The value of avian genomics to the conservation of wildlife

Abstract

BackgroundGenomic 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.ResultsGenotyping 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.ConclusionMining 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.

Stripes, sex and sparrows: what processes underlie heteromorphic chromosome evolution?

“…Similarly, a chromosomal inversion and fusion event in the black muntjac within the past 0.5 million years also bears an imprint of accumulated mutation on the neo-Y chromosome (Zhou et al, 2008). In marked contrast to these studies, the ZAL2 m chromosome, which is estimated to have split from ZAL2 two million years ago, does not show significant signs of genetic degeneration (Thomas et al, 2008;Romanov et al, 2009;Huynh et al, 2011). What might underlie the differences between these cases?…”

“…Indeed, the extent of sequence divergence and LD between the ZAL2 forms, revealing the suppression of recombination and their long-term coexistence, suggests that both functional haplotypes are actively maintained, and it was suggested that they might encode coadapted combinations of multiple traits (Falls and Kopachena, 1994;Romanov et al, 2009)-a form of giant supergene combining behavioural as well as plumage variation (Mather, 1950;Clarke et al, 1968;Joron et al, 2006). One remarkable finding is indeed the sheer number of genes locked into very large non-recombining units maintained by balancing selection.…”

“…Several lines of evidence also suggest that the divergence between the chromosome forms occurred before the radiation of the Zonotrichia clade (Thomas et al, 2008;Romanov et al, 2009;Huynh et al, 2011), which raises the question of the processes favouring long-term maintenance of the haplotypes in the clade, and the possibility of similar cryptic behavioural polymorphisms occurring in other species in the absence of plumage dimorphism. It is then tempting to speculate that the stripe pattern might represent a male signalling display (Tuttle, 2003) more recently recruited onto the polymorphic chromosome, with optimal effects in combination with the other male behaviours correlated with the ZAL2 m haplotype.…”

Deforestation and avian infectious diseases

“…First, genomics is revolutionizing all aspects of biology, and will play an important role in the conservation of wildlife (Romanov et al, 2009). Soon it may be possible to perform metagenomic analyses of whole forest ecosystems, to assess the effects of deforestation on the spread of EIDs.…”

“…R. N. M. Sehgal Future studies of the disease ecology of deforestation will take advantage of several technologies that will accelerate the research and increase scientific understanding. First, genomics is revolutionizing all aspects of biology, and will play an important role in the conservation of wildlife (Romanov et al, 2009). Soon it may be possible to perform metagenomic analyses of whole forest ecosystems, to assess the effects of deforestation on the spread of EIDs.…”