Taxon sampling may be critically important for phylogenetic accuracy because adding taxa can help to subdivide misleading long branches. Although the idea that added taxa can break up long branches was exemplified by a study of "incomplete" fossil taxa, the issue of taxon completeness (i.e., proportion of missing data) has been largely ignored in most subsequent discussions of taxon sampling an...

BACKGROUND Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ab...

Phylogenetic systematics seeks to describe and reconstruct the evolutionary relationships among and between organisms making use of molecular data. This field has become immensely popular in recent years, with the associated computational demands growing in leaps and bounds. Here, we review the progress made in statistical phylogenetics, compare the various methods and highlight the recent tren...

Because biological processes can result in different loci having different evolutionary histories, species tree estimation requires multiple loci from across multiple genomes. While many processes can result in discord between gene trees and species trees, incomplete lineage sorting (ILS), modeled by the multi-species coalescent, is considered to be a dominant cause for gene tree heterogeneity....

MOTIVATION Restriction-site-associated genomic markers are a powerful tool for investigating evolutionary questions at the population level, but are limited in their utility at deeper phylogenetic scales where fewer orthologous loci are typically recovered across disparate taxa. While this limitation stems in part from mutations to restriction recognition sites that disrupt data generation, an ...

The reconstruction of phylogenies is becoming an increasingly simple activity. This is mainly due to two reasons: the democratization of computing power and the increased availability of sophisticated yet user-friendly software. This review describes some of the latest additions to the phylogenetic toolbox, along with some of their theoretical and practical limitations. It is shown that Bayesia...

With 3,480 E. coli strains isolated from the Yeongsan River basin, South Korea, correlations between phylogenetic groups and horizontal fluorophore enhanced rep-PCR (HFERP) genotypes were examined, and environmental factors affecting E. coli phylogenetic groups in the river water were determined. Interestingly, multidimentional scaling (MDS) analyses based on HFERP DNA fingerprint data indicate...

St. Louis encephalitis virus belongs to the Japanese encephalitis virus serocomplex of the genus Flavivirus, family Flaviviridae. Since the first known epidemic in 1933, the virus has been isolated from a variety of geographical, temporal, and host origins. We have sequenced 10,236 nucleotides of the open reading frame (93.6% of the full-length genome) of 23 of these strains, and have used the ...

The monotypic fern genus Dryopolystichum Copel. combines a unique assortment of characters that obscures its relationship to other ferns. Its thin-walled sporangium with a vertical and interrupted annulus, round sorus with peltate indusium, and petiole with several vascular bundles place it in suborder Polypodiineae, but more precise placement has eluded previous authors. Here we investigate it...

The rapid increase in genomic and genome-scale data is resulting in unprecedented levels of discrete sequence data available for phylogenetic analyses. Major analytical impasses exist, however, prior to analyzing these data with existing phylogenetic software. Obstacles include the management of large data sets without standardized naming conventions, identification and filtering of orthologous...