Using cytochrome b to identify nests and museum specimens of cryptic songbirds
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METHODS AND RESOURCES ARTICLE
Using cytochrome b to identify nests and museum specimens of cryptic songbirds A. Elizabeth Arnold1 · Erik M. Andersen2 · Michael J. Taylor2 · Robert J. Steidl2
Received: 21 June 2016 / Accepted: 28 December 2016 © Springer Science+Business Media Dordrecht 2017
Abstract Understanding demography of vertebrate populations requires quantifying reproductive success. For taxa that are difficult to distinguish, estimates of reproductive success can be biased if species are misidentified or if breeding concludes before identification is confirmed. We surveyed desert grasslands where three species of cryptic sparrows breed: Peucaea botterii, P. cassinii, and Aimophila ruficeps (Emberizidae). Nests, eggs, and nestlings of these species are similar, making it difficult to differentiate nests without observing adults, which can be challenging. We collected seven types of material from nests for DNA analysis: maternal cells from exterior surfaces of unhatched eggs, epithelial cells from the oropharyngeal cavity of nestlings, eggshells, feathers, feather sheaths, feces, and fecal sacs. From these materials, we amplified and sequenced a fragment of the diagnostic locus, mitochondrial cytochrome b (cyt b), and analyzed the data in a phylogenetic framework to classify nests to species. We validated our classification by sequencing the same locus from feathers of museum specimens. Overall, 72% of samples from nests yielded high-quality sequences. We identified to species 44 of 51 nests and identified museum specimens with archival Electronic supplementary material The online version of this article (doi:10.1007/s12686-016-0680-2) contains supplementary material, which is available to authorized users. * A. Elizabeth Arnold [email protected] 1
School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, 1140 E. South Campus Drive, Forbes 303, Tucson, AZ 85721, USA
2
School of Natural Resources and the Environment, The University of Arizona, Tucson, USA
ages of up to 47 years. Our study extends previous research by demonstrating the efficacy of standard kits, inexpensive reagents, low DNA concentrations, and diverse materials in classifying nests of grassland sparrows. Compared to more invasive methods of acquiring DNA, the approaches we describe are less likely to affect nesting behavior and bias estimates of nesting success of birds, issues especially important for species of conservation concern. Keywords Aimophila · Cyt b · Emberizidae · Mitochondrial · Nest success · Peucaea · Polymerase chain reaction
Introduction Understanding mechanisms that govern demography and dynamics of vertebrate populations requires quantifying reproductive success. A key component of reproduction for birds is nest success, but classifying nests by species can be challenging for groups of species where nesting females are secretive, have similar morphology and cryptic coloration, and nest sympatrically. Identification is especially difficult when eggs, nestli
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