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  • 1
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    Adaptive radiation of Darwin's finches revisited using whole genome sequencing (2015)
    Wiley
    In: BioEssays
    Details
    Publication Date: 2015-11-26
    Description: We recently used genome sequencing to study the evolutionary history of the Darwin's finches. A prominent feature of our data was that different polymorphic sites in the genome tended to indicate different genetic relationships among these closely related species. Such patterns are expected in recently diverged genomes as a result of incomplete lineage sorting. However, we uncovered conclusive evidence that these patterns have also been influenced by interspecies hybridisation, a process that has likely played an important role in the radiation of Darwin's finches. A major discovery was that segregation of two haplotypes at the ALX1 locus underlies variation in beak shape among the Darwin's finches, and that differences between the two haplotypes in a 240 kb region in blunt and pointed beaked birds involve both coding and regulatory changes. As we review herein, the evolution of such adaptive haplotypes comprising multiple causal changes appears to be an important mechanism contributing to the evolution of biodiversity. Whole genome studies, when combined with field data, provide a powerful method of investigating evolution. We review an example with two discoveries in Darwin's finches. Interspecific hybridisation has occurred throughout the radiation, and involved a locus encoding the ALX1 transcription factor that controls variation in beak shape and hence diets.
    Print ISSN: 0265-9247
    Electronic ISSN: 1521-1878
    Topics: Biology , Medicine
    Published by Wiley
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  • 2
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    Optical properties of InAsBi and optimal designs of lattice-matched and strain-balanced III-V semiconductor superlattices (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-06-09
    Description: The optical properties of bulk InAs 0.936 Bi 0.064 grown by molecular beam epitaxy on a (100)-oriented GaSb substrate are measured using spectroscopic ellipsometry. The index of refraction and absorption coefficient are measured over photon energies ranging from 44 meV to 4.4 eV and are used to identify the room temperature bandgap energy of bulk InAs 0.936 Bi 0.064 as 60.6 meV. The bandgap of InAsBi is expressed as a function of Bi mole fraction using the band anticrossing model and a characteristic coupling strength of 1.529 eV between the Bi impurity state and the InAs valence band. These results are programmed into a software tool that calculates the miniband structure of semiconductor superlattices and identifies optimal designs in terms of maximizing the electron-hole wavefunction overlap as a function of transition energy. These functionalities are demonstrated by mapping the design spaces of lattice-matched GaSb/InAs 0.911 Sb 0.089 and GaSb/InAs 0.932 Bi 0.068 and strain-balanced InAs/InAsSb, InAs/GaInSb, and InAs/InAsBi superlattices on GaSb. The absorption properties of each of these material systems are directly compared by relating the wavefunction overlap square to the absorption coefficient of each optimized design. Optimal design criteria are provided for key detector wavelengths for each superlattice system. The optimal design mid-wave infrared InAs/InAsSb superlattice is grown using molecular beam epitaxy, and its optical properties are evaluated using spectroscopic ellipsometry and photoluminescence spectroscopy.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    Whole-genome resequencing reveals loci under selection during chicken domestication (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-03-12
    Description: Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rubin, Carl-Johan -- Zody, Michael C -- Eriksson, Jonas -- Meadows, Jennifer R S -- Sherwood, Ellen -- Webster, Matthew T -- Jiang, Lin -- Ingman, Max -- Sharpe, Ted -- Ka, Sojeong -- Hallbook, Finn -- Besnier, Francois -- Carlborg, Orjan -- Bed'hom, Bertrand -- Tixier-Boichard, Michele -- Jensen, Per -- Siegel, Paul -- Lindblad-Toh, Kerstin -- Andersson, Leif -- England -- Nature. 2010 Mar 25;464(7288):587-91. doi: 10.1038/nature08832. Epub 2010 Mar 10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-75123 Uppsala, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20220755" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Biological Evolution ; Chickens/*genetics ; Female ; Genetic Loci/*genetics ; Genome/*genetics ; Male ; Molecular Sequence Data ; Polymorphism, Single Nucleotide ; Selection, Genetic/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Deletion
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Cross‐Shelf Transport of Submarine Groundwater Discharge Tracers: A Sensitivity Analysis (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract The coastal mass balance for environmental tracers can be used to evaluate submarine groundwater discharge (SGD) and is often estimated using advective‐dispersive cross‐shelf transport models. Here we evaluate the sensitivity of different types of SGD tracers to key variables in this transport model under a wide range of environmental conditions. Salinity and long‐lived radionuclides (here represented by 226Ra; half‐life = 1,600 years) were transported by a combination of advection and dispersion under the scenarios considered, but short‐lived radionuclides (here represented by 224Ra; half‐life = 3.66 days) were mostly dispersed unless the offshore coefficient of solute dispersivity (Kx) was very low (〈1 m2/s). Sensitivity to variations in key transport variables was further evaluated by reinterpreting the cross‐shelf trends in Ra activity in the semiarid Gulf St Vincent of South Australia (GSV). In GSV, the trends in most Ra isotopes (223Ra, 228Ra, and 226Ra) in seawater could be explained similarly by a large number of parameter combinations, implying these tracers would provide highly uncertain SGD estimates in this environment. However, the range of possible parameter combinations was relatively smaller for 224Ra, suggesting that SGD estimates derived from this tracer would be most reliable for GSV. In both the sensitivity analysis and the reevaluation of the GSV data, Kx was the most sensitive parameter in the transport equation. Because Kx is an empirical parameter potentially encompassing different dispersion processes in time and space (tidal currents, storms, etc.), it is likely to be tracer, time, and site specific.
    Print ISSN: 2169-9275
    Electronic ISSN: 2169-9291
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
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    The genomic signature of dog domestication reveals adaptation to a starch-rich diet (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-01-29
    Description: The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Axelsson, Erik -- Ratnakumar, Abhirami -- Arendt, Maja-Louise -- Maqbool, Khurram -- Webster, Matthew T -- Perloski, Michele -- Liberg, Olof -- Arnemo, Jon M -- Hedhammar, Ake -- Lindblad-Toh, Kerstin -- England -- Nature. 2013 Mar 21;495(7441):360-4. doi: 10.1038/nature11837. Epub 2013 Jan 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75237 Uppsala, Sweden. Erik.Axelsson@imbim.uu.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23354050" target="_blank"〉PubMed〈/a〉
    Keywords: Amylases/genetics ; Animals ; Animals, Domestic/*genetics ; Diet/*veterinary ; Dogs/*genetics ; Genome/*genetics ; Glycogen Storage Disease Type II ; Mutation ; *Starch ; Wolves/genetics ; alpha-Glucosidases/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    A beak size locus in Darwin's finches facilitated character displacement during a drought (2016)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2016-04-23
    Description: Ecological character displacement is a process of morphological divergence that reduces competition for limited resources. We used genomic analysis to investigate the genetic basis of a documented character displacement event in Darwin's finches on Daphne Major in the Galapagos Islands: The medium ground finch diverged from its competitor, the large ground finch, during a severe drought. We discovered a genomic region containing the HMGA2 gene that varies systematically among Darwin's finch species with different beak sizes. Two haplotypes that diverged early in the radiation were involved in the character displacement event: Genotypes associated with large beak size were at a strong selective disadvantage in medium ground finches (selection coefficient s = 0.59). Thus, a major locus has apparently facilitated a rapid ecological diversification in the adaptive radiation of Darwin's finches.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lamichhaney, Sangeet -- Han, Fan -- Berglund, Jonas -- Wang, Chao -- Almen, Markus Sallman -- Webster, Matthew T -- Grant, B Rosemary -- Grant, Peter R -- Andersson, Leif -- New York, N.Y. -- Science. 2016 Apr 22;352(6284):470-4. doi: 10.1126/science.aad8786.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden. ; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA. ; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden. Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA. leif.andersson@imbim.uu.se.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27102486" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Beak/*anatomy & histology ; Body Size/genetics ; *Droughts ; Ecuador ; Female ; Finches/*anatomy & histology/classification/*genetics ; Genomics ; Genotype ; HMGA2 Protein/genetics ; Haplotypes ; Organ Size/genetics ; Phylogeny ; *Quantitative Trait Loci ; *Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Avidity-tuned nanoparticles reach the brain [Medical Sciences] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-05-22
    Description: Receptor-mediated transcytosis across the blood–brain barrier (BBB) may be a useful way to transport therapeutics into the brain. Here we report that transferrin (Tf)-containing gold nanoparticles can reach the brain parenchyma from systemic administration in mice through a receptor-mediated transcytosis pathway. This transport is aided by tuning the nanoparticle avidity...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Local interactions and global properties of wild, free-ranging stickleback shoals (2017)
    Royal Society
    Details
    Publication Date: 2017-07-13
    Description: Collective motion describes the global properties of moving groups of animals and the self-organized, coordinated patterns of individual behaviour that produce them. We examined the group-level patterns and local interactions between individuals in wild, free-ranging shoals of three-spine sticklebacks, Gasterosteus aculeatus . Our data reveal that the highest frequencies of near-neighbour encounters occur at between one and two body lengths from a focal fish, with the peak frequency alongside a focal individual. Fish also show the highest alignment with these laterally placed individuals, and generally with animals in front of themselves. Furthermore, fish are more closely matched in size, speed and orientation to their near neighbours than to more distant neighbours, indicating local organization within groups. Among the group-level properties reported here, we find that polarization is strongly influenced by group speed, but also the variation in speed among individuals and the nearest neighbour distances of group members. While we find no relationship between group order and group size, we do find that larger groups tend to have lower nearest neighbour distances, which in turn may be important in maintaining group order.
    Keywords: behaviour
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 9
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    Evolution of Darwin's finches and their beaks revealed by genome sequencing (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-02-18
    Description: Darwin's finches, inhabiting the Galapagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin's finch species and two close relatives. Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (Geospiza fortis), a species that has undergone rapid evolution of beak shape in response to environmental changes. The ALX1 haplotype has contributed to diversification of beak shapes among the Darwin's finches and, thereby, to an expanded utilization of food resources.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lamichhaney, Sangeet -- Berglund, Jonas -- Almen, Markus Sallman -- Maqbool, Khurram -- Grabherr, Manfred -- Martinez-Barrio, Alvaro -- Promerova, Marta -- Rubin, Carl-Johan -- Wang, Chao -- Zamani, Neda -- Grant, B Rosemary -- Grant, Peter R -- Webster, Matthew T -- Andersson, Leif -- England -- Nature. 2015 Feb 19;518(7539):371-5. doi: 10.1038/nature14181. Epub 2015 Feb 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden. ; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden. ; 1] Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden [2] Department of Plant Physiology, Umea University, SE-901 87 Umea, Sweden. ; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA. ; 1] Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden [2] Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden [3] Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25686609" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Avian Proteins/genetics/metabolism ; Beak/*anatomy & histology ; Ecuador ; *Evolution, Molecular ; Female ; Finches/*anatomy & histology/classification/embryology/*genetics ; Gene Flow ; Genome/genetics ; Haplotypes/genetics ; Hybridization, Genetic ; Indian Ocean Islands ; Male ; Molecular Sequence Data ; Phylogeny ; Transcription Factors/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 10
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    Specific sequence homology and three-dimensional structure of an aminoacyl transfer RNA synthetase (1984)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1984-12-14
    Description: Few and limited amino acid sequence homologies have been found among eight bacterial aminoacyl transfer RNA (tRNA) synthetases whose primary structures are known. The entire 939-amino acid primary structure of Escherichia coli isoleucyl-tRNA synthetase is now reported. In a sequence of 11 consecutive amino acids matching a sequence in E. coli methionyl-tRNA synthetase, there are ten identical residues and one conservative change. This is the strongest homology recorded between any two aminoacyl tRNA synthetases. This part of the methionine enzyme's three-dimensional structure has been determined, and it occurs in a mononucleotide binding fold; a close three-dimensional structural homology of this part of the enzyme with Bacillus stearothermophilus tyrosyl-tRNA synthetase has also been reported. The three synthetases probably fold identically in this region.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Webster, T -- Tsai, H -- Kula, M -- Mackie, G A -- Schimmel, P -- GM15539/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1984 Dec 14;226(4680):1315-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6390679" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Amino Acyl-tRNA Synthetases ; Escherichia coli/enzymology ; Geobacillus stearothermophilus/enzymology ; Isoleucine-tRNA Ligase ; Methionine-tRNA Ligase ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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