Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity.
Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity.
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DOI：
10.1093/sysbio/syab020
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发表时间：
2021-10-13
影响因子：
6.5
通讯作者：
Rothfels CJ
中科院分区：
文献类型：
--
作者：
May MR;Contreras DL;Sundue MA;Nagalingum NS;Looy CV;Rothfels CJ
系统发育分化时间估计已经被两个最近的发展彻底改变：（1）全证据测年法（或“tip-dating”）方法，其允许将化石作为tips并入分析中，以及它们与从数据中推断的现存分类群的系统发育和时间关系; 2）树模型的系统化出生-死亡（FBD）类，其捕获产生树的过程（物种形成，灭绝和灭绝），从而提供了一个连贯的和生物学上可解释的树先验。为了探索这些方法的行为，我们将它们应用于marattialean蕨类植物，一组是主导石炭纪景观之前下降到其适度的现存的多样性略高于100种。我们发现，树模型有一个显着的影响，估计发散时间和拓扑关系。这种影响是由均匀树先验的强的、反直觉的信息性和发散时间模型的固有不可识别性驱动的。与树模型的强烈影响相反，我们发现不同的形态过渡模型或形态时钟模型的微小影响。我们使用后验预测模拟和贝叶斯因子的组合来比较大量候选模型的性能。值得注意的是，具有特定时代物种形成和灭绝率的FBD模型受到贝叶斯因子的强烈青睐。我们的最佳拟合模型推断茎和冠分歧的Marattiales在泥盆纪中期和晚白垩世，分别与密西西比和升高灭绝率在西苏拉导致的高峰多样性的2800种在石炭纪结束时，代表全盛时期的Psaroniaceae的物种形成率升高。这一高峰之后是Psaroniaceae的迅速衰落和最终灭绝，其后代Marattiaceae一直保持着近似稳定的多样性水平，直到现在。这种一般的多样化模式似乎是不敏感的潜在偏见的化石记录，尽管优势的化石是从宾夕法尼亚州的煤球，纳入化石化率的变化并不能提高模型拟合。此外，通过将时间数据直接纳入模型，并允许推断化石的系统发育位置，我们的研究做出了令人惊讶的推断，即现存Marattiales的分支相对年轻，比历史上认为与现存物种同属的任何化石都年轻。这一结果是一个戏剧性的演示的危险基于节点的方法来估计分歧时间，其中指定的化石特定的分支是先验的（早期的基于节点的研究，限制了现存属的最小年龄的基础上，这些化石的年龄估计比我们的研究要老得多）和实用的明确模型的形态进化和谱系多样化。[贝叶斯模型比较;石炭纪;发散时间估计;化石记录;出生-死亡的简化;血统多样化;马拉蒂亚莱斯;形态演化模型;普萨罗尼乌斯;[RevBayes]
Phylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or "tip-dating") approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization) and thus provide a coherent and biologically interpretable tree prior. To explore the behavior of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior, and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the mid-Devonian and Late Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of 2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades is made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification. [Bayesian model comparison; Carboniferous; divergence-time estimation; fossil record; fossilized birth–death; lineage diversification; Marattiales; models of morphological evolution; Psaronius; RevBayes.]
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影响因子：
2.6
作者：
Escapa, Ignacio H.;Bomfleur, Benjamin;Scasso, Roberto
通讯作者：
Scasso, Roberto
影响因子：
1.9
作者：
DOYLE, JA;DONOGHUE, MJ
通讯作者：
DONOGHUE, MJ
DOI：
10.1098/rstb.2016.0020
发表时间：
2016-07-19
期刊：
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
影响因子：
--
作者：
Donoghue PC;Yang Z
通讯作者：
Yang Z
影响因子：
9.8
作者：
Drummond AJ;Ho SY;Phillips MJ;Rambaut A
通讯作者：
Rambaut A
DOI：
10.1098/rspb.2019.0685
发表时间：
2019-05-01
影响因子：
4.7
作者：
Barido-Sottani, Joelle;Aguirre-Fernandez, Gabriel;Warnock, Rachel
通讯作者：
Warnock, Rachel