Abstract
Fossils provide our only direct window into evolutionary events in the distant past. Incorporating them into phylogenetic hypotheses of living clades can help time-calibrate divergences, as well as elucidate macroevolutionary dynamics. However, the effect fossils have on phylogenetic reconstruction from morphology remains controversial. The consequences of explicitly incorporating the stratigraphic ages of fossils using tip-dated inference are also unclear. Here, we use simulations to evaluate the performance of inference methods across different levels of fossil sampling and missing data. Our results show that fossil taxa improve phylogenetic analysis of morphological datasets, even when highly fragmentary. Irrespective of inference method, fossils improve the accuracy of phylogenies and increase the number of resolved nodes. They also induce the collapse of ancient and highly uncertain relationships that tend to be incorrectly resolved when sampling only extant taxa. Furthermore, tip-dated analyses under the fossilized birth–death process outperform undated methods of inference, demonstrating that the stratigraphic ages of fossils contain vital phylogenetic information. Fossils help to extract true phylogenetic signals from morphology, an effect that is mediated by both their distinctive morphology and their temporal information, and their incorporation in total-evidence phylogenetics is necessary to faithfully reconstruct evolutionary history.
Highlights
Phylogenies underpin our ability to make sense of life on Earth in the context of its shared evolutionary history
Fossil terminals increase the accuracy of phylogenetic reconstruction across all inference methods
In the absence of missing data, topological precision increases with fossil sampling when measured using bipartitions, but decreases under quartets
Summary
Phylogenies underpin our ability to make sense of life on Earth in the context of its shared evolutionary history. Many analyses that seek to reconstruct past evolutionary events do so using data from only living organisms. This might not be enough to faithfully recover events that occurred in the distant past, as extant-only trees often lack the information necessary to distinguish between alternative scenarios [1] and can even favour incorrect results [2]. Placing fossils in a phylogenetic framework is necessary to understand their affinities and to obtain an accurate picture of evolutionary history
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