Kareleheliste Pulmonaria angustifolia L. ja Myosotis laxa s. lato (Boraginaceae) geneetiline mitmekesisus ja evolutsioon

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Taimeliikide püsimine looduses sõltub nende võimest kohastuda muutuvate keskkonnatingimustega, kohastumise aluseks aga on liigi geneetiline mitmekesisus. Teadmised geneetilise mitmekesisuse kohta võimaldavad välja selgitada liike mõjutavaid tegureid ning hinnata haruldaste liikide väljasuremise riski. Käesolevas doktoritöös uurisin geneetilist mitmekesisust kareleheliste (Boraginaceae) sugukonnas: sinisel kopsurohul (Pulmonaria angustifolia) ning muru-lõosilmal (Myosotis laxa s. lato). Sinine kopsurohi on areaali põhjapiiril, Eestis ja Lätis väheneva arvukusega ohustatud liik. Võrdlusmaterjalina kasutasin samas piirkonnas kasvava hariliku kopsurohu (Pulmonaria obscura Dumort.) ning sinise kopsurohu areaali keskosast (Poolast) pärit taimi. Selgus, et kõik uuritud sinise kopsurohu isendid sisaldasid hariliku kopsurohu DNA järjestusi. Sinise kopsurohu arvukuse vähenemine Eesti populatsioonides võib seega olla lokaalse hübridiseerumise tagajärg, kuid ei saa välistada, et liik tervikuna ongi hübriidne. Muru-lõosilm on morfoloogiliselt väga varieeruv liik, mille harvaesinevat teadmata päritoluga rannikuvormi on kirjeldatud ka kui balti lõosilma (Myosotis baltica Sam.). Kuigi osa muru-lõosilma rannikuvormi taimi olid morfoloogiliselt ülejäänud taimedest erinevad, geneetilist erinevust rannikuvormi ja ülejäänud taimede vahel ei olnud. Muru-lõosilma geneetiline varieeruvus populatsioonides oli positiivses korrelatsioonis populatsioone ümbritseva maastiku struktuuriga, mis näitab suunatud geenivoolu maastikul. Geenivool vee abil leviva muru-lõosilma populatsioonide vahel on tõenäoliselt suunatud kaugemalt maismaalt rannikule ega ei võimalda rannikupopulatsioonide geneetilist eristumist. Morfoloogiliste tunnuste varieeruvus muru-lõosilma populatsioonides ei olnud korrelatsioonis maastiku struktuuri ega keskkonnatingimustega. Seega ei ole rannikuvormi eristumise põhjuseks geneetiline kohastumine ega morfoloogiline plastilisus, vaid tõenäoliselt keskkonnast sõltuv taimede elutsükli epigeneetiline regulatsioon. Käesolev töö tõestab esmakordselt geneetiliste andmete põhjal sinise ja hariliku kopsurohu hübridiseerumise looduses ning toob välja, et muru- lõosilma rannikuvorm ei ole geneetiliselt eristunud takson.The ability of plants to adapt to changing environmental conditions is strongly dependent on their genetic diversity. Knowledge of genetic diversity helps us to understand the dynamics of the species as well as the threat level in terms of extinction. This thesis aims to characterize the genetic diversity of two species in the family Boraginaceae: firstly, Pulmonaria angustifolia L. and secondly, Myosotis laxa s. lato. P. angustifolia is extremely rare and in in decline in Estonia and Latvia, on the northern border of its range. To investigate genetic diversity of P. angustifolia in Estonia and Latvia, samples of Pulmonaria obscura Dumort. from the same area and the samples of P. angustifolia from its core area (Poland) were compared. All studied individuals of P. angustifolia contained genetic material from P. obscura. Thus, local hybridization is a likely explanation for the decline in the populations of P. angustifolia in Estonia. However, a hybrid origin for the whole species is also possible. M. laxa s. lato is morphologically highly variable and has a sporadically distributed coastal form with unknown origin and phylogeny. This coastal form has been described as a separate species, Myosotis baltica Sam. The study revealed that some of the specimens of the coastal form of M. laxa differed from the others in morphological characters but not on the basis of genetic data. The genetic variation of M. laxa s. lato populations was positively correlated to the structure of the surrounding landscape, which indicates the presence of directed gene flow across the landscape. As M. laxa s. lato disperses via water, the gene flow is likely directed from the mainland populations to the coastal populations and so genetic adaptation of coastal populations is not viable. The phenotypic variation of M. laxa s. lato was correlated neither to the structure of landscape nor to the environmental conditions. Thus, the phenotypic differences of the coastal form are not caused by genetic adaptation or phenotypic plasticity but likely, by the temperature-dependent epigenetic regulation of the life cycle. This thesis confirms for the first time hybridization of P. angustifolia and P. obscura on the basis of genetic data and reveals that the coastal form of M. laxa is not genetically different from the mainland form, but likely arises due to epigenetic regulation of the life cycle of plants

Soontaimede evolutsioon ja süstemaatika

BeSt programmi toetusel loodud e-kursuse "Soontaimede evolutsioon ja süstemaatika" õppematerjalid

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

A collaborative, individual-level analysis compared longitudinal outcomes across the International Network of Chronic Kidney Disease (iNETCKD) cohorts.

Rates of chronic kidney disease (CKD) progression, end stage kidney disease (ESKD), all-cause mortality, and cardiovascular (CVD) events among individuals with CKD vary widely across countries. Well-characterized demographic, comorbidity, and laboratory markers captured for prospective cohorts may explain, in part, such differences. To investigate whether core characteristics of individuals with CKD explain differences in rates of outcomes, we conducted an individual-level analysis of eight studies that are part of iNET-CKD, an international network of CKD cohort studies. Overall, the rate of CKD progression was 40 events/1000 person-year (95% confidence interval 39 - 41), 28 (27 - 29) for ESKD, 41 (40 - 42) for death, and 29 (28 - 30) for CVD events. However, standardized rates were highly heterogeneous across studies (over 92.5%). Interactions by study group on the association between baseline characteristics and outcomes were then identified. For example, the adjusted hazard ratio for CKD progression was 0.44 (95% confidence interval 0.35 - 0.56) for women vs. men among the Japanese (CKD-JAC), while it was 0.66 (0.59 - 0.75) among the Uruguayan (NRHP). The adjusted hazard ratio for ESKD was 2.02 (95% CI 1.88 - 2.17) per 10 units lower baseline eGFR among Americans (CRIC), while it was 3.01 (2.57 - 3.53) among Canadians (CanPREDDICT) (significant interaction for comparisons across all studies). The risks of CKD progression, ESKD, death, and CVD vary across countries even after accounting for the distributions of age, sex, comorbidities, and laboratory markers. Thus, our findings support the need for a better understanding of specific factors in different populations that explain this variation

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press