Recognizing the mechanisms of speciation and the limits of species is essential to understand the origin of biodiversity and how to conserve it. The general aims of my investigations during my doctoral studies were two-fold: to study evolutionary patterns and processes, and to provide specific and superspecific taxonomic classifications that try to reflect evolutionary history. I have focused my research on anurans in their biodiversity hotspot, the American Tropics. I have used morphological, behavioral (mating calls), and genetic (DNA sequences) characters to study species boundaries between frogs of the genus Pristimantis and the family Centrolenidae (glassfrogs). The results show that the exclusive use of single lines of evidence or the application of arbitrary thresholds impair and bias our ability to recognize new species and limit the possibility to understand evolutionary processes. Only an integrative approach combining every source of evidence provides the necessary feedback to discover all species and test their identity by comparing independent sets of data. This approach further allows identifying those species that probably represent stable comparative units (well supported species hypotheses) and to flag taxa that require further assessment. Phylogenetic reconstructions based on seven nuclear and mitochondrial genes for about 100 species of glassfrogs revealed that previous hypotheses of relationships were mislead by rampant convergent evolution at the phenotypic level. None of the previously suggested classifications fit with the reconstructed evolutionary history. Consequently, we proposed a new classification consistent with this phylogeny. I also studied the tempo and mode of diversification among glassfrogs. Based on sequences from ten genes in 87 species, I estimated species divergence times, age-range correlation between sister species, and reconstructed ancestral areas and dispersal/vicariance events. The results revealed a complex model of diversification where geographical isolation seems to be the dominant scenario for speciation and only clades of altitudinal generalists have been able to spread across the Neotropical rainforests.

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 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.

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.

Heliosperma (nom. cons prop.) comprises 15—20 taxa, most of them endemic to the Balkan Peninsula. DNA sequences from the chloroplast (rps16 intron, psbE-petG spacer) and the nuclear genome (ITS and four putatively unlinked RNA polymerase genes) are used to elucidate phylogenetic relationships within Heliosperma, and its position within Sileneae. Three main lineages are found within Heliosperma: Heliosperma alpestre, H. macranthum and the H. pusillum-clade. The relationships among the lineages differ between the plastid and the nuclear trees. Relative dates are used to discriminate among inter- and intralineage processes causing such incongruences, and ancient homoploid hybridisation is the most likely explanation. The chloroplast data strongly support two, geographically correlated clades in the H. pusillum-group, whereas the relationships appear poorly resolved by the ITS data, when analysed under a phylogenetic tree model. However, a network analysis finds a geographic structuring similar to that in the chloroplast data. Ancient vicariant divergence followed by hybridisation events best explains the observed pattern. The morphological and taxonomical diversity in the H. pusillum-group is possibly ecology-induced, and is not correlated with the molecular data. Phylogenetic patterns regarding the origin of Heliosperma are complicated, probably influenced by reticulate and sorting events. At least two ancient lineages have been involved in its evolution, one most closely related to Viscaria/Atocion and the other to Eudianthe/Petrocoptis. Atocion and Viscaria are sister genera, most species-rich on the Balkans, and including six/three species. Phylogenies do not support their traditional classification, and provide a framework for a taxonomic revision. Atocion compactum is found in three different positions in the chloroplast tree, and in a single clade in the nuclear gene trees. Using relative dates we demonstrate that hybridisation with subsequent chloroplast capture is a feasible explanation for the pattern observed. This, and other observed reticulate patterns, highlights the importance of hybridisation in plant evolution.