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Mitochondrial DNA Part B
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Volume 5, 2020 - Issue 3
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Complete mitochondrial genomes provide current refined phylogenomic hypotheses for relationships among ten Hirundo species

Javan K. Cartera Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USACorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0001-5104-9283View further author information
ORCID Icon,
Peter Innesa Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
,
April M. Goebla Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
,
Benjamin Johnsona Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
,
Matthew Geberta Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
,
Ziv Attiaa Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
,
Zachariah Gabania Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
,
Ruiqi Lia Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
,
Tina Meliea Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
,
Chiara Darta Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Ali Maresa Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Chrisopher Greidanusa Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Jaime Patersona Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Brianna Walla Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Gabriela Cortesea Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Kevin Thirouina Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Gabrielle Glimea Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Joseph Ruttena Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Cameron Poyda Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Erin Posta Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Brianna Walla Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Ahmed A. Elhadia Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Katherine Feldmanna Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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August Danza Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Thomas Blancharda Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Samantha Amatoa Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Stephan Reinerta Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Cloe S. Pogodaa Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAORCID Iconhttps://orcid.org/0000-0002-6808-7718View further author information
ORCID Icon,
Elizabeth S. C. Scordatob Department of Biological Science, California State Polytechnic University, Pomona, CA, USAView further author information
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Amanda K. Hunda Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA;c Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USAView further author information
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Rebecca J. Safrana Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Nolan C. Kanea Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USAView further author information
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Pages 2881-2885 | Received 16 Mar 2020, Accepted 20 Jun 2020, Published online: 20 Jul 2020

References

  • Anmarkrud JA, Lifjeld JT. 2017. Complete mitochondrial genomes of eleven extinct or possibly extinct bird species. Mol Ecol Resour. 17(2):334–341.
  • Bankevich A, Nurk S, Antipov D, Gurevich A A, Dvorkin M, Kulikov A S, Lesin V M, Nikolenko S I, Pham S, Prjibelski A D, et al. 2012. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J. Comput. Biol. 19(5):455–477. doi:10.1089/cmb.2012.0021.
  • Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler P F. 2013. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69(2):313–319. doi:10.1016/j.ympev.2012.08.023.
  • Bolger A M, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120. doi:10.1093/bioinformatics/btu170.
  • Boore J L. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27(8):1767–1780. doi:10.1093/nar/27.8.1767.
  • Brown CR, Brown MB. 1999. Barn swallow (Hirundo rustica). Birds North Am. 452:32.
  • Dor R, Safran RJ, Sheldon FH, Winkler DW, Lovette IJ. 2010. Phylogeny of the genus Hirundo and the Barn Swallow subspecies complex. Mol Phylogenet Evol. 56(1):409–418.
  • Held P, Buehrer L. 2003. The Synergy™ HT: a unique multi-detection microplate reader for HTS and drug discovery. J Assoc Lab Autom. 8(2):44–49.
  • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
  • Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, et al. 2013. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol. 30(11):2531–2540.
  • Li H. 2011. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 27(21):2987–2993.
  • Li, Heng. “Aligning sequence reads, clone sequence and assembly contigs with BWA-MEM.” arXiv preprint arXiv:1303.3997 (2013).
  • Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25(5):955–964.
  • Maddison WP, Knowles LL. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst Biol. 55(1):21–30.
  • Ovcharenko I, Loots GG, Hardison RC, Miller W, Stubbs L. 2004. zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res. 14(3):472–477.
  • Sheldon F H, Whittingham L A, Moyle R G, Slikas B, Winkler D W. 2005. Phylogeny of swallows (Aves: Hirundinidae) estimated from nuclear and mitochondrial DNA sequences. Mol. Phylogenet. Evol. 35(1):254–270. doi:10.1016/j.ympev.2004.11.008.
  • Sheldon FH, Winkler DW. 1993. Intergeneric phylogenetic relationships of swallows estimated by DNA-DNA hybridization. Auk. 110(4):798–824.
  • Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313.
  • Wiens JJ, Kuczynski CA, Smith SA, Mulcahy DG, Sites JW, Townsend TM, Reeder TW. 2008. Branch lengths, support, and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes. Syst Biol. 57(3):420–431.

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