@misc{HuynenSuzukiOguraetal.2014,
  author    = {Huynen, Leon and Suzuki, Takayuki and Ogura, Toshihiko and Watanabe, Yusuke and Millar, Craig D. and Hofreiter, Michael and Smith, Craig and Mirmoeini, Sara and Lambert, David M.},
  title     = {Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes)},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1117},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43159},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431599},
  pages     = {10},
  year      = {2014},
  abstract  = {Background The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures. Results To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya. Conclusions The results suggests that, as in mice, moa tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa's remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa.},
  language  = {en}
}
@article{HuynenSuzukiOguraetal.2014,
  author    = {Huynen, Leon and Suzuki, Takayuki and Ogura, Toshihiko and Watanabe, Yusuke and Millar, Craig D. and Hofreiter, Michael and Smith, Craig and Mirmoeini, Sara and Lambert, David M.},
  title     = {Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes)},
  series = {BMC evolutionary biology},
  volume    = {14},
  journal   = {BMC evolutionary biology},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2148},
  doi       = {10.1186/1471-2148-14-75},
  pages     = {8},
  year      = {2014},
  abstract  = {Background: The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures. Results: To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya.},
  language  = {en}
}
@article{LeDucRenaudKrishnanetal.2015,
  author    = {Le Duc, Diana and Renaud, Gabriel and Krishnan, Arunkumar and Almen, Markus Sallman and Huynen, Leon and Prohaska, Sonja J. and Ongyerth, Matthias and Bitarello, Barbara D. and Schioth, Helgi B. and Hofreiter, Michael and Stadler, Peter F. and Pr{\"u}fer, Kay and Lambert, David and Kelso, Janet and Sch{\"o}neberg, Torsten},
  title     = {Kiwi genome provides insights into evolution of a nocturnal lifestyle},
  series = {Genome biology : biology for the post-genomic era},
  volume    = {16},
  journal   = {Genome biology : biology for the post-genomic era},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1465-6906},
  doi       = {10.1186/s13059-015-0711-4},
  pages     = {15},
  year      = {2015},
  abstract  = {Background: Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. Results: We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi's odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle. Conclusions: The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.},
  language  = {en}
}