Comparative mapping among subsection Australes (genus Pinus, family Pinaceae)

Comparative mapping in conifers has not yet been used to test for small-scale genomic disruptions such as inversions, duplications, and deletions occurring between closely related taxa. Using comparative mapping to probe this smaller scale of inquiry may provide clues about speciation in a phylogenetically problematic taxon, the diploxylon pine subsection Australes (genus Pinus, family Pinaceae). Genetic maps were constructed for two allopatric species of Australes, P. elliottii var. elliottii and P. caribaea var. hondurensis, using microsatellites and an F₁ hybrid. A third map was generated directly from the meiotic products of an adult F₁ hybrid, eliminating the need for an F₂ generation. Numerous small-scale disruptions were detected in addition to synteny and collinearity, and these included (1) map shrinkage, (2) a paracentric inversion, (3) transmission ratio distortion, and (4) mild selection against a parental haplotype. Such cryptic signatures of genomic divergence between closely related interfertile species are useful in elucidating this problematic evolutionary history.