Enhancing Evolutionary Timelines: The Impact of Stratigraphic Range Information on Phylogenetic Inference

Abstract

5 6 7 8 9 10 11 12 15 Coherent phylogenetic analyses of molecular and fossil datasets have deepened our under- 16 standing of evolutionary biology. A core model facilitating such coherent analyses is the fossilised 17 birth-death (FBD) model which directly incorporates fossils within phylogenetic trees. How- 18 ever, a limitation of the FBD model is that it cannot assign multiple fossil occurrences of the 19 same species, limiting our ability to accurately represent age information for species which have 20 been sampled repeatedly. To address this gap, the Stratigraphic Ranges Fossilized Birth-Death 21 (SRFBD) model has recently been introduced. This model can account for sampled strati- 22 graphic ranges and integrate over occurrences within the range, enabling us to include more 23 complete fossil age information within the inference. Here, building upon this mathematical 24 work, we develop a computational method making the model accessible to the community, for 25 more accurate total-evidence inference of dated phylogenetic trees and evolutionary parameters. 26 In particular, we integrate the SRFBD model into BEAST2, facilitating the use of a diverse ar- 27 ray of genomic substitution models and the inclusion of both morphological and molecular data 28 when inferring phylogenies. We present a thorough validation of the SRFBD implementation 29 against simulated data. We then demonstrate the differences in posterior parameter estimates 30 and phylogenies when applying FBD and SRFBD models to two example datasets, the Sphenis- 31 cidae (penguins) and the Canidae (dogs). In both examples, the SRFBD model produces older 32 divergence times, lower diversification and turnover rates, and considerably higher sampling 33 proportions compared to FBD model. 1 bioRxiv preprint doi: https://doi.org/10.1101/2025.04.17.649084; this version posted April 22, 2025. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 1