| 1. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 2. |
- Lento, Jennifer, et al.
(författare)
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Temperature and spatial connectivity drive patterns in freshwater macroinvertebrate diversity across the Arctic
- 2022
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Ingår i: Freshwater Biology. - : John Wiley & Sons. - 0046-5070 .- 1365-2427. ; 67:1, s. 159-175
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Tidskriftsartikel (refereegranskat)abstract
- Warming in the Arctic is predicted to change freshwater biodiversity through loss of unique taxa and northward range expansion of lower latitude taxa. Detecting such changes requires establishing circumpolar baselines for diversity, and understanding the primary drivers of diversity. We examined benthic macroinvertebrate diversity using a circumpolar dataset of >1,500 Arctic lake and river sites. Rarefied α diversity within catchments was assessed along latitude and temperature gradients. Community composition was assessed through region-scale analysis of β diversity and its components (nestedness and turnover), and analysis of biotic–abiotic relationships. Rarefied α diversity of lakes and rivers declined with increasing latitude, although more strongly across mainland regions than islands. Diversity was strongly related to air temperature, with the lowest diversity in the coldest catchments. Regional dissimilarity was highest when mainland regions were compared with islands, suggesting that connectivity limitations led to the strongest dissimilarity. High contributions of nestedness indicated that island regions contained a subset of the taxa found in mainland regions. High Arctic rivers and lakes were predominately occupied by Chironomidae and Oligochaeta, whereas Ephemeroptera, Plecoptera, and Trichoptera taxa were more abundant at lower latitudes. Community composition was strongly associated with temperature, although geology and precipitation were also important correlates. The strong association with temperature supports the prediction that warming will increase Arctic macroinvertebrate diversity, although low diversity on islands suggests that this increase will be limited by biogeographical constraints. Long-term harmonised monitoring across the circumpolar region is necessary to detect such changes to diversity and inform science-based management.
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| 3. |
- Lindblad-Toh, Kerstin, et al.
(författare)
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Genome sequence, comparative analysis and haplotype structure of the domestic dog.
- 2005
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 438:7069, s. 803-19
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Tidskriftsartikel (refereegranskat)abstract
- Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
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| 4. |
- Ricci, C., et al.
(författare)
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A Tight Correlation between Millimeter and X-Ray Emission in Accreting Massive Black Holes from
- 2023
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Ingår i: Astrophysical Journal Letters. - 2041-8213 .- 2041-8205. ; 952:2
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies have proposed that the nuclear millimeter continuum emission observed in nearby active galactic nuclei (AGNs) could be created by the same population of electrons that gives rise to the X-ray emission that is ubiquitously observed in accreting black holes. We present the results of a dedicated high-spatial-resolution (∼60-100 mas) Atacama Large Millimeter/submillimeter Array (ALMA) campaign on a volume-limited (<50 Mpc) sample of 26 hard X-ray (>10 keV) selected radio-quiet AGNs. We find an extremely high detection rate (25/26 or 94 − 6 + 3 % ), which shows that nuclear emission at millimeter wavelengths is nearly ubiquitous in accreting SMBHs. Our high-resolution observations show a tight correlation between the nuclear (1-23 pc) 100 GHz and the intrinsic X-ray emission (1σ scatter of 0.22 dex). The ratio between the 100 GHz continuum and the X-ray emission does not show any correlation with column density, black hole mass, Eddington ratio, or star formation rate, which suggests that the 100 GHz emission can be used as a proxy of SMBH accretion over a very broad range of these parameters. The strong correlation between 100 GHz and X-ray emission in radio-quiet AGNs could be used to estimate the column density based on the ratio between the observed 2-10 keV ( F 2 - 10 keV obs ) and 100 GHz (F 100 GHz) fluxes. Specifically, a ratio log ( F 2 - 10 keV obs / F 100 GHz ) ≤ 3.5 strongly suggests that a source is heavily obscured ( log ( N H / cm − 2 ) ≳ 23.8 ). Our work shows the potential of ALMA continuum observations to detect heavily obscured AGNs (up to an optical depth of one at 100 GHz, i.e., N H ≃ 1027 cm−2), and to identify binary SMBHs with separations <100 pc, which cannot be probed by current X-ray facilities.
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| 5. |
- Wang, Zhaoming, et al.
(författare)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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