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Lineage specific inference about QTL evolution among three Mimulus species of contrasting relationship and inbreeding Chen, Charles


Complex traits including those involved with natural adaptation are determined by the contributions of numerous genes, the environment, and their interactions. Although quantitative trait locus (QTL) mapping approaches have been successful in dissecting complex traits, few studies have adopted a comparative approach of contrasting species pairs that differ in relationship, for the purpose of dissecting evolutionary changes of QTL. Furthermore, no QTL mapping approaches have explicitly inferred QTLs along lineages in a species network. This thesis brings such a comparative approach into QTL mapping. The evolution of inbreeding in the Mimulus guttatus species complex provides an excellent system where lineage-specific QTL changes can be inferred. Three intercrossable species were chosen: M. guttatus, M. platycalyx and M. micranthus, the latter two taxa being independent derived inbreeders from the first one. Five floral characters were selected as representative traits for the evolution of inbreeding in these species. A three-species crossing design was implemented, upon which QTL analyses were conducted. As expected in QTL mapping studies, the estimated number of genetic factors varies among crosses. An important role of dominance in the evolution of selfing from outcrossing taxa is supported by the data, owing to the consistency of directional dominance towards selfing taxa. The extensiveness of epistasis identified in this study suggests that in Mimulus, genes related to floral characters are co-adapted gene complexes, where genetic interdependency evolves as species diverge. Moreover, such genetic interdependency may be a key element in the evolution of stable mixed mating systems. A model for the inference of lineage specific QTL in a three-taxon network is described, and used to infer lineage-specific changes for floral traits among the three Mimulus taxa. After mapping QTL onto lineages, one can determine if QTL at the same map position are homologous (arising in an ancestral lineage leading to two taxa) or non-homologous (arising independently in derived lineages or via convergent evolution). In Mimulus, shared negative QTLs of dominant effect that arise from convergent evolution seem to play a prominent role in the early evolution of inbreeding; then derived, independent changes fine-tune further evolutionary changes of inbreeding.

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