Table 2 - uploaded by Erki Õunap
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Primers and annealing temperature for PCR and cycle sequencing (CS) used in wider phylogenetic analysis of Sterrhinae (section 4.4). COI and ND1 were in some occasions amplified as four or three partially overlapping sections.
Source publication
Väitekirja elektrooniline versioon ei sisalda publikatsioone. This thesis focuses on problems related to the systematics of the moth subfamily Sterrhinae, one of the largest subfamilies of ‘loopers’ (Geometridae). Molecular phylogenetic analysis proved that the European ‘blood-vein’ is a complex of two closely related species, namely Timandra grise...
Contexts in source publication
Context 1
... mitochondrial (COI, ND1) and four nuclear [EF-1α, wgl, 28S rRNA expansion segment D1 (28S D1) and 28S D2] gene fragments were used for the broader phylogenetic analysis of Sterrhinae (chapter 4.4). Both PCR and cycle sequencing reaction conditions are presented in Table 2. The sequences were resolved on ABI 377 automated sequencer. ...
Context 2
... the position of one T. griseata and one T. comae specimen, collected at Nigula Nature Reserve, SW Estonia in 1990 and at Põõsaspea Cape, NW Estonia in 2001, respectively (article I, Table 1) did pose a question about monophyly of these species. Both COI and ND1 sequences of these specimens were identical to commonest haplotypes of the 'wrong' species (article I, Table 2, Fig. 2). Phylogenetic analyses therefore inevitably positioned those speci- mens into the 'wrong' clades (article I, Figs. 2 and 3). ...
Citations
... Furthermore, the genus Lythria Hübner, 1823 (Lythriini) was placed in the Sterrhinae, grouping together with the Rhodometrini, agreeing with the recent finding [22] that Lythria is a genus in the subfamily Sterrhinae, not the Larentiinae. On a more detailed level, the Cosymbiini, Timandrini and Rhodometrini were found to be related in the same sequence in the present study as in Sihvonen and Kaila [13], Õunap [37] and Strutzenberger et al. [24]. Holloway [9] treated these three tribes as an unresolved trichotomy. ...
... In the present analysis the Rhodostrophiini and Cyllopodini grouped together, as did the Sterrhini and Scopulini. The same pattern was proposed by Holloway [9], Sihvonen and Kaila [13], Õunap [37] and Strutzenberger et al. [24], although the latter two did not have Cyllopodini included in the analysis. The systematic position of Lissoblemma Warren, 1902 and related genera, see [13], remains problematic. ...
... Sterrhinae were found to have two major lineages, supporting the earlier morphology-based results [9], [13], and molecular-based results [24], [37]. Furthermore, the genus Lythria Hübner, 1823 (Lythriini) was placed in the Sterrhinae, grouping together with the Rhodometrini, agreeing with the recent finding [22] that Lythria is a genus in the subfamily Sterrhinae, not the Larentiinae. ...
The moth family Geometridae (inchworms or loopers), with approximately 23,000 described species, is the second most diverse family of the Lepidoptera. Apart from a few recent attempts based on morphology and molecular studies, the phylogeny of these moths has remained largely uninvestigated.
We performed a rigorous and extensive molecular analysis of eight genes to examine the geometrid affinities in a global context, including a search for its potential sister-taxa. Our maximum likelihood analyses included 164 taxa distributed worldwide, of which 150 belong to the Geometridae. The selected taxa represent all previously recognized subfamilies and nearly 90% of recognized tribes, and originate from all over world. We found the Geometridae to be monophyletic with the Sematuridae+Epicopeiidae clade potentially being its sister-taxon. We found all previously recognized subfamilies to be monophyletic, with a few taxa misplaced, except the Oenochrominae+Desmobathrinae complex that is a polyphyletic assemblage of taxa and the Orthostixinae, which was positioned within the Ennominae. The Sterrhinae and Larentiinae were found to be sister to the remaining taxa, followed by Archiearinae, the polyphyletic assemblage of Oenochrominae+Desmobathrinae moths, Geometrinae and Ennominae.
Our study provides the first comprehensive phylogeny of the Geometridae in a global context. Our results generally agree with the other, more restricted studies, suggesting that the general phylogenetic patterns of the Geometridae are now well-established. Generally the subfamilies, many tribes, and assemblages of tribes were well supported but their interrelationships were often weakly supported by our data. The Eumeleini were particularly difficult to place in the current system, and several tribes were found to be para- or polyphyletic.
The Iranian taxa of the tribe Scopulini are taxonomically revised. The systematic positions of the genera Cinglis Guenée, 1858, Glossotrophia Prout, 1913, Pseudocinglis Hausmann, 1994 and Scopuloides Hausmann, 1994, with uncertain validity and/or position within the tribe Scopulini Duponchel, 1845 (Lepidoptera: Sterrhinae), are further elucidated by use of one mitochondrial and up to nine protein-coding nuclear gene regions. Available type specimens of the described species and more than 2,600 additional specimens were morphologically investigated. In addition, over 400 genitalia preparations were made and examined together with distribution data and DNA barcodes. As a result of the multigene analysis, the genera Cinglis stat. rev. and Scopuloides stat. rev. are re-validated at the genus level. The genus Pseudocinglis syn. nov. is regarded as a junior synonym of the genus Cinglis stat. rev. and Glossotrophia syn. nov. is regarded as a junior synonym of the genus Scopula. Cinglis eurata (Prout, 1913) comb. nov. and Cinglis benigna (Brandt, 1941) comb. nov. are combined with the genus Cinglis. Additionally, Cinglis benigna amseli (Wiltshire, 1967) syn. nov. is regarded as a synonym of C. benigna. Scopula adulteraria (Erschov, 1874) stat. nov. is raised from subspecies to species rank; Scopula iranaria Bytinski-Salz & Brandt, 1937 syn. nov. is synonymized with S. flaccidaria (Zeller, 1852); S. transcaspica taftanica Brandt, 1941 syn. nov. is synonymized with S. transcaspica Prout, 1935; S. diffinaria asiatica (Brandt, 1938) syn. nov. is synonymized with S. diffinaria (Prout, 1913) and Glossotrophia bullata Vojnits, 1986 syn. nov. is synonymized with Scopula sacraria ariana (Ebert, 1965). The female genitalia of Scopula lactarioides Brandt, 1941 are described and illustrated for the first time. In total, the presence of 33 species of Scopulini in Iran is confirmed.Wing patterns, male and female genitalia and diagnostic characters of most Iranian Scopulini species are depicted andtheir distribution ranges are mapped.
Fungi represent one of the largest and diverse kingdoms of eukaryotes, and Basidiomycota is the second most species-rich group within Fungi. Despite the ecological importance of basidial fungi, i.e., their leading role in decomposition of wood in terrestrial ecosystems, their diversity and taxonomy are insufficiently known. Fulfilling this knowledge gap, the thesis presents taxonomic studies in a class of basidal fungi called Dacrymycetes. Dacrymycetes occur only on dead wood and produce either of the two types of fruitbodies: gelatinous voluminous yellow or dry flat bleak-coloured. The latter type, also called corticioid fruitbodies, is the primary focus of this thesis. Traditionally, such corticioid fruitbodies in dacrymycetes were strictly associated with the family Cerinomycetaceae and its only genus Cerinomyces. This emphasis on a single character led to inclusion of dissimilar species into Cerinomyces, and over the time the genus became overly broad and polyphyletic. Thus, aim of the present thesis was to revise Cerinomyces and related taxa on a basis of DNA sequence-based phylogenetic analyses and morphological studies. As a result, Cerinomyces was reshaped to a more natural scope and became monophyletic. Priority for the corticioid morphology was abandoned, and gelatinous members were introduced to the genus. Instead of fruitbody type, the genus is now united by a set of microscopic characters: simple clamps, thin-walled aseptate basidiospores, and low amount of carotenoid pigments. Moreover, investigating taxa morphologically similar to Cerinomyces, the rest of dacrymycetes was partially revised. Special attention was paid to notable morphological structures called “dendrohyphidia” that are common in Cerinomyces, but were also found in other dacrymycetes. To accommodate such taxa in the Dacrymycetaceae family, a new genus Dendrodacrys was raised. In total, the thesis proposes 42 nomenclatural novelties to science, including one new genus, 27 new species, and 14 new combinations.
Knowledge of population genetics and phylogeography of living organisms are
important for conservation and management of species, since they provide
information about species viability and integrity. There have been numerous
genetic studies of brown bears in parts of the species’ range to inform local
management and conservation approaches, and due to the status of the brown
bear as a ‘model species’ in phylogeographic studies. However, there is little
information about brown bear genetics in the largest part of the distribution
area: northern continental Eurasia. The goal of this thesis was to provide new
information about the population genetics, diet and phylogeography of brown
bears in this region, to describe population genetic structure and to assess the
importance of historical and ecological conditions in generating and main-
taining structure.
Modern day human genomes are mixtures of ancient components. Thanks to advancements in ancient DNA (aDNA) research, we can detect the origins of these components and study them. However, aDNA might either not be available or be of low quality in many situations due to DNA structure being subject to degradation related to time and different environmental factors. Thankfully, we can identify and extract these ancient layers also from contemporary human genomes with local ancestry inference methods. With this approach, we can study admixed populations, which have highly divergent ancestral components, in terms of demography and functional analyses. This thesis particularly focuses on two such groups: South Asian populations, which are composed of West Eurasian and South Asian ancestries, and Ethiopian populations, which are composed of Eurasian and African ancestries. In the first part, past demographic events, diverse genomic variation and post-admixture natural selection in South Asia are investigated by generating surrogates for the two main ancestral components of contemporary South Asian genomes. In the second part, a local ancestry inference-based method is evaluated for improving selection detection in ancestral components of admixed genomes and it is applied on South Asian genomes. In the third and the last part, a similar approach to the first part is conducted for Ethiopian genomes to pinpoint the source of Eurasian ancestry in contemporary Ethiopians.
Eurasian wild boar is the most widespread species of the Suidae family and its populations increased significantly in the second half of the 20th century – a change that has been largely associated with the continuing spread of agriculture, as well as the widespread practice of supplementary feeding. However, due to its omnivorous diet, high population density of wild boar can have disastrous effects on other animals, particularly on ground-nesting birds, whose populations have suffered from loss of habitat as well as predation.Wild boar can also play an important role in disease outbreaks as a reservoir of various pathogens shared between wildlife and domestic animals. The purpose of this thesis was to examine the potential consequences of supplementary feeding of wild boar for ground-nesting birds and wild boar infection with endoparasites, because increased overall abundance of wild boar and increased contact rates at feeding sites can promote the spread of various diseases.
In this study, supplementary feeding had a key role in determining wild boar abundance and grain from feeding sites constituted a major food category even in the warm season, when food availability was not hindered by low temperatures and deep snow. However, despite having access to supplemental food, wild boar acted as a predator of nests and chicks of forest grouse and the concentration of wild boar and other predators near feeding sites resulted in locally increased predation risk for ground-nesting birds. What is more, the novel molecular method applied in this study revealed that faecal diet analysis based on morphology, which is still a popular method in diet studies, underestimates the proportion of bird in wild boar diet, indicating that previous studies might suffer from the same error. In addition to its contribution to increased predation of ground-nesting birds, supplementary feeding was shown to influence endoparasite infection in wild boar both directly and indirectly through increased abundance. Supplementary feeding sites had become hot-spots for acquiring lungworm infection and parasites with a direct life cycle benefited from the overall high host abundance. These unwanted effects should be reckoned with in wild boar management.
