Single copy genes produce a clearer phylogeny of the Apioideae

Analysis of over 3300 single copy genes has produced a well-supported topology with some significant changes.

The Apioideae is the largest of four subfamilies of the Apiaceae, or Umbelliferae, as well as the most taxonomically complex. Containing just over 400 genera and around 2900 species, the evolutionary relationships among its tribes and subtribes are controversial and the groups themselves may not be entirely monophyletic. A wide range of individual marker genes have been used to determine the phylogeny of the subfamily in the past, but these have often produced conflicting results, which may be due to hybridization or incomplete lineage sorting.

In a recent article published in Annals of Botany, Jun Wen and colleagues used over 3300 single copy genes (SCGs) to construct a phylogeny of the Apioideae. SCGs are useful because their orthology is easily assessed and they have a higher proportion of informative sites than many coding sequences from the mitochondria and chloroplasts. The researchers constructed a species tree based on the coalescent method. They then used the tree to study the evolution of fruit types and the possible biogeography of the Apioideae.

Morphological variation and evolutionary histories of Apioideae. Source Wen et al. 2020.

The analyses resulted in a well-supported phylogeny in which the positions of several major lineages have shifted from previous work. The pattern of gene tree topology frequencies and branch lengths suggests incomplete lineage sorting rather than hybridization as the cause for previous conflicting results. Investigation of fruit types in light of this new phylogeny suggests that the fruits of Apioideae have diversified in two directions, with one group tending toward water dispersal, and the other tending toward wind dispersal. Fruits with ribs facilitating animal dispersal appear to be derived from those that are wind dispersed.

Looking at the biogeography of the subfamily, molecular dating points to the uplift of the Qinghai–Tibetan Plateau (QTP) and a changing climate as driving forces behind Apioideae speciation. “Overall, our studies indicate that the QTP was likely to be an origin and differentiation centre of Apioideae,” the authors write, “and the taxa of [two east Asian endemic clades, Acronema and Physospermopsis] might provide details regarding the significance of the QTP orogeny on the evolution of Apioideae.”

One of the authors has this paper listed on their ResearchGate site.

Erin Zimmerman

Erin Zimmerman is a botanist turned science writer and sometimes botanical illustrator. She did her PhD at the University of Montréal and worked as a post-doctoral fellow with the Canadian Ministry of Agriculture. She was a plant morphologist, but when no one wanted to pay her to do that anymore, she started writing about them instead. Her other plant articles (and occasional essays) appear in Smithsonian Magazine, Undark, New York Magazine, Narratively, and elsewhere. Read her stuff at
Erin can also be found talking about plants and being snarky on Twitter @DoctorZedd.

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