Incongruence in the phylogenomics era

JL Steenwyk, Y Li, X Zhou, XX Shen… - Nature Reviews Genetics, 2023 - nature.com
Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Viruses and metabolism: the effects of viral infections and viral insulins on host metabolism

K Girdhar, A Powis, A Raisingani… - Annual review of …, 2021 - annualreviews.org
Over the past decades, there have been tremendous efforts to understand the cross-talk
between viruses and host metabolism. Several studies have elucidated the mechanisms …

Incomplete lineage sorting and phenotypic evolution in marsupials

S Feng, M Bai, I Rivas-González, C Li, S Liu, Y Tong… - Cell, 2022 - cell.com
Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during
rapid speciation events, inducing incongruences between gene trees and species trees. ILS …

Selection-driven trait loss in independently evolved cavefish populations

RL Moran, EJ Richards, CP Ornelas-García… - Nature …, 2023 - nature.com
Laboratory studies have demonstrated that a single phenotype can be produced by many
different genotypes; however, in natural systems, it is frequently found that phenotypic …

Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae)

Y Cao, F Almeida-Silva, WP Zhang… - Molecular biology …, 2023 - academic.oup.com
When challenged by similar environmental conditions, phylogenetically distant taxa often
independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme …

Mutational background influences P. aeruginosa ciprofloxacin resistance evolution but preserves collateral sensitivity robustness

S Hernando-Amado, P Laborda… - Proceedings of the …, 2022 - National Acad Sciences
Collateral sensitivity is an evolutionary trade-off whereby acquisition of the adaptive
phenotype of resistance to an antibiotic leads to the nonadaptive increased susceptibility to …

Genome annotation: From human genetics to biodiversity genomics

R Guigó - Cell Genomics, 2023 - cell.com
Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced.
Identifying genes in these sequences is essential to understand the biology of the species …

Avian Island Radiations Shed Light on the Dynamics of Adaptive and Nonadaptive Radiation

JC Illera, JC Rando, M Melo… - Cold Spring …, 2024 - cshperspectives.cshlp.org
Understanding the mechanisms underlying species formation and differentiation is a central
goal of evolutionary biology and a formidable challenge. This understanding can provide …

Reinventing the wheel? Reassessing the roles of gene flow, sorting and convergence in repeated evolution

JM Waters, GA McCulloch - Molecular Ecology, 2021 - Wiley Online Library
Biologists have long been intrigued by apparently predictable and repetitive evolutionary
trajectories inferred across a variety of lineages and systems. In recent years, high …

Habitat Adaptation Drives Speciation of a Streptomyces Species with Distinct Habitats and Disparate Geographic Origins

J Wang, Y Li, AA Pinto-Tomás, K Cheng, Y Huang - MBio, 2022 - Am Soc Microbiol
Microbial diversification is driven by geographic and ecological factors, but how the relative
importance of these factors varies among species, geographic scales, and habitats remains …