@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}, 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}, 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}, 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={Abstract}, 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} }