Genetic Diversity and Population Structure of Reddish Egrets Along the Texas Coast

Abstract

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

Genetic diversity and population structure of North America’s rarest heron, the reddish egret (Egretta rufescens)

“…Results from program STRUCTURE also suggest the existence of three major regions of distinct genetic units. A previous study using mtDNA to look at population structure of reddish egrets along the Texas coast found no structuring among 16 colonies; our results in Texas using microsatellites support these earlier findings (Bates et al 2009). …”

“…Program BOTTLENECK failed to detect evidence of any recent genetic bottleneck in any of the populations in this study. Bates et al (2009) did not detect reduced genetic diversity in reddish egrets from Texas but did find signals of a population expansion indicating a possible recovery from a previous low. Initial impacts of a genetic bottleneck include the loss of unique alleles, but a population can preserve genetic diversity if recovery occurs quickly (Allendorf 1986;Coates 1992).…”

“…The objectives of our study were to assess the genetic diversity and the genetic structure of reddish egret populations throughout most of its range and to assess genetic differentiation between color morphs using polymorphic microsatellite markers. Using mtDNA, Bates et al (2009) found no evidence of genetic structure for reddish egrets within the state of Texas. Disjunct populations, subspecies designations, varying color morph frequencies and the residential nature of reddish egrets suggests possible differentiation across the range.…”

Avian Resources of the Northern Gulf of Mexico

“…Fish and Wildlife Service (USFWS) (Bates et al 2009); (3) they are a species of moderate concern as evaluated by the U.S. Shorebird Conservation Plan (Elliott and McKnight 2000), as well as the Southeast U.S. Regional Waterbird Conservation Plan ; (4) they are a priority species for habitat planning by the Gulf Coast Joint Venture (Vermillion and Wilson 2009); (5) their populations were greatly impacted by plume hunting and their populations never recovered (Paul et al 1975;Lowther and Paul 2002;Hunter et al 2006); and (6) they are extremely coastal.…”

“…Only in the last 30 years have Reddish Egret populations begun to increase in Florida Bay enough to spread up the Gulf Coast on their own (Paul et al 1975;Powell et al 1989). Currently, about 2,000 breeding pairs are in the United States, and 75 % of the U.S. population resides in Texas (Lowther and Paul 2002;Bates et al 2009). The Bahamas are an important site for Reddish Egrets (Moore and Gape 2008), although surveys there indicate more than a 50 % decline in numbers since the 1980s (Green et al 2011), which is a cause for concern.…”