Molecular phylogenetics and genotypic variation in Coleoptera - a bioinformatics approach
File(s)
Supplementary material
Supplementary material
Author(s)
Barton, Christopher
Type
Thesis
Abstract
A custom-built bioinformatics pipeline is used to costruct a species-level phylogeny for beetles (Coleoptera) using publicly available sequences from Genbank, including 8441 terminals 5 gene loci. 152 of 189 described beetle families are included, representing 2.17% of described species. The overall structure of publicly available data and its fit with Linnaean classifications are discussed. The dataset is further expanded by the inclusion of additional gene loci and relaxation of concatenation conditions, bringing total species to ~12,000. To overcome incomplete or incorrect identifications, a multi-partite matching algorithm is applied, for concatenation of partially conflicting taxon labels between gene loci, using species-level sequence clusters. The method is modified through the addition of country/specimen weighting between loci, and the incorporation of the the GMYC method of sequence-based species delimitation into the bioinformatics pipeline. GMYC and BlastClust approaches are compared, in terms of accuracy of species delimitation, supermatrix structure and topology of resulting trees. GMYC clusters are used as a framework for broad-scale comparisons of intraspecificvariation across the Coleoptera. The Coleoptera tree is used to illustrate a novel method for estimating total extant diversity by extrapolating from higher-taxon diversification rates, generating an estimate of 3.1 million beetle species globally. The sensitivity of the method to phylogenetic uncertainty within the data, and undersampling of families and subfamilies, is examined. Partial and complete mitochondrial genomes are used to generate the largest and most comprehensive phylogeny ever produced fromthis type of data. This tree is used as the basis for a molecular dating analysis, and the quantification of compositional heterogeneity among genes, taxa and sites within protein-coding genes. Non-homogenous substitution models are applied to help resolve problematic regions of the phylogeny, and the effects on topology and phylogenetic diversity of adding a previously unsampled regional fauna from Borneo are assessed.
Version
Open Access
Date Issued
2014-01
Date Awarded
2014-10
Copyright Statement
Attribution NoDerivatives 4.0 International Licence (CC BY-ND)
Advisor
Vogler, Alfried
Sponsor
Leverhulme Trust
Grant Number
F/00696/P
Publisher Department
Life Sciences
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)