Data from: Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification

The binary-state speciation and extinction (BiSSE) model has been used in
many instances to identify state-dependent diversification and reconstruct
ancestral states. However, recent studies have shown that the standard
procedure of comparing the fit of the BiSSE model to constant-rate
birth–death models often inappropriately favours the BiSSE model when
diversification rates vary in a state-independent fashion. The newly
developed HiSSE model enables researchers to identify state-dependent
diversification rates while accounting for state-independent
diversification at the same time. The HiSSE model also allows researchers
to test state-dependent models against appropriate state-independent null
models that have the same number of parameters as the state-dependent
models being tested. We reanalyse two data sets that originally used BiSSE
to reconstruct ancestral states within squamate reptiles and reached
surprising conclusions regarding the evolution of toepads within Gekkota
and viviparity across Squamata. We used this new method to demonstrate
that there are many shifts in diversification rates across squamates. We
then fit various HiSSE submodels and null models to the state and
phylogenetic data and reconstructed states under these models. We found
that there is no single, consistent signal for state-dependent
diversification associated with toepads in gekkotans or viviparity across
all squamates. Our reconstructions show limited support for the recently
proposed hypotheses that toepads evolved multiple times independently in
Gekkota and that transitions from viviparity to oviparity are common in
Squamata. Our results highlight the importance of considering an adequate
pool of models and null models when estimating diversification rate
parameters and reconstructing ancestral states.

二元状态成种与灭绝模型（binary-state speciation and extinction, BiSSE）已在诸多场景中被用于识别状态依赖型多样化过程，并重建祖先状态。然而，近期研究表明，当多样化速率以状态独立的方式变化时，将BiSSE模型与恒定速率生灭模型的拟合优度进行比较的标准流程，往往会不适当地偏向BiSSE模型。新近开发的HiSSE模型能够让研究者在考量状态独立型多样化过程的同时，识别状态依赖型多样化速率。此外，HiSSE模型还允许研究者将状态依赖型模型与适配的状态独立型零模型进行检验——这类零模型与待检验的状态依赖型模型拥有相同的参数数量。我们重新分析了两项最初使用BiSSE模型重建有鳞目爬行动物祖先状态的数据集，并针对壁虎下目趾垫的演化以及整个有鳞目的胎生演化得出了令人意外的结论。我们借助这一新方法证明，有鳞类的多样化速率存在诸多转变事件。随后我们将多种HiSSE子模型与零模型适配至状态数据与系统发育数据中，并基于这些模型重建了祖先状态。我们发现，无论是壁虎下目与趾垫相关的状态依赖型多样化，还是所有有鳞类的胎生相关多样化，都不存在单一且一致的信号。我们的重建结果显示，对于新近提出的两项假说——壁虎下目趾垫曾多次独立演化，以及有鳞目中从胎生向卵生的转变较为常见——仅提供了有限的支持证据。我们的研究结果强调，在估算多样化速率参数与重建祖先状态时，考虑足够丰富的模型与零模型集合具有重要意义。