Doctoral Dissertation Improvement: Testing for archaic hominid introgression in Eritrean and Yemeni modern human genomes

科学家们一致认为，现代人类在非洲进化，然后在大约6万年前分散在欧洲和亚洲。直到最近，这一过程被认为是在没有来自尼安德特人或其他古代人类的任何遗传输入的情况下发生的。相比之下，人类学遗传学的最新研究表明，尼安德特人和西伯利亚丹尼索瓦洞穴中新描述的“丹尼索瓦人”之间存在轻微的基因杂交。这些论点是基于尼安德特人基因组草图与许多人类全基因组序列的比较;然而，没有一个完整的人类基因组来自非洲之角或阿拉伯半岛南部，这是研究第一批人类走出非洲的关键地区。也有人质疑尼安德特人杂交繁殖的证据是否可能是祖先人口的人工制品，而不是随机繁殖（即，反映了古代非洲人口的遗传结构）。 使用来自厄立特里亚和也门的全基因组序列，博士生Deven Vyas（佛罗里达大学）在Connie Mulligan博士的指导下，将测试与非洲古代人口结构的古代人类遗传杂交的对比假设。最新的下一代测序技术将用于生成整个人类基因组序列，新开发的分析方法将从统计学上检验这两种相互竞争的假设是否得到支持。这些数据对我们理解人类的进化历史以及我们对现代人类基因库的人口和过程的了解具有重要意义。这些来自厄立特里亚和也门的新基因数据将向全世界的研究人员公开，以促进未来的研究。此外，对科学研究感兴趣的本科生将协助这一项目，继续指导和培训本科生在由Mulligan博士指导的佛罗里达大学人类学系人类遗传学实验室进行科学研究的优良传统。

There is strong consensus among scientists that modern humans evolved in Africa and then dispersed throughout Europe and Asia around 60 thousand years ago. Until recently, this process was thought to have occurred without any genetic input from Neanderthals or other archaic humans. In contrast, recent research in anthropological genetics has suggested there were minor levels of genetic interbreeding with Neanderthals and the newly described "Denisovans" from Denisova cave in Siberia. These arguments are based on comparisons of the draft Neanderthal genome to a number of human whole genomes sequences; however, none of the whole human genomes came from the Horn of Africa or southern Arabia, which are regions critical to studies of the first human dispersals out of Africa. It also has been questioned whether the evidence for Neanderthal interbreeding could instead be an artifact of the ancestral human population not randomly breeding (i.e., reflective of genetic structure in the ancient African population). Using whole genome sequences from Eritrea and Yemen, doctoral student Deven Vyas (University of Florida), under the guidance of Dr. Connie Mulligan, will test the contrasting hypotheses of genetic interbreeding with archaic humans versus ancient population structure in Africa. The latest next-generation sequencing technologies will be utilized to generate whole human genome sequences, and newly developed analytical methods will statistically test support for the two competing hypotheses. The data have significant implications for our understanding of the evolutionary history of humans and our knowledge of the populations and processes that contributed to the modern human gene pool. These novel genetic data from Eritrean and Yemeni individuals will be publicly available to researchers all over the world, facilitating future research. In addition, undergraduate students interested in scientific research will be assisting in this project, continuing the strong tradition of mentoring and training undergraduates to conduct scientific research in the Department of Anthropology's Human Genetics Laboratory at the University of Florida, directed by Dr. Mulligan.