The chromosomal polymorphism linked to variation in social behavior in the white-throated sparrow (Zonotrichia albicollis) is a complex rearrangement and suppressor of recombination

Abstract

Variation in social behavior and plumage in the white-throated sparrow (Zonotrichia albicollis) is linked to an inversion polymorphism on chromosome 2. Here we report the results of our comparative cytogenetic mapping efforts and population genetics studies focused on the genomic characterization of this balanced chromosomal polymorphism. Comparative chromosome painting and cytogenetic mapping of 15 zebra finch BAC clones to the standard (ZAL2) and alternative (ZAL2(m)) arrangements revealed that this chromosome is orthologous to chicken chromosome 3, and that at a minimum, ZAL2 and ZAL2(m) differ by a pair of included pericentric inversions that we estimate span at least 98 Mb. Population-based sequencing and genotyping of multiple loci demonstrated that ZAL2(m) suppresses recombination in the heterokaryotype and is evolving as a rare nonrecombining autosomal segment of the genome. In addition, we estimate that the first inversion within the ZAL2(m) arrangement originated 2.2+/-0.3 million years ago. Finally, while previously recognized as a genetic model for the evolution of social behavior, we found that the ZAL2/ZAL2(m) polymorphism also shares genetic and phenotypic features with the mouse t complex and we further suggest that the ZAL2/ZAL2(m) polymorphism is a heretofore unrecognized model for the early stages of sex chromosome evolution.

Figure 1.—

Cytogenetic mapping of the ZAL2 and ZAL2^m chromosomes. Metaphase chromosome spreads from WS females were used for FISH mapping. Note that the karyotype of the white-throated sparrow, like other birds, is composed of a few large macrochromosomes and numerous microchromosomes. (A) Chicken chromosome 3 painting probe hybridization to ZAL2 and ZAL2^m. (B–E) Localization of zebra finch BAC clones orthologous to chicken chromosome 3 on ZAL2 and ZAL2^m. The color-coded arrows corresponding to each BAC represent the position of each probe on each chromosome. Note the change in relative order between the alternative arrangements for BACs 64A1, 71A1, and 5K13, and the shift in proximity toward the telomere of the long arm for 21H11, 55A1, and 352K14 on ZAL2^m relative to ZAL2.

Figure 2.—

Summary of the cytogenetic mapping of ZAL2 and ZAL2^m and gene flow between the chromosomes. The positions of the zebra finch BAC clones mapped by FISH to the ZAL2 (left) and ZAL2^m (right) chromosomes are indicated. In cases where the order of the BAC clones could not be reliably resolved, the clones were grouped together (vertical line) and listed in an arbitrary order. Lines between the chromosomes indicate the relative position of the markers on the two chromosomes. Centromeres are represented by solid circles. The gene names and F_ST values for loci included in the population genetics studies are listed to the right of ZAL2^m in their respective positions along this chromosome. The positions of the genes were directly determined by FISH (*) or inferred on the basis of flanking markers and the orthologous position on GGA3 (†). The subset of the loci that were genotyped in a larger panel of WS and TS birds are denoted by “‡.” The “§” indicates that the VIP genotyping results were previously reported in Michopoulos et al. (2007).

Figure 3.—

Phylogeny of the loci that map within the region rearranged between the ZAL2 and ZAL2^m chromosomes. A neighbor-joining phylogenetic tree was constructed on the basis of 7231 bp of concatenated sequence corresponding to nine loci included within the region rearranged between ZAL2 and ZAL2^m chromosomes. These nine loci were sequenced in six WS and four TS birds and in one individual from each of three closely related species: Z. leucophry (ZLE), Z. querula (ZQU), and J. hyemalis (JHY). Bootstrap values of 1000 replicates are indicated for the main nodes. Sequences from each white-throated sparrow are labeled with the bird identification number. For the WS individuals, the sequences of the ZAL2 and ZAL2^m chromosomes are labeled as 2 and 2m, respectively. For all other individuals, the estimated haplotypes were arbitrarily labeled A and B. In the cases of ZQU, ZLE, and JHY, nucleotide variants were randomly assigned to a haplotype.

Figure 4.—

Model for the generation of the ZAL2^m rearrangement. A minimum of two pericentric inversions, represented by the pairs of dashed lines, are hypothesized to have led to the ZAL2/ZAL2^m polymorphism. ZAL2 (left) and ZAL2^m (right) are shown along with a hypothetical intermediate chromosomal arrangement (middle). The depicted movement of a small chromosomal segment present on the short arm of ZAL2 to the long arm of ZAL2^m is only predicted by the model and is not based on empirical data. The illustrated order in which the inversions occurred is arbitrary, and a model with the inversions occurring in the reverse order is also possible. Centromeres are represented by solid circles. Open boxes and solid boxes represent the short and long arms of ZAL2 or chromosomal segments originating on those arms, respectively. Arrowheads indicate the orientation of the chromosomal segments.