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1
Changing effective population size and the McDonald-Kreitman test.有效种群大小的变化与麦克唐纳-克里特曼检验
Genetics. 2002 Dec;162(4):2017-24. doi: 10.1093/genetics/162.4.2017.
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Changing Population Size in McDonald-Kreitman Style Analyses: Artifactual Correlations and Adaptive Evolution between Humans and Chimpanzees.麦当劳-克里坦风格分析中的种群大小变化：人类和黑猩猩之间的人为关联和适应性进化。
Genome Biol Evol. 2022 Feb 4;14(2). doi: 10.1093/gbe/evac022.
3
Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations.密码子使用偏好会影响适应性氨基酸固定分数的估算。
Mol Biol Evol. 2016 Jun;33(6):1580-9. doi: 10.1093/molbev/msw027. Epub 2016 Feb 12.
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Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome.果蝇基因组中反复出现的有益氨基酸替换的搭便车效应。
Genome Res. 2007 Dec;17(12):1755-62. doi: 10.1101/gr.6691007. Epub 2007 Nov 7.
5
Why time matters: codon evolution and the temporal dynamics of dN/dS.时间为何重要：密码子进化与dN/dS的时间动态
Mol Biol Evol. 2014 Jan;31(1):212-31. doi: 10.1093/molbev/mst192. Epub 2013 Oct 14.
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impMKT: the imputed McDonald and Kreitman test, a straightforward correction that significantly increases the evidence of positive selection of the McDonald and Kreitman test at the gene level.impMKT：推断的 McDonald-Kreitman 检验，一种简单直接的校正方法，可极大地增强基因水平 McDonald-Kreitman 检验阳性选择的证据。
G3 (Bethesda). 2022 Sep 30;12(10). doi: 10.1093/g3journal/jkac206.
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Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale.在系统发育尺度上发生适应的基因和位点也表现出种群遗传尺度上的适应。
Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2214977120. doi: 10.1073/pnas.2214977120. Epub 2023 Mar 10.
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Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change.在存在轻微有害突变和种群大小变化的情况下估计适应性分子进化的速率。
Mol Biol Evol. 2009 Sep;26(9):2097-108. doi: 10.1093/molbev/msp119. Epub 2009 Jun 17.
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Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes.细菌基因组中的同义多态性和非同义多态性与分歧
Mol Biol Evol. 2008 Oct;25(10):2199-209. doi: 10.1093/molbev/msn166. Epub 2008 Jul 30.
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The effects of linkage on comparative estimators of selection.连锁效应对选择的比较估计量的影响。
BMC Evol Biol. 2013 Nov 7;13:244. doi: 10.1186/1471-2148-13-244.
引用本文的文献
1
Lineage-specific targets of positive selection in three leaf beetles correspond with defence capacity against their shared parasitoid wasp.三种叶甲中正向选择的谱系特异性靶点与它们对共同寄生蜂的防御能力相对应。
Heredity (Edinb). 2025 Sep 8. doi: 10.1038/s41437-025-00794-6.
2
Population Genomics of from Four African Countries.来自四个非洲国家的……的群体基因组学 （原文此处不完整）
medRxiv. 2024 Sep 9:2024.09.07.24313132. doi: 10.1101/2024.09.07.24313132.
3
Increased Positive Selection in Highly Recombining Genes Does not Necessarily Reflect an Evolutionary Advantage of Recombination.高度重组基因中增加的正向选择并不一定反映重组的进化优势。
Mol Biol Evol. 2024 Jun 1;41(6). doi: 10.1093/molbev/msae107.
4
Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data.关于患者体内严重急性呼吸综合征冠状病毒2（SARS-CoV-2）多态性数据解读的群体遗传学考量
Nat Commun. 2024 Apr 16;15(1):3240. doi: 10.1038/s41467-024-46261-4.
5
An efficient and robust ABC approach to infer the rate and strength of adaptation.一种高效稳健的 ABC 方法，用于推断适应的速度和强度。
G3 (Bethesda). 2024 Apr 3;14(4). doi: 10.1093/g3journal/jkae031.
6
Population Genomics of the Mostly Thelytokous Diplolepis rosae (Linnaeus, 1758) (Hymenoptera: Cynipidae) Reveals Population-specific Selection for Sex. Mostly 胎生的玫瑰短须盘长尾小蜂（膜翅目：长尾小蜂科）的种群基因组学揭示了种群特异性的性选择。
Genome Biol Evol. 2023 Oct 6;15(10). doi: 10.1093/gbe/evad185.
7
Inferring the distributions of fitness effects and proportions of strongly deleterious mutations.推断适应度效应的分布和强有害突变的比例。
G3 (Bethesda). 2023 Aug 30;13(9). doi: 10.1093/g3journal/jkad140.
8
Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale.在系统发育尺度上发生适应的基因和位点也表现出种群遗传尺度上的适应。
Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2214977120. doi: 10.1073/pnas.2214977120. Epub 2023 Mar 10.
9
Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations.生态进化灭绝和再殖民化动态减少了高度近亲繁殖种群的遗传负荷并增加了灭绝时间。
Evolution. 2022 Nov;76(11):2482-2497. doi: 10.1111/evo.14620. Epub 2022 Sep 28.
10
Two decades of suspect evidence for adaptive molecular evolution-negative selection confounding positive-selection signals.二十年关于适应性分子进化的可疑证据——负选择混淆正选择信号。
Natl Sci Rev. 2021 Dec 3;9(5):nwab217. doi: 10.1093/nsr/nwab217. eCollection 2022 May.
本文引用的文献
1
The Distribution of Gene Frequencies Under Irreversible Mutation.不可逆突变下基因频率的分布
Proc Natl Acad Sci U S A. 1938 Jul;24(7):253-9. doi: 10.1073/pnas.24.7.253.
2
Quantifying the slightly deleterious mutation model of molecular evolution.量化分子进化的轻度有害突变模型。
Mol Biol Evol. 2002 Dec;19(12):2142-9. doi: 10.1093/oxfordjournals.molbev.a004039.
3
Testing the neutral theory of molecular evolution with genomic data from Drosophila.利用果蝇的基因组数据检验分子进化的中性理论。
Nature. 2002 Feb 28;415(6875):1024-6. doi: 10.1038/4151024a.
4
Adaptive protein evolution in Drosophila.果蝇中的适应性蛋白质进化。
Nature. 2002 Feb 28;415(6875):1022-4. doi: 10.1038/4151022a.
5
Positive and negative selection on the human genome.人类基因组的正向和负向选择
Genetics. 2001 Jul;158(3):1227-34. doi: 10.1093/genetics/158.3.1227.
6
The evolution of isochores.等密度区带的演化
Nat Rev Genet. 2001 Jul;2(7):549-55. doi: 10.1038/35080577.
7
The frequency distribution of nucleotide variation in Drosophila simulans.拟暗果蝇核苷酸变异的频率分布。
Mol Biol Evol. 2001 Jul;18(7):1343-52. doi: 10.1093/oxfordjournals.molbev.a003918.
8
Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans.黑腹果蝇和拟暗果蝇中X连锁和常染色体核苷酸变异的对比模式。
Mol Biol Evol. 2001 Mar;18(3):279-90. doi: 10.1093/oxfordjournals.molbev.a003804.
9
Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees.人类与其他类人猿之间的基因组差异以及人类和黑猩猩共同祖先的有效种群大小。
Am J Hum Genet. 2001 Feb;68(2):444-56. doi: 10.1086/318206. Epub 2001 Jan 15.
10
Deleterious mutations and the evolution of sex.有害突变与性别的进化
Science. 2000 Oct 13;290(5490):331-3. doi: 10.1126/science.290.5490.331.
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