Skyline Fossilized Birth-Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating

doi:10.1093/sysbio/syad054

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	Skyline Fossilized Birth-Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating
	Zhang, Chi 1; Ronquist, Fredrik 2; Stadler, Tanja 3,4
	2023-11-01
发表期刊	SYSTEMATIC BIOLOGY
ISSN	1063-5157
卷号	72 期号:6 页码:1316-1336
通讯作者	Zhang, Chi([email protected])
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.
关键词	Deep root attraction fossilized birth-death OU process skyline total-evidence dating
DOI	10.1093/sysbio/syad054
收录类别	SCI
语种	英语
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]
项目资助者	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
WOS研究方向	Evolutionary Biology
WOS类目	Evolutionary Biology
WOS记录号	WOS:001186215100003
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.205/handle/311034/23472
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.Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing 100044, Peoples R China 2.Swedish Museum Nat Hist, Dept Bioinformat & Genet, SE-10405 Stockholm, Sweden 3.Eidgenoss Tech Hsch Zurich, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland 4.Swiss Inst Bioinformat SIB, CH-1015 Lausanne, Switzerland
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.