Patterns of genomic diversity and linkage disequilibrium across the disjunct range of the Australian forest tree Eucalyptus globulus

Abstract

The evolutionary trajectory of a population both influences and is influenced by characteristics of its genome. A disjunct population, for example is likely to exhibit genomic features distinct from those of continuous populations, reflecting its specific evolutionary history and influencing future recombination outcomes. We examined genetic diversity, population differentiation and linkage disequilibrium (LD) across the highly disjunct native range of the Australian forest tree Eucalyptus globulus, using 203,337 SNPs genotyped in 136 trees spanning seven races. We found support for four broad genetic groups, with moderate FST, high allelic diversity and genome-wide LD decaying to an r2 of 0.2 within 4 kb on average. These results are broadly similar to those reported previously in Eucalyptus species and support the ‘ring’ model of migration proposed for E. globulus. However, two of the races (Otways and South-eastern Tasmania) exhibited a much slower decay of LD with physical distance than the others and were also the most differentiated and least diverse, which may reflect the effects of selective sweeps and/or genetic bottlenecks experienced in their evolutionary history. We also show that FST and rates of LD vary within and between chromosomes across all races, suggestive of recombination outcomes influenced by genomic features, hybridization or selection. The results obtained from studying this species serve to illustrate the genomic effects of population disjunction and further contribute to the characterisation of genomes of woody genera.