@article{shimizu_reininga_caicedo_mays_moore_olsen_ruzsa_coop_bustamante_purugganan_2008, title={Darwinian selection on a selfing locus (vol 306, pg 2081, 2004)}, volume={320}, number={5873}, journal={Science}, author={Shimizu, K. K. and Reininga, J. M. and Caicedo, A. L. and Mays, C. A. and Moore, R. C. and Olsen, K. M. and Ruzsa, S. and Coop, G. and Bustamante, C. D. and Purugganan, M. D.}, year={2008}, pages={176–176} } @article{caicedo_williamson_hernandez_boyko_fledel-alon_york_polato_olsen_nielsen_mccouch_et al._2007, title={Genome-wide patterns of nucleotide polymorphism in domesticated rice}, volume={3}, ISSN={["1553-7404"]}, DOI={10.1371/journal.pgen.0030163}, abstractNote={Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation.}, number={9}, journal={PLOS GENETICS}, author={Caicedo, Ana L. and Williamson, Scott H. and Hernandez, Ryan D. and Boyko, Adam and Fledel-Alon, Adi and York, Thomas L. and Polato, Nicholas R. and Olsen, Kenneth M. and Nielsen, Rasmus and McCouch, Susan R. and et al.}, year={2007}, month={Sep}, pages={1745–1756} } @article{mather_caicedo_polato_olsen_mccouch_purugganan_2007, title={The extent of linkage disequilibrium in rice (Oryza sativa L.)}, volume={177}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.107.079616}, abstractNote={Abstract Despite its status as one of the world's major crops, linkage disequilibrium (LD) patterns have not been systematically characterized across the genome of Asian rice (Oryza sativa). Such information is critical to fully exploit the genome sequence for mapping complex traits using association techniques. Here we characterize LD in five 500-kb regions of the rice genome in three major cultivated rice varieties (indica, tropical japonica, and temperate japonica) and in the wild ancestor of Asian rice, Oryza rufipogon. Using unlinked SNPs to determine the amount of background linkage disequilibrium in each population, we find that the extent of LD is greatest in temperate japonica (probably >500 kb), followed by tropical japonica (∼150 kb) and indica (∼75 kb). LD extends over a shorter distance in O. rufipogon (≪40 kb) than in any of the O. sativa groups assayed here. The differences in the extent of LD among these groups are consistent with differences in outcrossing and recombination rate estimates. As well as heterogeneity between groups, our results suggest variation in LD patterns among genomic regions. We demonstrate the feasibility of genomewide association mapping in cultivated Asian rice using a modest number of SNPs.}, number={4}, journal={GENETICS}, author={Mather, Kristie A. and Caicedo, Ana L. and Polato, Nicholas R. and Olsen, Kenneth M. and McCouch, Susan and Purugganan, Michael D.}, year={2007}, month={Dec}, pages={2223–2232} } @article{olsen_caicedo_polato_mcclung_mccouch_purugganan_2006, title={Selection under domestication: Evidence for a sweep in the rice Waxy genomic region}, volume={173}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.106.056473}, abstractNote={Abstract Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems.}, number={2}, journal={GENETICS}, author={Olsen, Kenneth M. and Caicedo, Ana L. and Polato, Nicholas and McClung, Anna and McCouch, Susan and Purugganan, Michael D.}, year={2006}, month={Jun}, pages={975–983} } @article{stinchcombe_weinig_ungerer_olsen_mays_halldorsdottir_purugganan_schmitt_2004, title={A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA}, volume={101}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0306401101}, abstractNote={ A latitudinal cline in flowering time in accessions of Arabidopsis thaliana has been widely predicted because the environmental cues that promote flowering vary systematically with latitude, but evidence for such clines has been lacking. Here, we report evidence of a significant latitudinal cline in flowering time among 70 Northern European and Mediterranean ecotypes when grown under ecologically realistic conditions in a common garden environment. The detected cline, however, is found only in ecotypes with alleles of the flowering time gene FRIGIDA ( FRI ) that lack major deletions that would disrupt protein function, whereas there is no relationship between flowering time and latitude of origin among accessions with FRI alleles containing such deletions. Analysis of climatological data suggests that late flowering in accessions with putatively functional FRI was associated with reduced January precipitation at the site of origin, consistent with previous reports of a positive genetic correlation between water use efficiency and flowering time in Arabidopsis , and the pleiotropic effects of FRI of increasing water use efficiency. In accessions collected from Southern latitudes, we detected that putatively functional FRI alleles were associated with accelerated flowering relative to accessions with nonfunctional FRI under the winter conditions of our experiment. These results suggest that the ecological function of the vernalization requirement conferred by FRI differs across latitudes. More generally, our results indicate that by combining ecological and molecular genetic data, it is possible to understand the forces acting on life history transitions at the level of specific loci. }, number={13}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Stinchcombe, JR and Weinig, C and Ungerer, M and Olsen, KM and Mays, C and Halldorsdottir, SS and Purugganan, MD and Schmitt, J}, year={2004}, month={Mar}, pages={4712–4717} } @article{shimizu_cork_caicedo_mays_moore_olsen_ruzsa_coop_bustamante_awadalla_et al._2004, title={Darwinian selection on a selfing locus (Retracted Article. See vol 320, pg 176, 2008)}, volume={306}, ISSN={["1095-9203"]}, DOI={10.1126/science.1103776}, abstractNote={ The shift to self-pollination is one of the most prevalent evolutionary transitions in flowering plants. In the selfing plant Arabidopsis thaliana , pseudogenes at the SCR and SRK self-incompatibility loci are believed to underlie the evolution of self-fertilization. Positive directional selection has driven the evolutionary fixation of pseudogene alleles of SCR , leading to substantially reduced nucleotide variation. Coalescent simulations indicate that this adaptive event may have occurred very recently and is possibly associated with the post-Pleistocene expansion of A. thaliana from glacial refugia. This suggests that ancillary morphological innovations associated with self-pollination can evolve rapidly after the inactivation of the self-incompatibility response. }, number={5704}, journal={SCIENCE}, author={Shimizu, KK and Cork, JM and Caicedo, AL and Mays, CA and Moore, RC and Olsen, KM and Ruzsa, S and Coop, G and Bustamante, CD and Awadalla, P and et al.}, year={2004}, month={Dec}, pages={2081–2084} } @article{caicedo_stinchcombe_olsen_schmitt_purugganan_2004, title={Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait}, volume={101}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0406232101}, abstractNote={ Epistatic gene interactions are believed to be a major factor in the genetic architecture of evolutionary diversification. In Arabidopsis thaliana , the FRI and FLC genes mechanistically interact to control flowering time, and here we show that this epistatic interaction also contributes to a latitudinal cline in this life history trait within the species. Two major FLC haplogroups ( FLC A and FLC B ) are associated with flowering time variation in A. thaliana in field conditions, but only in the presence of putatively functional FRI alleles. Significant differences in latitudinal distribution of FLC haplogroups in Eurasia and North Africa also depend on the FRI genotype. There is significant linkage disequilibrium between FRI and FLC despite their location on separate chromosomes. Although no nonsynonymous polymorphisms differentiate FLC A and FLC B , vernalization induces the expression of an alternatively spliced FLC transcript that encodes a variant protein with a radical amino acid replacement associated with the two FLC haplogroups. Numerous polymorphisms differentiating the FLC haplogroups also occur in intronic regions implicated in the regulation of FLC expression. The features of the regulatory gene interaction between FRI and FLC in contributing to the latitudinal cline in A. thaliana flowering time are consistent with the maintenance of this interaction by epistatic selection. These results suggest that developmental genetic pathways and networks provide the molecular basis for epistasis, contributing to ecologically important phenotypic variation in natural populations and to the process of evolutionary diversification. }, number={44}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Caicedo, AL and Stinchcombe, JR and Olsen, KM and Schmitt, J and Purugganan, MD}, year={2004}, month={Nov}, pages={15670–15675} } @article{olsen_halldorsdottir_stinchcombe_weinig_schmitt_purugganan_2004, title={Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles}, volume={167}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.103.024950}, abstractNote={Abstract The selfing plant Arabidopsis thaliana has been proposed to be well suited for linkage disequilibrium (LD) mapping as a means of identifying genes underlying natural trait variation. Here we apply LD mapping to examine haplotype variation in the genomic region of the photoperiod receptor CRYPTOCHROME2 and associated flowering time variation. CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene; in addition, a haplotype possessing a radical glutamine-to-serine replacement (AS) occurs within the more common haplogroup. Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering. Data from six genes flanking CRY2 indicate that these haplogroups are limited to an ∼65-kb genomic region around CRY2. Whereas the B haplogroup cannot be delimited to <16 kb around CRY2, the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype. This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.}, number={3}, journal={GENETICS}, author={Olsen, KM and Halldorsdottir, SS and Stinchcombe, JR and Weinig, C and Schmitt, J and Purugganan, MD}, year={2004}, month={Jul}, pages={1361–1369} } @article{olsen_2004, title={SNPs, SSRs and inferences on cassava's origin}, volume={56}, ISSN={["1573-5028"]}, DOI={10.1007/s11103-004-5043-9}, abstractNote={Despite its importance as a staple food throughout the tropics, the root crop cassava (it Manihot esculenta ssp. esculenta) has traditionally not been a major focus of research. One basic question about cassava that remained unresolved until recently concerns the crop's origin. This paper describes analyses of SNPs (single nucleotide polymorphisms) and SSR (simple sequence repeat) variation as a means of tracing cassava's evolutionary and geographical origins. Genetic diversity was examined in a sample of 20 cassava varieties that are representative of germplasm diversity within the crop, and in 212 individuals collected from wild populations of two closely related Manihot species. SNP and indel variation was examined in portions of two low copy nuclear genes, BglA and Hnl. Inferences from these genes were compared to those from previously examined loci, including the low copy nuclear gene G3pdh and 5 SSR loci. For all genes examined, SNPs and SSR alleles are shared between domesticated cassava and a specific geographical subset of wild Manihot populations, which suggests the following: (1) Cassava was likely domesticated from a single wild Manihot species, M. esculenta ssp. flabellifolia, rather than from multiple hybridizing species, as traditionally believed; and (2) the crop most likely originated in the southern Amazon basin.}, number={4}, journal={PLANT MOLECULAR BIOLOGY}, author={Olsen, KM}, year={2004}, month={Nov}, pages={517–526} } @article{olsen_womack_garrett_suddith_purugganan_2002, title={Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway}, volume={160}, number={4}, journal={Genetics}, author={Olsen, K. M. and Womack, A. and Garrett, A. R. and Suddith, J. I. and Purugganan, M. D.}, year={2002}, pages={1641–1650} } @article{olsen_purugganan_2002, title={Molecular evidence on the origin and evolution of glutinous rice}, volume={162}, number={2}, journal={Genetics}, author={Olsen, K. M. and Purugganan, M. D.}, year={2002}, pages={941–950} } @article{olsen_2002, title={Population history of Manihot esculenta (Euphorbiaceae) inferred from nuclear DNA sequences}, volume={11}, ISSN={["0962-1083"]}, DOI={10.1046/j.1365-294X.2002.01493.x}, abstractNote={AbstractThe nature of gene flow in plants — including the propensity for interspecific introgression — makes them interesting candidates for phylogeographical analysis. Plant phylogeography studies have been limited, however, by the availability of suitable intraspecific variation. In this study, DNA sequence variation from a nuclear gene [Glyceraldehyde 3‐phosphate dehydrogenase; (G3pdh)] was used to examine the population history of Manihot esculenta ssp. flabellifolia and a potentially hybridizing species, M. pruinosa. These species occur in the rainforest–savanna ecotone adjoining the Amazon basin, a region believed to have undergone major habitat shifts since the Pleistocene. Geographical distributions of the G3pdh haplotypes indicate genetic isolation‐by‐distance across the range of M. esculenta ssp. flabellifolia. However, there is greater genetic similarity between northeastern and western populations than would be expected given the present species distribution. A nested clade analysis suggests that northeastern and western populations were connected by gene flow until relatively recently, when they became fragmented. This inferred fragmentation event is consistent with post‐Pleistocene habitat shifts proposed for the Amazon basin. At the interspecific level, haplotype sharing with M. pruinosa may reflect either recent interspecific introgression or incomplete lineage sorting between these closely related species.}, number={5}, journal={MOLECULAR ECOLOGY}, author={Olsen, KM}, year={2002}, month={May}, pages={901–911} } @article{bustamante_nielsen_sawyer_olsen_purugganan_hartl_2002, title={The cost of inbreeding in Arabidopsis}, volume={416}, ISSN={["0028-0836"]}, DOI={10.1038/416531a}, abstractNote={Population geneticists have long sought to estimate the distribution of selection intensities among genes of diverse function across the genome. Only recently have DNA sequencing and analytical techniques converged to make this possible. Important advances have come from comparing genetic variation within species (polymorphism) with fixed differences between species (divergence). These approaches have been used to examine individual genes for evidence of selection. Here we use the fact that the time since species divergence allows combination of data across genes. In a comparison of amino-acid replacements among species of the mustard weed Arabidopsis with those among species of the fruitfly Drosophila, we find evidence for predominantly beneficial gene substitutions in Drosophila but predominantly detrimental substitutions in Arabidopsis. We attribute this difference to the Arabidopsis mating system of partial self-fertilization, which corroborates a prediction of population genetics theory that species with a high frequency of inbreeding are less efficient in eliminating deleterious mutations owing to their reduced effective population size.}, number={6880}, journal={NATURE}, author={Bustamante, CD and Nielsen, R and Sawyer, SA and Olsen, KM and Purugganan, MD and Hartl, DL}, year={2002}, month={Apr}, pages={531–534} } @article{olsen_schaal_2001, title={Microsatellite variation in cassava (Manihot esculenta, Euphorbiaceae) and its wild relatives: Further evidence for a southern Amazonian origin of domestication}, volume={88}, ISSN={["0002-9122"]}, DOI={10.2307/2657133}, abstractNote={Genetic variation at five microsatellite loci was used to investigate the evolutionary and geographical origins of cassava (Manihot esculenta subsp. esculenta) and the population structure of cassava's wild relatives. Two hundred and twelve individuals were sampled, representing 20 crop accessions, 27 populations of cassava's closest wild relative (M. esculenta subsp. flabellifolia), and six populations of a potentially hybridizing species (M. pruinosa). Seventy‐three alleles were observed across all loci and populations. These data indicate the following on cassava's origin: (1) genetic variation in the crop is a subset of that found in the wild M. esculenta subspecies, suggesting that cassava is derived solely from its conspecific wild relative. (2) Phenetic analyses group cassava with wild populations from the southern border of the Amazon basin, indicating this region as the likely site of domestication. (3) Manihot pruinosa, while closely related to M. esculenta (and possibly hybridizing with it where sympatric), is probably not a progenitor of the crop. Genetic differentiation among the wild populations is moderately high (FST = 0.42, ρST = 0.54). This differentiation has probably arisen primarily through random genetic drift (rather than mutation) following recent population divergence.}, number={1}, journal={AMERICAN JOURNAL OF BOTANY}, author={Olsen, KM and Schaal, BA}, year={2001}, month={Jan}, pages={131–142} }