ggplot2: Elegant Graphics for Data Analysis by WICKHAM, H.

Wilkinson, Leland

doi:10.1111/j.1541-0420.2011.01616.x

Cited by 5,686 publications

(6,350 citation statements)

References 5 publications

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“…Additionally, in order to investigate the relationship between median dN/dS and genomic features associated to each genome, we applied the "cor.test" function with the Spearman method. Mean comparisons and correlation plots were visualized through the ggplot2 package (Wilkinson 2011). Also, we explored the distance between epipelagic and mesopelagic Marinimicrobia genomes employing the genomic features and median dN/dS values through a PCA analysis with the "prcomp" function available on R. Euclidean distance was visualized using the "ggbiplot" function within the ggplot2 package (Wilkinson 2011).…”

Section: Marinimicrobia Genomes Distribution and Statistical Analysesmentioning

confidence: 99%

Strong Purifying Selection Contributes to Genome Streamlining in Epipelagic Marinimicrobia

Martínez-Gutiérrez¹,

Aylward²

2019

Preprint

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Marine microorganisms inhabiting nutrient-depleted waters play critical roles in global biogeochemical cycles due to their abundance and broad distribution. Many of these microbes share similar genomic features including small genome size, low % G+C content, short intergenic regions, and low nitrogen content in encoded amino acids, but the evolutionary drivers of these characteristics are unclear. Here we compared the strength of purifying selection across the Marinimicrobia, a candidate phylum which encompasses a broad range of phylogenetic groups with disparate genomic features, by estimating the ratio of non-synonymous and synonymous substitutions (dN/dS) in conserved marker genes. Our analysis shows significantly lower dN/dS values in epipelagic Marinimicrobia that exhibit features consistent with genome streamlining when compared to their mesopelagic counterparts. We found a significant positive correlation between median dN/dS values and genomic traits associated to streamlined organisms, including % G+C content, genome size, and intergenic region length. Our findings are consistent with genome streamlining theory, which postulates that small, compact genomes with low G+C contents are adaptive and the product of strong purifying selection. Our results are also in agreement with previous findings that genome streamlining is common in epipelagic waters, suggesting that genomes inhabiting this region of the ocean have been shaped by strong selection together with prevalent nutritional constraints characteristic of this environment.

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Section: Marinimicrobia Genomes Distribution and Statistical Analysesmentioning

confidence: 99%

Strong Purifying Selection Contributes to Genome Streamlining in Epipelagic Marinimicrobia

Martínez-Gutiérrez¹,

Aylward²

2019

Preprint

View full text Add to dashboard Cite

show abstract

“…The correlation matrix and the significance test were visualized by R function "corrplot" [55]. Pie chart, donut chart, violin plot, box plot, heatmap, bar chart and circle bar chart were plotted using ggplot2 [56].…”

Section: Bioinformatics Analysis and Statistical Analysismentioning

confidence: 99%

The microbiome of captive hamadryas baboon

Trivedi

Brejnrod

et al. 2020

Preprint

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Hamadryas baboon is a highly social primate that lives in complex multilevel societies exhibiting a wide range of group behaviors akin to humans. Here, we report the comprehensive 16s rRNA gene analyses of groupliving baboon microbiota across different body sites. Additionally, we compared the baboon and human microbiome of the oral cavity, gut and vagina. Our analyses show that the baboon microbiome is distinct from the human and baboon cohabitants share similar microbial profiles in multiple body sites. The oral, gut and vagina shared more bacterial ASVs in group-living baboons than in humans. The shared ASVs in baboons had significantly positive correlations, suggesting a potential bacterial exchange throughout the body. No significant differences in baboon gut microbiome composition within the maternity line and between maternity lines were detected, suggesting that the offspring acquire their gut microbiota primarily through bacterial exchange among cohabitants. Besides, Lactobacillus was not so predominant in baboon vagina as in the human vagina but was the most abundant genus in baboon gut. These data and findings can form the basis of future microbiome studies in baboons and be used as a reference to research where the microbiome is expected to impact human modeling with baboons.

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“…We used Kendall's τ correlation coefficient to compare the association between increasing bin number and corresponding d N /d S (coding) and substitution rates (non-coding) for each gene. Statistical analysis was conducted using the scipy library in Python, and graphs were produced using the 'tidyverse' package in R (Wilkinson 2011) and the 'matplotlib' package in Python. Phylogenies were produced using the 'phytools' package in R (Revell 2012).…”

Section: Phenotype and Pathway Ontologies Protein Databases And Statmentioning

confidence: 99%

Noncoding regions underpin avian bill shape diversification at macroevolutionary scales

Yusuf

Heatley

Palmer

et al. 2019

Preprint

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AbstractRecent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence and speciation, as a model trait. We integrate class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1,434 protein coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. They are associated with embryonic stem cells pathways, including BMP and Wnt signalling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a genome wide scale over macroevolutionary time is feasible. While the coding and noncoding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to noncoding loci. Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times.

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ggplot2: Elegant Graphics for Data Analysis by WICKHAM, H.

Cited by 5,686 publications

References 5 publications

Strong Purifying Selection Contributes to Genome Streamlining in Epipelagic Marinimicrobia

Strong Purifying Selection Contributes to Genome Streamlining in Epipelagic Marinimicrobia

The microbiome of captive hamadryas baboon

Noncoding regions underpin avian bill shape diversification at macroevolutionary scales

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