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

The Genomic Signature of Crop-Wild Introgression in Maize

The Genomic Signature of Crop-Wild Introgression in Maize
Matthew B. Hufford, Pesach Lubinksy, Tanja Pyhäjärvi, Michael T. Devengenzo, Norman C. Ellstrand, Jeffrey Ross Ibarra
(Submitted on 19 Aug 2012)

The evolutionary significance of hybridization and introgression has long been appreciated, but evaluation of the genome-wide effects of these phenomena has only recently become possible. Crop-wild study systems represent ideal opportunities to examine evolution through hybridization. For example, maize and the conspecific wild teosinte Zea mays ssp. mexicana are known to hybridize in the fields of highland Mexico. Despite widespread evidence of gene flow, maize and mexicana maintain distinct morphologies and have done so in sympatry for thousands of years. Neither the genomic extent nor the evolutionary importance of introgression between these taxa is understood. We assessed patterns of genome-wide introgression based on 39,029 single nucleotide polymorphisms genotyped in 189 individuals from nine sympatric maize-mexicana populations and reference allopatric populations. While portions of these genomes were particularly resistant to introgression (notably near known cross-incompatibility and domestication loci), we detected widespread evidence for introgression in both directions of gene flow. Through further characterization of these regions and a growth chamber experiment we found evidence consistent with the incorporation of adaptive mexicana alleles into maize during its expansion to the highlands of central Mexico. In contrast, very little evidence was found indicating introgression from maize to mexicana altered the niche of this wild taxon, increasing its capacity to persist commensal to agriculture. The methods we have applied here can be replicated widely across species, greatly informing our understanding of evolution through introgressive hybridization. Crop species, due to their exceptional genomic resources and frequent histories of diffusion into sympatry with relatives, should be particularly influential in these studies.