IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era

BQ Minh, HA Schmidt, O Chernomor… - Molecular biology …, 2020 - academic.oup.com
Abstract IQ-TREE (http://www. iqtree. org, last accessed February 6, 2020) is a user-friendly
and widely used software package for phylogenetic inference using maximum likelihood …

Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars

G Hu, J Feng, X Xiang, J Wang, J Salojärvi, C Liu… - Nature …, 2022 - nature.com
Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar 'Feizixiao'was
assembled into 15 pseudochromosomes, totaling~ 470 Mb. High heterozygosity (2.27%) …

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

AM Kozlov, D Darriba, T Flouri, B Morel… - …, 2019 - academic.oup.com
Motivation Phylogenies are important for fundamental biological research, but also have
numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree …

UFBoot2: improving the ultrafast bootstrap approximation

DT Hoang, O Chernomor… - Molecular biology …, 2018 - academic.oup.com
The standard bootstrap (SBS), despite being computationally intensive, is widely used in
maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap …

Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths

AY Kawahara, D Plotkin, M Espeland… - Proceedings of the …, 2019 - National Acad Sciences
Butterflies and moths (Lepidoptera) are one of the major superradiations of insects,
comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey …

[HTML][HTML] Fungal Planet description sheets: 1284–1382

PW Crous, ER Osieck, Ž Jurjević, J Boers… - … and Evolution of …, 2021 - ncbi.nlm.nih.gov
Novel species of fungi described in this study include those from various countries as
follows: Antartica, Cladosporium austrolitorale from coastal sea sand. Australia …

The critically endangered vaquita is not doomed to extinction by inbreeding depression

JA Robinson, CC Kyriazis, SF Nigenda-Morales… - Science, 2022 - science.org
In cases of severe wildlife population decline, a key question is whether recovery efforts will
be impeded by genetic factors, such as inbreeding depression. Decades of excess mortality …

Phytophthora: taxonomic and phylogenetic revision of the genus

ZG Abad, TI Burgess, T Bourret, K Bensch… - Studies in …, 2023 - ingentaconnect.com
Many members of the Oomycota genus Phytophthora cause economic and environmental
impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of …

Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex

DM Geiser, AMS Al-Hatmi, T Aoki, T Arie… - …, 2021 - Am Phytopath Society
Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that
considers the end-user's needs and established successful practice. In 2013, the Fusarium …

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 …