Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae )

Ecology and Evolution
Stephen A L TrevoyF A H Sperling

Abstract

Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome-wide single-nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted resampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principal components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex-linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species' genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research.

References

Dec 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·J M WatsonJ A Graves
Dec 2, 1999·Nature Genetics·E PassargeR A Farber
Feb 12, 2004·European Journal of Human Genetics : EJHG·Louise HoskingChun-Fang Xu
Feb 27, 2004·Evolution & Development·H Frederik Nijhout
Jun 3, 2005·Heredity·D CharlesworthG Marais
Jul 19, 2005·Chromosoma·James M A Turner
Aug 4, 2005·PLoS Biology·Thomas L TurnerSergey V Nuzhdin
Mar 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·T Ohta
Feb 20, 2007·Molecular Ecology·Amy Bouck, Todd Vision
Mar 26, 2008·Nature·UNKNOWN Tribolium Genome Sequencing ConsortiumGregor Bucher
Sep 10, 2008·Genetica·Jon SlateJosephine M Pemberton
Oct 15, 2008·PloS One·Nathan A BairdEric A Johnson
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
May 12, 2010·Proceedings of the National Academy of Sciences of the United States of America·Andrew P MichelJeffrey L Feder
May 27, 2010·Heredity·N H Barton
Jun 30, 2010·Genome Biology·Daniel S DayPeter V Kharchenko
Nov 5, 2010·Annual Review of Genetics·Vera B Kaiser, Doris Bachtrog
May 17, 2011·PloS One·Robert J ElshireSharon E Mitchell
May 19, 2011·Nature Reviews. Genetics·Rasmus NielsenYun S Song
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jun 18, 2011·Nature Reviews. Genetics·John W DaveyMark L Blaxter
Jul 7, 2011·Evolution; International Journal of Organic Evolution·Sam Yeaman, Michael C Whitlock
Aug 13, 2011·Current Biology : CB·John P McCutcheon, Carol D von Dohlen
Aug 16, 2011·Nature·Mathieu JoronRichard H ffrench-Constant
Oct 4, 2011·Trends in Genetics : TIG·Sarah P OttoBryant F McAllister
Dec 28, 2011·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Matthew W HahnNora J Besansky
Jun 27, 2012·Environmental Entomology·John D ReeveScott T Kelley
Jul 28, 2012·Ecology and Evolution·Catherine I CullinghamDavid W Coltman
Mar 30, 2013·Genome Biology·Christopher I KeelingJoerg Bohlmann
May 25, 2013·Molecular Ecology·Julian CatchenWilliam A Cresko
May 29, 2013·Molecular Ecology·Shawn R NarumPaul A Hohenlohe
May 8, 2014·Molecular Biology and Evolution·Jasmine K JanesFelix A H Sperling
Sep 5, 2014·Molecular Ecology Resources·René M MalenfantCorey S Davis
Oct 29, 2014·Nucleic Acids Research·UNKNOWN UniProt Consortium
Nov 18, 2014·Ecological Entomology·Leanna E Lachowsky, Mary L Reid

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
PCA

Software Mentioned

LDHeatmap
LDna Heatmap
BWA
NextSeq
FastQC
BLAST
VCFtools
R
MEM
Cutadapt

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.