Medindo diversidade filogenética
Nesta prática trataremos do conceito de diversidade filogenética e suas implicações. Primeiro aprenderemos a medir diversidade filogenética. Considere a seguinte filogenia:
library(ape)
tr<-read.tree(text="((espécie_X:0.5,espécie_Y:0.5):0.5,espécie_Z:1);")
plot(tr)
axisPhylo()
Quanta história evolutiva está representada nessa filogenia? Se a escala abaixo está em uma escala de milhões de anos, temos 1 milhão de anos levando desde o ancestral de todas as espécies e a espécie Z, 0.5 mihão de anos entre o ancestral de todas as espécies e o ancestral das espécies X e Y e mais 0.5 milhão de anos desde então até o presente = 1 + 0.5 + 0.5 + 0.5= 2.5. Podemos fazer uma função para o R nos calcular isso diretamente.
divfilo<-function(tr){
res<-sum(tr$edge.length)
res
}
divfilo(tr)## [1] 2.5Digamos que temos uma filogenia maior e gostaríamos de calcular a diversidade filogenética de diferentes subconjuntos destas espécies.
#agora vamos abrir uma árvore um pouco maior do que a anterior para facilitar a visualização
tr<-read.tree(text="((t1:0.53,t2:0.53):0.07,(((t6:0.1,t7:0.1):0.19,(t4:0.11,(t5:0.11,((t9:0.028,t10:0.028):0.0009,t8:0.029):0.083):0.00039):0.18):0.024,t3:0.32):0.28);")
plot(tr)
subA<-drop.tip(tr, c("t1","t2","t3"))
subB<-drop.tip(tr, c("t10","t5","t6"))
divfilo(subA)## [1] 0.95929divfilo(subB)## [1] 2.47529Note como cada subconjunto tem o mesmo número de espécies, mas diversidades filogenéticas muito diferentes. Por que? Uma dica pode ser obtida plotando as ávores:
layout(matrix(1:3, nrow=1))
plot(tr)
axisPhylo()
plot(subA)
axisPhylo()
plot(subB)
axisPhylo()
Podemos avaliar o quanto a extinção de espécies pode apagar a diversidade filogenética. Podemos simular uma grande filogenia e podar cada vez mais espécies.
library(phytools)## Loading required package: mapstr<-pbtree(n=1000)
terminais<-tr$tip.label
terminais## [1] "t393" "t394" "t531" "t532" "t280" "t704" "t877" "t878"
## [9] "t770" "t771" "t72" "t500" "t724" "t725" "t8" "t455"
## [17] "t456" "t185" "t707" "t708" "t367" "t358" "t352" "t353"
## [25] "t316" "t757" "t758" "t625" "t626" "t468" "t591" "t592"
## [33] "t331" "t285" "t305" "t306" "t70" "t286" "t814" "t815"
## [41] "t722" "t723" "t519" "t520" "t204" "t686" "t687" "t610"
## [49] "t194" "t195" "t115" "t257" "t435" "t436" "t999" "t1000"
## [57] "t108" "t499" "t670" "t671" "t109" "t229" "t451" "t645"
## [65] "t646" "t881" "t993" "t994" "t288" "t59" "t60" "t400"
## [73] "t401" "t366" "t307" "t913" "t914" "t682" "t683" "t665"
## [81] "t202" "t203" "t14" "t4" "t250" "t251" "t161" "t875"
## [89] "t876" "t90" "t193" "t921" "t922" "t173" "t635" "t795"
## [97] "t796" "t91" "t958" "t959" "t923" "t987" "t988" "t319"
## [105] "t477" "t478" "t730" "t731" "t997" "t998" "t944" "t699"
## [113] "t177" "t310" "t799" "t800" "t832" "t855" "t856" "t560"
## [121] "t628" "t629" "t116" "t117" "t542" "t738" "t739" "t638"
## [129] "t138" "t336" "t751" "t752" "t480" "t481" "t299" "t300"
## [137] "t28" "t215" "t216" "t801" "t802" "t540" "t541" "t13"
## [145] "t25" "t132" "t133" "t85" "t569" "t570" "t86" "t31"
## [153] "t120" "t142" "t278" "t279" "t119" "t396" "t397" "t182"
## [161] "t342" "t450" "t691" "t692" "t989" "t990" "t221" "t332"
## [169] "t333" "t73" "t616" "t617" "t889" "t890" "t379" "t9"
## [177] "t21" "t210" "t260" "t261" "t504" "t505" "t222" "t223"
## [185] "t151" "t853" "t854" "t51" "t426" "t427" "t24" "t2"
## [193] "t503" "t556" "t557" "t5" "t620" "t621" "t175" "t176"
## [201] "t865" "t866" "t54" "t121" "t122" "t69" "t639" "t640"
## [209] "t198" "t822" "t823" "t253" "t26" "t245" "t604" "t605"
## [217] "t491" "t492" "t672" "t673" "t96" "t525" "t582" "t766"
## [225] "t767" "t553" "t734" "t735" "t513" "t572" "t573" "t516"
## [233] "t517" "t84" "t282" "t283" "t247" "t248" "t421" "t422"
## [241] "t104" "t849" "t850" "t637" "t357" "t269" "t740" "t741"
## [249] "t917" "t918" "t736" "t423" "t764" "t765" "t857" "t858"
## [257] "t29" "t19" "t785" "t786" "t94" "t789" "t790" "t643"
## [265] "t644" "t36" "t166" "t726" "t727" "t826" "t827" "t596"
## [273] "t345" "t380" "t381" "t190" "t191" "t350" "t351" "t137"
## [281] "t897" "t898" "t227" "t975" "t976" "t974" "t899" "t900"
## [289] "t167" "t930" "t931" "t313" "t314" "t254" "t255" "t160"
## [297] "t774" "t928" "t929" "t482" "t581" "t608" "t609" "t158"
## [305] "t606" "t607" "t416" "t74" "t75" "t66" "t42" "t334"
## [313] "t335" "t208" "t209" "t159" "t246" "t274" "t787" "t788"
## [321] "t67" "t938" "t939" "t465" "t544" "t545" "t816" "t817"
## [329] "t192" "t275" "t276" "t95" "t11" "t493" "t494" "t83"
## [337] "t838" "t839" "t536" "t537" "t354" "t388" "t777" "t778"
## [345] "t527" "t320" "t39" "t57" "t550" "t658" "t659" "t184"
## [353] "t424" "t425" "t371" "t775" "t776" "t369" "t207" "t463"
## [361] "t464" "t749" "t750" "t518" "t936" "t937" "t126" "t107"
## [369] "t374" "t375" "t270" "t432" "t433" "t178" "t759" "t760"
## [377] "t861" "t862" "t391" "t392" "t65" "t88" "t157" "t947"
## [385] "t948" "t641" "t871" "t872" "t323" "t438" "t439" "t376"
## [393] "t45" "t46" "t599" "t761" "t762" "t230" "t231" "t364"
## [401] "t365" "t287" "t259" "t995" "t996" "t124" "t125" "t1"
## [409] "t563" "t564" "t92" "t587" "t588" "t128" "t263" "t264"
## [417] "t962" "t963" "t595" "t718" "t719" "t127" "t129" "t130"
## [425] "t22" "t201" "t514" "t515" "t434" "t437" "t585" "t586"
## [433] "t131" "t61" "t62" "t934" "t935" "t567" "t172" "t650"
## [441] "t651" "t574" "t575" "t403" "t281" "t271" "t324" "t325"
## [449] "t293" "t663" "t664" "t224" "t225" "t343" "t344" "t12"
## [457] "t35" "t105" "t233" "t309" "t909" "t910" "t705" "t706"
## [465] "t632" "t633" "t268" "t783" "t784" "t444" "t445" "t150"
## [473] "t484" "t485" "t228" "t241" "t242" "t668" "t669" "t820"
## [481] "t821" "t405" "t406" "t404" "t213" "t214" "t487" "t488"
## [489] "t234" "t235" "t469" "t715" "t716" "t688" "t418" "t402"
## [497] "t327" "t945" "t946" "t562" "t284" "t308" "t561" "t882"
## [505] "t883" "t355" "t114" "t262" "t954" "t955" "t407" "t272"
## [513] "t273" "t970" "t971" "t654" "t689" "t690" "t772" "t773"
## [521] "t636" "t149" "t47" "t497" "t498" "t38" "t983" "t984"
## [529] "t322" "t41" "t410" "t411" "t16" "t859" "t860" "t243"
## [537] "t186" "t187" "t146" "t147" "t474" "t475" "t212" "t169"
## [545] "t63" "t168" "t301" "t302" "t200" "t3" "t589" "t590"
## [553] "t810" "t811" "t627" "t508" "t258" "t252" "t442" "t443"
## [561] "t106" "t828" "t829" "t568" "t630" "t631" "t385" "t386"
## [569] "t93" "t720" "t721" "t337" "t338" "t318" "t148" "t298"
## [577] "t489" "t490" "t139" "t140" "t7" "t179" "t180" "t30"
## [585] "t20" "t40" "t220" "t232" "t486" "t684" "t685" "t56"
## [593] "t303" "t304" "t529" "t530" "t647" "t952" "t953" "t543"
## [601] "t398" "t399" "t34" "t459" "t803" "t804" "t737" "t408"
## [609] "t471" "t538" "t539" "t417" "t818" "t819" "t236" "t170"
## [617] "t249" "t382" "t383" "t87" "t808" "t809" "t457" "t118"
## [625] "t143" "t893" "t894" "t528" "t779" "t780" "t729" "t979"
## [633] "t980" "t330" "t509" "t510" "t960" "t961" "t949" "t317"
## [641] "t346" "t347" "t341" "t452" "t521" "t830" "t831" "t660"
## [649] "t755" "t756" "t551" "t552" "t867" "t868" "t377" "t873"
## [657] "t874" "t466" "t467" "t152" "t431" "t768" "t769" "t111"
## [665] "t112" "t702" "t703" "t956" "t957" "t634" "t370" "t27"
## [673] "t558" "t559" "t144" "t879" "t880" "t458" "t576" "t577"
## [681] "t972" "t973" "t226" "t153" "t460" "t461" "t924" "t925"
## [689] "t615" "t991" "t992" "t110" "t33" "t506" "t507" "t15"
## [697] "t676" "t677" "t915" "t916" "t101" "t64" "t339" "t340"
## [705] "t80" "t81" "t102" "t103" "t674" "t675" "t619" "t472"
## [713] "t473" "t932" "t933" "t905" "t906" "t753" "t711" "t712"
## [721] "t113" "t483" "t911" "t912" "t797" "t798" "t211" "t495"
## [729] "t496" "t164" "t217" "t523" "t524" "t895" "t896" "t886"
## [737] "t695" "t696" "t535" "t919" "t920" "t717" "t642" "t188"
## [745] "t328" "t329" "t218" "t219" "t700" "t701" "t742" "t743"
## [753] "t781" "t782" "t754" "t618" "t678" "t679" "t600" "t601"
## [761] "t244" "t652" "t653" "t597" "t598" "t414" "t378" "t833"
## [769] "t834" "t289" "t82" "t655" "t656" "t479" "t413" "t697"
## [777] "t698" "t37" "t926" "t927" "t356" "t359" "t360" "t43"
## [785] "t44" "t368" "t501" "t502" "t744" "t745" "t361" "t661"
## [793] "t662" "t593" "t594" "t446" "t447" "t428" "t429" "t462"
## [801] "t522" "t805" "t966" "t967" "t315" "t693" "t694" "t840"
## [809] "t841" "t123" "t239" "t240" "t77" "t78" "t6" "t154"
## [817] "t602" "t603" "t387" "t430" "t578" "t863" "t864" "t237"
## [825] "t238" "t199" "t79" "t415" "t622" "t950" "t951" "t68"
## [833] "t713" "t714" "t985" "t986" "t657" "t409" "t100" "t579"
## [841] "t580" "t549" "t968" "t969" "t746" "t747" "t296" "t297"
## [849] "t611" "t612" "t256" "t419" "t420" "t76" "t162" "t163"
## [857] "t10" "t17" "t533" "t534" "t174" "t940" "t941" "t171"
## [865] "t666" "t667" "t842" "t843" "t58" "t189" "t869" "t870"
## [873] "t134" "t135" "t98" "t99" "t326" "t384" "t793" "t794"
## [881] "t847" "t848" "t395" "t981" "t982" "t277" "t412" "t887"
## [889] "t888" "t546" "t884" "t885" "t680" "t681" "t136" "t362"
## [897] "t363" "t565" "t566" "t181" "t183" "t348" "t349" "t613"
## [905] "t614" "t267" "t623" "t624" "t145" "t977" "t978" "t835"
## [913] "t547" "t548" "t824" "t825" "t907" "t908" "t571" "t903"
## [921] "t904" "t836" "t837" "t48" "t321" "t891" "t892" "t763"
## [929] "t32" "t97" "t901" "t902" "t470" "t476" "t554" "t555"
## [937] "t845" "t846" "t844" "t709" "t710" "t292" "t728" "t964"
## [945] "t965" "t389" "t390" "t71" "t290" "t291" "t511" "t512"
## [953] "t18" "t648" "t649" "t311" "t312" "t155" "t156" "t851"
## [961] "t852" "t748" "t791" "t792" "t205" "t206" "t50" "t141"
## [969] "t942" "t943" "t583" "t584" "t89" "t453" "t454" "t732"
## [977] "t733" "t806" "t807" "t526" "t440" "t441" "t196" "t197"
## [985] "t52" "t53" "t372" "t373" "t49" "t55" "t265" "t266"
## [993] "t23" "t812" "t813" "t448" "t449" "t165" "t294" "t295"Vc pode notar que em terminais temos todos os nomes das espécies da filogenia. Agora podemos fazer amostras aleatórias desdes nomes para serem podados.
del10<-sample(terminais, 100) # uma amostra aleatória de 10% das espécies (100 das 1000) e assim por diante.
del20<-sample(terminais, 200)
del30<-sample(terminais, 300)
del40<-sample(terminais, 400)
del50<-sample(terminais, 500)
del60<-sample(terminais, 600)
del70<-sample(terminais, 700)
del80<-sample(terminais, 800)
del90<-sample(terminais, 900)Agora podemos podar estas espécies e calcular as diversidades filogenéticas
treedel10<-drop.tip(tr, del10)
treedel20<-drop.tip(tr, del20)
treedel30<-drop.tip(tr, del30)
treedel40<-drop.tip(tr, del40)
treedel50<-drop.tip(tr, del50)
treedel60<-drop.tip(tr, del60)
treedel70<-drop.tip(tr, del70)
treedel80<-drop.tip(tr, del80)
treedel90<-drop.tip(tr, del90)
divfilo(treedel10)## [1] 922.2292divfilo(treedel20)## [1] 847.834divfilo(treedel30)## [1] 805.3763divfilo(treedel40)## [1] 760.7609divfilo(treedel50)## [1] 669.6512divfilo(treedel60)## [1] 595.2575divfilo(treedel70)## [1] 490.856divfilo(treedel80)## [1] 390.1199divfilo(treedel90)## [1] 246.0758Podemos fazer um gráfico para visualizar isso melhor.
diversidade_filogenetica<-c(divfilo(treedel10),divfilo(treedel20),divfilo(treedel30),divfilo(treedel40),divfilo(treedel50),divfilo(treedel60),divfilo(treedel70),divfilo(treedel80),divfilo(treedel90))
extincoes<-c(10,20,30,40,50,60,70,80,90)
plot(diversidade_filogenetica, extincoes, type="l")
Exercícios para serem entregues:
- Explique em suas palavras o conceito de diversidade filogenética.
- Com base nos resultados da prática, discuta como a extinção de espécies afeta a diversidade filogenética em um dado clado.