ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

C Zhang, M Rabiee, E Sayyari, S Mirarab - BMC bioinformatics, 2018 - Springer
Background Evolutionary histories can be discordant across the genome, and such
discordances need to be considered in reconstructing the species phylogeny. ASTRAL is …

Revisiting metazoan phylogeny with genomic sampling of all phyla

CE Laumer, R Fernández, S Lemer… - … of the royal …, 2019 - royalsocietypublishing.org
Proper biological interpretation of a phylogeny can sometimes hinge on the placement of
key taxa—or fail when such key taxa are not sampled. In this light, we here present the first …

[HTML][HTML] EvoRegen in animals: Time to uncover deep conservation or convergence of adult stem cell evolution and regenerative processes

AG Lai, AA Aboobaker - Developmental biology, 2018 - Elsevier
How do animals regenerate specialised tissues or their entire body after a traumatic injury,
how has this ability evolved and what are the genetic and cellular components underpinning …

Mapping single-cell atlases throughout Metazoa unravels cell type evolution

AJ Tarashansky, JM Musser, M Khariton, P Li, D Arendt… - Elife, 2021 - elifesciences.org
Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the
origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison …

Fast coalescent-based computation of local branch support from quartet frequencies

E Sayyari, S Mirarab - Molecular biology and evolution, 2016 - academic.oup.com
Species tree reconstruction is complicated by effects of incomplete lineage sorting,
commonly modeled by the multi-species coalescent model (MSC). While there has been …

Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees

Z He, H Zhang, S Gao, MJ Lercher… - Nucleic acids …, 2016 - academic.oup.com
Evolview is an online visualization and management tool for customized and annotated
phylogenetic trees. It allows users to visualize phylogenetic trees in various formats …

Embracing the comparative approach: how robust phylogenies and broader developmental sampling impacts the understanding of nervous system evolution

A Hejnol, CJ Lowe - … Transactions of the Royal Society B …, 2015 - royalsocietypublishing.org
Molecular biology has provided a rich dataset to develop hypotheses of nervous system
evolution. The startling patterning similarities between distantly related animals during the …

ASTRAL-III: increased scalability and impacts of contracting low support branches

C Zhang, E Sayyari, S Mirarab - RECOMB international workshop on …, 2017 - Springer
Discordances between species trees and gene trees can complicate phylogenetics
reconstruction. ASTRAL is a leading method for inferring species trees given gene trees …

Spiralian phylogeny informs the evolution of microscopic lineages

CE Laumer, N Bekkouche, A Kerbl, F Goetz, RC Neves… - Current Biology, 2015 - cell.com
Despite rapid advances in the study of metazoan evolutionary history [1], phylogenomic
analyses have so far neglected a number of microscopic lineages that possess a unique …

Phylogenomics of Lophotrochozoa with consideration of systematic error

KM Kocot, TH Struck, J Merkel, DS Waits… - Systematic …, 2017 - academic.oup.com
Phylogenomic studies have improved understanding of deep metazoan phylogeny and
show promise for resolving incongruences among analyses based on limited numbers of …