复发性混合机制模型中混合比例的推断。
Inference on admixture fractions in a mechanistic model of recurrent admixture.
作者信息
Buzbas Erkan Ozge, Verdu Paul
机构信息
Department of Statistical Science, University of Idaho, United States.
CNRS/MNHN/Université Paris Diderot/Sorbonne Paris Cité, France.
出版信息
Theor Popul Biol. 2018 Jul;122:149-157. doi: 10.1016/j.tpb.2018.03.006. Epub 2018 Mar 28.
Abstract
Signatures of recent historical admixture are ubiquitous in human populations. We present a mechanistic model of admixture with two source populations, encompassing recurrent admixture periods and study the distribution of admixture fractions for finite but arbitrary genome size. We provide simulation-based methods to estimate the introgression parameters and discuss the implications of reaching stationarity on estimability of parameters when there are recurrent admixture events with different rates.
摘要
近期历史混合的特征在人类群体中普遍存在。我们提出了一个包含两个源群体的混合机制模型，涵盖了反复混合的时期，并研究了有限但任意基因组大小下混合比例的分布。我们提供了基于模拟的方法来估计基因渗入参数，并讨论了在存在不同速率的反复混合事件时达到平稳状态对参数可估计性的影响。
相似文献
1
Inference on admixture fractions in a mechanistic model of recurrent admixture.复发性混合机制模型中混合比例的推断。
Theor Popul Biol. 2018 Jul;122:149-157. doi: 10.1016/j.tpb.2018.03.006. Epub 2018 Mar 28.
2
Complex genetic admixture histories reconstructed with Approximate Bayesian Computation.利用近似贝叶斯计算重建复杂的遗传混合历史。
Mol Ecol Resour. 2021 May;21(4):1098-1117. doi: 10.1111/1755-0998.13325. Epub 2021 Feb 26.
3
Population divergence with or without admixture: selecting models using an ABC approach.群体的分化是否存在混合：使用 ABC 方法选择模型。
Heredity (Edinb). 2012 May;108(5):521-30. doi: 10.1038/hdy.2011.116. Epub 2011 Dec 7.
4
AABC: approximate approximate Bayesian computation for inference in population-genetic models.AABC：用于群体遗传模型推断的近似近似贝叶斯计算
Theor Popul Biol. 2015 Feb;99:31-42. doi: 10.1016/j.tpb.2014.09.002. Epub 2014 Sep 26.
5
Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0).使用 DIYABC（v1.0）软件通过 DNA 序列和微卫星数据进行群体历史推断和模型检验。
BMC Bioinformatics. 2010 Jul 28;11:401. doi: 10.1186/1471-2105-11-401.
6
Statistical inference on genetic data reveals the complex demographic history of human populations in central Asia.遗传数据的统计推断揭示了中亚人群复杂的人口历史。
Mol Biol Evol. 2015 Jun;32(6):1411-24. doi: 10.1093/molbev/msv030. Epub 2015 Feb 11.
7
On the use of kernel approximate Bayesian computation to infer population history.关于使用核近似贝叶斯计算来推断种群历史。
Genes Genet Syst. 2015;90(3):153-62. doi: 10.1266/ggs.90.153.
8
Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone.在推断物种形成历史时，我们能否继续忽视基因渗入率中的基因组变异？贻贝杂交带的一个案例研究。
J Evol Biol. 2014 Aug;27(8):1662-75. doi: 10.1111/jeb.12425. Epub 2014 Jun 10.
9
PSMIX: an R package for population structure inference via maximum likelihood method.PSMIX：一个用于通过最大似然法进行群体结构推断的R软件包。
BMC Bioinformatics. 2006 Jun 22;7:317. doi: 10.1186/1471-2105-7-317.
10
Multiple introductions, admixture and bridgehead invasion characterize the introduction history of Ambrosia artemisiifolia in Europe and Australia.多次引入、混合以及桥头入侵是欧洲和澳大利亚豚草引入历史的特征。
Mol Ecol. 2017 Oct;26(20):5421-5434. doi: 10.1111/mec.14293. Epub 2017 Sep 11.
引用本文的文献
1
Temporal Variation in Introgressed Segments' Length Statistics Computed from a Limited Number of Ancient Genomes Sheds Light on Past Admixture Pulses.从有限数量的古代基因组计算得出的渐渗片段长度统计的时间变化揭示了过去的混合脉冲。
Mol Biol Evol. 2023 Dec 1;40(12). doi: 10.1093/molbev/msad252.
2
A genetic and linguistic analysis of the admixture histories of the islands of Cabo Verde.对佛得角群岛的混合历史的遗传和语言分析。
Elife. 2023 Apr 25;12:e79827. doi: 10.7554/eLife.79827.
3
Human genetic admixture through the lens of population genomics.透过群体基因组学视角看人类遗传混合
Philos Trans R Soc Lond B Biol Sci. 2022 Jun 6;377(1852):20200410. doi: 10.1098/rstb.2020.0410. Epub 2022 Apr 18.
4
Complex genetic admixture histories reconstructed with Approximate Bayesian Computation.利用近似贝叶斯计算重建复杂的遗传混合历史。
Mol Ecol Resour. 2021 May;21(4):1098-1117. doi: 10.1111/1755-0998.13325. Epub 2021 Feb 26.
5
Exploring Cuba's population structure and demographic history using genome-wide data.利用全基因组数据探索古巴的人口结构和人口历史。
Sci Rep. 2018 Jul 30;8(1):11422. doi: 10.1038/s41598-018-29851-3.
本文引用的文献
1
THE INFLUENCE OF POPULATION SIZE AND ISOLATION ON GENE FLOW BY POLLEN IN SILENE ALBA.种群大小和隔离对白麦瓶草花粉基因流动的影响
Evolution. 1999 Feb;53(1):63-73. doi: 10.1111/j.1558-5646.1999.tb05333.x.
2
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.西蒙斯基因组多样性项目：来自142个不同群体的300个基因组。
Nature. 2016 Oct 13;538(7624):201-206. doi: 10.1038/nature18964. Epub 2016 Sep 21.
3
The Demographic Development of the First Farmers in Anatolia.安纳托利亚首批农民的人口发展情况。
Curr Biol. 2016 Oct 10;26(19):2659-2666. doi: 10.1016/j.cub.2016.07.057. Epub 2016 Aug 4.
4
Reliable ABC model choice via random forests.基于随机森林的可靠 ABC 模型选择。
Bioinformatics. 2016 Mar 15;32(6):859-66. doi: 10.1093/bioinformatics/btv684. Epub 2015 Nov 20.
5
Beyond 2/3 and 1/3: The Complex Signatures of Sex-Biased Admixture on the X Chromosome.超越三分之二与三分之一：X染色体上性别偏向性混合的复杂特征
Genetics. 2015 Sep;201(1):263-79. doi: 10.1534/genetics.115.178509. Epub 2015 Jul 24.
6
POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.群体遗传学。美洲原住民更新世及近代群体历史的基因组证据。
Science. 2015 Aug 21;349(6250):aab3884. doi: 10.1126/science.aab3884. Epub 2015 Jul 21.
7
Genetic evidence for two founding populations of the Americas.美洲两个奠基人群体的遗传学证据。
Nature. 2015 Sep 3;525(7567):104-8. doi: 10.1038/nature14895. Epub 2015 Jul 21.
8
Ancient human genomes suggest three ancestral populations for present-day Europeans.古代人类基因组表明当今欧洲人有三个祖先群体。
Nature. 2014 Sep 18;513(7518):409-13. doi: 10.1038/nature13673.
9
Autosomal admixture levels are informative about sex bias in admixed populations.常染色体混合水平有助于了解混合群体中的性别偏差。
Genetics. 2014 Nov;198(3):1209-29. doi: 10.1534/genetics.114.166793. Epub 2014 Sep 5.
10
Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers.非洲雨林狩猎采集者中侏儒表型的适应性趋同起源。
Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):E3596-603. doi: 10.1073/pnas.1402875111. Epub 2014 Aug 18.
Zotero 插件