How can we most accurately reconstruct the
evolutionary history of organisms from their genomes?

How have reproductive interactions
(e.g., introgression, character displacement)
shaped the evolutionary history of lineages?

Pedicularis L. (Orobanchaceae)

  • >600 species globally, >300 endemic to Hengduan Mountains.
  • Many collections from 1996-present: KIB, HUH, FMNH
  • Spectacular floral diversity; convergent evolution (Ree 2005)
  • Form species rich assemblages; species interactions

Reproductive interference

Negative fitness consequences imposed by one organism on another by disrupting successful reproduction (a form of selection on reproductive traits/timing/behavior)

Floral diversity in Pedicularis

Morphological terminology

The beak of the galea directs pollen placement and pickup

Elongate styles

Elongate styles have evolved multiple times (Ree 2005) and facilitate pollen competition among species (Tong and Huang 2016).

Evolutionary process: character displacement

Selection drives divergence of competitors in sympatry, but not allopatry, reducing competition for limited resources.

Evolutionary process: character displacement

With many co-occurring species, it is difficult to identify a focal competitor. Rather, we are developing a community model of character displacement .

Reproductive character displacement

  • Hypothesis: Differences among populations (within species) are a result of interspecific interactions driving character displacement in local communities.
  • Test using widespread variable species.

Example sampled Pedicularis communities

New projects: Genomes, transcriptomes, and 3D models.

NSF CAREER: phylogenomic methods and Pedicularis species and population diversity.

Ongoing work: Reference genome assemblies

  • P. cranolopha var. longicornuta reference genome (nanopore + Illumina + Hi-C).
  • Diploid, 1.2Gb, highly heterozygous, chromosome-scale assembly.
  • Xu et al. Comparative Genomics of Orobanchaceae. Accepted in Mol Plant

  • 7 additional reference genomes (Pacbio HiFi + Hi-C) in progress (hifiasm).

Jianjun Jin

Ongoing work: Comparative phylogeography

Dense phylogeographic sampling and 3RAD seq. of 12 widespread taxa

Jared Meek

Ongoing work: Comparative phylogeography

Jared Meek


  • Massive community sampling to investigate reproductive interactions.

  • Massive 3RAD sequencing of both species and population diversity.
  • RNA-seq and 3D morphometric data for PhyloGWAS.
  • High quality genome assemblies for trait mapping and phylogenomics.

  • Come join us. Recruiting students now!