2020

Whittle CA, Kulkarni A, Extavour CG. 2020.
Absence of a Faster-X Effect in Beetles (Tribolium, Coleoptera). G3 (Bethesda) 10:1125-1136.

2019

Bernal MA, Dixon GB, Matz MV, Rocha LA. 2019.
Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon). PeerJ 7:e6541.

Okamura Y, Sato A, Tsuzuki N, Murakami M, Heidel-Fischer H, Vogel H. 2019.
Molecular signatures of selection associated with host plant differences in Pieris butterflies. Molecular Ecology 28:4958-4970.

Marks RA, Smith JJ, Cronk Q, Grassa CJ, McLetchie DN. 2019.
Genome of the tropical plant Marchantia inflexa: implications for sex chromosome evolution and dehydration tolerance. Scientific Reports 9:8722.

Qu Z, Li W, Zhang N, Li L, Yan H, Li T, Cui J, Yang Y, Jia W, Fu B. 2019.
Comparative Genomic Analysis of Trichinella spiralis Reveals Potential Mechanisms of Adaptive Evolution. Biomed Res Int 2019:2948973.

Wang RH, Li MD, Wu XM, Wang JB. 2019.
The Gene Structure and Expression Level Changes of the GH3 Gene Family in Brassica napus Relative to Its Diploid Ancestors. Genes 10.

2018

Bast J, Parker DJ, Dumas Z, Jalvingh KM, Tran Van P, Jaron KS, Figuet E, Brandt A, Galtier N, Schwander T. 2018.
Consequences of Asexuality in Natural Populations: Insights from Stick Insects. Molecular Biology and Evolution 35:1668-1677.

Davies KTJ, Bennett NC, Faulkes CG, Rossiter SJ. 2018.
Limited Evidence for Parallel Molecular Adaptations Associated with the Subterranean Niche in Mammals: A Comparative Study of Three Superorders. Molecular Biology and Evolution 35:2544-2559.

地中生活を送る哺乳類で修練進化したタンパク質遺伝子を検証．収斂進化の兆候は地中生活を送らない哺乳類でも見られたことから，地中生活を送る哺乳類で見られる表現型の収斂進化は，異なる遺伝子座に選択圧がかかって生じたと結論．オーソログ判定は Ensembl-API による．正の自然淘汰を受けた遺伝子を codeml によって判定。

Fujimoto A. 2018.
ゲノムシークエンスデータの情報解析. 生物物理 58:149-151.

Ghiselli F, Iannello M, Puccio G, Chang PL, Plazzi F, Nuzhdin SV, Passamonti M. 2018.
Comparative Transcriptomics in Two Bivalve Species Offers Different Perspectives on the Evolution of Sex-Biased Genes. Genome Biology and Evolution 10:1389-1402.

Goodswen SJ, Kennedy PJ, Ellis JT. 2018.
A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen. Front Genet 9:332.

Hawkins JA, Kaczmarek ME, Muller MA, Drosten C, Press WH, Sawyer SL. 2019.
A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species. Proceedings of the National Academy of Sciences of the United States of America 116:11351-11360.

2017

Abry MF, Kimenyi KM, Masiga D, Kulohoma BW. 2017.
Comparative genomics identifies male accessory gland proteins in five Glossina species. Wellcome Open Res 2:73.

Hawkins AK, Garza ER, Dietz VA, Hernandez OJ, Hawkins WD, Burrell AM, Pepper AE. 2017.
Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant. Genome Biology and Evolution 9:3478-3494.

Pespeni MH, Ladner JT, Moczek AP. 2017. Signals of selection in conditionally expressed genes in the diversification of three horned beetle species. Journal of Evolutionary Biology 30:1644-1657.

Sabater-Munoz B, Toft C, Alvarez-Ponce D, Fares MA. 2017.
Chance and necessity in the genome evolution of endosymbiotic bacteria of insects. ISME J 11:1291-1304.
J. Y. 2019. Positively Selected Orthologous Genes Identified in Sesame (Sesamum indicum) by Deep Resequencing. Plant Breed. Biotech.

Tong C, Fei T, Zhang CF, Zhao K. 2017.
Comprehensive transcriptomic analysis of Tibetan Schizothoracinae fish Gymnocypris przewalskii reveals how it adapts to a high altitude aquatic. BMC Evolutionary Biology 17.

2016

Biswas K, Chakraborty S, Podder S, Ghosh TC. 2016.
Insights into the dN/dS ratio heterogeneity between brain specific genes and widely expressed genes in species of different complexity. Genomics 108:11-17.

Enard D, Cai L, Gwennap C, Petrov DA. 2016.
Viruses are a dominant driver of protein adaptation in mammals. Elife 5.

Fujimoto A, Furuta M, Totoki Y, Tsunoda T, Kato M, Shiraishi Y, Tanaka H, Taniguchi H, Kawakami Y, Ueno M, et al. 2016.
Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nature Genetics 48:500-509.

発癌に重要は役割を果たすドライバー遺伝子の検出に dN/dS 検定を利用 (< Fujimoto 2018)。

Gradnigo JS, Majumdar A, Norgren RB, Jr., Moriyama EN. 2016.
Advantages of an Improved Rhesus Macaque Genome for Evolutionary Analyses. PloS One 11:e0167376.

Hoffmann RD, Palmgren M. 2016.
Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana. BMC Genomics 17:456.

Tiwary BK. 2016.
Evolution of the SRGAP2 Gene Is Linked to Intelligence in Mammals. Biomed Hub 1:1-12.

2015

Brand P, Ramirez SR, Leese F, Quezada-Euan JJ, Tollrian R, Eltz T. 2015.
Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini). BMC Evolutionary Biology 15:176.

Jeffares DC, Tomiczek B, Sojo V, dos Reis M. 2015.
A beginners guide to estimating the non-synonymous to synonymous rate ratio of all protein-coding genes in a genome. Methods in Molecular Biology 1201:65-90.

dN/dS 解析のチュートリアル。ゲノムワイドなデーターからオーソログ抽出、コドンを保持したコード配列のアライメント方法など。Plasmodium (マラリア原虫) のテストデータを利用。Perl scripts とともに、こちらから配布。

河村正二．2015.
適応進化遺伝学．東京大学新領域. PDF.

テキスト．

Kusumi J, Tsumura Y, Tachida H. 2015.
Evolutionary rate variation in two conifer species, Taxodium distichum (L.) Rich. var. distichum (baldcypress) and Cryptomeria japonica (Thunb. ex L.f.) D. Don (Sugi, Japanese cedar). Genes and Genetic Systems 90:305-315.

Lv WH, Zheng JJ, Luan MW, Shi M, Zhu HJ, Zhang MM, Lv HC, Shang ZW, Duan L, Zhang RJ, et al. 2015.
Comparing the evolutionary conservation between human essential genes, human orthologs of mouse essential genes and human housekeeping genes. Briefings in Bioinformatics 16:922-931.

Zhou X, Seim I, Gladyshev VN. 2015.
Convergent evolution of marine mammals is associated with distinct substitutions in common genes. Scientific Reports 5:16550.

2014

Zahng et al. 2014.
Comparative genomics reveals insights into avian genome evolution and adaptation.

2011

Wang Z, et al. 2011.
Domestication relaxed selective constraints on the yak mitochondrial genome. Mol. Biol. Evol. 28(5):1553-1556.

ミトコンドリアゲノム・12 タンパク質遺伝子配列データに基づいて枝モデルで ω を推定し，家畜化されたヤク集団で野生ヤク集団よりも有意に高い ω を尤度比検定で検出．
　ミトコンドリアにはエネルギー生産に関わるサブユニット (タンパク質群など) が多数存在し，ミトコンドリア DNA はこれらの一部をコードする．このため，家畜化ヤクで検出された高い ω 値は，エネルギー代謝低下につながる突然変異の蓄積を示す．家畜化されたヤクでは自然選択圧が低下し，野生で生きるための形質が多少劣化しても許容されると示唆．

2009

dos Reis M, Wernisch L (2009)
Estimating translational selection in eukaryotic genomes. Mol Biol Evol 26:451–461

Lefébure T, Stanhope MJ (2009)
Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res 19:1224–1232

寄生生物のゲノムで dN/dS 解析を行う。宿主の免疫システムとの間に繰り広げられた evolutionary arms race (進化的な軍備競争) の期間に、急速に変化した遺伝子を検出 (< Jeffares et al. 2015)。

Sato Y, Hashiguchi Y, & Nishida M (2009)
Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway BMC Systems Biology.

Yang Z. 2009.
分子系統学への統計的アプローチ - 計算分子進化学 (Computational Molecular Evolution). 藤博幸ら訳. 共立出版，東京.

「8.3 適応進化を受けている系統」などに，正の選択を検出する系統学的な方法について詳しい説明があります．

Voolstra CR, Sunagawa S, Schwarz JA, Coffroth MA, Yellowlees D, Leggat W, Medina M. 2009.
Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium). Comparative Biochemistry and Physiology: Part D, Genomics & Proteomics 4:67-74.

2008

Kosiol C, Vinar T, da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A (2008)
Patterns of positive selection in six Mammalian genomes. PLoS Genet 4:e1000144

dN/dS 比は、遺伝子の進化速度を要約する。それは、(1) 最も保存的か (あるいはそうでない) 遺伝子を示す、(2) 適応進化の期間に多様化した (?) 遺伝子を示す、ためである (< Jeffares et al. 2015)。

2008

Matsui A, Rakotondraparany F, Horai S, & Hasegawa M (2008)
霊長類のミトコンドリア DNA における進化速度. 統計数理 56(1):101–116. Web.

霊長類のミトコンドリア・全タンパク質遺伝子を枝モデルで解析し，推定された ML tree で極端に枝が長い真猿類では，DNA 変異率ではなくアミノ酸置換速度が増大したと示唆 (P109 中段)．このため機能的制約が緩んでいるか，あるいは適応的な進化が起きている可能性を指摘．尤度比検定について詳しい解説がある (P108 下の段落)．ミトコンドリアおよびそこにコードされている遺伝子の生理学的役割，および加速された進化速度に関する記述も詳しい．枝長の差異を「分子時計一定性の検定」で検出 (P107下)．
意見: まずはこの論文を熟読すると良いです．

Yang Z, Nielsen R (2008)
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol 25:568–579

2007

Clark et al (2007)
Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203–218

適応進化の研究に dN/dS 比を利用 (Jeffares et al. 2015)。

Jeffares DC, Pain A, Berry A, Cox AV, Stalker J, Ingle CE, Thomas A, Quail MA, Siebenthall K, Uhlemann AC, et al. 2007.
Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nature Genetics 39:120-125.

マラリア原虫。

Hashiguchi Y, Furuta Y, Kawahara R, & Nishida M (2007)
Diversification and adaptive evolution of putative sweet taste receptors in threespine stickleback. Gene 396(1):170–179.

Jeffares DC, Pain A, Berry A, Cox AV, Stalker J, Ingle CE, Thomas A, Quail MA, Siebenthall K, Uhlemann A-C, Kyes S, Krishna S, Newbold C, Dermitzakis ET, Berriman M (2007)
Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet 39:120–125

マラリア原虫ゲノムでゲノムの機能を dN/dS 比を用いて比較 (Jeffares et al. 2015)。

2005

Bustamante CD (2005)
Population genetics of molecular evolution. In: Nielsen R (ed)
Statistical methods in molecular evolution. Springer, New York

dN/dS 比の数学的な議論 (Jeffares et al. 2015)。

Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE (2005)
Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res 33:1141–1153

2003

Yang W, Bielawski JP, Yang Z (2003)
Widespread adaptive evolution in the human immunodefi ciency virus type 1 genome. J Mol Evol 57:212–221

寄生生物のゲノムで dN/dS 解析を行う。宿主の免疫システムとの間に繰り広げられた evolutionary arms race (進化的な軍備競争) の期間に、急速に変化した遺伝子を検出 (< Jeffares et al. 2015)。

2002

Anisimova M, Bielawski JP, Yang Z (2002)
Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol 19:950–958

2001

Anisimova M, Bielawski JP, Yang Z (2001)
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18:1585–1592

Swanson, W. J., Z. Yang, M. F. Wolfner, and C. F. Aquadro. 2001.
Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc. Natl. Acad. Sci. USA 98:2509-2514

2000

Ziheng Y, Bielawski JP (2000)
Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503

Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen. 2000b.
Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.

1998

Yang, Z. 1998.
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Molecular Biology and Evolution 15:568-573.

適応進化の研究に dN/dS 比を利用 (Jeffares et al. 2015)。