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Genomics of natural bird populations



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Molecular Ecology 2008 17 964 980 doi 10 1111 j 1365 294X 2007 03551 x Genomics of natural bird populations a gene based set of reference markers evenly spread across the avian genome Blackwell Publishing Ltd N I C L A S B A C K S T R M S O F I E FA G E R B E R G and H A N S E L L E G R E N Department of Evolutionary Biology Evolutionary Biology Centre Uppsala University Norbyv gen 18D SE 752 36 Uppsala Sweden Abstract Although there is growing interest to take genomics into the complex realms of natural populations there is a general shortage of genomic resources and tools available for wild species This applies not at least to birds for which genomic approaches should be helpful to questions such as adaptation speciation and population genetics In this study we describe a genome wide reference set of conserved avian gene markers broadly applicable across birds By aligning protein coding sequences from the recently assembled chicken genome with orthologous sequences in zebra finch we identified particularly conserved exonic regions flanking introns of suitable size for subsequent amplification and sequencing Primers were designed for 242 gene markers evenly distributed across the chicken genome with a mean inter marker interval of 4 2 Mb Between 78 and 93 of the markers amplified a specific product in five species tested chicken peregrine falcon collared flycatcher great reed warbler and blue tit Two hundred markers were sequenced in collared flycatcher yielding a total of 122 41 kb of genomic DNA sequence 12096 bp coding sequence and 110 314 bp noncoding Intron size of collared flycatcher and chicken was highly correlated as was GC content A polymorphism screening using these markers in a panel of 10 unrelated collared flycatchers identified 871 single nucleotide polymorphisms 0 0029 and 33 indels mainly very short Avian genome characteristics such as uniform genome size and low rate of syntenic rearrangements suggest that this marker set will find broad utility as a genome wide reference resource for molecular ecological and population genomic analysis of birds We envision that it will be particularly useful for obtaining large scale orthologous targets in different species important in for instance phylogenetics and for large scale identification of evenly distributed single nucleotide polymorphisms needed in linkage mapping or in studies of gene flow and hybridization Keywords chicken collared flycatcher comparative anchored tagged sequences linkage mapping QTL analysis single nucleotide polymorphism Received 22 May 2007 revision accepted 15 August 2007 Introduction There is a growing interest in exploring the possibility to merge knowledge hypotheses and technologies from the fields of genomics and evolutionary biology Feder Mitchell Olds 2003 Impetus for this would be for instance the long term goals to understand and trace the genetic background to phenotypic traits under selection in natural populations and subsequently to study adaptation using the combined information from genotypes and phenotypes Correspondence Hans Ellegren Fax 46 18 4716310 E mail hans ellegren ebc uu se Other motivations could be to reveal the genetic basis of reproductive isolation and to scale up analyses of population processes using population genomics approaches However although there is rapid progress in the generation and establishment of genomic resources in model species we still lack resources and tools for the vast majority of wild species and this is so even for initial and small scale attempts to access the genome Before the era of eukaryotic whole genome sequences O Brien et al 1993 and Lyons et al 1997 introduced the concept of comparative anchor tagged sequences CATS CATS are anchored reference loci with known location in a model genome that based on evolutionary conservation 2007 The Authors Journal compilation 2007 Blackwell Publishing Ltd A R E F E R E N C E S E T O F AV I A N G E N E M A R K E R S 965 can be analysed in other species and used for comparative mapping By designing markers evenly spread in a model human genome the idea was that the markers would simplify the construction of genetic maps of other mammalian species to allow transfer of map information between species and to make inference on chromosome evolution Specifically the selection of an even distribution of CATS markers in the model was expected to reduce the number of markers needed to construct maps of other species given that related species tend to show conserved synteny Moreover by focusing on markers evolving under strong functional constraint like many protein coding genes the possibility of cross species analysis would be facilitated The access to CATS played an important role in the development of the first genetic maps of several mammals O Brien et al 1993 Lyons et al 1999 LahbibMansais et al 2000 Although the suggested use for CATS was initially based on probe hybridization of Southern blots O Brien et al 1993 the approach found more widespread use when converted to polymerase chain reaction PCR based detection The idea was to design primers in two adjacent and conserved exons flanking an intron of suitable size for PCR amplification The rationale behind including exonic sequence was that it should not only increase amplification success but also aid in the ability to confirm orthology between sequences from different species In addition amplification of introns would increase the likelihood of finding polymorphic sites Although not presented in the context of deriving sets of reference markers evenly spread across the whole genome other investigators independently or subsequently used this approach on smaller scales and termed it traced orthologous amplified sequence tags TOAST Jiang et al 1998 or exon primed intron crossing EPIC PCR Palumbi Baker 1994 More recently the concept of using conserved exonic intron spanning primers has been frequently used in obtaining short sequence tags STS of relatively uncharacterized genomes Venta et al 1996 Touriya et al 2003 Aitken et al 2004 Cogan et al 2006 If we can start to unveil the links between genotypes and phenotypes in natural populations this would clearly advance our knowledge on fundamental evolutionary processes Birds are important study organisms in this respect because there is ample background information on many general aspects of ecology and evolutionary biology including mate choice sexual selection life history evolution and speciation


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