Amplified fragment length polymorphism (AFLP) DNA fingerprinting is a firmly established molecular marker technique, with broad applications in population genetics, shallow phylogenetics, linkage mapping, parentage analyses, and single-locus PCR marker development. Technical advances have presented new opportunities for data analysis, and recent studies have addressed specific areas of the AFLP...

Multidrug-resistant Escherichia coli is an emerging clinical challenge in domestic species. Treatment options in many cases are limited. This study characterized MDR E. coli isolates from urinary tract infections in dogs, collected between 2002 and 2011. Isolates were evaluated in terms of β-lactamase production, phylogenetic group, ST type, replicon type and virulence marker profile. Compariso...

Next-generation sequencing of restriction site associated DNA, or RADseq, was introduced in 2008 as a rapid genotyping method that does not require prior marker development. Developed for linkage mapping, genome-wide association, and population genetic studies, RADseq was initially viewed as ill-suited to interspecific phylogenetic questions. However, since 2012, approximately a dozen RADseq ph...

Gene content has been shown to contain a strong phylogenetic signal, yet its usage for phylogenetic questions is hampered by horizontal gene transfer and parallel gene loss and until now required completely sequenced genomes. Here, we introduce an approach that allows the phylogenetic signal in gene content to be applied to any set of sequences, using signature genes for phylogenetic classifica...

A large number of studies in evolutionary biology utilize phylogenetic information obtained from mitochondrial DNA. Researchers place trust in this molecule and expect it generally to be a reliable marker for addressing questions ranging from population genetics to phylogenies among distantly related lineages. Yet, regardless of the phylogenetic method and weighting treatment, individual mitoch...