Insights Into Microbial Evolution and Ecology from Genetic Analysis of Diverse Archaeological Materials
Total Page:16
File Type:pdf, Size:1020Kb
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`!D-*#!QHJK! 30#&'"(&455"%,6$12"%&7"(,"$'$#8%#-&HJ!M)C%3>%&!QHJK! ! ! ! Q! ! ! 6.-/0()5(7)"'0"'#( JF! V*'&)?-6'#)*FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!`! JFJ! G*6#%*'!3#6&)>#(.!4%*)3#6$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!L! JFQ! =0#/'#*4!*(&&('#C%$!)*!'0%!)#*$!)/!'->%&6-.)$#$FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!a! JFQFJ! +0%!&#$%!(*?!/(..!)/!'0%!E96)>(6'%&#-3!>)C#$!098)'0%$#$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!a! JFQFQ! G*6#%*'!"MG!(*?!'->%&6-.)$#$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!K! JFQFZ! "#$6&%8(*6#%$!>%'N%%*!?#//%&%*'!.#*%$!)/!%C#?%*6%!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JH! JFZ! G*6#%*'!3%'(4%*)3#6$!)/!0-3(*!3#6&)>#)'(!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JJ! JFZFJ! "%*'(.!6(.6-.-$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JQ! JFZFQ! 7(.%)/%6%$!(*?!6)8&).#'%$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JZ! QF! G#3!)/!'0%!'0%$#$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!J`! ZF! bC%&C#%N!)/!3(*-$6'$!(*?!(-'0)&c$!6)*'&#>-'#)*!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JI! ZFJ! E(*-$6'!G!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JI! ZFQ! E(*-$6'!A!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!J_! ZFZ! E(*-$6'!@!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!Ja! `F! E(*-$6'!G!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!QH! LF! E(*-$6'!A!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!_I! IF! E(*-$6'!@!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JHQ! _F! "#$6-$$#)*!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JZQ! _FJ! @0(..%*4%$!#*!-*6)C%&#*4!'0%!)#*$!)/!'->%&6-.)$#$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JZQ! _FJFJ! G&60(%).)4#6(.!$)-&6%$!)/!E+A@!"MG!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JZQ! _FJFQ! G-'0%*'#6('#)*!(*?!%*C#&)*3%*'(.!396)>(6'%&#(FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JZ`! _FJFZ! @0(..%*4%$!)/!?%3)4&(80#6!#*/%&%*6%!(*?!3).%6-.(&!?('#*4!-$#*4!(*6#%*'!"MG ! JZ`! _FJF`! Y0%&%!')!(#3!/)&!/-'-&%!$'-?#%$FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JZI! _FQ! @0(&(6'%&#d#*4!(*6#%*'!0-3(*!3#6&)>#)'(FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JZ_! _FQFJ! ,(6#.#'('#*4!2-(.#'('#C%!#*'%&8&%'(>#.#'9!)/!.(&4%!3%'(4%*)3#6!?('($%'$!FFFFFFFFFFFFF!JZ_! _FQFQ! e#3#'('#)*$!)/!3)?%&*!?('(>($%$!(*?!'(U)*)3#6!6.($$#/#%&$!FFFFFFFFFFFFFFFFFFFFFFFFFFF!JZa! _FQFZ! V*/%&&#*4!3#6&)>#)3%!?9*(3#6$!(*?!:*)&3(.f!3#6&)>#)3%$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JZa! _FQF`! "%*'#*!($!(!8)'%*'#(.!$)-&6%!/)&!)&(.!3#6&)>%$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JZK! _FZ! @0(..%*4%$!#*!$'-?9#*4!(*6#%*'!%-P(&9)'#6!8(&($#'%$!N#'0!(*6#%*'!"MG!FFFFFFFFFFFFFF!J`H! _F`! @)*6.-$#)*!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!J`J! aF! 1%/%&%*6%$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!J`Z! KF! =-33(&9!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JIQ! JHF! g-$(33%*/($$-*4!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JI`! JJF! h#4%*$'i*?#4P%#'$%&P.(%&-*4!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JII! JQF! @-&-.-3!\#'(%!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!JI_! JZF! G6P*)N.%?43%*'$!FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF!J_J! ! Z! ( 89( !"',)32+'$)"( +0%!$'-?9!)/!0-3(*!0%(.'0!)C%&!'#3%!)//%&$!C(.-(>.%!8('0N(9$!/)&!-*?%&$'(*?#*4! 3-.'#8.%!($8%6'$!)/!0-3(*!%U8%&#%*6%!(*?!>#).)49F!"%'%&3#*#*4!'0%!8&%$%*6%!)/!(!?#$%($%!#*! (*!(*6#%*'!#*?#C#?-(.!)&!6)33-*#'9!6(*!4#C%!-$!#*$#40'$!#*')!?(#.9!.#/%!?-&#*4!'0('!'#3%X!(*?! 6)38(&#*4!0-3(*!3#6&)>#)'(!>%'N%%*!?#//%&%*'!0-3(*!4&)-8$!)C%&!'#3%!(*?!$8(6%!6(*!)//%&! #*$#40'$!#*')!>%0(C#)&!(*?!?#%'F!G$$%$$#*4!'0%!0%(.'0!)/!8($'!8)8-.('#)*$!3(9!8&)C#?%!*%N! 8%&$8%6'#C%$!)*!6)*6)3#'(*'!$)6#(.!)&!8).#'#6(.!60(*4%$X!(*?!6)*'&#>-'%!')!)-&!-*?%&$'(*?#*4! )/!0)N!'0)$%!8)8-.('#)*$!3(*(4%?X!)&!/(#.%?!')!3(*(4%X!6&#$%$!(*?!60(*4%F!b*!(!>&)(?%&! .%C%.X!#?%*'#/9#*4!(*?!#*'%&&)4('#*4!0-3(*#'9c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d(>(.(4(X!QHHQj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kA.(P%.9X!JKaKj!1-44X!QHHH<F!"#$%($%!8&)6%$$%$!6(*!.%(C%!'&(6%$!#*!$-&C#C#*4!$)/'! '#$$-%!#*!'0%!6($%!)/!3-33#/#%?!#*?#C#?-(.$!)&!#*!0(&?!'#$$-%X!(*?!($!0-3(*!&%3(#*$!'0('! $-&C#C%!#*!'0%!(&60(%).)4#6(.!&%6)&?!(&%!3)$'.9!$P%.%')*#d%?X!>)*%!'%*?$!')!>%!'0%!3)$'! 6)33)*!3%?#-3!/&)3!N0#60!8(.%)8('0).)4#$'$!(''%38'!')!?#(4*)$%!?%6%($%?X! (&60(%).)4#6(.!#*?#C#?-(.$F!W)N%C%&X!8('0).)4#6(.!60(*4%$!#*!>)*%!(&%!*)'!(.N(9$!$8%6#/#6!')! (!$#*4.%!6)*?#'#)*!)&!#*/%6'#)*X!(*?!*)'!(..!6)*?#'#)*$!(*?!#*/%6'#)*$!.%(C%!$#4*$!#*!'0%! ! `! "#$%&'()$*&#! ! $P%.%')*F!,)&!'0)$%!6)*?#'#)*$!'0('!10%!.%(C%!$#4*$!#*!'0%!$P%.%')*X!N0%'0%&!)&!*)'!'0#$!)66-&$! ?%8%*?$!)*!*-3%&)-$!/(6')&$X!$-60!($X!/)&!%U(38.%X!'0%!#33-*)6)38%'%*69!)/!'0%! #*?#C#?-(.!)&!'0%!$%C%&#'9!)/!'0%!#*/%6'#)*F!hC%*!#*!'0%!%C%*'!'0('!'0%&%!(&%!8('0)4*)3)*#6! $#4*$!)/!(!$8%6#/#6!#*/%6'#)*!#?%*'#/#%?!#*!(!$P%.%')*#d%?!#*?#C#?-(.X!'0('!#*/)&3('#)*!6(**)'!>%! -$%?!')!#*/%&!%C).-'#)*(&9!?9*(3#6$!)/!'0%!#*/%6'#*4!)&4(*#$3F!! G&60(%)4%*%'#6$X!N#'0!%U#$'#*4!'%60*).)4#%$!(*?!#*!#'$!6-&&%*'!$'('%k)/k'0%k(&'X!6(*!)//%&! ?#&%6'!3).%6-.(&!%C#?%*6%!)/!#*?#C#?-(.!3#6&)>%$!(*?!3#6&)>#(.!6)33-*#'#%$!#*!'0%!8($'F!V/!N%! (&%!(>.%!')!8($$!'0%!'0&%$0).?!)/!(62-#&#*4!'&-$'N)&'09!(*6#%*'!"MGX!N%!6(*!'%..!'0%!$')&9!)/! %C).-'#)*(&9!60(*4%!#*!(!8('0)4%*!?)N*!')!'0%!.%C%.!)/!(!$#*4.%!3-'('#)*X!(*?!#..-$'&('%!'0%! $#3#.(&#'#%$!(*?!?#//%&%*6%$!>%'N%%*!0-3(*k($$)6#('%?!6)33-*#'#%$!)/!3#6&))&4(*#$3$!)C%&! '#3%!(*?!$8(6%F!W)N%C%&X!3#6&)>#(.!(&60(%)4%*%'#6$!#$!$'#..!(!9)-*4!/#%.?F!+0#$!'0%$#$! #..-$'&('%$!'0%!8)'%*'#(.!)/!(*6#%*'!"MG!')!(*$N%&!&%.%C(*'!2-%$'#)*$!(>)-'!0-3(*!0%(.'0!>9! d))3#*4!#*!')!(!$#*4.%!8('0)4%*!4%*)3%!%*<%?!/&)3!(!3%'(4%*)3#6!>(6P4&)-*?!(*?! d))3#*4!)-'!')!N0).%!3#6&)>#(.!6)33-*#'#%$!%U'&(6'%?!/&)3!(&60(%).)4#6(.!3('%&#(.$F!W%&%X! '0%!)#*$!)/!(!/(3#.9!)/!8('0)4%*$!l!'0%!9:1*;01,"($8+&,8;"(186*/$/&6)38.%U!;E+A@<!l!#$! /-&'0%&!%.-6#?('%?!N#'0!(!$#*4.%!(*6#%*'!4%*)3%X!(*?!3%'(4%*)3#6$!#$!.%C%&(4%?!')!%U8.)&%! 8&%$%&C('#)*!?9*(3#6$!/)&!0-3(*k($$)6#('%?!3#6&)>#(.!"MG!#*!?#//%&%*'!(&60(%).)4#6(.! 6)*'%U'$F!+0%!%*6.)$%?!8&)m%6'$!%3%&4%?!/&)3!3%'(4%*)3#6!$0)'4-*!$6&%%*#*4!)/!"MG! %U'&(6'%?!/&)3!(!6(.6#/#%?!.-*4!*)?-.%X!?%*'#*X!?%*'(.!6(.6-.-$X!(*?!>-.P!.('&#*%!$%?#3%*'$F!