Genomics insights into the evolutionary success of bats
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BAT1K break-out session at the G10K meeting, 29 August 2019
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Genomics insights into the evolutionary success of bats
- 1. The genomics of why there are so many species of bats Liliana M. Dávalos + the Bat1K Team BAT1K Break-Out Session Rockefeller University 29 August 2019
- 2. The genomics of why there are so many species of bats Liliana M. Dávalos + Huang Zixia, David Jebb, Martin Pippel, Graham Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars Jermiin, Emilia Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David Ray, Juliana G Roscito, Bogdan Kirilenko, Angelique P. Corthals, Megan Power, Gareth Jones, Roger Ransome, Dina Dechmann, Andrea Locatelli, Erich Jarvis, Mark Springer, Michael Hiller, Sonja Vernes, Eugene Myers, Emma Teeling
- 3. Credits: Merlin Tuttle/Bat Conservation International, Bryan Bongey
- 4. Four facts about bats • Bats fly • Bats are crepuscular/ nocturnal • Bats live longer than expected by size • Viral pathogens circulate among bats • That kill other mammals Photo by S.J. Rossiter
- 5. Why are there so many bat species? • How to answer a question like this? Photo by Winifred Frick
- 6. The ecological theory of adaptive radiation Simpson 1953 Major features of evolution Drawings by John Gould
- 7. Credits: Merlin Tuttle/Bat Conservation International, Bryan Bongey
- 8. Nycteridae Emballonuridae Phyllostomidae Mormoopidae Noctilionidae Furipteridae ThyropteridaeM ystacinidae M yzopodidae Vespertilionidae NatalidaePteropodidae Rhinolophidae M egaderm atidae Craseonycteridae Rhinopomatidae Miniopteridae Molossidae Rhinonycteridae Hipposideridae Cistugidae Bat1K Drawings by Fiona Reid Yangochiroptera Yinpterochiroptera
- 10. A pipeline for testing hypotheses 0 20 40 60 80 100 1k 20 40 60 80 100 N(x) % N(x) % Recent transposon insertions (fraction of genome) DNA LINE LTR Rolling−circle SINE or Retroposon Unknown no transposon Completeness of non-exonic regions in assemblies (197 non-exonic ultraconserved elements) Canis Equus Sus Rhinolophus Rousettus Phyllostomus Molossus Pipistrellus Myotis Bos Felis present missing due to assembly gap diverged sequence Bat1K Canis Mus Homo Equus Sus Rhinolophus Rousettus Phyllostomus Pipistrellus Myotis Bos Felis Bat1K Molossus 19235 21893 19113 20386 20742 19122 21182 20953 19577 21303 21423 19823 20221 10095 96 97 98 99 complete fragmented missing Completeness of gene annotations (4104 BUSCO genes in %) Number of annotated genes Sus Bos Equus Felis Canis Mus Homo Myotis Molossus Phyllostomus Rousettus Rhinolophus Pipistrellus Bat1K CESAR aBSREL
- 11. Nycteridae Emballonuridae Phyllostomidae Mormoopidae Noctilionidae Furipteridae ThyropteridaeM ystacinidae M yzopodidae Vespertilionidae Natalidae Rhinolophidae M egaderm atidae Craseonycteridae Rhinopomatidae Miniopteridae Molossidae Cistugidae Bat1K back sign Biological process biological adhesion biological regulation cell proliferation cellular component organization or biogenesis developmental process immune system process localization metabolic process multicellular organismal process other reproduction response to stimulus Drawings by Fiona Reid Credits: Merlin Tuttle/Bat Conservation International, Bryan Bongey
- 12. Nycteridae Emballonuridae Pteropodidae Rhinolophidae M egaderm atidae Craseonycteridae Rhinopomatidae Rhinonycteridae Hipposideridae Ba back sign Biological process biological adhesion biological regulation cell proliferation cellular component organization or biogenesis developmental process immune system process localization metabolic process multicellular organismal process other reproduction response to stimulus Drawings by Fiona Reid Credits: Hélder Conceição
- 13. Nycteridae Emballonuridae Pteropodidae Rhinolophidae M egaderm atidae Craseonycteridae Rhinopomatidae Rhinonycteridae Hipposideridae Ba back sign Biological process biological adhesion biological regulation cell proliferation cellular component organization or biogenesis developmental process immune system process localization metabolic process multicellular organismal process other reproduction response to stimulus Drawings by Fiona Reid Credits: Joel Sartore
- 14. Yinpterochiroptera • No positively selected genes • No disproportionate “hearing” signal • Pre-adaptation for constant-frequency echolocation • Instead, diet does have clear signal Photo by H. Conceção
- 15. back sign Biological process biological adhesion biological regulation cell proliferation cellular component organization or biogenesis developmental process immune system process localization metabolic process multicellular organismal process other reproduction response to stimulus Yangochiroptera Credits: Friedrich Seidler, Marco Mello
- 16. back sign Biological process biological adhesion biological regulation cell proliferation cellular component organization or biogenesis developmental process immune system process localization metabolic process multicellular organismal process other reproduction response to stimulus Vespertilionidae Credits: Friedrich Seidler, Jorge Espier
- 17. Mormoopidae Noctilionidae Furipteridae ThyropteridaeM ystacinidae M yzopodidae Vespertilionidae Natalidae Miniopteridae Molossidae Cistugidae Bat1K back sign Biological process biological adhesion biological regulation cell proliferation cellular component organization or biogenesis developmental process immune system process localization metabolic process multicellular organismal process other reproduction response to stimulus Drawings by Fiona Reid Credits: Jorge Espier
- 18. Mormoopidae Noctilionidae Furipteridae ThyropteridaeM ystacinidae M yzopodidae Vespertilionidae Natalidae Miniopteridae Molossidae Cistugidae Bat1K back sign Biological process biological adhesion biological regulation cell proliferation cellular component organization or biogenesis developmental process immune system process localization metabolic process multicellular organismal process other reproduction response to stimulus Drawings by Fiona Reid Credits: Merlin Tuttle
- 19. Nycteridae Emballonuridae Phyllostomidae Mormoopidae Noctilionidae Furipteridae ThyropteridaeM ystacinidae M yzopodidae Vespertilionidae Natalidae Rhinolophidae M egaderm atidae Craseonycteridae Rhinopomatidae Miniopteridae Molossidae Cistugidae Bat1K back sign Biological process biological adhesion biological regulation cell proliferation cellular component organization or biogenesis developmental process immune system process localization metabolic process multicellular organismal process other reproduction response to stimulus Drawings by Fiona Reid Credits: Marco Mello
- 20. Yangochiroptera • Several positively selected genes • e.g., immune process • Vesper positive in metabolic process • Signal of hibernation? • Diet shift also evident in Phyllostomus Photo by S.J. Rossiter
- 21. ACSL6 ADGRG7 AMPD2 ANPEP ASAH2 BCL11A BLOC1S1 CCNB3 CD79BCDHR5CDSNCOG5COX20CRNN CX3CL1CXCL13 CYBBDDOST DGKI DTX3L EFR3B EIF3A ESPL1 FBLL1 FLVCR2 GID4 GP1BA IDH3B IDO1 IGF1R ITGB2 KCNK7 LACRT LAS1L MAGED2 MBD1 MKRN3 MRPL234UEN PAPOLG PARD6G PCDHA6 PCDHGB5 PDE10A PDZD2 PLEC PRDM11 REST RFWD3 RTP4 SELP SI SLC12A4 SLC9A8 SM R 3A SPAG 8SPAM 1SYNCTACC1 TBC1D12TBPTEAD1TJP2 TLR8 TOR4A TPTE2 UGT1A7 UGT1A9 YRDC ZDHHC1 ZNF691 biological adhesion biological regulation cellproliferation nentorganizationorbiogenesis developmentalimmunesystem localization metabolic m ulticellular organism al reproduction response to stimulus ancestral tip both Branch
- 22. Back to the ecological theory • Bats fly • Bats are crepuscular/ nocturnal • New niche! • Opportunity but challenge • “hearing” adaptations Photo by J. Flanders
- 23. Back to the ecological theory • Bats live longer than expected by size • Hibernation? • Viral pathogens circulate among bats • That kill other mammals • Immune process genes at origin of bats Photo by S.J. Rossiter
- 24. Three challenges • Diversity • Function • Correlation Photo by S.J. Rossiter
- 25. Mormoopidae Macrotinae Rhinophyllinae Stenodermatinae Carolliinae Phyllostominae Noctilionidae Micronycterinae Desmodontinae Glyphonycterinae Lonchorhininae Glossophaginae Million Years Ago 5 10 15 20 25 30 35 40 45 95% CI Node Age Lonchophyllinae Dumont, Dávalos et al. 2012 Proc R Soc Lond B Biol Sci
- 27. Scale collection to address lack of replication Yohe et al. 2019 JoVE
- 28. Thanks!