Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding.
Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding.
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DOI：
10.1098/rsos.201229
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发表时间：
2021-06-16
影响因子：
3.5
通讯作者：
Amos W
中科院分区：
文献类型：
--
作者：
Amos W
尽管古人类遗产在人类中的存在被认为是理所当然的，但对于这些数据如何与人类殖民世界的方式相吻合，人们几乎没有给予关注。在这里，我展示了尼安德特人和丹尼索瓦人的遗产是密切相关的，并且推断的遗产大小，如杂合度，显示出与距离非洲的强烈相关性。模拟证实，一旦创建，遗产大小是极其稳定的：通过与较低的遗产种群混合，它可以减少，但不能通过中性漂移显著增加。因此，携带最高遗产的种群很可能是其祖先与古人杂交最多的种群。然而，具有最高遗产的种群是全球分散和统一的，不是因为起源于已知的尼安德特人范围内，而是因为生活在离非洲最远的地方。此外，西蒙斯基因组多样性项目的数据揭示了尼安德特人和丹尼索瓦人之间的两种截然不同的相关性，一种是从北非开始，从西向东穿过欧亚大陆并进入大洋洲的一些地区，另一种是从非洲开始的更陡峭的趋势，以圣人和朱氏/‘环西人为顶峰，如果推断，这两种古生物在大洋洲/澳大利亚发现的大量推断遗产。在Qin和Stoneking(Qin&Stoneking，2015Mol)发布的第二个大型数据集中，也观察到了类似的自回归统计f4趋势。比奥尔。埃沃尔。32,2665-2674(doi：10.1093/molbev/msv141)。这些趋势似乎与关于内向如何发生的简单模型不一致，尽管更复杂的内向模式可能会产生更好的匹配。此外，用大猩猩的基因组取代古老的基因组会产生类似的、但在生物学上不可能产生的渐渗信号，这表明这些指标捕获的信号来自人类内部，在很大程度上独立于测试组。有趣的是，这些数据似乎确实符合一种推测模型，即当人类从非洲迁徙到更远的地方时，多样性的丧失造成了杂合性的梯度，这反过来又逐渐降低了突变率，从而使距离非洲最远的种群与我们共同的祖先的分歧更小，从而与古生物的分歧也更小。从这个角度来看，这两个截然不同的趋势可以用两个“走出非洲”的事件来解释，一个是早期在大洋洲和澳大利亚结束的事件，另一个是在欧亚大陆和美洲殖民的事件。
Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance from Africa. Simulations confirm that, once created, legacy size is extremely stable: it may reduce through admixture with lower legacy populations but cannot increase significantly through neutral drift. Consequently, populations carrying the highest legacies are likely to be those whose ancestors inter-bred most with archaics. However, the populations with the highest legacies are globally scattered and are unified, not by having origins within the known Neanderthal range, but instead by living in locations that lie furthest from Africa. Furthermore, the Simons Genome Diversity Project data reveal two distinct correlations between Neanderthal and Denisovan legacies, one that starts in North Africa and increases west to east across Eurasia and into some parts of Oceania, and a second, much steeper trend that starts in Africa, peaking with the San and Ju/’hoansi and which, if extrapolated, predicts the large inferred legacies of both archaics found in Oceania/Australia. Similar ‘double’ trends are observed for the introgression statistic f4 in a second large dataset published by Qin and Stoneking (Qin & Stoneking 2015 Mol. Biol. Evol. 32, 2665–2674 (doi:10.1093/molbev/msv141)). These trends appear at odds with simple models of how introgression occurred though more complicated patterns of introgression could potentially generate better fits. Moreover, substituting archaic genomes with those of great apes yields similar but biologically impossible signals of introgression, suggesting that the signals these metrics capture arise within humans and are largely independent of the test group. Interestingly, the data do appear to fit a speculative model in which the loss of diversity that occurred when humans moved further from Africa created a gradient in heterozygosity that in turn progressively reduced mutation rate such that populations furthest from Africa have diverged less from our common ancestor and hence from the archaics. In this light, the two distinct trends could be interpreted in terms of two ‘out of Africa’ events, an early one ending in Oceania and Australia and a later one that colonized Eurasia and the Americas.
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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：
3.7
作者：
Amos W
通讯作者：
Amos W
DOI：
10.1073/pnas.1418652112
发表时间：
2015-03-17
影响因子：
11.1
作者：
Harris, Kelley
通讯作者：
Harris, Kelley
影响因子：
10.7
作者：
Martin, Simon H.;Davey, John W.;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.