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 Examination of signatures of recent positive selection on genes involved in human sialic acid biology

2017 ◽  
Author(s):  
Jiyun M. Moon ◽  
David M. Aronoff ◽  
John A. Capra ◽  
Patrick Abbot ◽  
Antonis Rokas
Keyword(s):  
Sialic Acid ◽  
Positive Selection ◽  
Transfer Functions ◽  
Demographic History ◽  
Neutral Evolution ◽  
Human Lineage ◽  
Selective Sweeps ◽  
Frequency Spectra ◽  
Recent Positive Selection ◽  
Soft Selective Sweeps

AbstractSialic acids are nine carbon sugars ubiquitously found on the surfaces of vertebrate cells and are involved in various immune response-related processes. In humans, at least 58 genes spanning diverse functions, from biosynthesis and activation to recycling and degradation, are involved in sialic acid biology. Because of their role in immunity, sialic acid biology genes have been hypothesized to exhibit elevated rates of evolutionary change. Consistent with this hypothesis, several genes involved in sialic acid biology have experienced higher rates of non-synonymous substitutions in the human lineage than their counterparts in other great apes, perhaps in response to ancient pathogens that infected hominins millions of years ago (paleopathogens). To test whether sialic acid biology genes have also experienced more recent positive selection during the evolution of the modern human lineage, reflecting adaptation to contemporary cosmopolitan or geographically-restricted pathogens, we examined whether their protein-coding regions showed evidence of recent hard and soft selective sweeps. This examination involved the calculation of four measures that quantify changes in allele frequency spectra, extent of population differentiation, and haplotype homozygosity caused by recent hard and soft selective sweeps for 55 sialic acid biology genes using publicly available whole genome sequencing data from 1,668 humans from three ethnic groups. To disentangle evidence for selection from confounding demographic effects, we compared the observed patterns in sialic acid biology genes to simulated sequences of the same length under a model of neutral evolution that takes into account human demographic history. We found that the patterns of genetic variation of most sialic acid biology genes did not significantly deviate from neutral expectations and were not significantly different among genes belonging to different functional categories. Those few sialic acid biology genes that significantly deviated from neutrality either experienced soft sweeps or population-specific hard sweeps. Interestingly, while most hard sweeps occurred on genes involved in sialic acid recognition, most soft sweeps involved genes associated with recycling, degradation and activation, transport, and transfer functions. We propose that the lack of signatures of recent positive selection for the majority of the sialic acid biology genes is consistent with the view that these genes regulate immune responses against ancient rather than contemporary cosmopolitan or geographically restricted pathogens.

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 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

scholarly journals Detecting Recent Positive Selection with High Accuracy and Reliability by Conditional Coalescent Tree

2014 ◽  
Vol 31 (11) ◽  
pp. 3068-3080 ◽  
Author(s):  
Minxian Wang ◽  
Xin Huang ◽  
Ran Li ◽  
Hongyang Xu ◽  
Li Jin ◽  
...  
Keyword(s):  
Positive Selection ◽  
High Accuracy ◽  
Recent Positive Selection ◽  
Coalescent Tree
Sign in / Sign up

Export Citation Format

Share Document