Showing papers by "John E. McCormack published in 2013"

A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing.

Abstract: Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.

Next‐generation phylogenetics takes root

Abstract: It has been a tumultuous 5 years in phylogeography and phylogenetics during which both fields have struggled to harness the power of next-generation sequencing (NGS) (Ekblom & Galindo 2010; McCormack et al. 2012a). Fortunately, several methodological approaches appear to be taking root. In this issue of Molecular Ecology, O'Neill et al. 2013) employ one such method – parallel tagged sequencing (PTS) – to elucidate the phylogeography of a tiger salamander (Ambystoma tigrinum) species complex. This study demonstrates a practical application of NGS on a scale appropriate (and not overkill) for most biologists interested in phylogeography (~100 loci for ~100 individuals), and their results highlight several analytical challenges that lie ahead for researchers employing NGS techniques.

A distinctive genetic footprint of Ancient hybridizAtion

Abstract: . Ancient hybridization is difficult to detect and is often surmised from conflicting patterns between phenotypic and genetic data sets that are difficult to explain with alternative hypotheses. Here, a fortuitous macromutation in a microsatellite locus allows an unusually distinctive footprint of ancient introgression to be inferred between two highly divergent bird species that began to speciate in the Late Miocene. A cline of distinctive high-repeat-number (large) alleles at a locus in the Mexican Jay (Aphelocoma wollweberi), which predominantly has low-repeat-number (small) alleles, reaches its highest frequency near the range border with Transvolcanic Jays (A. ultramarina), which are fixed for large alleles, indicating gene flow. The gene flow is not recent, however, because very few of the allelic states are shared between Mexican Jays and Transvolcanic Jays. Ancient gene flow is also more plausible than current gene flow because prior mitochondrial DNA results show no evidence of current di...