Our paper: The Genomic Signature of Crop-Wild Introgression in Maize

Our inaugural author post is by Matt Hufford and Jeff Ross-Ibarra [@lab_ri] on their paper:
The Genomic Signature of Crop-Wild Introgression in Maize ArXived here.

Evolutionary biologists have long been fascinated by introgressive hybridization. Numerous examples in which introgression has played an important evolutionary role are known, but genetic characterization has typically focused on only a handful of loci.

We took advantage of the recent development of inexpensive genotyping to address a long-standing question of introgression in maize evolution. Maize was domesticated in the warm low elevations of southwest Mexico, and likely colonized the highlands of central Mexico only thousands of years later. Maize is frequently cultivated in sympatry with its wild relatives the teosintes and is known to hybridize with them. Hybridization is especially common in the highlands, where maize and teosinte share several derived morphological features thought to be adaptive to high elevation.

We set out to discover the genomic extent of introgression in highland maize and teosinte populations and the degree to which this has been adaptive. We genotyped 9 sympatric population pairs of maize and teosinte at ~39,000 SNPs. We used two different algorithms (in the software STRUCTURE and HAPMIX) to model chromosomes as mosaics of maize and teosinte, and characterized regions of putative introgression. Surprisingly, we found shared regions of introgression across many populations and primarily only from teosinte into maize. To test whether this introgression may have facilitated maize adaptation to the highlands, we conducted a growth chamber experiment that revealed significant differences in putatively adaptive morphological traits between maize populations with and without introgression.

We submitted the paper to arXiv because this is a fast-moving area for empirical evolutionary genomics and we hoped to start the dialogue early on how to move forward with our results. We’d like feedback on the paper and specifically the following questions:

Are there recent advances in modeling admixture and introgression that we should apply?

Are our main findings surprising considering the putative history of maize diffusion?

Matt Hufford and Jeff Ross Ibarra

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2 thoughts on “Our paper: The Genomic Signature of Crop-Wild Introgression in Maize

  1. Great to see this set up! I’ll be eager to read the paper. You may be interested in some of the methods Simon Gravel has for estimating admixture time based on ancestry track length. We also have a new(er) version of PCAdmix for ancestry deconvolution that might be fun to try if you have good training data for the teosinte vs modern PCs. If not, we can EM it…

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