Araxi O Urrutia

• PhD at University of Bath
• Lecturer at University of Bath

Evolution has shaped the diversity of life on Earth for billions of years. Proposed by Charles Darwin in 1859, natural and sexual selection have emerged as important drivers in this process. Sexual selection — especially evident in mammals and birds— drives extreme differences between sexes in physical and behavioral traits. Recent studies have exp...

In mammals, sexual size dimorphism often reflects the intensity of sexual selection, yet its connection to genomic evolution remains unexplored. Gene family size evolution can reflect shifts in the relative importance of different molecular functions. Here, we investigate the associate between brain development gene repertoire to sexual size dimorp...

Gut microbiotas have important impacts on host health, reproductive success, and survival. While extensive research in mammals has identified the exogenous (e.g. environment) and endogenous (e.g. phylogeny, sex and age) factors that shape the gut microbiota composition and functionality, yet avian systems remain comparatively less understood. Shore...

Gut microbiotas have important impacts on host health, reproductive success, and survival. While extensive research in mammals has identified the exogenous (e.g. environment) and endogenous (e.g. phylogeny, sex, and age) factors that shape the gut microbiota composition and functionality, yet avian systems remain comparatively less understood. Shor...

Sexual selection has long been thought to promote speciation, but evidence is inconclusive. In Odonata - which includes dragonflies and damselflies-, wing pigmentation has been found to be influenced by sexual selection. Past evidence shows that wing pigmentation in males is a driver of speciation in damselflies. However, whether sexual dimorphism...

Indices of morphological disparity seek to summarise the highly multivariate morphological variation across groups of species within clades, time bins or other groups. Morphological variation can be quantified using geometric morphometric, outline or surface-based methods. These are most effective when morphological differences are relatively modes...

Sexual selection has long been thought to promote speciation, but evidence is inconclusive. In Odonata - which includes dragonflies and damselflies-, wing pigmentation has been found to be influenced by sexual selection. Past evidence shows that wing pigmentation in males is a driver of speciation in damselflies. However, whether sexual dimorphism...

Females and males often exhibit different survival in nature, and it has been hypothesized that sex chromosomes may play a role in driving differential survival rates. For instance, the Y chromosome in mammals and the W chromosome in birds are often degenerated, with reduced numbers of genes, and loss of the Y chromosome in old men is associated wi...

Males and females often exhibit differences in behaviour, life histories and ecology, many of which typically are reflecting in their brains. Neuronal protection and maintenance include complex processes led by the microglia, which also interacts with metabolites such as hormones or immune components. Despite increasing interest in sex-specific bra...

• In dragonflies, species richness shows a marked variation between lineages. Species diversification in this lineage has been linked with habitat variation, but the role of other factors, such as wing pigmentation, arguably one of the most conspicuous traits in dragonflies, have not yet been explored. • In this study, using novel methodology that...

Selection leaves signatures in the DNA sequence of genes, with many test statistics devised to detect its action. While these statistics are frequently used to support hypotheses about the adaptive significance of particular genes, the effect these genes have on reproductive fitness is rarely quantified experimentally. Consequently, it is unclear h...

Transcriptomes are known to organize themselves into gene co-expression clusters or modules where groups of genes display distinct patterns of coordinated or synchronous expression across independent biological samples. The functional significance of these co-expression clusters is suggested by the fact that highly coexpressed groups of genes tend...

Alzheimer’s disease (AD)-related degenerative decline is associated to the presence of amyloid beta (Aβ) plaque lesions and neuro fibrillary tangles (NFT). However, the precise molecular mechanisms linking Aβ deposition and neurological decline are still unclear. Here we combine genome-wide transcriptional profiling of the insular cortex of 3xTg-AD...

Background: Vertebrates exhibit diverse sex determination systems and reptiles stand out by having highly variable sex determinations that include temperature-dependent and genotypic sex determination (TSD and GSD, respectively). Theory predicts that populations living in either highly variable or cold climatic conditions should evolve genotypic s...

Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups....

Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups....

Understanding how incipient species are maintained with gene flow is a fundamental question in evolutionary biology. Whole genome sequencing of multiple individuals holds great potential to illustrate patterns of genomic differentiation as well as the associated evolutionary histories. Kentish (Charadrius alexandrinus) and the white-faced (C. dealb...

Understanding how incipient species are maintained with gene flow is a fundamental question in evolutionary biology. Whole genome sequencing of multiple individuals holds great potential to illustrate patterns of genomic differentiation as well as the associated evolutionary histories. Kentish (Charadrius alexandrinus) and the white-faced (C. dealb...

Social monogamy, typically characterized by the formation of a pair bond, increased territorial defense, and often biparental care, has independently evolved multiple times in animals. Despite the independent evolutionary origins of monogamous mating systems, several homologous brain regions and neuropeptides and their receptors have been shown to...

Different cell types have different postmitotic maintenance requirements. Nerve cells, however, are unique in this respect as they need to survive and preserve their functional complexity for the entire lifetime of the organism, and failure at any level of their supporting mechanisms leads to a wide range of neurodegenerative conditions. Whether th...

A fundamental question in biology is how the extraordinary range of living organisms arose. In this theme issue, we celebrate how evolutionary studies on the origins of morphological diversity have changed over the past 350 years since the first publication of the Philosophical Transactions of The Royal Society . Current understanding of this topic...

Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative spli...

Increased brain size is thought to have played an important role in the evolution of mammals and is a highly variable trait across lineages. Variations in brain size are closely linked to corresponding variations in the size of the neocortex, a distinct mammalian evolutionary innovation. The genomic features that explain and/or accompany variations...

Background: During early development of the nervous system, gene expression patterns are known to vary widely depending on the specific developmental trajectories of different structures. Observable changes in gene expression profiles throughout development are determined by an underlying network of precise regulatory interactions between individu...

Table S1 Genome sequence versions. Table S2 Drosophila and primate genes orthology relationships. Table S3 SHRiMP default parameters used for short read alignment. Table S4 Orthologous gene detection using alternative annotation strategies for total sequences (total) and single‐match sequences (SM). Table S5 GO slim terms with zero gene detecti...

Increased brain size is thought to have played an important role in the evolution of mammals and is a highly variable trait across lineages. Variations in brain size are closely linked to corresponding variations in the size of the neocortex, a distinct mammalian evolutionary innovation. The genomic features that explain and/or accompany variations...

Next generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA-seq annotation methods using reference genomes from related species have yet to be robustly characterised...

Genomic and transcriptomics analyses have revealed human head and body lice to be almost genetically identical; although con-specific, they nevertheless occupy distinct ecological niches and have differing feeding patterns. Most importantly, while head lice are not known to be vector competent, body lice can transmit three serious bacterial disease...

Rapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the 'edges' of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the...

Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of...

What at the genomic level underlies organism complexity? Although several genomic features have been associated with organism complexity, in the case of alternative splicing, which has long been proposed to explain the variation in complexity, no such link has been established. Here, we analyzed over 39 million expressed sequence tags available for...

Genomic determinants underlying increased encephalization across mammalian lineages are unknown. Whole genome comparisons have revealed large and frequent changes in the size of gene families, and it has been proposed that these variations could play a major role in shaping morphological and physiological differences among species. Using a genome-w...

The control of RNA splicing is often modulated by exonic motifs near splice sites. Chief amongst these are exonic splice enhancers (ESE). Well described ESEs in mammals are purine rich and cause predictable skews in codon and amino acid usage towards exonic ends. Looking across species, those with relatively abundant intronic sequence are those wit...

The sequencing of multiple genomes of the same plant species has revealed polymorphic gene and exon loss. Genes associated with disease resistance are overrepresented among those showing structural variations, suggesting an adaptive role for gene and exon presence–absence variation (PAV). To shed light on the possible functional relevance of polymo...

In female mammals most X-linked genes are subject to X-inactivation. However, in humans some X-linked genes escape silencing, these escapees being candidates for the phenotypic aberrations seen in polyX karyotypes. These escape genes have been reported to be under stronger purifying selection than other X-linked genes. While it is known that escape...

The control of RNA splicing is often modulated by exonic motifs near splice sites. Chief amongst these are exonic splice enhancers (ESE). Well described ESEs in mammals are purine rich and cause predictable skews in codon and amino acid usage towards exonic ends. Looking across species, those with relatively abundant intronic sequence are those wit...

Alternative splicing (AS) is a common posttranscriptional process in eukaryotic organisms, by which multiple distinct functional transcripts are produced from a single gene. The release of the human genome draft revealed a much smaller number of genes than anticipated. Because of its potential role in expanding protein diversity, interest in altern...

Large brains relative to body size represent an evolutionarily costly adaptation as they are metabolically expensive and demand substantial amounts of time to reach structural and functional maturity thereby exacerbating offspring mortality while delaying reproductive age. In spite of its cost and adaptive impact, no genomic features linked to brai...

Recent genome-wide analyses have detected numerous cancer-specific alternative splicing (AS) events. Whether transcripts containing cancer-specific AS events are likely to be translated into functional proteins or simply reflect noisy splicing, thereby determining their clinical relevance, is not known. Here we show that consistent with a noisy-spl...

Groups represent the 20% most highly, least highly, and medium expressed genes for peak and breadth. Points for 'high' and 'low' groups significantly different from medium expression levels (Student's t-tests using Bonferroni correction) are represented by closed circles. Each point represents the Alu content in sliding windows of 1 kb (moving 200...

From left to right and top to bottom: differences in total breadth; number of switches from expressed to non-expressed; differences in peak of expression; quantitative expression divergence assessed as correlation coefficients between orthologous pairs; and quantitative expression divergence, assessed as Euclidean distances between orthologous pair...

From top to bottom, each panel shows the following: difference in breadth of expression; number of switches from expressed to non-expressed; ranked peak of expression difference; expression intensity divergence estimated by using correlation coefficients as measure of distance; and expression intensity divergence estimated by using Euclidean distan...

From left to right and top to bottom: differences in total breadth; number of switches from expressed to non-expressed; differences in peak of expression; quantitative expression divergence, assessed as Euclidean distances between orthologous pairs; and quantitative expression divergence, assessed as correlation coefficients between orthologous pai...

Of all repetitive elements in the human genome, Alus are unusual in being enriched near to genes that are expressed across a broad range of tissues. This has led to the proposal that Alus might be modifying the expression breadth of neighboring genes, possibly by providing CpG islands, modifying transcription factor binding, or altering chromatin s...

In diverse organisms, neighbouring genes in the genome tend to be positively coexpressed more than expected by chance. When the similarity of transcription regulation is controlled for, adjacent genes have much higher coexpression rates than unlinked genes, supporting a role for chromatin modelling. Consequently, many incidences of low-to-moderate...

It is often supposed that a protein's rate of evolution and its amino acid content are determined by the function and anatomy of the protein. Here we examine an alternative possibility, namely that the requirement to specify in the unprocessed RNA, in the vicinity of intron-exon boundaries, information necessary for removal of introns (e.g., exonic...

Plot of Standardised Residuals for the Regression of AC Content Versus rho Grey lines indicate top and bottom 95% confidence intervals. (41 KB DOC)

Periodicity Analysis of Glycine and Proline For (A) glycine and (B) proline the distribution of homologous residues in the flanking sequence was determined. The first such residue in the sequence was taken as the reference point 0; once frequency data for the same amino acid were obtained, for the 150 flanking residues, the reference point moved al...

Trends in Relative Levels of Amino Acid Usage as a Function of the Distance from Intron–Exon Boundaries at Both 5′ and 3′ Ends (183 KB PDF)

Correlations and Partial Correlations between Rate of Protein Evolution (KA or KA/KS), Proportion of Sequence within 50, 70, or 100 bp of an Intron–Exon Junction, and Measures of Expression of the Relevant Gene in Mouse (36 KB DOC)

Relationship between Slope of Regression Line (between Proportion of Amino Acid and Distance from Boundary) and HPI Score For (A) 5′ and (B) 3′ ends. (47 KB DOC)

Relationship between the Correlation between Proportion of Amino Acid and Distance from Boundary (rho) and the Mean of HPI and DPI For (A) 5′ and (B) 3′ ends. (43 KB DOC)

Glycine Usage as a Function of Frame of Exon and Exonic End The first number in the title is the exonic end (5′ or 3′); the second is the phase (0, 1, or 2). (115 KB DOC)

Rates of Evolution in Enhancer and Nonenhancer Domains as a Function of Distance from the Boundary for Exons Longer than 200 bp All exons contribute equally to all data points. Here we merge 3′ and 5′ data. (55 KB DOC)

The human genome is a mosaic structure on many levels: there exist cytogenetic bands, GC composition bands (isochores) and clusters of broadly expressed genes. How might these inter-relate? It has been proposed that to optimize gene regulation, housekeeping genes should concentrate on transcriptionally competent chromosomal domains. Prior evidence...

As the efficacy of natural selection is expected to be a function of population size, in humans it is usually presumed that selection is a weak force and hence that gene characteristics are mostly determined by stochastic forces. In contrast, in species with large population sizes, selection is expected to be a much more effective force. Evidence f...

There is increasing evidence that X chromosomes have an unusual complement of genes, especially genes that have sex-specific expression. However, whereas in worm and fly the X chromosome has a dearth of male-specific genes, in mice genes that are uniquely expressed in spermatogonia are especially abundant on the X chromosome. Is this latter enrichm...

It is often supposed that, except for tandem duplicates, genes are randomly distributed throughout the human genome. However, recent analyses suggest that when all the genes expressed in a given tissue (notably placenta and skeletal muscle) are examined, these genes do not map to random locations but instead resolve to clusters. We have asked three...

In numerous species, from bacteria to Drosophila, evidence suggests that selection acts even on synonymous codon usage: codon bias is greater in more abundantly expressed genes, the rate of synonymous evolution is lower in genes with greater codon bias, and there is consistency between genes in the same species in which codons are preferred. In con...