The value of avian genomics to the conservation of wildlife

Abstract

Background: Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affecting genetic variation, adaptation and evolution.Developing genomic tools and resources including genomic libraries and a genetic map of the California condor is a prerequisite for identification of candidate loci for a heritable embryonic lethal condition. The white-throated sparrow exhibits a stable genetic polymorphism (i.e. chromosomal rearrangements) associated with variation in morphology, physiology, and behavior (e.g., aggression, social behavior, sexual behavior, parental care).In this paper we outline the utility of these species as well as report on recent advances in the study of their genomes.

Results: Genotyping of the condor resource population at 17 microsatellite loci provided a better assessment of the current population's genetic variation. Specific New World vulture repeats were found in the condor genome. Using condor BAC library and clones, chicken-condor comparative maps were generated. A condor fibroblast cell line transcriptome was characterized using the 454 sequencing technology.Our karyotypic analyses of the sparrow in combination with other studies indicate that the rearrangements in both chromosomes 2m and 3a are complex and likely involve multiple inversions, interchromosomal linkage, and pleiotropy. At least a portion of the rearrangement in chromosome 2m existed in the common ancestor of the four North American species of Zonotrichia, but not in the one South American species, and that the 2m form, originally thought to be the derived condition, might actually be the ancestral one.

Conclusion: Mining and characterization of candidate loci in the California condor using molecular genetic and genomic techniques as well as linkage and comparative genomic mapping will eventually enable the identification of carriers of the chondrodystrophy allele, resulting in improved genetic management of this disease.In the white-throated sparrow, genomic studies, combined with ecological data, will help elucidate the basis of genic selection in a natural population. Morphs of the sparrow provide us with a unique opportunity to study intraspecific genomic differences, which have resulted from two separate yet linked evolutionary trajectories. Such results can transform our understanding of evolutionary and conservation biology.

Figure 1

California condor pedigree of 69 individuals used for genetic studies. A pedigree includes founders and early generation offspring used for the DNA fingerprint [8], mtDNA [9] and microsatellite (msat; current study) analyses. All individuals are designated using their studbook numbers.

Figure 2

Morphs of the white-throated sparrow. Photographs of the morphs of the white-throated sparrow; A) white morphs are heterozygous for a chromosomal rearrangement on autosome 2, while B) tan morphs are homozygous for the non-inverted form of autosome 2.

Figure 3

An example of microsatellite genotyping profile at the loci C5 and D6. The DNA from a condor male (SB #162) was amplified with the C5 and D5 primers labeled with two different fluorescent dyes. The bird is heterozygous for C5 (green alleles, 179 and 191 bp) and homozygous for D5 (blue alleles, 256 bp both). Red peaks are size standards. Values along the y-axis represent the intensity of fluorescence (a.u.), values along the x-axis mark the size of the DNA fragments (a function of time).

Figure 4

Molecular assay for morph determination. Molecular assay for morph determination in the white-throated sparrow, modified in the Tuttle laboratory for use on automated sequencers from primers described in [50]. Panel A shows a tan morph with a single peak at 284 bp amplified from chromosome 2. Panel B shows a white morph with a band for chromosome 2 (at 284 bp) and two additional bands at 88 bp and 189 bp, which occur when PCR product amplified from chromosome 2^m is digested with restriction endonuclease DraI. If they occur in nature, we assume that birds homozygous for 2^m ("super whites") would produce a pattern showing only the 88 bp and 189 bp bands. This technique has been verified in adults of known plumage. Values along the y-axis represent the intensity of fluorescence (a.u.), values along the x-axis mark the size of the DNA fragments (a function of time).

Figure 5

California condor FISH mapping. An example of FISH using metaphase chromosomes of the California condor and a biotinylated BAC clone containing the ACVR2B gene located on GCA2.

Figure 6

Distribution of the condor 454 transcripts across the chicken chromosomes. The distribution of the condor transcripts based on their orthology to the chicken chromosomes.

Figure 7

Complete karyotype of white female. Complete karyotype of white (2^m/2) female (Z/W) KB15793, showing 82 macro- and microchromosomes, including 40 autosome pairs and two sex chromosomes (Z and W); data generated at the San Diego Zoo's Institute for Conservation Research, Zoological Society of San Diego. In addition to the rearrangement of 2, chromosome 3 also sometimes exhibits an alternate form (3^a; as seen here).

Figure 8

G-banded chromosomes 1–9 and Z from the sparrow. G-banded chromosomes 1–9 and Z from a 2^m/2 3^a/3 white-throated sparrow (KB15794; San Diego Zoo's Institute for Conservation Research, Zoological Society of San Diego).

Figure 9

VIP restriction site mapped on Zonotrichia tree. Phylogenetic tree for Zonotrichia from [75] showing branch lengths (% nucleotide differentiation). Mapped on the tree are presence (+), absence (-), or both presence and absence (+/-) of the DraI restriction site in the VIP fragment. Data for the restriction site were derived from Table 1. Only the four North American Zonotrichia species show polymorphism for the VIP fragment, suggesting that the polymorphism arose in the common ancestor of those four species.

Figure 10

VIP sequence for several passerine species. Sequence alignment for an intron of the vasoactive intestinal peptide (VIP) gene (primers described in [50]). Bases highlighted in gray show differences between the white-throated sparrow (Zonotrichia albicollis; WTSP of both morphs), Harris's sparrow (Z. querula; HASP), the white-crowned sparrow (Z. leucophrys, WCSP), the rufous-collared sparrow (Z. capensis, RUFS), the dark-eyed junco (Junco hyemalis; DEJU), the song sparrow (Melospiza melodia; SOSP), and the swamp sparrow (M. georgiana; SWSP). Yellow highlighting indicates the DraI restriction site, which is found in dark-eyed juncos and song sparrows, as well as white morphs (W) white-throated sparrows; green highlighting shows the lack of a DraI restriction site found in tan (T) morph white-throated sparrows.