Phylogeny | Nature

Article
20 March 2024 | Open Access

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche

A study reveals that Fusobacterium nucleatum subspecies animalis is bifurcated into two distinct clades, and shows that only one of these dominates the colorectal cancer niche, probably through increased colonization of the human gastrointestinal tract.

Martha Zepeda-Rivera
, Samuel S. Minot
& Christopher D. Johnston

Article
21 February 2024 | Open Access

Prevalence of persistent SARS-CoV-2 in a large community surveillance study

Using viral sequence data, individuals with persistent SARS-CoV-2 infections were identified, and had higher odds of self-reporting long COVID, in a large community surveillance study.

Mahan Ghafari
, Matthew Hall
& Katrina Lythgoe

Matters Arising
15 February 2023 | Open Access

Reply to: The case for standardizing gene nomenclature in vertebrates

Constantina Theofanopoulou
& Erich D. Jarvis

Article
11 August 2022 | Open Access

Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape

A new phylogenomic method is developed that can detect recombinations in virus lineages in pandemic-scale datasets.

Yatish Turakhia
, Bryan Thornlow
& Russell Corbett-Detig

Article | 25 August 2021

Clonal dynamics in early human embryogenesis inferred from somatic mutation

Adult human tissues from diverse sites around the body are used to reconstruct cellular phylogenies from early development, using somatic mutations as an internal barcode.

Seongyeol Park
, Nanda Maya Mali
& Young Seok Ju

Article
11 November 2020 | Open Access

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

The Progressive Cactus program can create reference-free alignments of hundreds of large vertebrate genomes efficiently, and is used for the alignment of more than 600 amniote genomes.

Joel Armstrong
, Glenn Hickey
& Benedict Paten

Article | 18 April 2018

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

A new version of the phylogenetic bootstrap method enables assessment of the robustness of phylogenies that are based on large datasets of hundreds or thousands of taxa.

F. Lemoine
, J.-B. Domelevo Entfellner
& O. Gascuel

Letter | 24 May 2017

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

Virus genomes reveal the establishment of Zika virus in Brazil and the Americas, and provide an appropriate timeframe for baseline (pre-Zika) microcephaly in different regions.

N. R. Faria
, J. Quick
& O. G. Pybus

Article
21 May 2014 | Open Access

The ctenophore genome and the evolutionary origins of neural systems

The draft genome of the ctenophore Pleurobrachia bachei (Pacific sea gooseberry) is presented, together with ten other ctenophore transcriptomes — these genomes have a very different neurogenic, immune and developmental gene content when compared with other animal genomes, and it is proposed that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.

Leonid L. Moroz
, Kevin M. Kocot
& Andrea B. Kohn

Article | 08 May 2013

Inferring ancient divergences requires genes with strong phylogenetic signals

Determining major branches in the tree of life generally relies on concatenating as much genetic information as possible, but, as shown here, phylogenomic analysis often produces results that are incongruent with the results of concatenation; a method that gives credence to genes or internodes with high average internode support reduces the incongruence.