| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Breznau, Nate, et al.
(författare)
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Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:44
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Tidskriftsartikel (refereegranskat)abstract
- This study explores how researchers analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each teams workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.
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| 3. |
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| 4. |
- Bartels, Pia, et al.
(författare)
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Water transparency drives intra-population divergence in Eurasian perch (Perca fluviatilis)
- 2012
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Ingår i: PLOS ONE. - San Francisco : Public Library of Science (PLoS). - 1932-6203. ; 7:8
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Tidskriftsartikel (refereegranskat)abstract
- Trait combinations that lead to a higher efficiency in resource utilization are important drivers of divergent natural selection and adaptive radiation. However, variation in environmental features might constrain foraging in complex ways and therefore impede the exploitation of critical resources. We tested the effect of water transparency on intra-population divergence in morphology of Eurasian perch (Perca fluviatilis) across seven lakes in central Sweden. Morphological divergence between near-shore littoral and open-water pelagic perch substantially increased with increasing water transparency. Reliance on littoral resources increased strongly with increasing water transparency in littoral populations, whereas littoral reliance was not affected by water transparency in pelagic populations. Despite the similar reliance on pelagic resources in pelagic populations along the water transparency gradient, the utilization of particular pelagic prey items differed with variation in water transparency in pelagic populations. Pelagic perch utilized cladocerans in lakes with high water transparency and copepods in lakes with low water transparency. We suggest that under impaired visual conditions low utilization of littoral resources by littoral perch and utilization of evasive copepods by pelagic perch may lead to changes in morphology. Our findings indicate that visual conditions can affect population divergence in predator populations through their effects on resource utilization.
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| 5. |
- Hirsch, Philipp E, et al.
(författare)
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Indirect trophic interactions with an invasive species affect phenotypic divergence in a top consumer
- 2013
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Ingår i: Oecologia. - : Springer Science and Business Media LLC. - 0029-8549 .- 1432-1939. ; 172:1, s. 245-256
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Tidskriftsartikel (refereegranskat)abstract
- While phenotypic responses to direct species interactions are well studied, we know little about the consequences of indirect interactions for phenotypic divergence.In this study we used lakes with and without the zebra mussel to investigate effects ofindirect trophic interactions on phenotypic divergence between littoral and pelagic perch. We found a greater phenotypic divergence between littoral and pelagic individuals inlakes with zebra mussels and propose a mussel-mediated increase in pelagic and benthic resource availability as a major factor underlying this divergence. Lakes withzebra mussels contained higher densities of large plankton taxa and large invertebrates. We suggest that this augmented resource availability improved perch foraging opportunities in both the littoral and pelagic zones. Perch in both habitats could hence express a more specialized foraging morphology, leading to an increased divergence of perch forms in lakes with zebra mussels. As perch do not prey on mussels directly, we conclude that the increased divergence results from indirect interactions with the mussels. Our results hence suggest that species at lower food web levels can indirectlyaffect phenotypic divergence in species at the top of the food chain.
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| 6. |
- Hirsch, Philipp E
(författare)
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Phenotypic Processes Triggered by Biological Invasions
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Individuals within a single population can vary widely in their phenotype e.g. in their body shape. These differences are an important source of biodiversity and they can precede evolutionary divergence within a population. In this thesis we use the biological invasion of the zebra mussels into Swedish lakes to investigate which processes create or maintain phenotypic diversity within populations of the two native fish species perch and roach and the mussel itself. Both fishes have specially adapted body shapes that depend on whether they feed in the near-shore or open-water habitat of lakes. This habitat-specific divergence was more pronounced in lakes with zebra mussels, probably because resources in both habitats were in higher supply due to the mussels’ effects on the lakes. Divergence in perch body shapes between habitats was also higher in lakes with a higher water clarity, suggesting that visual conditions can affect the resource use and thus also the expression of a habitat-specific body shape. When investigating the diversity of body shapes in the mussel itself we found that mussels from one lake changed their shell shape when exposed to different predators: fish predators induced a more elongated shell shape while crayfish predators induced a rounder shell. These specific shell shapes probably serve as two alternative predator defenses protecting the mussel from predation. We conclude that the availability and use of distinct resources is an important source of diversity within populations. Abiotic conditions can play a previously underappreciated role by promoting or impairing the use of the distinct resources thus affecting the divergence. The diversity of shell shapes we found in the zebra mussels complements our study by demonstrating that not only consumer responses to resources but also resources’ responses to predators can generate phenotypic diversity.
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| 7. |
- Hirsch, Philipp E, et al.
(författare)
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Plastic Responses of a Sessile Prey to Multiple Predators : A Field and Experimental Study
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:12, s. e115192-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Theory predicts that prey facing a combination of predators with different feeding modes have two options: to express a response against the feeding mode of the most dangerous predator, or to express an intermediate response. Intermediate phenotypes protect equally well against several feeding modes, rather than providing specific protection against a single predator. Anti-predator traits that protect against a common feeding mode displayed by all predators should be expressed regardless of predator combination, as there is no need for trade-offs. Principal Findings: We studied phenotypic anti-predator responses of zebra mussels to predation threat from a handling-time-limited (crayfish) and a gape-size-limited (roach) predator. Both predators dislodge mussels from the substrate but diverge in their further feeding modes. Mussels increased expression of a nonspecific defense trait (attachment strength) against all combinations of predators relative to a control. In response to roach alone, mussels showed a tendency to develop a weaker and more elongated shell. In response to crayfish, mussels developed a harder and rounder shell. When exposed to either a combination of predators or no predator, mussels developed an intermediate phenotype. Mussel growth rate was positively correlated with an elongated weaker shell and negatively correlated with a round strong shell, indicating a trade-off between anti-predator responses. Field observations of prey phenotypes revealed the presence of both anti-predator phenotypes and the trade-off with growth, but intra-specific population density and bottom substrate had a greater influence than predator density. Conclusions: Our results show that two different predators can exert both functionally equivalent and inverse selection pressures on a single prey. Our field study suggests that abiotic factors and prey population density should be considered when attempting to explain phenotypic diversity in the wild.
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| 8. |
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| 9. |
- Samson, Emma, et al.
(författare)
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Early Engagement of Stakeholders with Individual-Based Modeling Can Inform Research for Improving Invasive Species Management : The Round Goby as a Case Study
- 2017
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Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media S.A.. - 2296-701X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Individual-based models (IBMs) incorporating realistic representations of key range-front processes such as dispersal can be used as tools to investigate the dynamics of invasive species. Managers can apply insights from these models to take effective action to prevent further spread and prioritize measures preventing establishment of invasive species. We highlight here how early-stage IBMs (constructed under constraints of time and data availability) can also play an important role in defining key research priorities for providing key information on the biology of an invasive species in order that subsequent models can provide robust insight into potential management interventions. The round goby, Neogobius melanostomus, is currently spreading through the Baltic Sea, with major negative effects being reported in the wake of its invasion. Together with stakeholders, we parameterize an IBM to investigate the goby's potential spread pattern throughout the Gulf of Gdansk and the Baltic Sea. Model parameters were assigned by integrating information obtained through stakeholder interaction, from scientific literature, or estimated using an inverse modeling approach when not available. IBMs can provide valuable direction to research on invasive species even when there is limited data and/or time available to parameterize/fit them to the degree to which we might aspire in an ideal world. Co-development of models with stakeholders can be used to recognize important invasion patterns, in addition to identifying and estimating unknown environmental parameters, thereby guiding the direction of future research. Well-parameterized and validated models are not required in the earlier stages of the modeling cycle where their main utility is as a tool for thought.
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