Category Archives: Population genetics analysis

Blood ties: ABO is a trans-species polymorphism in primates

Posted on by
3

Blood ties: ABO is a trans-species polymorphism in primates
Laure Ségurel, Emma E. Thompson, Timothée Flutre, Jessica Lovstad, Aarti Venkat, Susan W. Margulis, Jill Moyse, Steve Ross, Kathryn Gamble, Guy Sella, Carole Ober, Molly Przeworski
(Submitted on 22 Aug 2012)

The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid changes responsible for A and B specificity in all species sequenced to date. Whether this recurrence of A and B antigens is the result of an ancient polymorphism maintained across species or due to numerous, more recent instances of convergent evolution has been debated for decades, with a current consensus in support of convergent evolution. We show instead that genetic variation data in humans and gibbons as well as in Old World Monkeys are inconsistent with a model of convergent evolution and support the hypothesis of an ancient, multi-allelic polymorphism of which some alleles are shared by descent among species. These results demonstrate that the ABO polymorphism is a trans-species polymorphism among distantly related species and has remained under balancing selection for tens of millions of years, to date, the only such example in Hominoids and Old World Monkeys outside of the Major Histocompatibility Complex.

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

Posted on by
2

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

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

Posted on by
3

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster

Mark F. Richardson, Lucy A. Weinert, John J. Welch, Raquel S. Linheiro, Michael M. Magwire, Francis M. Jiggins, Casey M. Bergman
(Submitted on 25 May 2012 (v1), last revised 2 Aug 2012 (this version, v2))

Wolbachia are maternally-inherited symbiotic bacteria commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. Here we use whole genome resequencing data from 290 lines of Drosophila melanogaster from North America, Europe and Africa to predict Wolbachia infection status, estimate cytoplasmic genome copy number, and reconstruct Wolbachia and mtDNA genome sequences. Complete Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with strict vertical transmission through the maternal cytoplasm and recurrent loss of Wolbachia in multiple populations. Bayesian phylogenetic analysis reveals that the most recent common ancestor of all Wolbachia and mitochondrial genomes in D. melanogaster dates to around 8,000 years ago. We find evidence for a recent incomplete global replacement of ancestral Wolbachia and mtDNA lineages, which is likely to be one of several similar incomplete replacement events that have occurred since the out-of-Africa migration that allowed D. melanogaster to colonize worldwide habitats.