Beginner's guide on the use of PAML to detect positive selection

S Álvarez-Carretero, P Kapli… - Molecular biology and …, 2023 - academic.oup.com
The CODEML program in the PAML package has been widely used to analyze protein-
coding gene sequences to estimate the synonymous and nonsynonymous rates (d S and d …

On the origin and continuing evolution of SARS-CoV-2

X Tang, C Wu, X Li, Y Song, X Yao, X Wu… - National science …, 2020 - academic.oup.com
The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since
impacted a large portion of China and raised major global concern. Herein, we investigated …

Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences

H Jiang, J Tian, J Yang, X Dong, Z Zhong… - BMC Plant …, 2022 - Springer
Abstract Background Polystachya Hook. is a large pantropical orchid genus (c. 240 species)
distributed in Africa, southern Asia and the Americas, with the center of diversity in Africa …

Meta‐analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species

DC Dearborn, S Warren, F Hailer - Molecular ecology, 2022 - Wiley Online Library
Pathogen‐mediated selection and sexual selection are important drivers of evolution. Both
processes are known to target genes of the major histocompatibility complex (MHC), a gene …

Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae)

D Jiang, X Cai, M Gong, M Xia, H Xing, S Dong, S Tian… - BMC genomics, 2023 - Springer
Abstract Background The genus Zingiber of the Zingiberaceae is distributed in tropical,
subtropical, and in Far East Asia. This genus contains about 100–150 species, with many …

Adaptive evolution of the spike protein in coronaviruses

X Tang, Z Qian, X Lu, J Lu - Molecular Biology and Evolution, 2023 - academic.oup.com
Coronaviruses are single-stranded, positive-sense RNA viruses that can infect many
mammal and avian species. The Spike (S) protein of coronaviruses binds to a receptor on …

Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance

L Tao, H Duan, K Tao, Y Luo, Q Li, L Li - BMC genomics, 2023 - Springer
Background The taxonomy and infrageneric delimitation of Phalaenopsis Blume has been
significantly disputed due to some overlapping morphological features between species …

The genomic basis of temporal niche evolution in a diurnal rodent

R Richardson, CY Feigin, B Bano-Otalora, MR Johnson… - Current Biology, 2023 - cell.com
Patterns of diel activity—how animals allocate their activity throughout the 24-h daily cycle—
play key roles in shaping the internal physiology of an animal and its relationship with the …

A multifunctional Wnt regulator underlies the evolution of rodent stripe patterns

MR Johnson, S Li, CF Guerrero-Juarez… - Nature ecology & …, 2023 - nature.com
Animal pigment patterns are excellent models to elucidate mechanisms of biological
organization. Although theoretical simulations, such as Turing reaction–diffusion systems …

Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism

G Potente, É Léveillé-Bourret, N Yousefi… - Molecular Biology …, 2022 - academic.oup.com
Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple,
coadapted genes. Despite the importance of supergenes in adaptation, little is known on …