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1
Faller, Beáta. "Combinatorial and probabilistic methods in biodiversity theory". Thesis, University of Canterbury. Mathematics and Statistics, 2010. http://hdl.handle.net/10092/3985.
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Phylogenetic diversity (PD) is a measure of species biodiversity quantified by how
much of an evolutionary tree is spanned by a subset of species. In this thesis, we study
optimization problems that aim to find species sets with maximum PD in different scenarios,
and examine random extinction models under various assumptions to predict the
PD of species that will still be present in the future.
Optimizing PD with Dependencies is a combinatorial optimization problem in
which species form an ecological network. Here, we are interested in selecting species
sets of a given size that are ecologically viable and that maximize PD. The NP-hardness
of this problem is proved and it is established which special cases of the problem are
computationally easy and which are computationally hard. It is also shown that it is
NP-complete to decide whether the feasible solution obtained by the greedy algorithm is
optimal. We formulate the optimization problem as an integer linear program and find
exact solutions to the largest food web currently in the empirical literature. In addition,
we give a generalization of PD that can be used for example when we do not know the
true evolutionary history. Based on this measure, an optimization problem is formulated.
We discuss the complexity and the approximability properties of this problem.
In the generalized field of bullets model (g-FOB), species are assumed to become
extinct with possibly different probabilities, and extinction events are independent. We
show that under this model the distribution of future phylogenetic diversity converges to
a normal distribution as the number of species grows. When extinction probabilities are
influenced by some binary character on the tree, the state-based field of bullets model
(s-FOB) represents a more realistic picture. We compare the expected loss of PD under
this model to that under the associated g-FOB model and find that the former is always
greater than or equal to the latter. It is natural to further generalize the s-FOB model to
allow more than one binary character to affect the extinction probabilities. The expected
future PD obtained for the resulting trait-dependent field of bullets model (t-FOB) is
compared to that for the associated g-FOB model and our previous result is generalized.
2
Jirásková, Kristýna. "Metody rekonstrukce fylogenetických superstromů". Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2012. http://www.nusl.cz/ntk/nusl-219518.
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The phylogenetic reconstruction has noted great development in recent decades. The development of computers and device for sequencing biopolymers have been an enormous amount od phylogenetic data from different sources and different types. The scientists are trying to reconstruct a comlet tree of life from these data. The phylogenetic supertree are theoretically this option because a supertree alow a combination of all information gathered so far – in contras to the phylogenetic trees. This thesis present the method of reconstruction supertrees using average konsensus method.
3
Kosíř, Kamil. "Metody rekonstrukce fylogenetických superstromů". Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2014. http://www.nusl.cz/ntk/nusl-220860.
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The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.
4
Tokac, Nihan. "Efficiency of algorithms in phylogenetics". Thesis, Durham University, 2016. http://etheses.dur.ac.uk/11768/.
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Phylogenetics is the study of evolutionary relationships between species. Phylogenetic trees have long been the standard object used in evolutionary biology to illustrate how a given set of species are related. There are some groups (including certain plant and fish species) for which the ancestral history contains reticulation events, caused by processes that include hybridization, lateral gene transfer, and recombination. For such groups of species, it is appropriate to represent their ancestral history by phylogenetic networks: rooted acyclic digraphs, where arcs represent lines of genetic inheritance and vertices of in-degree at least two represent reticulation events. This thesis is concerned with the efficiency, accuracy, and tractability of mathematical models for phylogenetic network methods. Three important and related measures for summarizing the dissimilarity in phylogenetic trees are the minimum number of hybridization events required to fit two phylogenetic trees onto a single phylogenetic network (the hybridization number), the (rooted) subtree prune and regraft distance (the rSPR distance) and the tree bisection and reconnection distance (the TBR distance) between two phylogenetic trees. The respective problems of computing these measures are known to be NP-hard, but also fixed-parameter tractable in their respective natural parameters. This means that, while they are hard to compute in general, for cases in which a parameter (here the hybridization number and rSPR/TBR distance, respectively) is small, the problem can be solved efficiently even for large input trees. Here, we present new analyses showing that the use of the “cluster reduction” rule – already defined for the hybridization number and the rSPR distance and introduced here for the TBR distance – can transform any O(f(p) · n)-time algorithm for any of these problems into an O(f(k) · n)-time one, where n is the number of leaves of the phylogenetic trees, p is the natural parameter and k is a much stronger (that is, smaller) parameter: the minimum level of a phylogenetic network displaying both trees. These results appear in [9]. Traditional “distance based methods” reconstruct a phylogenetic tree from a matrix of pairwise distances between taxa. A phylogenetic network is a generalization of a phylogenetic tree that can describe evolutionary events such as reticulation and hybridization that are not tree-like. Although evolution has been known to be more accurately modelled by a network than a tree for some time, only recently have efforts been made to directly reconstruct a phylogenetic network from sequence data, as opposed to reconstructing several trees first and then trying to combine them into a single coherent network. In this work, we present a generalisation of the UPGMA algorithm for ultrametric tree reconstruction which can accurately reconstruct ultrametric tree-child networks from the set of distinct distances between each pair of taxa. This result will also appear in [15]. Moreover, we analyse the safety radius of the NETWORKUPGMA algorithm and show that it has safety radius 1/2. This means that if we can obtain accurate estimates of the set of distances between each pair of taxa in an ultrametric tree-child network, then NETWORKUPGMA correctly reconstructs the true network.
5
Douady, Christophe Jean Gabriel. "Molecular phylogenetics of the insectivora". Thesis, Queen's University Belfast, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394635.
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Fletcher, W. A. J. "Computational statistics in molecular phylogenetics". Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1306705/.
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Simulation remains a very important approach to testing the robustness and accuracy of phylogenetic inference methods. However, current simulation programs are limited, especially concerning realistic models for simulating insertions and deletions (indels). In this thesis I implement a new, portable and flexible application, named INDELible, which can be used to generate nucleotide, amino acid and codon sequence data by simulating indels (under several models of indel length distribution) as well as substitutions (under a rich repertoire of substitution models). In particular, I introduce a simulation study that makes use of one of INDELible’s many unique features to simulate data with indels under codon models that allow the nonsynonymous/synonymous substitution rate ratio to vary among sites and branches. This data is used to quantify, for the first time, the precise effects of indels and alignment errors on the false-positive rate and power of the widely used branch-site test of positive selection. Several alignment programs are used and assessed in this context. Through the simulation experiment, I show that insertions and deletions do not cause the test to generate excessive false positives if the alignment is correct, but alignment errors can lead to unacceptably high false positives. Previous selection studies that use inferior alignment programs are revisited to demonstrate the applicability of my results in real world situations. Further work uses simulated data from INDELible to examine the effects of tree-shape and branch length on the alignment accuracy of several alignment programs, and the impact of alignment errors on different methods of phylogeny reconstruction. In particular, analysis is performed to explore which programs avoid generating the kind of alignment errors that are most detrimental to the process of phylogeny reconstruction.
7
Kim, Cheol-Min. "Phylogenetics of Trigynaspida (Acari: Mesostigmata) /". The Ohio State University, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=osu1486572165276144.
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Cooke, Patrick Alan. "BioInformatics, Phylogenetics, and Aspartate Transcarbamoylase". Thesis, University of North Texas, 2000. https://digital.library.unt.edu/ark:/67531/metadc2580/.
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In this research, the necessity of understanding and using bioinformatics is demonstrated using the enzyme aspartate transcarbamoylase (ATCase) as the model enzyme. The first portion of this research focuses on the use of bioinformatics. A partial sequence of the pyrB gene found in Enterococcus faecalis was submitted to GenBank and was analyzed against the contiguous sequence from its own genome project. A BLAST (Basic Local Alignment Search Tool; Atschul, et al., 1990) was performed in order to hypothesize the remaining portion of the gene from the contiguous sequence. This allowed a global comparison to other known aspartate transcarbamoylases (ATCases) and once deduced, a translation of the sequence gave the stop codon and thus the complete sequence of the open reading frame. When this was complete, upstream and downstream primers were designed in order to amplify the gene from genomic DNA. The amplified product was then sequenced and used later in phylogenetic analyses concerning the evolution of ATCase. The second portion of this research involves taking multiple ATCase nucleotide sequences and performing phenetic and phylogenetic analyses of the archaea and eubacter families. From these analyses, ancestral relationships which dictate both structure and function were extrapolated from the data and discussed.
9
Buckman, Rebecca S. "Phylogenetics of Thysanoptera (Insecta: Paraneoptera)". BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/2999.
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The order Thysanoptera (Insecta: Paraneoptera), commonly known as thrips, includes organisms that exhibit a wide range of social and feeding behaviors that are of particular interest in evolutionary studies. These studies within thrips have been inhibited by the lack of knowledge of thrips relationships. The recognized classification scheme strives to reflect evolutionary relationships and is based upon morphology. Molecular data is next as morphology alone is not enough to resolve relationships. Few molecular studies have been conducted and all were limited in their taxon sampling and genetic sampling. To provide a foundation of future evolutionary studies, the objectives of this study are to (1) test the monophyly of the suborders Terebrantia and Tubulifera, (2) test the monophyly of the families and decipher their relationships, and (3) test the monophyly of the recognized subfamilies. Phylogenies were reconstructed based upon 5299 bp, from five genetic loci: 18S ribosomal DNA, 28S ribosomal DNA, Histone 3 (H3), Tubulin-alpha (TubA) and cytochrome oxidase c subunit I (COI). 99 thrips species from seven of the nine families, all six subfamilies and 70 genera were sequenced. Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian analysis all strongly support a monophyletic Tubulifera and Terebrantia. Phlaeothripidae, Aeolothripidae, Melanthripidae and Thripidae are all monophyletic families. The relationship between Aeolothripidae and Merothripidae to the rest of Terebrantia is equivocal. Morphological and molecular data suggest Aeolothripidae or Merothripidae could be the basal lineage of Terebrantia. Four of the six subfamilies are recovered as monophyletic. The two largest subfamilies, Phlaeothripinae and Thripinae, are paraphyletic and require further study to understand relationships within them.
10
Farid, Arian. "Molecular Phylogenetics of Floridian Boletes". Scholar Commons, 2018. https://scholarcommons.usf.edu/etd/7618.
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The boletes are macrofungi which have undergone extensive taxonomic revisions since the advent of molecular tools. To further our understanding of the boletes in peninsular Florida, we sequenced two common Floridian boletes, and analyzed them with molecular phylogenetic tools. Boletus rubricitrinus, a common Florida bolete often found in lawns under Quercus, and likely has a distribution that extends to Texas. Based on ITS and LSU sequences and morphological studies, this species belongs in the genus Pulchroboletus. As the holotype is in poor condition, an epitype is established here. A thorough description of macroscopic and microscopic features is also provided for the species. Fungi in the genus Phylloporus are lamellate boletes that occur worldwide, but primarily in the tropics. Phylloporus boletinoides is a species which was described from Florida, and is found growing near Pinus spp. Based on ITS, LSU, and RPB1 sequences, we establish the novel genus Pseudophylloporus, which is allied to Bothia and Solioccasus. Morphological data are also provided from our collections, and one from Belize. Based on molecular data and a review of bolete literature, the delimitation of this genus suggests that there are three distinct lineages of boletes that have a lamellate hymenium in the Boletaceae. These molecular and morphological data will be useful to further improve our understanding of bolete taxonomy.
11
CICCOLELLA, SIMONE. "Practical algorithms for Computational Phylogenetics". Doctoral thesis, Università degli Studi di Milano-Bicocca, 2022. http://hdl.handle.net/10281/364980.
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In questo manoscritto vengono discussi le principali sfide computazionali
nel campo della inferenza di filogenesi tumorale a vengono proposte
diverse soluzione per i tre principali problemi di
(i) ricostruzione dell'evoluzioni di un campione tumorale,
(ii) clustering di dati SCS per una piu' pulita e veloce inferenza
e (iii) il confronto di diverse filogenesi.
Inoltre viene discusso come combinare le diverse soluzioni
in una singola pipeline per una piu' rapida analisi.In this manuscript we described the main computational challenges of the cancer phylogenetic field and we proposed different solutions for the three main problems of (i) the progression reconstruction of a tumor sample, (ii) the clustering of SCS data to allow for a cleaner and faster inference and (iii) the evaluation of different phylogenies. Furthermore we combined them into a usable pipeline to allow for a faster analysis.
12
Powell, Robyn Faye. "Systematics, diversification and ecology of the Conophytum-clade (Ruschieae; Aizoaceae)". University of the Western Cape, 2016. http://hdl.handle.net/11394/5453.
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Philosophiae Doctor - PhDThe Ruschieae is the most diverse and speciose tribe within the large subfamily Ruschioideae (Aizoaceae), with approximately 71 genera and a distribution centred in the arid parts of the Greater Cape Floristic Region (GCFR) of South Africa. Recent phylogenetic analyses provided the first insights into generic relationships within the tribe, with a number of novel generic relationships discovered. The tribal phylogeny recovered 12 large clades, of which the Conophytum-clade was one the most morphologically diverse based on leaf and capsule characters. The Conophytum-clade is an early-diverging lineage of the Ruschieae and includes the following 10 genera: Cheiridopsis N.E.Br., Conophytum N.E.Br., Enarganthe N.E.Br., Ihlenfeldtia H.E.K.Hartmann, Jensenobotrya A.G.J.Herre, Namaquanthus L.Bolus, Octopoma N.E.Br., Odontophorus N.E.Br., Ruschianthus L.Bolus and Schlechteranthus Schwantes. The present study presents an expanded phylogenetic analysis of the Conophytum-clade, with the sampling of the majority of species in the genera and a representative sampling (56% of species) of the speciose genus Conophytum. Phylogenetic data for up to nine plastid gene regions (atpB–rbcL, matK, psbJ–petA, rpl16, rps16, trnD– trnT, trnL–F, trnQᶷᶷᶢ–rps16, trnS–trnG) were produced for each of the sampled species. The produced plastid data was analyses using maximum parsimony, maximum likelihood and Bayesian inference. The combined plastid phylogenetic analyses were used in combination with morphological, anatomical and palynological data to assess generic and subgeneric circumscriptions within the clade. Upon assessment of generic circumscriptions in the Conophytum-clade, the number of recognised genera in the clade decreased from ten to seven. Arenifera A.G.J.Herre, which had not been sampled in any phylogeny of the Ruschieae, and Octopoma were recovered as polyphyletic, with species placed in the Conophytum-clade, while the type species was placed in the xeromorphic clade of the tribal phylogeny. The species of Arenifera and Octopoma placed in the Conophytum-clade were subsequently included in Schlechteranthus upon assessment of generic circumscriptions between the taxa. Two morphological groupings were recognised within Schlechteranthus, one including the species of Schlechteranthus and the other including species previously recognised as Arenifera and Octopoma. These two morphological groupings were treated as subgenera, with the erection of the new subgenus Microphyllus R.F.Powell. A detailed taxonomic revision of subgenus Microphyllus is presented with a key to species, descriptions of the species (including a new species: S. parvus R.F.Powell & Klak), known geographical distributions and illustrations of the species. In addition to the changes mentioned above, the expanded sampling and phylogenetic analyses of the Conophytum-clade recovered Ihlenfeldtia and Odontophorus embedded in Cheiridopsis. The species of Ihlenfeldtia were recovered with species of heiridopsis subgenus Aequifoliae H.E.K.Hartmann, while the species of Odontophorus were recovered as polyphyletic within the Cheiridopsis subgenus Odontophoroides H.E.K.Hartmann clade. Cheiridopsis was subsequently expanded to include the species of Ihlenfeldtia and Odontophorus, with these species accommodated in the subgenera of Cheiridopsis. The phylogenetic placement and relationship of these species was supported by the shared capsule morphology. The expanded sampling of the clade did not resolve the phylogenetic relationship of the monotypic genera Enarganthe, Jensenobotrya, Namaquanthus and Ruschianthus, with these genera unresolved in the Conophytum-clade. These genera however, exhibit a unique combination of morphological characters, such as a glabrous leaf epidermis and variation in pollen exine and colpi structure, in contrast to the other genera of the clade. The assessment of the generic circumscription of these genera, based on the molecular, morphological, anatomical and palynological data suggested that the generic statuses of these monotypic genera should be maintained. The expanded phylogenetic sampling of the morphologically diverse and speciose genus Conophytum recovered the genus as monophyletic. This monophyly was supported by the unique floral type in Conophytum, with the fused petaloid staminodes forming a tube. None of the sectional classifications were recovered as monophyletic but the phylogenetic analyses did recover a few clades which more or less corresponded to the current sectional classification of the genus. A number of clades were also recovered which included species from a range of different sections. Diverse leaf and floral traits were shown to have evolved numerous times across the genus. This was particularly interesting with regards to the selected floral traits, as the phylogeny indicated a number of switches in floral morphologies across the genus. The floral diversity was assessed in complex species communities of Conophytum across the GCFR, where up to 11 species of Conophytum are found occurring sympatrically, and floral traits were shown to be different across the species within the communities. Pollination competition and adaptation were suggested as possible drivers of floral diversity in the genus, with differences in phenology, anthesis and floral morphology within the species complex communities. The unique floral type of Conophytum has enabled the species to develop a diverse range of specialised flowers, with a variety of structures, scents and colours, resulting in the diverse floral morphologies found across the genus. The complex Conophytum species communities included both closely as well as distantly related species, suggesting the soft papery capsules of Conophytum are wind dispersed. This adaptation to long distance seed dispersal resulted in a significantly higher phylogenetic diversity in Conophytum when compared to its sister genus, Cheiridopsis. A population genetics study of Conophytum also suggested that the capsules may be wind dispersed, with an indication of genetic connectivity between the geographically isolated populations of C. marginatum Lavis across the Bushmanland Inselberg Region. Although the capsules are dispersed by wind, the seeds are released from the hygrochastic capsules by runoff during rainfall events. The relationship between seed dispersal and runoff is evident from the genetic structure of populations of C. maughanii N.E.Br. and C. ratum S.A.Hammer that occur on the tops and the surrounding bases of the inselbergs, as the drainage pattern was found to directly influence population structure in these species. In addition, the AFLP analyses provided insight into the conservation of the flagship species C. ratum. The summit populations of this species were shown to sustain the populations at the base of the Gamsberg. This finding is especially important, as the distribution of the species is restricted to the Gamsberg inselberg, where mining has already commenced as of this year.
National Research Foundation (NRF)
13
Kist, Nicolaas Christiaan. "Bayesian phylogenetic approaches to retroviral evolution : recombination, cross-species transmission, and immune escape". Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:997289db-0a6e-4cd4-b465-9fc962ce40b8.
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Catanzaro, Daniele. "Models and methods for molecular phylogenetics". Doctoral thesis, Universite Libre de Bruxelles, 2008. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210453.
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Un des buts principaux de la biologie évolutive et de la médecine moléculaire consiste à reconstruire les relations phylogénétiques entre organismes à partir de leurs séquences moléculaires. En littérature, cette question est connue sous le nom d’inférence phylogénétique et a d'importantes applications dans la recherche médicale et pharmaceutique, ainsi que dans l’immunologie, l’épidémiologie, et la dynamique des populations. L’accumulation récente de données de séquences d’ADN dans les bases de données publiques, ainsi que la facilité relative avec laquelle des données nouvelles peuvent être obtenues, rend l’inférence phylogénétique particulièrement difficile (l'inférence phylogénétique est un problème NP-Hard sous tous les critères d’optimalité connus), de telle manière que des nouveaux critères et des algorithmes efficaces doivent être développés. Cette thèse a pour but: (i) d’analyser les limites mathématiques et biologiques des critères utilisés en inférence phylogénétique, (ii) de développer de nouveaux algorithmes efficaces permettant d’analyser de plus grands jeux de données.Doctorat en Sciences
info:eu-repo/semantics/nonPublished
15
Chang, Ying. "Molecular phylogenetics of mosses and relatives". Thesis, University of British Columbia, 2011. http://hdl.handle.net/2429/37148.
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Substantial ambiguities still remain concerning the broad backbone of moss phylogeny. I surveyed 17 slowly evolving plastid genes from representative taxa to reconstruct phylogenetic relationships among the major lineages of mosses in the overall context of land-plant phylogeny. I first designed 78 bryophyte-specific primers and demonstrated that they permit straightforward amplification and sequencing of 14 core genes across a broad range of bryophytes (three of the 17 genes required more effort). In combination, these genes can generate sturdy and well-resolved phylogenetic inferences of higher-order moss phylogeny, with little evidence of conflict among different data partitions or analyses. Liverworts are strongly supported as the sister group of the remaining land plants, and hornworts as sister to vascular plants. Within mosses, besides confirming some previously published findings based on other markers, my results substantially
improve support for major branching patterns that were ambiguous before. The monogeneric classes Takakiopsida and Sphagnopsida likely represent the first and second split within moss phylogeny, respectively. However, this result is shown to be sensitive to the strategy used to estimate DNA substitution model parameter values and to different data partitioning methods. Regarding the placement of remaining nonperistomate lineages, the [[[Andreaeobryopsida, Andreaeopsida], Oedipodiopsida], peristomate mosses] arrangement receives moderate to strong support. Among peristomate mosses, relationships among Polytrichopsida, Tetraphidopsida and
Bryopsida remain unclear, as do the earliest splits within sublcass Bryidae. A Funariidae, [Timmiidae, [Dicranidae, Bryidae]]] arrangement is strongly supported, as are major relationships within subclasses Funariidae and Dicranidae. I also reconstructed the phylogeny of the nonperistomate moss family Andreaeaceae, with a focus on costate taxa, using two complementary sets of plastid markers and taxa. The major subgenera (Andreaea and Chasmocalyx) and sections of Andreaea (Andreaea and Nerviae) are rejected as monophyletic. Well-supported lineages include clades comprising: (1) Andreaea nivalis and A. rigida (northern hemisphere members of subgenus Chasmocalyx) and A. blyttii (section Nerviae); (2) most of the remainder of Nerviae; (3) a mixture of costate and ecostate species from Chasmocalyx, Nerviae,
all sampled members of section Andreaea, and subgenus Acroschisma. Relationships among the major lineages, including the root of the family, are all well supported.
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Subramanian, Ayshwarya. "Inferring tumor evolution using computational phylogenetics". Research Showcase @ CMU, 2013. http://repository.cmu.edu/dissertations/275.
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Cancer research has made tremendous progress in understanding the basic biology of tumors. One of the key insights that has informed work in this area is the recognition that a tumor is an evolutionary system, in which individual cells undergo a process of rapid mutation and selection leading to a progression in phenotypes and, typically, aggressiveness of the tumor. Tumor phylogenetics is a strategy for interpreting the evolution of tumors using computer algorithms for phylogenetics, i.e., the inference of evolutionary trees. The approach takes advantage of a large body of phylogenetic theory and algorithms, developed primarily for inferring evolution among species, to interpret complex tumor data sets as evidence for evolutionary processes. The result is a tumor phylogeny, or phylogenetic tree, a reconstruction of the sequences of mutations that cells within a tumor or class of tumors accumulate over the course of their progression. The goals of finding such trees are to better interpret heterogeneity within and among tumors, identify and classify tumor subtypes with possible underlying mechanisms of action, learn markers of progression for key steps in tumor evolution, and enable predictive modeling of likely tumor progression steps that may ultimately assist in diagnosis and treatment.
In this dissertation, we discuss a computational framework for reconstructing phylogenies from genome-scale tumor array and sequencing data. We first present a novel phylogenetic pipeline for building tumor phylogenies from whole-genome copy number variation data. The steps included computational unmixing for resolving heterogeneity in genomic data from tumors, a statistical method for progression marker discovery, a statistical method for data discretization, application of character-based phylogeny reconstruction, and analyses of the resulting trees to draw biological significance. We then describe HMM-CNA, an improved model for discovering progression markers from cohorts of patient tumor copy number data that are especially relevant for phylogeny reconstruction via a custom multi-sample Hidden Markov model (HMM). We next present a novel strategy for phylogeny building from single cell sequencing data by inferring features that can accurately capture the composition of the individual genome sequences and distinguish among stages of tumor progression. We demonstrate these contributions on both simulated and human breast tumor biopsy and cell line data assuming a maximum parsimony model of evolution. Finally, we discuss future directions for building a more realistic model of tumor evolution by integrating patterns in genome structural changes with the functional elements they encode. We close with a discussion of recent research, current trends, and challenges and opportunities facing the field.
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Heibl, Christoph. "R programming in phylogenetics and evolution". Diss., Ludwig-Maximilians-Universität München, 2014. http://nbn-resolving.de/urn:nbn:de:bvb:19-178834.
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This dissertation addresses the application of the statistical computing language
R in the study of evolution and diversification of plants. The topics included
range from the worldwide historical biogeography of the cucurbit family and the
phylogenetic composition of the Mediterranean Oxalis flora in central Chile to the
interplay between population genetics and climatic niche evolution in four Horde-
um clades in the Americas. In these studies, I drew on existing methods in R and
on java and C programs that could be easily integrated with R. Whenever necessary,
I created additional software available in four new R packages. R's features,
e.g., intersystem-interfaces, extensibility, reproducibility and advanced graphical
capability, proved well suited for evolutionary and phylogenetic research.
My coauthors and I addressed the history of Cucurbitaceae, one of the most economically
important families of plants, using a multi-gene phylogeny for 114 of the
115 genera and 25 per cent of the 960 species. Worldwide sampling was achieved by
using specimens from 30 herbaria. Results reveal an Asian origin of Cucurbitaceae
in the Late Cretaceous, followed by the repeated spread of lineages into the African,
American and Australian continents via transoceanic long-distance dispersal
(LDD). North American cucurbits stem from at least seven range expansions of
Central and South American lineages; Madagascar was colonized 13 times, always
from Africa; Australia was reached 12 times, apparently always from Southeast
Asia. Overall, Cucurbitaceae underwent at least 43 successful LDD events over
the past 60 Myr, which would translate into an average of seven LDDs every 10
Myr. These and similar findings from other angiosperms stress the need for an increased
tapping of museum collections to achieve extensive geographical sampling in plant phylogenetics.
The second study focused on the interplay of population demography with the
evolution of ecological niches during or after speciation in Hordeum. While large
populations maintain a high level of standing genetic diversity, gene
ow and recombination buffers against fast alterations in ecological adaptation. Small populations harbor lower allele diversity but can more easily shift to new niches if
they initially survive under changed conditions. Thus, large populations should
be more conservative regarding niche changes in comparison to small populations.
My coauthors and I used environmental niche modeling together with phylogenetic,
phylogeographic and population genetic analyses to infer the correlation of
population demography with changes in ecological niche dimensions in 12 diploid
Hordeum species from the New World, forming four monophyletic groups. Our
analyses found both shifts and conservatism in certain niche dimensions within
and among clades. Speciation due to vicariance resulted in three species with no
pronounced climate niche differences, while species originating due to long-distance
dispersals or otherwise encountering genetic bottlenecks mostly revealed climate
niche shifts. Niche convergence among clades indicates a niche-filling pattern during
the last 2 Myr in South American Hordeum. We provide evidence that species
that did not encounter population reductions mainly show ecoclimatic niche conservatism,
while major niche shifts have occurred in species that have undergone
population bottlenecks. Our analyses allow the conclusion that population demography
influences adaptation and niche shifts or conservatism in South American
Hordeum species.
Finally, I studied the phylogenetic composition of Oxalis flora of Mediterranean
zone of Chile by asking whether in such a species-rich clade xerophytic adaptations
arose in parallel, at different times, or simultaneously. Answering this type
of question has been a major concern of evolutionary biology over the past few
years, with a growing consensus that lineages tend to be conservative in their vegetative
traits and niche requirements. Combined nuclear and chloroplast DNA
sequences for 112 species of Oxalidales (4900 aligned nucleotides) were used for
a fossil-calibrated phylogeny that includes 43 of the 54 species of Chilean Oxalis,
and species distribution models (SDMs) incorporating precipitation, temperature,
and fog, and the phylogeny were used to reconstruct ancestral habitat preferences,
relying on likelihood and Bayesian techniques. Since uneven collecting can reduce the power of SDMs, we compared 3 strategies to correct for collecting effort. Unexpectedly,
the Oxalis flora of Chile consists of 7 distant lineages that originated
at different times prior to the last Andean uplift pulse; some had features preadapting
them to seasonally arid or xeric conditions. Models that incorporated fog
and a `collecting activity surface' performed best and identified the Mediterranean
zone as a hotspot of Oxalis species as well as lineage diversity because it harbors
a mix of ancient and young groups, including insuficiently arid-adapted species.
There is no evidence of rapid adaptive radiation.
18
Winney, Bruce Joseph. "Cormorant population genetics and Turaco phylogenetics". Thesis, University of Nottingham, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285767.
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Kidd, Sarah E. "Molecular Phylogenetics of the Hawaiian Geraniums". Bowling Green State University / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1131138585.
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Robertson, Charles E. "Ecology, phylogenetics, and ultrastructure of Archaea". Connect to online resource, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3337146.
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Arab, Daej A. Kh A. M. "Australian Nasutitermitinae: Phylogenetics, Evolution, and Biodiversity". Thesis, The University of Sydney, 2015. http://hdl.handle.net/2123/13671.
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The Nasutitermitinae is a termite subfamily within the family Termitidae that contains 596 species in 77 genera, distributed globally. The group is characterised by the presence of soldiers with a pointed snout at the front of their heads, known as a nasus, which they use to spray chemicals at predators, as well as highly reduced or absent mandibles. A diverse array of nesting and feeding habits are found among the Nasutitermitinae. They are known to feed on sound and decaying wood, grass, leaf litter, and other decaying vegetable matter, as well as soil. They build their nests under the ground, sometimes under rocks or decaying wood, as well as inside wood, in trees, and as mounds. In Australia, 44 Nasutitermitinae species in six genera have been described. Many of these build mounds, including some of the largest on earth. In this study, I investigated phylogenetic relationships in the Nasutitermitinae, focusing on Australian representatives. I sequenced three mitochondrial genes from a total of 184 specimens, performed phylogenetic and molecular clock analyses to understand the pattern and timing of Nasutitermitinae evolution, and inferred the evolution of nest-building and feeding using ancestral state reconstruction (Chapter 2). The study represents the first detailed molecular investigation of Australian Nasutitermitinae. Previous morphological studies of this group suggested the presence of cryptic species within a number of recognized taxa. I examined species boundaries among Australian Nasutitermitinae samples using the generalised mixed yule coalescent approach, and detected a number of putative species that warrant further investigation (Chapter 3). Based on my results I propose tentative systematic revisions for the group, which require further sampling as well as sequencing and morphological studies for confirmation.
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Hanson-Smith, Victor 1981. "Error and Uncertainty in Computational Phylogenetics". Thesis, University of Oregon, 2011. http://hdl.handle.net/1794/12151.
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xi, 119 p. : ill. (some col.)The evolutionary history of protein families can be difficult to study because necessary ancestral molecules are often unavailable for direct observation. As an alternative, the field of computational phylogenetics has developed statistical methods to infer the evolutionary relationships among extant molecular sequences and their ancestral sequences. Typically, the methods of computational phylogenetic inference and ancestral sequence reconstruction are combined with other non-computational techniques in a larger analysis pipeline to study the inferred forms and functions of ancient molecules. Two big problems surrounding this analysis pipeline are computational error and statistical uncertainty. In this dissertation, I use simulations and analysis of empirical systems to show that phylogenetic error can be reduced by using an alternative search heuristic. I then use similar methods to reveal the relationship between phylogenetic uncertainty and the accuracy of ancestral sequence reconstruction. Finally, I provide a case-study of a molecular machine in yeast, to demonstrate all stages of the analysis pipeline. This dissertation includes previously published co-authored material.
Committee in charge: John Conery， Chair； Daniel Lowd， Member； Sara Douglas， Member； Joseph W. Thornton， Outside Member
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Hou, Chen. "Proteomics and phylogenetics of the Gnetales". Licentiate thesis, Stockholms universitet, Institutionen för ekologi, miljö och botanik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-102194.
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A central point of Darwin’s theory of evolution is that accumulation of many small changes during the evolutionary process can result in significant change over time. In light of his theory, plant scientists seek for and compare different plant traits among species e.g., from morphology, DNA or proteins in order to discover the underlying evolutionary patterns and processes. The Gnetales, an intriguing family that comprises Ephedra, Gnetum and Welwitschia, have puzzled scientists for over a century. Their features are evolutionarily difficult to understand in comparison with other seed plants and this has hampered analyses of evolution and phylogeny regardless of whether morphological or molecular data has been utilized. In this thesis, I first attempt (Paper I) to seek for a new evolutionary indicator; a protein profile from pollination drops of Ephedra is compiled, and the results are compared with those from conifers and other seed plants. The aim of this proteomic study was also to investigate whether proteomic profiles vary among Ephedra species and are affected by different selection factors, e.g., pollination mode, ovule protection etc. The results indicate, however, that proteins are present only in very small amounts in pollination drops of Ephedra, and mainly as waste products from degrading cells. This is surprising since proteins are considered important for defense of the naked ovules of gymnosperms, e.g., against pathogens. Pollination drops of Ephedra have a very high sugar concentration and it is possible that carbohydrates are responsible for ovule defense in Ephedra. The second chapter of my thesis (Paper II) is devoted to Gnetum; a phylogenetic study based on genetic markers derived from both nuclear ribosomal regions and chloroplast regions is conducted. Previous studies have been hampered by difficulties with outgroup comparison and homology assessments of informative gene regions. A few attempts have been made to estimate the deepest splits in the genus, all with a limited ingroup sampling. We address the phylogeny of Gnetum and make a first assessment of the monophyly of species, using a denser sampling of taxa and a combination of faster and more slowly evolving molecular markers. The results are discussed in comparison with previous classification and morphology, and will provide a basis for further studies of taxonomy, ecology, and biogeography in Gnetum.
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Hernandez, Rosales Maribel. "The Orthology Road". Doctoral thesis, Universitätsbibliothek Leipzig, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-127823.
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The evolution of biological species depends on changes in genes. Among these changes are the gradual accumulation of DNA mutations, insertions and deletions, duplication of genes, movements of genes within and between chromosomes, gene losses and gene transfer. As two populations of the same species evolve independently, they will eventually become reproductively isolated and become two distinct species. The evolutionary history of a set of related species through the repeated occurrence of this speciation process can be represented as a tree-like structure, called a phylogenetic tree or a species tree. Since duplicated genes in a single species also independently accumulate point mutations, insertions and deletions, they drift apart in composition in the same way as genes in two related species. The divergence of all the genes descended from a single gene in an ancestral species can also be represented as a tree, a gene tree that takes into account both speciation and duplication events.
In order to reconstruct the evolutionary history from the study of extant species, we use sets of similar genes, with relatively high degree of DNA similarity and usually with some functional resemblance, that appear to have been derived from a common ancestor. The degree of similarity among different instances of the “same gene” in different species can be used to explore their evolutionary history via the reconstruction of gene family histories, namely gene trees.
Orthology refers specifically to the relationship between two genes that arose by a speciation event, recent or remote, rather than duplication. Comparing orthologous genes is essential to the correct reconstruction of species trees, so that detecting and identifying orthologous genes is an important problem, and a longstanding challenge, in comparative and evolutionary genomics as well as phylogenetics.
A variety of orthology detection methods have been devised in recent years. Although many of these methods are dependent on generating gene and/or species trees, it has been shown that orthology can be estimated at acceptable levels of accuracy without having to infer gene trees and/or reconciling gene trees with species trees. Therefore, there is good reason to look at the connection of trees and orthology from a different angle: How much information about the gene tree, the species tree, and their reconciliation is already contained in the orthology relation among genes? Intriguingly, a solution to the first part of this question has already been given by Boecker and Dress [Boecker and Dress, 1998] in a different context. In particular, they completely characterized certain maps which they called symbolic ultrametrics. Semple and Steel [Semple and Steel, 2003] then presented an algorithm that can be used to reconstruct a phylogenetic tree from any given symbolic ultrametric. In this thesis we investigate a new characterization of orthology relations, based on symbolic ultramterics for recovering the gene tree.
According to Fitch’s definition [Fitch, 2000], two genes are (co-)orthologous if their last common ancestor in the gene tree represents a speciation event. On the other hand, when their last common ancestor is a duplication event, the genes are paralogs. The orthology relation on a set of genes is therefore determined by the gene tree and an “event labeling” that identifies each interior vertex of that tree as either a duplication or a speciation event. In the context of analyzing orthology data, the problem of reconciling event-labeled gene trees with a species tree appears as a variant of the reconciliation problem where genes trees have no labels in their internal vertices. When reconciling a gene tree with a species tree, it can be assumed that the species tree is correct or, in the case of a unknown species tree, it can be inferred. Therefore it is crucial to know for a given gene tree whether there even exists a species tree. In this thesis we characterize event-labelled gene trees for which a species tree exists and species trees to which event-labelled gene trees can be mapped. Reconciliation methods are not always the best options for detecting orthology. A fundamental problem is that, aside from multicellular eukaryotes, evolution does not seem to have conformed to the descent-with-modification model that gives rise to tree-like phylogenies. Examples include many cases of prokaryotes and viruses whose evolution involved horizontal gene transfer. To treat the problem of distinguishing orthology and paralogy within a more general framework, graph-based methods have been proposed to detect and differentiate among evolutionary relationships of genes in those organisms. In this work we introduce a measure of orthology that can be used to test graph-based methods and reconciliation methods that detect orthology. Using these results a new algorithm BOTTOM-UP to determine whether a map from the set of vertices of a tree to a set of events is a symbolic ultrametric or not is devised. Additioanlly, a simulation environment designed to generate large gene families with complex duplication histories on which reconstruction algorithms can be tested and software tools can be benchmarked is presented.
25
Spinks, Phillip Quinton. "Molecular phylogenetics and conservation of freshwater turtles /". For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2004. http://uclibs.org/PID/11984.
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Silva, Dylan De. "Phylogenetics of the genus Echium L. (Boraginaceae)". Thesis, University of Reading, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485364.
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Maximum parsimony and Bayesian analysis of the ITS 1&2, tm T-F and 5s rDNA spacer regions was performed for a selection ofmainland and island taxa from the genus Eehium. ITS and tm datasets reveal that both mainland and island taxa separate into two distinct clades. All but two of the island taxa show the characteristic of insular woodiness, suggesting that the evolution of this character may have been a 'key innovation' assisting the diversity ofthe genus on the Macaronesian islands. Lack of basal resolution in the trees generated from the ITS dataset meant that the relative ancestral vs. derived status of these two clades was unclear. Analysis of tm T-F data confirmed the split between mainland and island taxa with the latter being in a derived position in the tree. This is concordant with the results of a number of other studies undertaken for island taxa such as Aeonium, So'!ehus and Argyranthemum. Conflicts ~n the data meant that the combined ITS 1&2 and tm T-F tree was not basally resolved and the question of (', evolutionary polarity was again unclear. Both datasets showed a paucity of characters and lack of I teirninal resolution in the island clade. Hybridisation and long generations time is rejected as a possible cause of this genetic homogeneity and it is concluded that the island EeMa have instead undergone a recent and rapid radiative speciation. Relationships amongst island taxa were similarly unresolved following analysis of clones of the 5s NTS. Given that the 5s region is one of the most rapidly mutating regions of the plant genome, it is concluded that robust cladistic resolution is unlikely to be achievable with single or groups of genes in instances of rapid species radiations. It has been suggested that morphological characters, as direct manifestations of the evolutionary process, are better suited to the study of rapid species radiations. A morphological data matrix for a suite of 25 characters was constructed for Eehium and analysed using maximum parsimony. The perennial difficulty of recognising between convergence and true synapomorphy in morphological characters was highlighted by the paraphyletic nature of the resulting tree in which the mainland/island disjunction defined by molecular analyses was distorted and several outgroup taxa were placed deep within the ingroup. The validity of defming taxic relationships based on morphology in Eehium is therefore considered questionable. The implication associated with the lack of genetic variation in many island plant groups is discuSsed in the context of recognising conservation priorities. Should this minimal genetic diversity be a cause to reassess the conservation importance of island floras?
27
Seears, Heidi. "Biogeography and phylogenetics of the planktonic foraminifera". Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/11879/.
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The planktonic foraminifera are a highly abundant and diverse group of marine pelagic protists that are ubiquitously distributed throughout the worlds’ oceans. These unicellular eukaryotes are encased in a calcareous (CaCO3) shell or ‘test’, the morphology of which is used to identify individual ‘morphospecies’. The foraminifera have an exceptional fossil record, spanning over 180 million years, and as microfossils provide a highly successful paleoproxy for dating sedimentary rocks and archiving past climate. Molecular studies, using the small subunit (SSU) ribosomal (r) RNA gene are used here to investigate the biogeographical distributions and phylogenetic relationships of the planktonic foraminifera. Biogeographical surveys of two markedly different areas of the global ocean, the tropical Arabian Sea, and the transitional/sub-polar North Atlantic Ocean, revealed significant genotypic variation within the planktonic foraminifera, with some genetic types being sequenced here for the first time. The foraminiferal genotypes displayed non-random geographical distributions, suggestive of distinct ecologies, giving insight into the possible mechanisms of diversification in these marine organisms. The ecological segregation of genetically divergent but morphologically cryptic genetic types could, however, have serious repercussions on their use as paleoproxies of past climate change. Phylogenetic analyses of the foraminifera based firstly on a partial ~1,000 bp terminal 3´ fragment of the SSU rRNA gene, and secondly on the ~3,000 bp almost complete gene supported the hypothesis of the polyphyletic origins of the planktonic foraminifera, which appear to be derived from up to 5 separate benthic ancestral lineages. The almost complete gene is sequenced here in the planktonic taxa for the first time, though amplification was problematic. In a first step to addressing a pressing need for new genetic markers to support data gained from the SSU rRNA gene, a culture system was established for the benthic foraminifera, in order to provide a reliable source of DNA for EST library construction or full genome sequencing. Finally, to overcome difficulties associated with the PCR amplification of the foraminifera, a new lysis buffer and DNA extraction procedure was developed. A highly successful buffer was created, allowing high quality DNA to be extracted from foraminiferal specimens, whilst leaving the delicate calcitic shell intact for morphological reference.
28
Hone, David William Elliott. "The phylogenetics and macroevolution of the Archosauromorpha". Thesis, University of Bristol, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.432067.
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Eales, James Matthew. "Text-mining of experimental methods in phylogenetics". Thesis, University of Manchester, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.529251.
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Morris, Kirsty Janet. "North Atlantic octocorals : distribution, ecology and phylogenetics". Thesis, University of Southampton, 2011. https://eprints.soton.ac.uk/338892/.
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Most studies of deep-sea benthic fauna have concentrated on soft sediments with little sampling in rocky areas and even less on non-vent mid-ocean ridges and within submarine canyons, mainly as a result of difficulty accessing them. To assess the distribution and abundance of cold-water corals along an Axial Volcanic Ridges along the Mid-Atlantic ridge at 45oN 27oW, and within the Whittard Canyon along the Irish Margin video footage from the ROV Isis taken during a three scientific cruises was analysed. Samples were also taken to allow taxonomic and phylogentic work to be completed. Abundance of octocorals per 100 m transect were calculated and mapped using Arc GIS, with a maximum of 59 in the AVR compared to 855 within the Whittard Canyon. Thirty-one putative species were identified within the Whittard Canyon including some scleractinians, Eleven more than were found in along the AVR. Both locations indicated differences in coral assemblages dependent on substratum type with sedimented areas having increased occurrence of Pennatulidae and Chrysogorgiidae within the AVR and an increased abundance of Acanella and Radicipes upon sediment in comparison to rock within the Whittard Canyon. It is suggested that these differences in abundance and assemblage structure, both within and between the AVR and Whittard Canyon sites, reflects higher food availability as well as differences in substratum type on which coral larvae settle. Taxononomic investigations identified 4 new species from samples taken along the AVR, and are described within the thesis. Phylogenetic analysis of novel sequences obtained throughout this study, as well as published sequences, showed the presence of 3 clades A) Calcaxonia and some Alcyoniidae B) Holoaxonia and Pennatulacea C) some Alcyoniidae, Corallium and Paragorgia. When individual MSH1 and ND2 genes were combined the Pennatulacea separated out as a fourth clade. This was attributed to an increase in resolution when two or more genes are used for analysis. Results indicate that morphological taxonomy and molecular analysis are not in agreement and there is a requirement for some taxonomic revisions using molecular data to confirm species boundaries and help guide taxonomic decisions.
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Rebholz, Wilhelmus Ewald Reinaard. "Molecular phylogenetics and conservation aspects of antelopes". Doctoral thesis, University of Cape Town, 1996. http://hdl.handle.net/11427/26971.
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This thesis concerns the molecular phylogenetics of three tribes of the family Bovidae, the Antilopini, Neotragini, and Tragelaphini. None of these tribes have been studied extensively with molecular techniques. The tribe Antilopini is one of the most speciose tribes (it includes 6 genera with 20 species) and the classification of several species of the genus Gazella is not clear. The tribe Neotragini is thought to be paraphyletic. Mitochondrial sequences of the cytochrome c oxidase ill and cytochrome b genes totalling 1083 base pairs have been determined for 52 taxa and used to determine phylogenetic relationships using cladistic and distance methods. Karyological analysis identified polymorphisms in several species (especially in Gazella saudiya and G. subgutturosa). Karyotypes of G. dorcas pelzelni and an XXY karyotype of a G. dorcas individual are shown for the first time. The main conclusions are that the Antilopini and the Tragelaphini are monophyletic and that the tribe Neotragini is paraphyletic. There is a lack of phylogenetic resolution between tribes which is probably due to the rapid radiation of the different tribes about 20 million years ago. The genus Taurotragus in the tribe Tragelaphini is shown to be paraphyletic and it would be appropriate to incorporate these taxa in the genus Tragelaphus. The genus Gazella could be paraphyletic, due to the position of Antilope cervicapra, in which case the genus needs to be split into two genera or renamed as Antilope. It is also argued that the use of the subgenus Trachelocele should be discontinued and that its only species, G. subgutturosa should be included in the subgenus Gazella. G. rufifrons and G. thomsonii may be more appropriately considered as conspecific. Cytogenetic and sequence data reveal that the herd of G. saudiya in Al Areen Wildlife Park is hybridised with G. bennettii and it is argued that it is important to identify unhybridised G. saudiya in other collections, since this species is on the brink of extinction. This case study demonstrates the need to genetically screen individuals which are part of a captive breeding program, especially if they are intended for reintroduction into the wild.
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dos, Santos Ferreira Lins Luana. "Molecular phylogenetics, evolution and systematics of isopoda". Thesis, The University of Sydney, 2014. http://hdl.handle.net/2123/12705.
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Isopods are a remarkably diverse group of crustaceans that can be found in virtually all environments. Although the monophyly of this group is well supported, there remains uncertainty about the phylogenetic relationships within the group. The use of molecular data to infer the phylogeny of isopods offers a promising complement to the evidence provided by morphological data. This study uses a range of techniques to shed light on various aspects of isopod evolution. I inferred the phylogenetic relationships among isopod lineages and evaluated support for several major suborders. I estimated the timeframe for the isopods colonisation of the deep sea, freshwater and terrestrial habitats. Using mitochondrial genomes, I investigated patterns of evolutionary rate variation in isopods and other crustaceans. Lastly, I described two new species of asellotan isopods from the Australian deep sea, and extended the occurrence of one species to New South Wales, and one genus to Australia, improving our knowledge of Australian fauna. My thesis shows that the isopods colonised different environments many millions of years ago. In the case of the deep-sea clades, this study contradicts the hypothesis that the deep-sea fauna went extinct during anoxic events. The colonisation of continental environments coincided with the formation of the supercontinent Pangaea and with the diversification of vascular plants. Some suborders were found to be paraphyletic, conflicting with classical morphological views. My analyses of isopods and other crustaceans’ mitogenomes did not reveal any impact of lineage-by-gene interactions. This indicates that standard molecular-clock analysis can be used for analysing the mitogenomes of isopods and other crustaceans. Together with the other analyses presented in this thesis, my work contributes to the discussion of isopod systematics, to the understanding of the evolution of isopods, and to the provision of data for comparisons with other crustaceans.
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Cherlin, Svetlana. "Rooting major cellular radiations using statistical phylogenetics". Thesis, University of Newcastle upon Tyne, 2016. http://hdl.handle.net/10443/3492.
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Phylogenetics focuses on learning about evolutionary relationships between species. These relationships can be represented by phylogenetic trees, where similar species are grouped together as sharing a recent common ancestor. The common ancestor of all the species of the tree is the root of the tree. The root is fundamental to the biological interpretation of the tree, providing a critical reference point for polarising ancestor-descendant relation- ships and determining the order in which key traits evolved along the tree (Embley and Martin, 2006). Despite its importance, most models of sequence evolution are unable to infer the root of a phylogenetic tree. They are based on homogeneous continuous time Markov processes (CTMPs) that are assumed to be stationary and time-reversible, with the mathematical consequence that the likelihood of a tree does not depend on where it is rooted. As a result, the root of the tree cannot be inferred as part of the analysis. Other methods which are generally used to root evolutionary trees can be problematic. For example, the outgroup rooting method is susceptible to a long-branch attraction arte- fact. Paralogue rooting requires pairs of paralogous genes which underwent an ancient gene duplication event to be present in all species being analysed, and the number of such genes is limited. In this thesis we explore an alternative model-based approach, adopting a substitution model in which changing the root position changes the likelihood of the tree. We explore the e ect of relaxing reversibility and stationarity assumptions and allowing the position of the root to be another unknown quantity in the model. We propose two hierarchical non-reversible models which are centred on a reversible model but perturbed to allow non- reversibility. The models di er in the degree of structure imposed on the perturbations. We also explore non-stationary models, and the combination of relaxing both the reversibility and the stationarity assumptions. The analysis is performed in the Bayesian framework using Markov chain Monte Carlo methods. We illustrate the performance of the models in analyses of simulated datasets using two types of topological priors. We also investigate the e ect of di erent topologies and branch lengths on the inference. Our results illustrate the usefulness of modelling non- reversibility and non-stationarity for root inference, and also demonstrate the sensitivity of the analysis to topological priors. We then apply the models to real biological datasets, the radiation of polyploid yeasts and the radiation of primates, for which there is a robust biological opinion about the root position. Finally we apply the models to an open question in biology: rooting the ribosomal tree of life.
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au, V. Andjic@murdoch edu, i Vera Andjic. "Phylogeny, phylogeography and movement of Kirramyces spp. associated with leaf blight diseases of plantation eucalypts". Murdoch University, 2008. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20080805.133632.
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When this study commenced in early 2004, only five Phaeophleospora species. had been reported from eucalypts of which only two; P. destructans (STE-U 1336) and P. epicoccoides (STE-U 1346) had been sequenced. In a former study, Phaeophleospora species emerged in two separate clades suggesting that Phaeophelospora is polyphyletic. The appearance and severity of lesions on eucalypt leaves are generally used to recognise the species of Phaeophleospora responsible for disease. However, depending on host and climate, the symptoms associated with infection by P. epicoccoides, P. eucalypti and P. destructans can be almost identical and incorrect diagnosis is a common problem. Thus, Phaeophleospora species were compared based on DNA sequences and multi gene genealogies were constructed. In addition species- specific primers were designed and tested on leaf material.
Many isolates of Phaeophleospora spp. were collected and sequenced, and all Phaeophleospora spp. from eucalypts were shown to cluster together and are closely related to the most important leaf pathogens associated with eucalypts namely Colletogloeopsis zuluensis, Mycosphaerella cryptica and M. nubilosa. In contrast, these fungi are distantly related to the type specimen of the genus Phaeophleospora, P. eugeniae. Furthermore, all DNA sequences of isolates of P. destructans examined in this thesis, including the ex-type culture, were identical but different to one previously lodged in GenBank.
This phylogenetic separation led to a morphological study of the species assigned to Phaeophleospora and compared the species from eucalypts with P. eugeniae the type specimen of Phaeophleospora. The phylogenetic and morphological studies show that P. eugeniae is well separated from Phaeophleospora spp. occurring on eucalypts and led to the resurrection of the previous generic name, Kirramyces for Phaeophleospora spp. occurring on eucalypts. Furthermore, phylogenetic analysis and morphological observation of Kirramyces spp. and Colletogloeopsis spp. occurring on eucalypts showed considerable overlap between these two genera. Therefore, Colletogloeopsis was reduced to synonymy with Kirramyces. Consequently, the genus Kirramyces was expanded from five to 14 species, and included the description of two new species, K. angophorae and K. corymbiae. In order to assist with their identification a key based on morphology of conidia for Kirramyces species was developed.
Kirramyces destructans is a devastating pathogen originally described from Indonesia in 1996 and has since been found throughout Asia where all common tropical and subtropical plantation eucalypt species and hybrids are susceptible. K. destructans is considered a major biosecurity threat in Australia, both to native eucalypt forests and the tropical plantation industry. Prior to the current study, there had been no investigation into the origin and movement of this important pathogen. Thus, five gene regions and six microsatellite loci were sequenced for 43 representative isolates of K. destructans from a range of geographical locations and hosts. Two microsatellite markers detected very low nucleotide polymorphism (three haplotypes for each loci); five other gene regions, including four microsatellite region were uniform. This low level of genetic diversity provides strong evidence that K. destructans was introduced into Indonesia as a founder population and that it has subsequently been spread throughout Asia via human-mediated movement of germplasm. Timor and Northern Australia were considered to be a possible source of origin of this fungus, but the high susceptibility of native E. urophylla to K. destructans in Timor indicates that the pathogen is unlikely to be endemic to Timor.
The current distribution of Kirramyces eucalypti is New South Wales, Queensland, Victoria, Tasmania and New Zealand (North Island). The main host of this pathogen is E. nitens which is native to Victoria and New South Wales. Kirramyces eucalypti has not been found in South Africa, yet it causes a severe disease on eucalypt hybrids originating from South Africa growing in New South Wales indicating movement to these hybrids from either native eucalypts or nearby plantations. As such, K. eucalypti poses a threat for the plantation industry in sub-tropical and tropical Australia. The phylogeography of K. eucalypti in Australia and New Zealand was studied by sequencing three gene regions and one microsatellite locus of fifty-seven representative isolates of K. eucalypti from Queensland, New South Wales, Victoria, Tasmania and New Zealand. The highest genetic variation was found among isolates from NSW suggesting that K. eucalypti originates from NSW. Isolates in New Zealand appear to have been introduced from NSW. Isolates from Queensland were consistently different to those from other regions and may in fact represent a cryptic species or a hybrid.
During monitoring of eucalypt taxa trials in far North Queensland, infected leaves resembling symptoms typical of K. destructans were collected and examined. Phylogenetic data based on three gene regions and some morphological characteristics revealed a new taxon described in this study as K. viscidus. Kirramyces viscidus was also shown to be closely related to the devastating pathogen K. destructans. Kirramyces viscidus had been found to cause extensive damage to eucalypt hybrids originating from South America, and less damage to E. grandis from Australia, indicating that this pathogen is probably endemic to Australia. Kirramyces viscidus has the potential to seriously damage tropical eucalypt plantations, especially if clonal and planted off-site.
In conclusion, this study resurrected genus Kirramyces for the Phaeophleospora and Coletoglloeopsis spp. occurring on eucalypts. It also studied the phylogeography and gene flow of the two most important Kirramyces species, K. destructans and K. eucalypti and describes three new Kirramcyes spp. found on eucalypts in Australia. Very recently, K. destructans has been discovered in Northern Australia. This raises a whole series of new issues as there are now several pathogens, K. eucalypti, K. viscidus and K. destructans present in Australia that known to cause serious damage on plantation eucalypts. Recent investigations have also revealed several undescribed Kirramyces spp. in Northern Australia. Their impact, distribution, movement and potential for hybridization now need to be examined.
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Bordewich, Magnus. "The complexity of counting and randomised approximation". Thesis, University of Oxford, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289352.
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Wanke, Stefan, Mendoza Carolina Granados, Julia Naumann, Marie-Stéphanie Samain, Paul Goetghebeur i Smet Yannick De. "A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea". Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-192196.
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Background
Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other "fast" evolving plastid markers.
Results
Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae).
Conclusions
While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.
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Svennblad, Bodil. "On Estimating Topology and Divergence Times in Phylogenetics". Doctoral thesis, Uppsala University, Mathematical Statistics, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8441.
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This PhD thesis consists of an introduction and five papers, dealing with statistical methods in phylogenetics.
A phylogenetic tree describes the evolutionary relationships among species assuming that they share a common ancestor and that evolution takes place in a tree like manner. Our aim is to reconstruct the evolutionary relationships from aligned DNA sequences.
In the first two papers we investigate two measures of confidence for likelihood based methods, bootstrap frequencies with Maximum Likelihood (ML) and Bayesian posterior probabilities. We show that an earlier claimed approximate equivalence between them holds under certain conditions, but not in the current implementations of the two methods.
In the following two papers the divergence times of the internal nodes are considered. The ML estimate of the divergence time of the root is improved if longer sequences are analyzed or if more taxa are added. We show that the gain in precision is faster with longer sequences than with more taxa. We also show that the algorithm of the software package PATHd8 may give biased estimates if the global molecular clock is violated. A change of the algorithm to obtain unbiased estimates is therefore suggested.
The last paper deals with non-informative priors when using the Bayesian approach in phylogenetics. The term is not uniquely defined in the literature. We adopt the idea of data translated likelihoods and derive the so called Jeffreys' prior for branch lengths using Jukes Cantor model of evolution.
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Sebastian, Patrizia. "Phylogenetics and biogeography of two clades of Cucurbitaceae". Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-146298.
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Jewell, Sean William. "Divide and conquer sequential Monte Carlo for phylogenetics". Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/54514.
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Recently reconstructing evolutionary histories has become a computational issue due to the increased availability of genetic sequencing data and relaxations of classical modelling assumptions. This thesis specializes a Divide & conquer sequential Monte Carlo (DCSMC) inference algorithm to phylogenetics to address these challenges. In phylogenetics, the tree structure used to represent evolutionary histories provides a model decomposition used for DCSMC. In particular, speciation events are used to recursively decompose the model into subproblems. Each subproblem is approximated by an independent population of weighted particles, which are merged and propagated to create an ancestral population. This approach provides the flexibility to relax classical assumptions on large trees by parallelizing these recursions.Science, Faculty of
Statistics, Department of
Graduate
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Nylander, Johan A. A. "Bayesian Phylogenetics and the Evolution of Gall Wasps". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3996.
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Randall, Ryan Nicole. "Experimental phylogenetics: a benchmark for ancestral sequence reconstruction". Thesis, Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/48998.
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The field of molecular evolution has benefited greatly from the use of ancestral sequence reconstruction as a methodology to better understand the molecular mechanisms associated with functional divergence. The method of ancestral sequence reconstruction has never been experimentally validated despite the method being exploited to generate high profile publications and gaining wider use in many laboratories. The failure to validate such a method is a consequence of 1) our inability to travel back in time to document evolutionary transitions and 2) the slow pace of natural evolutionary processes that prevent biologists from ‘witnessing’ evolution in action (pace viruses). In this thesis research, we have generated an experimentally known phylogeny of fluorescent proteins in order to benchmark ancestral sequence reconstruction methods. The tips/leaves of the fluorescent protein experimental phylogeny are used to determine the performances of various ASR methods. This is the first example of combining experimental phylogenetics and ancestral sequence reconstruction.
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Idid, Mohammed Rizman. "Phylogenetics and population structure of Lake Malawi cichlids". Thesis, University of Hull, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418795.
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Corfe, Ian J. "Competing hypotheses and character conflict in palaeontological phylogenetics". Thesis, University of Bristol, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.496222.
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What happens in the case where more than one morphologic dataset is used to generate hypotheses of phylogeny for fossil taxa? Sometimes the different investigations produce congruent results, but more often than not, a degree of conflict between the relationships hypothesised is observed. Little work has been carried out on quantifying this conflict, and still less on discerning the source(s) and cause(s) of such conflict, especially for morphological (as opposed to molecular) data. As evolutionary studies are critically dependent upon the accuracy of phylogenies, finding the cause of phylogenetic conflict becomes a keystone of accurate evolutionary biology. Here, two case studies are examined in which conflict is identified between competing morphological, palaeontological phylogenetic hypotheses. The first, investigating the relationships of sauropod dinosaurs, focuses on two more or less independently derived datasets. By quantifying and identifying sources of statistically significant conflict between the phylogenetic hypotheses produced, it highlights priority areas for further study in order to produce more congruent estimates of relationship. It is shown that congruence has increased through time between competing sauropod phylogenies. By following a stepped methodology, increasingly more detail can be resolved regarding the presence, statistical significance, source(s) and cause(s) of the remaining conflict. The second involves a very small number of rescorings and recodings to an existing dataset based on a recently described specimen of Archaeopteryx. These result in a dramatically different phylogenetic hypothesis - namely, the polyphyly of Aves. It is shown that this is not statistically significantly betterer supported than the original hypothesis of a monophyletic Aves, and that relationshij general within coelurosaurian dinosaurs are very uncertain, and subject to change with extremely minor differences in character scoring.
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Gardiner, Laura Maria. "Phylogenetics and conservation of the Genus Vanda (Orchidaceae)". Thesis, University of East Anglia, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.446457.
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The most comprehensive molecular study of the genus Vanda Jones ex R. Br and closely affiliated taxa to date is presented here, greatly contributing to the understanding of this diverse genus, horticulturally important, yet threatened in the wild. Using sequence data from three chloroplast regions, it is shown that Vanda s. l. forms a monophyletic Glade containing approximately 70 species, including the genera Ascocentrum, Euanthe, Christensonia, Neofinetia, and Trudelia, and the species Aerides flabellata. Resolution of the relationships between these groups of species within Vanda s. I. is low and Ascocentrum and Neofinetia, with their distinctive morphological character sets, may form separate monophyletic and basal sister genera to the rest of the genus. Existing morphological classification systems for the genus Vanda are partially incongruent to the phylogenies produced, and some novel species relationships are revealed. A potential 'out of Asia' colonisation route for the genus and affiliated genera is inferred from the phylogeny and geographic distributions of taxa. A single morphologically diverse species from the genus, V. tricolor, is found to exhibit genetic and geographic structure across its range in Java and Bali, and is assessed in the context of a reintroduction programme taking place in Java. A hypothesised historical route of dispersal is inferred from the data, with the most recent common ancestor as being from the Philippines/Sulawesi region and estimated at having diverged into Java and Bali in the early Pleistocene era. A novel study of the relationship between genetic and geographic distances between species in selected orchid genera shows that a degree of phylogenetic signal is carried by present day distribution data. Very simple, non-specific data sources and basic methods are used to reveal this signal and future research in this area could provide a useful conservation tool for rapid assessment of phylogenetic relatedness of taxa
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Gillett, C. P. D. T. "Molecular phylogenetics of the superfamily Curculionoidea (Insecta: Coleoptera)". Thesis, University of East Anglia, 2014. https://ueaeprints.uea.ac.uk/67069/.
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This thesis examines higher-level evolutionary history within the superfamily Curculionoidea, the most speciose family-level taxon, which includes beetles commonly known as weevils. This is achieved using a phylogenetic approach incorporating the largest datamatrix yet employed for weevil molecular systematics, and includes an investigation into the prospect of obtaining short phylogenetically informative amplicons from archival museum specimens. Newly obtained DNA sequence data is analysed from a variety of mitochondrial and nuclear loci, including 92 mitogenomes assembled through the approach of next-generation sequencing of pooled genomic DNA. The resulting trees are used to test previous morphological- and molecular-based hypotheses of weevil relationships and classification schemes. Mitogenomic-derived trees reveal topologies that are highly congruent with previous molecular studies, but that conflict with some morphological hypotheses. Strong nodal support strengthens inferences into the relationships amongst most weevil families and suggests that the largest family, the Curculionidae, is monophyletic, if the subfamily Platypodinae is excluded. Division of the Curculionidae into two large clades is well supported and the wood-boring habit adopted by three subfamilies is shown to have arisen multiple times, contradicting most morphological analyses. Addition of several nuclear loci to the mitogenomic data is found to provide little additional value, in terms of improving nodal bootstrap support. A suggestion is made that future efforts to enhance understanding of relationships should focus on improving taxon sampling. Statistical tests of an augmented dataset, derived from public database sequences for single mitochondrial genes, wherein multiple tribes and subfamilies within the broad-nosed weevils are constrained as monophyletic, indicate that three entimine tribes, as currently defined, are each not consistent with the hypothesis for their monophyly. Incongruences between molecular data and classical morphological taxonomy are suggestive that the current weevil classification system is misleading if used to interpret species richness, geographic distributions or ecological traits within currently recognised lineages.
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Bozkus, Nebahat. "Cluster detection by lifting with application to phylogenetics". Thesis, University of Leeds, 2018. http://etheses.whiterose.ac.uk/21300/.
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In this thesis, we propose a new algorithm which automatically detects the number of clusters in a tree structure data set by denoising some generalized node values in the tree using lifting “one coefficient at a time” (LOCAAT) algorithm introduced by Jansen et al. (2001). Our algorithm can be applied to any multidimensional data set using compactness value as a node value or to phylogenetic data sets, DNA sequences, using either compactness value or dissimilarity score as a node value. Compactness value is defined as the average distance from the centroid of each possible cluster in the tree, and the dissimilarity score is the average number of loci, where at least one of them does not share the same nucleotide between sequences under the node of interest. For multidimensional data sets, we consider each node in the tree as a possible location of a cluster after denoising the tree by LOCAAT. Thus, for each possible cluster, we check how much departure we can allow from the centroid of the cluster to assign the objects under the node of interest as a cluster. Then if a node and all its child nodes are denoised less than or equal to the allowed amount of departure from the centroid of their clusters, a cluster is located at this node. We also propose another version of our algorithm based on non-decimated lifting (Knight & Nason, 2009) in which we generate a probability of being clustered for each node. If a node and all its child nodes have a probability of being clustered less than or equal to the probability of acceptance, θ∈[0; 1], a cluster is located at this node. We provide a comparison study between our algorithms and some available internal cluster validity indices (CVIs) in the literature using some artificial data sets and a real data set. In addition, we compare the performance of each method using some available external cluster validity scores. For phylogenetic data sets, we check the performance of our algorithms and other CVIs using both compactness value and dissimilarity score as a node value. To be able to compute compactness value for a phylogenetic tree, we need to find the position of each specie in Rp using multidimensional scaling (MDS), and then we can find which species share the similar features using our algorithm. If we use the dissimilarity score as a node value, we will cluster similar species together by finding how much difference we can allow between species. We check the performance of our algorithms using some artificial and a real data sets. In the final part of our thesis, we propose a visualization tool for cophylogenetic data sets. We only consider the associated two phylogenetic trees case, and we apply our algorithm to both host and parasite trees separately to provide a summary of these data sets. We check the performance of our algorithm using two well-known cophylogenetic data sets.
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Pereira, da Conceicoa Lyndall Louise. "Phylogenetics and historical biogeography of the Teloganodidae (Ephemeroptera)". Thesis, Rhodes University, 2016. http://hdl.handle.net/10962/64900.
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The Teloganodidae are a mayfly family endemic to the southwestern Cape (South Africa), with relatives in Madagascar and Asia. Like many other aquatic invertebrates in Africa, they have been considerably understudied. Research into biodiversity and biogeography allows an understanding of the earth’s biota, producing knowledge which can be used to develop strategies to preserve and monitor this biota. Mismanagement of water systems places biodiversity of river fauna under an ever-increasing extinction threat. This investigation explores rivers in under-collected areas to determine how well teloganodids have been represented in the literature, with four genera and five species described at the onset of this study. A lectotype for Lestagella penicillata Barnard (1940) has been elected and described in detail, setting “benchmark” characters for future descriptions. Standard DNA sequencing methods provide portions of three mitochondrial genes; cytochrome oxidase subunit I (COI), small subunit ribosomal 16S RNA (16S), 12S ribosomal DNA (12S) and two nuclear genes, Histone 3 (H3) and 28S ribosomal DNA (28S) for up to 255 specimens. Fore and hind wings of 79 teloganodid adults were used to examine phylogenetic signal and evolutionary divergence using geometric morphometrics. A multi-faceted approach is used to investigate relationships between clades and the effects of deep-time climatic and landform changes which have influenced the diversity and distribution seen today. Tree (Bayesian Inference and Maximum Likelihood) and network (parsimony) phylogenies, ancestral reconstruction, historical biogeography and wingevolution of the Teloganodidae are investigated. Species tree analyses discovered 27 species and six genera. Distinct lineages are restricted to catchments, and strong phylogeographic structure was found within most genera. Southern African Teloganodidae are shown to have originated in the Cretaceous, with divergence and dispersal of lineages depended on their established locality at the time of tectonic events (uplift) and climatic changes (sea level regressions and transgressions). Geographic clines in wing-shape of Lestagella across its range imply evolutionary adaptations to specific catchment landscape and environment. A detailed analysis of biodiversity has many valuable contributions, from directing future research, understanding adaptive processes, fine-tuning phylogeographical and evolutionary hypotheses, to improving management and conservation decisions in order to preserve endemic biodiversity hotspots.
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Barnes, Keith N. "The phylogenetics and evolution of Africa's larks (Alaudidae)". Doctoral thesis, University of Cape Town, 2007. http://hdl.handle.net/11427/6228.
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Includes bibliographical references.The larks are a group of dull coloured birds that are conservative in plumage coloration and pattern due to the requirements for camouflage in open habitats. Because many species inhabit structurally similar habitats the group is also characterised by a great deal of morphological convergence. Variation in plumage and morphology is frequently as great within species as it is between species, leading to many inconsistent and controversial taxonomic treatments and classifications at an intra- and inter-generic level, and when defining specific and sub-specific boundaries. The advent of genetic techniques and success at applying these to species complexes in southern Africa suggested that a molecular phylogeny of the family would elucidate relationships that could not be determined via traditional taxonomic practices. In this study 2009 nucleotides of two mitochondrial DNA genes, cytochrome b and 16S rRNA (Chapter 2), and 2872 nucleotides of the nuclear exon RAG-l (Chapter 3) were used to generate a robust phylogeny of the family Alaudidae. The former analysis included 55 species and the latter 25. These data were also combined to construct a combined evidence phylogeny (Chapter 7). Within the family, several genera recognised by more traditional taxonomies are polyphyletic, including Ammomanes, Eremalauda .and Certhilauda. Two other genera, Calandrella and Mirafra, are best treated as multiple genera (Chapter 2). The sampled Alaudidae can be divided into three main radiations, the ammomanid larks, mirafrid larks and alaudid larks (Chapter 3). Within the ammomanid larks, there is strong support for: (1) a southern African' radiation comprising Chersomanes, the Long-billed Lark complex (Certhilauda) and Ammomanes (Ammomanopsis) grayi ,with Alaemon allied to this radiation; and (2) a .Saharo-Sindian radiation comprising Ramphocoris c1otbey, Ammomanes cinc(urus, and A. deserti sister to the Afro-Sindian sparrowlark Eremopterix clade. The Madagascan endemic Mirafra hova was a surprise basal member of Eremopterix.
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Aguiar, Alexandre Pires. "Phylogenetics and systematics of the World Stephanidae (Hymenoptera) /". The Ohio State University, 2000. http://rave.ohiolink.edu/etdc/view?acc_num=osu1488195154356513.
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Lopez-Osorio, Federico. "Phylogenetics And Molecular Evolution Of Highly Eusocial Wasps". ScholarWorks @ UVM, 2016. http://scholarworks.uvm.edu/graddis/569.
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Societies where workers sacrifice their own reproduction and cooperatively nurture the offspring of a reproductive queen caste have originated repeatedly across the Tree of Life. The attainment of such reproductive division of labor enabled the evolution of remarkable diversity in development, behavior, and social organization in the Hymenoptera (ants, bees, and wasps). Wasps of the family Vespidae exhibit a gamut of social levels, ranging from solitary to highly social behavior. The highly social yellowjackets and hornets (Vespinae) have well developed differences in form and function between queens and workers, large colony sizes, and intricate nest architecture. Moreover, certain socially parasitic species in the Vespinae have secondarily lost the worker caste and rely entirely on the workers of a host species to ensure the survival of parasitic offspring. Understanding the evolution of behavioral traits in the Vespinae over long periods of time would be greatly enhanced by a robust hypothesis of historical relationships.
In this study, I analyze targeted genes and transcriptomes to address three goals. First, infer phylogenetic relationships within yellowjackets (Vespula and Dolichovespula) and hornets (Vespa and Provespa). Second, test the hypothesis that social parasites are more closely related to their hosts than to any other species (Emery's rule). Third, test the protein evolution hypothesis, which states that accelerated evolution of protein coding genes and positive selection operated in the transition to highly eusocial behavior. The findings of this study challenge the predominant understanding of evolutionary relationships in the Vespinae. I show that yellowjacket genera are not sister lineages, instead recovering Dolichovespula as more closely related to the hornets, and placing Vespula as sister to all other vespine genera. This implies that traits such as large colony size and high paternity are mostly restricted to a particular evolutionary trajectory (Vespula) from an early split in the Vespinae. I demonstrate that obligate and facultative social parasites do not share immediate common ancestry with their hosts, indicating that socially parasitic behavior likely evolved independently of host species. Moreover, obligate social parasites share a unique evolutionary history, suggesting that their parasitic behavior might have a genetic component. Lastly, I analyze transcriptomic data to infer a phylogeny of vespid wasps and use this phylogeny to discover lineage-specific signatures of positive selection. I identify more than two hundred genes showing signatures of positive selection on the branch leading to the highly eusocial yellowjackets and hornets. These positively selected genes involve functions related mainly to carbohydrate metabolism and mitochondrial activity, in agreement with insights from studies of bees and ants. Parallels of functional categories for genes under positive selection suggests that at the molecular level the evolution of highly eusocial behavior across the Hymenoptera might have followed similar and narrow paths.