Collaborative Research: The evolutionary mechanics of hybridization across a primate radiation

这是一项关于近亲物种之间的杂交是否在灵长类动物的进化中起着重要作用的研究。最近的研究发现，许多现代人高达5%的DNA来自古代与尼安德特人的杂交，这引发了一个更广泛的问题：一个物种的基因构成是否包括通过偶尔的杂交而聚集在一起的基因。在本研究中，将比较一组猴子物种的基因组，以确定DNA片段是否在进化过程中在物种之间转移。该项目将通过与麦克奈尔学者计划（McNair Scholars Program，一项联邦计划，旨在识别有前途的第一代、低收入和/或在博士项目中代表性不足的本科生）的合作，以及与其他专注于类似高中生群体的组织合作，如哈莱姆儿童协会（Harlem Children’s Society）、BridgeUp:STEM和纽约市的ARISE，扩大在科学领域代表性不足群体的参与。该项目还将通过在互联网上免费提供所有定制编写的软件，并在泛非生物信息学组织H3ABioNet的年度会议上展示这些软件，从而加强研究的基础设施。据报道，许多物种与Cercopithecins杂交。因此，如果历史上的杂交确实在一个物种的基因组上留下了印记，那么这些证据应该很容易在这些动物身上找到，并作为研究灵长类动物杂交的模型系统。本文将讨论两个核心问题。首先，基因是更容易在亲缘关系密切的物种（例如，在一个属内）之间交换，还是在进化上存在深度分离的物种（例如，不同的属）之间交换？前一种情况允许更高的杂交频率，因为更大的整体生物相似性，而后一种情况允许更多的变异，可能更有利的基因形式在物种之间进化和转移。第二，通过杂交交换的基因是独一无二的吗？还是会发现具有相似功能的基因模式在物种之间反复杂交？如果是后者，这些模式将通过识别可能是灵长类动物进化过程的基本驱动因素的基因来揭示更普遍的模式。这些猴子物种之间的“共识”进化关系将来自对非编码DNA序列的分析；这相当于基因组的大部分，反映了进化关系的“真实”集。然后对编码序列进行单独分析，并在所有可能的物种对之间进行比较；一些序列将遵循共识模式，但那些不遵循共识模式的序列可能反映通过杂交交换的基因。一系列的统计计算将测量这些基因通过杂交被正确识别为转移的概率。

This is an investigation of whether hybridization between closely-related species has been a significant force in the evolution of primates. Recent research has uncovered that up to 5% of the DNA of many modern humans originated from ancient interbreeding with Neanderthal populations, raising the broader question of whether a species' genetic makeup includes genes brought together through occasional episodes of hybridization. In the present study, the genomes of a group of monkey species will be compared to determine whether segments of DNA have been transferred between species over evolutionary time. The project will broaden participation of groups under-represented in science through a partnership with the McNair Scholars Program (a federal program that identifies promising undergraduates who are first-generation, low-income and/or under-represented in PhD programs) and by working with other organizations that focus on similar groups of high school students, such as the Harlem Children's Society, BridgeUp:STEM, and ARISE in New York City. The project will also enhance infrastructure for research by making all custom-written software freely available on the internet and by presenting such software in workshops at the annual conference of H3ABioNet, a pan-African bioinformatics group. Hybridization has been reported among numerous species with the Cercopithecins. Thus, if historical interbreeding indeed leaves its mark on a species' genome, such evidence should be readily identified in these animals and serve as a model system for investigating hybridization in primates. Two central questions will be addressed. First, are genes more likely to be exchanged between closely related species (e.g., within a genus), or species with deep evolutionary separation (e.g., different genera)? The former scenario allows for a higher frequency of hybridization due to greater overall biological similarity, while the latter scenario allows for more variant, and possibly more advantageous, forms of genes to evolve and transfer between species. Second, will genes exchanged through hybridization be unique, or will patterns of genes with similar functions be found to repeatedly cross between species? If the latter, such patterns will reveal a more general pattern by identifying genes that are likely the essential drivers of the evolutionary process in primates. "Consensus" evolutionary relationships among these monkey species will be derived from an analysis of the total non-coding DNA sequence; this amounts to the majority of the genome and reflects the "true" set of evolutionary relationships. Coding sequences will then be analyzed individually and compared across all possible pairs of species; some sequences will follow the consensus pattern, but those that do not will likely reflect genes exchanged through hybridization. A series of statistical calculations will measure the probability of such genes being correctly identified as transfers via hybridization.