Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification

• Published in: Molecular phylogenetics and evolution 2017-01, Vol.106, p.86-102
• Main Authors: Springer, Mark S., Emerling, Christopher A., Meredith, Robert W., Janečka, Jan E., Eizirik, Eduardo, Murphy, William J.
• Format: Article
• Language: English
• Subjects: Animals; Biodiversity; Body Size; Divergence time; Female; Fossils; Ghost lineage; Long fuse model; Longevity; Mammals - classification; Mammals - physiology; Models, Theoretical; Paleontology; Phylogeny; Placenta; Placental mammal; Pregnancy; Zombie lineage
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2016.09.017

[Display omitted] •By contrast with ghost lineages, zombie lineages occur when a crown fossil is older than a molecular divergence time.•Rate transference errors in rates of molecular evolution can drag estimated divergence times backward or forward.•Timetree analyses that address rate transference problems support the long fuse model of placental mammal diversification. The explosive, long fuse, and short fuse models represent competing hypotheses for the timing of placental mammal diversification. Support for the explosive model, which posits both interordinal and intraordinal diversification after the KPg mass extinction, derives from morphological cladistic studies that place Cretaceous eutherians outside of crown Placentalia. By contrast, most molecular studies favor the long fuse model wherein interordinal cladogenesis occurred in the Cretaceous followed by intraordinal cladogenesis after the KPg boundary. Phillips (2016) proposed a soft explosive model that allows for the emergence of a few lineages (Xenarthra, Afrotheria, Euarchontoglires, Laurasiatheria) in the Cretaceous, but otherwise agrees with the explosive model in positing the majority of interordinal diversification after the KPg mass extinction. Phillips (2016) argues that rate transference errors associated with large body size and long lifespan have inflated previous estimates of interordinal divergence times, and further suggests that most interordinal divergences are positioned after the KPg boundary when rate transference errors are avoided through the elimination of calibrations in large-bodied and/or long lifespan clades. Here, we show that rate transference errors can also occur in the opposite direction and drag forward estimated divergence dates when calibrations in large-bodied/long lifespan clades are omitted. This dragging forward effect results in the occurrence of more than half a billion years of ‘zombie lineages’ on Phillips’ preferred timetree. By contrast with ghost lineages, which are a logical byproduct of an incomplete fossil record, zombie lineages occur when estimated divergence dates are younger than the minimum age of the oldest crown fossils. We also present the results of new timetree analyses that address the rate transference problem highlighted by Phillips (2016) by deleting taxa that exceed thresholds for body size and lifespan. These analyses recover all interordinal divergence times in the Cretaceous and are consistent with the long fuse model of placenta