A first-generation microsatellite-based genetic linkage map of the Siberian jay (Perisoreus infaustus): insights into avian genome evolution

High fidelity--no evidence for extra-pair paternity in Siberian jays (Perisoreus infaustus)

Extra-pair paternity (EPP) in birds is related to a number of ecological and social factors. For example, it has been found to be positively related with breeding density, negatively with the amount of paternal care and especially high rates have been observed in group-living species. Siberian jays (Perisoreous infaustus) breed at low densities and have extended parental care, which leads to the expectation of low rates of EPP. On the other hand, Siberian jays live in groups which can include also unrelated individuals, and provide opportunities for extra-pair matings. To assess the potential occurrence of EPP in Siberian jays, we analysed a large data pool (n = 1029 offspring) covering ca. 30 years of samples from a Finnish Siberian jay population. Paternities were assigned based on up to 21 polymorphic microsatellite markers with the additional information from field observations. We were unable to find any evidence for occurrence of EPP in this species. Our findings are in line with earlier studies and confirm the generally low rates of EPP in related Corvid species. These results suggest that ecological factors may be more important than social factors (group living) in determining costs and benefits of extra-pair paternity.

No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps

Revealing the genetic basis of reproductive isolation is fundamental for understanding the speciation process. Chromosome speciation models propose a role for chromosomal rearrangements in promoting the build up of reproductive isolation between diverging populations and empirical data from several animal and plant taxa support these models. The pied flycatcher and the collared flycatcher are two closely related species that probably evolved reproductive isolation during geographical separation in Pleistocene glaciation refugia. Despite the short divergence time and current hybridization, these two species demonstrate a high degree of intrinsic post-zygotic isolation and previous studies have shown that traits involved in mate choice and hybrid viability map to the Z-chromosome. Could rearrangements of the Z-chromosome between the species explain their reproductive isolation? We developed high coverage Z-chromosome linkage maps for both species, using gene-based markers and large-scale SNP genotyping. Best order maps contained 57-62 gene markers with an estimated average density of one every 1-1.5 Mb. We estimated the recombination rates in flycatcher Z-chromosomes to 1.1-1.3 cM/Mb. A comparison of the maps of the two species revealed extensive co-linearity with no strong evidence for chromosomal rearrangements. This study does therefore not provide support the idea that sex chromosome rearrangements have caused the relatively strong post-zygotic reproductive isolation between these two Ficedula species.

Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution

Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the zebra finch, provides, for the first time, an ideal opportunity to analyze the relationship between structural genomic variation (chromosomal and CNV) and recombination on a genome-wide level. The aims of this study were therefore threefold: (1) to combine bioinformatics, physical mapping to produce comprehensive comparative maps of the genomes of chicken and zebra finch. In so doing, this allowed the identification of evolutionary chromosomal rearrangements distinguishing them. The previously reported interchromosomal conservation of synteny was confirmed, but a larger than expected number of intrachromosomal rearrangements were reported; (2) to hybridize zebra finch genomic DNA to a chicken tiling path microarray and identify CNVs in the zebra finch genome relative to chicken; 32 interspecific CNVs were identified; and (3) to test the hypothesis that there is an association between CNV, chromosomal rearrangements, and recombination by correlating data from (1) and (2) with recombination rate data from a high-resolution genetic linkage map of the zebra finch. We found a highly significant association of both chromosomal rearrangements and CNVs with elevated recombination rates. The results thus provide support for the notion of recombination-based processes playing a major role in avian genome evolution.

Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome

The extent of nonrandom association of alleles at two or more loci, termed linkage disequilibrium (LD), can reveal much about population demography, selection, and recombination rate, and is a key consideration when designing association mapping studies. Here, we describe a genome-wide analysis of LD in the zebra finch (Taeniopygia guttata) using 838 single nucleotide polymorphisms and present LD maps for all assembled chromosomes. We found that LD declined with physical distance approximately five times faster on the microchromosomes compared to macrochromosomes. The distribution of LD across individual macrochromosomes also varied in a distinct pattern. In the center of the macrochromosomes there were large blocks of markers, sometimes spanning tens of mega bases, in strong LD whereas on the ends of macrochromosomes LD declined more rapidly. Regions of high LD were not simply the result of suppressed recombination around the centromere and this pattern has not been observed previously in other taxa. We also found evidence that this pattern of LD has remained stable across many generations. The variability in LD between and within chromosomes has important implications for genome wide association studies in birds and for our understanding of the distribution of recombination events and the processes that govern them.

Sex-specific population structure, natural selection, and linkage disequilibrium in a wild bird population as revealed by genome-wide microsatellite analyses

Background

Sexual dimorphism in ecologically important traits is widespread, yet the differences in the genomic architecture between the two sexes are largely unexplored. We employed a genome-wide multilocus approach to examine the sexual differences in population subdivision, natural selection and linkage disequilibrium (LD) in a wild Siberian jay (Perisoreus infaustus) population, using genotypes at a total of 107 autosomal and Z-chromosomal microsatellites.

Results

Mean observed heterozygosity was significantly higher in females (H_O = 0.567) than in males (H_O = 0.532), and autosomal markers (H_O = 0.561) were more variable than Z-chromosomal markers (H_O = 0.512). Genetic differentiation (F_ST = 0.002, P < 0.05) between the two sexes was low but significant and males were on average significantly more genetically related to each other than females. Genomescan analyses revealed that 3 out of 101 (3%) autosomal loci were under directional selection, while 4 out of 6 (67%) Z-chromosomal markers were indicated to be under balancing selection. This suggests a significantly greater but contrasting selection force on the Z-chromosome in comparison to autosomes, which is consistent with an overall significantly (P < 0.05) lower F_STvalue for Z-chromosomal (-0.014, 95% CI: -0.025 - -0.011) than for the autosomal loci (0.003, 95% CI: 0.001 - 0.004). Analysis of syntenic marker pairs revealed high levels of LD in both sexes but significantly (P < 0.05) lower levels of LD in the females both on autosomes and Z-chromosome, probably due to the higher rate of dispersal and the higher recombination rates on autosomes, as well as the pseudoautosomal markers. In both sexes LD decayed rapidly with genetic distance in a similar fashion on autosomes, while a more rapid decay of LD in Z-chromosome was detected in females than in males.

Conclusion

We conclude that there are many clear differences in genomic architecture between the sexes studied here which can be at least partly understood in the light of higher dispersal rate of females as compared to males and the unusual structure of the Z-chromosome of the species.

Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora

A high-resolution genetic linkage map for the coral Acropora millepora is constructed and compared with other metazoan genomes, revealing syntenic blocks.

Background

Worldwide, coral reefs are in decline due to a range of anthropogenic disturbances, and are now also under threat from global climate change. Virtually nothing is currently known about the genetic factors that might determine whether corals adapt to the changing climate or continue to decline. Quantitative genetics studies aiming to identify the adaptively important genomic loci will require a high-resolution genetic linkage map. The phylogenetic position of corals also suggests important applications for a coral genetic map in studies of ancestral metazoan genome architecture.

Results

We constructed a high-resolution genetic linkage map for the reef-building coral Acropora millepora, the first genetic map reported for any coral, or any non-Bilaterian animal. More than 500 single nucleotide polymorphism (SNP) markers were developed, most of which are transferable in populations from Orpheus Island and Great Keppel Island. The map contains 429 markers (393 gene-based SNPs and 36 microsatellites) distributed in 14 linkage groups, and spans 1,493 cM with an average marker interval of 3.4 cM. Sex differences in recombination were observed in a few linkage groups, which may be caused by haploid selection. Comparison of the coral map with other metazoan genomes (human, nematode, fly, anemone and placozoan) revealed synteny regions.

Conclusions

Our study develops a framework that will be essential for future studies of adaptation in coral and it also provides an important resource for future genome sequence assembly and for comparative genomics studies on the evolution of metazoan genome structure.

Extensive linkage disequilibrium in a wild bird population

Knowledge about the extent and patterns of linkage disequilibrium (LD) can provide important insights into demographic processes and strategies to identify the genetic basis of complex phenotypes in wild populations. However, data on the extent and patterns of LD from non-model vertebrate species from the wild are still scarce. We conducted so far the most extensive and detailed examination of LD in a pedigreed wild bird population using genotypes from 97 autosomal and 6 gonosomal microsatellites and a recently established linkage map of Siberian jays (Perisoreus infaustus). Analysis of syntenic marker pairs showed high levels of LD that extended over tens of centimorgans or several megabases and generally decayed as an increasing function of intermarker distance. In addition, significant LD was also very common between nonsyntenic markers. Patterns of LD varied across different linkage groups possibly because of the differences in chromosomal structure (macro-, micro-, and Z-chromosome). In particular, the level of LD was significantly lower on the Z-chromosome than on the autosomes at comparable genetic distances. In general, the high levels and extent of LD in this population are likely owing to its relatively small size, significant intrapopulation genetic structure, and occurrence of inbreeding. Whatever the cause, the long-range LD between syntenic loci suggests that LD mapping of phenotypic traits in this population using low-density markers maps is feasible. However, the frequent occurrence of LD between nonsyntenic markers suggests that the combined use of linkage and LD methods is needed to reduce the likelihood of false-positive associations between marker loci and traits of ecological and evolutionary interest.