The promise and pitfalls of synteny in phylogenomics

JL Steenwyk, N King - Plos Biology, 2024 - journals.plos.org
Reconstructing the tree of life remains a central goal in biology. Early methods, which relied
on small numbers of morphological or genetic characters, often yielded conflicting …

Common methods for phylogenetic Tree Construction and their implementation in R

Y Zou, Z Zhang, Y Zeng, H Hu, Y Hao, S Huang, B Li - Bioengineering, 2024 - mdpi.com
A phylogenetic tree can reflect the evolutionary relationships between species or gene
families, and they play a critical role in modern biological research. In this review, we …

Evolution and genetic architecture of sex-limited polymorphism in cuckoos

J Merondun, CI Marques, P Andrade… - Science …, 2024 - science.org
Sex-limited polymorphism has evolved in many species including our own. Yet, we lack a
detailed understanding of the underlying genetic variation and evolutionary processes at …

Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family

S Das, E Greenbaum, J Brecko, OSG Pauwels… - Scientific Reports, 2024 - nature.com
Asian mock vipers of the genus Psammodynastes and African forest snakes of the genus
Buhoma are two genera belonging to the snake superfamily Elapoidea. The phylogenetic …

Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

JL Steenwyk, C Balamurugan, HA Raja… - Microbiology …, 2024 - Am Soc Microbiol
Modern taxonomic classification is often based on phylogenetic analyses of a few molecular
markers, although single-gene studies are still common. Here, we leverage genome-scale …

The Bryophyte Phylogeny Group: A revised familial classification system based on plastid phylogenomic data

YF Li, L Luo, Y Liu, Q He, NN Yu… - … of Systematics and …, 2024 - Wiley Online Library
Bryophytes, a monophyletic group comprising three major lineages, diversified soon after
the terrestrialization of land plants. However, their internal phylogenetic relationships remain …

Ancient and recent origins of shared polymorphisms in yeast

N Tellini, M De Chiara, S Mozzachiodi… - Nature Ecology & …, 2024 - nature.com
Shared genetic polymorphisms between populations and species can be ascribed to
ancestral variation or to more recent gene flow. Here, we mapped shared polymorphisms in …

Putative genome contamination has minimal impact on the GTDB taxonomy

AJ Mussig, PA Chaumeil, M Chuvochina… - Microbial …, 2024 - microbiologyresearch.org
The Genome Taxonomy Database (GTDB) provides a species to domain classification of
publicly available genomes based on average nucleotide identity (ANI)(for species) and a …

Phylogenomic perspectives on speciation and reproductive isolation in a North American biodiversity hotspot: an example using California sages (Salvia subgenus …

JP Rose, R Kriebel, KJ Sytsma, BT Drew - Annals of Botany, 2024 - academic.oup.com
Abstract Background and Aims The California Floristic Province (CA-FP) is the most species-
rich region of North America north of Mexico. One of several proposed hypotheses …

Genomic incongruence accompanies the evolution of flower symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales)

L Pokorny, J Pellicer, Y Woudstra… - Frontiers in Plant …, 2024 - frontiersin.org
Reconstructing evolutionary trajectories and transitions that have shaped floral diversity
relies heavily on the phylogenetic framework on which traits are modelled. In this study, we …