| 1. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 2. |
- Haycock, Philip C., et al.
(författare)
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Association Between Telomere Length and Risk of Cancer and Non-Neoplastic Diseases A Mendelian Randomization Study
- 2017
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Ingår i: JAMA Oncology. - : American Medical Association. - 2374-2437 .- 2374-2445. ; 3:5, s. 636-651
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Tidskriftsartikel (refereegranskat)abstract
- IMPORTANCE: The causal direction and magnitude of the association between telomere length and incidence of cancer and non-neoplastic diseases is uncertain owing to the susceptibility of observational studies to confounding and reverse causation. OBJECTIVE: To conduct a Mendelian randomization study, using germline genetic variants as instrumental variables, to appraise the causal relevance of telomere length for risk of cancer and non-neoplastic diseases. DATA SOURCES: Genomewide association studies (GWAS) published up to January 15, 2015. STUDY SELECTION: GWAS of noncommunicable diseases that assayed germline genetic variation and did not select cohort or control participants on the basis of preexisting diseases. Of 163 GWAS of noncommunicable diseases identified, summary data from 103 were available. DATA EXTRACTION AND SYNTHESIS: Summary association statistics for single nucleotide polymorphisms (SNPs) that are strongly associated with telomere length in the general population. MAIN OUTCOMES AND MEASURES: Odds ratios (ORs) and 95% confidence intervals (CIs) for disease per standard deviation (SD) higher telomere length due to germline genetic variation. RESULTS: Summary data were available for 35 cancers and 48 non-neoplastic diseases, corresponding to 420 081 cases (median cases, 2526 per disease) and 1 093 105 controls (median, 6789 per disease). Increased telomere length due to germline genetic variation was generally associated with increased risk for site-specific cancers. The strongest associations (ORs [ 95% CIs] per 1-SD change in genetically increased telomere length) were observed for glioma, 5.27 (3.15-8.81); serous low-malignant-potential ovarian cancer, 4.35 (2.39-7.94); lung adenocarcinoma, 3.19 (2.40-4.22); neuroblastoma, 2.98 (1.92-4.62); bladder cancer, 2.19 (1.32-3.66); melanoma, 1.87 (1.55-2.26); testicular cancer, 1.76 (1.02-3.04); kidney cancer, 1.55 (1.08-2.23); and endometrial cancer, 1.31 (1.07-1.61). Associations were stronger for rarer cancers and at tissue sites with lower rates of stem cell division. There was generally little evidence of association between genetically increased telomere length and risk of psychiatric, autoimmune, inflammatory, diabetic, and other non-neoplastic diseases, except for coronary heart disease (OR, 0.78 [ 95% CI, 0.67-0.90]), abdominal aortic aneurysm (OR, 0.63 [ 95% CI, 0.49-0.81]), celiac disease (OR, 0.42 [ 95% CI, 0.28-0.61]) and interstitial lung disease (OR, 0.09 [ 95% CI, 0.05-0.15]). CONCLUSIONS AND RELEVANCE: It is likely that longer telomeres increase risk for several cancers but reduce risk for some non-neoplastic diseases, including cardiovascular diseases.
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| 3. |
- Hiron, Matthew, et al.
(författare)
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Crop damage by granivorous birds despite protection efforts by human bird scarers in a sorghum field in western Kenya
- 2014
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Ingår i: Ostrich: Journal of African Ornithology. - : National Inquiry Services Center (NISC). - 0030-6525. ; 85, s. 153-159
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Tidskriftsartikel (refereegranskat)abstract
- Cereal crop damage from granivorous birds poses a serious food security problem for subsistence farmers in sub-Saharan Africa. In this region, farmers may rely on human 'bird scarers' to limit crop damage. Here we report feeding behaviour and crop damage patterns caused by Village Weavers Ploceus cucullatus and African Mourning Doves Streptopelia decipiens during four days in a 0.12 ha sorghum field protected by two full-time bird scarers in western Kenya. Despite the scarers' efforts, almost 60% of the seed was lost before harvest. Bird abundance was largely determined by the presence of the bird scarers, with seed loss patterns being a function of distance from these people. Throughout the day, an average of 18 weavers (maximum 120) was present on the crop in any five-minute period. The number of mud projectiles thrown at the birds per 15 min showed only minor diurnal fluctuations, further suggesting that seed eaters attacked the crop throughout the day. Village Weaver individuals took an average 16 seeds per visit, whereas dove individuals took 32 seeds (maximum 105 and 455, respectively). Our study illustrates that avian crop pests can be extremely persistent and, even with consistent diurnal bird scaring activity, severely damage a small crop field. Bird scarers need to be active throughout daylight hours and patrol both the centres and edges of fields to create maximum disturbance to foraging seed eating birds. Further research is needed in order to investigate effects of local-and landscape-level land use patterns on the feeding behaviour of crop pests and the effectiveness of crop protection measures.
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| 4. |
- Josefsson, Jonas, et al.
(författare)
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Improving scientific rigour in conservation evaluations and a plea deal for transparency on potential biases
- 2020
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Ingår i: Conservation Letters. - : Wiley. - 1755-263X. ; 13:5
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Forskningsöversikt (refereegranskat)abstract
- The delivery of rigorous and unbiased evidence on the effects of interventions lay at the heart of the scientific method. Here we examine scientific papers evaluating agri-environment schemes, the principal instrument to mitigate farmland biodiversity declines worldwide. Despite previous warnings about rudimentary study designs in this field, we found that the majority of studies published between 2008 and 2017 still lack robust study designs to strictly evaluate intervention effects. Potential sources of bias that arise from the correlative nature are rarely mentioned, and results are still promoted by using a causal language. This lack of robust study designs likely results from poor integration of research and policy, while the erroneous use of causal language and an unwillingness to discuss bias may stem from publication pressures. We conclude that scientific reporting and discussion of study limitations in intervention research must improve and propose some practices toward this goal.
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| 5. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 6. |
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| 7. |
- Rosin, Zuzanna, et al.
(författare)
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Village modernization may contribute more to farmland bird declines than agricultural intensification
- 2021
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Ingår i: Conservation Letters. - : Wiley. - 1755-263X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- The central tenet of European farmland ecology is that agricultural intensification during the 20th century was largely responsible for dramatic declines in species abundances. However, during this time, human rural settlements were also undergoing radical changes through modernization, with undocumented biodiversity impacts in this important wildlife habitat. We performed the first ever large-scale study to disentangle the impact of these simultaneous processes on farmland bird diversity in 104 Polish villages. We show that modernized villages and their surrounding agricultural fields had 50-60% fewer birds than those in and around comparable older villages. The relative contribution of modernization versus agricultural intensification to predicted bird declines was 88% versus 12% for bird communities in villages and 56% versus 44% in surrounding croplands, with considerable variation among ecological species subgroups. These results challenge our current understanding of agricultural ecosystem ecology and how best to implement conservation measures costing billions of euros annually.
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| 8. |
- Arlt, Debora, et al.
(författare)
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Effect of Geolocators on Migration and Subsequent Breeding Performance of a Long-Distance Passerine Migrant
- 2013
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Geolocators are small light-weight data loggers used to track individual migratory routes, and their use has increasedexponentially in birds. However, the effects of geolocators on individual performance are still poorly known. Westudied geolocator effects on a long-distance migrating passerine bird, the northern wheatear (Oenanthe oenantheL.). We asked the general question of whether geolocators affect migratory behaviour and subsequent reproductiveperformance of small passerines by comparing arrival time, breeding time, breeding success and survival ofgeolocator versus control birds of known identity and breeding history. During two years geolocator birds (n=37)displayed a lower apparent survival (30%) as compared to controls (45%, n=164). Furthermore, returning geolocatorbirds (n=12) arrived on average 3.5 days later, started laying eggs 6.3 days later, and had lower nest success (25%)than control birds (78%). Our results suggest that geolocators affect migratory performance with carry-over effects tothe timing of breeding and reproductive success in the subsequent breeding season. We discuss the implications ofsuch geolocator effects for the study of migratory strategies of small passerines in general and suggest how toidentify and investigate such effects in the future.
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| 9. |
- Arlt, Debora, et al.
(författare)
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Prolonged stopover duration characterises migration strategy and constraints of a long-distance migrant songbird
- 2015
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Ingår i: Animal Migration. - : Walter de Gruyter GmbH. - 2084-8838. ; 2, s. 47-62
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Tidskriftsartikel (refereegranskat)abstract
- Stopover behaviour is a central element ofmigration strategies. But in recent geolocator studies,despite now being able to track individual songbirdsduring their entire migration, their stopover behaviourhas received little attention. We used light-sensitivegeolocators to identify the migratory routes and schedulesof 12 northern wheatears (Oenanthe oenanthe) breedingin Sweden. Three geolocators collected temperature datacomplementing inferences from light data by providingadditional information on behaviour during migration.The wheatears performed a slow migration withconsiderable stopover time (84%/76% of autumn/springmigration), with short stops while traveling throughEurope, and a prolonged stopover period in both autumnand spring in the Mediterranean region. Spring migrationwas faster than autumn migration, mainly because ofdecreased stopover time. Migration routes and timeschedules were similar to those from a German breedingpopulation. Compared to wheatears breeding in Alaskawith a three-fold migration distance, Swedish wheatearsspent more time during stopovers during autumn andspring migration, suggesting less time constraints andpotential flexibility in migration schedules. The findingof prolonged stopovers, similar to other recent geolocatorstudies, shows that temporary residency periods maybe common. This changes our current view on stopoverecology to one where temporary residency periods arepart of spatio-temporal strategies optimising resource useduring the entire annual cycle.
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| 10. |
- Aronsson, Malin, et al.
(författare)
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Intensity of space use reveals conditional sex-specific effects of prey and conspecific density on home range size
- 2016
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 6, s. 2957-2967
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Tidskriftsartikel (refereegranskat)abstract
- Home range (HR) size variation is often linked to resource abundance, with sex differences expected to relate to sex-specific fitness consequences. However, studies generally fail to disentangle the effects of the two main drivers of HR size variation, food and conspecific density, and rarely consider how their relative influence change over spatiotemporal scales. We used location data from 77 Eurasian lynx (Lynx lynx) from a 16-year Scandinavian study to examine HR sizes variation relative to prey and conspecific density at different spatiotemporal scales. By varying the isopleth parameter (intensity of use) defining the HR, we show that sex-specific effects were conditional on the spatial scale considered. Males had larger HRs than females in all seasons. Females' total HR size declined as prey and conspecific density increased, whereas males' total HR was only affected by conspecific density. However, as the intensity of use within the HR increased (from 90% to 50% isopleth), the relationship between prey density and area showed opposing patterns for females and males; for females, the prey density effect was reduced, while for males, prey became increasingly important. Thus, prey influenced the size of key regions within male HRs, despite total HR size being independent of prey density. Males reduced their HR size during the mating season, likely to remain close to individual females in estrous. Females reduced their HR size postreproduction probably because of movement constrains imposed by dependent young. Our findings highlight the importance of simultaneously considering resources and intraspecific interactions as HR size determinants. We show that sex-specific demands influence the importance of prey and conspecific density on space use at different spatiotemporal scales. Thus, unless a gradient of space use intensity is examined, factors not related to total HR size might be disregarded despite their importance in determining size of key regions within the HR.
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