Collaborative Research: Advancing Bayesian Phylogenetic Methods for Synthesizing Paleontological and Neontological Data
合作研究:推进贝叶斯系统发育方法来合成古生物学和新生物学数据
基本信息
- 批准号:1556615
- 负责人:
- 金额:$ 62万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Standard Grant
- 财政年份:2016
- 资助国家:美国
- 起止时间:2016-05-01 至 2021-04-30
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
Combining data from living species and the fossil record provides a rich perspective for understanding the evolutionary processes responsible for generating the biodiversity observed in nature. Although methods for combining these data have made significant advances, these approaches still do not consider the completeness and sampling of the fossil record or the geographical distributions of living and fossil species. For this project, the investigators will integrate statistical models for describing how fossils are sampled over time and where species are found. These models for estimating species relationships will be developed in widely used software packages, making them broadly accessible to other researchers. These new methods will be tested using both simulated and real datasets. Specifically, two vertebrate groups with rich fossil records will be studied: penguins and crocodyliforms (crocodiles, alligators, gharials, and extinct relatives). This work will help to uncover how rates of speciation and extinction have changed over time for these species. The methods developed as part of this project will be taught in workshops for evolutionary biologists. Additionally, results from analyses of data from living and fossil penguins will be contributed to a public museum exhibit at the Bruce Museum in Greenwich, CT. In recent years, advances in phylogenetic inference methods have provided ways to integrate fossil and extant taxa. These approaches allow simultaneous estimation of the divergence times and phylogenetic relationships of extant and fossil species, thus making full use of morphological and temporal data, rather than just molecular sequence data from living species. Approaches combining fossil and extant taxa have opened the door for fully integrative phylogenetic methods that use more sources of biological data, including stratigraphy, sampling, and biogeography. Thus, there is a need for comprehensive statistical models and methods that accommodate this information. The investigators will develop new, Bayesian statistical models, extensions of stochastic birth-death processes, that will integrate information about the fossil record and biogeography for use in phylogenetic methods that consider both extant and fossil taxa. The new models will be implemented in the program RevBayes. The performance and adequacy of new and previously described models will be evaluated using simulated and empirical datasets. New methods will be used to investigate macroevolutionary patterns in two exemplar clades: Sphenisciformes (penguins) and Crocodyliformes, addressing key hypotheses about phylogenetic relationships, lineage diversification, and biogeography.
结合来自活物种和化石记录的数据,为理解自然界中观察到的生物多样性产生的进化过程提供了丰富的视角。虽然结合这些数据的方法已经取得了重大进展,但这些方法仍然没有考虑化石记录的完整性和采样或活物种和化石物种的地理分布。在这个项目中,研究人员将整合统计模型来描述化石是如何随着时间的推移取样的,以及物种是在哪里发现的。这些用于估计物种关系的模型将被开发成广泛使用的软件包,使其他研究人员可以广泛使用。这些新方法将使用模拟和真实的数据集进行测试。具体来说,将研究两个具有丰富化石记录的脊椎动物群:企鹅和鳄鱼形目(鳄鱼,短吻鳄,gharials和灭绝的亲戚)。这项工作将有助于揭示这些物种的物种形成和灭绝速度如何随着时间的推移而变化。作为该项目的一部分开发的方法将在进化生物学家的研讨会上教授。此外,对活企鹅和化石企鹅数据的分析结果将贡献给康涅狄格州格林威治的布鲁斯博物馆的公共博物馆展览。近年来,系统发育推断方法的进步提供了整合化石和现存分类群的途径。这些方法允许同时估计现存物种和化石物种的分化时间和系统发育关系,从而充分利用形态和时间数据,而不仅仅是活物种的分子序列数据。结合化石和现存分类群的方法为完全整合的系统发育方法打开了大门,这些方法使用更多的生物数据来源,包括地层学,采样和地理学。因此,需要有一个全面的统计模型和方法,以适应这一信息。研究人员将开发新的贝叶斯统计模型,随机出生-死亡过程的扩展,将整合有关化石记录和植物地理学的信息,用于考虑现存和化石分类群的系统发育方法。新模型将在RevBayes程序中实现。新的和以前描述的模型的性能和充分性将使用模拟和经验数据集进行评估。新的方法将被用来调查macroevolutionary模式在两个范例分支:Sphenisciformes(企鹅)和Crocodyliformes,解决有关系统发育关系,谱系多样化和speechography的关键假设。
项目成果
期刊论文数量(5)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates
评估不完整的物种采样对物种形成和灭绝率估计的影响
- DOI:10.1017/pab.2020.12
- 发表时间:2020
- 期刊:
- 影响因子:2.7
- 作者:Warnock, Rachel C.;Heath, Tracy A.;Stadler, Tanja
- 通讯作者:Stadler, Tanja
Total-evidence analysis resolves the phylogenetic position of an enigmatic group of Paederinae rove beetles (Coleoptera: Staphylinidae)
- DOI:10.1016/j.ympev.2020.107059
- 发表时间:2021-01-10
- 期刊:
- 影响因子:4.1
- 作者:Zyla, Dagmara;Bogri, Amalia;Solodovnikov, Alexey
- 通讯作者:Solodovnikov, Alexey
Putting the F into FBD analysis: tree constraints or morphological data?
将 F 放入 FBD 分析:树约束还是形态数据?
- DOI:10.1111/pala.12679
- 发表时间:2023
- 期刊:
- 影响因子:2.6
- 作者:Barido‐Sottani, Joëlle;Pohle, Alexander;De Baets, Kenneth;Murdock, Duncan;Warnock, Rachel C. M.
- 通讯作者:Warnock, Rachel C. M.
Lessons learned from organizing and teaching virtual phylogenetics workshops
从组织和教授虚拟系统发育学研讨会中汲取的经验教训
- DOI:10.18061/bssb.v1i2.8425
- 发表时间:2022
- 期刊:
- 影响因子:0
- 作者:Barido-Sottani, Joëlle;Justison, Joshua A.;Borges, Rui;Brown, Jeremy M.;Dismukes, Wade;Do Rosario Petrucci, Bruno;Guimarães Fabreti, Luiza;Höhna, Sebastian;Landis, Michael J.;Lewis, Paul O.
- 通讯作者:Lewis, Paul O.
Ancient crested penguin constrains timing of recruitment into seabird hotspot
古代冠企鹅限制了海鸟热点地区的招募时间
- DOI:10.1098/rspb.2020.1497
- 发表时间:2020
- 期刊:
- 影响因子:0
- 作者:Thomas, Daniel B.;Tennyson, Alan J.;Scofield, R. Paul;Heath, Tracy A.;Pett, Walker;Ksepka, Daniel T.
- 通讯作者:Ksepka, Daniel T.
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Tracy Heath其他文献
Tracy Heath的其他文献
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{{ truncateString('Tracy Heath', 18)}}的其他基金
Collaborative Research: Improving the stability, usability, and speed of the RevBayes platform for phylogenetic analysis
协作研究:提高 RevBayes 系统发育分析平台的稳定性、可用性和速度
- 批准号:
1759909 - 财政年份:2018
- 资助金额:
$ 62万 - 项目类别:
Standard Grant
NSF PostDoctoral Research Fellowship in Biology
NSF 生物学博士后研究奖学金
- 批准号:
0805631 - 财政年份:2008
- 资助金额:
$ 62万 - 项目类别:
Fellowship Award
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