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

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

Jul 06, 2023 169 likes •561 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

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Why fly when you can walk?

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Flightlessness occurs often

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Takahe and Pukeko

Porphyrio

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Pukeko distribution

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Weka and Banded Rail

Gallirallus

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Banded Rail distribution

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Flightless rails:

  • Have shorter wings
  • Are generally bigger
  • Produce less eggs
  • Expend less energy
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MtDNA selection relaxation?

Flightless Flightless Flightless

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PAML: Codeml

  • designate 1 or more

dN/dS ratios (ω) over the tree

  • calculate log likelihood

for the different trees

  • are they significantly

different?

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MtDNA selection relaxation

Significance level Gene *** (p<0.001) CoI ** p(<0.01) ND1 ND4 CoIII cytb * (p<0.05) ND2 ND5 Atp8 not significant (p>0.05) ND3 ND4L ND6 Co2 Atp6 Rag1

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MtDNA selection relaxation

Significance level Gene *** (p<0.001) CoI ** p(<0.01) ND1 ND4 CoIII cytb * (p<0.05) ND2 ND5 Atp8 not significant (p>0.05) ND3 ND4L ND6 Co2 Atp6 Rag1 Significance level Gene *** (p<0.001) cytb ** p(<0.01) ND4 CoI * (p<0.05) ND1 CoIII Atp8 not significant (p>0.05) ND2 ND3 ND4L ND5 ND6 Co2 Atp6 Rag1

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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

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46 25 172 169 61 99 38 52 53 48 128

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Ancient DNA

  • Gallirallus modestus
  • Gallirallus dieffenbachi
  • Porphyrio mantelli
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Future directions

  • Is dN/dS a useful measure – how informative is

it?

  • What is happening with the nuclear-coded

genes?

  • More flightless species:

Ancient DNA

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Thanks for listening!

Phoenix Evolutionary Ecology & Genetics www.evolves.massey.ac.nz

Thanks to: Steve Trewick Juan-Carlos Garcia-Ramirez Dave Wheeler Massey University Rutherford Foundation

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AA changes on branches

20 40 60 80 100 120 140 160 180 200 Gallinula_chloropus

  • Fulica_atra
  • Eulabeornis_castaneoventris

Gallirallus_philippensis Gallirallus_okinawae Gallirallus_australis Lewinia_muelleri Rallina_eurizonoides Coturnicops_exquisitus Porphyrio_porphyrio Porphyrio_hochste eri 8+9 10+11 8+9+10+11 4+5 3+4+5 3+4+5+6 3+4+5+6+7 3+4+5+6+7+8+9+10+11 1+2 1 2 3 4 5 6 7 8 9 1011121314151617181920 ND1 ND2 ND3 ND4L ND4 ND5 ND6 CoI CoII CoIII cytb ATP8 ATP6

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AA changes on branches, adjusted for branch length

2000 4000 6000 8000 10000 12000 14000 16000 Gallinula_chloropus

  • Fulica_atra
  • Eulabeornis_castaneoventris

Gallirallus_philippensis Gallirallus_okinawae Gallirallus_australis Lewinia_muelleri Rallina_eurizonoides Coturnicops_exquisitus Porphyrio_porphyrio Porphyrio_hochste eri 8+9 10+11 8+9+10+11 4+5 3+4+5 3+4+5+6 3+4+5+6+7 3+4+5+6+7+8+9+10+11 1+2 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 ND1 ND2 ND3 ND4L ND4 ND5 ND6 CoI CoII CoIII cytb ATP8 ATP6

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Amino acid changes, adjusted for branch and gene length

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Nuclear genes

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

chicken

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Ancient DNA

  • Gallirallus modestus
  • Gallirallus dieffenbachi
  • Capellirallus karamu
  • Porphyrio mantelli
  • Fulica prisca
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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
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350bp 12S, Trewick 1997

SI takahe Pukeko Weka Dieffenbach’s rail Chatham rail Banded rail NI takahe