| 1. |
- Pang, Jun-Feng, et al.
(författare)
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mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves.
- 2009
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 1537-1719 .- 0737-4038. ; 26:12, s. 2849-64
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Tidskriftsartikel (refereegranskat)abstract
- There is no generally accepted picture of where, when, and how the domestic dog originated. Previous studies of mitochondrial DNA (mtDNA) have failed to establish the time and precise place of origin because of lack of phylogenetic resolution in the so far studied control region (CR), and inadequate sampling. We therefore analyzed entire mitochondrial genomes for 169 dogs to obtain maximal phylogenetic resolution and the CR for 1,543 dogs across the Old World for a comprehensive picture of geographical diversity. Hereby, a detailed picture of the origins of the dog can for the first time be suggested. We obtained evidence that the dog has a single origin in time and space and an estimation of the time of origin, number of founders, and approximate region, which also gives potential clues about the human culture involved. The analyses showed that dogs universally share a common homogenous gene pool containing 10 major haplogroups. However, the full range of genetic diversity, all 10 haplogroups, was found only in southeastern Asia south of Yangtze River, and diversity decreased following a gradient across Eurasia, through seven haplogroups in Central China and five in North China and Southwest (SW)Asia, down to only four haplogroups in Europe. The mean sequence distance to ancestral haplotypes indicates an origin 5,400-16,300 years ago (ya) from at least 51 female wolf founders. These results indicate that the domestic dog originated in southern China less than 16,300 ya, from several hundred wolves. The place and time coincide approximately with the origin of rice agriculture, suggesting that the dogs may have originated among sedentary hunter-gatherers or early farmers, and the numerous founders indicate that wolf taming was an important culture trait.
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| 2. |
- Meadows, Jennifer, et al.
(författare)
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Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
- 2023
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24
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Tidskriftsartikel (refereegranskat)abstract
- Background: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 x data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.Results: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.Conclusions: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
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| 3. |
- Wang, Xin ping, et al.
(författare)
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Spatiotemporal variation of soil water potential and its significance to water balance for a desert shrub area
- 2022
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Ingår i: Soil and Tillage Research. - : Elsevier BV. - 0167-1987. ; 224
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Tidskriftsartikel (refereegranskat)abstract
- In dry sandy soil, soil water is naturally redistributed by forces owing to matric and gravitational potential, and temperature gradients. Occurring shrub vegetation strongly influences these patterns by hydraulic redistribution within the soil. This means that plants can move water from moist to drier soil areas to extract nutrients from the drier soil and enhance nutrient uptake. This incorporates both upward and downward transport of water through the roots. Diel soil water potential (ψs) and soil temperature fluctuation were investigated at 30-min intervals for a respectively vegetated desert shrub area and non-vegetated bare area. Soil water potential fluctuations at the vegetated area reflected daytime depletion and nocturnal re-supply of water due to hydraulic redistribution while corresponding fluctuations at the non-vegetated area were mainly due to variation in soil temperature. Thus, the greatest diel ψs variability occurred in the vegetated area that averaged −0.401 MPa with a smaller variation in the non-vegetated area with an average of −0.009 MPa. At the shrub scale, ψs was strongly correlated with root distribution pattern that corroborates that diel variation in the active root zone of the shrub was mainly attributed to hydraulic redistribution. In the non-vegetated area, ψs responded more strongly to temperature gradients. The total of hydraulic redistribution of soil water storage increment accounted for 27 % of the total rainfall through the growing season from April to September. The study shows that it is important to consider biotic-factors such as hydraulic redistribution when analyzing water balance changes and hydrological niche segregation for desert ecosystems.
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| 4. |
- Zhu, Zhenke, et al.
(författare)
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Microorganisms maintain C:N stoichiometric balance by regulating the priming effect in long-term fertilized soils
- 2021
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Ingår i: Applied Soil Ecology. - : Elsevier BV. - 0929-1393. ; 167
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Tidskriftsartikel (refereegranskat)abstract
- Labile carbon (C) inputs affect the soil carbon:nitrogen (C:N) ratio and microbial stoichiometric homeostasis, which control the intensity and direction of the priming effect (PE). Here, we clarified how soil microorganisms regulate enzyme production and PE to maintain the C:N stoichiometric balance. Specifically, we conducted an incubation experiment by adding 13C-labeled glucose to four long-term fertilized paddy soils: no fertilization; fertilization with mineral nitrogen, phosphorus, and potassium (NPK); NPK combined with straw; and NPK with manure (NPKM). After glucose addition, the dissolved organic carbon-to-ammonium (DOC:NH4+) ratio (24–39) initially increased, but subsequently decreased after day 2 following glucose exhaustion. In parallel, the microbial C:N imbalance [(DOC:NH4+):(microbial biomass C:microbial biomass N)] rapidly decreased from day 2 (4.6–7.2) to day 20 (<0.5). Thus, microorganisms became C limited after 20 days of incubation. Excess C, resulting from glucose addition, increased N-hydrolase (chitinase) production and N mining from soil organic matter (SOM) through positive PEs. However, C hydrolase (β-1,4-glucosidase and β-xylosidase) activity increased, while that of N hydrolase (chitinase) decreased, following glucose exhaustion. Consequently, the C:N microbial biomass ratio increased as the DOC:NH4+ ratio decreased, leading to negative PEs. NPKM-fertilized soil had the largest cumulative PE (2.3% of soil organic carbon) because it had the highest microbial biomass and iron (Fe) reduction rate. Thus, this increased N mining from SOM maintained the microbial C:N stoichiometric balance. We concluded that soil microorganisms regulate C- and N-hydrolase production to control the intensity and direction of PE, maintaining the C:N stoichiometric balance in response to labile C inputs.
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