Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny.
Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a 'traditional' Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina's HiSeq and MiSeq, Roche's 454 GS FLX, and Life Technologies' Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case.
Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom.|Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom.|Department of Animal Management, Reaseheath College, Nantwich, CW5 6DF, United Kingdom.
Simon T
ST
Maddock
Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom.
Andrew G
AG
Briscoe
Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom.
Mark
M
Wilkinson
Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom.
Andrea
A
Waeschenbach
Department of Zoology and Physical Anthropology, Complutense University of Madrid, 28040, Madrid, Spain.
Diego
D
San Mauro
Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom.
Julia J
JJ
Day
Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom.
D Tim J
DT
Littlewood
Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom.
Peter G
PG
Foster
Museum of Zoology, University of Michigan, Ann Arbor, MI, 48109-1079, United States of America.|Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109-1079, United States of America.
Ronald A
RA
Nussbaum
Department of Life Sciences, Natural History Museum, London, SW7 5BD, United Kingdom.
David J
DJ
Gower
D000663:Amphibians / Q000145:classification / Q000235:genetics*; D000818:Animals; D001499:Bayes Theorem; D004272:DNA, Mitochondrial / Q000235:genetics*; D005819:Genetic Markers; D014644:Genetic Variation; D054629:Genome, Mitochondrial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D012750:Seychelles; D013045:Species Specificity
D004272:DNA, Mitochondrial; D005819:Genetic Markers