Abstract
Abstract Western Scrub-Jays (Aphelocoma californica) range throughout the western United States and Mexico and exhibit substantial geographic variation in morphology and behavior. Western Scrub-Jays are a polytypic species complex with three distinct groups (californica, woodhouseii, and sumichrasti) associated with geography and distinguished by morphology, genetics, and behavior. Until recently, the Island Scrub-Jay (A. insularis) and the Florida Scrub-Jay (A. coerulescens) were considered subspecies within the Western Scrub-Jay complex. We analyzed mitochondrial DNA sequences (control region I) to reveal the phylogenetic relationships within Western Scrub-Jays and used maximum likelihood, a Bayesian approach, and a relaxed phylogenetic approach to construct phylogenies. In addition, we used several methods to estimate divergence time between clades. Our results reveal that the interior woodhouseii group, which contains the sumichrasti subclade, and the coastal californica group have had a long and inde...
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