Complete mitochondrial genomes offer insights into the evolutionary relationships and comparative genetic diversity of New Zealand’s iconic kiwi (Apteryx spp.)

References

• Alvarenga HMF. 1983. Uma ave ratitae do Paleoceno Brasileiro: bada calcarla de Itaboraí, Estado do Rio de Janeiro, Brasil. Boletim do Museu Nacional de Rio de Janeiro Geologia. 41:1–11.
   Google Scholar
• Bergsten J. 2005. A review of long-branch attraction. Cladistics. 21(2):163–193.
   PubMed Web of Science ®Google Scholar
• Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):313–319.
   PubMed Web of Science ®Google Scholar
• Boles WE. 1992. Revision of Dromaius gidju Patterson and Rich 1987 from Riversleigh, northwestern Queensland, Australia, with a reassessment of its generic position. Natural History Museum of LA County Science Series. 36:195–208.
   Google Scholar
• Buller SWL, Keulemans JG. 1888. A history of the birds of New Zealand. Selbstverl.
   Google Scholar
• Chevreux B, Wetter T, Suhai S. Others 1999. Genome sequence assembly using trace signals and additional sequence information. German Conference on Bioinformatics. 99:45–56.
   Google Scholar
• Colbourne R. 2005. Kiwi (Apteryx spp.) on offshore New Zealand islands. NZ Dep Conserv Res Dev Ser. 208. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.214.4423&rep=rep1&type=pdf.
   Google Scholar
• Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J, Ward R. 2001. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature. 409(6821):704–707.
   PubMed Web of Science ®Google Scholar
• Cooper RA, Millener PR. 1993. The New Zealand biota: Historical background and new research. Trends Ecol Evol. 8(12):429–433.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7(1):214–214.
   PubMed Web of Science ®Google Scholar
• Grealy A, Phillips M, Miller G, Gilbert MTP, Rouillard J-M, Lambert D, Bunce M, Haile J. 2017. Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Mol Phylogenet Evol. 109:151–163.
   PubMed Web of Science ®Google Scholar
• Haddrath O, Baker AJ. 2001. Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proc Biol Sci. 268(1470):939–945.
   PubMed Web of Science ®Google Scholar
• Haddrath O, Baker AJ. 2012. Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an early Cretaceous origin of modern birds. Proc Biol Sci. 279(1747):4617–4625.
   PubMed Web of Science ®Google Scholar
• Hahn C, Bachmann L, Chevreux B. 2013. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Res. 41(13):e129–e129.
   PubMed Web of Science ®Google Scholar
• Hurles ME, Matisoo-Smith E, Gray RD, Penny D. 2003. Untangling Oceanic settlement: the edge of the knowable. Trends Ecol Evol. 18(10):531–540.
   Web of Science ®Google Scholar
• Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO. 2012. The global diversity of birds in space and time. Nature. 491(7424):444–448.
   PubMed Web of Science ®Google Scholar
• Jiang H, Lei R, Ding S-W, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 15(1):182–182.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
   PubMed Web of Science ®Google Scholar
• Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649.
   PubMed Web of Science ®Google Scholar
• Korneliussen TS, Albrechtsen A, Nielsen R. 2014. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics. 15(1):356–356.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA x: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 35(6):1547–1549.
   PubMed Web of Science ®Google Scholar
• Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. 2017. Partitionfinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol. 34(3):772–773.
   PubMed Web of Science ®Google Scholar
• Lanfear R, Welch JJ, Bromham L. 2010. Watching the clock: studying variation in rates of molecular evolution between species. Trends Ecol Evol. 25(9):495–503.
   PubMed Web of Science ®Google Scholar
• Leigh JW, Bryant D. 2015. popart: full-feature software for haplotype network construction. Methods Ecol Evol. 6(9):1110–1116.
   Web of Science ®Google Scholar
• Lewis AR, Marchant DR, Ashworth AC, Hedenäs L, Hemming SR, Johnson JV, Leng MJ, Machlus ML, Newton AE, Raine JI, et al. 2008. Mid-Miocene cooling and the extinction of tundra in continental Antarctica. Proc Natl Acad Sci U S A. 105(31):10676–10680.
   PubMed Web of Science ®Google Scholar
• Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–wheeler transform. Bioinformatics. 25(14):1754–1760.
   PubMed Web of Science ®Google Scholar
• Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. 1000 genome Project data Processing Subgroup. The Sequence Alignment/Map Format and SAMtools. Bioinformatics. 25(16):2078–2079.
   PubMed Web of Science ®Google Scholar
• Mindell DP, Sorenson MD, Dimcheff DE. 1998. An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles. Mol Biol Evol. 15(11):1568–1571.
   PubMed Web of Science ®Google Scholar
• Mitchell KJ, Llamas B, Soubrier J, Rawlence NJ, Worthy TH, Wood J, Lee MSY, Cooper A. 2014. Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution. Science. 344(6186):898–900.
   PubMed Web of Science ®Google Scholar
• Nabholz B, Glémin S, Galtier N. 2008. Strong Variations of mitochondrial mutation rate across Mammals—the Longevity Hypothesis. Mol Biol Evol. 25(1):120–130.
   PubMed Web of Science ®Google Scholar
• Peat N. 1990. The incredible kiwi: A wild south book. Random Century.
   Google Scholar
• Phillips MJ, Gibb GC, Crimp EA, Penny D. 2010. Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Syst Biol. 59(1):90–107.
   PubMed Web of Science ®Google Scholar
• Rambaut A, Suchard MA, Xie D, Drummond AJ. 2013. Tracer 1.6. Edinburgh: University of Edinburgh.
   Google Scholar
• Ramstad KM, Miller HC, Kolle G. 2016. Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds. BMC Genomics. 17(1):410–410.
   PubMed Web of Science ®Google Scholar
• Ramstad KM, Pfunder M, Robertson HA, Colbourne RM, Allendorf FW, Daugherty CH. 2010. Fourteen microsatellite loci cross-amplify in all five kiwi species (Apteryx spp.) and reveal extremely low genetic variation in little spotted kiwi (A. owenii). Conserv Genet Resour. 2(1):333–336.
   Web of Science ®Google Scholar
• Robertson HA, Baird K, Dowding JE, Elliott GP, Hitchmough RA, Miskelly CM, McArthur N, O’Donnell CFJ, Sagar PM, Scofield RP, et al. 2017. Conservation status of New Zealand birds, 2016. https://www.doc.govt.nz/documents/science-and-technical/nztcs19entire.pdf.
   Google Scholar
• Sackton TB, Grayson P, Cloutier A, Hu Z, Liu JS, Wheeler NE, Gardner PP, Clarke JA, Baker AJ, Clamp M, et al. 2019. Convergent regulatory evolution and loss of flight in paleognathous birds. Science. 364(6435):74–78.
   PubMed Web of Science ®Google Scholar
• Schmieder R, Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 27(6):863–864.
   PubMed Web of Science ®Google Scholar
• Shepherd LD, Lambert DM. 2008. Ancient DNA and conservation: lessons from the endangered kiwi of New Zealand. Mol Ecol. 17(9):2174–2184.
   PubMed Web of Science ®Google Scholar
• Shepherd LD, Worthy TH, Tennyson AJD, Scofield RP, Ramstad KM, Lambert DM. 2012. Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp.) and a recently extinct lineage of spotted kiwi. PLoS One. 7(8):e42384–e42384.
   PubMed Web of Science ®Google Scholar
• Shevenell AE, Kennett JP, Lea DW. 2004. Middle Miocene Southern Ocean cooling and Antarctic cryosphere expansion. Science. 305(5691):1766–1770.
   PubMed Web of Science ®Google Scholar
• Tennyson AJD. 2010. The origin and history of New Zealand’s terrestrial vertebrates. N Z J Ecol. 34(1):6–6.
   Web of Science ®Google Scholar
• Weir JT, Haddrath O, Robertson HA, Colbourne RM, Baker AJ. 2016. Explosive ice age diversification of kiwi. Proc Natl Acad Sci U S A. 113(38):E5580–7.
   PubMed Web of Science ®Google Scholar
• Worthy TH, Holdaway RN. 2002. The lost world of the Moa: Prehistoric life of New Zealand. Bloomington, IN: Indiana University Press.
   Google Scholar
• Zachos J, Pagani M, Sloan L, Thomas E, Billups K. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science. 292(5517):686–693.
   PubMed Web of Science ®Google Scholar