Chenopodium quinoa Willd., an ancient Andean pseudocereal almost exclusively consumed in South America, jumped onto the global stage when Western cultures noted quinoa's advantageous nutritional profile. Quinoa seed's high protein content, nutritionally balanced amino acid profile, low glycemic index, and high fiber, vitamin, and mineral content, make it a highly sought-after 'superfood'. Pitseed goosefoot (C. berlandieri Moq.), a closely related North American species sharing quinoa's genome composition (AABB), grows across the North American continent, inhabiting diverse environments including the saline coastal soils of the Gulf of Texas and the drought-prone regions of the Southwest. Quinoa and pitseed goosefoot, along with South American avian goosefoot (C. hircinum Schrad.), make up the Allotetraploid Goosefoot Complex (ATGC). We hypothesize that an ancient hybridization event between A- and B-genome diploids, with a subsequent whole-genome duplication, gave rise to the common ancestor of the ATGC. Prior data indicate that allopolyploidization most likely occurred within North America, with long-range dispersal of the ATGC to South America. We have sequenced the genome of the North American AA-genome diploid C. watsonii and identified via DNA marker analyses the closest extant species to the AA-genome diploid ancestor of the ATGC from among a panel of 41 AA-genome diploid resequenced accessions, encompassing 30 putative AA-genome diploid species, from North and South America. We also present evidence for reciprocal long-range dispersal of Chenopodium diploids between North and South America.

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.

The North American genus Speyeria is an especially challenging radiation of butterflies due to ongoing hybridization, incomplete lineage sorting, and similar morphological characters among species. Adaptive radiations often require considerable evidence in order to resolve the evolutionary relationships of closely related individuals. Previous studies of this genus have found paraphyly among species and have been unable to disentangle these taxa due to a lack of data and/or incomplete sampling of the genus. As a result, the interspecific relationships among Speyeria remain unresolved. In an attempt to achieve phylogenetic resolution of the genus, we conducted population genomic and phylogenomic analyses of all North American Speyeria species, as well as several subspecies, based on genome wide markers using the SbfI restriction enzyme and restriction site associated DNA sequencing (RADseq). Together, our analyses recovered 16 species within Speyeria, validating previous taxonomic work. However, consistent with recent molecular analyses, internal relationships have poor support. This lack of resolution indicates Speyeria represent an ongoing adaptive radiation, with incomplete lineage sorting, hybridization, and lack of postzygotic reproductive barriers, supporting this hypothesis.

Peregrine falcon subspecies taxonomy is widely debated due to uncertainty in their evolutionary history and unresolved phylogenetic reconstruction using both morphological and molecular data. Previous genetic work has shown limited support for subspecies taxonomy largely as a result of molecular markers used, potential contemporary gene flow, incomplete lineage sorting, and ancestral polymorphisms. With the advent of next-generation sequencing, the cost of generating large amounts of sequence data has dropped significantly, making whole genome re-sequencing (WGR) studies of non-model organisms more tangible. In this study, WGR methods have been utilized to investigate the phylogenetic relationships among all 20 currently recognized peregrine falcon subspecies. By generating whole-genome data for all 20 subspecies, subspecies specific diagnostic SNPs have been identified to aid in subspecies delimitation. Results of this study broadly support current subspecies, however, reveal that further study is needed to investigate regional relationships among subspecies in Asia, Australia, and western North America. With these results, conservation efforts can be further supported by allowing for accurate delimitation of local subspecies and subspecies boundaries.

Once thought to be an evolutionary dead-end, hybridization is now being detected in genomes across kingdoms, perhaps even playing an integral role in evolution. In chapter 1, I investigated the potential influences of hybridization on the evolution of a group of vagrant, asexual species in the Rhizoplaca melanophthalma species group. I sequenced the mitochondrial and nuclear genomes of 55 specimens and found well-supported nuclear phylogenies of both datasets. There were, however, multiple instances of discordance between the mitochondrial and nuclear trees, which can be caused by hybridization. PhyloNet and ABBA-BABA also detected widespread hybridization among this group. In chapter 2, I shifted to the Holarctic clade of lichen-forming fungi in Xanthoparmelia to characterize gene tree conflict and investigate the potential for hybrization. Here, I used three different tests for hybridization that account for incomplete lineage sorting "ABBA-BABA, PhyloNet, and SplitsTree" as well as PhyParts to characterize gene tree conflict. Like the Rhizoplaca species group, widespread hybridization was detected in the Holarctic clade despite robust phylogenies. My research underscores the value of investigating hybridization when studying species boundaries and evolutionary history.

Coleoptera is currently the most diverse lineage of life on Earth with more than 400,000 described species. The group also contains unbelievable ecological and morphological variation that has been evolving since the early Carboniferous (>350 MYA). The group provides the perfect playground to test evolutionary hypotheses with large-scale phylogenies. First, a newly developed bioinformatics tool is presented that allows for the critical assessment of the stability of phylogenetic nodes with even minor changes in taxon sampling (i.e. a single taxon jackknifed). The tool, TANOS, is capable of performing tests on large genomics-scale datasets. The case study included is a widely used phylogenomics effort to resolve the higher level relationships of all Insecta. The specific beetle group chosen for the remaining products is the superfamily Cucujoidea, and more specifically the family Nitidulidae, or sap beetles. Several taxonomic and nomenclatural projects were necessary to provide a more stable classification and begin the process of establishing the group as a model system for questions concerning feeding behavior evolution. Several new species of the genus Carpophilus were described from both the West Indies and the New World tropics and subtropics. Several type designations were also needed for many species in the subfamily Carpophilinae. In addition, the fossil diversity of Nitidulidae was reviewed with the addition of the oldest known member of the Cillaeinae from amber (Dominican). With the reviewed fossil fauna, as well as many more from across the Cucujoidea more broadly, a divergence-time estimated phylogeny was generated for >250 species of the superfamily. The phylogeny, based on the combination of multiple published Sanger datasets and supplemented with newly generated data for a further 50 species, was used to date multiple feeding shifts in the group. Specifically, the clade ages were used to compare with published clade ages for the corresponding food resource each clade is known to exploit. A significant relationship was recovered between age of the beetle clade and the corresponding food resource clade. Interestingly, it was found that clades that shifted to a food resource first, in the absence of existing beetle competitors, were significantly more diverse over subsequent lineages that shifted to the same resource. A feeding ecology of specific importance, at least to many groups of nitidulid, is anthophily, or flower-visiting. An extreme variation in eye size is observable across the family and so multiple factors including; sex, day-night activity, and feeding behavior were tested in a phylogenetic context. No sexual dimorphism nor variation consistent with activity period was found. Relative eye size of flower visiting species was significantly larger than that of all other feeding behaviors in sap beetles. This correlation was also tested in a phylogenetic context, with the increase in morphological investment in vision repeatedly shown to correspond to shifts in flower associated behavior. In an attempt to investigate the interplay between behavior, morphology, and genetics in the same process, opsin data was captured as part of a large targeted enrichment sequencing effort (AHE) across Nitidulidae and their relatives. The first phylogenomic estimate was generated for the group, with a taxon sampling of 192, and data sampling depth of 703 loci. A newly updated pipeline was developed for AHE data and is presented herein. Topological results support the recent idea of a non-monophyletic Cucujoidea. Results also demonstrate multiple classification issues within the Nitidulidae with several new subfamilies/tribes necessary to maintain diagnosable monophyletic groups in the family. The vast majority of sampled genera were supported, with the exception of Brachypeplus and Pallodes. Preliminary opsin diversity across the group is much greater than previously estimated. Opsin copy number is potentially plastic even within individual genera, although consistently duplications are associated with taxa that visit flowers. It is clear that the complexity of cucujoid visual systems increases with anthophilous behavior.

<p dir="ltr">Sepidiini is a large and morphologically diverse tribe of darkling beetles (Tenebrionidae) in the subfamily Pimeliinae, containing ~1,000 species and subspecies. Despite the presence of many large and charismatic species and the cultural significance of some of its members, the toktokkie beetles, this tribe has been lacking revision at all taxonomic levels. To develop a framework for taxonomic revisionary work, in Chapter 1, I reconstructed a phylogeny of the tribe using targeted enrichment sequencing data. I also scored a comprehensive suite of diagnostic characters for the tribe to test in a phylogenetic context. Based on the results of the study, I proposed revising the subtribe Oxurina Koch, 1955, <b>sens. nov. </b>(now containing the genera <i>Oxura </i>Kirby, 1918, and <i>Miripronotum </i>Louw, 1979) and moving the genera <i>Decoriplus </i>Louw, 1979, <i>Pterostichula </i>Koch, 1952, <i>Stenethmus </i>Gebien, 1937b, and <i>Synhimba </i>Koch, 1952 to a new subtribe Stenethina <b>subtr. nov. </b>The tree topology also supports revising or synonymizing the genera <i>Dichtha </i>Haag Rutenberg, 1871, and <i>Amiantus </i>Fåhraeus, 1870,<i> </i>and revising the genus <i>Somaticus </i>Hope, 1840.</p><p dir="ltr">In Chapter 2, I performed a partial revision of the subtribe Hypomelina Koch 1955. A new genus <i>Bufoniopsis </i><b>gen. nov. </b>is erected containing one newly described species <i>Bufoniopsis hypnosis</i> <b>sp. nov. </b>The genus <i>Hypomelus </i>Solier, 1843, and all of its species are redescribed, and three new species are described: <i>Hypomelus johnprinei</i> <b>sp. nov</b>., <i>Hypomelus lorettalynnae</i> <b>sp. nov.</b>, and <i>Hypomelus tomhalli</i> <b>sp. nov</b>. One species was moved from <i>Hypomelus </i>to <i>Triangulipenna</i><i> </i>Louw 1979<i> </i>and redescribed, <i>Triangulipenna vulipnus </i>(Haag Rutenberg, 1873)<i> </i><b>comb. nov. </b><i>Triangulipenna </i>was redescribed and three new species were described, <i>Triangulipenna tylerchildersi </i><b>sp. nov.</b>, <i>Triangulipenna dollypartonae</i> <b>sp. nov</b>., and <i>Triangulipenna ralphstanleyi</i> <b>sp. nov</b>. A revised key to the genera of Hypomelina is provided as well as keys to the species of <i>Hypomelus </i>and <i>Triangulipenna</i>.</p><p dir="ltr">Toktokkie beetles—members of the subtribe Molurina Solier, 1843—are known for their substrate tapping behavior which is a form of sexual communication in which beetles tap their abdomens on the ground to locate mates. Despite the fact that this behavior is well-known among people in southern Africa, very little research has been done on the topic. In Chapter 3, I document variation in tapping patterns across the subtribe Molurina. Three characters of tap trains were found to vary: length of tap trains, tapping rate, and tapping pattern. Ancestral state reconstruction was performed for each of the characters. Characters were found to be only partially linked to ancestry. Additionally, in any given locality sampled, no two species had the same “song”. This suggests that signal partitioning could be influencing species “songs”.</p>

No description available.

Plants and animals are characterized by intimate, enduring, often indispensable, and always complex associations with microbes. Therefore, it should come as no surprise that when the genome of a eukaryote is sequenced, a medley of bacterial sequences are produced as well. These sequences can be highly informative about the interactions between the eukaryote and its bacterial cohorts; unfortunately, they often comprise a vanishingly small constituent within a heterogeneous mixture of microbial and host sequences. Genomic analyses typically avoid the bacterial sequences in order to obtain a genome sequence for the host. Metagenomic analysis typically avoid the host sequences in order to analyze community composition and functional diversity of the bacterial component. This dissertation describes the development of a novel approach at the intersection of genomics and metagenomics, aimed at the extraction and characterization of bacterial sequences from heterogeneous sequence data using phylogenomic and bioinformatic tools. To achieve this objective, three interoperable workflows were constructed as modular computational pipelines, with built-in checkpoints for periodic interpretation and refinement. The MetaMiner workflow uses 16S small subunit rDNA analysis to enable the systematic discovery and classification of bacteria associated with a host genome sequencing project. Using this information, the ReadMiner workflow comprehensively extracts, assembles, and characterizes sequences that belong to a target microbe. Finally, AssemblySifter examines the genes and scaffolds of the eukaryotic genome for sequences associated with the target microbe. The combined information from these three workflows is used to systemically characterize a bacterial target of interest, including robust estimation of its phylogeny, assessment of its signature profile, and determination of its relationship to the associated eukaryote. This dissertation presents the development of the described methodology and its application to three eukaryotic genome projects. In the first study, the genomic sequences of a single, known endosymbiont was extracted from the genome sequencing data of its host. In the second study, a highly divergent endosymbiont was characterized from the assembled genome of its host. In the third study, genome sequences from a novel bacterium were extracted from both the raw sequencing data and assembled genome of a eukaryote that contained significant amounts of sequence from multiple competing bacteria. Taken together, these results demonstrate the usefulness of the described approach in singularly disparate situations, and strongly argue for a sophisticated, multifaceted, supervised approach to the characterization of host-associated microbes and their interactions. / Ph. D.

A phylogenetic tree is used to model gene evolution and species evolution using molecular sequence data. For artifactual and biological reasons, a gene tree may differ from a species tree, a phenomenon known as gene tree-species tree incongruence. Assuming the presence of one or more evolutionary events, e.g., gene duplication, gene loss, and lateral gene transfer (LGT), the incongruence may be explained using a reconciliation of a gene tree inside a species tree. Such information has biological utilities, e.g., inference of orthologous relationship between genes. In this thesis, we present probabilistic models and methods for orthology analysis and species tree inference, while accounting for evolutionary factors such as gene duplication, gene loss, and sequence evolution. Furthermore, we use a probabilistic LGT-aware model for inferring gene trees having temporal information for duplication and LGT events. In the first project, we present a Bayesian method, called DLRSOrthology, for estimating orthology probabilities using the DLRS model: a probabilistic model integrating gene evolution, a relaxed molecular clock for substitution rates, and sequence evolution. We devise a dynamic programming algorithm for efficiently summing orthology probabilities over all reconciliations of a gene tree inside a species tree. Furthermore, we present heuristics based on receiver operating characteristics (ROC) curve to estimate suitable thresholds for deciding orthology events. Our method, as demonstrated by synthetic and biological results, outperforms existing probabilistic approaches in accuracy and is robust to incomplete taxon sampling artifacts. In the second project, we present a probabilistic method, based on a mixture model, for species tree inference. The method employs a two-phase approach, where in the first phase, a structural expectation maximization algorithm, based on a mixture model, is used to reconstruct a maximum likelihood set of candidate species trees. In the second phase, in order to select the best species tree, each of the candidate species tree is evaluated using PrIME-DLRS: a method based on the DLRS model. The method is accurate, efficient, and scalable when compared to a recent probabilistic species tree inference method called PHYLDOG. We observe that, in most cases, the analysis constituted only by the first phase may also be used for selecting the target species tree, yielding a fast and accurate method for larger datasets. Finally, we devise a probabilistic method based on the DLTRS model: an extension of the DLRS model to include LGT events, for sampling reconciliations of a gene tree inside a species tree. The method enables us to estimate gene trees having temporal information for duplication and LGT events. To the best of our knowledge, this is the first probabilistic method that takes gene sequence data directly into account for sampling reconciliations that contains information about LGT events. Based on the synthetic data analysis, we believe that the method has the potential to identify LGT highways. / <p>QC 20150529</p>