A well-tested set of primers to amplify regions spread across the avian genome

Abstract

1. IntroductionDNA markers have been used to examine a broad range ofbiological problems, including those in phylogen etics, populationgenetics and the identiÞcatio n of individuals. Nuclear loci providea rich source of information regarding evolutionary history andthey allow researche rs to examine many unlinked markers thathave the potential to provide insight the coalescent process as wellas introgress ion or hybridizatio n events (e.g. Maddison, 1997; Nic-hols, 2001 ). Information about the nuclear genome can be collectedby sequencing or by examining single nucleotide polymorphis ms(SNPs) (Sunnucks, 2000; Avise, 2004 ). Unlike mitochondr ialregions where virtually universal primers are available for verte-brates (e.g., Sorenson et al., 1999 ), extensively tested primer setsfor nuclear regions that are likely to work on the majority of spe-cies within a group are not available.In phylogenetic studies, nuclear sequence data have providedadditional insights into avian evolution (e.g., Avise, 2004; Hackettet al., 2008 ). The nuclear genome is heterogeneous , consisting ofcoding regions, introns, untranslated regions (UTRs), andintergeni c regions. The markers exhibit varying patterns of molec-ular evolution (e.g., mutation rates, base composition, etc.), andthus can be used at a variety of different taxonomi c levels for dif-ferent types of phylogeneti c questions. In addition to substitution alvariation , non-coding regions often exhibit length variation , pro-viding indel (insertionÐdel etion) characters that can be added tothe regionOs information content (e.g., Fain and Houde, 2004 ).Populatio n-level questions can be examined using non-codingregions such as introns. Substitutional (and indel) variation of mul-tiple individuals of a single species or a set of closely relatedspecies provide insights into population divergence times andancestral population sizes (e.g., Jennings and Edwards, 2005;Aitken et al., 2004 ). SNPs present in these rapidly evolving regionsare increasingly being used as markers because they provide anopportun ity to assess a large number of unlinked loci for a rangeof population questions (BrumÞeld et al., 2003; Morin et al.,2004 ). In addition to population genetics, SNPs also have thepotential to be used in parentage studies and for quantitativegenetic studies in wild populations.In birds, there are several studies which have published sets ofprimers to amplify nuclear regions, particularly intron regions (e.g.,Friesen et al., 1999, 1997; Primmer et al., 2002; Waltari andEdwards, 2002; Slade et al., 1993; Backstršm et al., 2008 ). How-ever, many of these primers have been tested on a limited set of