Evolutionary inferences from phylogenies: a review of methods

BC O'Meara - Annual Review of Ecology, Evolution, and …, 2012 - annualreviews.org
There are many methods for making evolutionary inferences from phylogenetic trees. Many
of these can be divided into three main classes of models: continuous-time Markov chain …

Understanding angiosperm diversification using small and large phylogenetic trees

SA Smith, JM Beaulieu, A Stamatakis… - American journal of …, 2011 - Wiley Online Library
How will the emerging possibility of inferring ultra‐large phylogenies influence our ability to
identify shifts in diversification rate? For several large angiosperm clades (Angiospermae …

Constructing a broadly inclusive seed plant phylogeny

SA Smith, JW Brown - American journal of botany, 2018 - Wiley Online Library
Premise of the Study Large phylogenies can help shed light on macroevolutionary patterns
that inform our understanding of fundamental processes that shape the tree of life. These …

treePL: divergence time estimation using penalized likelihood for large phylogenies

SA Smith, BC O'Meara - Bioinformatics, 2012 - academic.oup.com
Ever larger phylogenies are being constructed due to the explosion of genetic data and
development of high-performance phylogenetic reconstruction algorithms. However, most …

The age and diversification of the angiosperms re‐revisited

CD Bell, DE Soltis, PS Soltis - American journal of botany, 2010 - Wiley Online Library
• Premise of the study: It has been 8 years since the last comprehensive analysis of
divergence times across the angiosperms. Given recent methodological improvements in …

Cell-type homologies and the origins of the neocortex

J Dugas-Ford, JJ Rowell, CW Ragsdale - Proceedings of the National …, 2012 - pnas.org
The six-layered neocortex is a uniquely mammalian structure with evolutionary origins that
remain in dispute. One long-standing hypothesis, based on similarities in neuronal …

Building the C oleoptera tree‐of‐life for> 8000 species: composition of public DNA data and fit with L innaean classification

L Bocak, C Barton, A Crampton‐Platt… - Systematic …, 2014 - Wiley Online Library
The species representation of public databases is growing rapidly and permits increasingly
detailed phylogenetic inferences. We present a supermatrix based on all gene sequences of …

Molecular systematics and character evolution in Caryophyllaceae

AK Greenberg, MJ Donoghue - Taxon, 2011 - Wiley Online Library
The aim of the present study was to infer a substantially larger, more evenly sampled,
phylogenetic tree for Caryophyllaceae in order to more confidently resolve relationships …

Extended implied weighting

PA Goloboff - Cladistics, 2014 - Wiley Online Library
Several extensions to implied weighting, recently implemented in TNT, allow a better
treatment of data sets combining morphological and molecular data sets, as well as those …

[HTML][HTML] A phylogenomic supertree of birds

RT Kimball, CH Oliveros, N Wang, ND White, FK Barker… - Diversity, 2019 - mdpi.com
It has long been appreciated that analyses of genomic data (eg, whole genome sequencing
or sequence capture) have the potential to reveal the tree of life, but it remains challenging …