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479 results on '"Carvalho, Gary R"'

1. Demographic reconstruction from ancient DNA supports rapid extinction of the great auk

Author

Thomas, Jessica E, Carvalho, Gary R, Haile, James, Rawlence, Nicolas J, Martin, Michael D, Ho, Simon YW, Sigfússon, Arnór Þ, Jósefsson, Vigfús A, Frederiksen, Morten, Linnebjerg, Jannie F, Castruita, Jose A Samaniego, Niemann, Jonas, Sinding, Mikkel-Holger S, Sandoval-Velasco, Marcela, Soares, André ER, Lacy, Robert, Barilaro, Christina, Best, Juila, Brandis, Dirk, Cavallo, Chiara, Elorza, Mikelo, Garrett, Kimball L, Groot, Maaike, Johansson, Friederike, Lifjeld, Jan T, Nilson, Göran, Serjeanston, Dale, Sweet, Paul, Fuller, Errol, Hufthammer, Anne Karin, Meldgaard, Morten, Fjeldså, Jon, Shapiro, Beth, Hofreiter, Michael, Stewart, John R, Gilbert, M Thomas P, and Knapp, Michael

Subjects
Biological Sciences, Ecology, Genetics, Life on Land, Animals, Charadriiformes, DNA, Ancient, DNA, Mitochondrial, Extinction, Biological, Genetic Variation, Genome, Mitochondrial, Humans, Phylogeny, Population Dynamics, 19th century extinction, ancient DNA, evolutionary biology, genetics, genomics, hunting, paleogenetics, seabird exploitation, Biochemistry and Cell Biology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.

Published
2019

2. Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms.

Author

Seymour, Mathew, Durance, Isabelle, Cosby, Bernard J, Ransom-Jones, Emma, Deiner, Kristy, Ormerod, Steve J, Colbourne, John K, Wilgar, Gregory, Carvalho, Gary R, de Bruyn, Mark, Edwards, François, Emmett, Bridget A, Bik, Holly M, and Creer, Simon

Abstract

Accurate quantification of biodiversity is fundamental to understanding ecosystem function and for environmental assessment. Molecular methods using environmental DNA (eDNA) offer a non-invasive, rapid, and cost-effective alternative to traditional biodiversity assessments, which require high levels of expertise. While eDNA analyses are increasingly being utilized, there remains considerable uncertainty regarding the dynamics of multispecies eDNA, especially in variable systems such as rivers. Here, we utilize four sets of upland stream mesocosms, across an acid-base gradient, to assess the temporal and environmental degradation of multispecies eDNA. Sampling included water column and biofilm sampling over time with eDNA quantified using qPCR. Our findings show that the persistence of lotic multispecies eDNA, sampled from water and biofilm, decays to non-detectable levels within 2 days and that acidic environments accelerate the degradation process. Collectively, the results provide the basis for a predictive framework for the relationship between lotic eDNA degradation dynamics in spatio-temporally dynamic river ecosystems.

Published
2018

5. Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries

Author

Maggini, Sara, primary, Jacobsen, Magnus Wulff, additional, Urban, Paulina, additional, Hansen, Brian Klitgaard, additional, Kielgast, Jos, additional, Bekkevold, Dorte, additional, Jardim, Ernesto, additional, Martinsohn, Jann T., additional, Carvalho, Gary R., additional, Nielsen, Einar E., additional, and Papadopulos, Alexander S. T., additional

Published
2024
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6. Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries

Author

Maggini, Sara, Jacobsen, Magnus Wulff, Urban, Paulina, Hansen, Brian Klitgaard, Kielgast, Jos, Bekkevold, Dorte, Jardim, Ernesto, Martinsohn, Jann T., Carvalho, Gary R., Nielsen, Einar E., Papadopulos, Alexander S.T., Maggini, Sara, Jacobsen, Magnus Wulff, Urban, Paulina, Hansen, Brian Klitgaard, Kielgast, Jos, Bekkevold, Dorte, Jardim, Ernesto, Martinsohn, Jann T., Carvalho, Gary R., Nielsen, Einar E., and Papadopulos, Alexander S.T.

Abstract

Bycatch and discards, representing unwanted catches, undermine sustainable fisheries and hinder the conservation of vulnerable and endangered species. To effectively monitor bycatch and enhance the effectiveness of management measures while promoting sustainable fishing practices, reliable data is essential. Here, we explore the use of Nanopore metabarcoding to analyze the catch composition in demersal bottom fisheries. We collected eDNA samples directly from an onboard catch holding tank (catch water) for 10 fishing hauls from a fishing vessel operating in the Skagerrak (North-East Atlantic). The approach involved sequencing a combination of long (~2 kb) and short (~170–313 bp) mitochondrial amplicons and was validated by analyzing a fishery-related mock community sample and fishing haul replicates. Overall, the detection rate accuracy was 95% for landed species, and replicates obtained from the same fishing haul showed consistent results, validating the robustness of this approach. The detection rate accuracy for all caught species observed on board (including the non-landed fraction) was 81%. Undetected species were always limited to species in low abundance, but may also be attributed to problems with identifying closely related species due to the impact of sequencing errors and limited diagnostic variation in the genetic regions used. In the future, such biases may be reduced by using additional markers to increase species discrimination power and applying newly available technological advantages in flow cell chemistry to improve sequencing accuracy. In conclusion, this study demonstrates the effectiveness of Nanopore eDNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries, including catches of non-commercial and threatened and vulnerable species, without disrupting fishing activities. Incorporating eDNA analysis of catch water may therefore help facilitate effective monitoring, leading to better

Published
2024

8. SNP Discovery Using Next Generation Transcriptomic Sequencing in Atlantic Herring (Clupea harengus)

Author

Helyar, Sarah J, Limborg, Morten T, Bekkevold, Dorte, Babbucci, Massimiliano, van Houdt, Jeroen, Maes, Gregory E, Bargelloni, Luca, Nielsen, Rasmus O, Taylor, Martin I, Ogden, Rob, Cariani, Alessia, Carvalho, Gary R, Consortium, FishPopTrace, and Panitz, Frank

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Ecology, Genetics, Human Genome, Generic health relevance, Animals, Atlantic Ocean, Base Sequence, Fishes, Gene Frequency, Genetic Association Studies, Genotyping Techniques, Geography, Microsatellite Repeats, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, RNA, Messenger, Reproducibility of Results, Sequence Analysis, DNA, Species Specificity, Transcriptome, FishPopTrace Consortium, General Science & Technology
Abstract

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.

Published
2012

35. Biocomplexity in a Highly Migratory Pelagic Marine Fish, Atlantic Herring

Author

Ruzzante, Daniel E., Mariani, Stefano, Bekkevold, Dorte, André, Carl, Mosegaard, Henrik, Clausen, Lotte A. W., Dahlgren, Thomas G., Hutchinson, William F., Hatfield, Emma M. C., Torstensen, Else, Brigham, Jennifer, Simmonds, E. John, Laikre, Linda, Larsson, Lena C., Stet, René J. M., Ryman, Nils, and Carvalho, Gary R.

Published
2006
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49. Validation of the barcoding gene COI for use in forensic genetic species identification

Author

Dawnay, Nick, Ogden, Rob, McEwing, Ross, Carvalho, Gary R., and Thorpe, Roger S.

Subjects
DNA testing -- Methods, Bar codes -- Usage, Cytochrome oxidase -- Identification and classification, Wildlife -- Identification and classification, Law
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.forsciint.2006.09.013 Byline: Nick Dawnay (a), Rob Ogden (b), Ross McEwing (b), Gary R. Carvalho (a), Roger S. Thorpe (a) Keywords: DNA barcoding; Cytochrome c oxidase I; COI; Wildlife forensics; Validation; Cytochrome b Abstract: The application of forensics to wildlife crime investigation routinely involves genetic species identification based on DNA sequence similarity. This work can be hindered by a lack of authenticated reference DNA sequence data resulting in weak matches between evidence and reference samples. The introduction of DNA barcoding has highlighted the expanding use of the mtDNA gene, cytochrome c oxidase I (COI), as a genetic marker for species identification. Here, we assess the COI gene for use in forensic analysis following published human validation guidelines. Validation experiments investigated reproducibility, heteroplasmy, mixed DNA, DNA template concentration, chemical treatments, substrate variation, environmental conditions and thermocycling parameters. Sequence similarity searches using both GenBank BLASTn and BOLD search engines indicated that the COI gene consistently identifies species where authenticated reference sequence data exists. Where misidentification occurred the cause was attributable to either erroneous reference sequences from published data, or lack of primer specificity. Although amplification failure was observed under certain sample treatments, there was no evidence of environmentally induced sequence mutation in those sequences that were generated. A simulated case study compared the performance of COI and cytochrome b mtDNA genes. Findings are discussed in relation to the utility of the COI gene in forensic species identification. Author Affiliation: (a) School of Biological Sciences, University of Wales, Bangor LL57 2UW, United Kingdom (b) Wildlife DNA Services, Science Campus, University of Wales, Bangor LL57 2UW, United Kingdom Article History: Received 12 May 2006; Revised 2 August 2006; Accepted 13 September 2006

Published
2007

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