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Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling
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 …
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
Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two
genomic enrichment strategies for applying next-generation sequencing technologies to …
genomic enrichment strategies for applying next-generation sequencing technologies to …
Quartet inference from SNP data under the coalescent model
Motivation: Increasing attention has been devoted to estimation of species-level
phylogenetic relationships under the coalescent model. However, existing methods either …
phylogenetic relationships under the coalescent model. However, existing methods either …
Anchored hybrid enrichment for massively high-throughput phylogenomics
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 …
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 …
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 …
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
With the increasing availability of whole genome data, many species trees are being
constructed from hundreds to thousands of loci. Although concatenation analysis using …
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 …
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 …
of Life. Currently, two divergent systematic methods are commonly applied to such datasets …
Multi-allele species reconstruction using ASTRAL
Genome-wide phylogeny reconstruction is becoming increasingly common, and one driving
factor behind these phylogenomic studies is the promise that the potential discordance …
factor behind these phylogenomic studies is the promise that the potential discordance …