Biology subjects

Jeffrey Ross-Ibarra

Publications and source records attributed to Jeffrey Ross-Ibarra.

8 recordsLinked to original sources

bioRxiv2016

Evolutionary genomics of peach and almond domestication

The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originate on opposite sides of Asia and were independently domesticated approximately 5000 years ago. While interfertile, they possess alternate mating systems and differ in a number of morpholog-ical and physiological traits. Here we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has [~]7X the genetic diversity of peach, and high genome-wide FST values support their status as separate species. We estimated a divergence time of approximately 8 Mya, coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application and further the understanding of evolution in these species.

Evolutionary Biology↗

bioRxiv2015

Extending the Stress-Gradient hypothesis: greater adaptation between teosinte and soil biota at higher stress sites

The outcomes of many species interactions are conditional on the environments in which they occur. A common pattern is that outcomes grade from being more positive under stressful conditions to more antagonistic or neutral under benign conditions. The evolutionary implications of conditionality in interactions have received much less attention than the documentation of conditionality itself, with a few notable exceptions. Here, we predict patterns of adaptation and co-adaptation between partners along abiotic gradients, positing that when interactions become more positive in stressful environments, fitness outcomes for mutations affecting interactions align across partners and selection should favor greater mutualistic adap-tation and co-adaptation between interacting species. As a corollary, in benign environments, if interactions are strongly antagonistic, we predict antagonistic co-adaptation resulting in Red Queen or arms-race dynamics, or reduction of antagonism through character displacement and niche partitioning. We predict no adaptation if interactions are more neutral. We call this the CoCoA hypothesis: (Co)-adaptation and Conditionality across Abiotic gradients. We describe experimental designs and statistical models that allow testing predictions of CoCoA, with a focus on positive interactions. While only one study has included all the elements to test CoCoA, we briefly review the literature and summarize study findings relevant to CoCoA and highlight opportunities to test CoCoA further.

Ecology↗

bioRxiv2015

Construction of the third generation Zea mays haplotype map

BackgroundCharacterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole genome sequencing data from 1,218 maize lines, covering pre-domestication and domesticated Zea mays varieties across the world.\n\nResultsA new computational pipeline was set up to process over 12 trillion bp of sequencing data, and a set of population genetics filters were applied to identify over 83 million variant sites.\n\nConclusionsWe identified polymorphisms in regions where collinearity is largely preserved in the maize species. However, the fact that the B73 genome used as the reference only represents a fraction of all haplotypes is still an important limiting factor.

Bioinformatics↗

bioRxiv2015

The origin and evolution of maize in the American Southwest

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.

Evolutionary Biology↗

bioRxiv2015

Independent molecular basis of convergent highland adaptation in maize

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica 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 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.

Evolutionary Biology↗

bioRxiv2014

Transposable elements contribute to activation of maize genes in response to abiotic stress

Transposable elements (TEs) account for a large portion of the genome in many eukaryotic species. Despite their reputation as "junk" DNA or genomic parasites deleterious for the host, TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression. It has been hypothesized that TEs and genes they insert near may be transcriptionally activated in response to stress conditions. The maize genome, with many different types of TEs interspersed with genes, provides an ideal system to study the genome-wide influence of TEs on gene regulation. To analyze the magnitude of the TE effect on gene expression response to environmental changes, we profiled gene and TE transcript levels in maize seedlings exposed to a number of abiotic stresses. Many genes exhibit up- or down-regulation in response to these stress conditions. The analysis of TE families inserted within upstream regions of up-regulated genes revealed that between four and nine different TE families are associated with up-regulated gene expression in each of these stress conditions, affecting up to 20% of the genes up-regulated in response to abiotic stress and as many as 33% of genes that are only expressed in response to stress. Expression of many of these same TE families also responds to the same stress conditions. The analysis of the stress- induced transcripts and proximity of the transposon to the gene suggests that these TEs may provide local enhancer activities that stimulate stress-responsive gene expression. Our data on allelic variation for insertions of several of these TEs show strong correlation between the presence of TE insertions and stress-responsive up-regulation of gene expression. Our findings suggest that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize.

Genomics↗

bioRxiv2014

Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)

Premise of the studyThe teosinte branched1 (tb1) gene is a major QTL controlling branching differences between maize and its wild progenitor, teosinte. The insertion of a transposable element (Hopscotch) upstream of tb1 is known to enhance the genes expression, causing reduced tillering in maize. Observations of the maize tb1 allele in teosinte and estimates of an insertion age of the Hopscotch that predates domestication led us to investigate its prevalence and potential role in teosinte.\n\nMethodsPrevalence of the Hopscotch element was assessed across an Americas-wide sample of 837 maize and teosinte individuals using a co-dominant PCR assay. Population genetic summaries were calculated for a subset of individuals from four teosinte populations in central Mexico. Phenotypic data were also collected using seed from a single teosinte population where Hopscotch was found segregating at high frequency.\n\nKey resultsGenotyping results indicate the Hopscotch element is found in a number of teosinte populations and linkage disequilibrium near tb1 does not support recent introgression from maize. Population genetic signatures are consistent with selection on this locus revealing a potential ecological role for Hopscotch in teosinte, but a greenhouse experiment does not detect a strong association between tb1 and tillering in teosinte.\n\nConclusionsOur findings suggest the role of Hopscotch differs between maize and teosinte. Future work should assess tb1 expression levels in teosinte with and without the Hopscotch and more comprehensively phenotype teosinte to assess the ecological significance of the Hopscotch insertion and, more broadly, the tb1 locus in teosinte.

Evolutionary Biology↗

bioRxiv2014

Diversity and evolution of centromere repeats in the maize genome

Centromere repeats are found in most eukaryotes and play a critical role in kinetochore formation. Though CentC repeats exhibit considerable diversity both within and among species, little is understood about the mechanisms that drive cen- tromere repeat evolution. Here, we use maize as a model to investigate how a complex history involving polyploidy, fractionation, and recent domestication has impacted the diversity of the maize CentC repeat. We first validate the existence of long tan- dem arrays of repeats in maize and other taxa in the genus Zea. Although we find considerable sequence diversity among CentC copies genome-wide, genetic similar- ity among repeats is highest within these arrays, suggesting that tandem duplica- tions are the primary mechanism for the generation of new copies. Genetic clustering analyses identify similar sequences among distant repeats, and simulations suggest that this pattern may be due to homoplasious mutation. Although the two ancestral subgenomes of maize have contributed nearly equal numbers of centromeres, our analysis shows that the vast majority of all CentC repeats derive from one of the parental genomes. Finally, by comparing maize with its wild progenitor teosinte, we find that the abundance of CentC has decreased through domestication while the peri- centromeric repeat Cent4 has drastically increased.

Genomics↗