Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)

The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous–Paleogene (K–Pg; 65.5 Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14,539 bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock and strict-clock models, we inferred a time-calibrated molecular phylogeny for 225 of the 291 extant Galliform taxa. These analyses suggest that crown Galliformes diversified in the Cretaceous and that three-stem lineages survived the K–Pg mass extinction. Ideally, characterizing the tempo and mode of diversification involves a taxonomically complete phylogenetic hypothesis. We used simple constraint structures to incorporate 66 data-deficient taxa and inferred the first taxon-complete phylogenetic hypothesis for the Galliformes. Diversification analyses conducted on 10,000 timetrees sampled from the posterior distribution of candidate trees show that the evolutionary history of the Galliformes is best explained by a rate-shift model including 1–3 clade-specific increases in diversification rate. We further show that the tempo and mode of diversification in the Galliformes conforms to a three-pulse model, with three-stem lineages arising in the Cretaceous and inter and intrafamilial diversification occurring after the K–Pg mass extinction, in the Paleocene–Eocene (65.5–33.9 Ma) or in association with the Eocene–Oligocene transition (33.9 Ma).

鸡形目（Galliformes，陆禽）的系统发育关系已得到广泛深入的研究，但近期其配套的年代学框架因化石校准点放置不当或鉴定错误而受到质疑。因此，目前尚不清楚是否存在任何冠群支系起源于白垩纪并幸存于白垩纪-古近纪（K-Pg；65.5 Ma）大灭绝事件。
本研究针对覆盖14539个碱基对的线粒体与核DNA序列比对数据集，结合4个化石校准点，同时采用无相关对数正态分布松弛分子钟与严格分子钟模型，通过贝叶斯系统发育推断，对291种现存鸡形目类群中的225种进行了时间校准的分子系统发育重建。分析结果显示，鸡形目冠群于白垩纪发生分化，且有3个干谱系幸存了K-Pg大灭绝事件。
理想情况下，精准刻画类群分化的速率与模式需要基于分类学完整的系统发育假说。本研究通过设置简单约束结构纳入66个数据缺失类群，首次构建了覆盖全部现存类群的鸡形目全分类单元系统发育假说。
基于候选树后验分布中抽样得到的10000棵时间树开展分化速率分析，结果表明鸡形目的进化历史最符合包含1~3次分支特异性分化速率提升的速率转移模型。研究进一步发现，鸡形目的分化速率与模式符合三脉冲模型：3个干谱系起源于白垩纪，科间与科内的分化则发生在K-Pg大灭绝之后的古新世-始新世（65.5~33.9 Ma），或是与始新世-渐新世过渡事件（33.9 Ma）相关联。