| 1. |
- Kurland, Sara, et al.
(författare)
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Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species
- 2019
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9, s. 11448-11463
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Tidskriftsartikel (refereegranskat)abstract
- Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F-ST) between the two introduced populations exceeds that of the naturally sympatric populations (F-ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (pi over bar approximate to 0.002 and pi over bar approximate to 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.
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| 2. |
- Ademuyiwa, Adesoji O., et al.
(författare)
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Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries
- 2016
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Ingår i: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4
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Tidskriftsartikel (refereegranskat)abstract
- Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
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| 3. |
- Andersson, Anastasia, et al.
(författare)
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Complex genetic diversity patterns of cryptic, sympatric brown trout (Salmo trutta) populations in tiny mountain lakes
- 2017
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Ingår i: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 18:5, s. 1213-1227
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Tidskriftsartikel (refereegranskat)abstract
- Intraspecific genetic variation can have similar effects as species diversity on ecosystem function; understanding such variation is important, particularly for ecological key species. The brown trout plays central roles in many northern freshwater ecosystems, and several cases of sympatric brown trout populations have been detected in freshwater lakes based on apparent morphological differences. In some rare cases, sympatric, genetically distinct populations lacking visible phenotypic differences have been detected based on genetic data alone. Detecting such cryptic sympatric populations without prior grouping of individuals based on phenotypic characteristics is more difficult statistically, though. The aim of the present study is to delineate the spatial connectivity of two cryptic, sympatric genetic clusters of brown trout discovered in two interconnected, tiny subarctic Swedish lakes. The structures were detected using allozyme markers, and have been monitored over time. Here, we confirm their existence for almost three decades and report that these cryptic, sympatric populations exhibit very different connectivity patterns to brown trout of nearby lakes. One of the clusters is relatively isolated while the other one shows high genetic similarity to downstream populations. There are indications of different spawning sites as reflected in genetic structuring among parr from different creeks. We used > 3000 SNPs on a subsample and find that the SNPs largely confirm the allozyme pattern but give considerably lower F (ST) values, and potentially indicate further structuring within populations. This type of complex genetic substructuring over microgeographical scales might be more common than anticipated and needs to be considered in conservation management.
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| 4. |
- Andersson, Anastasia, 1987-
(författare)
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Hidden biodiversity in an alpine freshwater top predator : Existence, characteristics, and temporal dynamics of cryptic, sympatric brown trout populations
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- 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).
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| 5. |
- Andersson, Anastasia, et al.
(författare)
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Lack of trophic polymorphism despite substantial genetic differentiation in sympatric brown trout (Salmo trutta) populations
- 2017
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Ingår i: Ecology of Freshwater Fish. - : Wiley. - 0906-6691 .- 1600-0633. ; 26:4, s. 643-652
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Tidskriftsartikel (refereegranskat)abstract
- Sympatric populations occur in many freshwater fish species; such populations are typically detected through morphological distinctions that are often coupled to food niche and genetic separations. In salmonids, trophic and genetically separate sympatric populations have been reported in landlocked Arctic char, whitefish and brown trout. In Arctic char and brown trout rare cases of sympatric, genetically distinct populations have been detected based on genetic data alone, with no apparent morphological differences, that is cryptic structuring. It remains unknown whether such cryptic, sympatric structuring can be coupled to food niche separation. Here, we perform an extensive screening for trophic divergence of two genetically divergent, seemingly cryptic, sympatric brown trout populations documented to remain in stable sympatry over several decades in two interconnected, tiny mountain lakes in a nature reserve in central Sweden. We investigate body shape, body length, gill raker metrics, breeding status and diet (stomach content analysis and stable isotopes) in these populations. We find small significant differences for body shape, body size and breeding status, and no evidence of food niche separation between these two populations. In contrast, fish in the two lakes differed in body shape, diet, and nitrogen and carbon isotope signatures despite no genetic difference between lakes. These genetically divergent populations apparently coexist using the same food resources and showing the same adaptive plasticity to the local food niches of the two separate lakes. Such observations have not been reported previously but may be more common than recognised as genetic screenings are necessary to detect the structures.
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| 6. |
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| 7. |
- Andersson, Annika, et al.
(författare)
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Membrane integration and topology of RIFIN and STEVOR proteins of the Plasmodium falciparum parasite
- 2020
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Ingår i: The FEBS Journal. - : Wiley. - 1742-464X .- 1742-4658. ; 287:13, s. 2744-2762
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Tidskriftsartikel (refereegranskat)abstract
- The malarial parasite Plasmodium exports its own proteins to the cell surfaces of red blood cells (RBCs) during infection. Examples of exported proteins include members of the repetitive interspersed family (RIFIN) and subtelomeric variable open reading frame (STEVOR) family of proteins from Plasmodium falciparum. The presence of these parasite-derived proteins on surfaces of infected RBCs triggers the adhesion of infected cells to uninfected cells (rosetting) and to the vascular endothelium potentially obstructing blood flow. While there is a fair amount of information on the localization of these proteins on the cell surfaces of RBCs, less is known about how they can be exported to the membrane and the topologies they can adopt during the process. The first step of export is plausibly the cotranslational insertion of proteins into the endoplasmic reticulum (ER) of the parasite, and here, we investigate the insertion of three RIFIN and two STEVOR proteins into the ER membrane. We employ a well-established experimental system that uses N-linked glycosylation of sites within the protein as a measure to assess the extent of membrane insertion and the topology it assumes when inserted into the ER membrane. Our results indicate that for all the proteins tested, transmembranes (TMs) 1 and 3 integrate into the membrane, so that the protein assumes an overall topology of Ncyt-Ccyt. We also show that the segment predicted to be TM2 for each of the proteins likely does not reside in the membrane, but is translocated to the lumen.
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| 8. |
- Andersson, Anastasia, 1987-, et al.
(författare)
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Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator
- 2022
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31:24, s. 6422-6439
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Tidskriftsartikel (refereegranskat)abstract
- 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 populations, all retained over time. Twelve of the 27 lakes harboured more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne ≤ 500) in 20 populations with five showing Ne < 100. Statistically significant genetic 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 appropriate for managers to initiate monitoring of genetic biodiversity.
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| 9. |
- Andersson, Anastasia, et al.
(författare)
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Two shades of boldness : novel object and anti-predator behavior reflect different personality dimensions in domestic rabbits
- 2014
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Ingår i: Journal of ethology. - : Springer Science and Business Media LLC. - 0289-0771 .- 1439-5444. ; 32:3, s. 123-136
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Tidskriftsartikel (refereegranskat)abstract
- It is increasingly common to quantify and describe behavioral variation in domestic and wild animals in terms of personality. Correlating behavioral traits are referred to as personality dimensions or factors and different dimensions have been reported in different species. Boldness is a well-described personality dimension in several species, although some issues remain unclear. Previous models of boldness include both novelty and risk taking, but recent studies indicate that these types of behaviors may reflect separate personality dimensions. In this study, we developed a behavioral test battery for domestic rabbits, and recorded behaviors of 61 individuals in four different situations (novel object, novel arena, social, and predator interactions). We used domestic rabbits as a model because behavioral variation in rabbits has rarely been quantified in terms of personality dimensions, although rabbit behavior is described. We also wanted to investigate behavioral variation in a Swedish rabbit breed of conservation concern - the Gotland rabbit. Factor analysis of the behavioral test measures suggested three personality dimensions: exploration, boldness, and anxiety. Novel object scores clustered in the exploration and boldness factors, whereas scores associated with predator interactions were explained by anxiety, indicating that novel object and anti-predator behavior reflect different personality dimensions in rabbits.
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| 10. |
- Gallardo-Dodd, Carlos J., et al.
(författare)
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Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells
- 2023
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Ingår i: Science Advances. - 2375-2548. ; 9:34
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Tidskriftsartikel (refereegranskat)abstract
- The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3(+) T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.
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