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The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny. [ABSTRACT FROM AUTHOR]

The American plains bison (Bison bison) was pushed to the brink of extinction in the late 1800s but has since rebounded. Less than 5% of animals currently exist in conservation herds that are critical for maintaining genetic variability. Here, we use 25 microsatellite loci to assess genetic diversity and patterns of mating success over a 3-year period in a managed conservation herd at Konza Prairie Biological Station, Kansas (total number of individuals genotyped = 587). Heterozygosity was comparable to and allelic diversity higher than that in 11 other wild and managed herds for which similar estimates are available. Parentage analyses revealed that males within the oldest age classes (5–7 years) sired >90% of calves over the study period, consistent with a polygynous breeding system. Asymmetries in siring success also were observed within age classes, with the same males enjoying high siring success over multiple seasons. Empirical results of paternity will facilitate future modeling and empirical efforts to determine how demographic factors, population size, and variation in siring success interact to determine the retention (or loss) of genetic diversity in natural and managed herds, thus allowing informed recommendations for management practices and conservation efforts of this symbolic North American species. [ABSTRACT FROM PUBLISHER]

Hybridization and abiotic stress are natural agents hypothesized to influence activation and proliferation of transposable elements in wild populations. In this report, we examine the effects of these agents on expression dynamics of both quiescent and transcriptionally active sublineages of long terminal repeat (LTR) retrotransposons in wild sunflower species with a notable history of transposable element proliferation. For annual sunflower species Helianthus annuus and H. petiolaris, neither early generation hybridization nor abiotic stress, alone or in combination, induced transcriptional activation of quiescent sublineages of LTR retrotransposons. These treatments also failed to further induce expression of sublineages that are transcriptionally active; instead, expression of active sublineages in F1 and backcross hybrids was nondistinguishable from, or intermediate relative to, parental lines, and abiotic stress generally decreased normalized expression relative to controls. In contrast to findings for early generation hybridization between H. annuus and H. petiolaris, ancient sunflower hybrid species derived from these same two species and which have undergone massive proliferation events of LTR retrotransposons display 2× to 6× higher expression levels of transcriptionally active sublineages relative to parental sunflower species H. annuus and H. petiolaris. Implications and possible explanations for these findings are discussed. [ABSTRACT FROM AUTHOR]

Hybridization is a natural phenomenon that has been linked in several organismal groups to transposable element derepression and copy number amplification. A noteworthy example involves three diploid annual sunflower species from North America that have arisen via ancient hybridization between the same two parental taxa, Helianthus annuus and H. petiolaris. The genomes of the hybrid species have undergone large-scale increases in genome size attributable to long terminal repeat (LTR) retrotransposon proliferation. The parental species that gave rise to the hybrid taxa are widely distributed, often sympatric, and contemporary hybridization between them is common. Natural H. annuus × H. petiolaris hybrid populations likely served as source populations from which the hybrid species arose and, as such, represent excellent natural experiments for examining the potential role of hybridization in transposable element derepression and proliferation in this group. In the current report, we examine multiple H. annuus × H. petiolaris hybrid populations for evidence of genome expansion, LTR retrotransposon copy number increases, and LTR retrotransposon transcriptional activity. We demonstrate that genome expansion and LTR retrotransposon proliferation are rare in contemporary hybrid populations, despite independent proliferation events that took place in the genomes of the ancient hybrid species. Interestingly, LTR retrotransposon lineages that proliferated in the hybrid species genomes remain transcriptionally active in hybrid and nonhybrid genotypes across the entire sampling area. The finding of transcriptional activity but not copy number increases in hybrid genotypes suggests that proliferation and genome expansion in contemporary hybrid populations may be mitigated by posttranscriptional mechanisms of repression. [ABSTRACT FROM AUTHOR]

Quantitative trait locus (QTL) mapping has become an established and effective method for studying the genetic architecture of complex traits. In this report, we use a QTL mapping approach in combination with data from a large selection experiment in Arabidopsis thaliana to explore a response to selection of experimental populations with differentiated genetic backgrounds. Experimental populations with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were exposed to multiple generations of fertility and viability selection. This selection resulted in phenotypic shifts in a number of life-history and fitness-related characters including early development time, flowering time, dry biomass, longevity, and fruit production. Quantitative trait loci were mapped for these traits and their positions were compared to previously characterized allele frequency changes in the experimental populations (Ungerer et al. 2003). Quantitative trait locus positions largely colocalized with genomic regions under strong and consistent selection in populations with differentiated genetic backgrounds, suggesting that alleles for these traits were selected similarly in differentiated genetic backgrounds. However, one QTL region exhibited a more variable response; being positively selected on one genetic background but apparently neutral in another. This study demonstrates how QTL mapping approaches can be combined with map-based population genetic data to study how selection acts on standing genetic variation in populations. [ABSTRACT FROM AUTHOR]

Examines the inflorescence development patterns in Arabidopsis thaliana under different, ecologically relevant photoperiod environments for two recombinant inbred mapping populations using a combination of quantitative genetics and quantitative trait locus (QTL) mapping. Changes in magnitude of effect of QTL; Plasticity and genotype-environment interactions; Use of high-resolution mapping to distinguish between the alternative explanations of pleiotropy and tight linkage among multiple genes.

The extent to which genetic background can influence allelic fitness is poorly understood, despite having important evolutionary consequences. Using experimental populations of Arabidopsis thaliana and map-based population generic data, we examined a multigeneration response to selection in populations with differentiated genetic backgrounds. Replicated experimental populations of A. thaliana with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were subjected to strong viability and fertility selection by growing individuals from each population at high density for three generations in a growth chamber. Patterns of genome-wide selection were evaluated by examining deviations from expected frequencies of mapped molecular markers. Estimates of selection coefficients for individual genomic regions ranged from near 0 to 0.685. Genomic regions demonstrating the strongest response to selection most often were selected similarly in both genetic backgrounds. The selection response of several weakly selected regions, however, appeared to be sensitive to genetic background, but only one region showed evidence of positive selection m one background and negative selection in another. These results are most consistent with models of adaptive evolution in which allelic fitnesses are not strongly influenced by genetic background and only infrequently change in sign due to variation at other loci. [ABSTRACT FROM AUTHOR]

Examines the quantitative trait of loci for inflorescence development in Arabidopsis thaliana. Variation in inflorescence development patterns; Discussions on Arabidopsis ecotypes and mapping population; Isolation of genes and genetic polymorphism from the inflorescence developmental phenotypes.

Reports the first study of quantitative trait loci (QTL) for date of bolting (the transition from vegetative to reproductive growth) in A. thaliana in natural seasonal field environments and compares the results with those obtained under typical growth-chamber conditions. Two QTL specific to long days in the chamber were expressed only in spring-germinating cohorts in the field, and two loci specific to short days in the chamber were expressed only in fall-germinating cohorts, suggesting differential involvement of the photoperiod pathway in different seasonal environments. However, several other photoperiod-specific QTL with large effects in controlled conditions were undetectable in natural environments, indicating that expression of allelic variation at these loci was overridden by environmental factors specific to the field. Moreover, a substantial number of QTL with major effects on bolting date in one or more field environments were undetectable under controlled environment conditions. These novel loci suggest the involvement of additional genes in the transition to flowering under ecologically relevant conditions.

Mutations are crucial to evolution, providing the ultimate source of variation on which natural selection acts. Due to their key role, the distribution of mutational effects on quantitative traits is a key component to any inference regarding historical selection on phenotypic traits. In this paper, we expand on a previously developed test for selection that could be conducted assuming a Gaussian mutation effect distribution by developing approaches to also incorporate any of a family of heavy-tailed Laplace distributions of mutational effects. We apply the test to detect directional natural selection on five traits along the divergence of Columbia and Landsberg lineages of Arabidopsis thaliana, constituting the first test for natural selection in any organism using quantitative trait locus and mutation accumulation data to quantify the intensity of directional selection on a phenotypic trait. We demonstrate that the results of the test for selection can depend on the mutation effect distribution specified. Using the distributions exhibiting the best fit to mutation accumulation data, we infer that natural directional selection caused divergence in the rosette diameter and trichome density traits of the Columbia and Landsberg lineages. [ABSTRACT FROM AUTHOR]

Reports that selection on quantitative trait loci (QTL) for fitness traits in the model plant species Arabidopsis thaliana differs among natural ecological settings and genetic backgrounds. Suggestion that the allelic fitness effects of two QTL reversed direction depending on the genotype at the other locus; Indication that both environmental heterogeneity and epistatic selection may maintain genetic variation for fitness in wild plant species.