Many animal species are still undiscovered, even in Sweden. This thesis deals with the wasps of the subfamily Eucoilinae (of Figitidae, Cynipoidea), a poorly known group of small parasitoids of Dipteran flies. In this group, old classifications are chaotic, knowledge of old taxa is scant, phylogenetic work has recently started, and many new taxa remain to be described. In this thesis, an identification key is given to the European genera of Eucolinae, and a tribal classification of the subfamily is reintroduced, based on recent phylogenetic results. Most of the thesis focuses on the tribe Eucoilini. That tribe is analyzed phylogenetically in two analyses, one based on a large morphological dataset, the other on two molecular markers, ribosomal 28S and mitochondrial Cytochrome B. The monophyletic core group of Eucoilini is the Eucoila/Trybliographa complex. It is treated in a big taxonomic revision, based on studies of several hundred possibly relevant type specimens and several thousands of other specimens, and on the phylogenetic analyses. More than 500 names of possible members of this group are investigated, and many new combinations are proposed, of species found not to belong within the group, as well as those that did, including some which are transferred to other genera in accordance with the new phylogenetic results. The new genus Quasimodoana is erected, and 20 new species described (8 from Northern Europe, 12 from elsewhere). More than 180 new combinations, more than 50 new species-level synonyms and ca 10 genus-level synonyms, are proposed. Within this complex, the basal split is found to have been between a Paleotropic, specis-poor lineage (Bothrochacis), and a species-rich and largely Holarctic lineage, dominated by Trybliographa but also including the small genera Eucoila and Linoeucoila. The three are not satisfactorily resolved in the analysis, but still maintained as separate genera for pragmatic reasons. It is hypothesized that this group originated in Asia during the Eocene or Oligocene, attacking calyptrate flies in herbivore dung. Then it separated in a tropical branch retaining the ancestral life history mode, and a Holarctic branch, where some lineages specialised in Anthomyiidae and colonised the microhabitats of fungi and plants, speciating extensively in the boreal forests.

The phylogenetic relationships within subfamily Ixoroideae of the coffee family are investigated by phylogenetic reconstruction of molecular data, including regions of the chloroplast DNA (matK, ndhF, rbcL, rps16, trnH-psbA, trnS-G, and trnT-F), and the nuclear ribosomal DNA (ITS). The evolution of morphological characters within the group are inferred, with focus on characters used in classification. Ixoroideae have primarily been characterized by secondary pollen presentation, contorted corolla aestivation, and fleshy fruits. Secondary pollen presentation appears synapomorhic of a clade comprising the Ixoroideae crown group together with Retiniphyllum, whereas contorted corolla aestivation has evolved earlier and is synapomorphic for the crown group, Retiniphyllum, and Steenisia. Capsules likely represent a plesiomorphy from which various dry or fleshy indehiscent fruits have evolved independently in different clades. Reductions in seed number have also occured in many clades, none of which shows a secondary increase in the number of seeds. Within Ixoroideae, the phylogeny and tribal delimitations of Alberteae and Condamineeae are studied in more detail. The former appears restricted to Alberta, Nematostylis, and Razafimandimbisonia, a new genus described here. The Condamineeae are a diverse tribe largely unresolved in previous molecular phylogenetic studies. Our results support a synonymization of both Calycophylleae and Hippotideae, because these are nested within the Condamineeae. Ancestral state reconstructions indicate that intrapetiolar stipules, poricidal anthers, and protogyny, otherwise uncommon characters in Rubiaceae, all have evolved more than once in the Condamineeae. The rare genera Jackiopsis, Glionnetia, and Trailliaedoxa previously not included in molecular phylogenetic analyses, are all found nested within the Ixoroideae, and their systematic positions are discussed. The genera Bathysa, Calycophyllum, Elaeagia, and Rustia do not appear monophyletic. Consequently, resurrections of the names Holtonia, Schizocalyx, and Semaphyllanthe, and synonymizations of Phitopis (as Schizocalyx) and Tresanthera (as Rustia) are proposed. Also proposed are five new tribal names for clades that are not associated with any previously described tribes in the phylogenetic hypotheses presented. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.

This thesis comprises studies of the phylogenetic relationships in the flowering plant clade Potentilleae in Rosaceae. The relationships were elucidated by using DNA sequence data from the nuclear genome as well as from the plastid genome. In particular, the focus of the studies was the investigation of allopolyploidy, i.e. speciation as a result of hybridization and subsequent chromosome doubling. A phylogenetic method was used for identifying allopolyploidy through comparison of trees resulting from the analyses of different DNA sequences. Five sub-clades were investigated. First, both the sister clades that together contain all of Potentilleae: Fragariinae and Potentilla. Secondly, three subclades of Fragariinae, namely Alchemilla in wide sense, Sibbaldia and relatives, and Fragaria. The aim was to unravel the phylogenetic relationships, including instances of allopolyploidy. Classification issues were discussed in relation to the phylogenetic results. The split between Potentilla (=Potentillinae) and Fragariinae received better support than in previous studies. The phylogeny of Fragariinae was found to be consistent with classifying ten genera: Alchemilla in wide sense (incl. Aphanes and Lachemilla), Comarum, Sibbaldia, Sibbaldianthe, Sibbaldiopsis, Chamaerhodos, Drymocallis, Dasiphora, Potaninia, Fragaria, and also including a few orphan Potentilla species. The segregated genera Ivesia, Horkelia, Horkeliella and Duchesnea were found to be nested within Potentilla, corroborating earlier studies, while the segregated genus Argentina (P. anserina and close relatives) showed an ambiguous position. Plastid and nuclear (ribosomal) phylogenies were compared and incongruences were detected as potential instances of allopolyploid speciation. Five strongly supported incongruences were detected in Fragariinae and four of them were considered to be potentially caused by allopolyploidy. In addition, five supported incongruences were found in Potentilla. Alchemilla in the wide sense was found to contain four major clades, African Alchemilla, Eurasian Alchemilla, Lachemilla and Aphanes. Both Lachemilla and Aphanes were nested within Alchemilla and it was suggested that the name Alchemilla should be used in the wide sense, i.e. including both the genera Lachemilla and Aphanes. The genus Sibbaldia as commonly classified was shown to be polyphyletic in five different places in Potentilleae. Three Sibbaldia clades ended up in Fragariinae and two in Potentilla. A phylogeny of Fragaria, based on a nuclear low/single copy DNA region was estimated. The gene copy phylogeny was used to construct a reticulate tree hypothesizing allopolyploid speciation events. The evolution of Fragaria was shown to have been shaped by polyploidy. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript.

The Brachiopoda, a major group of the Lophotrochozoa, experienced a rapid early evolutionary diversification during the well-known Cambrian explosion and subsequently dominated the Palaeozoic benthos with its diversity and abundance. Even though the phylogeny of the Lophotrochozoa is still hotly debated, it is now known that the Brachiopoda are a monophyletic grouping. However, the early evolutionary rates for the Brachiopoda have never been studied in the framework of a study combining molecular data and fossil time calibration points. In order to investigate the expected higher evolutionary rates of the Phylum at its origin, we conducted phylogenetic studies combining different methodologies and datasets. This work has at its foundation Maximum Likelihood and Bayesian analyses of 18S and 28S rRNA datasets followed by analyses of phylogenomic sequences. All material was obtained from previously available sequences and from sequencing of genetic material from specimens from a concerted worldwide collection effort.       While the analyses of the phylogenomic dataset produced a robust phylogeny of the Brachiopoda with good support, both the results of the novel rRNA and phylogenomic dating analyses provided limited insights into the early rates of evolution of the Brachiopoda from a newly assembled dataset, demonstrating some limitations in calibration dating using the software package BEAST2. Future studies implementing fossil calibration, possibly incorporating morphological data, should be attempted to elucidate the early rates of evolution of Brachiopoda and the effect of the Push of the Past in this clade. / Det är ofta antaget att evolution (förändringar i arvsmassan hos en grupp organismer) sker i en konstant hastighet men i slutändan ändå osäkert om så är fallet. Stora grupper av organismer har ofta associerats med en högre evolutionär hastighet, speciellt nära deras uppkomst, vilket ökar sannolikheten för överlevnad.  Armfotingar (Brachiopoda) är marina ryggradslösa djur med skal som tidigare var allmänt spridd, idag är istället musslor (Bivalvia) betydligt mer spridda. Armfotingar har funnits och utvecklats under flera miljoner år med ursprung under tidigt kambrium. Genom år av forskning och många fossil har vi fått mer information om utseendet hos utdöda organismer vilket har bidragit till att antalet fossila arter som vi känner till har ökat tusenfalt. Under den senaste tiden har det också skett innovationer inom molekylära tekniker som gjort det möjligt att applicera dessa kunskaper även på utdöda arter. Dessa molekylära tekniker har nyligen hjälpt till att bestämma några av släktskapsförhållandena inom armfotingar som tidigare ansetts vara väldigt svåra att lösa.  Det finns fortfarande vissa släktskapsförhållanden inom armfotingar som inte är kända och man vet ännu inte hur fort de utvecklades. Genom att undersöka just evolutionens hastighet kan man börja förstå gruppens tidiga framgång under Kambrium och Ordovicium samt minskningen som följde. Syftet med den här studien var att beräkna evolutionshastigheten hos armfotingar med särskild fokus på den tidiga diversifieringen av gruppen. För att undersöka detta använde vi oss av molekylära data för att analysera släktskapsförhållandena inom armfotingar. Dessutom använde vi fossil för att datera stora händelser i armfotingarnas evolutionära historia. Med hjälp av statistiska analyser kunde vi beräkna evolutionshastighet och släktskapsförhållandena inom gruppen. Vi kom fram till att armfotingar härstammar från en gemensam förfader. Dateringen kring när detta skedde blev inte fastställd då det beräknades ske miljoner år före det äldsta djurfossilet. Det kommer behövas mer forskning för att ta reda på om armfotingar hade en högre evolutionär hastighet i tidigt skede.

The species of Amomum Roxb. (Zingiberaceae) in Cambodia, Laos and Vietnam are revised. Thirty-five species and two varieties are recognised, all names are typified, and detailed descriptions and a key are provided. Nine new species are described and one species is validated. Whilst revising Amomum for the Flore du Cambodge, du Laos et du Viêtnam, we have proposed to conserve the name Amomum villosum Lour. with a recent collection from Laos, which was not included in the protologue, as its type. Our research on the use of Amomum focuses on the use of plants during pregnancy, parturition, postpartum recovery and infant healthcare among three ethnic groups, the Brou, Saek and Kry. The investigations aim to identify culturally important traditions that may facilitate implementation of culturally appropriate healthcare. Data were collected in Khammouane province, Lao PDR, through group and individual interviews with women by female interviewers. More than 55 plant species are used in women's healthcare, of which > 90 % are used in postpartum recovery. This wealth of novel insights into plant use and preparation will help to understand culturally important practices such as confinement, dietary restrictions, mother roasting and herbal steam baths and their incorporation into modern healthcare. Through chemical analyses of Amomum we have recorded compounds with antimicrobial, analgesic and sedative effects that point to an empirical development of the traditional treatments around childbirth. Essential oils of three species used in hotbed and mother roasting, Amomum villosum Lour. Amomum microcarpum C.F.Liang & D.Fang and Blumea balsamifera (L.) DC. were found to contain significant amounts of the following terpenes: b-pinene, camphor, bornylacetate, borneol, linalool, D-limonene, fenchone, terpinen-4-ol and a-terpinene.

The focus for the first part of the thesis is on the systematics of species belonging to Silene subgenus Silene. Phylogenetic relationships are inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ITS, intron of the RPB2 gene) genomes. Silene section Rigidulae is shown to be non-monophyletic in its previous circumscription, but instead consisting of six separate clades, each correlated to the geographical distribution of the included species. The taxonomic consequences for each clade are discussed. One of the clades is recognized as a new section and described as Silene sect. Arenosae sect. nov. The morphological descriptions of the species are formalized using a novel implementation of the Prometheus Description Model. Two proposals are included in the thesis, one to reject the name Silene polyphylla L., which is a senior synonym to S. portensis L. Silene linearis Decne. is proposed for conservation against the rarely used S. linearis Sweet. Silene antirrhina, a weedy American annual, is strongly supported as sister to the Hawaiian endemic species of Silene, suggesting an American origin for these. Two of the endemics have evolved woodiness after introduction to Hawaii. In the second part of the thesis we use four nuclear DNA regions, (introns from RPA2, RPB2, RPD2a, RPD2b), and the chloroplast psbE-petG spacer. A framework is developed to evaluate different phylogenetic explanations for conflicting gene trees, where divergence times are used to discriminate among inter- and intralineage processes. The incongruences observed regarding the relationships among the three major lineages of Heliosperma are best explained by homoploid hybridization. The pattern regarding the origin of Heliosperma itself is more complicated and is likely to include several reticulate events. Two lineages have probably been involved in the origin of Heliosperma, one leading to Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.

In this thesis relationships and the occurrence of reticulate evolutionary events in the club moss genus Diphasiastrum are investigated. Diphasiastrum is initially established as a monophyletic group within Lycopodiaceae using non recombinant chloroplast sequence data. Support is obtained for eight distinct parental lineages in Diphasiastrum, and relationships among the putative parent taxa in the hypothesized hybrid complexes; D. alpinum, D. complanatum, D. digitatum, D. multispicatum, D. sitchense, D. tristachyum and D. veitchii are presented. Feulgen DNA image densitometry data and sequence data obtained from three nuclear regions, RPB2, LEAFY and LAMB4, were used to infer the origins of three different taxa confirmed to be allopolyploid; D. zanclophyllum from South Africa, D. wightianum from Malaysia and an undescribed taxon from China. The two Asian polyploids have originated from two different hybrid combinations, D. multispicatum x D. veitchii and D. tristachyum x D. veitchii. Diphasiastrum zanclophyllum originates from a cross between D. digitatum and an unidentified diploid taxon. The occurrence of three homoploid hybrid combinations commonly recognized in Europe, D. alpinum x D. complanatum, D. alpinum x D. tristachyum and D. complanatum x D. tristachyum, are verified using the same three nuclear regions. Two of the three hybrid combinations are also shown to have originated from reciprocal crosses. Admixture analyses performed on an extended, dataset similarly identified predominately F1 hybrids and backcrosses. The observations and common recognition of hybrid species in the included populations are hence most likely due to frequent observations of neohybrids in hybrid zones. Reticulate patterns are, however, prominent in the presented dataset. Hence future studies addressing evolutionary and ecological questions in Diphasiastrum should emphasize the impact of gene flow between parent lineages rather than speciation as the result of hybridization.

Haematophagous parasites and disease vectors such as leeches, ticks, mites, lice, bed bugs, mosquitoes, and myiasis-causing fly larvae are common health problems in Lao Peoples Democratic Republic (Lao PDR). A main aim of my field work in Lao PDR in 2006-2010 was to document traditional knowledge among different ethnic groups about plants that people use to repel or to kill blood-feeding invertebrates. We carried out structured interviews in 66 villages comprising 17 ethnic groups, covering a range of ethnic group, throughout Lao PDR and recorded a total of 92 plant species - in 123 different plant-ectoparasite combinations - that are used as traditional repellents and/or as “pesticides” to kill "pest" invertebrates. Traditional use was confirmed in the scientific literature for 74 of these plant species, and for an additional 13 species based on literature on closely related species. We concluded that repellents and pesticides from many plant species are commonly used in the Lao countryside. We also investigated traditionally used Lao plants for their activity to repel or to kill certain disease vectors and parasites. Target organisms were mosquitoes (Diptera, Culicidae), fly larvae (Diptera, Cyclorrhapha) in fermented fish production, and terrestrial blood-sucking leeches (Hirudinea, Haemadipsidae). The potential mosquito repellent activities of essential oils of Croton roxburghii (Euphorbiaceae), Hyptis suaveolens (Lamiaceae), and Litsea cubeba (Lauraceae) were evaluated in the field near Vientiane. Oils at concentrations of 1.7-6.7 µg/cm2 were significantly repellent to Aedes, Armigeres and Culex attracted to human baits. The activities against fly larvae, infesting fermenting fish, of three plant species, Tadehagi triquetrum (Fabaceae), Uraria crinita (Fabaceae) and Bambusa multiplex (Poaceae) were investigated: When fresh material of the plants was added on top of fermenting fish infested with fly larvae significant proportions of the larvae were repelled or killed. The total protective effect, i.e., repellent and killing effect combined, of T. triquetrum, U. crinita, and B. multiplex was 60-83 %, 77-90 %, and 60-93 %, respectively. Field evaluation of the potential leech repellent activities of water extracts of Sapindus rarak (Sapindaceae), Catunaregam spathulifolia (Rubiaceae) and Vernonia elaeagnifolia, (Asteraceae) impregnated on stockings and worn by persons in two leech-infested biotopes revealed leech repellent activities of 82.6%, 62.6% and 63.0%, respectively. The corresponding repellencies of deltamethrin and diethyl-3-methyl-benzamide (DEET) were 73.1% and 88.4%, respectively. Identification of the active components in certain of the plants with the ultimate aim to develop more optimal, less costly repellents, insecticides, acaricides, and anti-leech compounds as alternatives to synthetic repellents and pesticides against blood-feeding insects, ticks, mites, and leeches is in progress.

Phylogeny, the study of evolutionary relationships among species and other taxa, plays a crucial role in understanding the history of life. Bayesian analysis using Markov chain Monte Carlo (MCMC) is a widely used approach for inferring phylogenetic trees, but it suffers from slow convergence in higher dimensions and is slow to converge. This thesis focuses on exploring variational inference (VI), a methodology that is believed to lead to improved speed and accuracy of phylogenetic models. However, VI models are known to concentrate the density of the learned approximation in high-likelihood areas. This thesis evaluates the current state of Variational Inference Bayesian Phylogenetics (VBPI) and proposes a solution using a mixture of components to improve the VBPI method's performance on complex datasets and multimodal latent spaces. Additionally, we cover the basics of phylogenetics to provide a comprehensive understanding of the field. / Fylogeni, vilket är studien av evolutionära relationer mellan arter och andra taxonomiska grupper, spelar en viktig roll för att förstå livets historia. En ofta använd metod för att dra slutsatser om fylogenetiska träd är bayesiansk analys med Markov Chain Monte Carlo (MCMC), men den lider av långsam konvergens i högre dimensioner och kräver oändligt med tid. Denna uppsats fokuserar på att undersöka hur variationsinferens (VI) kan nyttjas inom fylogenetisk inferens med hög noggranhet. Vi fokuserar specifik på en modell kallad VBPI. Men VI-modeller är allmänt kända att att koncentrera sig på höga sannolikhetsområden i posteriorfördelningar. Vi utvärderar prestandan för Variatinal Inference Baysian Phylogenetics (VBPI) och föreslår en förbättring som använder mixturer av förslagsfördelningar för att förbättra VBPI-modellens förmåga att hantera mer komplexa datamängder och multimodala posteriorfördelningar. Utöver dettta går vi igenom grunderna i fylogenetik för att ge en omfattande förståelse av området.

This thesis focuses on phylogenetic relationships among some of the major lineages in Silene subgenus Behenantha (Caryophyllaceae) using DNA sequences from multiple, potentially unlinked gene regions from a large taxonomic and geographic sample. Both traditional phylogenetic analyses and a strategy to infer species trees and gene trees in a joint approach are used. A new strategy to optimize species classifications, based on the likelihoods of the observed gene trees, is presented. Silene latifolia, S. dioica and the other dioecious species previously classified in section Elisanthe are not closely related to the type of the section (S. noctiflora). The correct name for the group of dioecious species is section Melandrium. The chloroplast DNA data presented indicate a geographic, rather than a taxonomic, structure in section Melandrium. The nuclear genes investigated correlate more to the current taxonomy, although hybridization has likely been influencing the relationships within section Melandrium. Incongruence between different parts of the gene SlXY1 in two Silene lineages is investigated, using phylogenetic methods and a novel probabilistic, multiple primer-pair PCR approach. The incongruence is best explained by ancient hybridization and recombination events. A survey of mitochondrial substitution rate variation in Sileneae is presented. Silene section Conoimorpha, S. noctiflora and the closely related S. turkestanica have elevated synonymous substitution rates in the mitochondrial genes investigated. Morphological and phylogenetic data reject that the Californian S. multinervia should be treated as a synonym to the Asian S. coniflora, as has previously been suggested. Furthermore, none of the genes investigated, or a chromosome count, support the inclusion of S. multinervia in section Conoimorpha. Data from multiple genes suggest that S. noctiflora and S. turkestanica form a sister group to section Conoimorpha. The calyx nervature, which is a potential synapomorphy for S. multinervia and section Conoimorpha, may be explained either by parallelism or by sorting effects.