Molecular cytogenetics of the california condor: evolutionary and conservation implications

Abstract

Evolutionary cytogenetic comparisons involved 5 species of birds (California condor, chicken, zebra finch, collared flycatcher and black stork) belonging to divergent taxonomic orders. Seventy-four clones from a condor BAC library containing 80 genes were mapped to condor chromosomes using FISH, and 15 clones containing 16 genes were mapped to the stork Z chromosome. Maps for chicken and finch were derived from genome sequence databases, and that for flycatcher from the published literature. Gene content and gene order were highly conserved when individual condor, chicken, and zebra finch autosomes were compared, confirming that these species largely retain karyotypes close to the ancestral condition for neognathous birds. However, several differences were noted: zebra finch chromosomes 1 and 1A are homologous to condor and chicken chromosomes 1, the CHUNK1 gene appears to have transposed on condor chromosome 1, condor chromosomes 4 and 9 and zebra finch chromosomes 4 and 4A are homologous to chicken chromosome arms 4q and 4p, and novel inversions on chromosomes 4, 12 and 13 were found. Condor and stork Z chromosome gene orders are collinear and differentiated by a series of inversions/transpositions when compared to chicken, zebra finch, or flycatcher; phylogenetic analyses suggest independent rearrangement along the chicken, finch, and flycatcher lineages.

Fig. 1

Gene localization on California condor metaphase chromosomes following FISH using BAC clones labeled with biotin and counterstained with propidium iodide (a, b), or 2-color FISH using biotin- and digoxigenin-labeled clones withHoechst 33258 counterstaining (c, d). a SUPT3H and RUNX2 (clone 13G5) on chromosome 3q, b BTK (1N8) near the centromere of chromosome 9 with hybridization of an uncharacterized repeat to the W chromosome (green arrowhead), c OVM (5J24, biotin) and NR3C1 (29N19, digoxigenin) on chromosome 14, d USP5 (1D23, biotin) and OCA2 (5D3, digoxigenin) on chromosome 1. In figures 1 and 2, biotin-FITC signals appear yellow or green, while digoxigenin-CY3 probes are red.

Fig. 2

Gene localization on black stork Z chromosomes following one-color (biotin) (a–c), or 2-color (d) FISH. a TAL2 (3O23) on Zq near centromere, b UHRF2 (6C12) on Zq, c PALM2 (42P15) on Zp, d UBE2R2 (37I2, biotin) on Zq near telomere and SNCAIP (184F6, digoxigenin) on Zp near centromere.

Fig. 3

Ideogrammatic comparisons between autosomes of zebra finch, chicken and California condor. Maps for finch and chicken are from the UCSC (finch July 2008; chicken May 2006) and NCBI (finch build 1.1; chicken build 2.1) genome browsers, those for condor are present FISH results. Unresolved gene orders are indicated by brackets (]).

Fig. 4

Ideogrammatic comparisons of the Z chromosomes of zebra finch, chicken, California condor and black stork. Maps for zebra finch and chicken were based upon genome sequences, those for condor and stork are current FISH results.

Fig. 5

Comparisons of Z chromosomes from chicken, zebra finch, and collared flycatcher using different genes than those presented in figure 4. Data for chicken and finch are based upon genome sequences, those for flycatcher are from the linkage map [Backstrom et al., 2007].