5 results on '"Driskell, Amy C."'
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2. DNA barcoding fishes.
- Author
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Weigt LA, Driskell AC, Baldwin CC, and Ormos A
- Subjects
- Animals, DNA isolation & purification, Polymerase Chain Reaction, DNA genetics, DNA Barcoding, Taxonomic methods, Fishes genetics
- Abstract
This chapter is an overview of the techniques for DNA barcoding of fishes from field collection to DNA sequence analysis. Recommendations for modifications of field protocols and best tissue sampling practices are made. A variety of DNA extraction protocols is provided, including high-throughput robot-assisted methods. A pair of well-tested forward and reverse primers for PCR amplification and sequencing are presented. These primers have been successfully used for DNA barcode on a wide array of marine fish taxa and also work well in most freshwater and cartilaginous fishes. Recipes and cycling protocols for both PCR amplification and sequencing and cleanup methods for the reaction products are provided. A method for the consistent production of high-quality DNA barcodes from DNA sequence data is given and stringent guidelines for judging the quality of raw sequence data are laid out.
- Published
- 2012
- Full Text
- View/download PDF
3. Introduction to animal DNA barcoding protocols.
- Author
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Weigt LA, Driskell AC, Ormos A, Meyer C, and Collins A
- Subjects
- Animals, DNA isolation & purification, Polymerase Chain Reaction, DNA genetics, DNA Barcoding, Taxonomic methods
- Abstract
Procedures and protocols common to many DNA barcoding projects are summarized. Planning for any project should emphasize front-end procedures, especially the "genetic lockdown" of collected materials for downstream genetic procedures. Steps further into the DNA barcoding process chain, such as sequencing, data processing, and other back-end functions vary slightly, if at all, among projects and are presented elsewhere in the volume. Point-of-collection sample and tissue handling and data/metadata handling are stressed. Specific predictions of the future workflows and mechanics of DNA barcoding are difficult, so focus is on that which most or all future methods and technologies will surely share.
- Published
- 2012
- Full Text
- View/download PDF
4. Whole-genome analyses resolve early branches in the tree of life of modern birds
- Author
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Jarvis, Erich D, Mirarab, Siavash, Aberer, Andre J, Li, Bo, Houde, Peter, Li, Cai, Ho, Simon YW, Faircloth, Brant C, Nabholz, Benoit, Howard, Jason T, Suh, Alexander, Weber, Claudia C, da Fonseca, Rute R, Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Munch, Kasper, Schierup, Mikkel, Lindow, Bent, Warren, Wesley C, Ray, David, Green, Richard E, Bruford, Michael W, Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P, Bertelsen, Mads Frost, Sheldon, Frederick H, Brumfield, Robb T, Mello, Claudio V, Lovell, Peter V, Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego, José Alfredo, Vargas Velazquez, Amhed Missael, Alfaro-Núñez, Alonzo, Campos, Paula F, Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M, Zhou, Qi, Perelman, Polina, Driskell, Amy C, Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E, Braun, Michael, Fjeldsa, Jon, Orlando, Ludovic, Barker, F Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus-Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A, Rahbek, Carsten, Willerslev, Eske, Graves, Gary R, Glenn, Travis C, McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V, Stamatakis, Alexandros, Mindell, David P, and Cracraft, Joel
- Subjects
Human Genome ,Genetics ,Animals ,Avian Proteins ,Base Sequence ,Biological Evolution ,Birds ,DNA Transposable Elements ,Genes ,Genetic Speciation ,Genome ,INDEL Mutation ,Introns ,Phylogeny ,Sequence Analysis ,DNA ,General Science & Technology - Abstract
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
- Published
- 2014
5. A multigene phylogeny examining evolutionary and ecological relationships in the Australo-papuan wrens of the subfamily Malurinae (Aves)
- Author
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Driskell, Amy C., Norman, Janette A., Pruett-Jones, Stephen, Mangall, Elizabeth, Sonsthagen, Sarah, and Christidis, Les
- Subjects
- *
AUSTRALIAN robins , *MOLECULAR phylogeny , *MALURIDAE , *MITOCHONDRIA , *PASSERIFORMES , *DNA , *ANIMAL genetics - Abstract
Abstract: Nucleotide sequences from four mitochondrial genes and three nuclear introns were used to examine phylogenetic relationships within the Australo-papuan fairy-wrens (Passeriformes: Maluridae: Malurinae). A well-resolved and well-supported phylogenetic hypothesis of all species in the subfamily was generated. The tree contained three clades corresponding to groups with similar plumages previously identified in earlier studies: the “bi-color,” “blue,” and “chestnut-shouldered” groups. The genus Malurus was not monophyletic –Malurus grayi formed a clade with two New Guinean genera Sipodotus and Clytomyias. We recommend M. grayi be reclassified into the genus Chenorhamphus Oustalet 1898. One other taxonomic change is recommended based on the large genetic distance between the two subspecies of Chenorhamphus grayi – the elevation of C. g. campbelli to specific status (= C. campbelli). Although the family Maluridae appears to have had its origins in Australia, the DNA data supports a New Guinean origin for the Malurini (Sipodotus, Clytomyias, Chenorhamphus, Malurus). [Copyright &y& Elsevier]
- Published
- 2011
- Full Text
- View/download PDF
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