Is self‐fertilization an evolutionary dead end?

B Igic, JW Busch - New Phytologist, 2013 - Wiley Online Library
A compound hypothesis positing that self‐fertilization is an evolutionary dead end conflates
two distinct claims: the transition from outcrossing to selfing is unidirectional; and the …

Comparison of methods for molecular species delimitation across a range of speciation scenarios

A Luo, C Ling, SYW Ho, CD Zhu - Systematic Biology, 2018 - academic.oup.com
Species are fundamental units in biological research and can be defined on the basis of
various operational criteria. There has been growing use of molecular approaches for …

The fossilized birth–death process for coherent calibration of divergence-time estimates

TA Heath, JP Huelsenbeck… - Proceedings of the …, 2014 - National Acad Sciences
Time-calibrated species phylogenies are critical for addressing a wide range of questions in
evolutionary biology, such as those that elucidate historical biogeography or uncover …

Diversification in vipers: Phylogenetic relationships, time of divergence and shifts in speciation rates

LRV Alencar, TB Quental, FG Grazziotin… - Molecular phylogenetics …, 2016 - Elsevier
Snakes of the cosmopolitan family Viperidae comprise around 329 venomous species
showing a striking heterogeneity in species richness among lineages. While the subfamily …

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 …

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 …

Recent synchronous radiation of a living fossil

NS Nagalingum, CR Marshall, TB Quental, HS Rai… - Science, 2011 - science.org
Modern survivors of previously more diverse lineages are regarded as living fossils,
particularly when characterized by morphological stasis. Cycads are often cited as a classic …

Multiple Continental Radiations and Correlates of Diversification in Lupinus (Leguminosae): Testing for Key Innovation with Incomplete Taxon Sampling

CS Drummond, RJ Eastwood, STS Miotto… - Systematic …, 2012 - academic.oup.com
Replicate radiations provide powerful comparative systems to address questions about the
interplay between opportunity and innovation in driving episodes of diversification and the …

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 …

SimPhy : Phylogenomic Simulation of Gene, Locus, and Species Trees

D Mallo, L de Oliveira Martins, D Posada - Systematic biology, 2016 - academic.oup.com
We present a fast and flexible software package—SimPhy—for the simulation of multiple
gene families evolving under incomplete lineage sorting, gene duplication and loss …