Integrating fossil observations into phylogenetics using the fossilized birth–death model

AM Wright, DW Bapst, J Barido-Sottani… - Annual Review of …, 2022 - annualreviews.org
Over the past decade, a new set of methods for estimating dated trees has emerged.
Originally referred to as the fossilized birth–death (FBD) process, this single model has …

Studying speciation and extinction dynamics from phylogenies: addressing identifiability issues

H Morlon, S Robin, F Hartig - Trends in Ecology & Evolution, 2022 - cell.com
A lot of what we know about past speciation and extinction dynamics is based on statistically
fitting birth–death processes to phylogenies of extant species. Despite their wide use, the …

State-dependent evolutionary models reveal modes of solid tumour growth

MA Lewinsohn, T Bedford, NF Müller… - Nature Ecology & …, 2023 - nature.com
Spatial properties of tumour growth have profound implications for cancer progression,
therapeutic resistance and metastasis. Yet, how spatial position governs tumour cell division …

Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability

BT Kopperud, AF Magee… - Proceedings of the …, 2023 - National Acad Sciences
The birth–death model is commonly used to infer speciation and extinction rates by fitting the
model to phylogenetic trees with exclusively extant taxa. Recently, it was demonstrated that …

Pulled diversification rates, lineages-through-time plots, and modern macroevolutionary modeling

AJ Helmstetter, S Glemin, J Käfer… - Systematic …, 2022 - academic.oup.com
Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees
of extant species (timetrees), and determining how and why they vary, is key to …

[HTML][HTML] Why extinction estimates from extant phylogenies are so often zero

S Louca, MW Pennell - Current Biology, 2021 - cell.com
Time-calibrated phylogenies of extant species (" extant timetrees") are widely used to
estimate historical speciation and extinction rates by fitting stochastic birth-death models. 1 …

Unifying phylogenetic birth–death models in epidemiology and macroevolution

A MacPherson, S Louca, A McLaughlin… - Systematic …, 2022 - academic.oup.com
Birth–death stochastic processes are the foundations of many phylogenetic models and are
widely used to make inferences about epidemiological and macroevolutionary dynamics …

Explanations for latitudinal diversity gradients must invoke rate variation

EE Saupe - Proceedings of the National Academy of …, 2023 - National Acad Sciences
The latitudinal diversity gradient (LDG) describes the pattern of increasing numbers of
species from the poles to the equator. Although recognized for over 200 years, the …

A class of identifiable phylogenetic birth–death models

B Legried, J Terhorst - … of the National Academy of Sciences, 2022 - National Acad Sciences
In a striking result, Louca and Pennell [S. Louca, MW Pennell, Nature 580, 502–505 (2020)]
recently proved that a large class of phylogenetic birth–death models is statistically …

Cross-disciplinary information for understanding macroevolution

LH Liow, J Uyeda, G Hunt - Trends in Ecology & Evolution, 2023 - cell.com
Many different macroevolutionary models can produce the same observations. Despite
efforts in building more complex and realistic models, it may still be difficult to distinguish the …