Supplemental Table 1. Mass competitive fitness values of all deletion strains in our dataset across both species and all three nutrient limitations. NAs are samples for which there are no fitness values. ORF Hybrid Glucose Fitness Hybrid Phosphate Fitness Hybrid Sulfate Fitness Purebred Glucose Fitness Purebred Phosphate Fitness Purebred Sulfate Fitness YAL001C NA NA NA -0.051597292 -0.003543806 -0.026972383 YAL002W NA NA NA 0.004274964 0.002418171 0.007835905 YAL003W 0.004435595 -0.056524858 -0.023682202 -0.016205745 -0.002671671 -0.002014808 YAL004W -0.017575734 0.037783618 -0.011656632 -0.011668649 -0.018361244 -0.024005617 YAL005C -0.002512395 0.051521066 -0.009673695 NA NA NA YAL007C 0.015585788 0.053039459 -0.00209392 -0.021342372 -0.004910773 -0.023196948 YAL008W 0.002931293 0.002927123 -0.007431229 -0.013292814 -0.00678601 -0.015950233 YAL009W 0.012481815 -0.05526886 -2.99E-05 -0.01020191 0.001825868 -0.009520509 YAL010C -0.014213211 0.052935057 -0.041510353 -0.016659407 0.004696169 -0.01170187 YAL011W NA 0.016069794 -0.19829219 -0.01435629 -0.027783027 -0.039577986 YAL012W NA NA NA -0.026993719 -1.83E-05 -0.000905108 YAL013W 0.009144527 0.06846662 -0.015900049 -0.014063196 0.010179577 -0.004051667 YAL014C NA NA NA 0.033120293 0.006512643 -0.009675883 YAL015C -0.012462789 -0.065761508 -0.000863007 0.014750708 -0.002442067 -0.007355686 YAL016W NA NA NA -0.029423546 0.016314129 -0.107509142 YAL017W -0.003239047 0.054479277 -0.002217492 NA -0.009449201 NA YAL018C -0.010237539 0.004909059 -0.011578905 -0.008942492 -0.00306254 -0.01199704 YAL019W 0.004055722 -0.001640717 0.010664408 0.010858153 -0.006075673 0.008499557 YAL020C -0.000173406 0.004807124 -0.012435818 -0.014800153 -0.005009774 -0.01705136 YAL021C -0.025863028 -0.066087669 -0.031691852 -0.020726283 -0.008343896 0.026924252 YAL022C -0.018575476 0.004808014 -0.006299839 -0.004496932 -0.000954299 -0.008349104 YAL023C -0.00405683 0.042332138 -0.022224205 -0.022042948 -0.012983212 -0.052824637 YAL024C NA NA NA -0.012134985 0.002791998 0.000370376 YAL025C -0.036214482 -0.058383164 -0.032253021 0.016610278 -0.004730578 -0.017156052 YAL026C -0.048242221 0.004652844 0.011504309 0.00109178 -0.002621485 -0.003302059 YAL027W -0.00062055 -0.017489209 -0.005178439 -0.005963162 0.00534154 -0.008946101 YAL029C NA NA NA 0.003033057 -0.001926314 -0.007578081 YAL030W 0.002372624 0.03481365 0.003235655 -0.000419631 0.008085224 0.001942782 YAL031C NA NA NA 0.001397551 -0.004728975 0.003337804 YAL032C NA NA NA -0.016918745 0.001984203 -0.004798891 YAL033W -0.03197014 -0.030884889 -0.037024613 0.001308183 -0.006655833 -0.013116997 YAL034C -0.001568438 -0.058863333 0.002455986 -0.008635137 0.00338256 0.019806095 YAL034W-A 0.009586998 -0.040460655 -0.028562782 -0.013419405 -0.005348629 -0.106683316 YAL035C-A NA NA NA -0.011905795 -0.00709897 -0.115080689 YAL036C -0.013169958 0.036980194 -0.009490549 NA NA NA YAL037W NA NA NA 0.007922719 -0.024053072 -0.036399482 YAL038W NA NA NA 0.001451674 -0.002223715 -0.007984557 YAL039C NA NA NA -0.012577581 0.004126494 -0.000317737 YAL040C NA 0.032687969 NA -0.055239521 -0.00467876 0.006128562 YAL041W NA NA NA -0.009530382 -0.010453662 -0.018789852 YAL042W NA NA NA -0.035902288 -0.025273014 -0.025528531 YAL043C -0.052081547 -0.102192276 -0.023405665 -0.02228085 -0.033347753 -0.028760473 YAL044C NA NA -0.018822521 NA 0.037292289 0.016909857 YAL045C -0.005506227 -0.004859762 0.002128777 0.01539534 -0.005183947 -0.067741743 YAL046C NA NA NA -0.012175791 0.000828697 -0.003399317 YAL047C 0.009801602 -0.067065551 -0.022889268 -0.023130936 -0.002703436 -0.006629597 YAL048C NA NA NA -0.01130415 0.010011875 -0.002196707 YAL049C NA NA NA NA NA -0.001884495 YAL051W NA NA NA NA 0.016614764 NA YAL053W NA NA NA -0.020456239 0.005381154 -0.009339131 YAL054C NA NA NA -0.009145916 -0.003916762 0.006578964 YAL055W -0.008526977 0.041837769 0.004678025 -0.017283512 0.010007197 0.000222133 YAL056W 0.055697484 -0.058742898 0.037317663 0.025663094 0.000377214 0.001996575 YAL058C-A NA NA NA -0.006107555 -0.003272894 -0.001591864 YAL058W 0.011762928 -0.059799147 -0.006182597 -0.00503816 0.000188926 -0.00914752 YAL059W NA NA NA -0.013258302 -0.001937616 -0.014978116 YAL060W 0.006633195 -0.036163083 -0.009544041 -0.010279506 -0.000379767 -0.007423609 YAL061W NA NA NA -0.028176627 -0.003907743 -0.016284648 YAL062W NA 0.028202213 -0.210170571 -0.004326686 -0.00514429 -0.013696047 YAL064C-A 0.002726326 -0.024975135 -0.012693911 -0.005915858 0.003251576 -0.006999689 YAL065C NA 0.034323951 -0.241057674 -0.004377903 -0.00266133 -0.006756369 YAL066W NA NA NA -0.002147952 -0.002686305 -0.014148317 YAL067C 0.008369201 -0.084434868 0.002316967 NA 0.000650933 NA YAL068C -0.00213257 -0.012220029 -0.004043042 NA -0.012208198 NA YAR002C-A -0.000895295 -0.017473311 -0.009282946 -0.003610868 -0.002865471 -0.019143754 YAR003W NA 0.045096103 -0.248750788 -0.004138468 -0.001466732 -0.008246376 YAR007C -0.046628022 -0.049038351 -0.02449652 -0.007413936 -0.006346139 -0.00523502 YAR008W NA NA NA -0.008530156 0.002121238 -0.007868443 YAR014C -0.011339368 0.025308464 -0.024758941 -0.015745533 -0.006703347 -0.017839175 YAR015W -0.014607773 0.028396704 -0.008572882 -0.023606035 0.00145599 -0.00931441 YAR019C NA NA NA -0.006711419 0.000352937 -0.006203988 YAR020C NA NA NA -0.015933059 0.003726782 0.001216304 YAR023C NA NA NA 0.004789711 0.003298033 -0.001829402 YAR027W NA NA NA 0.00610501 0.000285373 -0.007381587 YAR028W 0.001895484 -0.01353175 0.006061917 -0.003710304 0.006928884 0.00073965 YAR029W NA NA NA -0.006726319 -0.005152423 -0.007860534 YAR030C -0.003155731 0.022619098 -0.010472081 -0.006559664 -0.006220737 -0.005925597 YAR031W 0.002472914 -2.05E-05 -0.001286738 -0.00575549 -3.75E-05 0.002853622 YAR035W 0.000694129 -0.063393116 0.00620215 0.005171051 0.007258729 -0.00198068 YAR037W -0.008593043 0.006559861 -0.003355571 -0.009962467 0.004197517 0.003968223 YAR040C -0.002505435 -0.030617172 -0.009470497 -0.01362427 -0.002257771 -0.005847126 YAR042W NA NA NA 0.000961985 -0.003138734 0.001537944 YAR043C NA NA NA 0.004333538 -0.005913008 0.003474579 YAR044W NA NA NA 0.005184995 -0.007571957 -0.022761655 YAR047C NA NA NA 0.000664399 -0.000205801 -0.017498783 YAR050W NA 0.014798021 NA -0.028848499 -0.003749305 -0.001981026 YBL003C -0.021010316 -0.039298731 0.003419478 NA -0.019472535 NA YBL004W -0.136442043 -0.072939095 0.014634901 -0.007723011 -0.002362743 -0.006121058 YBL005W 0.046092232 -0.036809198 0.013957218 NA NA NA YBL006C -0.020448563 0.089323612 0.012613981 -0.041853646 -0.008129422 -0.036201156 YBL007C 0.00531014 0.044031705 0.02917481 NA NA NA YBL008W 0.005049861 -0.077448273 0.004393228 0.0025451 0.011293484 -0.006499671 YBL009W 0.005203455 -0.064475032 0.005185304 -0.026642978 0.00733842 0.014001554 YBL010C 0.01410434 -0.07205673 0.018387315 -0.023167621 -0.003450263 -0.00758968 YBL011W -0.000527178 -0.076798623 -0.002104851 NA NA NA YBL012C -0.009933005 -0.073836087 -0.007864142 -0.004501544 -0.028935227 -0.009831088 YBL013W -0.005883228 -0.053181501 0.015625769 -0.058650967 -0.042200228 0.099093086 YBL015W -0.04907624 -0.041621441 -0.004277342 -0.020373532 0.001164156 -0.010904118 YBL016W NA 0.01509093 -0.215965319 -0.013978303 -0.008308012 -0.009278123 YBL017C NA NA NA -0.100541828 -0.051189172 -0.020026609 YBL018C NA NA NA -0.021523046 0.004604509 0.010868374 YBL019W NA NA NA -0.014378507 -0.003090048 -0.002651513 YBL020W -0.010544626 0.059712593 0.041103608 -0.019301942 0.000678743 0.009715344 YBL024W 0.010187027 -0.06507736 0.004652467 -0.015377413 0.00488466 0.002117301 YBL025W NA NA NA -0.024555547 -0.000127076 0.004212434 YBL026W -0.140856877 -0.051829043 0.009871482 -0.046748555 -0.02109809 0.099037085 YBL027W -0.013483651 0.060590023 0.023753161 0.010416792 -0.035372638 -0.004720345 YBL028C 0.01357213 -0.051194066 0.008636183 -0.012677821 -0.005187492 -0.003403464 YBL029W -0.001749143 -0.031265399 0.005815791 -0.023104065 -0.012586206 -0.005099642 YBL031W -0.021513974 -0.076209745 -0.005989431 -0.003471301 -0.004223181 -0.007470116 YBL032W NA NA 0.022456219 -0.021720566 -0.017032086 -0.00386338 YBL033C NA NA NA -0.003686356 -0.000398421 -0.002916011 YBL034C NA NA NA -0.015121692 -0.004668654 0.004322487 YBL035C NA NA NA -0.020516606 -0.012402914 -0.013952473 YBL036C -0.002045966 -0.06153733 -0.002721022 -0.001809999 0.000661943 -0.003520974 YBL037W -0.007857885 -0.056336537 0.003901073 -0.018905657 -0.010204867 -0.005238383 YBL038W -0.068935736 -0.051231574 0.012326567 -0.010283875 -0.004194779 -0.006997777 YBL039C -0.000249545 -0.112206882 0.0073395 -0.007761424 0.000632987 -0.001968826 YBL040C 0.029303442 0.036492368 0.035926017 -0.022455004 -0.015893315 0.006501744 YBL041W NA NA NA 0.018502196 0.037599157 0.013657376 YBL042C 0.010220599 -0.053836273 0.003066429 -0.005867148 -0.000389026 -0.002684472 YBL045C 0.005447388 -0.034743897 0.001015486 0.012081346 -0.014871658 0.004557801 YBL046W NA NA NA NA -0.070052886 -0.035841432 YBL047C NA NA NA NA NA 0.090925234 YBL048W -0.024781399 -0.062159473 -0.000211869 0.027232207 -0.000175305 -0.000390811 YBL049W NA NA NA -0.006992508 -0.005891738 -0.001925832 YBL050W NA NA NA -0.008392896 -0.029646812 -0.032697229 YBL051C -0.005342334 -0.056182902 0.002584244 -0.007846199 -0.009077234 0.021784701 YBL052C -0.002223885 0.045429312 0.00126379 NA NA NA YBL053W -0.001190047 -0.042836411 0.00047671 -0.009918415 -0.005166424 0.00119705 YBL054W -0.004377187 -0.065811134 0.002542296 -0.000639612 -0.012911229 -0.005558543 YBL055C -0.01795825 -0.090560527 0.000426167 -0.007631828 -0.008807349 -0.007304293 YBL056W 0.00162797 -0.014739117 0.000750226 0.004448851 -0.002278388 0.006327419 YBL057C -0.013898448 -0.04773047 0.003072146 -0.008807212 0.000574116 -0.003478609 YBL059W -0.003687402 -0.044915554 0.004658913 0.000162381 -0.002982292 -0.007355159 YBL060W -0.006190391 -0.073939302 0.003885469 -0.015045463 0.001496381 0.001321355 YBL061C 0.002503934 -0.063284241 0.00587558 -0.006306654 0.001156277 0.001573287 YBL062W -0.013138028 -0.061798665 -0.003932989 0.014897768 -0.015513045 -0.022743728 YBL063W 0.00690104 -0.051940996 -0.000111878 0.002398643 -0.004020685 -0.002252478 YBL064C NA NA NA 0.015143978 -0.006569546 -0.004793735 YBL065W NA NA NA -0.075995489 -0.095737365 -0.060231142 YBL066C -0.007287505 -0.088757496 0.010241779 -0.001360248 0.000462414 -0.003108324 YBL067C NA 0.022019753 NA NA NA NA YBL068W 0.012420681 -0.056437244 0.004388161 -0.008665946 -0.000862772 -0.00055637 YBL069W -0.007554359 0.016812159 0.009344392 NA 0.011736646 NA YBL070C -0.004531842 -0.051661769 -0.000156103 -0.008963397 -8.30E-05 -0.002755543 YBL071C 0.002339495 -0.070564724 -0.001379722 -0.002424365 -0.01225049 -0.005998794 YBL072C -0.022637434 0.060159861 0.02878886 -0.057954185 -0.006170921 -0.021199208 YBL073W -0.123312873 -0.051468274 0.019176822 -0.014889302 -0.009036276 -0.009020257 YBL074C NA 0.016860454 -0.158050873 -0.008311691 -0.002527438 0.010815227 YBL076C -0.053154487 0.061614224 0.024036318 -0.004818862 -0.002598357 -0.001015694 YBL077W -0.107460559 -0.060720419 0.015280141 -0.018746091 -0.000716447 -0.003362966 YBL078C NA NA NA -0.00453279 -0.00207426 -0.004535853 YBL079W NA 0.040723615 -0.192155253 0.050453435 -0.002420072 -0.000938669 YBL080C NA NA NA NA NA 0.014339577 YBL081W -0.020037443 -0.042189597 -0.002636235 -0.02013704 -0.003940509 -0.005228766 YBL082C 0.061258727 -0.007817146 -0.010125875 -0.00929028 -0.004805931 -0.005376583 YBL083C -0.02569967 -0.07587687 0.007119748 NA NA -0.001702398 YBL084C -0.017846936 0.16594932 0.008930631 -0.004941442 -0.007630463 -0.003234866 YBL085W 0.00142893 -0.065513475 0.002522497 -0.00699449 -0.00351475 -0.003526159 YBL086C 0.061812857 0.18414221 0.000872627 NA NA NA YBL087C NA NA NA -0.0180887 -0.027291312 -0.009727864 YBL088C -0.006957542 0.012228666 0.001664459 0.032336337 -0.006495198 -0.005991329 YBL089W -0.021523425 -0.037196533 0.001456303 -0.003962939 0.000328193 -0.003149667 YBL090W -0.127148805 0.03594772 0.018351647 -0.018183755 -0.004291318 -0.004572478 YBL091C-A -0.005158287 -0.044053778 -0.00041927 0.020917827 -0.000226166 -0.059813441 YBL092W -0.017102254 0.053309964 -0.005677224 -0.036090758 0.01929129 0.087945412 YBL093C -0.030459803 -0.014906278 0.037652208 -0.016461969 -0.001987889 -0.055225563 YBL094C 0.003322091 -0.02383445 0.001679762 -0.009492167 -0.00327577 -0.003146409 YBL095W NA NA NA 0.000789393 -0.010847729 -0.012353246 YBL096C 0.00057756 -0.031638825 -0.004742451 -0.020970196 -0.006870614 -0.007794286 YBL097W NA NA NA -0.006572222 -0.002587762 0.008227829 YBL098W -0.018852855 -0.028996615 0.008468852 -0.014688965 0.000345478 0.014260293 YBL099W -0.020812974 0.172820209 0.013843102 NA NA NA YBL100C -0.02207337 0.049415761 -3.66E-06 -0.054008112 -0.009003562 0.000297049 YBL101C -0.0080175 0.037649396 -0.005239494 -0.010437219 -0.00023012 -0.021509929 YBL102W NA NA NA -0.0005994 -0.005321998 0.001508291 YBL103C NA NA NA NA -0.030976907 -0.000623215 YBL104C 0.002335431 -0.028587912 -0.011805467 -0.015763593 0.004091236 -0.006588397 YBL105C 0.001500507 0.065088033 0.027327726 -0.008243408 0.00105418 0.003863463 YBL106C -0.000972364 0.030898407 -0.002229146 -0.005125544 -0.004121436 -0.006467262 YBL107C -0.001123518 0.026903725 -0.002881432 -0.016766895 -0.002263991 -0.004662135 YBR001C -0.012668274 0.030051555 -0.004090391 -0.011024189 -0.000833272 -0.002806022 YBR002C -0.106644278 -0.066377792 -0.068732861 -0.041274721 -0.021610068 -0.017332423 YBR003W 0.009041372 -0.037430272 -0.001970957 0.026695249 -0.007110856 -2.62E-05 YBR005W -0.005837924 -0.006085085 0.000854472 -0.000554934 -0.002182358 -0.005788313 YBR006W -0.016054779 -0.020891528 0.007826653 -0.00446246 -0.006956737 -0.005970912 YBR007C 0.005059729 -0.024699508 0.0090271 -0.038026948 0.006903415 -0.025836094 YBR008C 0.002826854 -0.033133159 0.001150411 -0.022734546 -0.001485367 -0.002038486 YBR009C 0.004555664 0.03141652 -0.007807362 NA NA NA YBR010W 0.002355763 0.03241681 -0.009214835 NA NA NA YBR011C NA NA NA -0.010111668 0.002268817 -0.005366593 YBR012C NA 0.030748643 NA -0.014896845 -0.00384546 -0.003023564 YBR013C NA NA NA 0.010778576 -0.000290931 -0.006682781 YBR015C 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0.000835341 -0.061866824 0.001361322 -0.019782971 -0.002544302 0.010007406 YKL201C -0.000573855 -0.069821362 0.001231941 0.007234316 0.000930489 0.000350555 YKL202W -0.01443305 -0.009338328 0.002660826 0.015826129 -0.009509515 -0.010457909 YKL203C -0.150443792 0.009638387 0.031001223 0.002572819 0.008086971 -0.014679862 YKL204W -0.03295442 0.10261368 0.026186643 -0.063033885 -0.002228086 -0.00201428 YKL205W -0.002787609 0.056827132 -0.001358374 0.006065483 0.001108721 -0.015036114 YKL207W -0.008034903 -0.020600733 -0.004654774 -0.016426687 0.001019968 0.024389785 YKL208W 0.006638373 -0.02176594 -0.001049281 -0.008457715 -0.000240836 -0.00356189 YKL209C -0.03629684 0.00027244 0.024397359 -0.007688559 -0.002037242 -0.007489625 YKL209C-1 NA NA NA -0.027448108 0.001744838 0.000914161 YKL210W -0.011709943 0.060187119 0.032471602 -0.016349601 0.005774796 -0.001774242 YKL211C -0.014498688 -0.00250966 -0.00548361 -0.00623463 -0.002595998 -0.00527653 YKL212W -0.120924146 -0.036714561 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0.006647459 -0.048330731 -0.000953786 -0.01270818 -0.000421849 -0.070352752 YKR020W 0.009879771 0.005783881 0.000317944 -0.017807627 -0.000339719 -0.005033312 YKR021W 0.085444958 -0.02623107 0.025122912 -0.025928253 0.000485049 0.003652271 YKR022C -0.133002822 -0.026865931 0.028467846 -0.017125969 0.002610993 -0.004225777 YKR023W -0.013957711 -0.081230902 0.002409061 -0.009764033 -0.002117213 -0.011299986 YKR024C -0.040469945 0.041787142 0.033994647 -0.018013358 0.001102419 0.002985395 YKR026C -0.01249444 -0.047031946 -0.013514146 -0.001512989 -0.004617139 -0.011825484 YKR027W -0.02406087 -0.05166136 0.006458175 -0.020302162 -0.006253369 -0.004105934 YKR028W -0.003073752 0.037171079 0.010121301 0.027986235 0.008973354 -0.008158294 YKR029C -0.005252464 0.022367833 0.004785652 0.003524228 -0.005325077 -0.023896294 YKR030W -0.015585735 -0.031386741 -0.004662581 -0.006356501 0.000361872 -0.019117646 YKR032W -0.003980926 -0.038859088 0.00711937 -0.023010958 -0.009617284 -0.008111285 YKR033C 0.00733006 -0.068744977 -0.002285822 -0.026757845 -0.011406716 0.004257959 YKR034W -0.010418278 -0.043590425 -0.004195097 -0.027893941 -0.006202827 -0.002311336 YKR035C 0.00611769 -0.039989339 0.00328446 -0.006369314 -0.010041166 -0.013190516 YKR035W-A -0.002347122 -0.089149144 0.001575659 0.00888316 -0.013429522 -0.022185576 YKR036C -0.002064278 -0.039688858 0.004195302 -0.012278554 -0.001530228 -0.005901046 YKR037C NA NA NA -0.021799698 -0.04059625 -0.054366642 YKR038C NA NA NA -0.001698915 0.002594877 -0.006153816 YKR039W -0.009213606 -0.071429362 0.000428291 -0.011703805 0.001424173 0.002222735 YKR040C 0.030085179 0.008447774 0.02009885 -0.01051659 -0.003196073 -0.003152378 YKR041W -0.003842124 -0.036043701 0.002024952 -0.009874895 -0.002121287 -0.006472482 YKR042W 0.004645043 -0.08791704 0.001273409 -0.016481014 -0.005664726 0.011399241 YKR043C -0.004313718 -0.036296723 -0.00018462 0.000880161 0.003517679 0.000373157 YKR044W -0.010464609 -0.015604943 -0.001208014 -0.022775471 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