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when you can walk? Flightlessness occurs often Takahe and Pukeko - PowerPoint PPT Presentation

Jul 06, 2023 •169 likes •558 views

Why fly when you can walk? Flightlessness occurs often Takahe and Pukeko Porphyrio Pukeko distribution Weka and Banded Rail Gallirallus Banded Rail distribution Flightless rails: Have shorter wings Are generally bigger Produce

  1. Why fly when you can walk?

  3. Flightlessness occurs often

  4. Takahe and Pukeko Porphyrio

  5. Pukeko distribution

  6. Weka and Banded Rail Gallirallus

  7. Banded Rail distribution

  9. Flightless rails: • Have shorter wings • Are generally bigger • Produce less eggs • Expend less energy

  12. Flightless MtDNA selection relaxation? Flightless Flightless

  13. PAML: Codeml • designate 1 or more d N /d S ratios ( ω ) over the tree • calculate log likelihood for the different trees • are they significantly different?

  14. MtDNA selection relaxation Significance level Gene *** (p<0.001) CoI ** p(<0.01) ND1 ND4 CoIII cyt b * (p<0.05) ND2 ND5 Atp8 not significant (p>0.05) ND3 ND4L ND6 Co2 Atp6 Rag1

  15. MtDNA selection relaxation Significance level Gene *** (p<0.001) CoI ** p(<0.01) ND1 ND4 CoIII cyt b * (p<0.05) ND2 ND5 Atp8 not significant (p>0.05) ND3 ND4L ND6 Co2 Atp6 Rag1 Significance level Gene *** (p<0.001) cyt b ** p(<0.01) ND4 CoI * (p<0.05) ND1 CoIII Atp8 not significant (p>0.05) ND2 ND3 ND4L ND5 ND6 Co2 Atp6 Rag1

  17. NADH 1-6 Cyt b COI-III Atp 6&8 ** p<0.01 NADH all *** p<0.001 COX all ** p<0.01 Atp all

  18. 46 25 172 169 61 99 38 52 53 48 128

  20. Ancient DNA • Gallirallus modestus • Gallirallus dieffenbachi • Porphyrio mantelli

  21. Future directions • Is d N /d S a useful measure – how informative is it? • What is happening with the nuclear-coded genes? • More flightless species: Ancient DNA

  22. Thanks for listening! Thanks to: Steve Trewick Juan-Carlos Garcia-Ramirez Dave Wheeler Phoenix Evolutionary Ecology & Genetics Massey University www.evolves.massey.ac.nz Rutherford Foundation

  23. AA changes on branches 1� 2� 3� 4� 5� 6� 7� 8� 9� 10�11�12�13�14�15�16�17�18�19�20� 1+2� 3+4+5+6+7+8+9+10+11� 3+4+5+6+7� ND1� 3+4+5+6� ND2� 3+4+5� 4+5� ND3� 8+9+10+11� ND4L� 10+11� ND4� 8+9� ND5� Porphyrio_hochste eri� ND6� Porphyrio_porphyrio� Coturnicops_exquisitus� CoI� Rallina_eurizonoides� CoII� Lewinia_muelleri� CoIII� Gallirallus_australis� cytb� Gallirallus_okinawae� Gallirallus_philippensis� ATP8� Eulabeornis_castaneoventris� ATP6� Fulica_atra� � Gallinula_chloropus� � 0� 20� 40� 60� 80� 100� 120� 140� 160� 180� 200�

  24. AA changes on branches, adjusted for branch length 1� 2� 3� 4� 5� 6� 7� 8� 9� 10� 11� 12� 13� 14� 15� 16� 17� 18� 19� 20� 1+2� 3+4+5+6+7+8+9+10+11� 3+4+5+6+7� 3+4+5+6� ND1� 3+4+5� ND2� 4+5� ND3� 8+9+10+11� ND4L� 10+11� ND4� 8+9� ND5� Porphyrio_hochste eri� ND6� Porphyrio_porphyrio� CoI� Coturnicops_exquisitus� Rallina_eurizonoides� CoII� Lewinia_muelleri� CoIII� Gallirallus_australis� cytb� Gallirallus_okinawae� ATP8� Gallirallus_philippensis� ATP6� Eulabeornis_castaneoventris� Fulica_atra� � Gallinula_chloropus� � 0� 2000� 4000� 6000� 8000� 10000� 12000� 14000� 16000�

  25. Amino acid changes, adjusted for branch and gene length

  26. Nuclear genes • AmiGO gene ontology database • 79 genes associated with limb development in chicken

  33. Ancient DNA • Gallirallus modestus • Gallirallus dieffenbachi • Capellirallus karamu • Porphyrio mantelli • Fulica prisca

  37. Predicted number of reads… • Gallirallus modestus 4.2 million • Gallirallus dieffenbachi 16 million • Capellirallus karamu 5.5 million • Porphyrio mantelli 18 million • Fulica prisca 5.7 million

  38. Dieffenbach ’ s rail Chatham rail Banded rail Weka SI takahe Pukeko NI takahe 350bp 12S, Trewick 1997

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