Peter W Harrison

University College London | UCL · Department of Genetics, Evolution and Environment (GEE)

Gene expression differences between the sexes account for the majority of sexually dimorphic phenotypes, and the study of sex-biased gene expression is important for understanding the genetic basis of complex sexual dimorphisms. However, it has been difficult to test the nature of this relationship due to the fact that sexual dimorphism has traditi...

Males and females experience differences in gene dose for loci in the nonrecombining region of heteromorphic sex chromosomes. If not compensated, this leads to expression imbalances, with the homogametic sex on average exhibiting greater expression due to the doubled gene dose. Many organisms with heteromorphic sex chromosomes display global dosage...

Changes in gene expression underlie the adaptive evolution in many complex phenotypes, and the recent increase in the availability of multi-species comparative transcriptome data has made it possible to scan whole transcriptomes for loci that have experienced adaptive changes in expression. However, despite the increase in data availability, curren...

What adaptive changes in brain structure and function underpin the evolution of increased cognitive performance in humans and our close relatives? Identifying the genetic basis of brain evolution has become a major tool in answering this question. Numerous cases of positive selection, altered gene expression or gene duplication have been identified...

Ruditapes philippinarum, one of the major contributors to the global mollusc production, is susceptible to perkinsosis, a disease caused by the protozoan Perkinsus olseni (Alveolata, Perkinsidae). Understanding the molecular response of Manila clam defence cells (haemocytes) to this parasite is essential to head towards controlling this disease. He...

In many diploid species, sex determination is linked to a pair of sex chromosomes that evolved from a pair of autosomes. In these organisms, the degeneration of the sex-limited Y or W chromosome causes a reduction in gene dose in the heterogametic sex for X- or Z-linked genes. Variations in gene dose are detrimental for large chromosomal regions wh...

The protistan parasite Perkinsus olseni is a deadly causative agent of perkinsosis, a molluscan disease affecting Manila clam (Ruditapes philippinarum), having a significant impact on world mollusc production. Deciphering the underlying molecular mechanisms in R. philippinarum-P. olseni interaction is crucial for controlling this parasitosis. The p...

Regional variation in sex-specific gene regulation has been observed across sex chromosomes in a range of animals, and is often a function of sex chromosome age. The avian Z chromosome exhibits substantial regional variation in sex-specific regulation, where older regions show elevated levels of male-biased expression. Distinct sex-specific regulat...

Brain size varies substantially across the animal kingdom and is often associated with cognitive ability; however, the genetic architecture underpinning natural variation in these key traits is virtually unknown. In order to identify the genetic architecture and loci underlying variation in brain size, we analysed both coding sequence and expressio...

The elevated rate of evolution for genes on sex chromosomes compared to autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex, or from non-adaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed p...

Significance Genes with different expression between males and females (sex-biased genes) show rapid rates of sequence and expression divergence in a range of taxa. These characteristics have led many to assume that sex-biased genes are the product of sexual selection and sexual conflict, but this assumption remains to be rigorously tested. Using a...

Higher rates of coding sequence evolution have been observed on the Z chromosome relative to the autosomes across a wide range of species. However, despite a considerable body of theory, we lack empirical evidence explaining variation in the strength of the Faster-Z Effect. To assess the magnitude and drivers of Faster-Z Evolution, we assembled six...

Background: Enteromyxosis caused by the intestinal myxozoan parasite Enteromyxum scophthalmi is a serious threat for turbot (Scophthalmus maximus, L.) aquaculture, causing severe catarrhal enteritis leading to a cachectic syndrome, with no therapeutic options available. There are still many aspects of host-parasite interaction and disease pathogen...

With the greater availability of genetic data, large genome-wide scans for positive selection increasingly incorporate data from a range of sources. These data sets may be derived from different sequencing methods, each of which has potential sources of error. Sequencing errors, compounded by alignment errors, greatly increase the number of false p...

Supplementary Figure S1. Comparison of results using row-based SWAMP and column-based G-Blocks filtering. Results show the rank order of the Likelihood ratio test (LRT) for the top 100 genes under a branch-site model for four species as in Figure 2. The dashed grey lines are the results from the unfiltered alignments. Orange circles show the G-Bloc...

Supplemental Figure Legends

We used a comparative approach spanning three species and 90 million years to study the evolutionary history of the avian sex chromosomes. Using whole transcriptomes, we assembled the largest cross-species dataset of W-linked coding content to date. Our results show that recombination suppression in large portions of the avian sex chromosomes has e...

Manila clam (Ruditapes philippinarum) with its high commercial value has become a major contributor to the world´s clam production from both bivalve fishery and aquaculture ventures. But, the production of manila clam is at greater risk from diseases, especially caused by Perkinsus olseni. Considering the limited genomic resources of R. philippinar...

Sexually dimorphic phenotypes are thought to largely result from sex differences in gene expression, and genes with sex-biased expression have been well characterized in adults of many species. Although most sexual dimorphisms manifest in adults, many result from sex-specific developmental trajectories, implying that juveniles may exhibit significa...

Expression level and sex-bias. Relationship between expression level and sex-bias for male-biased genes in dominant males (panel A), subordinate males (panel B) and females (panel C). Relationship between expression level and sex-bias for female-biased genes in dominant males (panel D), subordinate males (panel E) and females (panel F). Pairwise te...

Number of sex-biased autosomal genes expressed in the spleen, brain and gonad of the turkey. Genes are sex biased if they are expressed at least two-fold higher in one sex with an adj. p-value<0.05. (DOCX)

Number and percentage of genes that reside in close proximity to at least one testosterone DNA binding motif and are male-biased. P-values are calculated using a two-sided Z-test by comparison to the actual number of male-biased genes in the genome (2217, 22.46%). (DOCX)

Average log2 fold change between subordinate and dominant males for genes that reside in close proximity to at least one predicted testosterone DNA binding motif. Significant difference from overall average log2 fold change (0.00044) was calculated by a permutation test with 1000 replicates. (DOCX)

Male and female sexual dimorphisms in Meleagris gallopavo. Females are smaller than males, and lack both beards and iridescent plumage. In addition to size and plumage differences, males exhibit more vivid coloration on the head and neck, elongated snoods, enlarged caruncles, and a larger wattle or dewlap. (PDF)

Factor analysis of gonad and spleen average gene expression for females, subordinate males and dominant males. Shown are the first two factors accounting for 48.2% and 33.7% of the variance respectively. Factor analysis was performed using the R package ‘factanal’. Suitability of the data for factor analysis was confirmed with a Kaiser-Meyer-Olkin...

List of significantly different GO terms for genes shared between female and subordinate male turkeys. GO term enrichment analysis for 195 genes shared between female and subordinate males. (DOCX)

List of genes differentially expressed between subordinate and dominant male turkeys. Binomial p-values, adjusted for multiple comparisons, were calculated in DESeq. An asterisk indicates the single differentially expressed gene found to lie within 10 kb of a testosterone receptor binding site. (DOCX)

Expression differences between sexual morphs for unbiased and female-biased autosomal genes. Panel A. Average expression for autosomal unbiased genes in females, subordinate males, and dominant males. The increase (2.76%) in average expression between subordinate and dominant male morphs is less than the decrease observed for male-biased (11.35%) o...

Expression differences between sexual morphs is not dependent upon how sex-bias is defined. Panel A. Expression differences between sexual morphs for autosomal sex-biased genes where sex-bias is defined as those genes expressed two-fold higher in subordinate males or females, with an adjusted p-value<0.05. Statistical difference between subordinate...

List of significantly different GO terms for genes shared between dominant and subdominant male turkeys. GO term enrichment analysis for 490 genes shared between dominant and subordinate males. (DOCX)

We assembled a de novo transcriptome of short-read Illumina RNA-Seq data generated from telencephalon and diencephalon tissue samples from the Kentish plover, Charadrius alexandrinus. This is a species of considerable interest in behavioural ecology for its highly variable mating system and parental behaviour, but it lacks genomic resources and is...

We investigated the genomic diversity of a local population of the symbiotic bacterium Sinorhizobium medicae, isolated from the roots of wild Medicago lupulina plants, in order to assess genomic diversity, to identify genomic regions influenced by duplication, deletion or strong selection, and to explore the composition of the pan-genome. Partial g...

In addition to the main chromosome, approximately one in ten bacterial genomes have a 'second chromosome' or 'megaplasmid'. Here, we propose that these represent a single class of elements that have a distinct and consistent set of properties, and suggest the term 'chromid' to distinguish them from both chromosomes and plasmids. Chromids carry some...

The aim of this study was to examine whether flux through the pathways of carbohydrate oxidation is accurately reflected in the pattern of (14)CO(2) release from positionally labelled [(14)C]substrates in conventional radiolabel feeding studies. Heterotrophic cell suspension cultures of Arabidopsis thaliana were used for this work. The presence of...