Knowledge of phylogenetic relationships among organisms is essential for anchoring evolutionary studies. Phylogenomic studies use large amounts of genetic data in analyses, which is particularly important for highly phenotypically variable taxa that are difficult to distinguish from one another without the use of genetic data, due to the abundance of homoplasy in morphological characters typically used in morphological classification. Use of genome-scale molecular data has thus become the gold standard for identifying these phylogenetic relationships, specifically in comparison to past studies based on fewer genes. Greater quantities of genetic data, in addition to finer taxon sampling, may lead to different conclusions about phylogenetic relationships among organisms compared to previous studies, necessitating new analyses on organisms when new discoveries of populations and new sources of genetic data arise. Ranitomeya poison frogs (Amphibia: Dendrobatidae) are an Amazonian lineage of dendrobatid frogs consisting of 16 species possessing remarkable diversity in color pattern, range size, and parental care behavior. I present the first phylogeny based on genomic data for all species in Ranitomeya, using maximum likelihood and multi-species coalescent methods. I used ultraconserved elements (UCEs), a genome-scale nuclear marker, as my source of molecular data to construct the tree. I also present divergence time estimations using the MCMCTree program. My results indicate several differences from previous analyses in terms of interspecific relationships. Notably, I find R. toraro and R. defleri constitute different species groups, and recover R. uakarii as paraphyletic. I also designate former populations of R. fantastica from Isla Pongo, Peru and Tarapoto as R. summersi, and transfer the French Guianan R. amazonica populations to R. variabilis. My study clarifies both interspecific and intraspecific relationships within Ranitomeya, and provides key insights into phylogeny that pave the way for future studies testing hypotheses on color pattern evolution and historical biogeography.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24457号 / 理博第4956号 / 新制||理||1707(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 中野 隆文, 教授 本川 雅治, 教授 森 哲 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24079号 / 理博第4846号 / 新制||理||1693(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 田村 実, 教授 工藤 洋, 教授 松下 智直 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Doctor of Philosophy / Department of Entomology / David C. Margolies / Yoonseong Park / The predatory mite Phytoseiulus persimilis (Acari, Phytoseiidae) is one of the most frequently released natural enemies for biological control of spider mites in greenhouse and outdoors crops. In this research, I utilized Expresses Sequence Tags (ESTs), the most cost effective approach for transcriptome exploration, to study three different aspects of this arachnid species for which there is little genomic information. I combined two EST datasets from different whole body cDNA libraries and analyzed by bioinformatics means. Approximately 54% of 10,256 uniESTs were annotated based on the homology to sequences in the National Center for Biotechnological Information (NCBI) database. A list of these uniESTs, sorted from most to least likelihood based on the expected value from the blast search in public databases, was used to create tools for each of the three studies. First, I described sixty-one genes encoding products known to be important in pesticide metabolism and in endocrinology, including cytochrome P450s, glutathione-S-transferases, acetylcholinesterase homologs, neuropetides and neurohormones. Findings on arachnid specific esterases and neuropetides, and possible benefits to pest management programs, were discussed. Next, I inferred divergence time for Acari and the point of divergence of two lineages within anactinotrichid mites, Ixodes scapularis and Phytoseiulus persimilis. I used expresses sequence tags from the predatory mite P. persimilis to pull out 74 orthologous amino acid sequences of invertebrates species: nine insect species, Daphnia pulex, Ixodes scapularis, and Caenorhabditis elegans. I estimated a similar origin for Chelicerata (578.1 ± 38.2 - 482.2 ± 7.2 Mya) as in other recent studies. However, divergence dating using amino acid sequences suggested a Devonian origin of anactinotrichid mites (487.6 ± 32.2 - 410.1 ± 6.1 Mya) based on four reference dates (two fossil records and two molecular clocks) and four amino acid substitution methods; this estimate is much earlier that those in the current literature. This discrepancy of divergence times may be due to the use of a global clock. Finally, I developed molecular markers from the EST dataset to examine inheritance in the haplodiploid system in P. persimilis. Biparental contribution of chromosomes is required among the predatory mites but the paternal chromosome set seems to be eliminated or loss (Paternal genome loss, PGL) in male offspring. However, genetic studies in other two phytoseiid species were suggested diploid males with PGL only in the germ cells. In the present study, haploid adult males of P. persimilis have been observed using five independent EST-derived markers. Single mites derived from inter-population crosses were genotyped after whole genome amplification. The parahaploid genetic system in P. persimilis is supported by this study, in which both sexes arise from fertilized eggs but the paternal chromosome set is subsequently lost in males.

<p>This PhD thesis consists of an introduction and five papers, dealing with statistical methods in phylogenetics.</p><p>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.</p><p>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.</p><p>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.</p><p>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.</p>

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.

The flightless Cape High-mountain stag beetle genus Colophon (Coleoptera: Lucanidae) is studied. Represented by 17 species, which are restricted to the highest mountain peaks of the Cape Floristic Region in the Western Cape, South Africa, and show a strict association with the fynbos biome. The study aimed to determine the specific and phylogenetic status of the described species of Colophon and to determine the main factors driving their evolution by testing hypotheses of relationship and of a lowland origin. This was achieved by analysing DNA sequence data from three gene regions, the mitochondrial COI and 16S rRNA and the nuclear CAD, using a Maximum Likelihood (ML) and Bayesian approach. Timing of key biogeographical events in the diversification of Colophon was estimated in BEAST. The study also undertook to determine diagnostic larval characters for Colophon species and also to determine their phylogenetic implications for the sub-familial placement of the genus. Lastly, the study aimed to collate biological information on Colophon species so as to make suggestions for their revised conservation status in terms of IUCN and ToPS criteria. Most species of Colophon showed an allopatric distribution, although contact zones between geographically adjacent species are likely. Climate seems to be the main driving factor behind Colophon evolution and the hypothesis of a lowland origin appears to be supported. Larvae are soil-living and feed on humus, a habit unique to the family. There are only small inter-specific differences between larvae, with larval characters contributed little equivocal information from which phylogenetic support for family placement of Colophon could be deduced. The main threats to Colophon survival include overexploitation by commercial collectors, decline in habitat quality and habitat loss due to projected changes in climate. It is suggested that out of the 17 currently described species, eight should be listed as Critically Endangered, seven as Endangered, two as Data Deficient. Lastly, in light of this project‟s findings, it is suggested that future considerations in terms of Colophon research should focus on obtaining more information on their biology, behaviour and population size and in so doing contribute knowledge for the effective conservation management of each species. A taxonomic revision of the species, focusing on the C. stokoei varieties and C. eastmani subspecies, should be done and a complete taxonomic key of all described species compiled. Future fieldwork should focus on sampling the five species that remained elusive during the project, to eventually be included in phylogenetic analyses. / Dissertation (MSc)--University of Pretoria, 2013. / gm2013 / Zoology and Entomology / unrestricted

京都大学 / 新制・課程博士 / 博士(地球環境学) / 甲第24064号 / 地環博第227号 / 新制||地環||43(附属図書館) / 京都大学大学院地球環境学舎地球環境学専攻 / (主査)准教授 西川 完途, 教授 瀬戸口 浩彰, 教授 本川 雅治 / 学位規則第4条第1項該当 / Doctor of Global Environmental Studies / Kyoto University / DGAM

Composed of a chromophore bound to an integral membrane protein (opsin), visual pigments are phenotypically characterized by the wavelength of maximal absorption (λmax). The underlying molecular mechanism controlling λmax is the interaction between the opsin amino acid sequence and the chromophore. While a plethora of studies have looked at structure/function relationships in vertebrate opsins, fewer studies have investigated similar issues in invertebrates. Furthermore, those few studies undertaken in invertebrate systems suggest different mechanisms of spectral tuning and photoactivation compared to vertebrate systems. This dissertation research is focused on expanding our knowledge of opsin evolution in invertebrate systems, particularly from non-insect taxa. First, issues related to opsin evolution and the maintenance of supposedly ‘non-functional’ genes were explored in a review of regressive and reverse evolution. Second, in order to place studies of crustacean opsin evolution in context, phylogenetic studies of two crustacean groups (Mysidae and Decapoda) were completed. Studies of Mysidae utilized 16S mtDNA, and 18S and 28S rDNA to reconstruct phylogenetic relationships and assess newly developed Bayesian methods of assessing pattern heterogeneity. Using this suite of genetic markers, there are incongruencies between current taxonomy and inferred phylogenetic relationships. Studies of Decapoda assessed phylogenetic relationships and estimated divergence times using 16S mtDNA, H3 nDNA, and 18S and 28S rDNA sequence data in conjunction with a set of eight fossil calibrations. Reconstructed phylogenies show support for two well supported nodes corresponding to the Pleocyemata and the informal ‘Reptantia’ and place the emergence of the Decapod lineage in the early Devonian (407 MYA. Finally, opsin sequences and spectral sensitivity data from species within the Mysidae and Decapoda were combined with previously characterized invertebrate sequences to investigate opsin evolution. Standard dN/dS methods did not detect any evidence of selection. Methods investigating selection on amino acid properties, however, identified four properties (coil tendencies, compressibility, power to be at the middle of the alpha helix, and refractive index) to be under positive destabilizing selection. These properties occurred mostly at sites in transmembrane helices and included residues previously identified to affect spectral tuning as well as identifying novel sites.

This dissertation focuses on increasing the understanding of the evolution processes that have contributed to the diversification of freshwater crayfish. Chapter one estimates the divergence time of the three crayfish families and tests the hypothesis that diversification is tied to the break-up of Pangaea, Gondwanna, and Laurasia. I find that the families of crayfish diverged prior to or in association with the break-up of the three super continents. Chapter two addresses the evolutionary history of the genus Cambarus, using molecular data to test hypotheses of relationships based on chela and carapace morphology. The results provide evidence that the morphology used to determine Cambarus relationships do not reflect evolutionary history and that convergent evolution of morphological traits is common in crayfish. Chapter three addresses evolution at the population level and tests for differences in the genetic population structure of two crayfish with different physiological needs. I find that physiological requirements of these crayfish have influenced their population genetic structure. The last chapter addresses a molecular based hypothesis that rates of mitochondrial evolution are reduced in cave crayfish that have increased longevity, reduced metabolism, and restricted diets compared to surface crayfish. I find that cave crayfish rates of mitochondrial evolution do not significantly differ from surface crayfish. Therefore, increased longevity, reduced metabolism, and restricted diets do not slow the rate of mitochondrial evolution as predicted in this group of cave crayfish.