Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures.
Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures.
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DOI：
10.1038/s41467-021-25524-4
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发表时间：
2021-09-07
影响因子：
16.6
通讯作者：
Schierup MH
中科院分区：
文献类型：
--
作者：
Coll Macià M;Skov L;Peter BM;Schierup MH
在主要的非洲事件之后，人类与尼安德特人杂交，留下了1-2%的尼安德特人DNA分散在今天所有非非洲基因组的小片段中。在这里，我们调查可以了解人类的人口统计过程，从这些片段的大小分布。我们观察到欧亚大陆的片段长度差异，东亚人的片段长度比西欧人长12%。现存种群与古代样本之间的比较表明，这些差异是由于自尼安德特人混合以来，通过重组而产生的不同衰减率造成的。在一致性，我们观察到的平均片段长度和突变积累之间的强相关性，类似于预期通过改变年龄在生殖估计从三人组的研究。总而言之，我们的研究结果表明，在过去的40，000年里，欧亚大陆的世代间隔差异增加了10- 20%。我们使用性别特异性突变特征来推断这些变化是否是由男性或女性生殖年龄的变化驱动的，或者两者兼而有之。我们还发现，以前报道的突变谱的变化可能在很大程度上解释了世代间隔的变化。我们的结论是，尼安德特人的片段长度提供了独特的洞察人类种群之间的差异在近代历史。尼安德特人和人类之间的历史杂交应该在现代人类基因组中留下历史人口统计学的签名。分析非非洲基因组中尼安德特人片段的大小分布表明，欧亚大陆的世代间隔存在一致的差异，这可以解释突变谱的变化。
After the main Out-of-Africa event, humans interbred with Neanderthals leaving 1–2% of Neanderthal DNA scattered in small fragments in all non-African genomes today. Here we investigate what can be learned about human demographic processes from the size distribution of these fragments. We observe differences in fragment length across Eurasia with 12% longer fragments in East Asians than West Eurasians. Comparisons between extant populations with ancient samples show that these differences are caused by different rates of decay in length by recombination since the Neanderthal admixture. In concordance, we observe a strong correlation between the average fragment length and the mutation accumulation, similar to what is expected by changing the ages at reproduction as estimated from trio studies. Altogether, our results suggest differences in the generation interval across Eurasia, by up 10–20%, over the past 40,000 years. We use sex-specific mutation signatures to infer whether these changes were driven by shifts in either male or female age at reproduction, or both. We also find that previously reported variation in the mutational spectrum may be largely explained by changes to the generation interval. We conclude that Neanderthal fragment lengths provide unique insight into differences among human populations over recent history. Historical interbreeding between Neanderthals and humans should leave signatures of historical demographics in modern human genomes. Analysing the size distribution of Neanderthal fragments in non-African genomes suggests consistent differences in the generation interval across Eurasia, and that this could explain mutational spectrum variation.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
64.8
作者：
Lazaridis, Iosif;Patterson, Nick;Mittnik, Alissa;Renaud, Gabriel;Mallick, Swapan;Kirsanow, Karola;Sudmant, Peter H.;Schraiber, Joshua G.;Castellano, Sergi;Lipson, Mark;Berger, Bonnie;Economou, Christos;Bollongino, Ruth;Fu, Qiaomei;Bos, Kirsten I.;Nordenfelt, Susanne;Li, Heng;de Filippo, Cesare;Pruefer, Kay;Sawyer, Susanna;Posth, Cosimo;Haak, Wolfgang;Hallgren, Fredrik;Fornander, Elin;Rohland, Nadin;Delsate, Dominique;Francken, Michael;Guinet, Jean-Michel;Wahl, Joachim;Ayodo, George;Babiker, Hamza A.;Bailliet, Graciela;Balanovska, Elena;Balanovsky, Oleg;Barrantes, Ramiro;Bedoya, Gabriel;Ben-Ami, Haim;Bene, Judit;Berrada, Fouad;Bravi, Claudio M.;Brisighelli, Francesca;Busby, George B. J.;Cali, Francesco;Churnosov, Mikhail;Cole, David E. C.;Corach, Daniel;Damba, Larissa;van Driem, George;Dryomov, Stanislav;Dugoujon, Jean-Michel;Fedorova, Sardana A.;Romero, Irene Gallego;Gubina, Marina;Hammer, Michael;Henn, Brenna M.;Hervig, Tor;Hodoglugil, Ugur;Jha, Aashish R.;Karachanak-Yankova, Sena;Khusainova, Rita;Khusnutdinova, Elza;Kittles, Rick;Kivisild, Toomas;Klitz, William;Kucinskas, Vaidutis;Kushniarevich, Alena;Laredj, Leila;Litvinov, Sergey;Loukidis, Theologos;Mahley, Robert W.;Melegh, Bela;Metspalu, Ene;Molina, Julio;Mountain, Joanna;Nakkalajarvi, Klemetti;Nesheva, Desislava;Nyambo, Thomas;Osipova, Ludmila;Parik, Jueri;Platonov, Fedor;Posukh, Olga;Romano, Valentino;Rothhammer, Francisco;Rudan, Igor;Ruizbakiev, Ruslan;Sahakyan, Hovhannes;Sajantila, Antti;Salas, Antonio;Starikovskaya, Elena B.;Tarekegn, Ayele;Toncheva, Draga;Turdikulova, Shahlo;Uktveryte, Ingrida;Utevska, Olga;Vasquez, Rene;Villena, Mercedes;Voevoda, Mikhail;Winkler, Cheryl A.;Yepiskoposyan, Levon;Zalloua, Pierre;Zemunik, Tatijana;Cooper, Alan;Capelli, Cristian;Thomas, Mark G.;Ruiz-Linares, Andres;Tishkoff, Sarah A.;Singh, Lalji;Thangaraj, Kumarasamy;Villems, Richard;Comas, David;Sukernik, Rem;Metspalu, Mait;Meyer, Matthias;Eichler, Evan E.;Burger, Joachim;Slatkin, Montgomery;Paeaebo, Svante;Kelso, Janet;Reich, David;Krause, Johannes
通讯作者：
Krause, Johannes
DOI：
10.1126/science.1224344
发表时间：
2012-10-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Meyer M;Kircher M;Gansauge MT;Li H;Racimo F;Mallick S;Schraiber JG;Jay F;Prüfer K;de Filippo C;Sudmant PH;Alkan C;Fu Q;Do R;Rohland N;Tandon A;Siebauer M;Green RE;Bryc K;Briggs AW;Stenzel U;Dabney J;Shendure J;Kitzman J;Hammer MF;Shunkov MV;Derevianko AP;Patterson N;Andrés AM;Eichler EE;Slatkin M;Reich D;Kelso J;Pääbo S
通讯作者：
Pääbo S
影响因子：
64.8
作者：
Mallick, Swapan;Li, Heng;Lipson, Mark;Mathieson, Iain;Gymrek, Melissa;Racimo, Fernando;Zhao, Mengyao;Chennagiri, Niru;Nordenfelt, Susanne;Tandon, Arti;Skoglund, Pontus;Lazaridis, Iosif;Sankararaman, Sriram;Fu, Qiaomei;Rohland, Nadin;Renaud, Gabriel;Erlich, Yaniv;Willems, Thomas;Gallo, Carla;Spence, Jeffrey P.;Song, Yun S.;Poletti, Giovanni;Balloux, Francois;van Driem, George;de Knijff, Peter;Romero, Irene Gallego;Jha, Aashish R.;Behar, Doron M.;Bravi, Claudio M.;Capelli, Cristian;Hervig, Tor;Moreno-Estrada, Andres;Posukh, Olga L.;Balanovska, Elena;Balanovsky, Oleg;Karachanak-Yankova, Sena;Sahakyan, Hovhannes;Toncheva, Draga;Yepiskoposyan, Levon;Tyler-Smith, Chris;Xue, Yali;Abdullah, M. Syafiq;Ruiz-Linares, Andres;Beall, Cynthia M.;Di Rienzo, Anna;Jeong, Choongwon;Starikovskaya, Elena B.;Metspalu, Ene;Parik, Juri;Villems, Richard;Henn, Brenna M.;Hodoglugil, Ugur;Mahley, Robert;Sajantila, Antti;Stamatoyannopoulos, George;Wee, Joseph T. S.;Khusainova, Rita;Khusnutdinova, Elza;Litvinov, Sergey;Ayodo, George;Comas, David;Hammer, Michael F.;Kivisild, Toomas;Klitz, William;Winkler, Cheryl A.;Labuda, Damian;Bamshad, Michael;Jorde, Lynn B.;Tishkoff, Sarah A.;Watkins, W. Scott;Metspalu, Mait;Dryomov, Stanislav;Sukernik, Rem;Singh, Lalji;Thangaraj, Kumarasamy;Paeaebo, Svante;Kelso, Janet;Patterson, Nick;Reich, David
通讯作者：
Reich, David
影响因子：
4.3
作者：
Kelleher J;Etheridge AM;McVean G
通讯作者：
McVean G