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This document provides a set of primer sequences for amplifying and sequencing the entire avian mitochondrial DNA. Most of the primers were originally developed as part of earlier studies (see refs) but many have since been revised or replaced with primers in different locations. All of the primers have been designed to work with most or all birds and most perform very well in this regard.This document is intended as a resource for those interested in using mtDNA for avian population genetics and systematics, whether that work involves sequencing complete mitochondrial genomes or single genes. A second goal is to encourage the use of genes other than cytochrome b, which is a poor choice for studies in which only one mitochondrial gene will be sequenced. If I'm going to sequence only one gene, which one should I choose? ND2! Why not cyt b?All mitochondrial protein genes have similarly high rates of substitution at 3 rd codon positions, but they vary greatly in the rate of amino acid substitution. Therefore, all mt protein genes provide similar information (per base pair sequenced) for very closely related taxa (e.g., individuals within a species) that differ primarily at degenerate 3 rd codon positions. For somewhat more distantly related taxa (including species within a genus, for example, and everything else up to and including comparisons between avian orders), more variable mt genes accumulate more informative variation at 1 st and 2 nd codon positions, whereas 3 rd positions increasingly accumulate multiple substitutions (i.e., homoplasy) in all genes. With cyt b, you get all of the noise and none of the signal! -with other mt genes, you get a little signal along with the noise. Why ND2?In terms of amino acid sequence, ND2 is the 3 rd most variable gene after ATPase 8, which is very short (~165-168 bp) and therefore provides relatively little information, and ND6, which is also relatively short (~519-522 bp) and is generally more difficult to amplify and sequence, given its unusual base composition and location near the control region. In contrast, the complete ND2 gene can be amplified in either one or two pieces with primers that have worked well on essentially all birds (L5216-H6313 for the whole gene; L5216-H5766 and L5758-H6313 for two pieces). We routinely amplify the gene in two pieces and run four sequencing reactions (both strands of each PCR product). What are all those Y's and R's in the primer sequences?Many of the primers listed below have several and as many as six or more "degenerate" positions. What this means is that there are actually different versions of the primer that have

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The reddish egret (Egretta rufescens) is the rarest heron in North America and much remains to be learned about in the ecology of the species. The reddish egret is a foraging habitat specialist and relies on shallow coastal ecosystems. There is a paucity of information on foraging habitat requirements and the availability of foraging habitat throughout the annual cycle. Characteristics of foraging habitat at locations within the Laguna Madre, Texas where reddish egrets were observed foraging were measured. These characteristics were used to conduct a geospatial analysis that estimated the spatial and temporal distributions of foraging habitat in the Laguna Madre across 120 weeks from 2012 to 2014. Reddish egrets (n = 372) foraged in an average water depth of 10.1 ± 0.68 cm and in areas with average seagrass cover of 12.3 ± 2.74%. Approximately, 75 000 ha of foraging habitat were delineated to be available in the Laguna Madre across the study period; of this, 4 003 ha were available ≥ 50% of the time. The amount of available foraging habitat was relatively high during the spring and summer, and decreased by ~50% during winter. This model-based approach can be used throughout the species' range to examine foraging habitat availability which is a current conservation need according to the Reddish Egret Conservation Action Plan.