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Rapid divergence of local populations with different color forms in the dung beetle Phelotrupes auratus revealed by population genomics analyses

Araki, Yoshifumi 京都大学 DOI:10.14989/doctor.k24310

2023.01.23

概要

生物の多様化機構、特に種分化機構の解明は、生物学における究極的な課題の一つである。しかし、種分化の最初期の段階である地域集団の形成と、そこで生じている進化的現象については未解明な部分が多い。本研究では、種分化につながる可能性のある集団間分化の一例として、地理的に顕著な色彩変異を示すオオセンチコガネ Phelotrupes auratus に着目した。本種は、特にシカなどの大型草食哺乳類の糞を利用する食糞性甲虫で、鞘翅の層構造により、大別して赤色、緑色、瑠璃色の 3 つの色彩を示すが、同所的に複数の色彩型が共存することは極めて稀であり、明瞭な地理的分化が成立している。しかし、先行研究におけるミトコンドリア DNA の部分配列を用いた全国レベルでの種内系統推定では、系統分化と色彩型の間の関係は明瞭ではなく、どのように地域集団が成立したのかはわかっていなかった。そこで本研究では、地域集団形成の過程と要因を明らかにすることを目的に、集団ゲノミクス的手法を用いて集団遺伝学的構造と歴史的集団動態を解明した。

まず、制限酵素関連サイト DNA のシーケンス(RAD-seq)によって取得したゲノムワイドな SNP を用いた集団遺伝学的構造解析、表現型および遺伝子型のクライン解析、およびゲノムワイド連関解析(GWAS)を実施した。その結果、近畿地方のオオセンチコガネは遺伝的に 3 系統に分かれるが、その地理的分化は色彩型の分布を反映しておらず、遺伝的系統(西、東、南)と色彩型(赤色型、緑色型、瑠璃色型)の組み合わせにより、5 つの地域集団(西/赤、東/赤、南/赤、南/緑、南/瑠璃)に分化していることが明らかになった。さらにクライン解析により、狭い交雑帯が 2 ヵ所存在することが明らかになり、系統間で遺伝子流動が制限されていることが示唆された。交雑帯の一方では位置や規模が色彩型の移行帯とは一致しなかったことから、体色は集団間の隔離に必ずしも寄与していないことが示唆された。また、色彩と相関を示す SNP が複数見つかったことから、本種の構造色が複数の遺伝子座によって複合的に制御されている可能性が示唆された。

続いて、集団遺伝学的構造推定によって明らかになった 5 つの地域集団間の遺伝子流動の大きさを評価し、集団分化の時期と有効集団サイズの変動を明らかにするために本種の全ゲノム配列を決定し、全ゲノムリシーケンシングで得られたより詳細な SNP でータを用いて、地域集団の過去の動態を推定した。その結果、5 つの地域集団は約 3,800 年前、2,100 年前、600 年前、200 年前に分化したことが示唆された。この集団分化には約4,000〜3,600年前の寒冷化と、約2,000年前以降のヒトの急速な人口増加にともなうシカなどの大型哺乳類の集団のサイズ縮小や生息地の分断化が影響している可能性が考えられた。また、5つの地域集団間には、有効な遺伝子流動が見られず、地理的な隔離が成立していることが明らかとなった。色彩型が各地域集団内に固定された経緯は不明だが、瑠璃色型および緑色型が分化した際に集団サイズの縮小が見られることから、遺伝的浮動が色彩の集団内への固定に寄与した可能性がある。本研究により、近畿地方のオオセンチコガネは過去3,800年間に、寒冷化や人間活動の影響によって5つの独立した地域集団へと急速に分化したこと、そして地域集団間に遺伝子流動を妨げる何らかの隔離機構が作用していることが示唆された。本研究の結果は、形質の異なる、遺伝的に独立した地域集団間の形成が、我々の想像以上に急速に、容易に、かつ微細なスケールで進行し、種分化の機会をもたらしている可能性を示すものである。

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