Skyline Fossilized Birth-Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating
文献类型：期刊论文
| 作者 | Zhang, Chi4; Ronquist, Fredrik3; Stadler, Tanja1,2 |
| 刊名 | SYSTEMATIC BIOLOGY
 |
| 出版日期 | 2023-11-01 |
| 卷号 | 72期号:6页码:1316-1336 |
| 关键词 | Deep root attraction fossilized birth-death OU process skyline total-evidence dating |
| ISSN号 | 1063-5157 |
| DOI | 10.1093/sysbio/syad054 |
| 通讯作者 | Zhang, Chi(zhangchi@ivpp.ac.cn) |
| 英文摘要 | Several total-evidence dating studies under the fossilized birth-death (FBD) model have produced very old age estimates, which are not supported by the fossil record. This phenomenon has been termed "deep root attraction (DRA)." For two specific data sets, involving divergence time estimation for the early radiations of ants, bees, and wasps (Hymenoptera) and of placental mammals (Eutheria), it has been shown that the DRA effect can be greatly reduced by accommodating the fact that extant species in these trees have been sampled to maximize diversity, so-called diversified sampling. Unfortunately, current methods to accommodate diversified sampling only consider the extreme case where it is possible to identify a cut-off time such that all splits occurring before this time are represented in the sampled tree but none of the younger splits. In reality, the sampling bias is rarely this extreme and may be difficult to model properly. Similar modeling challenges apply to the sampling of the fossil record. This raises the question of whether it is possible to find dating methods that are more robust to sampling biases. Here, we show that the skyline FBD (SFBD) process, where the diversification and fossil-sampling rates can vary over time in a piecewise fashion, provides age estimates that are more robust to inadequacies in the modeling of the sampling process and less sensitive to DRA effects. In the SFBD model we consider, rates in different time intervals are either considered to be independent and identically distributed or assumed to be autocorrelated following an Ornstein-Uhlenbeck (OU) process. Through simulations and reanalyses of Hymenoptera and Eutheria data, we show that both variants of the SFBD model unify age estimates under random and diversified sampling assumptions. The SFBD model can resolve DRA by absorbing the deviations from the sampling assumptions into the inferred dynamics of the diversification process over time. Although this means that the inferred diversification dynamics must be interpreted with caution, taking sampling biases into account, we conclude that the SFBD model represents the most robust approach currently available for addressing DRA in total-evidence dating. |
| 资助项目 | National Natural Science Foundation of China[42172006] ; Hundred Young Talents Program of Chinese Academy of Sciences[Y902061] ; European Research Council under the Seventh Framework Programme of the European Commission[335529] ; Swedish Research Council[2018-04620] ; Vinnova[2018-04620] ; Swedish Research Council[2018-04620] |
| WOS研究方向 | Evolutionary Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:001186215100003 |
| 出版者 | OXFORD UNIV PRESS |
| 资助机构 | National Natural Science Foundation of China ; Hundred Young Talents Program of Chinese Academy of Sciences ; European Research Council under the Seventh Framework Programme of the European Commission ; Swedish Research Council ; Vinnova ; Swedish Research Council |
| 源URL | [http://119.78.100.205/handle/311034/23471]  |
| 专题 | 中国科学院古脊椎动物与古人类研究所 |
| 通讯作者 | Zhang, Chi |
| 作者单位 | 1.Swiss Inst Bioinformat SIB, CH-1015 Lausanne, Switzerland 2.Eidgenoss Tech Hsch Zurich, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland 3.Swedish Museum Nat Hist, Dept Bioinformat & Genet, SE-10405 Stockholm, Sweden 4.Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing 100044, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhang, Chi,Ronquist, Fredrik,Stadler, Tanja. Skyline Fossilized Birth-Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating[J]. SYSTEMATIC BIOLOGY,2023,72(6):1316-1336. |
| APA | Zhang, Chi,Ronquist, Fredrik,&Stadler, Tanja.(2023).Skyline Fossilized Birth-Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating.SYSTEMATIC BIOLOGY,72(6),1316-1336. |
| MLA | Zhang, Chi,et al."Skyline Fossilized Birth-Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating".SYSTEMATIC BIOLOGY 72.6(2023):1316-1336. |
入库方式： OAI收割
来源：古脊椎动物与古人类研究所
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