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Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains

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A 15-Myr-old genetic bottleneck.

Timothy Paape¹, Boris Igic, Stacey D Smith

¹Section of Ecology, Behavior and Evolution, Department of Biological Sciences, University of California, San Diego, CA, USA.

Molecular Biology and Evolution

|January 23, 2008

Summary

Balancing selection maintains genetic diversity at the self-incompatibility locus (S-locus) in plants. This study reveals an ancient bottleneck in the Solanaceae family, occurring after the divergence of Iochrominae.

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Area of Science:

Evolutionary Biology
Population Genetics
Plant Reproductive Biology

Background:

Balancing selection at the self-incompatibility locus (S-locus) preserves genetic variation over millions of years in flowering plants.
This long-term variation allows for the detection of ancient demographic events predating extant species.
Restricted S-locus variation in Physalis and Witheringia suggests a common ancestral bottleneck.

Purpose of the Study:

To investigate S-locus diversity in the Iochrominae subtribe, sister to Physalis and Witheringia.
To determine the timing and impact of a potential bottleneck event in the Solanaceae family.
To assess the utility of S-locus polymorphism for deep evolutionary history inference.

Main Methods:

Sequencing of 14 S-alleles from Iochrominae taxa.
Phylogenetic analysis using chloroplast DNA (cpDNA) sequences.
Molecular clock dating using fossil calibrations and Bayesian methods.

Main Results:

Iochrominae taxa exhibit diverse S-locus variation, with at least 6 ancient lineages.
This contrasts with the restricted S-locus diversity observed in Physalis and Witheringia.
The bottleneck event occurred after the divergence of Iochrominae, estimated between 14.0-18.4 million years ago.

Conclusions:

The bottleneck event in the Solanaceae lineage occurred after the split from Iochrominae.
The S-locus retains ancient polymorphism, useful for inferring deep evolutionary history.
The findings highlight the deep age of Solanaceae and S-locus polymorphism.