dN/dS 検定を利用した論文
13 Mar. 2020. Jun Inoue

dN/dS 検定についてはこちらを参照してください。Wikipedia にも解説があります。



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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。

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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)。

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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。

適応進化遺伝学.東京大学新領域. PDF.


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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.


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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)。

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「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.

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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)。


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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.

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

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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)。


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

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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)。


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