Advances and applications in the quest for orthologs
Gene families evolve by the processes of speciation (creating orthologs), gene duplication
(paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and …
(paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and …
Amphioxus functional genomics and the origins of vertebrate gene regulation
Vertebrates have greatly elaborated the basic chordate body plan and evolved highly
distinctive genomes that have been sculpted by two whole-genome duplications. Here we …
distinctive genomes that have been sculpted by two whole-genome duplications. Here we …
Spider phylogenomics: untangling the Spider Tree of Life
ABSTRACT Spiders (Order Araneae) are massively abundant generalist arthropod
predators that are found in nearly every ecosystem on the planet and have persisted for over …
predators that are found in nearly every ecosystem on the planet and have persisted for over …
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces
Abstract The Orthologous Matrix (OMA) is a leading resource to relate genes across many
species from all of life. In this update paper, we review the recent algorithmic improvements …
species from all of life. In this update paper, we review the recent algorithmic improvements …
Convergent regulatory evolution and loss of flight in paleognathous birds
A core question in evolutionary biology is whether convergent phenotypic evolution is driven
by convergent molecular changes in proteins or regulatory regions. We combined …
by convergent molecular changes in proteins or regulatory regions. We combined …
The house spider genome reveals an ancient whole-genome duplication during arachnid evolution
Background The duplication of genes can occur through various mechanisms and is thought
to make a major contribution to the evolutionary diversification of organisms. There is …
to make a major contribution to the evolutionary diversification of organisms. There is …
Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics
Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly
include transcriptomes and low-coverage genomes that are incomplete and contain errors …
include transcriptomes and low-coverage genomes that are incomplete and contain errors …
Systematics, phylogeny, and evolution of orb-weaving spiders
The orb-weaving spiders (Orbiculariae) comprise more than 25% of the approximately
44,000 known living spider species and produce a remarkable variety of webs. The wheel …
44,000 known living spider species and produce a remarkable variety of webs. The wheel …
A phylogenomic solution to the origin of insects by resolving crustacean-hexapod relationships
Insects, the most diverse group of organisms, are nested within crustaceans, arguably the
most abundant group of marine animals. However, to date, no consensus has been reached …
most abundant group of marine animals. However, to date, no consensus has been reached …
Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal
Chelicerata represents one of the oldest groups of arthropods, with a fossil record extending
to the Cambrian, and is sister group to the remaining extant arthropods, the mandibulates …
to the Cambrian, and is sister group to the remaining extant arthropods, the mandibulates …