Riparian vegetation along the water courses is one of the places that are highly vulnerable to the spread of invasive alien plants. Water corridors allow their easy and rapid spread to new area. The diploma thesis occupies with changes in the distribution of the invasive neophytes in the riparian vegetation of the Berounka river during the years 2015-2018. The objective of this study was to find out how changes in the course of each year will be reflected and whether a certain trend of population development can be traced. In connection with this, the thesis occupies with the possible influence of extremely dry years 2015 and 2018 on the occurrence of invasive neophytes. Field research took place on the banks of the Berounka river from the village of Čilá near Skryje to the confluence of the Berounka and Vltava river in Prague-Lahovice during the summer months in 2015, 2016, 2017 and 2018. The riparian vegetation was divided into 500 ± 150 m long segments. There were 90 segments where the occurrence and abundance of 17 invasive neophytes were mapped. In total, occurrence of 14 taxons was registered. The most frequent taxons were Robinia pseudacacia, Impatiens glandulifera and Solidago sp. in the Berounka riverbank vegetation. The highest number of specimen was recorded for invasive neophyte...

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Environmental constraints can limit a population to a certain size, which is usually called the carrying capacity of a habitat. Besides to this 'external' factor, which is mainly determined by the limitation of resources, we investigate here another set of population-intrinsic factors that can limit a population size significantly below the maximum sustainable size. Firstly, density-independent mortality is a prominent factor in all organisms that show age-related and/or accidental death. Secondly, in sexually reproducing organisms the sex ratio and the success of pairing is important for finding reproductive partners. Using a simple model, we demonstrate how sex ratio, mating success and gender-specific mortality can strongly affect the speed of population growth and the maximum population size. In addition, we demonstrate that density-independent mortality, which is often neglected in population models, adds a very important feature to the system: it strongly enhances the negative influence of unbiased sex ratios and inefficient pairing to the maximum sustainable population size. A decrease of the maximum population size significantly affects a population's survival chance in inter-specific competition. Thus, we conclude that the inclusion of density-independent mortality is crucial, especially for models of species that reproduce sexually. We show that density-independent mortality, together with biased sex ratios, can significantly lower the abilities of a population to survive in conditions of strong inter-specific competition and due to the Allee effect. We emphasize that population models should incorporate the sex ratio, male success and density-independent mortality to make plausible predictions of the population dynamics in a gender-structured population. We show that the population size is limited by these intrinsic factors. This is of high ecological significance, because it means that there will always be resources available in any habitat that allows other species (e.g., invaders) to use these resources and settle successfully, if they are sufficiently adapted.

<p>Meteorological&nbsp; conditions&nbsp; have&nbsp; a&nbsp; significant influence on the time of occurrence, abundance and activity of the mosquito vector. In the current context of climate change, it is of great importance to assess the&nbsp; impact&nbsp; of&nbsp; shifts&nbsp; in&nbsp; climatic&nbsp; conditions&nbsp; on&nbsp; the suitability for the establishment and annual activity of&nbsp; the&nbsp; vector&nbsp; species.&nbsp; Moreover,&nbsp; changes&nbsp; in&nbsp; the variability&nbsp; of&nbsp; meteorological&nbsp; elements&nbsp; and&nbsp; their extremes&nbsp; can&nbsp; generate&nbsp; unexpected&nbsp; changes&nbsp; in&nbsp; the mosquito&nbsp; vector&nbsp; population&nbsp; which&nbsp; in&nbsp; turn&nbsp; have&nbsp; an&nbsp; important effect on human health. One of the ways to put&nbsp; these&nbsp; causes&nbsp; and&nbsp; effects&nbsp; into&nbsp; perspective&nbsp; is&nbsp; to simulate the activity of the vector within a processbased framework which allows for the analysis of the contribution of individual factors on the different life stages of the vector. Such analysis is presented by use of&nbsp; sophisticated&nbsp; dynamical&nbsp; models&nbsp; simulating&nbsp; the characteristics of the biological population, forced by observed&nbsp; meteorological&nbsp; data,&nbsp; capturing&nbsp; the&nbsp; localmicro-environment&nbsp; of&nbsp; the&nbsp; vector&nbsp; habitat,&nbsp; and validated by the observed entomology.Numerical&nbsp; models&nbsp; are&nbsp; being&nbsp; developed&nbsp; to&nbsp; model vector&nbsp; population&nbsp; dynamics&nbsp; and&nbsp; the&nbsp; expected circulation of the virus within a closed system. Two modelling&nbsp; approaches&nbsp; are&nbsp; standardly&nbsp; applied&nbsp; to modelling vector population dynamics: Mechanistic and&nbsp; Stochastic.&nbsp; The&nbsp; advantage&nbsp; of&nbsp; mechanistic&nbsp; over<br />statistical&nbsp; models&nbsp; is&nbsp; that&nbsp; they&nbsp; can&nbsp; provide&nbsp; a deterministic&nbsp; framework&nbsp; allowing&nbsp; for&nbsp; the&nbsp; isolated evaluation of each input parameter and their effect on the modelled system. Mechanistic dynamical models are used to describe the biophysical processes or part<br />of&nbsp; the&nbsp; process&nbsp; as&nbsp; a&nbsp; response&nbsp; to&nbsp; changes&nbsp; in&nbsp; the meteorological conditions.<br />The&nbsp; work&nbsp; carried&nbsp; out&nbsp; in&nbsp; this&nbsp; thesis&nbsp; can&nbsp; be summarized as follows: (i) Analysis of the association between&nbsp; the&nbsp; most&nbsp; important&nbsp; abiotic&nbsp; drivers influencing the population dynamics, annual activity and&nbsp; time&nbsp; of&nbsp; occurrence&nbsp; of Culex&nbsp; pipiens and Aedes aegypti;&nbsp; (ii)&nbsp; Identifying&nbsp; the&nbsp; most&nbsp; important&nbsp; climatic factors and model settings as a function of climatic characteristics of the study region; (iii) Modelling the vector population dynamics and stability analysis of the&nbsp; dynamical&nbsp; system&nbsp; (iv)&nbsp; Analysis&nbsp; of&nbsp; different verification techniques and implications in terms of model&nbsp; application;&nbsp; (v)&nbsp; Feasibility&nbsp; analysis&nbsp; of<br />improving&nbsp; the&nbsp; model&nbsp; with&nbsp; a&nbsp; Land-Surface Parametrization scheme and short-range forecasting of pest population dynamics.</p> / <p>Meteorolo&scaron;ki&nbsp; uslovi&nbsp; bitno&nbsp; utiču&nbsp; na&nbsp; vreme&nbsp; pojave, brojnost&nbsp; vektora&nbsp; i&nbsp; njihovu&nbsp; aktivnost.&nbsp; U&nbsp; uslovima evidentnih promene klime, od ogromne je važnosti sagledati&nbsp; uticaj&nbsp; očekivanih&nbsp; promena&nbsp; klime&nbsp; na pogodnost&nbsp; uslova&nbsp; na&nbsp; pojavu&nbsp; izabranih&nbsp; vektora.<br />Takodje, značajne promene kolebanja meteorolo&scaron;kih elemenata&nbsp; u&nbsp; odnosu&nbsp; na&nbsp; vi&scaron;egodi&scaron;nji&nbsp; prosek&nbsp; i&nbsp; sve če&scaron;će pojave nepovoljnih vremenskih prilika dovode do neočekivanog pona&scaron;anja populacije komarca &scaron;to značajno&nbsp; utiče&nbsp; na&nbsp; kvalitet&nbsp; života&nbsp; i&nbsp; zdravlje&nbsp; ljudi. Jedini&nbsp; način&nbsp; da&nbsp; se&nbsp; sagledaju&nbsp; uzroci&nbsp; i&nbsp; posledice navedenih pojava zasniva se na simulaciji aktivnosti i&nbsp; brojnosti&nbsp; vektora&nbsp; uz&nbsp; mogućnost&nbsp; testiranja&nbsp; uticaja svakog&nbsp; pojedinačnog&nbsp; faktora.&nbsp; Ovu&nbsp; mogućnost pružaju samo visoko sofistikovani dinamički modeli koju su pro&scaron;li proces kalibracije i validacije zasnovan<br />na izmerenim vrednostima meteorolo&scaron;kih elemenata i karakteristika biolo&scaron;ke populacije.<br />Sofistikovani&nbsp; modeli&nbsp; za&nbsp; simulaciju&nbsp; dinamike populacije vektora i očekivane cirkulacije vektorskih transmisivnih bolesti se koriste sa ciljem modeliranja potencijalnog rizika od zaraze i epidemije. Modeli zasimulaciju dinamike vektora mogu da se podele na dve&nbsp; glavne&nbsp; grupe:&nbsp; Mehanističke&nbsp; i&nbsp; Statističke. Prednost&nbsp; mehanističkih&nbsp; modela&nbsp; nad&nbsp; statističkim&nbsp; je &scaron;to&nbsp; mogu&nbsp; da&nbsp; se&nbsp; koriste&nbsp; za&nbsp; evaluaciju&nbsp; uticaja izolovanog&nbsp; faktora&nbsp; na&nbsp; dinamički&nbsp; sistem&nbsp; i odgovarajuće promene brojnosti unutar svake faze u razvoju&nbsp; vektora.&nbsp; Mehanistički&nbsp; dinamički&nbsp; sistemi&nbsp; se koriste&nbsp; kako&nbsp; bi&nbsp; se&nbsp; opisao&nbsp; mehanizam&nbsp; biofizičkog procesa&nbsp; ili&nbsp; dela&nbsp; procesa&nbsp; u&nbsp; zavisnosti&nbsp; od&nbsp; forsirajuće veličine.<br />Predmet&nbsp; istraživanja&nbsp; u&nbsp; ovom&nbsp; radu&nbsp; jeste identifikovanje&nbsp; najznačajnijih&nbsp; biolo&scaron;kih&nbsp; i&nbsp; fizičkih procesa&nbsp; kao&nbsp; i&nbsp; odgovarajućih&nbsp; faktora&nbsp; koji&nbsp; utiču&nbsp; na brojnost i aktivnost vektora roda Aedes i Culex. Ciljevi istraživanja mogu da se sumiraju na sledeći način: (i)<br />analiza najznačajnijih meteorolo&scaron;kih parametara koji utiču na vreme pojave, brojnost i aktivnost vektora Aedes&nbsp; i&nbsp; Culex&nbsp; roda;&nbsp; (ii)&nbsp; definisanje&nbsp; najznačajnijih klimatskih&nbsp; faktora&nbsp; i&nbsp; stepena&nbsp; osetljivosti&nbsp; procesa&nbsp; na njih; (iii) modeliranje dinamike populacije vektora i analiza&nbsp; stabilnosti&nbsp; dinamičkog&nbsp; sistema;&nbsp;&nbsp; (iv) verifikacija&nbsp; i&nbsp; analiza&nbsp; metoda&nbsp; verifikacije&nbsp; i&nbsp; validacije dinamičkog&nbsp; modela;&nbsp; (v)&nbsp; kratkoročna&nbsp; prognoza dinamike&nbsp; populacije&nbsp; komarca&nbsp; i&nbsp; formulacija hidrolo&scaron;kog modula upotrebom SURFEX povr&scaron;inske<br />&scaron;eme sa ECOCLIMAP fiziogeografskim podacima.</p>

This thesis attempts to provide new insight into some population-dynamical problems and also proposes a new perspective on certain models of ecological communities. Following a short introduction into the field of mathematical modelling of population dynamics, the first chapter investigates the paradoxical Hydra Effect, the increase of mean population size as a response to an increase in mortality rate, in a class of simple predator-prey models. The main result is that a Hydra Effect occurs if and only if the system dynamics are oscillatory, which has interesting implications for the theory of optimal harvesting and biocontrol of invasive species. The second chapter discusses how coordinate transformations change the structure of intraguild predation food webs, establishing a close connection of certain cases of intraguild predation to simpler community modules such as exploitative competition and food chains. These results and possible generalizations of them could have wide-ranging implications for the question of how structural properties of food webs determine population-dynamical properties such as ecological stability and persistence. The last chapter presents numerical investigations of how random environmental fluctuations affect the spatiotemporal dynamics of oscillatory reaction-diffusion models, such as classical predator-prey and simple lambda-omega systems. These results in particular question whether travelling waves arising from these models can explain similar spatiotemporal waves found in natural populations.

Seasonal shifts in predation habits, from a generalist in the summer to a specialist in the winter, have been documented for the great horned owl (Bulbo virginialis) in the boreal forest. This shift occurs largely due to varying prey availability. There is little study of this switching behaviour in the current literature. Since season length is predicted to change under future climate scenarios, it is important to understand resulting effects on species dynamics. Previous work has been done on a two-species seasonal model for the great horned owl and its focal prey, the snowshoe hare (Lepus americanus). In this thesis, we extend the model by adding one of the hare's most important predators, the Canadian lynx (Lynx canadensis). We study the qualitative behaviour of this model as season length changes using tools and techniques from dynamical systems. Our main approach is to determine when the lynx and the owl may invade the system at low density and ask whether mutual invasion of the predators implies stable coexistence in the three-species model. We observe that, as summer length increases, mutual invasion is less likely, and we expect to see extinction of the lynx. However, in all cases where mutual invasion was satisfied, the three species stably coexist.

Understanding the relative importance of density-dependent and density-independent factors in driving population dynamics is one of the oldest challenges in ecology, and may play a critical role in predicting the effects of climate change on populations. We used long-term observational data to describe patterns in plant population regulation for 57 forb and grass species from three different ecosystems (arid desert grassland, semiarid sagebrush steppe, and subhumid mixed-grass prairie). Using a hierarchical partitioning approach, we (i) quantified the relative influence of conspecific density, heterospecific composition, and climate on temporal variation in population growth rates, and (ii) asked how the relative importance of these drivers depends on site aridity, species growth form and life expectancy, and abundance and spatial patterns. The data from one of the sites in this analysis are presented in one of the chapters of this thesis. We found that density-dependence had the strongest effect on species. Climate often had a significant effect, but its strength depended on growth form. Community composition rarely explained significant variation in growth rates. The relative importance of density, composition, and climate did not vary among sites, but was related to species' life histories: compared to forbs, grasses were more sensitive to climate drivers. Abundance and spatial clustering were negatively correlated with the importance of density dependence, suggesting that local rarity is a consequence of self-limitation. Our results show that interspecific interactions play a weaker role than intraspecific interactions and climate variability in regulating plant populations. Forecasting the impacts of climate change on populations may require understanding how changes in climate variables will affect the strength of density-dependence, especially for rare species.

We estimated survival of ~ 1-day-old chicks to 42 days based on radio-marked individuals for the Parker Mountain greater sage-grouse (Centrocercus urophasianus) population. Chick survival was relatively high (low estimate of 0.41 and high estimate of 0.50) compared to other studies. Brood-mixing occurred for 21 % of radio-marked chicks, and within 43 % of radio-marked broods. Our study showed that brood-mixing may be an important ecological strategy for sage-grouse, because chicks that brood-mixed experienced higher survival. Additionally, modeling of chick survival suggested that arthropod abundance is important during the early brood-rearing period (1 - 21 days). We also used life-cycle modeling (perturbation analyses and Life Table Response Experiments) to assess the importance of various vital rates within this population. We determined that adult hen survival and production (chick and fledgling survival) had the most influence on growth rate. Moreover, we assessed various methods (walking, spotlight, and pointing dog) for counting sage-grouse broods. Spotlight and pointing dog methods were more effective than walking flush counts, and the latter may underestimate chick survival.

京都大学 / 0048 / 新制・課程博士 / 博士(情報学) / 甲第21914号 / 情博第697号 / 新制||情||120(附属図書館) / 京都大学大学院情報学研究科先端数理科学専攻 / (主査)教授 木上 淳, 教授 磯 祐介, 准教授 藤原 宏志 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

Although transposable elements (TEs) have been subjected to detailed study in various organisms such as humans, maize, and drosophila, this is not the case for all organisms. Despite numerous studies on the effects of TEs in the field of evolution and functional genomics, there has not been many studies yet on how much variation these elements show in populations. To address these questions, we identified TEs in Leptidea sinapis based on a newly produced high-quality genome assembly and identified novel TEs in this project. In the first step of the project, we manually curated consensus sequences of the 150 most abundant TE subfamilies. We could identify 145 of these subfamilies: two of which were non-curatable because of bad consensus sequences, three that were uncertain where they start and end, and one of the subfamilies were divided into two different subfamilies. Hence, we ended up with 146 different TE subfamilies, and the remaining part of the project was carried out using these. In the second step, we examined how the manually curated 146 subfamilies were distributed in 83 different L. sinapis individuals in the Swedish population. Before performing manual curation for our selected TEs, we looked at the TE landscape of the long-read sequenced L. sinapis genome and showed that 58.2% of the L. sinapis genome consists of TEs. In a recent study, it has been shown that 40% of L. sinapis consists of TEs. So, when compared to previous studies, our result showed that the L. sinapis genome contained more TEs than previously reported. When we made the same analysis after manual curation, we showed that this amount increased to 62.4%. The distribution of classified TEs by groups is as follows: LINE 22.6%, DNA 7.43%, SINE 4.76%, LTR 3.10%.  After creating the final TE landscape for our reference genome, we analyzed 83 different individuals collected from different regions of Sweden such as Uppland, Östergötland, Västmanland, Närke, Värmland, Dalarna, Hälsingland, Småland, Medelpad, and Västerbotten for the individual number of non-reference insertions using RelocaTE2. We observed that these 146 subfamilies showed different distributions among individuals based on their sequence coverage. We couldn’t find any correlation between the number of insertions and the latitude of locations where individuals had been collected. When we look at the total number of insertions, we realized type I transposable elements were more abundant compared to type II transposable elements. Also, we checked the percentage of covered bases per individual in our dataset and observed that individuals with greater coverage had more TE insertions. After realizing this, when we analyzed individuals from different locations with very similar coverage, we could not see a significant correlation between the number of TE insertions and the latitude of locations of butterflies from different locations. For this reason, we can say that for the most abundant 146 TE subfamilies in the reference genome, there is not a significant difference between regions of Sweden. This study contributes to a better analysis of TE content in L. sinapis, and the know-how and possible problems with technical bias for individual TE insertion studies in general.