Mammal madness: is the mammal tree of life not yet resolved?

NM Foley, MS Springer… - … Transactions of the …, 2016 - royalsocietypublishing.org
Most molecular phylogenetic studies place all placental mammals into four superordinal
groups, Laurasiatheria (eg dogs, bats, whales), Euarchontoglires (eg humans, rodents …

Causes, consequences and solutions of phylogenetic incongruence

A Som - Briefings in Bioinformatics, 2015 - academic.oup.com
Phylogenetic analysis is used to recover the evolutionary history of species, genes or
proteins. Understanding phylogenetic relationships between organisms is a prerequisite of …

Inferring the mammal tree: species-level sets of phylogenies for questions in ecology, evolution, and conservation

NS Upham, JA Esselstyn, W Jetz - PLoS biology, 2019 - journals.plos.org
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to
modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of …

A genomic timescale for placental mammal evolution

NM Foley, VC Mason, AJ Harris, KR Bredemeyer… - Science, 2023 - science.org
The precise pattern and timing of speciation events that gave rise to all living placental
mammals remain controversial. We provide a comprehensive phylogenetic analysis of …

[HTML][HTML] A comprehensive and dated phylogenomic analysis of butterflies

M Espeland, J Breinholt, KR Willmott, AD Warren… - Current Biology, 2018 - cell.com
Summary Butterflies (Papilionoidea), with over 18,000 described species [1], have
captivated naturalists and scientists for centuries. They play a central role in the study of …

Why do phylogenomic data sets yield conflicting trees? Data type influences the avian tree of life more than taxon sampling

S Reddy, RT Kimball, A Pandey, PA Hosner… - Systematic …, 2017 - academic.oup.com
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been
viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life …

Phylotranscriptomic consolidation of the jawed vertebrate timetree

I Irisarri, D Baurain, H Brinkmann, F Delsuc… - Nature ecology & …, 2017 - nature.com
Phylogenomics is extremely powerful but introduces new challenges as no agreement exists
on 'standards' for data selection, curation and tree inference. We use jawed vertebrates …

Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six …

EJM Koenen, DI Ojeda, R Steeves, J Migliore… - New …, 2020 - Wiley Online Library
Phylogenomics is increasingly used to infer deep‐branching relationships while revealing
the complexity of evolutionary processes such as incomplete lineage sorting, hybridization …

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

D Arcila, G Ortí, R Vari, JW Armbruster… - Nature Ecology & …, 2017 - nature.com
Much progress has been achieved in disentangling evolutionary relationships among
species in the tree of life, but some taxonomic groups remain difficult to resolve despite …

The gene tree delusion

MS Springer, J Gatesy - Molecular phylogenetics and evolution, 2016 - Elsevier
Higher-level relationships among placental mammals are mostly resolved, but several
polytomies remain contentious. Song et al.(2012) claimed to have resolved three of these …