| 1. |
- Ramirez, Kelly S., et al.
(författare)
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Detecting macroecological patterns in bacterial communities across independent studies of global soils
- 2018
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Ingår i: Nature Microbiology. - : NATURE PUBLISHING GROUP. - 2058-5276. ; 3:2, s. 189-196
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Tidskriftsartikel (refereegranskat)abstract
- The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.
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| 2. |
- Santangelo, James S., et al.
(författare)
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Global urban environmental change drives adaptation in white clover
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 375
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Tidskriftsartikel (refereegranskat)abstract
- Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural dines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
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| 3. |
- Fox, Graeme, et al.
(författare)
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Bespoke markers for ex-situ conservation : application, analysis and challenges in the assessment of a population of endangered undulate rays
- 2018
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Ingår i: Journal of Zoo and Aquarium Research. - 2214-7594. ; 6:2, s. 50-56
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Tidskriftsartikel (refereegranskat)abstract
- Genetic data are important and informative in the management of ex-situ populations. Where the risk of inbreeding is particularly great, it is critical that tools are employed that allow for the quantification of genetic variation and to identify potential breeding pairs. This study demonstrates the rapid application of laboratory and bioinformatics techniques to develop a novel microsatellite marker panel for use with a population of the endangered undulate ray (Raja undulata) and shows how a minimally invasive sampling method can be used with aquarium-dwelling individuals. The study assesses the population and investigates how informative a small microsatellite marker panel is to the conservation of a restricted ex-situ group. It was found that after a single captive generation of R. undulata there is no detectable evidence of reduced heterozygosity and no observable aquaria effects or differences between the generations. In conclusion, the study demonstrates that it is practical, quick and informative to develop a bespoke panel of markers to aid ex-situ conservation efforts of non-model species and make recommendations that these processes should constitute the minimum effort required in managing such a population.
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