Recent studies comparing genome-wide polymorphism and divergence in Drosophila have found evidence for a surprisingly high proportion of adaptive amino acid fixations, but results for other taxa are ...mixed. In particular, few studies have found convincing evidence for adaptive amino acid substitution in plants. To assess the generality of this finding, we have sequenced 257 loci in the outcrossing crucifer Capsella grandiflora, which has a large effective population size and low population structure. Using a new method that jointly infers selective and demographic effects, we estimate that 40% of amino acid substitutions were fixed by positive selection in this species, and we also infer a low proportion of slightly deleterious amino acid mutations. We contrast these estimates with those for a similar data set from the closely related Arabidopsis thaliana and find significantly higher rates of adaptive evolution and fewer nearly neutral mutations in C. grandiflora. In agreement with results for other taxa, genes involved in reproduction show the strongest evidence for positive selection in C. grandiflora. Taken together, these results imply that both positive and purifying selection are more effective in C. grandiflora than in A. thaliana, consistent with the contrasting demographic history and effective population sizes of these species.
Genome size varies by many orders of magnitude across plants and animals, but resolving the most important evolutionary forces driving this variation remains challenging. Since eukaryotic genome size ...variation is not associated with complexity, genetic drift of the amount of noncoding DNA could dominate, implicating population and species history as key drivers of shifts in DNA content. Alternatively, directional selection could be acting on DNA content, but if so, it has not been resolved which level of selection is most important. Since the predominant component of many eukaryotic genomes is comprised of selfish genetic elements such as transposable elements (TEs) and regions subject to meiotic drive, factors that influence their differential success across populations and species could account for much of the variation in genome size. 6 add to this rich literature by using a quantitative genetics framework to conduct a test of local adaptation, recognizing that genome size is a trait governed by an immense number of small-effect loci. ...it can be thought of as a quantitative trait under complete genetic control, since the variation in genome size is expected to be a simple function of the net number of insertion and deletion alleles individuals have across the genome. Conversely, other selective pressures on selfish genetic elements may provide an additional source of genome size variation in maize populations beyond the effects of flowering time. Since chromosomal knobs are known to have severe fitness costs, the extent of these costs may well depend on the environment 22, possibly explaining the disproportionate effect of altitude on knobs when genome size is controlled for in this study.
Abstract
Mutation rate estimates for vegetatively reproducing organisms are rare, despite their frequent occurrence across the tree of life. Here we report mutation rate estimates in two vegetatively ...reproducing duckweed species, Lemna minor and Spirodela polyrhiza. We use a modified approach to estimating mutation rates by taking into account the reduction in mutation detection power that occurs when new individuals are produced from multiple cell lineages. We estimate an extremely low per generation mutation rate in both species of duckweed and note that allelic coverage at de novo mutation sites is very skewed. We also find no substantial difference in mutation rate between mutation accumulation lines propagated under benign conditions and those grown under salt stress. Finally, we discuss the implications of interpreting mutation rate estimates in vegetatively propagating organisms.
Species in the Drosophila and Arabidopsis species groups share the feature of having relatively small, streamlined genomes. In Drosophila, evidence for pervasive negative and positive selection is ...overturning long-held views about the functional significance of noncoding DNA, the frequency of positive selection, and the extent to which coding and noncoding polymorphism and divergence between species is neutral. However, despite sharing some similarities with Drosophila, Arabidopsis shows quite distinct patterns of selective constraint and positive selection. Two conspicuous differences between these species groups are their effective population sizes and population structure, which may explain lower levels of selective constraint in coding and noncoding DNA of Arabidopsis, more evidence for balancing selection and less evidence for canonical signature of positive selection than in Drosophila species. As more comparative genomic data accumulate in the Arabidopsis group, the combination of polymorphism and divergence data allow these initial contrasts to be quantified on a genomic scale.
Our knowledge of recombination rates and patterns in plants is far from being comprehensive. However, compelling evidence indicates a central role for recombination, through its influences on ...mutation and selection, in the evolution of plant genomes. Furthermore, recombination seems to be generally higher and more variable in plants than in animals, which could be one of the primary reasons for differences in genome lability between these two kingdoms. Much additional study of recombination in plants is needed to investigate these ideas further.
population genomics of plant adaptation Siol, Mathieu; Wright, Stephen I.; Barrett, Spencer C. H.
The New phytologist,
October 2010, Letnik:
188, Številka:
2
Journal Article
Recenzirano
Odprti dostop
There has been an enormous increase in the amount of data on DNA sequence polymorphism available for many organisms in the last decade. New sequencing technologies provide great potential for ...investigating natural selection in plants using population genomic approaches. However, plant populations frequently show significant departures from the assumptions of standard models used to detect selection and many forms of directional selection do not fit with classical population genetics theory. Here, we explore the extent to which plant populations show departures from standard model assumptions, and the implications this has for detecting selection on molecular variation. A growing number of multilocus studies of nucleotide variation suggest that changes in population size, particularly bottlenecks, and strong subdivision may be common in plants. This demographic variation presents important challenges for models used to infer selection. In addition, selection from standing genetic variation and multiple independent adaptive substitutions can further complicate efforts to understand the nature of selection. We discuss emerging patterns from plant studies and propose that, rather than treating population history as a nuisance variable when testing for selection, the interaction between demography and selection is of fundamental importance for evolutionary studies of plant populations using molecular data.
Patterns of Selection in Plant Genomes Hough, Josh; Williamson, Robert J.; Wright, Stephen I.
Annual review of ecology, evolution, and systematics,
01/2013, Letnik:
44, Številka:
1
Journal Article
Recenzirano
Plants show a wide range of variation in mating system, ploidy level, and demographic history, allowing for unique opportunities to investigate the evolutionary and genetic factors affecting ...genome-wide patterns of positive and negative selection. In this review, we highlight recent progress in our understanding of the extent and nature of selection on plant genomes. We discuss differences in selection as they relate to variation in demography, recombination, mating system, and ploidy. We focus on the population genetic consequences of these factors and argue that, although variation in the magnitude of purifying selection is well documented, quantifying rates of positive selection and disentangling the relative importance of recombination, demography, and ploidy are ongoing challenges. Large-scale comparative studies that examine the relative and joint importance of these processes, combined with explicit models of population history and selection, are key and feasible goals for future work.
Spontaneous plastome mutants have been used as a research tool since the beginning of genetics. However, technical restrictions have severely limited their contributions to research in physiology and ...molecular biology. Here, we used full plastome sequencing to systematically characterize a collection of 51 spontaneous chloroplast mutants in Oenothera (evening primrose). Most mutants carry only a single mutation. Unexpectedly, the vast majority of mutations do not represent single nucleotide polymorphisms but are insertions/deletions originating from DNA replication slippage events. Only very few mutations appear to be caused by imprecise double-strand break repair, nucleotide misincorporation during replication, or incorrect nucleotide excision repair following oxidative damage. U-turn inversions were not detected. Replication slippage is induced at repetitive sequences that can be very small and tend to have high A/T content. Interestingly, the mutations are not distributed randomly in the genome. The underrepresentation of mutations caused by faulty double-strand break repair might explain the high structural conservation of seed plant plastomes throughout evolution. In addition to providing a fully characterized mutant collection for future research on plastid genetics, gene expression, and photosynthesis, our work identified the spectrum of spontaneous mutations in plastids and reveals that this spectrum is very different from that in the nucleus.
On the Trail of Linked Selection Josephs, Emily B; Wright, Stephen I
PLoS genetics,
08/2016, Letnik:
12, Številka:
8
Journal Article
Recenzirano
Odprti dostop
Since this alternative mechanism was first proposed, understanding the relative importance of positive and negative selection on linked neutral diversity has been an ongoing challenge in population ...genetics 7. While Elyashiv et al.\n However, this method's use of synonymous substitutions as a neutral control may not be effective in larger genomes, in which nonsynonymous substitutions may be more common in regions of low constraint, reduced background selection, and higher neutral diversity, masking the signals of selective sweeps 24. Because Elyashiv et al.'s 1 method can use the distribution of selected sites present in the actual genome under investigation, it may be more robust to variation in constraint across the genome and be useful for investigating linked selection in large genomes.
Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of their evolutionary history: the extent of ...parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 19 agricultural populations of common waterhemp (
), which we show to have undergone a massive expansion over the past century, with a contemporary effective population size estimate of 8 x 10
. We found variation at seven characterized TSR loci, two of which had multiple amino acid substitutions, and three of which were common. These three common resistance variants show extreme parallelism in their mutational origins, with gene flow having shaped their distribution across the landscape. Allele age estimates supported a strong role of adaptation from de novo mutations, with a median age of 30 suggesting that most resistance alleles arose soon after the onset of herbicide use. However, resistant lineages varied in both their age and evidence for selection over two different timescales, implying considerable heterogeneity in the forces that govern their persistence. Two such forces are intra- and inter-locus allelic interactions; we report a signal of extended haplotype competition between two common TSR alleles, and extreme linkage with genome-wide alleles with known functions in resistance adaptation. Together, this work reveals a remarkable example of spatial parallel evolution in a metapopulation, with important implications for the management of herbicide resistance.
PDF
