Stefan Prost presentation for the #ICG13 GigaScience Prize Track: Genome analyses show strong selection on coloration, morphological and behavioral phenotypes in birds-of-paradise. Shenzhen, 26th October, 2018

1. Comparative Genomics of Birds of Paradise
Genome analyses show strong selection on coloration, morphological and behavioral
phenotypes in birds-of-paradise.
Stefan Prost 1,2,3
1Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany
2Department of Integrative Biology, University of California, Berkeley, USA
3SANBI National Zoological Garden, Pretoria, South Africa
October 25th, 2018
Stefan Prost stefan.prost@berkeley.edu

2. Comparative Genomics of Birds of Paradise
Genome analyses show strong selection on coloration, morphological and behavioral phenotypes in birds-of-paradise.
Prost, S., Armstrong, E.E., Nylander, J., Thomas, G., Suh, A.S., Petersen, B., Dalen, L., Benz, B., Blom, M.,
Palkopoulou, E., Ericson, P.G.P. and Irestedt, M. - (2018) BioRxiv
Stefan Prost stefan.prost@berkeley.edu

3. Comparative Genomics of Birds of Paradise
Stefan Prost stefan.prost@berkeley.edu

4. Comparative Genomics of Birds of Paradise
Heads 2002, Journal of Biogeography
Stefan Prost stefan.prost@berkeley.edu

5. Comparative Genomics of Birds of Paradise
0.1
Paradisaea apoda
Paradisaea raggiana
0.88
Paradisaea minor
Paradisaea rubra
0.83
Paradisaea guilielmi
Paradisaea rudolphi
0.85
Diphyllodes magnificus
Diphyllodes respublica
Cicinnurus regius
Astrapia nigra
Astrapia splendidissima
Astrapia rothschildi
Astrapia stephaniae
0.82
0.98
Paradigalla brevicauda
Paradigalla carunculata
Epimachus fastuosus
Epimachus meyeri
Ptiloris intercedens
Ptiloris magnificus
Lophorina superba
0.65
Ptiloris paradiseus
Ptiloris victoriae
Semioptera wallacii
0.64
Drepanornis albertisi
Drepanornis bruijnii
Seleucidis melanoleucus
0.60
0.96
Parotia helenae
Parotia lawesii
0.96
Parotia sefilata
Parotia wahnesi
0.67
Parotia carolae
0.82
Pteridophora alberti
Manucodia ater
Manucodia jobiensis
0.97
Manucodia chalybatus
Phonygammus keraudrenii
0.99
Lycocorax pyrrhopterus
Corvus
Monarcha
0.87
Dicrurus
Gymnorhina
Batis
Passer
A
B
C
D
E
Irestedt et al. 2009
Stefan Prost stefan.prost@berkeley.edu

6. Comparative Genomics of Birds of Paradise
Stefan Prost stefan.prost@berkeley.edu

7. Comparative Genomics of Birds of Paradise
Stefan Prost stefan.prost@berkeley.edu

8. Comparative Genomics of Birds of Paradise
Stefan Prost stefan.prost@berkeley.edu

9. Comparative Genomics of Birds of Paradise
Xu et al. in prep
Xu et al. in prep
Stefan Prost stefan.prost@berkeley.edu

10. Comparative Genomics of Birds of Paradise
Stefan Prost stefan.prost@berkeley.edu

11. Comparative Genomics of Birds of Paradise
Positive Selection:
213 genes under positive selection only in birds-of-paradise (out of 8,134 genes)
42 remained significant after multiple-testing correction (FDR, <0.05)
Functions: coloration, feather and bone development, eye development, innate
immune response, etc.
Gene Family Expansion/Contraction:
18 significantly expanded gene families on the branch to the birds-of-paradise
21 significantly expanded gene families on the branch to the core
birds-of-paradise
Functions: startle response/locomotory behavior, odor receptors, etc.
Stefan Prost stefan.prost@berkeley.edu

12. Comparative Genomics of Birds of Paradise
Phase II: Sequenced 42 species - phylogeny and adaptive introgression (Mozes
Blom, NRM Stockholm)
Sex Chromosome Evolution - (Qi Zhou and Luohao Xu, University of Vienna
and Zhejiang University)
Evolution of Repeats on Sex Chromosomes - De novo assembly of the paradise
crow with pacbio, bionano and HiC (Alex Suh, Uppsala University)
Stefan Prost stefan.prost@berkeley.edu

13. Comparative Genomics of Birds of Paradise
Acknowledgements
Martin Irestedt (NRM, Sweden)
Per GP Ericson (NRM, Sweden)
Ellie E Armstrong (Stanford, USA)
Johan Nylander (NRM, Sweden)
Gregg WC Thomas (Indiana University, USA)
Alexander Suh (Uppsala University, SWE)
Bent Petersen (GeoScience, DEN)
Love Dalen (NRM, Sweden)
Brett W Benz (ANHM, USA)
Mozes PK Blom (NRM, Sweden)
Eleftheria Palkopoulou (NRM, Sweden)
Luoha Xu (Zhejiang University)
Qi Zhou (Zhejiang University)
and others
Photos by: Con Foley, Eric Baccega, Phil Savoie,
Bruce Beehler, Tim Laman, Fabrice Tortey and Tony
Tilford (www.arkive.org)
Stefan Prost stefan.prost@berkeley.edu