The effects of environment and niche on the distributions of dwarf chameleons, present and future

Includes bibliographical references.The niche and niche breadth of Dwarf Chameleons, Bradypodion, was assessed in terms of broad scale climatic factors. A niche-based modelling method was then used to construct present and future habitat suitability maps for 2050 and 2080, for species in the genus. Additionally, the relationship between environment and morphology was analysed for a representative Bradypodion species, the Cape Dwarf Chameleon, B. pumilum. The niche and niche breadth of species and phylogenetic clades were analysed and described via an ordination technique, the outlying mean index (OMI) analysis. Maxent (v2.3), a presence only niche modelling method, proved very useful in the construction of present and future habitat suitability maps for species within the genus. For analysis of the correspondence between environment and morphology for B. pumilum, regression trees were employed. Rainfall seasonality and maximum annual temperatures were shown to strongly effect the current distributions of the genus Bradypodion at both the species and clade level. Additionally, as closely related species inhabited similar environmental niches, the genus was shown to display a degree of niche conservatism. All species and clades were shown to respond to climate change scenarios for 2050 and 2080, but responses were individualistic. However, most demonstrated range contractions under predicted climate scenarios. Additionally, a strong correlation (p < 0.05) was found between the morphology of B. pumilum and its environment. Environmental factors explained over 40% of the variation in snout-vent length and tail length, and over 20% of the variation in head width and head height, thus supporting the hypothesis of a correspondence between vegetation and morphology in Bradypodion. These results have provided an understanding of the relationship between Bradypodion and their environments that could provide valuable information regarding their ecology. Additionally, the habitat suitability maps for 2050 and 2080 could prove useful in the construction of any future conservation plans for these species. Furthermore, the results support the hypothesis of a correspondence between environmental factors and morphological traits within the genus Bradypodion

Analysis and interpretation of next-generation sequencing data for the identification of genetic variants involved in cardiovascular malformation

PhD ThesisCongenital cardiovascular malformation (CVM) affects 7/1000 live births. Approximately 20% of cases are caused by chromosomal and syndromic conditions. Rare Mendelian families segregating particular forms of CVM have also been described. Among the remaining 80% of non-syndromic cases, there is a familial predisposition implicating as yet unidentified genetic factors. Since the reproductive consequences to an individual of CVM are usually severe, evolutionary considerations suggest predisposing variants are likely to be rare. The overall aim of my PhD was to use next generation sequencing (NGS) methods to identify such rare, potentially disease causing variants in CVM. First, I developed a novel approach to calculate the sensitivity and specificity of NGS data in detecting variants using publicly available population frequency data. My aim was to provide a method that would yield sound estimates of the quality of a sequencing experiment without the need for additional genotyping in the sequenced samples. I developed such a method and demonstrated that it provided comparable results to methods using microarray data as a reference. Furthermore, I evaluated different variant calling pipelines and showed that they have a large effect on sensitivity and specificity. Following this, the NovoAlign-Samtools and BWA-Dindel pipelines were used to identify single base substitution and indel variants in three pedigrees, where predisposition to a different disease appears to segregate following an autosomal dominant mode of inheritance. I identified potentially causative variants segregating with disease in all three of the pedigrees. In the pedigrees with Dilated Cardiomyopathy and Hereditary Sclerosing Poikiloderma these variants were in plausible candidate genes. Finally, NGS was used to identify rare, potentially disease causing indel variants in patients with sporadic, non-syndromic forms of CVM characterised by chamber hypoplasia. Two indel calling pipelines were used as a means to increase confidence in the identified indels. These two pipelines achieved the highest sensitivity calls using the method described above. In the 133 cases, evaluated for 403 candidate genes, indels were identified in 4 known causative genes for human cardiovascular disease, namely MYL1, NOTCH1, TNNT2, and DSC2

Using population data for assessing next-generation sequencing performance.

Motivation: During the past 4 years, whole-exome sequencing has become a standard tool for finding rare variants causing Mendelian disorders. In that time, there has also been a proliferation of both sequencing platforms and approaches to analyse their output. This requires approaches to assess the performance of different methods. Traditionally, criteria such as comparison with microarray data or a number of known polymorphic sites have been used. Here we expand such approaches, developing a maximum likelihood framework and using it to estimate the sensitivity and specificity of whole-exome sequencing data. Results: Using whole-exome sequencing data for a panel of 19 individuals, we show that estimated sensitivity and specificity are similar to those calculated using microarray data as a reference. We explore the effect of frequency misspecification arising from using an inappropriately selected population and find that, although the estimates are affected, the rankings across procedures remain the same. Availability and implementation: An implementation using Perl and R can be found at busso.ncl.ac.uk (Username: igm101; Password: Z1z1nts). Contact: [email protected]; [email protected]

Mutations in Three Genes Encoding Proteins Involved in Hair Shaft Formation Cause Uncombable Hair Syndrome

International audienceUncombable hair syndrome (UHS), also known as “spun glass hair syndrome,” “pili trianguli et canaliculi,” or “cheveux incoiffables” is a rare anomaly of the hair shaft that occurs in children and improves with age. UHS is characterized by dry, frizzy, spangly, and often fair hair that is resistant to being combed flat. Until now, both simplex and familial UHS-affected case subjects with autosomal-dominant as well as -recessive inheritance have been reported. However, none of these case subjects were linked to a molecular genetic cause. Here, we report the identification of UHS-causative mutations located in the three genes PADI3 (peptidylarginine deiminase 3), TGM3 (transglutaminase 3), and TCHH (trichohyalin) in a total of 11 children. All of these individuals carry homozygous or compound heterozygous mutations in one of these three genes, indicating an autosomal-recessive inheritance pattern in the majority of UHS case subjects. The two enzymes PADI3 and TGM3, responsible for posttranslational protein modifications, and their target structural protein TCHH are all involved in hair shaft formation. Elucidation of the molecular outcomes of the disease-causing mutations by cell culture experiments and tridimensional protein models demonstrated clear differences in the structural organization and activity of mutant and wild-type proteins. Scanning electron microscopy observations revealed morphological alterations in hair coat of Padi3 knockout mice. All together, these findings elucidate the molecular genetic causes of UHS and shed light on its pathophysiology and hair physiology in general