biodiversity informatics and prediction of disease dynamics a. townsend peterson natural history...
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Biodiversity Biodiversity Informatics Informatics
and Prediction and Prediction of Disease of Disease DynamicsDynamics A. Townsend PetersonA. Townsend Peterson
Natural History MuseumNatural History Museum
The University of KansasThe University of Kansas
Colleagues and CollaboratorsColleagues and Collaborators UNAMUNAM: Adolfo Navarro, Victor Sanchez-: Adolfo Navarro, Victor Sanchez-
Cordero, Enrique Martinez-Meyer (all UNAM), Cordero, Enrique Martinez-Meyer (all UNAM), Jorge Soberon (UNAM-CONABIO), Janine Jorge Soberon (UNAM-CONABIO), Janine RamseyRamsey
BRAZILBRAZIL: Ricardo Scachetti (CRIA), Jane Costa : Ricardo Scachetti (CRIA), Jane Costa (FIOCRUZ), Jeffrey Shaw (USP)(FIOCRUZ), Jeffrey Shaw (USP)
USAUSA: David Stockwell (SDSC), David Vieglais, : David Stockwell (SDSC), David Vieglais, Ed Wiley, Robert Anderson, Steve Egbert, Ed Wiley, Robert Anderson, Steve Egbert, Miguel Ortega-Huerta, Kris McNyset (all KU), Miguel Ortega-Huerta, Kris McNyset (all KU), Mark Benedict, Ben Beard, Jim Mills, Darin Mark Benedict, Ben Beard, Jim Mills, Darin Carroll (CDC)Carroll (CDC)
Ecological Niche Concept Ecological Niche Concept
The set of environmental conditions, resources, The set of environmental conditions, resources, interactions, etc., in which a species is able to interactions, etc., in which a species is able to maintain populations without immigrationmaintain populations without immigration
Geographical DomainEcological Domain
project
Geographic Space Ecological Space
occurrence points on native distribution
ecological niche modeling
Projection back onto geography
Native range prediction
Invaded range prediction
Essence of Ecological Niche ModelingEssence of Ecological Niche Modeling
temperature
Model of niche in ecological dimensions
pre
cip
itatio
nNote that there are fewer than 500 points … indeed, GARP
works with excellent predictive ability for quite small samples
Factors that Limit Species’ Factors that Limit Species’ DistributionsDistributions
HistoryHistory– Limited dispersalLimited dispersal– SpeciationSpeciation– ExtinctionExtinction
EcologyEcology– Abiotic environmentAbiotic environment– Biotic environmentBiotic environment
InteractionsInteractions– CompetitionCompetition– PredationPredation– ParasitismParasitism– MutualismsMutualisms
Predicting disease Predicting disease dynamicsdynamics
depends critically depends critically on ecological on ecological
niches as long-niches as long-term stable term stable
distributional distributional constraints on constraints on
species’ species’ geographic geographic
potentialpotential
West Nile Virus in West Nile Virus in the New Worldthe New World: :
Analysis of Analysis of Transport Transport
MechanismsMechanisms
West Nile Virus 1999West Nile Virus 1999
West Nile Virus 2000West Nile Virus 2000
West Nile Virus 2001West Nile Virus 2001
West Nile Virus TransportWest Nile Virus Transport
Mosquito-Mosquito-mediated mediated onlyonly
Mosquito- Mosquito- and bird-and bird-mediatedmediated
Mosquito DistributionsMosquito Distributions
Culex pipiens
C. restuans
C. salinarius
Culex Culex Suitability SurfaceSuitability Surface
West Nile Virus 2000West Nile Virus 2000
West Nile Virus 2001West Nile Virus 2001
West Nile Virus Arrival Until 2000West Nile Virus Arrival Until 2000
Spread Without BirdsSpread Without Birds
Winter Destinations of NY Winter Destinations of NY BirdsBirds
Spread With BirdsSpread With Birds
Spread With BirdsSpread With Birds
First Test ResultsFirst Test Results
Mosquito mediation
Mosquitos and Birds
Spring 2002Spring 2002
Successfully reconstructs mid-Atlantic disjunction, SE concentration, spread W to Rockies
Filoviruses …Filoviruses …
Distribution of Filovirus OutbreaksDistribution of Filovirus Outbreaks
Filovirus OutbreaksFilovirus Outbreaks
Filovirus Strain DistributionFilovirus Strain Distribution
Omitting Most Divergent Filovirus (Marburg)Omitting Most Divergent Filovirus (Marburg)
Ecological Distribution of Ebola IEcological Distribution of Ebola I
All of Africa
0
20
40
60
80
8 12 16 20 24 28 32
Annual mean temperature
Ann
ual m
ean
prec
ipita
tion Availability
Ebola
Land Use / Land Cover Types: Land Use / Land Cover Types: Proportion Predicted Appropriate for Proportion Predicted Appropriate for
EbolaEbola
0.00
0.10
0.20
0.30
0.40
0.50
0.60
Evergreenbroadleaf
forest
Woodland Woodedgrassland
Closedshrubland
Openshrubland
Grassland Cropland Bare ground
Pro
po
rtio
n
Ebola RestonEbola Reston
Mammal Reservoir Mammal Reservoir IdentificationIdentification
Species IC Zaire Marburg Sudan RestonFunisciurus anerythrus 1 1 1Funisciurus bayonii ?Funisciurus carruthersi 1 1Funisciurus congicus 1Funisciurus isabella 1Funisciurus lemniscatus 1Funisciurus leucogenys ?Funisciurus pyrropus 1 1 1 1Funisciurus substriatus 1Other Sciurinae 1
Bat Species Coinciding With Bat Species Coinciding With African EbolaAfrican Ebola
Eidolon helvumEpomophorus labiatusEpomops franquetiHypsignathus monstrosusMicropteropus pusillusRousettus aegyptiacusRousettus angolensisMegaloglossus woermanniColeura afraSaccolaimus peliTaphozous mauritianusTaphozous nudiventrisNycteris argeNycteris grandisNycteris hispidaNycteris intermediaNycteris macrotisNycteris majorNycteris nanaLavia frons
Rhinolophus alcyoneRhinolophus fumigatusRhinolophus landeriHipposideros cafferHipposideros commersoniHipposideros cyclopsHipposideros fuliginosusHipposideros ruberKerivoula lanosaChalinolobus poensisChalinolobus variegatusEptesicus capensisEptesicus guineensisEptesicus rendalliEptesicus somalicusEptesicus tenuipinnisMimetillus moloneyiMyotis bocageiMyotis tricolor
Pipistrellus nanusPipistrellus rusticusScotoecus albofuscusScotoecus hirundoScotophilus dinganiiScotophilus nigritaScotophilus robustusScotophilus viridisMiniopterus schreibersiChaerephon bemmeleniChaerephon pumilaMops brachypterusMops condylurusMops midasMops nanulusTadarida aegyptiaca
Example QuestionsExample Questions Emergence of visceral leishmaniasis as an urban Emergence of visceral leishmaniasis as an urban
disease in Brazil … which reservoir species are disease in Brazil … which reservoir species are involved?involved?
Transmission of leprosy in tropical America … Transmission of leprosy in tropical America … what is the role of armadillo distributions in what is the role of armadillo distributions in determining case distribution?determining case distribution?
Risk analysis for hantavirus in Mexico … what is Risk analysis for hantavirus in Mexico … what is the best way to summarize and combine reservoir the best way to summarize and combine reservoir species distributions?species distributions?
Chagas disease … how does a triatomine Chagas Chagas disease … how does a triatomine Chagas vector make the shift from sylvatic to domestic vector make the shift from sylvatic to domestic environments?environments?
And many more …And many more …
Ecological Niche Modeling and DiseasesEcological Niche Modeling and Diseases Large-scale ecological perspective on species’ Large-scale ecological perspective on species’
distributionsdistributions Tool for studyingTool for studying
– geographic distributiongeographic distribution– invasive potentialinvasive potential– effects of changeeffects of change– complex distributional and geographic effectscomplex distributional and geographic effects
Permits reconstruction of disease dynamics based Permits reconstruction of disease dynamics based on the ecological requirements of component on the ecological requirements of component speciesspecies
Demonstrates the critical role that biodiversity Demonstrates the critical role that biodiversity informatics can play in many issues of interest and informatics can play in many issues of interest and importance not just in BIOLOGY, but in public importance not just in BIOLOGY, but in public health and human welfarehealth and human welfare
Thanks ... Thanks ... Any Questions?Any Questions?
[email protected]@ukans.edu