Irrational exuberance for resolved species trees
Phylogenomics has largely succeeded in its aim of accurately inferring species trees, even
when there are high levels of discordance among individual gene trees. These resolved …
when there are high levels of discordance among individual gene trees. These resolved …
Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing
Many phylogenomic studies based on transcriptomes have been limited to “single-copy”
genes due to methodological challenges in homology and orthology inferences. Only a …
genes due to methodological challenges in homology and orthology inferences. Only a …
Sequence capture versus restriction site associated DNA sequencing for shallow systematics
Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two
genomic enrichment strategies for applying next-generation sequencing technologies to …
genomic enrichment strategies for applying next-generation sequencing technologies to …
GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno …
P Vinuesa, LE Ochoa-Sánchez… - Frontiers in …, 2018 - frontiersin.org
The massive accumulation of genome-sequences in public databases promoted the
proliferation of genome-level phylogenetic analyses in many areas of biological research …
proliferation of genome-level phylogenetic analyses in many areas of biological research …
An alternative root for the eukaryote tree of life
The root of the eukaryote tree of life defines some of the most fundamental relationships
among species. It is also critical for defining the last eukaryote common ancestor (LECA), the …
among species. It is also critical for defining the last eukaryote common ancestor (LECA), the …
Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets
Explosive diversification is widespread in eukaryotes, making it difficult to resolve
phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important …
phylogenetic relationships. Eudicots contain c. 75% of extant flowering plants, are important …
The impact of missing data on species tree estimation
Phylogeneticists are increasingly assembling genome-scale data sets that include hundreds
of genes to resolve their focal clades. Although these data sets commonly include a …
of genes to resolve their focal clades. Although these data sets commonly include a …
Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation
EJM Koenen, C Kidner, ÉR de Souza… - American Journal of …, 2020 - Wiley Online Library
PREMISE Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to
enhance phylogenetic resolution and elucidate why some parts of the “tree of life” are …
enhance phylogenetic resolution and elucidate why some parts of the “tree of life” are …
Phylogenetic signal, congruence, and uncertainty across bacteria and archaea
CA Martinez-Gutierrez… - Molecular Biology and …, 2021 - academic.oup.com
Reconstruction of the Tree of Life is a central goal in biology. Although numerous novel
phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic …
phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic …
Concordance and discordance in the phylogenomics of the wrasses and parrotfishes (Teleostei: Labridae)
Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic
tree topologies for large species groups, help test the accuracy of and improve resolution for …
tree topologies for large species groups, help test the accuracy of and improve resolution for …