High performance computing for haplotyping: Models and platforms

\u3cp\u3eThe reconstruction of the haplotype pair for each chromosome is a hot topic in Bioinformatics and Genome Analysis. In Haplotype Assembly (HA), all heterozygous Single Nucleotide Polymorphisms (SNPs) have to be assigned to exactly one of the two chromosomes. In this work, we outline the state-of-the-art on HA approaches and present an in-depth analysis of the computational performance of GenHap, a recent method based on Genetic Algorithms. GenHap was designed to tackle the computational complexity of the HA problem by means of a divide-et-impera strategy that effectively leverages multi-core architectures. In order to evaluate GenHap’s performance, we generated different instances of synthetic (yet realistic) data exploiting empirical error models of four different sequencing platforms (namely, Illumina NovaSeq, Roche/454, PacBio RS II and Oxford Nanopore Technologies MinION). Our results show that the processing time generally decreases along with the read length, involving a lower number of sub-problems to be distributed on multiple cores.\u3c/p\u3

The ecology and genetics of speciation in Heliconius butterflies (Lepidoptera: Nymphalidae)

Natural hybridisation between species offers an opportunity to study the processes of speciation. This thesis describes a study of hybridisation between Heliconius himera, which is endemic to dry forest in southern Ecuador and northern Peru, and H. erato, which is ubiquitous in wet forest throughout the neotropics. In a zone of contact in southern Ecuador hybrids are found at low frequency. Collections show that the contact zone is about 5 km wide, half the width of the narrowest clines between colour pattern races of H. erato, which implies that strong selection is maintaining the parapatric distributions of the species. Polymorphic protein and mitochondrial DNA markers were used to examine patterns of genetic differentiation and gene flow across the hybrid zone. Marked genetic differences between himera and erato are maintained in sympatry. Furthermore, analysis of linkage relationships between the allozyme markers showed that species differences are distributed widely across the genome. There was no evidence for any divergence in host plant ecology, but the hybrid zone between himera and erato was closely correlated with a habitat transition from wet to dry forest. Experiments showed that the barrier to gene flow was mainly due to strong assortative mating between himera and erato. Hybrid crosses showed no reduction in viability or fertility. Analysis of these broods showed that major gene control of pattern elements is similar to that found in previous studies of H. erato races, and the loci are homologous. Another species, H. charitonia, also has a genetically distinct sister species in the dry forests of Ecuador and Peru, peruviana. In both taxa, speciation is associated with divergence in habitat and warning colour, and in the case of himera and erato at least, there is a change in mating preferences but no evidence for genomic incompatibilities

Status and conservation goals for the critically endangered Arctic fox in Scandinavia. Is the mission completed?

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SYSTEMATICS OF THE GENUS COSMOSPORA (NECTRIACEAE, HYPOCREALES), AND COSPECIATION OF COSMOSPORA SPECIES WITH THEIR ASSOCIATED FUNGAL HOSTS.

Cosmospora (in the broad sense; Nectriaceae, Hypocreales, Ascomycota) are fungi that parasitize other fungi, particularly fungi in the Xylariales (Ascomycota), or scale insects. Morphologically, these fungi are known for having one of the most simplest and smallest sexual fruiting bodies (Cosmospora species have acremonium-like or fusarium-like asexual states. The name Cosmospora is derived from the ornamentation in the sexual spores (Gr. cosmos = ornamented + Gr. spora = spore). The main goals of this dissertation were to revise Cosmospora sensu stricto, and to determine the evolutionary relationship between Cosmospora species and their associated fungal hosts. Additionally, Corallomycetella (Nectriaceae, Hypocreales, Ascomycota), a lineage basal to Cosmospora sensu lato, was revised as well. Molecular and classical taxonomic tools were used to revise the genera. A genus was recognized if the clade met the following criteria: 1) the clade was well supported, 2) the clade was associated with a unique asexual state, and 3) the clade was ecologically different. A species was recognized if the clade met the following criteria: 1) the clade was well supported in the majority of single gene trees, 2) the clade was morphologically different, and/or 3) the clade was ecologically different in regards to host. Cosmospora species were observed to be highly host specific. Thus, host was recognized as an important character to delineate species, and the host specificity led us to hypothesize that Cosmospora species and their associated hosts were cospeciation (i.e., their association was not random). Two new genera, nine new combinations, and eleven new species were described in the taxonomic work included in this dissertation. A significant global congruence was determined between the Cosmospora and host phylogenies. However, host-switch events seemed more abundant in the early lineages of the host, while cospeciation events seemed more common in more recent lineages of the host. This phylogenetic signature is consistent with pseudocospeciation, but it could not be confirmed given that divergence estimates could not be estimated

The Molecular and behavioural ecology of click beetles (Coleoptera: Elateridae) in agricultural land

The larvae (wireworms) of some click beetle genera inhabit the soil in agricultural land and are crop pests. In the UK, a pest complex of Agriotes species, A. obscurus, A. sputator and A. lineatus, has been identified as the cause of the majority of damage. However, studies on their ecology are lacking, despite knowledge of this being important for the development of sustainable risk assessment and pest management strategies, in part due to the morphologically cryptic nature of wireworms. The ecology of economically important click beetle species was investigated, focusing on UK Agriotes species. The relationship between sex pheromone trapped male Agriotes adults and wireworms, identified using a molecular tool (T‐RFLP), was influenced by sampling method, and some environmental variables significantly correlated with species distributions. Scale of sampling influenced the observed distribution of wireworms and other soil insect larvae. Other wireworm species were trapped together with Agriotes species, but mitochondrial 16S rRNA sequences could not be matched to those of other UK species. Sequences from Canadian wireworm samples revealed possible cryptic species. Differences in adult movement rates were found in laboratory tests (A. lineatus > A. obscurus > A. sputator). Molecular markers (AFLPs) were developed to assess dispersal in adult male Agriotes but further protocol optimisation is required. The results show the importance of identifying wireworms to species for assessing adult and wireworm distributions, since the Agriotes pest complex may not be present or as 3 widespread as previously assumed. Sex pheromone trapping of adults may not be appropriate for risk assessment as the relationship between aboveground adult and belowground wireworm species distribution is not straightforward. The differences observed in Agriotes species’ ecology have implications for the implementation of pest management strategies. The techniques used here can be applied in future studies to provide information on other economically important click beetle species worldwide

Phylogeography and diversification of Taiwanese bats

PhDGene flow is a central evolutionary force that largely determines the level of differentiation among populations of organisms and thus their potential for divergence from each other. Identifying key factors that influence gene flow among populations or closely related taxa can thus provide valuable insights into how new species arise and are maintained. I undertook a comparative study of the factors that have shaped range-wide intraspecific differentiation in four related and broadly co-distributed Taiwanese bat species of the genera Murina and Kerivoula. Bats were sampled from sites across Taiwan and sequenced at two mitochondrial genes as well as genotyped at newly developed and/or existing multi-locus microsatellite markers. To improve phylogeographic inference of existing patterns of population genetic structure, I undertook spatial distribution modeling of the focal species at both the present time and at the Last Glacial Maximum. Genetic data were analysed using traditional and new methods, including Bayesian clustering, coalescent-based estimation of gene flow, and haplotype network reconstruction. My findings revealed contrasting signatures of population subdivision and demographic expansion that appear in part to reflect differences in the altitudinal ranges of the focal taxa. Mitochondrial analyses also revealed a putative sister relationship between two of the Taiwanese endemic taxa - M. gracilis and M. recondita, which - given the fact both are restricted to Taiwan - presents an unusual case of potential non-allopatric divergence. To dissect this divergence process in more detail, I used 454-Pyrosequencing to obtain ten nuclear loci sequences of these two taxa, and a third taxon from mainland Asia, M. eleryi. Based on these loci, Bayesian isolation-migration models provided no strong evidence of post-split gene flow and, therefore, did not support speciation within Taiwan. Instead, the divergence process reconstructed from ncDNA loci was found to be incompatible with the mtDNA tree, with M. recondita showing a sister relationship with M. eleryi. This conflict is best explained by the ancient introgression of mtDNA between the two insular species following their colonization of Taiwan at different times.Overseas Research Students Awards Scheme of the UK and the Taiwanese Ministry of Education, London Central Research Fund and the National Science Council of Taiwa