The origin and evolution of maize in the American Southwest

Rute R da Fonseca, Bruce D Smith, Nathan Wales, Enrico Cappellini, Pontus Skoglund, Matteo Fumagalli, José Alfredo Samaniego, Christian Carøe, María C Ávila-Arcos, David E Hufnagel, Thorfinn Sand Korneliussen, Filipe Garrett Vieira, Mattias Jakobsson, Bernardo Arriaza, Eske Willerslev, Rasmus Nielsen, Matthew B Hufford, Anders Albrechtsen, Jeffrey Ross-Ibarra, M Thomas P Gilbert
doi: http://dx.doi.org/10.1101/013540

Maize offers an ideal system through which to demonstrate the potential of ancient population genomic techniques for reconstructing the evolution and spread of domesticates. The diffusion of maize from Mexico into the North American Southwest (SW) remains contentious with the available evidence being restricted to morphological studies of ancient maize plant material. We captured 1 Mb of nuclear DNA from 32 archaeological maize samples spanning 6000 years and compared them with modern landraces including those from the Mexican West coast and highlands. We found that the initial diffusion of domesticated maize into the SW is likely to have occurred through a highland route. However, by 2000 years ago a Pacific coastal corridor was also being used. Furthermore, we could distinguish between genes that were selected for early during domestication (such as zagl1 involved in shattering) from genes that changed in the SW context (e.g. related to sugar content and adaptation to drought) likely as a response to the local arid environment and new cultural uses of maize.

SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in Warblers

Natasha Bloch, James M Morrow, Belinda SW Chang, Trevor D Price
doi: http://dx.doi.org/10.1101/013573

Distantly related clades that occupy similar environments may differ due to the lasting imprint of their ancestors – historical contingency. The New World warblers (Parulidae) and Old World warblers (Phylloscopidae) are ecologically similar clades that differ strikingly in plumage coloration. We studied genetic and functional evolution of the short-wavelength sensitive visual pigments (SWS2 and SWS1) to ask if altered color perception could contribute to the plumage color differences between clades. We show SWS2 is short-wavelength shifted in birds that occupy open environments, such as finches, compared to those in closed environments, including warblers. Sequencing of opsin genes and phylogenetic reconstructions indicate New World warblers were derived from a finch-like form that colonized from the Old World 15-20Ma. During this process the SWS2 gene accumulated 6 substitutions in branches leading to New World warblers, inviting the hypothesis that passage through a finch-like ancestor resulted in SWS2 evolution. In fact, we show spectral tuning remained similar across warblers as well as the finch ancestor. Results reject the hypothesis of historical contingency based on opsin spectral tuning, but point to evolution of other aspects of visual pigment function. Using the approach outlined here, historical contingency becomes a generally testable theory in systems where genotype and phenotype can be connected.

Independent molecular basis of convergent highland adaptation in maize

Shohei Takuno, Peter Ralph, Kelly Swarts, Rob J Elshire, Jeffrey C Glaubitz, Edward S. Buckler, Matthew B Hufford, Jeff Ross-Ibarra
doi: http://dx.doi.org/10.1101/013607

Convergent evolution occurs when multiple species/subpopulations adapt to similar environments via similar phenotypes. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mexico and South America using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection, and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide array of parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation, and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.

High-resolution genomic surveillance of 2014 ebolavirus using shared subclonal variants

Kevin J Emmett, Albert K Lee, Hossein Khiabanian, Raul Rabadan
doi: http://dx.doi.org/10.1101/013318

Viral outbreaks, such as the 2014 ebolavirus, can spread rapidly and have complex evolutionary dynamics, including coinfection and bulk transmission of multiple viral populations. Genomic surveillance can be hindered when the spread of the outbreak exceeds the evolutionary rate, in which case consensus approaches will have limited resolution. Deep sequencing of infected patients can identify genomic variants present in intrahost populations at subclonal frequencies (i.e. <50%). Shared subclonal variants (SSVs) can provide additional phylogenetic resolution and inform about disease transmission patterns. Here, we use metrics from population genetics to analyze data from the 2014 ebolavirus outbreak in Sierra Leone and identify phylogenetic signal arising from SSVs. We use methods derived from information theory to measure a lower bound on transmission bottleneck size that is larger than one founder population, yet significantly smaller than the intrahost effective population. Our results demonstrate the important role of shared subclonal variants in genomic surveillance.