiang Zhang
May 22, 2010·Trends in Ecology & Evolution·Katalin CsilléryOlivier François
Jan 5, 2013·Journal of Evolutionary Biology·D AudigeosI Scotti

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.