Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling

JP Bernot, CL Owen, JM Wolfe, K Meland… - Molecular Biology …, 2023 - academic.oup.com
The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group
of animals on earth, containing over 80% of animal species and half of animal biomass. It …

Sequence capture versus restriction site associated DNA sequencing for shallow systematics

MG Harvey, BT Smith, TC Glenn, BC Faircloth… - Systematic …, 2016 - academic.oup.com
Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two
genomic enrichment strategies for applying next-generation sequencing technologies to …

Quartet inference from SNP data under the coalescent model

J Chifman, L Kubatko - Bioinformatics, 2014 - academic.oup.com
Motivation: Increasing attention has been devoted to estimation of species-level
phylogenetic relationships under the coalescent model. However, existing methods either …

Anchored hybrid enrichment for massively high-throughput phylogenomics

AR Lemmon, SA Emme, EM Lemmon - Systematic biology, 2012 - academic.oup.com
The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of
data collection that leverage both genomic resources and recent advances in DNA …

Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent

G Jones - Journal of mathematical biology, 2017 - Springer
The focus of this article is a Bayesian method for inferring both species delimitations and
species trees under the multispecies coalescent model using molecular sequences from …

Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences

H Huang, LL Knowles - Systematic biology, 2016 - academic.oup.com
There is a lack of consensus on how next-generation sequence (NGS) data should be
considered for phylogenetic and phylogeographic estimates, with some studies excluding …

To include or not to include: the impact of gene filtering on species tree estimation methods

EK Molloy, T Warnow - Systematic biology, 2018 - academic.oup.com
With the increasing availability of whole genome data, many species trees are being
constructed from hundreds to thousands of loci. Although concatenation analysis using …

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 …

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

J Gatesy, MS Springer - Molecular phylogenetics and evolution, 2014 - Elsevier
Large datasets are required to solve difficult phylogenetic problems that are deep in the Tree
of Life. Currently, two divergent systematic methods are commonly applied to such datasets …

Multi-allele species reconstruction using ASTRAL

M Rabiee, E Sayyari, S Mirarab - Molecular phylogenetics and evolution, 2019 - Elsevier
Genome-wide phylogeny reconstruction is becoming increasingly common, and one driving
factor behind these phylogenomic studies is the promise that the potential discordance …