"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的热带地区，其中包括蜘蛛猴，howl猴，果猴和胶囊等著名和魅力的物种。如今，五个家庭中有170多种已知的物种，它们共同表现出各种不同的身体大小，饮食和活动。值得注意的是，所有这些多样性源自35-45万年前从非洲到达南美的单个共同祖先，可能是通过在海上运输的一大堆植被运输。为什么以及如何以及如何产生构成现代新世界灵长类动物辐射的所有多种物种？导致不同家庭多元化的驱动因素是什么？非生物因素是气候变化，安第斯山脉山脉的升高以及亚马逊河的发展，还是生物因素（与其他哺乳动物的竞争）在推动多样化中更为重要？我们可以确定不同新世界灵长类动物群体的体型，饮食和活动模式的变化以及为什么会发生变化吗？我们提议的项目将尝试回答这些问题。为此，我们将结合两种截然不同的数据类型：基因组数据，该数据提供有关生物物种和化石数据的详细信息，这些信息提供了有关过去多样性的（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，但是我们的研究将结合两者，以利用它们的不同优势并弥补彼此的弱点。首先，我们将检查不同新世界灵长类动物的基因组，以查看我们是否可以识别与饮食，体型和活动模式等性状有关的基因。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如何随着时间的流逝而改变。其次，我们将使用大量的基因组数据和复杂方法生产所有新世界灵长类动物的新进化树（系统发育），以产生该组最完整，最准确的系统发育，我们将使用“分子钟”来推断不同谱系分裂时的差异时间。随着我们的新系统发育和分歧时间，我们将研究多样化的速度随时间而变化，以及非常高或低的多样化速率是否与环境变化时期一致。我们还将确定以前未认可的物种，并重新评估所有已知物种的分类学。通过帮助确定最需要保护的物种以保护最大的生物多样性，这些信息将是保护工作的关键。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生命和灭绝血统如何随着时间的流逝而多样化。可以将这些数据与活的新世界灵长类动物的系统发育所指示的多样化模式进行比较，以查看它们是否与众不同。如果他们表现出重大差异，这表明灭绝在新世界灵长类动物的进化中起着关键作用。我们还将利用化石记录来检验以下假设：新世界灵长类动物以表面上的“灵长类动物般”哺乳动物（实际上是现代有袋动物的亲戚）在南美已经存在的新世界灵长类动物祖先从非洲抵达时已经存在。我们的项目将大大提高我们对新世界灵长类动物进化的理解，对一般的多元化和进化过程展示了新的启示，并帮助确定最容易灭绝的新世界灵长类动物。这样一来，我们的发现将吸引众多科学家，包括进化生物学家，基因组学家，生态学家和古生物学家。由于我们的项目通过严格澄清NWP物种数量和边界，我们的结果还将为政府和非政府机构的保护从业者和政策制定者提供更广泛的实用性。

项目成果

Total Evidence Tip-Dating Phylogeny of Platyrrhine Primates and 27 Well-Justified Fossil Calibrations for Primate Divergences

• DOI: 10.1101/2021.10.21.465342
• 发表时间: 2021-01-01
• 期刊: Evol. Biol.
• 作者: De Vries, D.;Beck, R.M.D.
• 通讯作者: Beck, R.M.D.

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

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.

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

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