A Guide to Phylogenomic Inference

JSL Patané, J Martins Jr, JC Setubal - Comparative Genomics: Methods …, 2024 - Springer
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into
account whole genomes or large fractions of genomes. Phylogenomics has significant …

The limits of the constant-rate birth–death prior for phylogenetic tree topology inference

MP Khurana, N Scheidwasser-Clow, MJ Penn… - Systematic …, 2024 - academic.oup.com
Birth–death models are stochastic processes describing speciation and extinction through
time and across taxa and are widely used in biology for inference of evolutionary timescales …

Evolution of the WRKY Family in Angiosperms and Functional Diversity under Environmental Stress

W Wu, J Yang, N Yu, R Li, Z Yuan, J Shi… - International Journal of …, 2024 - mdpi.com
The transcription factor is an essential factor for regulating the responses of plants to
external stimuli. The WRKY protein is a superfamily of plant transcription factors involved in …

Negative global-scale association between genetic diversity and speciation rates in mammals

AC Afonso Silva, O Maliet, L Aristide… - Nature …, 2025 - nature.com
Genetic diversity is critical for species evolution and their adaptability to global changes,
while speciation rate is critical for explaining large-scale patterns of species richness …

Around the World in 26 Million Years: Diversification and Biogeography of Pantropical Grass‐Yellow Eurema Butterflies (Pieridae: Coliadinae)

JV Leong, P Matos‐Maraví, R Núñez… - Journal of …, 2025 - Wiley Online Library
ABSTRACT Aim Grass‐yellow butterflies (Eurema) are a group of pantropical Pieridae
distributed throughout Asia, Australasia, Africa and the New World. However, little is known …

Mixture Models for Dating with Confidence

G Darlim, S Hoehna - bioRxiv, 2024 - biorxiv.org
Robust estimation of divergence times is commonly performed using Bayesian inference
with relaxed clock models. The specific choice of relaxed clock model and tree prior model …

Evolution is coupled with branching across many granularities of life

J Douglas, R Bouckaert, SC Harris, CW Carter Jr… - bioRxiv, 2024 - biorxiv.org
Across many different scales of life, the rate of evolutionary change is often accelerated at
the time when one lineage splits into two. The emergence of novel protein function can be …

[HTML][HTML] Phylogenetics and Evolutionary Dynamics of Yunnan Acrididae Grasshoppers Inferred from 17 New Mitochondrial Genomes

K Zhang, J Song, J Lu, L Zhao, W Deng, D Guan… - Insects, 2025 - mdpi.com
Yunnan Province, a global biodiversity hotspot, hosts a diverse array of Acrididae
grasshoppers essential for ecosystem dynamics and agriculture. To elucidate the …

A covariant model of molecular and diversification patterns through time and the history of large clades

GE Budd, RP Mann - bioRxiv, 2024 - biorxiv.org
Rate shifts in speciation and extinction have been recognised as important contributors to
the creation of evolutionary patterns. In particular, the distribution of modern clade sizes is …