Differential strengths of selection on S-RNases from Physalis and Solanum (Solanaceae)

<p>Abstract</p> <p>Background</p> <p>The S-RNases of the Solanaceae are highly polymorphic self-incompatibility (S-) alleles subject to strong balancing selection. Relatively recent diversification of S-alleles has occurred in the genus <it>Physalis </it>following a historical restriction of S-allele diversity. In contrast, the genus <it>Solanum </it>did not undergo a restriction of S-locus diversity and its S-alleles are generally much older. Because recovery from reduced S-locus diversity should involve increased selection, we employ a statistical framework to ask whether S-locus selection intensities are higher in <it>Physalis </it>than <it>Solanum</it>. Because different S-RNase lineages diversify in <it>Physalis </it>and <it>Solanum</it>, we also ask whether different sites are under selection in different lineages.</p> <p>Results</p> <p>Maximum-likelihood and Bayesian coalescent methods found higher intensities of selection and more sites under significant positive selection in the 48 <it>Physalis </it>S-RNase alleles than the 49 from <it>Solanum</it>. Highest posterior densities of dN/dS (ω) estimates show that the strength of selection is greater for <it>Physalis </it>at 36 codons. A nested maximum likelihood method was more conservative, but still found 16 sites with greater selection in <it>Physalis</it>. Neither method found any codons under significantly greater selection in <it>Solanum</it>. A random effects likelihood method that examines data from both taxa jointly confirmed higher selection intensities in <it>Physalis</it>, but did not find different proportions of sites under selection in the two datasets. The greatest differences in strengths of selection were found in the most variable regions of the S-RNases, as expected if these regions encode self-recognition specificities. Clade-specific likelihood models indicated some codons were under greater selection in background <it>Solanum </it>lineages than in specific lineages of <it>Physalis </it>implying that selection on sites may differ among lineages.</p> <p>Conclusions</p> <p>Likelihood and Bayesian methods provide a statistical approach to testing differential selection across populations or species. These tests appear robust to the levels of polymorphism found in diverse S-allele collections subject to strong balancing selection. As predicted, the intensity of selection at the S-locus was higher in the taxon with more recent S-locus diversification. This is the first confirmation by statistical test of differing selection intensities among self-incompatibility alleles from different populations or species.</p

Drop on a Bent Fibre

Inspired by the huge droplets attached on cypress tree leaf tips after rain, we find that a bent fibre can hold significantly more water in the corner than a horizontally placed fibre (typically up to three times or more). The maximum volume of the liquid that can be trapped is remarkably affected by the bending angle of the fibre and surface tension of the liquid. We experimentally find the optimal included angle ($\sim {36}{^\circ}$) that holds the most water. Analytical and semi-empirical models are developed to explain these counter-intuitive experimental observations and predict the optimal angle. The data and models could be useful for designing microfluidic and fog harvesting devices

Phylogenetic Signal Variation in the Genomes of Medicago (Fabaceae)

Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, then aligned these sequences to the Medicago truncatula reference genome to confidently identify 87 596 variable homologous sites. We used this data set to estimate phylogenetic relationships among Medicago species, to investigate the number of sites needed to provide robust phylogenetic estimates and to identify specific genomic regions supporting topologies in conflict with the genome-wide phylogeny. Our full genomic data set resolves relationships within the genus that were previously intractable. Subsampling the data reveals considerable variation in phylogenetic signal and power in smaller subsets of the data. Even when sampling 5000 sites, no random sample of the data supports a topology identical to that of the genome-wide phylogeny. Phylogenetic relationships estimated from 500-site sliding windows revealed genome regions supporting several alternative species relationships among recently diverged taxa, consistent with the expected effects of deep coalescence or introgression in the recent history of Medicago. [Medicago; phylogenomics; whole-genome resequencing.

Genome assembly and annotation ofArabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology

The self-incompatible species Arabidopsis halleri is a close relative of the self-compatible model plant Arabidopsis thaliana. The broad European and Asian distribution and heavy metal hyperaccumulation ability makes A. halleri a useful model for ecological genomics studies.We used long-insert mate-pair libraries to improve the genome assembly of the A. halleri ssp.gemmifera Tada mine genotype (W302) collected from a site with high contamination by heavy metals in Japan. After five rounds of forced selfing, heterozygosity was reduced to 0.04%, which facilitated subsequent genome assembly. Our assembly now covers 196 Mb or 78% of the estimated genome size and achieved scaffold N50 length of 712 kb. To validate assembly and annotation, we used synteny of A. halleri Tada mine with a previously published high quality reference assembly of a closely related species, Arabidopsis lyrata. Further validation of the assembly quality comes from synteny and phylogenetic analysis of the HEAVY METAL ATPASE4 (HMA4) and METAL TOLERANCE PROTEIN1 (MTP1) regions using published sequences from European A. halleri for comparison. Three tandemly duplicated copies of HMA4, key gene involved in cadmium and zinc hyperaccumulation, were assembled on a single scaffold.The assembly will enhance the genome-wide studies of A. halleri as well as the allopolyploid Arabidopsis kamchatica derived from A. lyrata and A. halleri

Fine-Scale Population Recombination Rates, Hotspots, and Correlates of Recombination in the Medicago truncatula Genome

Recombination rates vary across the genome and in many species show significant relationships with several genomic features, including distance to the centromere, gene density, and GC content. Studies of fine-scale recombination rates have also revealed that in several species, there are recombination hotspots, that is, short regions with recombination rates 10–100 greater than those in surrounding regions. In this study, we analyzed whole-genome resequence data from 26 accessions of the model legume Medicago truncatula to gain insight into the genomic features that are related to high- and low-recombination rates and recombination hotspots at 1 kb scales. We found that high-recombination regions (1-kb windows among those in the highest 5% of the distribution) on all three chromosomes were significantly closer to the centromere, had higher gene density, and lower GC content than low-recombination windows. High-recombination windows are also significantly overrepresented among some gene functional categories—most strongly NB–ARC and LRR genes, both of which are important in plant defense against pathogens. Similar to high-recombination windows, recombination hotspots (1-kb windows with significantly higher recombination than the surrounding region) are significantly nearer to the centromere than nonhotspot windows. By contrast, we detected no difference in gene density or GC content between hotspot and nonhotspot windows. Using linear model wavelet analysis to examine the relationship between recombination and genomic features across multiple spatial scales, we find a significant negative correlation with distance to the centromere across scales up to 512 kb, whereas gene density and GC content show significantly positive and negative correlations, respectively, only up to 64 kb. Correlations between recombination and genomic features, particularly gene density and polymorphism, suggest that they are scale dependent and need to be assessed at scales relevant to the evolution of those features

Evolutionary Genetics of an S-Like Polymorphism in Papaveraceae with Putative Function in Self-Incompatibility

Papaver rhoeas possesses a gametophytic self-incompatibility (SI) system not homologous to any other SI mechanism characterized at the molecular level. Four previously published full length stigmatic S-alleles from the genus Papaver exhibited remarkable sequence divergence, but these studies failed to amplify additional S-alleles despite crossing evidence for more than 60 S-alleles in Papaver rhoeas alone.Using RT-PCR we identified 87 unique putative stigmatic S-allele sequences from the Papaveraceae Argemone munita, Papaver mcconnellii, P. nudicuale, Platystemon californicus and Romneya coulteri. Hand pollinations among two full-sib families of both A. munita and P. californicus indicate a strong correlation between the putative S-genotype and observed incompatibility phenotype. However, we also found more than two S-like sequences in some individuals of A. munita and P. californicus, with two products co-segregating in both full-sib families of P. californicus. Pairwise sequence divergence estimates within and among taxa show Papaver stigmatic S-alleles to be the most variable with lower divergence among putative S-alleles from other Papaveraceae. Genealogical analysis indicates little shared ancestral polymorphism among S-like sequences from different genera. Lack of shared ancestral polymorphism could be due to long divergence times among genera studied, reduced levels of balancing selection if some or all S-like sequences do not function in incompatibility, population bottlenecks, or different levels of recombination among taxa. Preliminary estimates of positive selection find many sites under selective constraint with a few undergoing positive selection, suggesting that self-recognition may depend on amino acid substitutions at only a few sites.Because of the strong correlation between genotype and SI phenotype, sequences reported here represent either functional stylar S-alleles, tightly linked paralogs of the S-locus or a combination of both. The considerable complexity revealed in this study shows we have much to learn about the evolutionary dynamics of self-incompatibility systems

Corporate Governance for Sustainability

The current model of corporate governance needs reform. There is mounting evidence that the practices of shareholder primacy drive company directors and executives to adopt the same short time horizon as financial markets. Pressure to meet the demands of the financial markets drives stock buybacks, excessive dividends and a failure to invest in productive capabilities. The result is a ‘tragedy of the horizon’, with corporations and their shareholders failing to consider environmental, social or even their own, long-term, economic sustainability. With less than a decade left to address the threat of climate change, and with consensus emerging that businesses need to be held accountable for their contribution, it is time to act and reform corporate governance in the EU. The statement puts forward specific recommendations to clarify the obligations of company boards and directors and make corporate governance practice significantly more sustainable and focused on the long term

Patterns of polymorphism, recombination, and selection in Medicago truncatula

Resequencing of natural accessions of Medicago truncatula has enabled evolutionary analyses using population genomics to estimate genome wide patterns of diversity, recombination rates, and quantifying positive and purifying selection. The patterns of genome wide diversity and linkage disequilibrium (LD) in M. truncatula largely resembles genome wide patterns for the model species Arabidopsis thaliana. Nucleotide diversity in 100 kilobase (kb) windows was negatively correlated with gene density, as expected if diversity is shaped by selection acting against slightly deleterious mutations. The population-scaled recombination rate is approximately one third that of the mutation rate, consistent with expectations for a species with a high selfing rate. LD, however, is not extensive and therefore the low recombination rate is not likely a major constraint to adaptation. Fine scale recombination rate analysis revealed that high recombination regions on three well covered chromosomes were significantly closer to the centromere, had higher gene density, and lower GC content than low recombination windows. High recombination regions are also significantly over-represented among a few functional gene categories including NB-ARC and LRR genes, both of which are important in plant defense against pathogens. Based upon patterns of intraspecific diversity and interspecific divergence in 20 000 coding sequences, approximately 50–75% of the genic region appears to be under purifying selection. Estimates of the distribution of fitness effects (DFE) indicated that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (non-expressed). Genes expressed in only a single tissue and non-expressed genes show significantly greater proportions of neutral mutations. Together, genome wide analyses of genetic diversity, recombination, and selection has identified several interesting genomic regions and genes that have unique evolutionary patterns which may be relevant for agriculturally important legumes

Evolutionary genetics of self-incompatibility in solanaceae and papaveraceae

Flowering plants are able to avoid inbreeding by several genetically based mechanisms. Gametophytic self- incompatibility (GSI) occurs when pollen is rejected in the style or on the stigma if it possesses a matching allele with either of the ovule parent's S-alleles. This mechanism typically involves a single genetic locus that is highly polymorphic within populations and species. S- alleles are maintained by strong negative frequency dependent selection that essentially favors alleles when they become rare in a population. This type of balancing selection preserves variation at the S-locus for millions of years enabling us to infer ancient demographic patterns through phylogenetic analyses of genealogies of S-alleles. GSI has been described in several taxa of Solanaceae but only one genus of Papaveraceae, the genus Papaver. Although the molecular mechanisms of self-recognition in these respective families differ remarkably, the underlying theoretical predictions regarding their genetics and evolution are expected to be similar. In Chapter I of this dissertation, I first explore the evolutionary history of a genetic bottleneck in the Solanaceae. Self-incompatible species in the sister genera Physalis and Witheringia share restricted variation at the S-locus indicative of an ancient bottleneck that occurred in a common ancestor. Using phylogenic approaches to look at S-allele variation in species of the subtribe Iochrominae, the clade containing Physalis and Witheringia, we are able to determine when this bottleneck event occurred. We then use two chloroplast markers, fossil calibrations and a Bayesian relaxed molecular clock approach to determine the approximate date of the bottleneck. In Chapter II, I examine the molecular evolution of individual codons from S-alleles from the bottlenecked lineages of Physalis compared to those of the non-bottlenecked lineages of Solanum. Because Physalis S- RNases appear to have diversified more recently than those of Solanum, we find significantly different patterns among amino acids undergoing positive selection using maximum likelihood phylogenetic and Bayesian coalescent methods. (increase in subst. at 4 fold degenerate sites or 3rd position (general synonymous relative to 1-2nd pos.) HyPhy.docs, overall dS increase in Physalis relative to Solanum; overall increase in dN in Physalis?). In Chapter III, I explore the genetics of a putative S-locus polymorphism in three previously uncharacterized species of Papaveraceae native to California. Analyses of putative S-allele sequences from A. munita , P. californicus and Romneya coulteri sampled from natural populations have shown that each harbors substantial genetic polymorphism homologous to stylar S-alleles from Papaver rhoeas. These genes appear to be expressed only in female reproductive tissues as expected for stylar S-locus products. In A. munita and P. californicus, greenhouse crosses among full sibs with matching putative S-genotypes usually don't result in seed set while crosses among individuals with non-matching genotypes almost always do. In addition, potential duplications at or near this locus have been detected in diploid P. californicus. Contrary to other well known SI systems, allelic genealogies from Papaveraceae show a general pattern of monophyletic clustering according to species. Genealogies of these species' S-alleles and those from newly sequenced Papaver alleles show general patterns of monophyletic clustering. The reduced levels of trans-specific polymorphism may be explained by founder events or population bottlenecks in each of the species, though other possibilities must also be considered. We also employ maximum likelihood models to estimate positive selection among putative alleles from these tax