Building interpretable fuzzy models for high dimensional data analysis in cancer diagnosis

Background: Analysing gene expression data from microarray technologies is a very important task in biology and medicine, and particularly in cancer diagnosis. Different from most other popular methods in high dimensional bio-medical data analysis, such as microarray gene expression or proteomics mass spectroscopy data analysis, fuzzy rule-based models can not only provide good classification results, but also easily be explained and interpreted in human understandable terms, by using fuzzy rules. However, the advantages offered by fuzzy-based techniques in microarray data analysis have not yet been fully explored in the literature. Although some recently developed fuzzy-based modeling approaches can provide satisfactory classification results, the rule bases generated by most of the reported fuzzy models for gene expression data are still too large to be easily comprehensible. Results: In this paper, we develop some Multi-Objective Evolutionary Algorithms based Interpretable Fuzzy (MOEAIF) methods for analysing high dimensional bio-medical data sets, such as microarray gene expression data and proteomics mass spectroscopy data. We mainly focus on evaluating our proposed models on microarray gene expression cancer data sets, i.e., the lung cancer data set and the colon cancer data set, but we extend our investigations to other type of cancer data set, such as the ovarian cancer data set. The experimental studies have shown that relatively simple and small fuzzy rule bases, with satisfactory classification performance, can be successfully obtained for challenging microarray gene expression datasets. Conclusions: We believe that fuzzy-based techniques, and in particular the methods proposed in this paper, can be very useful tools in dealing with high dimensional cancer data. We also argue that the potential of applying fuzzy-based techniques to microarray data analysis need to be further explored. </p

Feature subset selection problem on microarray data

Recent advance of technology gave birth to tools such as microarray chips. The use of microarray chips enabled the scientists to measure the amount of protein production from their genes in a cell, known as the gene expression data. The classification of cell samples by means of their gene expression data is a hot research area. The data used for the analysis is massive and therefore the features, i.e., the genes, must be reduced to a reasonable level due to the computational cost of experiments and the possibility of misleading irrelevant genes. Therefore, usually, the analysis based on the classification of cell samples includes a feature subset selection phase. This thesis aims to develop a tool that can be used during the feature subset selection phase of such analyses. Three novel algorithms are proposed for the gene selection problem based on basic association rule mining. The first algorithm starts with fuzzy partitioning of the gene expression data and discovers highly confident IF-THEN rules that enable the classification of sample tissues. The second algorithm search the possible IFTHEN rules based on a heuristic pruning approach which is based on the beam search algorithm. Finally, the third algorithm focuses on the hierarchical information carried through gene expressions by constructing decision trees based on different performance measures. We found satisfactory results in Leukemia Dataset. In addition, in colon cancer dataset, algorithm that is based on construction of decision trees showed good performance

Fis suurendab Pseudomonas putida biofilmi hulka, tõstes lapA ekspressiooni

Väitekirja elektrooniline versioon ei sisalda publikatsiooneBakterid elavad looduses valdavalt biofilmis, pinnale kinnituvate bakterite kogumis. Biofilmis elamisel on bakterite jaoks mitmeid eeliseid. Biofilmis elavad bakterid on kahjulike keskkonnamõjude eest paremini kaitstud ja heades tingimustes aitab pinnale kinnitumine nendesse tingimusesse jäädagi. Biofilm ei ole kasulik mitte ainult bakteritele, vaid paljud biofilmi moodustavad bakterid on vajalikud ka taimedele. Üheks selliseks bakteriks on Pseudomonas putida, mida uurin oma doktoritöös. P. putida moodustab biofilmi taime juurtel ja kaitseb taimi, ka põllumajanduslikult olulisi kultuure, haigustekitajate eest ning soodustab nende kasvu. Käesoleva töö käigus leiti juhuslikult, et P. putida biofilmi mõjutab bakteri keskne regulaatorvalk Fis. Kui bakterid satuvad headesse tingimustesse, siis Fis-i roll on suunata nad kiirelt kasvama ja kui toitained saavad otsa, siis aeglustada kasv jälle maha. Me nägime, et liiga palju Fis-i tootvad bakterid ei suuda ringi liikuda. Sealt tekkis kahtlus, et äkki nad ei liigu sellepärast, et jäävad hoopis paigale ja moodustavad biofilmi. See teooria osutus tõeseks ja püstitas kohe järgmise küsimuse, kuidas Fis suunab bakterid biofilmi moodustama? Me leidsime, et Fis soodustab ühe väga suure kleepvalgu tootmist. See kleepvalk, LapA, on biofilmi tekkeks väga oluline, kuna võimaldab bakteritel nii pinnale kui teineteisega kleepuda. Käesolevas töös näitasime, et Fis seondub kahes kohas lapA geeni ette ja just neid kohti kasutades soodustab LapA tootmist. Lisaks kirjeldasime need kohad (promootorid), kust algab lapA mRNA tootmine. Kui tavaliselt on ühel geenil üks või kaks promootorit, siis lapA geenil on neid lausa kuus. Kokkuvõttes lõi see töö uusi teadmisi P. putida biofilmi regulatsioonist ja aitab seega paremini mõista selle kasuliku mullabakteri elu väga olulist etappi.Tartu Ülikool. Loodus- ja täppisteaduste valdkondBiofilms are the prevailing lifestyle of bacteria in most natural environments. This is because living in a biofilm gives bacteria a number of advantages. When the environment is hazardous, residing in a biofilm protects them; and when conditions are favourable, biofilm is a way to settle down and not be carried away from the good life. Biofilm is not only useful for bacteria but many biofilm-forming bacteria are also beneficial for plants. One of those beneficial bacteria is Pseudomonas putida, the focus of this thesis. P. putida forms biofilm on roots of plants, including agriculturally important crops, protecting them against disease-causing microorganisms and promoting plant growth. During this work, it was discovered that P. putida’s biofilm is regulated by the central regulator protein Fis. Fis is the regulator that starts fast growth in good conditions and when nutrients deplete, decelerates growth. We saw that bacteria producing elevated levels of Fis were unable to move around. This prompted the idea that maybe they are not moving because they are settling down and forming biofilm. This idea proved true and raised the next question, how does Fis lead the bacteria to form biofilm? We found that Fis upregulates the production of a huge adhesion protein. This protein, LapA, is a key factor for biofilm formation as it enables bacteria to stick both to surfaces and to one another. In this work, we show that Fis binds upstream of the lapA gene in two positions and utilizes these sites to boost the production of LapA. We also described the location of the promoter sites where the production of lapA mRNA is initiated. While many genes have one or two promoter, lapA has surprisingly many – six. Altogether, this work shed light onto P. putida biofilm regulation and thus helps us better understand a very important stage in this beneficial soil bacterium’s life

Elupaiga ja maastiku mõjud päevaliblikakooslustele majandatavates metsades

Väitekirja elektrooniline versioon ei sisalda publikatsiooneElurikkuse vähenemine on üleilmne probleem, mida peamiselt põhjustab looduslike ja poollooduslike elupaikade kadumine. Elupaikade liigilist mitmekesisust mõjutab ka ümbritsev maastik: mida rohkem on elupaigad üksteisest eraldatud, seda enam need liigiliselt vaesuvad. Ehkki kaitsealad on elurikkuse hoidmisel väga tähtsad, ainuüksi neist ei piisa. Järjest enam püütakse leida võimalusi liigirikkuse säilitamiseks ja suurendamiseks ka tugevate inimmõjutustega maastikes. Suurenev nõudlus puidu ja puidutoodete järele on järjest intensiivsemaks muutnud ka metsade majandamise. Metsamajanduse intensiivistumine on paljudele metsaliikidele ohuks, samas leidub ka neid, kellele majandatav metsamaastik elupaigaks sobib. Doktoritöö tulemused viitavad, et üheks selliseks liigirühmaks on metsapäevaliblikad. Paljude liikide röövikud toituvad puudel, põõsastel ja alustaimestiku taimedel, valmikud aga leiavad nektaritaimi raiesmikelt. Niisiis on metsapäevaliblikatele oluline mosaiikne metsamaastik tervikuna – doktoritöös leidsingi, et mida rohkem on ümbritsevas maastikus metsamaad, seda kõrgem on metsaliblikate liigirikkus raiesmikul. Oma töös lähen aga sammu võrra kaugemale ja näitan, et lisaks metsaliikidele pakub majandatav metsamaastik oma mitmesuguste avakooslustega elupaika ka paljudele avamaastikuliikidele. Selgus, et raiesmikud on elupaigaks enamikule regionaalsest päevaliblikafaunast, kellest suurt osa on tavapäraselt seostatud poollooduslike niitudega. Seejuures asustavad niiduliigid ka täielikult metsaga ümbritsetud raiesmikke, millest järeldub, et puistu raiesmikele jõudmisel neile oluliseks takistuseks ei ole. Nii niiduliikide kui metsaliikide koosluseid mõjutavad aga metsa lokaalsed kasvukohatingimused – teatud liigid esinevad sagedamini ja arvukamalt näiteks palumetsades, teised jällegi laane- või salumetsades. Seega on päevaliblikate liigirikkuse seisukohalt oluline elupaikade mitmekesisus, erinevad metsatüübid täiendavad teineteist.Decrease of biodiversity is a global problem mainly caused by loss of natural and semi-natural habitats. Local diversity is also affected by surrounding landscape: isolation of habitats leads to decline of species richness. Despite being important, protected areas alone may be insufficient to maintain biodiversity. The focus is shifting towards sustaining and enhancing species diversity in landscapes of significant human impact. Intensification of forest management due to increasing demand for timber, poses a threat for many forest species. However, some species may find favourable habitat in managed forests. The results of this thesis indicate that forest butterflies are among those. At caterpillar stage, forest butterflies feed on trees, bushes and understorey plants, whereas adults find nectar plants from clear-cuts. Therefore, the whole mosaic of managed forest landscape is important for forest butterflies. Indeed, I found higher species richness of forest butterflies in clear-cuts containing higher proportion of woodland in the surrounding landscape. Furthermore, my thesis shows that managed forest landscape containing various open habitats is also suitable for many open-habitat species. I found that clear-cuts serve as habitats for the majority of regional species pool of butterflies traditionally associated with semi-natural grasslands. Moreover, grassland species reach even to clear-cuts completely surrounded with forest, which implies that forest is not a significant barrier for colonisation. Assemblages of grassland species and forest species are both affected by local environmental conditions of forest: different forest types provide habitat for distinct butterfly assemblages. The diversity of forest types is therefore important for maintaining species richness of butterflies, as different forest habitat types complement each other.https://www.ester.ee/record=b524411

Sequential Event Prediction with Association Rules

We consider a supervised learning problem in which data are revealed sequentially and the goal is to determine what will next be revealed. In the context of this problem, algorithms based on association rules have a distinct advantage over classical statistical and machine learning methods; however, there has not previously been a theoretical foundation established for using association rules in supervised learning. We present two simple algorithms that incorporate association rules, and provide generalization guarantees on these algorithms based on algorithmic stability analysis from statistical learning theory. We include a discussion of the strict minimum support threshold often used in association rule mining, and introduce an "adjusted confidence" measure that provides a weaker minimum support condition that has advantages over the strict minimum support. The paper brings together ideas from statistical learning theory, association rule mining and Bayesian analysis

Globaalse regulaatorvalgu Fis-i roll lapF geeni ekspressiooni reguleerimisel ja rakupinna hüdrofoobsuse mõjutamisel mullabakteris Pseudomonas putida

Väitekirja elektrooniline versioon ei sisalda publikatsiooneBakteritel on pikaaegse evolutsiooni käigus välja kujunenud omadused ja mehhanismid selleks, et olla kohanemisvõimelised ja jääda ellu mitmesugustes keskkonnatingimustes. Vastavalt vajadusele muudavad bakterid oma eluvormi, ujudes vabalt keskkonnas ringi või olles paiksed ja moodustades koos teiste bakteritega ühise kooseluvormi, mida nimetatakse ka biofilmiks. Biofilmis elades on bakterid paremini kaitstud kahjulike keskkonnamõjude eest. Üleminek liikuvalt eluviisilt paiksele algab tavaliselt bakterite kinnitumisega elusale või elutule pinnale. Erinevatele pindadele kinnitudes võivad bakterid tekitada tõsist kahju näiteks meditsiini ja tööstusvaldkondades. Samas, biofilmi moodustavaid baktereid on kasutatud ka edukalt näiteks mürgiste ühendite eemaldamiseks keskkonnast. Üks peamisi bakteriraku pinna omadusi, mis aitab kinnitumisele kaasa, on hüdrofoobsus. Hüdrofoobsema pinnaga rakud liituvad ehk agregeeruvad omavahel paremini, tänu millele nad vähendavad kättesaadavat rakupinda kahjulikele ainetele. Näiteks mullabakter Pseudomonas putida muudab oma rakupinda hüdrofoobsemaks kokkupuutel erinevate toksiliste ainetega. P. putida on kosmopoliitne bakter, mis tihti elab taimejuurtel ja soodustab taimede kasvu. Üldiselt mullabakterid eelistavad elada taimejuurte ümber risosfääris, sest taimed eritavad juurte kaudu bakterite jaoks kergesti kasutatavaid toitaineid. Samas, taimed võivad juurte kaudu ümbritsevasse mulda eritada ka toksilisi ühendeid. Seega bakterid peavad kohanema nii kasvu soodustavate kui ka pärssivate tingimustega. Käesolevas töös kirjeldatakse P. putida pinna hüdrofoobsufaktorit LapF-i ning selle geeni regulatsiooni Fis-ga. Varem ei ole avaldatud seoseid LapF-i ja P. putida pinna hüdrofoobsuse vahel ega ole ka teada detailsemat infot lapF geeni ekspressiooni regulatsiooni kohta. P. putida rakud, mis toodavad pinnavalku LapF, on stressitingimustes hüdrofoobsemad võrreldes rakkudega, kus puudub LapF. LapF-st tulenev hüdrofoobsem rakupind võib omada potentsiaalset kaitsvat rolli P. putida’le. LapF-ga P. putida’l on soodustatud rakkude liitumine, tänu millele vähendatakse toksilistele ainetele kättesaadavat rakupinda. Kirjeldatud kaudne kaitsemehhanism võib olla üks seni avastamata LapF-i rolle mullabakteris P. putida.Bacteria have developed several mechanisms to cope with the changing conditions of the surrounding environment. The characteristics of cell surface can passively help to deal with unfavourable conditions or can be involved in the switch between two different life-forms: free-swimming aka planktonic lifestyle and surface-attached aka biofilm aka sessile lifestyle. When living in a biofilm, bacteria are better protected against harmful conditions. The transition from free-swimming to sessile happens when bacteria attach to the surface and/or each-other. The formation of bacterial biofilms can cause serious problems for humans. Hospital-related infections due to bacteria on surgical instruments are one of the examples. However, the human society has also learned to benefit from the bacterial biofilm by using microorganisms to remove contaminants from environment. In most cases, the adhesion properties of bacteria are defined by cell surface hydrophobicity. Bacteria with more hydrophobic surface attach to each-other, which helps reduce their surface to toxic compounds. For example, the surface of Pseudomonas putida becomes more hydrophobic in the presence of toxic chemicals. P. putida is a soil bacterium mainly residing on the roots of plants. That kind of habitation is strongly dependent on the roots exudates, which include both nutrients and toxic compounds for bacteria. In order to survive and outcompete other microorganisms on the plant roots P. putida must be able to quickly adapt to the changes in its surrounding environment. For example staying put by forming biofilm or moving freely to recolonize new parts of plant roots for better conditions. The aim of this research was to study and enlighten the role of surface protein LapF in P. putida and it`s regulation by global regulator Fis. Prior this work, LapF had only been described as a biofilm-related protein and there was no detailed information published about the lapF gene regulation in P. putida. We demonstrate, that LapF is the factor for making P. putida cells more hydrophobic and propose that LapF might have a potential role as a protective factor for P. putida. More hydrophobic bacteria can be more aggregative and therefore might help the cells reduce the surface exposed to the environment. This can be a passive protection mechanism against toxic compounds

Puuliikide mõju seente liigirikkusele ja liigilisele koosseisule

Väitekirja elektrooniline versioon ei sisalda publikatsiooneErinevad seenerühmad on looduses olulised orgaanilise aine lagundajad, haigustekitajad või juursümbiondid, kes aitavad puudel omastada mineraalaineid. Puud mõjutavad oma ümbrust läbi varise ja juureeritiste. Puuliikide kooskasvamine loob segametsades erinevad elupaigalaigud, mis suurendab muude organismide elurikkust metsades, kus kasvab rohkem puuliike. Elurikkus suurendab ökosüsteemide tootlikkust ja stabiilsust muutuvate keskkonnatingimuste vastu. Enda doktoritöös käsitlen seente elurikkuse seost puude varise ja peremeestaimede liigirikkusega ning teiste puuliikide naabruse mõjuga. Leidsin, et mida rohkem sisaldab lagunev lehevaris erinevate puuliikide lehti, seda suurem on selles seente liigirikkus. Samas juurte liigirikkuse mõju seente mitmekesisusele on nõrk. Lehevarise koosseis määrab ka lagundajate ja taimepatogeenide liigilise koosseisu. Kuuse ektomükoriisaseente liigiline koosseis erineb kase–kuuse segametsa ning kuuse monokultuuri vahel. Kase naabrus mõjutab mulla keemilisi omadusi ja seeläbi ektomükoriissete seente kooslusi. Ektomükoriisaseente liigirikkus on globaalsel skaalal seotud peremeestaimede liigirikkusega, kuid regionaalsel tasemel on seosed mulla omaduste ja konkreetsete puuliikidega tähtsamad. Oma tööst järeldan, et metsa liigirikkus tõepoolest suurendab seente elurikkust, mõju tugevus sõltub aga konkreetsetest puuliikidest ning mulla ja muu taimkatte omadustest.Fungi play key roles in forest ecosystems. Various groups of fungi drive organic matter decomposition and soil nutrient cycling, act as tree root symbionts or cause diseases. Trees are influential components of forest habitats that modify their surroundings via shedding litter and root exudates, but little is known about the functional importance of tree species diversity on soil organisms and soil biological processes. Mixtures of tree species can create fine-scale environmental heterogeneity that supports higher biodiversity in forest stands. Biodiversity enhances productivity and stability, buffering ecosystems against changing environmental conditions. In this thesis, I examined fungal diversity in relation to plant litter, host plant diversity and tree neighbourhood effects. Leaf litter mixtures with higher plant species richness harboured higher fungal diversity, indicating that heterogeneity of resources in litter mixtures provides more habitats and allows a larger number of fungal species to co-exist. Conversely, the root litter richness effect on fungal diversity was weak. Furthermore, leaf litter composition had a strong effect on composition of saprotrophic and plant pathogenic fungi. Richness of ectomycorrhizal fungi was positively related to host plant richness at global scale. At regional scale, fungal richness correlated with plant richness, but this effect was related to improved soil conditions in mixed forests. Communities of ectomycorrhizal fungi on spruce roots differed in spruce monocultures and mixed stands of birch and spruce, which points to the influence of birch on soil quality. To conclude, tree species richness and fungal diversity are usually positively correlated, but the direct impact of plant richness depends on the context, including the influence of particular plant species and analysis of other factors.https://www.ester.ee/record=b538405

Sisisev hoiatushäälitsus peegeldab emastel rasvatihastel (Parus major) käitumuslikku fenotüüpi ning sigimisedukust looduslikus populatsioonis

Väitekirja elektrooniline versioon ei sisalda publikatsiooneKisklus on üks peamisi tegureid looduses, mis mõjutab otseselt loomade ellujäämist ja sigimist. Kisklusvastane käitumine eri liiki loomadel ja isegi sama liigi isenditel on väga mitmekesine. Liigisiseste käitumuslike erinevuste üheks põhjuseks võib pidada erinevusi iseloomus. Paljudel lindudel, sealhulgas rasvatihasel, on välja arenenud iseloomulik hoiatushäälitsus ootamatu ohu korral – nad sisisevad –, kuid mitte kõik isendid. Uurisin emaste rasvatihaste sisisemist, kasutades selle esilekutsumiseks suur-kirjurähni topist, kuna tegemist on liigiga, kes sageli õõnelindude pesi rüüstab. Võrdlesin sigimisnäitajaid, rüüstatud pesade hulka, pesapaiga eelistust ja genotüübierinevusi neljal aastal. Tulemustest selgus, et emaste rasvatihaste vastus kiskja ootamatule ilmumisele varieerub asurkonnas, kuid isendi käitumine on ajas üsna püsiv. Munemise alustamise aeg või kurna suurus ei ennustanud emaste sisisemist või vaikimist, kuid lindudel, kes ei sisisenud, lennuvõimestus rohkem poegi. Seejuures ei erinenud munade koorumise edukus sisisejatel ja mittesisisejatel. Sisisejad eelistasid pesitseda liigikaaslastest kaugemal ning pigem okas- kui lehtmetsas. Pesa rüüstamise tõenäosus ei seostunud sisisemisega. Kokkuvõtlikult, sisisemine või selle puudumine sõltub ilmselt emase iseloomust ja on võimalik iseloomutunnus. Emased rasvatihased käituvad vastavalt oma iseloomule erinevalt nii suheldes liigikaaslastega kui ka kiskjatega ning iseloomust tulenevalt võib erineda ka nende vanemlik võimekus. Kuna loodusliku valiku tulemusel on erinevad käitumistüübid populatsioonis olemas, võib arvata, et nende püsimajäämise edukus peitub näiteks erinevustes ellujäämises või sigimisedukuses.Predation is a major aspect affecting animal survival and reproductive success in the wild. Anti-predator behaviours greatly vary between species but also among individuals of the same species. Differences within a species may be derived from differences in personalities. Several bird species, including the great tit, have evolved a specific vocal response towards a threatening situation – the hissing call – but not all individuals elicit hissing. I investigated the hissing behaviour of female great tits by presenting a great spotted woodpecker decoy – a species that is a common nest-predator of cavity-nesting birds. I compared breeding characteristics, the number of nests depredated by predators, nest-site preferences, and differences in the genotype over four years. According to my results, the response type of female great tits varied within the population, but the individual behavioural type remained relatively consistent in time. Start of egg-laying or clutch size did not predict whether the female hissed or not, but birds that did not hiss raised more fledglings. Hatching success did not differ between hissing and non-hissing birds. Hissing females preferred to nest further away from conspecifics and were more likely found in a coniferous than in a deciduous forest. Nest depredation rate was not related to the propensity of hissing birds. Taken together, whether a female hisses or not may depend on the female’s personality and may be regarded as a personality trait. The same as females differ in their personalities, they differ in the way they interact with conspecifics or predators, and they may even differ in their parental abilities. As natural selection has maintained different behavioural types within the population, it is likely that the success of the different behavioural types may be found in differences in survival or breeding success.https://www.ester.ee/record=b552435

Eukarüootse mullaelustiku seos maakasutuse muutuse ning peremeestaime identiteediga

Väitekirja elektrooniline versioon ei sisalda publikatsiooneMullaelustiku uurimine pole lihtne – lisaks sellele, et maa-alune elu jääb inimese igapäevasest tajuruumist kõrvale, on enamik mullas elutsevaid organisme kas mikroskoopilised või vähemalt piisavalt pisikesed, et nende leidmine, rääkimata liikide eristamisest, on keeruline. Õnneks tulevad siinkohal ökoloogidele appi DNA-põhised määramismeetodid. Selle tulemusena on tormiliselt arenema hakanud ökoloogiasuund, kus samaaegselt endisaegsete loodusuurijate tööga – kes kus elab? – uuritakse maapealsel elul põhinevate teooriate paikapidavust ka maa all. Doktoritöö käigus uurisin, kuidas mõjutab inimtegevus ühe olulise maa-aluse elustikurühma – peaaegu 80% maismaa taimeliikidega sümbioosis elavate arbuskulaarmükoriissete (AM) seente – elurikkust nii globaalsel skaalal ning Eestile omastes poollooduslikes kasvukohtades. Leidsin, et inimtegevusest (või selle tegevuse lõpetamisest) tingitud stress mõjutab suuresti koosluste koosseisu, kuid ei pruugi tingimata päädida vaadeldavate organismide liigirikkuse vähenemisega. Kuna liigilist koosseisu võib teatud lähenduses käsitleda koosluse funktsiooni indikaatorina, leidsin, et inimtegevuse mõju hindamiseks ei piisa pelgalt liikide loendamisest. Samuti leidsin, et looduslike ökosüsteemide AM seente liigirikkusele on inimtekkelistel häiringutel vastassuunaline mõju – vaesemates kasvukohtades elurikkust suurendav ning rikkamates vähendav. Puisniidul erinevaid organismirühmi uurides selgus, et inimtegevuse tõttu muutunud kasvukohtades muutuvad samaaegselt ja -suunaliselt mitmed päristuumsed organismirühmad, nii mükoriisaseened kui ka mullas elavad loomad. Lisaks leidsin vastupidiselt ootustele, et vaatamata enamiku taimeliikidega koos elavate AM seente väiksele globaalsele liigirikkusele (maismaa taimeliikide ning AM seeneliikide arvu suhe on umbes 300:1) ei ole taimejuurtesse „komplekteeritud“ AM seeneliikide kogum juhuslik, vaid mükoriisavõrgustikus eelistavad teatud peremeestaimed kindlaid seeneliike (või vastupidi).Doing research on belowground organisms is troublesome – in addition to being hidden from the everyday perspective on the world, most soil-dwellers are either microscopic or at least small enough to seriously hinder detection and identification. Luckily, recent decades have advanced molecular techniques enough to allow ecologists to delimit organisms based on DNA sequences, and rapid developments in quantifying and making sense of the belowground biosphere are underway. Still, due to the hasty pace in which this field of ecology is evolving – biogeographical works resembling that of early naturalists’ are being conducted in parallel with validating old and generating new ecological principles for soil – much of the results are contradictory and gaps in knowledge can span entire ecosystems. The PhD thesis in hand dealt with global and regional anthropogenic impact on one of the ubiquitous groups of soil organisms – arbuscular mycorrhizal (AM) fungi that form symbiosis with nearly 80% of land plants. We found that stress caused by human influence (or in some cases, cessation of) strongly influences the compositional structure of AM fungi, but does not always directly translate to loss of biodiversity. As the compositional structure could be viewed as a proxy of the functional characteristics we speculate that human disturbance might influence the function of the belowground biosphere. Further, we demonstrated that human disturbance could have an opposite effect at different ends of the natural biodiversity gradient – naturally species poor sites gain in biodiversity and vice versa. In order not to be confined to a single organism group, we showed co-varying changes of different groups of soil-dwelling eukaryotes, from symbiotrophic fungi to soil animals, in response to human-mediated change of habitat. To our great surprise, we also found that despite the great imbalance of the overall diversity of AM fungal species and plant species with whom they form symbiosis with (the ratio of land plant species to AM fungal species is about 300:1), the communities of AM fungi in plant roots are not assembled randomly. Instead, the plant-fungal interaction network follows certain structural principles that promote resilience and symbiotic partners seem to prefer some species to others.https://www.ester.ee/record=b538034

Seente perekonna Cerinomyces ja lähedaste taksonite süstemaatika ning fülogenees

Väitekirja elektrooniline versioon ei sisalda publikatsioonePäristuumsete hulgas on seened üks suuremaid ja liigirikkamaid eluslooduse riike. Kandseened on omakorda üks seente liigirikkam hõimkond, mille hulka kuuluvad nii surnud orgaanilise aine lagundajad kui ka taimejuurtega sümbioosis elavad organismid. Vaatamata kandseente olulisele ökoloogilisele rollile, on nende taksonoomia ja ökoloogia siiani ebapiisavalt uuritud. Käesolev doktoritöö hõlmab kandseente klassi pisarseened (Dacrymycetes) taksonoomia ja evolutsiooni uuringuid. Pisarseened kasvavad kõdupuidul ja neil areneb kahte tüüpi viljakehi: kollased sültjad või tuhmi värvi koorikjad viljakehad. Enne seda uurimistööd arvati koorikjate viljakehadega pisarseente liigid sugukonda Cerinomycetaceae ja selle ainsasse perekonda Cerinomyces. Selline lihtsustatud süstemaatika on viinud olukorrani, kus perekonda Cerinomyces kuulub palju liike, mis pole omavahel lähisuguluses. Käesoleva doktoritöö eesmärgiks oligi uurida perekonna Cerinomyces ja sellele morfoloogiliselt sarnaseid liike. Selleks kasutati nii DNA järjestusi kui ka morfoloogilisi ning anatoomilisi tunnuseid, mille põhjal viidi läbi fülogeneetilised analüüsid. Selle töö põhjal esitati teadusele uus monofüleetilise perekonna Cerinomyces kontseptsioon. Cerinomyces perekonda on nüüd arvatud nii sültjate kui ka liibuvate viljakehadega liigid. Esitati perekonnale Cerinomyces unikaalsete tunnuste kombinatsioon: seeneniitidel lihtsa ehitusega pandlad, kõver-silinderjad õhukesekestalised eosed ning vähene karotenoidsete pigmentide sisaldus seeneniitides ja eostes. Lisaks käsitleb doktoritöö perekonna Cerinomyces liikidele morfoloogiliselt sarnaseid taksoneid. Põhjalikult uuriti nn. dendrohüfiide, mis osutus perekonna Cerinomyces ja teisi lähedasi liike hästi eristavaks tunnuseks. Hüfiidid on ka doktoritöös kirjeldatud uue perekonna Dendrodacrys iseloomulikuks tunnuseks. Lisaks uuele perekonnale kirjeldati doktoritöös 27 teadusele uut liiki.Fungi represent one of the largest and diverse kingdoms of eukaryotes. Basidiomycota is the second most species-rich group within Fungi. Despite the ecological importance of Basidiomycota, i.e., its leading role in decomposition of wood in terrestrial ecosystems, its diversity and taxonomy are insufficiently known. Fulfilling the knowledge gap, the thesis presents taxonomic studies in dacrymycetes (Basidiomycota). 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 the 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.https://www.ester.ee/record=b553990