Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator

Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970–2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD) and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science- management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔFST, respectively) and assess the effective population size (Ne- indicator). We identified 29 genetically distinct popula-tions, all retained over time. Twelve of the 27 lakes harboured more than one popula-tion indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the thresh-old (Ne ≤ 500) in 20 populations with five showing Ne< 100. Statistically significant ge-netic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appro-priate for managers to initiate monitoring of genetic biodiversitypublishedVersio

Complex genetic diversity patterns of cryptic, sympatric brown trout (Salmo trutta) populations in tiny mountain lakes

publishedVersio

A weighted blanket increases pre-sleep salivary concentrations of melatonin in young, healthy adults

Weighted blankets have emerged as a potential non-pharmacological intervention to ease conditions such as insomnia and anxiety. Despite a lack of experimental evidence, these alleged effects are frequently attributed to a reduced activity of the endogenous stress systems and an increased release of hormones such as oxytocin and melatonin. Thus, the aim of the present in-laboratory crossover study (26 young and healthy participants, including 15 men and 11 women) was to investigate if using a weighted blanket (similar to 12% of body weight) at bedtime resulted in higher salivary concentrations of melatonin and oxytocin compared with a light blanket (similar to 2.4% of body weight). We also examined possible differences in salivary concentrations of the stress hormone cortisol, salivary alpha-amylase activity (as an indicative metric of sympathetic nervous system activity), subjective sleepiness, and sleep duration. When using a weighted blanket, the 1 hour increase of salivary melatonin from baseline (i.e., 22:00) to lights off (i.e., 23:00) was about 32% higher (p = 0.011). No other significant differences were found between the blanket conditions, including subjective sleepiness and total sleep duration. Our study is the first to suggest that using a weighted blanket may result in a more significant release of melatonin at bedtime. Future studies should investigate whether the stimulatory effect on melatonin secretion is observed on a nightly basis when frequently using a weighted blanket over weeks to months. It remains to be determined whether the observed increase in melatonin may be therapeutically relevant for the previously described effects of the weighted blanket on insomnia and anxiety

Genotyping of Genetically Monomorphic Bacteria: DNA Sequencing in Mycobacterium tuberculosis Highlights the Limitations of Current Methodologies

Because genetically monomorphic bacterial pathogens harbour little DNA sequence diversity, most current genotyping techniques used to study the epidemiology of these organisms are based on mobile or repetitive genetic elements. Molecular markers commonly used in these bacteria include Clustered Regulatory Short Palindromic Repeats (CRISPR) and Variable Number Tandem Repeats (VNTR). These methods are also increasingly being applied to phylogenetic and population genetic studies. Using the Mycobacterium tuberculosis complex (MTBC) as a model, we evaluated the phylogenetic accuracy of CRISPR- and VNTR-based genotyping, which in MTBC are known as spoligotyping and Mycobacterial Interspersed Repetitive Units (MIRU)-VNTR-typing, respectively. We used as a gold standard the complete DNA sequences of 89 coding genes from a global strain collection. Our results showed that phylogenetic trees derived from these multilocus sequence data were highly congruent and statistically robust, irrespective of the phylogenetic methods used. By contrast, corresponding phylogenies inferred from spoligotyping or 15-loci-MIRU-VNTR were incongruent with respect to the sequence-based trees. Although 24-loci-MIRU-VNTR performed better, it was still unable to detect all strain lineages. The DNA sequence data showed virtually no homoplasy, but the opposite was true for spoligotyping and MIRU-VNTR, which was consistent with high rates of convergent evolution and the low statistical support obtained for phylogenetic groupings defined by these markers. Our results also revealed that the discriminatory power of the standard 24 MIRU-VNTR loci varied by strain lineage. Taken together, our findings suggest strain lineages in MTBC should be defined based on phylogenetically robust markers such as single nucleotide polymorphisms or large sequence polymorphisms, and that for epidemiological purposes, MIRU-VNTR loci should be used in a lineage-dependent manner. Our findings have implications for strain typing in other genetically monomorphic bacteria

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Hidden biodiversity in an alpine freshwater top predator : Existence, characteristics, and temporal dynamics of cryptic, sympatric brown trout populations

Intraspecific genetic diversity is imperative to the survival of species in a changing environment, and it plays a vital role in ecosystem function. Since this type of diversity can be difficult to detect it is sometimes referred to as “hidden biodiversity”. When separate and genetically distinct populations of the same species coexist within the same habitat, without apparent barriers to migration and obvious phenotypic divergence, this form of hidden biodiversity is called cryptic sympatry. Knowledge of cryptic sympatry is limited, however, and the aim of this thesis is to increase our understanding of this phenomenon by focusing on a species group where several cases of sympatry have been documented – the salmonids. Using the brown trout (Salmo trutta) as a model, I characterized two previously reported cases of cryptic sympatry occurring in small Swedish alpine lakes with respect to both phenotypic and genetic characteristics. I explored the hypothesis that cryptic sympatry is more common than currently recognized by reviewing literature documenting sympatry, as well as by assessing the statistical power to detect sympatric populations with varying degrees of divergence using commonly applied sample sizes for loci and individuals. Further, I performed a large-scale search for sympatric populations in alpine lakes in central Sweden. I found that cryptic, sympatric populations can coexist while apparently utilizing the same food resources and exhibiting the same adaptive plasticity to their shared environment (Paper I). In one of the empirical cases there were indications that the populations used different creeks for spawning, suggesting that segregation in spawning location contributes to the maintenance of sympatry (Paper II). Further, I found that differences between cryptic, sympatric populations of the same lake may be large with respect to levels of genetic diversity, inbreeding, and connectivity with populations in nearby lakes (Papers II and III).  I found support for the hypothesis that cryptic sympatry is more common than generally acknowledged (Papers IV and V). In the literature, cryptic sympatry is rarely reported and typically associated with higher divergence levels than between sympatric populations that differ phenotypically. My results suggest that this to a large extent may be due to limited statistical power when commonly used sample sizes in terms of individuals and loci are applied and the amount of divergence between populations is small (Paper IV). Cryptic sympatry was observed in over 40% of the screened localities (27 lakes), and was shown to be temporally stable over at least 40 years (Paper V)

Investigation of stabilization and non-stabilization of MKBSC in multi-agent games

There are constructions called KBSC and MKBSC. KBSC is used to expand a player’s knowledge of the conditions in a game graph, while MKBSC works the same but for game graphs with at least two players working together towards a common goal. If you apply MKBSC several times to a game graph, the construction can potentially stabilize and there is no longer any point in running MKBSC. This report examines various multiplayer game graphs using a MKBSC tool written in Python. Possible explanations are then given as to why stabilization occurs or not intuitively based on the resulting iterated game graphs and with the help of mathematical notations that are usually being used in relation to MKBSC. The resulting findings show that the graphs generally tend to stabilize as long as there are not a number of conditions that are being fulfilled. These conditions include that there are at least three nodes where you can get from one node to another (though not necessarily with the use of a single action), there are partially overlapping observations for the players in the game and there is an uncertainty for the players about which upcoming state their individual choice of action leads to. In addition, the initial state of the game graph can affect whether or not MKBSC stabilizes. Det finns konstruktioner som kallas KBSC samt MKBSC. KBSC används för att utöka en spelares kunskap om tillstånden i en spelgraf medan MKBSC fungerar likadant men för spelgrafer med minst två spelare som samarbetar mot ett gemensamt mål. Om man applicerar MKBSC flera gånger på en spelgraf så kan konstruktionen potentiellt stabilisera sig och det finns inte längre någon mening att köra MKBSC. I den här rapporten undersöks diverse spelgrafer för flera spelare med ett MKBSC- verktyg skrivet i Python. Sedan ges möjliga förklaringar om varför stabilisering sker eller ej intuitivt utifrån de resulterande itererade spelgraferna samt med hjälp av matematiska notationer som brukar användas i samband med MKBSC. De resulterande upptäckterna visar att graferna generellt sett tenderar att stabilisera så länge det inte finns ett flertal villkor som uppfylls. Dessa villkor inkluderar att det finns minst tre noder där kan man ta sig från en nod till en annan (dock ej nödvändigtvis med en enda handling), det finns delvis överlappande observationer för spelarna i spelet och det finns en ovisshet för spelarna om vad deras individuella val av handling leder till för nästföljande tillstånd. Dessutom kan spelgrafens starttillstånd påverka om huruvida MKBSC stabiliserar eller ej

Renovering av flerfamiljsbostäder inom miljonprogrammet ur ett energi- och lönsamhetsperspektiv

Miljonprogram is a Swedish building program from 1964 to 1975. During that time about a million homes were constructed. Now, almost 50 years later, they are in desperate need of renovation. In order to fulfil the Swedish environmental objective to decrease energy consumption 50 per cent until 2050, considerable housing stock built under the Miljonprogram has to be renovated. Focus in this thesis is on the building services and theirs profitability that can decrease energy consumption in households build during the Miljonprogram. Building construction is not considered in this report. This thesis includes a literature review of existing housing stock and the exploration of the three renovated projects Brogården in Alingsås, Gårdsten in Gothenburg and Katjas Gata 119 in Gothenburg, where energy savings and profitability was evaluated. It turns out that the three real estate companies have different views on profitability, while one considers socio-economic profit the other one takes into consideration increase of rent level and construction experience. The three real estate companies use different repayment periods which affects the profitability of various measures considerably. I the case study on the miljonprogramʼs building Siriusgatan 24-28 various building services are examined and evaluated separately and in combination in order to estimate theirs energy saving and profitability. The results of the cost-benefit analysis show that charging for hot water, installation of low-flow faucet nozzle and replacement of exhaust fan is profitable whilst they are those measures that save least energy. Installation of ventilation system with heat recovery (FTX) and exhaust air heat pump (FVP) do not prove to be profitable. The option that provides the biggest profit while saving most energy is a combination consisting of charging for hot water, low-flow faucet nozzles, replacement of exhaust fan and installation of FVP system. At higher energy prices FTX system will be profitable because of the high energy savings that it provides. The results are affected by the assumptions and the fact that calculation models are a simplified reflection of reality

simulations_and_scripts

R-scripts for generating the figures presented in the paper