Simulations modelling the effect of budding speciation on phylogenies

Paleobiologists have long sought to explain how alternative modes of speciation, including budding and bifurcating cladogenesis, shape patterns of evolution. Methods introduced over the past decade have paved the way for a renewed enthusiasm for exploring modes of speciation in the fossil record. However, the field does not yet have a strong intuition for how ancestor-descendant relationships, especially those that arise from budding speciation, might influence the shape of trees reconstructed for fossil or living clades. We developed a simulation approach based on classic paleobiological theory to ask what proportion of ancestral nodes in paleontological phylogenies are expected to correspond to sampled lineages under a range of preservational regimes. We compared our simulated results to empirical estimates of absolute fossil record completeness gathered from the literature and found that many fossilized clades of marine invertebrates are likely to display upwards of 80% sampled ances..., , , # Simulations modelling the effect of budding speciation on phylogenies

[https://doi.org/10.5061/dryad.dr7sqvb6n](https://doi.org/10.5061/dryad.dr7sqvb6n)

## Description of the data and file structure

**completeness.csv** - completeness estimates for each fossil clade examined.

Columns are:

`Taxon`: Name of the clade

`Completeness`: Estimate of completeness, expressed as a percentage of total taxa inferred to have been sampled by the dataset, among all of the taxa that are inferred to have existed throughout the history of the clades.

`Level`: Taxonomic level at which the clade was sampled. All clades examined here were sampled either at the species or genus level.

`Scale`: Approximate estimation of the geographic scale at which the clade was sampled. Some were sampled globally, while others were sampled locally, at a single or small handful of nearby locality(ies)

`Epoch`: Geological interval for which the clade was sampled. \"All\" means that the clade was sampled over its enti...

古生物学家长期以来一直致力于阐释包括出芽成种与二分歧式成种在内的多种成种模式如何塑造演化格局。过去十年间提出的各类研究方法，重新点燃了学界探索化石记录中成种模式的研究热情。然而，当前学界尚未形成清晰的认知：祖先-后裔关系——尤其是由出芽成种所产生的这类关系——会如何影响针对化石或现生支系所重建的系统发育树的形态特征。

我们基于经典古生物学理论开发了一套模拟方法，旨在探究在不同保存条件下，古生物系统发育树中预期有多大比例的祖先节点对应于已采样的支系。我们将模拟结果与从文献中获取的绝对化石记录完整度的经验估算值进行了对比，结果发现，诸多海洋无脊椎动物的化石支系很可能拥有超过80%的采样祖先……

# 模拟出芽成种对系统发育树的影响
https://doi.org/10.5061/dryad.dr7sqvb6n

## 数据与文件结构说明
**completeness.csv**：本次研究涉及的所有化石支系的完整度估算值。
各列含义如下：
`Taxon`：支系名称
`Completeness`：完整度估算值，以数据集采样得到的总分类群数占该支系演化历史中所有推定存在过的分类群数的百分比表示。
`Level`：支系的采样分类层级。本次研究涉及的所有支系均在物种或属级进行采样。
`Scale`：支系采样的地理尺度近似估算值。部分支系为全球范围采样，其余则为局域范围采样，即仅在单个或少量邻近的化石点开展采样。
`Epoch`：支系的采样地质区间。"All"代表该支系在其整个演化历史中均被采样……