| 1. |
- Groenen, M. A., et al.
(författare)
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Analyses of pig genomes provide insight into porcine demography and evolution
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 491:7424, s. 393-398
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Tidskriftsartikel (refereegranskat)abstract
- For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.
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| 2. |
- Lionikas, Arimantas, et al.
(författare)
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Genomic Analysis of Variation in Hindlimb Musculature of Mice from the C57BL/6J and DBA/2J Lineage
- 2010
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Ingår i: Journal of Heredity. - : Oxford University Press (OUP). - 0022-1503 .- 1465-7333. ; 101:3, s. 360-367
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Tidskriftsartikel (refereegranskat)abstract
- The precise locations of attachment points of muscle to bone-the origin and insertion sites-are crucial anatomical and functional characteristics that influence locomotor performance. Mechanisms that control the development of these interactions between muscle, tendon, and bone are currently not well understood. In a subset of BXD recombinant inbred (RI) strains derived from the C57BL/6J and DBA/2J strains, we observed a soleus femoral attachment anomaly (SFAA) that was rare in both parental strains (Lionikas, Glover et al. 2006). The aim of the present study was to assess suitability of SFAA as a model to study the genetic mechanisms underlying variation in musculoskeletal anatomy. We scored the incidence of SFAA in 55 BXD strains (n = 9 to 136, median = 26, phenotyped animals per strain, for a total number of 2367). Seven strains (BXD1, 12, 38, 43, 48, 54, and 56) exhibited a high incidence of unilateral SFAA (47-89%), whereas 23 strains scored 0%. Exploration of the mechanisms underlying SFAA in 2 high incidence strains, BXD1 and BXD38, indicated that SFAA-relevant genes are to be found in both C57BL/6J and DBA/2J regions of the BXD1 genome. However, not all alleles relevant for the expression of the phenotype were shared between the 2 high-incidence BXD strains. In conclusion, the anatomical origin of the soleus muscle in mouse is controlled by a polygenic system. A panel of BXD RI strains is a useful tool in exploring the genetic mechanisms underlying SFAA and improving our understanding of musculoskeletal development.
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| 3. |
- Potapov, Anton M., et al.
(författare)
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Globally invariant metabolism but density-diversity mismatch in springtails
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Soil life supports the functioning and biodiversity of terrestrial ecosystems. Springtails (Collembola) are among the most abundant soil arthropods regulating soil fertility and flow of energy through above- and belowground food webs. However, the global distribution of springtail diversity and density, and how these relate to energy fluxes remains unknown. Here, using a global dataset representing 2470 sites, we estimate the total soil springtail biomass at 27.5 megatons carbon, which is threefold higher than wild terrestrial vertebrates, and record peak densities up to 2 million individuals per square meter in the tundra. Despite a 20-fold biomass difference between the tundra and the tropics, springtail energy use (community metabolism) remains similar across the latitudinal gradient, owing to the changes in temperature with latitude. Neither springtail density nor community metabolism is predicted by local species richness, which is high in the tropics, but comparably high in some temperate forests and even tundra. Changes in springtail activity may emerge from latitudinal gradients in temperature, predation and resource limitation in soil communities. Contrasting relationships of biomass, diversity and activity of springtail communities with temperature suggest that climate warming will alter fundamental soil biodiversity metrics in different directions, potentially restructuring terrestrial food webs and affecting soil functioning.
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| 4. |
- Li, L. S., et al.
(författare)
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CONFLICTING EFFECTS OF PREDATOR CUE AND OCEAN ACIDIFICATION ON THE MUSSEL MYTILUS CORUSCUS BYSSUS PRODUCTION
- 2015
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Ingår i: Journal of Shellfish Research. - : National Shellfisheries Association. - 0730-8000 .- 1943-6319. ; 34:2, s. 393-400
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the impact of ocean acidification and warming on communities and ecosystems is a researcher priority. This can only be achieved through a combination of experimental and field approaches that would allow developing a mechanistic understanding of impacts across level of biological organizations. Surprisingly, most published studies are still focusing on single species responses with little consideration for interspecific interactions. In this study, the impacts of a 3 days exposure to three parameters (temperature, pH, and presence/absence of the predator cue of the crab Charybdis japonica) and their interactions on an ecologically important endpoint were evaluated: the byssus production of the mussel Mytilus coruscus. Tested temperatures (25 degrees C and 30 degrees C) were within the present range of natural variability whereas pH (8.1, 7.7, and 7.4) covered present as well as near-future natural variability. As expected, the presence of the crab cue induced an antipredator response in Mytilus coruscus (significant 10% increase in byssus secretion rate, 22% increase in frequency of shed byssus, and 30% longer byssus). Decreased pH but not temperature had a significant negative impact on the same endpoints (up to a 17% decrease in byssus secretion rate, 40% decrease in frequency of shed byssus, and 10% shorter byssus at pH 7.3 as compared with pH 8.1) with no significant interactions between the three tested parameters. In this study, it has been hypothesized that pH and predator cue have different modes of action and lead to conflicting functional responses (escape response versus stronger attachment). Functional consequences for ecosystem dynamics still need to be investigated.
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| 5. |
- Settele, Josef, et al.
(författare)
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Rice ecosystem services in South-east Asia
- 2018
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Ingår i: Paddy and Water Environment. - : Springer. - 1611-2490 .- 1611-2504. ; 16:2, s. 211-224
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 6. |
- Tao, Feng, et al.
(författare)
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Microbial carbon use efficiency promotes global soil carbon storage
- 2023
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 618:7967, s. 981-985
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Tidskriftsartikel (refereegranskat)abstract
- Soils store more carbon than other terrestrial ecosystems. How soil organic carbon (SOC) forms and persists remains uncertain, which makes it challenging to understand how it will respond to climatic change. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.
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| 7. |
- Xiao, K., et al.
(författare)
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Crab bioturbation drives coupled iron-phosphate-sulfide cycling in mangrove and salt marsh soils
- 2022
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Ingår i: Geoderma. - : Elsevier BV. - 0016-7061. ; 424
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Tidskriftsartikel (refereegranskat)abstract
- Coastal wetlands sequestering abundant blue carbon in soils are biogeochemical hotspots and critical habitats for benthic animals like invertebrate fiddler crabs. Here, we reveal how crab bioturbation (i.e., burrowing activity) drives the redox geochemistry of ferrous iron (Fe(II)), phosphate (PO43-), and sulfide (S(-II)) under contrasting vegetation types and hydrological conditions. We used in-situ approaches of diffusive gradients in thin films to perform detailed mm-scale burrow observations in two subtropical wetlands with a vegetation gradient of mudflat-salt marsh-mangrove. Burrow flushing caused a top-down hydrologic connectivity through the crab burrows and thus created a deep depth for the occurrence of Fe(III) reduction and sulfate reduction which were accompanied by P mobilization. The burrow oxidation zone, indicated by lower concentrations of Fe(II), PO43- and S(-II), were shallower in mudflats and salt marshes than in mangroves due to the unique respiratory roots of mangrove plants. The redox of Fe(II), PO(4)(3-)and S(-II) in crab burrow was insensitive to the convection flow induced input of dissolved oxygen through the surrounding soil matrix, indicating the burrow soil is an independent microenvironment. Crab burrowing activities favored Fe-S coupling which is conductive the formation of pyrite and alkalinity generation. Overall, our in-situ high-resolution observations and porewater hydraulic dynamics revealed spatially variable soil geochemistry, active coupled cycling of Fe-P-S in crab burrows, and mm-scale hotspots of redox cycling within burrows.
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