Family Pinguipedidae belong to the class Actinopterygii, subclass Neopterygii, order Perciformes, suborder Trachinoidei. Currently the interrelationships of the genera within this family and among the families in the Trachinoidei remain unequivocal. Also, whether the Cheimarrichthys should be included in the family Pinguipedidae has also been a controversial issue. This study aimed to reconstruct phylogenetic hypotheses in order to resolve these questions. Species of the Parapercis and Kochichtys in the family Pinguipedidae occur Taiwan. This study used osteological characters, 16S rRNA and Cyt b sequences to conduct phylogenetic analysis such that hypotheses can be proposed. The results revealed the monophyly of Parapercis, a taxonomic view consistent to the prevailary classification. Summarizing all the results, the 17 Parapercis species analysed can be divided into 4 groups. They are (1) Parapercis aurantiaca¡BP. decemfasciata¡BP. mimaseana¡BP. multifasciata¡BP. muronis¡Btwo morphotypes of P. sexfasciata¡F(2) P. cephalopunctata¡BP. clathrata¡BP. hexophthalma¡BP. kamoharai¡BP. tetracantha¡BP. xanthozona¡F(3) P. cylindrica and P. snyderi¡F(4) P. maculata¡BP. ommatura and P. somaliensis. Two color morphotypes have been shown for Parapercis sexfasciata. Data of the present study revealed that the ¡§ autapomorphic¡¨ osteological character known only in Kochichtys also occurred in three Parapercis species. This result supports a close relationship between these species. However, it also challenges the validity of the generic status of Kochichtys. About the dabate of the phylogenetic position of Cheimarrichthys, it should be put into its own family, Cheimarichthyide, rather than placed in the Pinguipedidae. The hypothesis for the sister group of Pinguipedidae to the Cheimarichthyide is not supported by all the data in this study completely. Morphological and molecular evidences are incongruence for closest phylogenetic relationship. Similar results were also obtained when the molecular sequences were analysed using different methods. More data analyses are needed for complete and reliable results. The present study suggests that the Trachinoidei is not a monophyletic group.

Known as the Himalayan poppies or the blue poppies, Meconopsis is a genus with approximately 50 species distributed through the high altitude of the Himalaya and the Hengduan Mountains (SW China). This dissertation is a study of the systematics of Meconopsis primarily using molecular phylogenetic methods. DNA sequences of chloroplast matK, ndhF, trnL-trnF, rbcL, and nuclear ITS were collected to reconstruct the phylogenies of the genus. Results showed that traditional Meconopsis is a polyphyletic group and revealed extensive mismatches between the nuclear ITS tree and the chloroplast tree. Based on the phylogenies, the taxonomy of Meconopsis was revised, making Meconopsis monophyletic. Four new sections (sect. Meconopsis, sect. Aculeatae, sect. Primulinae, and sect. Grandes) were proposed as well as a species complex (M. horridula). The chloroplast phylogeny and a likelihood method (chromEvol) were applied to ancestral chromosome number estimation to reconstruct the polyploidy evolution history of the genus. The analysis recovered an ancient triploid ancestor shared by sect. Primulinae and sect. Grandes. A low-copy nuclear gene (GAPDH) network of Meconopsis was further reconstructed, which indicated that the ancient triploid ancestor was formed by hybridization. A hypothesis of reticulate history of Meconopsis was also proposed based on the GAPDH network. Using a reconstructed rbcL phylogeny of Ranunculales, the stem group of Meconopsis was estimated at ca. 22 Mya by molecular dating, which coincided with the time of Asian interior desertification and the onset of Asian monsoon. These climatic changes could possibly have been the impetus for the split between Meconopsis and its sister clade. Ancestral area reconstruction was further conducted using likelihood-based methods. The result indicated that Meconopsis originated in the Himalaya, most likely in the west Himalaya, followed by migration to the Hengduan Mountains. / text

Parasitoid wasps are an important group of organisms in need of systematic revision. This dissertation examines the cosmopolitan parasitoid wasp genus Cremnops. It is a compilation of three projects and significantly advances the taxonomic foundation of the genus. The New World species of the genus Cremnops are revised. Thirty-three species of Cremnops are treated; five are described as new, i.e., C. bertae sp. nov., C. cluttsis sp. nov., C. nymphius sp. nov., C. wileycoyotius sp. nov. and C. witkopegasus sp. nov. Six species are synonymized, i.e., Cremnops caribensis Berta 1998, is synonymized under C. guanicanus Wolcott 1924; C. nigrosternum (Morrison 1917) is synonymized under C. haematodes (Brullé 1846); C. punctatus Berta 1998, is synonymized under C. marshi Berta 1998; C. sharkei Berta 1998, is synonymized under C. montrealensis (Morrison 1917); C. turrialbae Berta de Fernandez 1998, is synonymized under C. ferrugineus (Cameron 1887); and C. misionensis Berta 1987, is synonymized under C. slossonae (Morrison 1917). Cremnops florissanticola is transferred to its original combination Bracon florissanticola Cockerell 1919, st. rev. The species concept Cremnops desertor and its complicated taxonomic history are discussed. A phylogenetic distance tree, based on COI data, is used to help delimit species. The recognition of C. alterans Enderlein and C. malayensis Bhat is proposed. I propose new combinations for five African species that are currently placed in Cremnops, i.e., C. atripennis Szépligeti 1914 and C. elegantissima Szépligeti 1908 are moved to Disophrys; C. borealis (Szépligeti 1914) and C. rubrigaster Masi 1944 are moved to Biroia; and C. pulchripennis Szépligeti 1905 is moved to and renamed Biroia neopulchipennis. These changes result in Disophrys atripennis (Szépligeti 1915) becoming a junior homonym, which is changed to Disophrys szatripennis. Additionally, two species are proposed as nomen dubia: C. rufitarsis Szépligeti 1913 and C. schubotzi Szépligeti 1915. Included are a molecular phylogeny, a dichotomous key, links to distribution maps, an electronic interactive key, images of holotypes, and suggestions for further research.

Species evolution can often be adequately described with a phylogenetic tree. Interestingly, this is the case also for the evolution of homologous genes; a gene in an ancestral species may – through gene duplication, gene loss, lateral gene transfer (LGT), and speciation events – give rise to a gene family distributed across contemporaneous species. However, molecular sequence evolution and genetic recombination make the history – the gene tree – non-trivial to reconstruct from present-day sequences. This history is of biological interest, e.g., for inferring potential functional equivalences of extant gene pairs. In this thesis, we present biologically sound probabilistic models for gene family evolution guided by species evolution – effectively yielding a gene-species tree reconciliation. Using Bayesian Markov-chain Monte Carlo (MCMC) inference techniques, we show that by taking advantage of the information provided by the species tree, our methods achieve more reliable gene tree estimates than traditional species tree-uninformed approaches. Specifically, we describe a comprehensive model that accounts for gene duplication, gene loss, a relaxed molecular clock, and sequence evolution, and we show that the method performs admirably on synthetic and biological data. Further-more, we present two expansions of the inference procedure, enabling it to pro-vide (i) refined gene tree estimates with timed duplications, and (ii) probabilistic orthology estimates – i.e., that the origin of a pair of extant genes is a speciation. Finally, we present a substantial development of the model to account also for LGT. A sophisticated algorithmic framework of dynamic programming and numerical methods for differential equations is used to resolve the computational hurdles that LGT brings about. We apply the method on two bacterial datasets where LGT is believed to be prominent, in order to estimate genome-wide LGT and duplication rates. We further show that traditional methods – in which gene trees are reconstructed and reconciled with the species tree in separate stages – are prone to yield inferior gene tree estimates that will overestimate the number of LGT events. / Arters evolution kan i många fall beskrivas med ett träd, vilket redan Darwins anteckningsböcker från HMS Beagle vittnar om. Detta gäller också homologa gener; en gen i en ancestral art kan – genom genduplikationer, genförluster, lateral gentransfer (LGT) och artbildningar – ge upphov till en genfamilj spridd över samtida arter. Att från sekvenser från nu levande arter rekonstruera genfamiljens framväxt – genträdet – är icke-trivialt på grund av genetisk rekombination och sekvensevolution. Genträdet är emellertid av biologiskt intresse, i synnerhet för att det möjliggör antaganden om funktionellt släktskap mellan nutida genpar. Denna avhandling behandlar biologiskt välgrundade sannolikhetsmodeller för genfamiljsevolution. Dessa modeller tar hjälp av artevolutionens starka inverkan på genfamiljens historia, och ger väsentligen upphov till en förlikning av genträd och artträd. Genom Bayesiansk inferens baserad på Markov-chain Monte Carlo (MCMC) visar vi att våra metoder presterar bättre genträdsskattningar än traditionella ansatser som inte tar artträdet i beaktning. Mer specifikt beskriver vi en modell som omfattar genduplikationer, genförluster, en relaxerad molekylär klocka, samt sekvensevolution, och visar att metoden ger högkvalitativa skattningar på både syntetiska och biologiska data. Vidare presenterar vi två utvidgningar av detta ramverk som möjliggör (i) genträdsskattningar med tidpunkter för duplikationer, samt (ii) probabilistiska ortologiskattningar – d.v.s. att två nutida gener härstammar från en artbildning. Slutligen presenterar vi en modell som inkluderar LGT utöver ovan nämnda mekanismer. De beräkningsmässiga svårigheter som LGT ger upphov till löses med ett intrikat ramverk av dynamisk programmering och numeriska metoder för differentialekvationer. Vi tillämpar metoden för att skatta LGT- och duplikationsraten hos två bakteriella dataset där LGT förmodas ha spelat en central roll. Vi visar också att traditionella metoder – där genträd skattas och förlikas med artträdet i separata steg – tenderar att ge sämre genträdsskattningar, och därmed överskatta antalet LGT-händelser. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 5: Manuscript.</p>

Rhadine is a Nearctic lineage of flightless ground beetles in the tribe Platynini notable for the slender and elongate habitus of the adults and, in the Southwest, the habitat preferences of many species, with several mountaintop endemics as well as microphthalmous species known from caves in central Texas. The genus is in need of a modern taxonomic revision as species identifications remain challenging, and a phylogenetic hypothesis for the overall structure of the group is needed in order to better understand the group's evolutionary history and test whether subterranean Rhadine are a monophyletic clade or not. To this end, a multigene phylogeny of Rhadine was inferred based on ~2.4-kb of aligned nucleotide sites from 3 molecular markers: cytochrome c oxidase subunit I (COI), 28S ribosomal DNA (28S), and carbamoylphosphate synthetase domain of the rudimentary gene (CAD). These gene fragments were obtained for 30 species or putative species of Rhadine as well as from members of their putative sister group, Tanystoma. Rhadine as currently circumscribed is reconstructed as paraphyletic with two species of subterranean beetles from caves in northern Mexico being resolved outside of Rhadine + Tanystoma. Rhadine sensu stricto (s. str.) is resolved with high support across analyses and is composed of two reciprocally monophyletic clades, clade I and II, the second of which is generally recovered in most analyses. Clade I includes those Rhadine with adult morphological characters defining the dissecta-, larvalis-, and subterranea-groups as well as a clade of macropthalmous subterranean perlevis-group species. Clade II, although not as robust as clade I, contains several surface-dwelling species from the western United States in the jejuna-, nivalis-, and perlevis-groups in addition to lineages of exclusively macropthalmous subterranean Rhadine. The troglobitic, cave-restricted, Rhadine classified in the subterranea-group are reconstructed in two different clades, and the clade contained within clade I also includes several species of large-eyed cavernicolous Rhadine. Those with a slender habitus (e.g., R. exilis, R. subterranea, R. austinica) evolved independently at least three times. Major biogeographic and evolutionary patterns based on these molecular results include: subterranea-group Rhadine north of the Colorado River in Texas (which all lack lateral pronotal setae) are found to comprise a monophyletic group, beetles in caves south of the Colorado River likely form another monophyletic group, and the "species pairs" of troglobitic Rhadine known to occur in the same caves that were sampled in our study are not resolved as each other's closest relatives suggesting that these caves were colonized independently by more than one lineage of Rhadine. The fine-scale attention given to populations of Rhadine isolated on mountain tops in the Madrean Sky Island region suggests that there is a great deal of genetic diversity among these lineages. In addition, these populations are resolved as reciprocally monophyletic with high support across all analyses. Haplotype networks constructed for these populations and compared with those of other described species for the same gene fragments reveal similar genetic distances between separate Sky Island Rhadine as compared to distances between described species from throughout the tree. Preliminary divergence time estimates of the Rhadine-Tanystoma lineage based on relaxed molecular clock analyses support a Miocene age for Rhadine and the Rhadine-Tanystoma lineage, with the crown ages of clade I and II being similar though not identical. All subterranean clade I Rhadine are dated to have begun diversifying within approximately the past 5 million years (Pliocene), an age that is compatible with the stratigraphy of the caves in the Balcones Escarpment. In addition, divergence estimates for the members of this clade support the climactic relict hypothesis, as they diversified during rapid temperature fluctuations during the Quaternary. However, the ages of the high altitude Sky Island Rhadine are estimated to be older than the most recent glacial maximum, suggesting that these distinct clades are considerably older than initially thought. We also performed character correlation tests using our phylogeny to test for patterns in form associated with cave habit and did not find statistical significance between subterranean habit and microphthalmy nor habit and development of the foveae of the mentum.Morphological characters that have been traditionally used to classify the genus into species groups were shown to be convergent in many cases. Despite these well-supported molecular clades, few morphological characters are consistent across all members, posing a challenge to the construction of identification tools. Nevertheless, a tentative update to the classification based on our findings is presented, and the future goals for reconstructing the phylogeny of Rhadine are discussed.

The cactophilic Drosophila mojavensis species group living in the deserts and dry tropical forests of the Southwestern United States and Mexico provides a valuable system for studies in diversification and speciation. My dissertation addresses a variety of evolutionary genetic questions using this system.Rigorous studies of the relationships between host races of D. mojavensis and the relationships among the members of the species group (D. mojavensis, D. arizona, and D. navojoa) are lacking. I used mitochondrial CO1 sequence data to address the phylogenetics and population genetics of this species group (Appendix A). In this study I have found that the sister species D. mojavensis and D. arizonae share no mitochondrial haplotypes and thus show no evidence for recent introgression. I estimate the divergence time between D. mojavensis and D. arizonae to be between 0.66 and 0.99 million years ago. I performed additional population genetic analyses of these species to provide a basis for future hypothesis testing.In Appendix B, I report the first example of substantial intraspecific polymorphism for genetic factors contributing to hybrid male sterility. I show that the occurrence of hybrid male sterility in crosses between Drosophila mojavensis and its sister species, D. arizonae is controlled by factors present at different frequencies in different populations of D. mojavensis. In addition, I show that hybrid male sterility is a complex phenotype; some hybrid males with motile sperm still cannot sire offspring.The large degree of variation between isofemale lines in producing sterile hybrid sons suggests a complex genetic basis to hybrid male sterility warranting quantitative genetic analysis. Since the genes underlying hybrid male sterility in these species are not yet fixed, I am able to perform explicit genetic analysis of this reproductive isolating mechanism. In Appendix C, I present the results of mapping QTL for hybrid male sterility within species. The genetic architecture underlying hybrid male sterility when analyzed directly in the F1 is highly complex. Thus, hybrid male sterility arises as a complex trait in this system and we propose a drift-based model for the evolution of this phenotype.

Teasing apart the evolutionary forces responsible for biological phenomena is difficult in the absence of a detailed evolutionary history, especially if this history is lacking a temporal component. RNA viruses, due to their rapid rate of molecular and phenotypic evolution, provide a unique biological system in which to study the temporal aspects of evolutionary processes. These types of studies are possible because of relaxed molecular clock dating techniques, which allow the rate of evolution to vary across a phylogenetic tree. The primary focus of the research presented here concerns the age of the simian immunodeficiency virus (SIV), the primate precursor to HIV. SIV has long been thought to be an ancient infection in non-human African primates, and it has been hypothesized that codivergence with its primate hosts has shaped the SIV phylogeny and resulted in a virus capable of apathogenic infection. The codivergence theory was tested by comparing the phylogeny of a group of monkeys thought to be exemplary of SIV-host codivergence to the phylogeny of their SIVs (Appendix A). These phylogenies were incongruent, suggesting that SIV may have infected these monkeys after their common ancestor speciated. The codivergence theory was investigated further by estimating the time of most recent common ancestor for the SIV lineages that directly gave rise to HIV, found in sooty mangabeys and chimpanzees (Appendix B). The temporal estimates suggest that these SIV lineages are only of hundreds of years old, much younger than expected under the codivergence hypothesis. Next, the same dating techniques were employed to elucidate the evolutionary history of an emerging RNA virus of shrimp, Taura syndrome virus (Appendix C). This analysis provided phylogenetic confirmation that Taura syndrome virus emerged out of the Americas and spread rapidly around the world. Finally, because all of these studies utilized relaxed molecular clocks, a simulation study was performed to test the hypothesis that relaxed molecular clocks provide higher quality phylogenetic inference compared with traditional time-free phylogenetic inference (Appendix D). This simulation found no difference in the overall quality of phylogenetic inference between these methods.

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.

Multiple gene phylogenetic analysis is of interest since single gene analysis often results in poorly resolved trees. Here the use of spectral techniques for analyzing multi-gene data sets is explored. The protein sequences are treated as categorical time series and a measure of similarity between a pair of sequences, the spectral covariance, is used to build trees. Unlike other methods, the spectral covariance method focuses on the relationship between the sites of genetic sequences. We consider two methods with which to combine the dissimilarity or distance matrices of multiple genes. The first method involves properly scaling the dissimilarity measures derived from different genes between a pair of species and using the mean of these scaled dissimilarity measures as a summary statistic to measure the taxonomic distances across multiple genes. We introduced two criteria for computing scale coefficients which can then be used to combine information across genes, namely the minimum variance (MinVar) criterion and the minimum coefficient of variation squared (MinCV) criterion. The scale coefficients obtained with the MinVar and MinCV criteria can then be used to derive a combined-gene tree from the weighted average of the distance or dissimilarity matrices of multiple genes. The second method is based on the singular value decomposition of a matrix made up of the p-vectors of pairwise distances for k genes. By decomposing such a matrix, we extract the common signal present in multiple genes to obtain a single tree representation of the relationship between a given set of taxa. Influence functions for the components of the singular value decomposition are derived to determine which genes are most influential in determining the combined-gene tree.

With rapid advances in sequencing technologies and precipitous decreases in cost, public sequence databases have increased in size apace. However, experimental characterization of novel genes and their products remains prohibitively expensive and time consuming. For these reasons, bioinformatics approaches have become increasingly necessary to generate hypotheses of biological function. Phylogenomic approaches use phylogenetic methods to place genes, chromosomes, or whole genomes within the context of their evolutionary history and can be used to predict the function of encoded proteins. In this thesis, two new phylogenomic methods and software implementations are presented that address the problems of subcellular localization prediction and functional divergence prediction within protein families respectively. Most of the widely used programs for subcellular localization prediction have been trained on model organisms and ignore phylogenetic information. As a result, their predictions are not always reliable when applied to phylogenetically divergent eukaryotes, such as unicellular protists. To address this problem, PhyloPred-HMM, a novel phylogenomic method was developed to predict sequences that are targeted to mitochondria or mitochondrion-related organelles (hydrogenosomes and mitosomes). This method was compared to existing prediction methods using an existing test dataset of mitochondrion-targeted sequences from well-studied groups, sequences from a variety of protists, and the whole proteomes of two protists: Tetrahymena thermophila and Trichomonas vaginalis. PhyloPred-HMM performed comparably to existing classifiers on mitochondrial sequences from well-studied groups such as animals, plants, and Fungi and better than existing classifiers on diverse protistan lineages. FunDi, a novel approach to the prediction of functional divergence was developed and tested on 11 biological datasets and two large simulated datasets. On the 11 biological datasets, FunDi appeared to perform comparably to existing programs, although performance measures were compromised by a lack of experimental information. On the simulated datasets, FunDi was clearly superior to existing methods. FunDi, and two other prediction programs, was then used to characterize the functional divergence in two groups of plastid-targeted glyceraldehyde-3-phosphate dehydrogenases (GAPDH) adapted to roles in the Calvin cycle. FunDi successfully identified functionally divergent residues supported by experimental data, and identified cases of potential convergent evolution between the two groups of GAPDH sequences.