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 …

ncOrtho: efficient and reliable identification of miRNA orthologs

F Langschied, MS Leisegang, RP Brandes… - Nucleic acids …, 2023 - academic.oup.com
MicroRNAs (miRNAs) are post-transcriptional regulators that finetune gene expression via
translational repression or degradation of their target mRNAs. Despite their functional …

Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance

MS Hibbins, LC Breithaupt, MW Hahn - Proceedings of the National …, 2023 - pnas.org
Phylogenetic comparative methods have long been a mainstay of evolutionary biology,
allowing for the study of trait evolution across species while accounting for their common …

Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk

JM Vazquez, VJ Lynch - Elife, 2021 - elifesciences.org
The risk of develo** cancer is correlated with body size and lifespan within species.
Between species, however, there is no correlation between cancer and either body size or …

Pollinator shifts despite hybridisation in the Cape's hyperdiverse heathers (Erica, Ericaceae)

SD Musker, MD Pirie, NM Nürk - Molecular Ecology, 2024 - Wiley Online Library
Interrogating the ecological and geographic factors that influence population divergence
dynamics can reveal why some groups of organisms diversify more prolifically than others …

Bactrocera dorsalis in the Indian Ocean: A tale of two invasions

P Deschepper, S Vanbergen, Y Zhang… - Evolutionary …, 2023 - Wiley Online Library
An increasing number of invasive fruit fly pests are colonizing new grounds. With this study,
we aimed to uncover the invasion pathways of the oriental fruit fly, Bactrocera dorsalis into …

Genome sequencing of 'Fuji'apple clonal varieties reveals genetic mechanism of the spur-type morphology

Y Cai, X Gao, J Mao, Y Liu, L Tong, X Chen… - Nature …, 2024 - nature.com
Somatic variations can give rise to bud sports with advantageous traits, serving as the
foundation for bud sport breeding in perennial plants. Here, we report a fully phased …

Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world's most threatened primates

J Malukiewicz, RA Cartwright, JA Dergam… - Scientific Reports, 2021 - nature.com
The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world's most
endangered primates, is threatened by anthropogenic hybridization with exotic, invasive …

AmAMP1 from Acropora millepora and damicornin define a family of coral-specific antimicrobial peptides related to the Shk toxins of sea anemones

B Mason, I Cooke, A Moya, R Augustin, MF Lin… - Developmental & …, 2021 - Elsevier
A candidate antimicrobial peptide (AmAMP1) was identified by searching the whole genome
sequence of Acropora millepora for short (< 125AA) cysteine-rich predicted proteins with an …

Genetic characterization of the first Deltacoronavirus from wild birds around Qinghai Lake

Y Tian, T Yu, J Wang, H Zhang, Y Jian, X Li… - Frontiers in …, 2024 - frontiersin.org
Deltacoronavirus, widely distributed among pigs and wild birds, pose a significant risk of
cross-species transmission, including potential human epidemics. Metagenomic analysis of …