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| 2. |
- Berg, Åke
(författare)
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Conservation of birds in fragmented landscapes requires protected areas
- 2022
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Ingår i: Frontiers in Ecology and the Environment. - : Wiley. - 1540-9295 .- 1540-9309. ; 20, s. 361-369
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Tidskriftsartikel (refereegranskat)abstract
- For successful conservation of biodiversity, it is vital to know whether protected areas in increasingly fragmented landscapes effectively safeguard species. However, how large habitat fragments must be, and what level of protection is required to sustain species, remains poorly known. We compiled a global dataset on almost 2000 bird species in 741 forest fragments varying in size and protection status, and show that protection is associated with higher bird occurrence, especially for threatened species. Protection becomes increasingly effective with increasing size of forest fragments. For forest fragments >50 ha our results show that strict protection (International Union for Conservation of Nature [IUCN] categories I-IV) is strongly associated with higher bird occurrence, whereas fragments had to be at least 175 ha for moderate protection (IUCN categories V and VI) to have a positive effect. This meta-analysis quantifies the importance of fragment size, protection status, and their interaction for the conservation of bird species communities, and stresses that protection should not be limited to large pristine areas.
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| 3. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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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. |
- Kacergyte, Ineta, et al.
(författare)
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Evaluating created wetlands for bird diversity and reproductive success
- 2021
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Ingår i: Biological Conservation. - : Elsevier BV. - 0006-3207 .- 1873-2917. ; 257
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Tidskriftsartikel (refereegranskat)abstract
- Wetland creation is a common conservation practice to mitigate biodiversity loss, caused by global wetland destruction. Despite this, there is a lack of large-scale evaluations of how created wetland characteristics and landscape context relate to bird diversity and reproductive success. We inventoried 89 created wetlands (0.2-20 ha) in central Sweden to investigate which local and landscape components were associated with breeding wetland bird species richness, pair abundance and reproductive success. Wetland size was positively associated with species richness, pair abundance and chick abundance. However, several small (1 ha) wetlands taken together were similar to or exceeded individual large wetlands of similar total wetland area, in terms of species richness, pair abundance, and chicks produced. While species richness showed a clear negative relationship with the proportion of the adjacent 50 m buffer composed of forest, pair abundance was positively related to the proportion of flooded grassland area and negatively related to the proportion of emergent water vegetation. Reproductive success measures showed no clear relationships to local habitat characteristics but tended to increase with a decreasing forest at the landscape scale. Our results suggest that breeding wetland bird populations could benefit from creating wetlands with a high flooded area, continuous management to minimise both the area of emergent water vegetation and the establishment of shrubs and trees in the immediate surroundings. We also suggest a practice of creating mainly small wetlands with a few larger ones to facilitate breeding wetland bird communities at the regional scale (gamma diversity).
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| 6. |
- Kacergyte, Ineta, et al.
(författare)
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Quantifying effects of wetland restorations on bird communities in agricultural landscapes
- 2022
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Ingår i: Biological Conservation. - : Elsevier BV. - 0006-3207 .- 1873-2917. ; 273
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Tidskriftsartikel (refereegranskat)abstract
- Restoring wetlands to improve habitats for birds has become an important conservation tool as many wetlands have deteriorated and wetland bird populations declined. To what extent such restorations are effective is not well known because surveys usually either lack data before the restoration or means of correcting for background population trends. We identified wetland restorations made in agricultural landscapes in Sweden and retrieved all available Before-After survey data of breeding birds. From the resulting heterogeneous surveys, we quantified the effectiveness of restorations for eight bird groups comprising 72 bird species from 30 wetlands. We used national survey data to correct for background population trends. We estimated that island breeder populations have increased by between 62 % and 315 % (95 % confidence intervals) following restorations. Deep water foragers, shallow water foragers and short meadow breeders also mainly increased following restoration. The direction of effect was uncertain for tall meadow breeders, reed breeders and predators. Shrubland breeder populations declined between-55 % and-4 % following restorations. While restoration measures seemed to generally benefit about half of the breeding wetland bird community, estimated species-and site-specific re-sponses varied greatly and were associated with large uncertainty. Such heterogeneity in responses can arise due to biotic and abiotic interactions, varying management actions and survey methods between wetlands. Thus, to improve the effectiveness of future wetland restorations, funding bodies and environmental agencies should require standardised Before-After bird surveys at both restored and non-restored reference sites. Such improved survey designs would facilitate the development of more efficient restoration efforts.
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| 7. |
- Ruete, Alejandro, et al.
(författare)
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Cannot see the diversity for all the species: Evaluating inclusion criteria for local species lists when using abundant citizen science data
- 2020
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 10, s. 10057-10065
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Tidskriftsartikel (refereegranskat)abstract
- Abundant citizen science data on species occurrences are becoming increasingly available and enable identifying composition of communities occurring at multiple sites with high temporal resolution. However, for species displaying temporary patterns of local occurrences that are transient to some sites, biodiversity measures are clearly dependent on the criteria used to include species into local species lists. Using abundant opportunistic citizen science data from frequently visited wetlands, we investigated the sensitivity of alpha- and beta-diversity estimates to the use raw versus detection-corrected data and to the use of inclusion criteria for species presence reflecting alternative site use. We tested seven inclusion criteria (with varying number of days required to be present) on time series of daily occurrence status during a breeding season of 90 days for 77 wetland bird species. We show that even when opportunistic presence-only observation data are abundant, raw data may not produce reliable local species richness estimates and rank sites very differently in terms of species richness. Furthermore, occupancy model based alpha- and beta-diversity estimates were sensitive to the inclusion criteria used. Total species lists (all species observed at least once during a season) may therefore mask diversity differences among sites in local communities of species, by including vagrant species on potentially breeding communities and change the relative rank order of sites in terms of species richness. Very high sampling effort does not necessarily free opportunistic data from its inherent bias and can produce a pattern in which many species are observed at least once almost everywhere, thus leading to a possible paradox: The large amount of biological information may hinder its usefulness. Therefore, when prioritizing among sites to manage or preserve species diversity estimates need to be carefully related to relevant inclusion criteria depending on the diversity estimate in focus.
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