Regions where trees grouped plants by color rather than location pointed to two known color loci: Flavia (yellow) and Rosea/Eluta (magenta). Coalescence times at these loci suggest selective sweeps and local barriers to gene flow.

The authors then used genealogical trees to analyze all four populations jointly. Four tree inference methods produced vastly different numbers of trees, yet recovered similar patterns of how genealogical relationships change along the genome.

Demographic models point to different histories of gene flow after secondary contact, with much more introgression at Planoles. The highly heterogeneous Fst landscape at Avellanet was largely driven by the history of its yellow population, not by barriers to gene flow.

Pal et al. sequenced plants from two of these zones, Planoles and Avellanet. Although both have the same two snapdragon varieties, the zones looked very different: genetic differentiation (Fst) between the varieties was over ten times higher at Avellanet than at Planoles.

Two snapdragon varieties, one magenta and one yellow, differ mainly in flower color but share habitats and bee pollinators. After isolation during the last ice age, they came into contact in several Pyrenean valleys forming independent hybrid zones.

Organellar genomes differ too! Animal mitochondrial DNA changes faster in sequence, while plant mitochondria appear to change faster in structure. Plants also have chloroplasts, adding an additional layer to cytonuclear interactions in this kingdom.

Sex chromosomes are more common and often more differentiated in animals. Their presence seems to underlie classic patterns like Haldane's Rule and the Large-X Effect. In plants, sex chromosomes are rarer and mostly homomorphic.

Karyotypes also evolve faster in plants, likely due to their more frequent whole-genome duplications and higher transposable element abundance. Translocations appear more common in plants, while fissions/fusions and inversions look broadly similar across kingdoms.

First, plants have had more ancient whole-genome duplications. These events create an immediate reproductive barrier, and over longer time scales can create hybrid incompatibilities when duplicated genes are lost differently in each lineage.

Do plants and animals speciate in the same way? Plants diversify ~2x as fast as animals, and their species barriers seem to arise earlier in divergence. Wang et al. review the role of genome architecture evolution in this process.

Overall, these results are consistent with ecological speciation theory, suggesting that divergent ecological adaptation can indeed promote intrinsic reproductive isolation over a few hundred generations.

F2 hybrid genomes showed vast instability. They had more structural variants (e.g., large indels and translocations) including those not observed in the parents or the F1s, suggesting disruption in hybrid meiosis.