Community phylogenomics of a rapid plant radiation:
Pedicularis in the Hengduan Mountains
Deren Eaton
Dept. of Ecology, Evolution, and Environmental Biology
Columbia University
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)
The Hengduan Mountains
The Hengduan Mountains
The Hengduan Mountains
The Hengduan Mountains
Floral diversity in Pedicularis
Current projects
- Large-scale community sampling to investigate reproductive interactions.
- Massive 3RAD sequencing of both species and population diversity
(117 species, >900 specimens). - Transcriptome and 3D morphometric flower data for PhyloGWAS.
- 7 chromosome-scale genome assemblies for trait mapping and phylogenomics.
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).
Ecological pattern: reproductive interference
- We have prevously shown evidence of RI in Pedicularis communities:
- Phenotypic overdispersion (co-occurring spp have dissimilar flowers)
- Eaton & Ree (2012) Ecology.
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.
Case study: Pedicularis cranolopha
Example sampled Pedicularis communities
P. cranolopha (widespread)
P. longiflora (widespread)
P. fetisowii (rare)
P. cranolopha phylogeography
- RAD-seq, PstI enzyme, ~5M reads/sample; 100 individuals; 15 locations.
- ipyrad assembly: ~20K loci, 21% missing, 286K SNPs
- raxml: reciprocal monophyly of all samples x site.
- structure/pca: 4-6 clades; gene flow at contact zones.
P. cranolopha phylogeography
Style length shows little variation within sites, but high variability across clades.
Systematics of the P. cranolopha complex
Orange clade is undescribed; Pink is P. tricolor; Three varieties of P. cranolopha are described in Flora of China, varying in calyx venation, and presence of a "forked beak" (crest).
In P. cranolopha pollen transfer occurs on the right side of bumblebee pollinators
but is not super precise, bees tend to squirm about.
In forked populations, bees are restrained by the "fork", which may increase precision.
Potential reinforcement of reproductive isolation.
Hybrid zones: contact between populations with "forked beak" and without.
Potential reinforcement of reproductive isolation.
Hybrid zones: contact between populations with "forked beak" and without.
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2
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Horned beak variation within hybrid zone 1.
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
Summary
- 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!
