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

“猴子大陆的崛起”：对新世界灵长类动物适应性辐射的综合基因组和化石分析

• 批准号: NE/T000341/1
• 负责人: Robin Beck
• 金额: $ 82.56万
• 依托单位: University of Salford
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FT000341%2F1
• 关键词: Rise; continent; monkeys; integrated; genomic

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.

新世界灵长类动物生活在中美洲和南美洲的热带地区，包括一些众所周知的有魅力的物种，如蜘蛛猴、吼猴、狨猴和卷尾猴。今天，已知的有5科170多种，它们共同表现出不同的体型、饮食和活动。值得注意的是，所有这些多样性都来自于一个共同的祖先，这个祖先在3500万到4500万年前从非洲到达南美洲，可能是通过一堆植被漂洋过海而来的。这个祖先为什么以及如何产生了构成现代新世界灵长类动物辐射的所有不同物种？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在体型、饮食和活动模式上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，我们将把两种截然不同但又互补的数据类型结合起来：基因组数据提供了现存物种的详细信息，而化石数据提供了（通常非常不完整的）过去物种多样性的信息。以前的研究通常使用基因组数据或化石数据，但我们将两者结合起来，利用它们的不同优势并弥补彼此的弱点。首先，我们将检查不同的新世界灵长类物种的基因组，看看我们是否能识别出与饮食、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大陆灵长类动物群体中是如何随着时间而变化的。其次，我们将利用大量的基因组数据和复杂的方法，为所有现存的新大陆灵长类物种建立一个新的进化树（系统发育），以产生最完整和准确的该群体的系统发育，我们将使用“分子钟”来推断不同谱系彼此分裂的分化时间。根据我们新的系统发育和分化时间，我们将研究多样化的速度如何随时间变化，以及非常高或低的多样化速度是否与环境变化时期相吻合。我们还将鉴定以前未被认识的物种，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的数据来模拟新世界现存和灭绝的灵长类谱系是如何随着时间的推移而多样化的。这些数据可以与现存新大陆灵长类动物的系统发育所显示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，这表明灭绝在新大陆灵长类动物进化中起了关键作用。我们还将使用化石记录来验证这样一个假设，即当新世界灵长类祖先从非洲来到南美洲时，新世界灵长类动物在竞争中战胜了表面上“类似灵长类动物”的哺乳动物（实际上是现代有袋动物的亲戚）。我们的项目将极大地增加我们对新大陆灵长类动物进化的理解，为多样性和进化过程提供新的视角，并帮助确定那些最容易灭绝的新大陆灵长类动物。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用价值。

项目成果

Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum.

• DOI: 10.24272/j.issn.2095-8137.2021.143
• 发表时间: 2021-11-18
• 期刊: Zoological research
• 影响因子: 4.9
• 作者: Boubli JP;Janiak MC;Porter LM;de la Torre S;Cortés-Ortiz L;Da Silva MNF;Rylands AB;Nash S;Bertuol F;Byrne H;Silva FE;Rohe F;de Vries D;Beck RMD;Ruiz-Gartzia I;Kuderna LFK;Marques-Bonet T;Hrbek T;Farias IP;Van Heteren AH;Roos C
• 通讯作者: Roos C

An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico) from the arc of deforestation.

• DOI: 10.1038/s41598-021-93943-w
• 发表时间: 2021-08-02
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Costa-Araújo R;Silva-Jr JS;Boubli JP;Rossi RV;Canale GR;Melo FR;Bertuol F;Silva FE;Silva DA;Nash SD;Sampaio I;Farias IP;Hrbek T
• 通讯作者: Hrbek T

Twenty-five well-justified fossil calibrations for primate divergences

• DOI: 10.26879/1249
• 发表时间: 2023-02-23
• 期刊: PALAEONTOLOGIA ELECTRONICA
• 影响因子: 2
• 作者: de Vries, Dorien;Beck, Robin M. D.
• 通讯作者: Beck, Robin M. D.

A New Diminutive Durophagous Miocene Dasyuromorphian (Marsupialia, Malleodectidae) from the Riversleigh World Heritage Area, Northern Australia

• DOI: 10.1080/02724634.2023.2170804
• 发表时间: 2022-09
• 期刊: Journal of Vertebrate Paleontology
• 影响因子: 1.4
• 作者: Timothy J. Churchill;M. Archer;S. Hand;Troy J Myers;A. Gillespie;R. Beck

Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline

使用新型免费软件管道比较狨猴和狨猴（Callitrichidae）与其他阔鼻灵长类动物的牙齿地形

• DOI: 10.1101/2023.08.31.555703
• 发表时间: 2023
• 作者: De Vries D