This study focuses on three phylogenetic problems related to Capsicum (Solanaceae): (1) the monophyly of the genus, (2) species delimitation within the genus, and (3) phylogenetic relationships of species within Capsicum. The chloroplast atpB-rbcL noncoding spacer region was used to derive a phylogeny for seven outgroup genera and 11 species of Capsicum. Data derived from five introns within th...

Haplotype phylogenies based on DNA sequence data are increasingly being used to test traditional species-level taxonomies based on morphology. However, few studies have critically compared species limits based on morphological and DNA data, and the methods used to delimit species using either type of data are only rarely explained. In this paper, we review three approaches for species delimitat...

In the spirit of recent calls for species delimitation studies to become more pluralistic, incorporating multiple sources of evidence, we adopted an integrative, phylogeographic approach to delimiting species and evolutionarily significant units (ESUs) in the Corallorhiza striata species complex. This rare, North American, mycoheterotrophic orchid has been a taxonomic challenge regarding specie...

Species are commonly delimited on the basis of gaps in patterns of morphological variation, but there seems to be little recent work on methods to objectively assess such gaps. Here, we introduce a statistical approach that uses measurements of continuous morphological characters and geographic variation in those characters to (i) measure the strength of the evidence for the existence of a gap ...

The estimation of species diversity in fungal endophyte communities is based either on species counts or on the assignment of operational taxonomic units (OTUs). Consequently, the application of different species recognition criteria affects not only diversity estimates but also the ecological hypotheses that arise from those observations. The main objective of the study was to examine how the ...

Both gene-tree discordance and unrecognized diversity are sources of error for accurate estimation of species trees, and can affect downstream diversification analyses by obscuring the correct number of nodes, their density, and the lengths of the branches subtending them. Although the theoretical impact of gene-tree discordance on evolutionary analyses has been examined previously, the effect ...

The focus of this article is a Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using molecular sequences from multiple loci. The species delimitation requires no a priori assignment of individuals to species, and no guide tree. The method is implemented in a package called STACEY for BEAST2, and is a extension of the author's DI...

Insect cuticular hydrocarbons (CHCs) play critical roles in reducing water loss and chemical communication. Species-specific CHC profiles have been used increasingly as an excellent character for species classification. However, considerably less is known about their potential for population delimitation within species. The aims of this study were to develop a solid-phase microextraction (SPME)...