On computing relative effective population size estimates and parameters from an equilibrium cycle of hermaphrodite frequency fluctuation due to mixed reproductive modes in filamentous fungi

Many filamentous ascomycete fungi reproduce primarily asexually, with only occasional sexual generations. This can lead to a departure from the 1:1 mating type ratio that is expected in obligate sexual populations. The relaxed selection on sexual traits also can lead to a decrease in the frequency of female fertile strains in field populations, while male fertility does not similarly decrease since male gametes also can serve as asexual spores. Both changes ultimately impact the strength of genetic drift in populations. The frequency of female sterility likely increases with the time since the last generation of sexual reproduction, such that it can be used to estimate the relative frequency of sexual reproduction. Here I provide additional details relevant to Leslie and Klein’s (1996) model of mixed sexual reproduction and vegetative propagation as related to the frequency of female sterility. This includes new or modified equations that allow for simpler calculations of i) two estimates of relative Ne, ii) the expected range of hermaphrodite frequencies during the cycles of mixed reproduction, and iii) the relative frequency of sex. These equations also are included in spreadsheet templates into which researchers can directly enter frequencies computed from their population data to estimate these parameters for their own populations. These resources will make the results of Leslie and Klein (1996) more accessible and should increase the use of this model in evaluating the frequency of sexual reproduction of filamentous fungi

Complex patterns of local adaptation in teosinte

Populations of widely distributed species often encounter and adapt to specific environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and a good understanding of population structure. We have used environmental and high-density genotype data to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found that altitude, dispersal events and admixture among subspecies formed a complex hierarchical genetic structure within teosinte. Patterns of linkage disequilibrium revealed four mega-base scale inversions that segregated among populations and had altitudinal clines. Based on patterns of differentiation and correlation with environmental variation, inversions and nongenic regions play an important role in local adaptation of teosinte. Further, we note that strongly differentiated individual populations can bias the identification of adaptive loci. The role of inversions in local adaptation has been predicted by theory and requires attention as genome-wide data become available for additional plant species. These results also suggest a potentially important role for noncoding variation, especially in large plant genomes in which the gene space represents a fraction of the entire genome

Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement

Citation: Liu, S. Z., Zheng, J., Migeon, P., Ren, J., Hu, Y., He, C., . . . Wang, G. Y. (2017). Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement. Scientific Reports, 7, 15. https://doi.org/10.1038/srep42444The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allelespecific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement

Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites

Peer reviewedPublisher PD

A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

Citation: Jordan, K. W., Wang, S., Lun, Y., Gardiner, L. J., MacLachlan, R., Hucl, P., . . . Akhunov, E. (2015). A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biology, 16(1). https://doi.org/10.1186/s13059-015-0606-4Background: Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. Results: A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. Conclusions: Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets. © 2015 Jordan et al.; licensee BioMed Central.Additional Authors: Talbert, L.;Bansal, U. K.;Bariana, H. S.;Hayden, M. J.;Pozniak, C.;Jeddeloh, J. A.;Hall, A

Exhibit Curriculum for Fighting for Democracy: Unit Two

Exhibit curriculum for the CUNY Dominican Studies Institute exhibit, Fighting for Democracy: Dominican Veterans from World War II. Students in Global History and U.S. History courses often spend extensive class time studying World War II. Dominicans were involved in virtually every facet of the U.S. war effort. The Dominican Studies Institute\u27s exhibit highlights Dominican veterans who served in both the European and Pacific theaters, in multiple branches of the U.S. armed forces. These same veterans, like other people of color, faced discrimination as soldiers in the U.S. An exploration of these veterans\u27 experiences would be memorable and valuable for secondary history students. Curriculum objective: Students will be able to describe the experiences of Dominicans who served in the U.S. military during World War II. The visual resources to support this curriculum are available on the JSTOR open collection site

Exhibit Curriculum for Fighting for Democracy: Unit Three

Exhibit curriculum for the CUNY Dominican Studies Institute exhibit, Fighting for Democracy: Dominican Veterans from World War II. Students in Global History and U.S. History courses often spend extensive class time studying World War II. Dominicans were involved in virtually every facet of the U.S. war effort. The Dominican Studies Institute\u27s exhibit highlights Dominican veterans who served in both the European and Pacific theaters, in multiple branches of the U.S. armed forces. These same veterans, like other people of color, faced discrimination as soldiers in the U.S. An exploration of these veterans\u27 experiences would be memorable and valuable for secondary history students. Curriculum objective: Students will be able to describe the experiences of Dominicans who served in the U.S. military during World War II. The visual resources to support this curriculum are available on the JSTOR open collection site

Exhibit Curriculum for Fighting for Democracy: Unit One

Exhibit curriculum for the CUNY Dominican Studies Institute exhibit, Fighting for Democracy: Dominican Veterans from World War II. Students in Global History and U.S. History courses often spend extensive class time studying World War II. Dominicans were involved in virtually every facet of the U.S. war effort. The Dominican Studies Institute\u27s exhibit highlights Dominican veterans who served in both the European and Pacific theaters, in multiple branches of the U.S. armed forces. These same veterans, like other people of color, faced discrimination as soldiers in the U.S. An exploration of these veterans\u27 experiences would be memorable and valuable for secondary history students. Curriculum objective: Students will be able to describe the experiences of Dominicans who served in the U.S. military during World War II. The visual resources to support this curriculum are available on the JSTOR open collection site

Fumonisin and beauvericin chemotypes and genotypes of the sister species Fusarium subglutinans and Fusarium temperatum

Fusarium subglutinans and Fusarium temperatum are common maize pathogens that produce mycotoxins and cause plant disease. The ability of these species to produce beauvericin and fumonisin mycotoxins is not settled, as reports of toxin production are not concordant. Our objective was to clarify this situation by determining both the chemotypes and genotypes for strains from both species. We analyzed 25 strains from Argentina, 13 F. subglutinans and 12 F. temperatum strains, for toxin production by ultraperformance liquid chromatography mass spectrometry (UPLC-MS). We used new genome sequences from two strains of F. subglutinans and one strain of F. temperatum, plus genomes of other Fusarium species, to determine the presence of functional gene clusters for the synthesis of these toxins. None of the strains examined from either species produced fumonisins. These strains also lack Fum biosynthetic genes but retain homologs of some genes that flank the Fum cluster in Fusarium verticillioides. None of the F. subglutinans strains we examined produced beauvericin although 9 of 12 F. temperatum strains did. A complete beauvericin (Bea) gene cluster was present in all three new genome sequences. The Bea1 gene was presumably functional in F. temperatum but was not functional in F. subglutinans due to a large insertion and multiple mutations that resulted in premature stop codons. The accumulation of only a few mutations expected to disrupt Bea1 suggests that the process of its inactivation is relatively recent. Thus, none of the strains of F. subglutinans or F. temperatum we examined produce fumonisins, and the strains of F. subglutinans examined also cannot produce beauvericin. Variation in the ability of strains of F. temperatum to produce beauvericin requires further study and could reflect the recent shared ancestry of these two species.Fil: Fumero, María Verónica. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigación en Micología y Micotoxicología. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación en Micología y Micotoxicología; ArgentinaFil: Villani, Alessandra. Institute of Sciences of Food Production; ItaliaFil: Susca, Antonia. Institute of Sciences of Food Production; ItaliaFil: Haidukowski, Miriam. Institute of Sciences of Food Production; ItaliaFil: Cimmarusti, María. Institute of Sciences of Food Production; ItaliaFil: Toomajian, Christopher. Kansas State University; Estados UnidosFil: Leslie, John Franklin. Kansas State University; Estados UnidosFil: Chulze, Sofia Noemi. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas Fisicoquímicas y Naturales. Instituto de Investigación en Micología y Micotoxicología. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación en Micología y Micotoxicología; ArgentinaFil: Moretti, Antonio. Institute of Sciences of Food Production; Itali