
Comparative and Population Genomics of Host-Pathogen Co-Evolution in Birds The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Shultz, Allison Jane. 2017. Comparative and Population Genomics of Host-Pathogen Co-Evolution in Birds. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:41142072 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use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`! ! /6"7),3!9! a4#/+!0+,#$+!2+A.+,1),0!'+*+&/2!'+1+,(!2)0,&(.'+2!#3!-+$#0'&%48!&,-!%#/80+,)1! 2+/+1()#,!),!(4+!D#.2+!S),14__________________________________N^W! ! ! /6"7),3!:! ?*#/.()#,!#3!(4+!),,&(+!)$$.,+!282(+$!&1'#22!(4+!6)'-!('++!#3!/)3+_____________NWX! ! ! /-0/+512-01_NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNJHW! ! ! "77,042;!8! :.%%/+$+,(&'8!$&(+')&/2F!"4&%(+'!JNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNJ^J! ! ! "77,042;!9! :.%%/+$+,(&'8!$&(+')&/2F!"4&%(+'!HNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNJ^H! ! ! "77,042;!:! :.%%/+$+,(&'8!$&(+')&/2F!"4&%(+'!^NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNJ^X! ! ! 3,.,3,0/,1NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNJYH! ! ! *! ! "/<0-=+,4>,?,0)1! ! R!Q#./-!/)\+!(#!(4&,\!$8!1#$$)((++!3#'!&//!#3!(4+!4&'-!Q#\!&,-!(4+)'!&22)2(&,1+!Q)(4!$8! -)22+'(&()#,!&,-!6+8#,-N!!='N!?-Q&'-2F!(4&,\!8#.!3#'!8#.'!+V%+'()2+F!0.)-&,1+F!&,-!&-*)1+! Q4+,+*+'!R!,++-+-!)(!),!'+0&'-2!(#!$8!'+2+&'14F!(4+!3)+/-!),!0+,+'&/F!#'!$8!%/&,2!3#'!(4+! 3.(.'+N!!='N!a&\+/+8F!(4&,\!8#.!3#'!8#.'!+V%+'()2+F!),%.(F!&,-!Q)//),0,+22!(#!2+'*+!&2!BR!3#'! $8!]:S!==RZN!!='N!D#+\2('&F!(4&,\!8#.!3#'!8#.'!),%.(!&,-!&-*)1+N! ! :%+1)&/!(4&,\2!(#!$8!3.,-),0!2#.'1+2N!!<4)2!'+2+&'14!Q&2!3.,-+-!),!%&'(!68!(4+! ]&()#,&/!:1)+,1+!S#.,-&()#,!6#(4!3#'!'+2+&'14!2.%%#'(!T=?@5R>:!IXH^IWWF!=?@5JbIJbbYU! &,-!3+//#Q24)%!2.%%#'(!TZcSB!HIIWIKYKJ^UN!!<4+!D&'*&'-!G.2+.$!#3!"#$%&'&()*+! d##/#08!B.(,&$!S.,-F!7$+')1&,!G.2+.$!#3!]&(.'&/!D)2(#'8F!7$+')1&,!>',)(4#/#0)2(2e! E,)#,F!:#1)+(8!3#'!(4+!:(.-8!#3!?*#/.()#,F!&,-!Z'&-.&(+!a#$+,!),!:1)+,1+!%'#*)-+-! 3.,-),0!3#'!6#(4!3)+/-!Q#'\!&,-!2+A.+,1),0N!!<4&,\!8#.!(#!(4+!D&'*&'-!E,)*+'2)(8!3#'! 2.%%#'(),0!$+!Q4)/+!1#,-.1(),0!'+2+&'14N! ! <4)2!%'#C+1(!Q#./-!,#(!4&*+!6++,!%#22)6/+!Q)(4#.(!(4+!1.'&(#'2F!1#//+1()#,2! $&,&0+'2F!&,-!$.2+.$2!(4&(!2+,(!()22.+!/#&,2!3#'!.2+!),!(4+!%'#C+1(N!7(!(4+!c#8&/!>,(&')#! G.2+.$F!7/&,!@&\+'!0&*+!$+!%+'$)22)#,!(#!.2+!(4+!()22.+2N!!7(!(4+!@.'\+!G.2+.$!#3! ]&(.'&/!D)2(#'8F!9#4,!f/)1\&!0&*+!$+!%+'$)22)#,!(#!.2+!(4+!()22.+2F!&,-!:4&'#,!@)'\2! 2.62&$%/+-!&,-!2+,(!$+!(4+!()22.+2N!!7(!(4+!S)+/-!G.2+.$!#3!]&(.'&/!D)2(#'8F!9#4,!@&(+2! 0&*+!$+!%+'$)22)#,!(#!.2+!(4+!()22.+2F!&,-!@+,!G&'\2!2.62&$%/+-!&,-!2+,(!$+!(4+!()22.+2N!! 7(!(4+!G.2+.$!#3!"#$%&'&()*+!d##/#08F!:1#((!?-Q&'-2!0&*+!$+!%+'$)22)#,!(#!.2+!(4+! ()22.+2F!&,-!@'+-&!d)$\.2!2.62&$%/+-!(4+!()22.+2N!!7(!(4+!G.2+.$!#3!P+'(+6'&(+!d##/#08F! c&.')!@#Q)+!0&*+!$+!%+'$)22)#,!(#!.2+!(4+!()22.+2F!&,-!"&'/&!")1+'#!2+,(!$+!(4+!()22.+2N!R,! *)! (4+!G"d!6)'-!1#//+1()#,F!9+'+$)&4!<')$6/+!&,-!f&(+!?/-')-0+!&/Q&82!$&-+!2.'+!R!4&-!Q4&(!R! ,++-+-F!),1/.-),0!+A.)%$+,(F!&11+22!(#!2%+1)$+,2F!&,-!%+'$)(2N! ! S#'!&22)2(&,1+!1&(14),0!D#.2+!S),14+2!),!7');#,&!R!Q#./-!/)\+!(#!(4&,\!f+*),! G1Z'&Q!&,-!B)+'1+!D.((#,N!R,!a&24),0(#,F!c#6!S&.1+((!4+/%+-!0+(!$+!(4+!+A.)%$+,(!R! ,++-+-!&,-!2+,-!$+!$8!2&$%/+2F!&,-!g)2+!")11#,)!%'#*)-+-!$.14!,++-+-!&22)2(&,1+!&,-!&! 3)+/-!2)(+N!R,!G&22&14.2+((2F!g)/8!g.F!:)$#,!:),!&,-!c&6)+!7,0&-)!4+/%+-!$+!1&(14!6)'-2F!&,-! :1#((!?-Q&'-2!&,-!G)14&+/!c++-!%'#*)-+-!3)+/-!2)(+2N!R,!"&/)3#',)&F!"&'/&!")1+'#!&,-!(4+! %'+%!/&6!(+&$!2&*+-!$+!D#.2+!S),14+2!(#!%'+%&'+!&,-!4+/%+-!2+,-!$+!()22.+!2&$%/+2N! ! S#'!4+/%!Q)(4!(4+!c7=2+A!/)6'&'8!%'+%&'&()#,!%'#(#1#/F!R!(4&,\!?$)/8!f&8!&,-!@'&,(! B+(+'2#,!3#'!2.00+2()#,2F!&,-!S/&*)&!<+'$)0)#,)!3#'!Q#'\),0!Q)(4!$+!(#!3)0.'+!#.(!(4+! %'#(#1#/N!!<4+!@&.+'!"#'+!2(&33!$+$6+'2!"4')2()&,!=&/8F!"/&)'+!c+&'-#,F!B&(')1\!=+,,+((F! &,-!9+,,)3+'!"#.0+(!Q+'+!+22+,()&/!3#'!('&),),0!&,-!1#,2./(&()#,!3#'!/)6'&'8!%'+%&'&()#,!&,-! 2+A.+,1),0F!&,-!:)$#,!:),!Q&2!&!.2+3./!'+2#.'1+!3#'!&,2Q+'),0!/&6!A.+2()#,2N!!<)$!:&1\(#,! %'#*)-+-!.2+3./!&-*)1+!#,!Q4)14!&,&/82+2!(#!'.,F!&,-!(4+!S7:!),3#'$&()12!(+&$!\+%(!(4+! >-822+8!1/.2(+'!.%!&,-!'.,,),0!Q)(4!(4+!2#3(Q&'+!(4&(!R!,++-+-N!!7,-+'2!7/6'+14(2+,!&,-! <4#'3),,!!f#',+/).22+,!4+/%+-!$+!0+(!(4+)'!2#3(Q&'+F!7]Z:=!.%!&,-!'.,,),0!Q)(4!$8! -&(&2+(N! ! <4&,\!8#.!(#!(4+!>?@!=+%&'($+,(!&,-!D&'*&'-!2(&33F!3#'!4+/%!),!&-$),)2('&()*+! $&((+'2N!!R!+2%+1)&//8!Q&,(!(#!(4&,\!7/)2#,!B)')+F!])\\)!D.04+2!&,-!f)'2(),!B+,,&'.,F!Q4#! &/Q&82!&,2Q+'+-!$8!A.+2()#,2!&,-!4+/%+-!$+!0+(!&,8!$&(+')&/2!#'!0'&,(2!R!,++-+-F!&,-! Q)(4#.(!Q4#!$8!/)3+!Q#./-!4&*+!6++,!$.14!$#'+!-)33)1./(N! ! <#!$8!3+//#Q!>?@!0'&-.&(+!2(.-+,(2F!(4&,\!8#.!3#'!8#.'!2.%%#'(F!),%.(F!&,-! 3')+,-24)%N!!h#.!('./8!$&-+!(4)2!%'#C+1(!&,!+,C#8&6/+!+V%+')+,1+F!&,-!4&*+!4+/%+-!$+!(4),\! *))! &6#.(!$&,8!-)33+'+,(!282(+$2!&,-!A.+2()#,2N!G&'\!g).F!S'&,\!c4+),-(F!"/+$+,2!f.%%+'F! G&((!S.C)(&F!"&22)+!:(#--&'-F!"4')2()+!c)+4/F!B&(')1\!7/6+'2F!G##2!@/#$F!?/)2&!=)+')1\VF! "8,(4)&!E'2),#F!G&.-+!@&/-Q),F!:4&,+!"&$%6+//5:(&,(#,F!:)$#,!:),F!B4)/!Z'&82#,F!f&(4'),! ]&%3/),F!f&()+!:('8C+Q2\)F!9#,&(4&,!:14$)((F!<)$!:&1\(#,F!Z.2(&*#!@'&*#F!:&,0++(! g&$)1\4&,+8F!7/)2#,!"/#.()+'F!B+,014&,0!a&,0F!9#4,!@.'/+8F!&,-!@+(./!f&1&'F!R!1#./-!,#(! 4&*+!&2\+-!3#'!$#'+!),(+//)0+,(!#'!6+((+'!/&6!$&(+2N!!R!Q)//!,+*+'!2(#%!14+')24),0!8#.'! 3')+,-24)%N! ! <#!&//!#3!$8!3')+,-2!&,-!3&$)/8F!(4&,\!8#.!3#'!8#.'!2.%%#'(!&,-!%&()+,1+N!!h#.!('./8! $&-+!$8!(4+2)2!%#22)6/+N!!<#!&//!#3!$8!%&'+,(2F!7$8!&,-!G)\+!:+Q+//F!&,-!c#6+'(!&,-!7,,! :4./(;F!R!Q#./-!,#(!4&*+!6++,!Q4+'+!R!&$!Q)(4#.(!8#.N!!h#.!4&*+!&/Q&82!2.%%#'(+-!$+!),!
Details
-
File Typepdf
-
Upload Time-
-
Content LanguagesEnglish
-
Upload UserAnonymous/Not logged-in
-
File Pages172 Page
-
File Size-