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

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 less eggs • Expend less energy

Flightless MtDNA selection relaxation? Flightless Flightless

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?

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

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

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

46 25 172 169 61 99 38 52 53 48 128

Ancient DNA • Gallirallus modestus • Gallirallus dieffenbachi • Porphyrio mantelli

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

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

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�

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�

Amino acid changes, adjusted for branch and gene length

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

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

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

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