scholarly journals Recent Positive Selection Has Acted on Genes Encoding Proteins with More Interactions within the Whole Human Interactome

2015 ◽  
Vol 7 (4) ◽  
pp. 1141-1154 ◽  
Author(s):  
Pierre Luisi ◽  
David Alvarez-Ponce ◽  
Marc Pybus ◽  
Mario A. Fares ◽  
Jaume Bertranpetit ◽  
...  
Keyword(s):  
Positive Selection ◽  
Human Interactome ◽  
Recent Positive Selection ◽  
Genes Encoding

scholarly journals Evidence for Very Recent Positive Selection in Mongolians

2017 ◽  
Vol 34 (8) ◽  
pp. 1936-1946 ◽  
Author(s):  
Kazuhiro Nakayama ◽  
Jun Ohashi ◽  
Kazuhisa Watanabe ◽  
Lkagvasuren Munkhtulga ◽  
Sadahiko Iwamoto
Keyword(s):  
Positive Selection ◽  
Recent Positive Selection

scholarly journals High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability

2018 ◽  
Author(s):  
Pier Francesco Palamara ◽  
Jonathan Terhorst ◽  
Yun S. Song ◽  
Alkes L. Price
Keyword(s):  
Positive Selection ◽  
Snp Array ◽  
Complex Trait ◽  
Joint Analysis ◽  
Background Selection ◽  
Sequencing Data ◽  
Data Set ◽  
Coalescence Time ◽  
Recent Positive Selection ◽  
Coalescence Times

AbstractInterest in reconstructing demographic histories has motivated the development of methods to estimate locus-specific pairwise coalescence times from whole-genome sequence data. We developed a new method, ASMC, that can estimate coalescence times using only SNP array data, and is 2-4 orders of magnitude faster than previous methods when sequencing data are available. We were thus able to apply ASMC to 113,851 phased British samples from the UK Biobank, aiming to detect recent positive selection by identifying loci with unusually high density of very recent coalescence times. We detected 12 genome-wide significant signals, including 6 loci with previous evidence of positive selection and 6 novel loci, consistent with coalescent simulations showing that our approach is well-powered to detect recent positive selection. We also applied ASMC to sequencing data from 498 Dutch individuals (Genome of the Netherlands data set) to detect background selection at deeper time scales. We observed highly significant correlations between average coalescence time inferred by ASMC and other measures of background selection. We investigated whether this signal translated into an enrichment in disease and complex trait heritability by analyzing summary association statistics from 20 independent diseases and complex traits (average N=86k) using stratified LD score regression. Our background selection annotation based on average coalescence time was strongly enriched for heritability (p = 7×10−153) in a joint analysis conditioned on a broad set of functional annotations (including other background selection annotations), meta-analyzed across traits; SNPs in the top 20% of our annotation were 3.8x enriched for heritability compared to the bottom 20%. These results underscore the widespread effects of background selection on disease and complex trait heritability.

scholarly journals Genomic evidence for recent positive selection at the human MDR1 gene locus

2004 ◽  
Vol 13 (8) ◽  
pp. 783-797 ◽  
Author(s):  
Kun Tang ◽  
Li Peng Wong ◽  
Edmund J.D. Lee ◽  
Samuel S. Chong ◽  
Caroline G.L. Lee
Keyword(s):  
Positive Selection ◽  
Gene Locus ◽  
Mdr1 Gene ◽  
Recent Positive Selection ◽  
Human Mdr1

scholarly journals Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
William C. Beckerson ◽  
Ricardo C. Rodríguez de la Vega ◽  
Fanny E. Hartmann ◽  
Marine Duhamel ◽  
Tatiana Giraud ◽  
...  
Keyword(s):  
Positive Selection ◽  
Plant Pathogens ◽  
Pfam Domain ◽  
Rapid Evolution ◽  
Host Specialization ◽  
Secreted Proteins ◽  
Smut Fungi ◽  
Core Proteins ◽  
Genes Encoding ◽  
Species Specific

ABSTRACT Plant pathogens utilize a portfolio of secreted effectors to successfully infect and manipulate their hosts. It is, however, still unclear whether changes in secretomes leading to host specialization involve mostly effector gene gains/losses or changes in their sequences. To test these hypotheses, we compared the secretomes of three host-specific castrating anther smut fungi (Microbotryum), two being sister species. To address within-species evolution, which might involve coevolution and local adaptation, we compared the secretomes of strains from differentiated populations. We experimentally validated a subset of signal peptides. Secretomes ranged from 321 to 445 predicted secreted proteins (SPs), including a few species-specific proteins (42 to 75), and limited copy number variation, i.e., little gene family expansion or reduction. Between 52% and 68% of the SPs did not match any Pfam domain, a percentage that reached 80% for the small secreted proteins, indicating rapid evolution. In comparison to background genes, we indeed found SPs to be more differentiated among species and strains, more often under positive selection, and highly expressed in planta; repeat-induced point mutations (RIPs) had no role in effector diversification, as SPs were not closer to transposable elements than background genes and were not more RIP affected. Our study thus identified both conserved core proteins, likely required for the pathogenic life cycle of all Microbotryum species, and proteins that were species specific or evolving under positive selection; these proteins may be involved in host specialization and/or coevolution. Most changes among closely related host-specific pathogens, however, involved rapid changes in sequences rather than gene gains/losses. IMPORTANCE Plant pathogens use molecular weapons to successfully infect their hosts, secreting a large portfolio of various proteins and enzymes. Different plant species are often parasitized by host-specific pathogens; however, it is still unclear whether the molecular basis of such host specialization involves species-specific weapons or different variants of the same weapons. We therefore compared the genes encoding secreted proteins in three plant-castrating pathogens parasitizing different host plants, producing their spores in plant anthers by replacing pollen. We validated our predictions for secretion signals for some genes and checked that our predicted secreted proteins were often highly expressed during plant infection. While we found few species-specific secreted proteins, numerous genes encoding secreted proteins showed signs of rapid evolution and of natural selection. Our study thus found that most changes among closely related host-specific pathogens involved rapid adaptive changes in shared molecular weapons rather than innovations for new weapons.

scholarly journals Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology

2018 ◽  
Vol 8 (4) ◽  
pp. 1315-1325 ◽  
Author(s):  
Jiyun M. Moon ◽  
David M. Aronoff ◽  
John A. Capra ◽  
Patrick Abbot ◽  
Antonis Rokas
Keyword(s):  
Sialic Acid ◽  
Positive Selection ◽  
Recent Positive Selection

scholarly journals Correction: A Map of Recent Positive Selection in the Human Genome

PLoS Biology ◽  
2006 ◽  
Vol 4 (4) ◽  
pp. e154 ◽  
Author(s):  
Benjamin F Voight ◽  
Sridhar Kudaravalli ◽  
Xiaoquan Wen ◽  
Jonathan K Pritchard
Keyword(s):  
Positive Selection ◽  
Human Genome ◽  
Recent Positive Selection

scholarly journals Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods

PLoS ONE ◽  
2013 ◽  
Vol 8 (5) ◽  
pp. e64280 ◽  
Author(s):  
Yuri Tani Utsunomiya ◽  
Ana Maria Pérez O’Brien ◽  
Tad Stewart Sonstegard ◽  
Curtis Paul Van Tassell ◽  
Adriana Santana do Carmo ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Positive Selection ◽  
Recent Positive Selection ◽  
Genome Wide ◽  
Genome Wide Scan
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