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Schnell I.B.,Copenhagen University | Schnell I.B.,Center for Zoo and Wild Animal Health | Bohmann K.,Copenhagen University | Bohmann K.,University of Bristol | And 2 more authors.
Molecular Ecology Resources | Year: 2015

Metabarcoding of environmental samples on second-generation sequencing platforms has rapidly become a valuable tool for ecological studies. A fundamental assumption of this approach is the reliance on being able to track tagged amplicons back to the samples from which they originated. In this study, we address the problem of sequences in metabarcoding sequencing outputs with false combinations of used tags (tag jumps). Unless these sequences can be identified and excluded from downstream analyses, tag jumps creating sequences with false, but already used tag combinations, can cause incorrect assignment of sequences to samples and artificially inflate diversity. In this study, we document and investigate tag jumping in metabarcoding studies on Illumina sequencing platforms by amplifying mixed-template extracts obtained from bat droppings and leech gut contents with tagged generic arthropod and mammal primers, respectively. We found that an average of 2.6% and 2.1% of sequences had tag combinations, which could be explained by tag jumping in the leech and bat diet study, respectively. We suggest that tag jumping can happen during blunt-ending of pools of tagged amplicons during library build and as a consequence of chimera formation during bulk amplification of tagged amplicons during library index PCR. We argue that tag jumping and contamination between libraries represents a considerable challenge for Illumina-based metabarcoding studies, and suggest measures to avoid false assignment of tag jumping-derived sequences to samples. © 2015 John Wiley & Sons Ltd.

Villar D.,University of Cambridge | Berthelot C.,European Bioinformatics Institute | Aldridge S.,University of Cambridge | Aldridge S.,Astrazeneca | And 14 more authors.
Cell | Year: 2015

The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These results provide important insight into the functional genetics underpinning mammalian regulatory evolution. © 2015 The Authors.

Jewgenow K.,Leibniz Institute for Zoo and Wildlife Research | Wiedemann C.,Leibniz Institute for Zoo and Wildlife Research | Bertelsen M.F.,Center for Zoo and Wild Animal Health | Ringleb J.,Leibniz Institute for Zoo and Wildlife Research
International Zoo Yearbook | Year: 2011

The ability to freeze unfertilized oocytes and the ovarian cortex is valuable for genetic resource banking, especially in the case of genetically important individuals that undergo castration or euthanasia for medical reasons. Although offspring have been produced from frozen-thawed oocytes in mice, humans, cattle and rabbits, the results have been variable and not sufficiently successful for routine use. This review provides an overview on the recent knowledge of female germ cell cryopreservation, with a focus on wildlife species, and introduces the Felid Gametes Rescue Project within European Association of Zoos and Aquaria zoos. © 2010 The Authors. International Zoo Yearbook © 2010 The Zoological Society of London.

Nilsson M.A.,Biodiversity and Climate Research Center | Nilsson M.A.,Lund University | Klassert D.,Biodiversity and Climate Research Center | Bertelsen M.F.,Center for Zoo and Wild Animal Health | And 3 more authors.
Molecular Biology and Evolution | Year: 2012

In the genome of Artiodactyla (cow, sheep, pigs, camels, and whales), a major retroposon group originated from a presumable horizontal transfer of BovB, a retrotransposon-like element retroposon, between 52 and 70 million years ago. Since then, BovB retroposons have proliferated and today occupy a quarter of the cow's genome sequence. The BovB-related short interspersed elements (SINEs) were used for resolving the phylogeny of Bovinae (cows, spiral-horned antelopes, and nilgais) and their relatives. In silico screening of 55,000 intronic retroposon insertions in the cow genome and experimental validation of 126 introns resulted in 29 informative retroposon markers for resolving bovine evolutionary relationships. A transposition-in-transposition analysis identifies three different phases of SINE activity and show how BovB elements have expanded in the cattle genome. © 2012 The Author.

Madsen J.,Copenhagen University | Bertelsen M.F.,Center for Zoo and Wild Animal Health
Journal of Animal Science | Year: 2012

The claimed low production of CH4 by kangaroos and marsupials in general has been questioned because of a lack of data. The extent of their CH4 production is of interest both from the point of view of discussing meat production of marsupials and as a basis for developing methods to reduce CH4 production from ruminants. In the present experiment, the CH4 production of 8 red-necked wallabies (Macropus rufogriseus) was measured of which 4 were fed 2 different diets in an open-circuit respiration chamber. These results were compared with a newly developed, inexpensive, and simple method that does not influence the behavior of the animal, and where the ratio between CH4 and CO2 is measured and used together with the calculated CO2 to quantify the CH4 production. The experiment demonstrated that the wallabies produce CH4. However, the amount of CH4 produced by these wallabies was between 1.6 and 2.5 L/d equivalent to 1.6 and 2.5% of GE or 2.2% and 3.5% of DE intake and 0.22 L/BW, kg0.75. This is between 25 and 33% of what can be expected from ruminants fed the same diet. Based on the uneven release of CH4 with time, it is most likely that the CH4 is excreted through flatulence and not through breathing as is seen in ruminants. The experiments also showed that a reasonably accurate determination of the CH4 production of a group of animals can be obtained by simply measuring the CH4/ CO2 ratio over a limited time span. This may represent the situation in a natural setting better than measurements in a respiration chamber. It was found that the CH4/CO2 ratio in itself represents a reasonable prediction of the proportion of feed GE that is lost as CH4, and that this method offers new opportunities for CH4 measurements on a large number of animals. © 2012 American Society of Animal Science. All rights reserved.

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