"Rise of the continent of the monkeys": an integrated genomic and fossil-based analysis of the adaptive radiation of New World primates

新世界灵长类动物生活在中美洲和南美洲的热带地区，包括蜘蛛猴、吼猴、绒猴和卷尾猴等著名的魅力物种。今天，已知有五个科的170多个物种，它们共同表现出广泛的不同体型，饮食和活动。值得注意的是，所有这些多样性都起源于一个单一的共同祖先，该祖先在3500万至4500万年前从非洲到达南美洲，可能是通过植被筏从海上运送过来的。为什么这个祖先又是如何产生了构成现代新大陆灵长类辐射的所有不同物种的？导致不同家庭多样化的驱动因素是什么？是气候变化、安第斯山脉的隆起和亚马逊河的发展等非生物因素，还是生物因素（与其他哺乳动物的竞争）在推动多样化方面更重要？我们能否确定不同的新大陆灵长类动物群体的体型、饮食和活动模式发生变化的时间和原因？我们提出的项目将试图回答这些问题。为此，我们将结合联合收割机两种非常不同但互补的数据类型：基因组数据，提供有关活物种的详细信息，以及化石数据，提供有关过去多样性的（通常非常不完整的）信息。以前的研究通常使用基因组数据或化石数据，但我们将联合收割机结合两者，利用它们不同的优势，弥补彼此的弱点。首先，我们将检查不同新世界灵长类物种的基因组，看看我们是否可以识别与饮食，体型和活动模式等特征相关的基因。通过这样做，我们将能够推断出这些特征在不同的新世界灵长类动物群体中是如何随着时间而变化的。其次，我们将使用大量的基因组数据和复杂的方法，为所有现存的新世界灵长类物种制作一个新的进化树（进化树），以产生该群体最完整和准确的进化树，我们将使用“分子钟”来推断不同谱系彼此分裂的分歧时间。随着我们新的多样性和分歧的时间，我们将研究如何随着时间的推移多样化的速度变化，以及非常高或低的多样化速度是否与环境变化的时期相吻合。我们还将确定以前未被识别的物种，并重新评估所有已知物种的分类。这些信息将是保护工作的关键，有助于确定最需要保护的物种，以最大限度地保护生物多样性。第三，我们将使用化石记录中的数据来模拟新世界灵长类动物的现存和灭绝谱系如何随着时间的推移而多样化。这些数据可以与现存的新大陆灵长类动物的生殖发育所表明的多样化模式进行比较，看看它们是否大致相似。如果它们表现出重大差异，这表明灭绝在新世界灵长类进化中发挥了关键作用。我们还将利用化石记录来检验一个假设，即新世界灵长类动物在竞争中战胜了表面上“类灵长类”的哺乳动物（实际上是现代有袋动物的亲戚），当新世界灵长类动物的祖先从非洲来到南美洲时，这些哺乳动物已经存在。我们的项目将大大增加我们对新世界灵长类动物进化的理解，为多样化和进化过程提供新的视角，并帮助识别那些最容易灭绝的新世界灵长类动物。在这样做的过程中，我们的发现将引起广泛的科学家的兴趣，包括进化生物学家，基因组学家，生态学家和古生物学家。因为我们的项目通过严格澄清NWP物种数量和边界，我们的结果也将对政府和非政府机构的保护从业者和政策制定者具有更广泛的实际效用。

New World primates live in the tropical regions of Central and South America, and include such well-known and charismatic species as spider monkeys, howler monkeys, marmosets and capuchins. Today, there are more than 170 species known in five families, which collectively exhibit a broad range of different body sizes, diets and activity. Remarkably, all this diversity originated from a single common ancestor that reached South America from Africa 35-45 million years ago, probably by being transported over sea on a raft of vegetation. Why and how did this ancestor give rise to all the varied species that make up modern New World primate radiation? What were the drivers leading to the diversification of the different families? Were abiotic factors like changes in climate, the uplift of the Andes mountains, and the development of the Amazon river, or were biotic factors (competition with other mammals) more important in driving diversification? Can we identify when and why there were changes in body size, diet and activity pattern in different New World primate groups? Our proposed project will attempt to answer these questions. To do so, we will combine two very different, but complementary, types of data: genomic data, which provides detailed information on living species, and fossil data, which provides (often very incomplete) information on past diversity. Previous studies have usually used either genomic data or fossil data, but ours will combine the two, to take advantage of their different strengths and to compensate for each other's weaknesses. Firstly, we will examine the genomes of different New World primate species to see if we can identify genes relating to traits like diet, body size and activity pattern. By doing so, we will be able to infer how these traits have changed through time in the different New World primate groups. Secondly we will produce a new evolutionary tree (phylogeny) of all the living New World primate species, using large amounts of genomic data and sophisticated methods to produce the most complete and accurate phylogeny of the group, and we will use "molecular clocks" to infer divergence times for when different lineages split from one another. With our new phylogeny and divergence times, we will examine how the rate of diversification has varied through time, and whether very high or low rates of diversification coincide with periods of environmental change. We will also identify previously unrecognised species and reassess the taxonomy of all known species. This information will be key to conservation efforts, by helping identify the species most in need of protection to conserve maximum biodiversity. Thirdly, we will use data from the fossil record to model how living and extinct lineages of New World primates have diversified through time. This data can be compared with the pattern of diversification indicated by the phylogeny of living New World primates, to see if they are broadly similar. If they show major differences, this suggests that extinction has played a key role in New World primate evolution. We will also use the fossil record to test the hypothesis that New World primates outcompeted superficially "primate-like" mammals (actually, relatives of modern marsupials) that were already present in South America when the New World primate ancestor arrived from Africa. Our project will massively increase our understanding of New World primate evolution, shed new light on diversification and evolutionary processes in general, and help identify those New World primates most vulnerable to extinction. In doing so our findings will be of interest to a wide range of scientists, including evolutionary biologists, genomicists, ecologists and palaeontologists. Because our project, by rigorously clarifying NWP species numbers and boundaries, our results will also have broader practical utility for conservation practitioners and policy makers in governmental and non-governmental agencies.