Recovering speciation and extinction dynamics based on phylogenies

T Stadler - Journal of evolutionary biology, 2013 - academic.oup.com
Phylogenetic trees of only extant species contain information about the underlying
speciation and extinction pattern. In this review, I provide an overview over the different …

The conditioned reconstructed process

T Gernhard - Journal of theoretical biology, 2008 - Elsevier
We investigate a neutral model for speciation and extinction, the constant rate birth–death
process. The process is conditioned to have n extant species today, we look at the tree …

Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains

NR Polato, BA Gill, AA Shah, MM Gray… - Proceedings of the …, 2018 - National Acad Sciences
Species richness is greatest in the tropics, and much of this diversity is concentrated in
mountains. Janzen proposed that reduced seasonal temperature variation selects for …

Sampling-through-time in birth–death trees

T Stadler - Journal of theoretical biology, 2010 - Elsevier
I consider the constant rate birth–death process with incomplete sampling. I calculate the
density of a given tree with sampled extant and extinct individuals. This density is essential …

On incomplete sampling under birth–death models and connections to the sampling-based coalescent

T Stadler - Journal of theoretical biology, 2009 - Elsevier
The constant rate birth–death process is used as a stochastic model for many biological
systems, for example phylogenies or disease transmission. As the biological data are …

Simulating trees with a fixed number of extant species

T Stadler - Systematic biology, 2011 - academic.oup.com
In this paper, I develop efficient tools to simulate trees with a fixed number of extant species.
The tools are provided in my open source R-package TreeSim available on CRAN. The new …

A phylogenetic comparative method for studying multivariate adaptation

K Bartoszek, J Pienaar, P Mostad, S Andersson… - Journal of Theoretical …, 2012 - Elsevier
Phylogenetic comparative methods have been limited in the way they model adaptation.
Although some progress has been made, there are still no methods that can fully account for …

The contour of splitting trees is a Lévy process

A Lambert - 2010 - projecteuclid.org
Splitting trees are those random trees where individuals give birth at a constant rate during a
lifetime with general distribution, to iid copies of themselves. The width process of a splitting …

Population dynamics and random genealogies

A Lambert - Stochastic models, 2008 - Taylor & Francis
We start with stochastic models of genealogies in discrete time, distinguishing models where
the population size is fixed (models of Cannings, Wright–Fisher, and Moran; compositions of …

Sampling trees from evolutionary models

K Hartmann, D Wong, T Stadler - Systematic biology, 2010 - academic.oup.com
A wide range of evolutionary models for species-level (and higher) diversification have been
developed. These models can be used to test evolutionary hypotheses and provide …