A Manipulative Experiment to Estimate Biparental Inbreeding in Monkeyflowers

Biparental inbreeding occurs when plants receive pollen from genetically related neighbors. The frequency of biparental inbreeding in natural populations is unknown but directly relevant to the evolution of plant mating systems. We suggest a simple manipulative experiment to distinguish the effects of biparental inbreeding from those of self‐fertilization. The basis of the method is to compare the levels of inbreeding in plants with and without the potential to outcross with genetic relatives. We eliminate the potential for biparental inbreeding by transplanting seedlings to different locations within a population. The level of inbreeding is then estimated from homozygosity at molecular markers. This method is applied in a study of two natural populations of Mimulus guttatus (the yellow monkeyflower) using microsatellites as marker loci. In contrast to previous studies of this species, our study finds no evidence of biparental inbreeding in either population

Organic amendment increases arbuscular mycorrhizal fungal diversity in primary coastal dunes

Plastic pots were inserted beneath seedlings of a shallow-rooted C4 grass species, Ischaemum indicum, with and without a root-impenetrable nylon sachet filled with organic matter (OM) amendment, at seven stations along an interrupted belt transect in which plant community and soil chemistry had been previously surveyed. The transect was perpendicular to mean high-water mark (MH-WM) across a primary coastal dune system in Goa, India, where summer monsoon is the predominant weather feature. The Quadrat survey of plant frequency was made in stations when the above-ground biomass was estimated to be highest. Arbuscular mycorrhiza fungal (AMF) spore density and diversity were determined morphologically in amended and control pots soils, and in OM sachet residues, after host-plant desiccation when monsoon rains had ceased. Twenty-seven AM fungal spore morphotypes were isolated from the pots containing OM amended rhizosphere soils, 19 from controls and 14 from OM residues in the sachets. Gigaspora margarita proved to be the dominant spore in all treatments. Eight morphotypes recovered from amended pots were not recovered from the controls. There was an increasing trend in species diversity in amended pots away from MH-WM. Spore recovery from the three regimes showed variable distribution that indicated differing AMF species strategies

Population structure and local selection yield high genomic variation in Mimulus guttatus

Across western North America, Mimulus guttatus exists as many local populations adapted to site-specific environmental challenges. Gene flow between locally adapted populations will affect genetic diversity both within demes and across the larger metapopulation. Here, we analyse 34 whole-genome sequences from the intensively studied Iron Mountain population (IM) in conjunction with sequences from 22 Mimulus individuals sampled from across western North America. Three striking features of these data address hypotheses about migration and selection in a locally adapted population. First, we find very high levels of intrapopulation polymorphism (synonymous =0.033). Variation outside of genes is likely even higher but difficult to estimate because excessive divergence reduces the efficiency of read mapping. Second, IM exhibits a significantly positive genomewide average for Tajima\u27s D. This indicates allele frequencies are typically more intermediate than expected from neutrality, opposite the pattern observed in many other species. Third, IM exhibits a distinctive haplotype structure with a genomewide excess of positive associations between rarer alleles at linked loci. This suggests an important effect of gene flow from other Mimulus populations, although a residual effect of population founding might also contribute. The combination of multiple analyses, including a novel tree-based analytic method, illustrates how the balance of local selection, limited dispersal and metapopulation dynamics manifests across the genome. The overall genomic pattern of sequence diversity suggests successful gene flow of divergent immigrant genotypes into IM. However, many loci show patterns indicative of local adaptation, particularly at SNPs associated with chromosomal inversions

Mapping of ionomic traits in Mimulus guttatus reveals Mo and Cd QTLs that colocalize with MOT1 homologues

Peer reviewedPublisher PD

Spatially and temporally varying selection on intra-population QTL for a life history tradeoff in Mimulus guttatus

This is the peer reviewed version of the following article: MOJICA, J. P., LEE, Y. W., WILLIS, J. H. and KELLY, J. K. (2012), Spatially and temporally varying selection on intrapopulation quantitative trait loci for a life history trade-off in Mimulus guttatus. Molecular Ecology, 21: 3718–3728. doi:10.1111/j.1365-294X.2012.05662.x, which has been published in final form at http://doi.org/10.1111/j.1365-294X.2012.05662.x. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Why do populations remain genetically variable despite strong continuous natural selection? Mutation reconstitutes variation eliminated by selection and genetic drift, but theoretical and experimental studies each suggest that mutation-selection balance insufficient to explain extant genetic variation in most complex traits. The alternative hypothesis of balancing selection, wherein selection maintains genetic variation, is an aggregate of multiple mechanisms (spatial and temporal heterogeneity in selection, frequency-dependent selection, antagonistic pleiotropy, etc.). Most of these mechanisms have been demonstrated for Mendelian traits, but there is little comparable data for loci affecting quantitative characters. Here, we report a three-year field study of selection on intra-population Quantitative Trait Loci (QTL) of flower size, a highly polygenic trait of Mimulus guttatus. The QTL exhibit antagonistic pleiotropy: alleles that increase flower size reduce viability but increase fecundity. The magnitude and direction of selection fluctuates yearly and on a spatial scale of meters. This study provides direct evidence of balancing selection mechanisms on QTL of an ecologically relevant trait

Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (\u3ci\u3eMimulus guttatus\u3c/i\u3e) lineage with cryptic CMS

Despite intense investigation for over 25 years, the in vivo structure of plant mitochondrial genomes remains uncertain. Mapping studies and genome sequencing generally produce large circular chromosomes, whereas electrophoretic and microscopic studies typically reveal linear and multi-branched molecules. To more fully assess the structure of plant mitochondrial genomes, the complete sequence of the monkeyflower (Mimulus guttatus DC. line IM62) mtDNA was constructed from a large (35 kb) paired-end shotgun sequencing library to a high depth of coverage (~30x). The complete genome maps as a 525,671 bp circular molecule and exhibits a fairly conventional set of features including 62 genes (encoding 35 proteins, 24 tRNAs, 3 rRNAs), 22 introns, 3 large repeats (2.7, 9.6, 29 kb), and 96 small repeats (40–293 bp). Most paired-end reads (71%) mapped to the consensus sequence at the expected distance and orientation across the entire genome, validating the accuracy of assembly. Another 10% of reads provided clear evidence of alternative genomic conformations due to apparent rearrangements across large repeats. Quantitative assessment of these repeat-spanning read pairs revealed that all large repeat arrangements are present at appreciable frequencies in vivo, although not always in equimolar amounts. The observed stoichiometric differences for some arrangements are inconsistent with a predominant master circular structure for the mitochondrial genome of M. guttatus IM62. Finally, because IM62 contains a cryptic cytoplasmic male-sterility (CMS) system, an in silico search for potential CMS genes was undertaken. The three chimeric ORFs identified in this study, in addition to the previously identified ORFs upstream of the nad6 gene, are the most likely CMS candidate genes in this line. Includes Supplementary Information

Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (\u3ci\u3eMimulus guttatus\u3c/i\u3e) lineage with cryptic CMS

Despite intense investigation for over 25 years, the in vivo structure of plant mitochondrial genomes remains uncertain. Mapping studies and genome sequencing generally produce large circular chromosomes, whereas electrophoretic and microscopic studies typically reveal linear and multi-branched molecules. To more fully assess the structure of plant mitochondrial genomes, the complete sequence of the monkeyflower (Mimulus guttatus DC. line IM62) mtDNA was constructed from a large (35 kb) paired-end shotgun sequencing library to a high depth of coverage (~30x). The complete genome maps as a 525,671 bp circular molecule and exhibits a fairly conventional set of features including 62 genes (encoding 35 proteins, 24 tRNAs, 3 rRNAs), 22 introns, 3 large repeats (2.7, 9.6, 29 kb), and 96 small repeats (40–293 bp). Most paired-end reads (71%) mapped to the consensus sequence at the expected distance and orientation across the entire genome, validating the accuracy of assembly. Another 10% of reads provided clear evidence of alternative genomic conformations due to apparent rearrangements across large repeats. Quantitative assessment of these repeat-spanning read pairs revealed that all large repeat arrangements are present at appreciable frequencies in vivo, although not always in equimolar amounts. The observed stoichiometric differences for some arrangements are inconsistent with a predominant master circular structure for the mitochondrial genome of M. guttatus IM62. Finally, because IM62 contains a cryptic cytoplasmic male-sterility (CMS) system, an in silico search for potential CMS genes was undertaken. The three chimeric ORFs identified in this study, in addition to the previously identified ORFs upstream of the nad6 gene, are the most likely CMS candidate genes in this line. Includes Supplementary Information