aDNA Analysis of Pre-Contact TB
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Transcript of aDNA Analysis of Pre-Contact TB
aDNA Analysis of Pre-aDNA Analysis of Pre-Contact TBContact TB
Frederika Kaestle, Jennifer Raff, Della CookFrederika Kaestle, Jennifer Raff, Della CookIndiana University Departments of Indiana University Departments of
Anthropology and BiologyAnthropology and Biology
Outline of TalkOutline of Talk
Background on TB complex evolutionBackground on TB complex evolution Introduction to tuberculosis in ancient North Introduction to tuberculosis in ancient North
AmericaAmerica Approaches in detecting and analyzing TB Approaches in detecting and analyzing TB
complex DNA from Schild populationcomplex DNA from Schild population Results of ancient TB complex strain Results of ancient TB complex strain
analysisanalysis Implications for evolution of TB complex in Implications for evolution of TB complex in
North AmericaNorth America
How has tuberculosis evolved How has tuberculosis evolved as a human pathogen?as a human pathogen?
Null hypothesis: Null hypothesis: M. M. tuberculosistuberculosis evolved from evolved from M. M. bovisbovis Domestication of Domestication of
cattle allowed jump cattle allowed jump from animal to from animal to human populationshuman populations
How has tuberculosis evolved How has tuberculosis evolved as a human pathogen?as a human pathogen?
Null hypothesis: Null hypothesis: M. M. tuberculosistuberculosis evolved from evolved from M. M. bovisbovis Domestication of Domestication of
cattle allowed jump cattle allowed jump from animal to from animal to human populationshuman populations
From Marmiesse et al., 2004 p 150 (modified from Brosch et al., 2002)
How has tuberculosis evolved How has tuberculosis evolved as a human pathogen?as a human pathogen?
Null hypothesis: Null hypothesis: M. M. tuberculosistuberculosis evolved from evolved from M. M. bovisbovis Domestication of Domestication of
cattle allowed jump cattle allowed jump from animal to from animal to human populationshuman populations
Genomic analysis: Genomic analysis: M. tuberculosisM. tuberculosis older than older than M. bovisM. bovis From Marmiesse et al., 2004 p 150 (modified from Brosch et al., 2002)
How has tuberculosis evolved How has tuberculosis evolved as a human pathogen?as a human pathogen?
Null hypothesis: Null hypothesis: M. M. tuberculosistuberculosis evolved evolved from from M. bovisM. bovis Domestication of cattle Domestication of cattle
allowed jump from allowed jump from animal to human animal to human populationspopulations
Genomic analysis: Genomic analysis: M. M. tuberculosistuberculosis older older than than M. bovisM. bovis Suggests very ancient Suggests very ancient
association between TB association between TB complex, humanscomplex, humans From Marmiesse et al., 2004 p 150 (modified from Brosch et al., 2002)
How has tuberculosis evolved How has tuberculosis evolved in North America?in North America?
Which member(s) of the TB complex Which member(s) of the TB complex infected prehistoric Native infected prehistoric Native Americans?Americans? Was TB brought to the New World in Was TB brought to the New World in
human populations?human populations? M. tuberculosisM. tuberculosis or other predominantly or other predominantly
human infecting specieshuman infecting species Was TB acquired by contact with Was TB acquired by contact with
infected animals?infected animals? M. bovisM. bovis or related species or related species
ApproachApproach
Determine the species of TB complex Determine the species of TB complex present in a pre-contact Native present in a pre-contact Native American population using ancient American population using ancient DNA techniquesDNA techniques Schild: a Late Woodland and Schild: a Late Woodland and
Mississippian burial population from Mississippian burial population from West-Central IllinoisWest-Central Illinois
The Schild site : AD 930-The Schild site : AD 930-13001300
Perino, 1971
Tuberculosis complex infection Tuberculosis complex infection at Schildat Schild
Previous studies (Perino, 1971;Buikstra 1977;Buikstra and Cook, 1978; Cook 1980;Buikstra and Cook 1981; Roberts and Buikstra 2003) have identified pathology consistent with TB complex infection in 11 individuals at Schild.
TB complex infection in individual at right, SB201, confirmed molecularly by Braun et al., 1998
SB201, a 20-25 year old female
MethodsMethods
Extract DNA from Schild skeletons and test Extract DNA from Schild skeletons and test for TB complex infection, using standard for TB complex infection, using standard aDNA precautions.aDNA precautions. Insertion sequence Insertion sequence IS6110IS6110
Amplify and sequence segments of genes Amplify and sequence segments of genes informative to complex evolution and informative to complex evolution and strain discriminationstrain discrimination DNA DNA Gyrase BGyrase B
Extend amplifications in overlapping Extend amplifications in overlapping fragmentsfragments
TB complex infected TB complex infected individualsindividuals
IS6110IS6110 was amplified and was amplified and sequenced from 5.3 % (8) sequenced from 5.3 % (8) of samples tested (n=150).of samples tested (n=150).
7/8 individuals had TB 7/8 individuals had TB lesionslesions
DNA amplified from non-DNA amplified from non-lesion sourceslesion sources
IS6110IS6110 sequence identical sequence identical to TB complex members to TB complex members published in literature. published in literature.
Knoll A: SA41, SA96a, Knoll A: SA41, SA96a, SA141SA141
Knoll B: SB201, SB250, Knoll B: SB201, SB250, SB259a, SB269, SB297SB259a, SB269, SB297
We amplified We amplified GyrBGyrB from four skeletons in from four skeletons in two overlapping two overlapping fragments: SA41, fragments: SA41, SA96a, SB201, SB297SA96a, SB201, SB297 165 base pairs of 165 base pairs of
sequence was sequence was obtained from SA41, obtained from SA41, SB201, SB297SB201, SB297
203 base pairs of 203 base pairs of sequence was sequence was obtained from SA96aobtained from SA96a
GyrB amplification product
SB
297
Neg
. extr
. co
ntr
ol
Neg
. am
plifi
cati
on
co
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Primer-dimer(50bp)
SB
201
GyrB amplification
Neg
. extr
. co
ntr
ol
Neg
. extr
. co
ntr
olS
A96a
Sequence analysisSequence analysis GyrBGyrB sequences showed numerous differences from all sequences showed numerous differences from all
other TB complex members. other TB complex members.
Sequence analysisSequence analysis GyrBGyrB sequences showed numerous differences from all other TB complex members. sequences showed numerous differences from all other TB complex members.
Do not appear more similar to any one species over another: at most 89% similarity to other Do not appear more similar to any one species over another: at most 89% similarity to other MycobacteriaMycobacteria
Samples are distinguished from each other by several polymorphisms, supporting lack of contamination.Samples are distinguished from each other by several polymorphisms, supporting lack of contamination.
Comparison of amino acid sequences of Comparison of amino acid sequences of
GyrB GyrB from ancient and modern from ancient and modern MycobacteriaMycobacteria
--Most changes are synonymous, suggesting purifying selection--Non-synonymous changes (e.g. K to R) conserve amino acid properties, do not alter protein structure significantly at that site.
ConclusionsConclusions A substantial number of individuals from Schild were A substantial number of individuals from Schild were
infected by a member of the TB complex.infected by a member of the TB complex.
Phylogenetic analysis of Phylogenetic analysis of GyrB GyrB sequences recovered from sequences recovered from four infected individuals suggests a long evolutionary four infected individuals suggests a long evolutionary separation from TB complex strains in the Old World.separation from TB complex strains in the Old World.
Cannot distinguish between human or animal origin for TB Cannot distinguish between human or animal origin for TB complex in New World on basis of these resultscomplex in New World on basis of these results
Based upon a survey of the literature, and of GenBank, it Based upon a survey of the literature, and of GenBank, it appears that a novel strain of TB complex was present in appears that a novel strain of TB complex was present in pre-contact North American populationspre-contact North American populations
AcknowledgmentsAcknowledgments
Kaestle LabGraduate StudentsAlison French DoubledayMarisa FennCharla McCormickUndergraduate StudentsJake EnkSam OrrRotation studentsSkye Chang Mike BarnoKate GiestingPK Moua
IUB Faculty Mark Braun Clay Fuqua Armin Moczek Jeff Palmer Rudy Raff Beth Raff Loren Rieseburg Bill Saxton Susan Strome
FundingNSF IGERT Evolution, Development and Genomics Training Grant to JARIUB Anthropology Skomp Research Feasibility Grant to JARIUB Start Up Grant to FAK
CollaboratorsJason EschlemanRipan Malhi