Supplementary Material 1 for

Dynamics of sex chromosome evolution in a rapid radiation of

cichlid fishes

Athimed El Taher, Fabrizia Ronco, Michael Matschiner, Walter Salzburger, Astrid Böhne* * corresponding author, email: [email protected]

This PDF file includes: Figs S1-S11

1 Haplochromini Cyprichromini

Lamprologini Ectodini

Fig. S1. Results of tribe-wise GWAS for an association with sex (approach 1). Manhattan plots of a GWAS analysis for an association with sex per tribe (indicated next to the plot) using the reference genome of the Nile tilapia (Oreochromis niloticus). Interchanging black and gray colors delimit chromosomes. Unplaced scaffolds were concatenated into an “UNPLACED” chromosome for visualization. Insets show zooms of regions with an accumulation of SNPs that show an association with sex, i.e. sex chromosomes.

2 Supplementary Figure 2

Haplochromini

LG19 1780354 1984669 2092049 2203083 2483170 2685108 2711638 2869192 3050657 3638570 3781684 3781786 3793071 3793082 3793815 3888769 4646015 4733190 4736796 4775809 4936523 5470756 5587819 5588416 5728838 6581016 6736165 6903808 7170634 7170680 7564848 7645577 8220396 8304853 8347969 8665960 8665961 8800955 9301296 11815251 12801443 13105384 13778806 13991882 14116388 14210815 14295942 14345776 14364546 14640894 14759144 14982759 14982910 15008349 15257989 15755206 15827397 16055602 16097439 16498107 16499168 16555456 16586902 16670396 16677183 17075422 17134511 17190265 17279942 17309610 17530063 17544406 17682087 17735196 17763791 17958537 17990855 17995566 18061088 18061188 18075477 18387476 18394941 18634103 19043155 19111626 19112370 19372148 19470569 20638333 21457792 21477997 21524650 21677988 22043812 25792700 28893291 29098528 29157984 29841859 M M M M F F M F F M M F M F M F M M M M M M F M F F M M M F F F M M M M M M F F F F F F F F F M M M M F M M F M M M F F F F F F F F M F F M M M M M M M M F M F M M F F M F F M M M M M M F F F M M F

T

T

P T. duboisi T T. P P. marginatus P T T T P. babaulti P T P T P P P L. labiatus P I. loocki T A. T P G. p P P P P. cu C. horei L. dardennii P S. diag P. babaulti H. P. marginatus T A. O P T P T. H. stappersii A. paludinosa H. P P P P P T. b P I. loocki P P P P T P T T H. C. polli P T C. horei T A. P L. dardennii P S. diag P. babaulti P. babaulti G. p P. marginatus P. marginatus P. cu P O O O H. A. fl A. st P. philander L. labiatus O T T T T. polli T T P ...... annectens . . b . moo . polli . . . o . . . . tr . ho . ephippium . . macrognathus . . . pol . . . duboisi . . . annectens . . . . b . . s s s . . . moo . . . . . o . . tr . . . ho . . . ephippium . pol . . macrognathus s s . . . . s s s inde s s s s f f s s s s s s b b s s s s s s s malaganenzis uvinzae mazimeroensis inde s s s s f s s s s f asciolatus a b s v s p p p p p p r asciolatus a p p p p p p p p p p r u u p p p p p p p p e r p p p f p p p p p p r a r ichardi anheusdeni m u p p e . "lukuga" . " . "mpimb . "b . "mu . "red" thognathus f ef ichardi . "lunatus" . "red" . "kirschfleck" . "kazumbae" . "moshi . "pol . "giant" . "macrog. . "o . "kipili br m r auschi r r . "mpimb . "mu . "b . "lunatus" . "kirschfleck" . " . "lukuga" . "chip r r thognathus w ef . "red" . "kipili br . "macrog. . "o . "red" . "giant" . "pol . "moshi . "kazumbae" viijosephi r r y . "kilossana" . "chip r w aeleni ii vifrons toni toni y ula ii vifrons toni f b odon r ula a r f b odon e a r r r ii amma e r lack" r v mau amma r ii lack" r r v mau r ichardi kipili" r thog. i asae ichardi kipili" i thog. i asa (North) i r y (South) (South) r y ago" (North) ago" odon t (South) (North) (South) w odon t w r a" r e i a" w y i w o y (North) o (South) (North) ell (South) e" ell k wn" e" wn" k r r ola" ainb ola" o ainb e o e w" xas" w" xas" o o w" w"

3 Supplementary Figure 2 (continued)

Cyprichromini

LG05 152487 236756 485843 485846 485852 1982243 2035360 2321451 2789744 3162428 3570652 4585091 4662701 4878747 4878748 4991748 5050019 5492243 5591488 6188053 6188055 7693903 7693906 7952745 8124004 8167713 8293924 8414205 8885698 8885707 8977539 9752847 9957420 10168629 10335335 10499008 10683251 11217887 11451959 11624312 12967701 13051960 13903746 13965766 13972017 14281249 15134154 15492779 15658516 15890822 15912025 16823704 16882326 17040588 17055591 17071454 17224191 17786073 17786075 18475351 18514095 18566751 18579458 18579467 18713340 19438795 19757831 20053845 20322991 20380843 20466052 20560544 20812754 20911893 20913460 20945479 20945480 21095449 21181784 21191590 21199519 21199520 21460466 21668338 21668340 21885383 22147798 22160812 22495563 22840937 22877045 24392467 28053633 28053635 29536583 29839920 29839921 29891735 30217632 30309068 M F F F M F F M M F F M M M M F F F M M M

C. leptosoma C. colo C. P P C. C. p C. C. microlepidotus P. C. zonatus P. nigripinnis P. P. brieni C. C. leptosoma C. C. coloratus C. pavo C. C. microlepidotus . nig . b sp. “brieni south” sp. “brieni south” sp. "dwarf jumbo" s s z sp. "jumbo" sp. "kibishi" r onatus p p a ieni . "d . "kibishi" v r o ipinnis r atus (No w (No arf jumbo" r r th) th)

4 Lamprologini LG15_14171023 LG15_14171122 LG15_14171336 LG20_21935453 LG20_21935699 LG20_21935735 LG20_21935762 LG20_21935833 LG20_21935846 LG20_21935859 LG20_21935871 LG20_21935945 LG20_21936306 LG20_21936337 LG20_21936357 LG20_21936422 LG20_21936467 LG20_21936468 LG20_21936612 LG20_21936720 LG20_21936741 LG20_21936869 LG20_21936884 LG20_21936887 LG20_21936920 LG20_21936979 LG20_21937019 LG20_21937030 LG20_21937031 LG20_21937097 LG20_21937101 LG20_21937112 LG20_21937153 LG20_21937170 LG20_21937172 LG20_21937324 LG20_21937485 LG20_21940577 LG20_21940584 LG20_21940596 LG20_21940611 LG20_21940643 LG20_21940665 LG20_21940684 LG20_21940721 LG20_21940819 LG20_21940893 contig695_58443 contig695_58618 contig695_58621 contig695_58628 M T. sp. "dhonti twiyu" M N. olivaceous M J. marksmithi M J. dickfeldi M J. sp. “regani south” M J. marlieri M J. transcriptus M C. sp. “ndobhoi” M C. sp. “bifrenatus” M C. cyanophleps M C. popelini M C. brichardi M N. mondabu M J. sp. "marlieri south" M J. ornatus M T. bifrenatus F T. brichardi M T. brichardi M J. regani M T. sp. "dhonti north" M N. toae M T. sp. "shell" M V. moorii F T. vittatus M J. sp. "kombe" M L. callipterus M L. kendalli M N. furcifer F L. tigripictilis M L. sp. "meeli kipili" M L. lemairii M N. devosi F N. tretocephalus M N. sp. "brevis magara" M N. brevis M N. calliurus M L. ocellatus M N. sp. "ventralis stripe" F N. cylindricus F C. popelini M N. sexfasciatus M L. cunningtoni M N. multifasciatus M N. savoryi F N. pulcher F L. signatus M N. brichardi F N. mondabu F J. marlieri F N. leloupi M N. sp. "gracilis tanzania" F N. sp. "falcicula mahale" F N. sp. "gracilis tanzania" F N. sp. "caudopunctatus kipili" M N. petricola M N. splendens M N. mustax M N. fasciatus M N. pulcher M N. walteri M N. tretocephalus M N. sp. “falcicula mahale” M N. timidus M N. splendens M N. hecqui F V. moorii M L. elongatus F L. elongatus F C. brichardi M L. attenuatus F N. fasciatus F N. mustax F N. brevis F L. ocellatus M N. sp. "kombe" F N. sp. "kombe" F N. obscurus F T. temporalis F L. kendalli M N. modestus F J. sp. "kombe" F N. sexfasciatus M A. calvus F A. calvus F L. lemairii M N. tetracanthus F N. tetracanthus M N. caudopunctatus F N. caudopunctatus F J. sp. “regani south” F N. multifasciatus M A. sp. "compressiceps shell" F A. sp. "compressiceps shell" F T. sp. "shell" M A. compressiceps F J. ornatus F A. compressiceps F N. christyi M N. crassus M L. signatus F N. savoryi M N. christyi F L. callipterus M N. meeli F N. meeli M L. sp. "ornatipinnis zambia" F L. sp. "ornatipinnis zambia" F L. laparogramma M L. laparogramma F N. sp. "ventralis stripe" M N. buescheri F N. buescheri F T. sp. "dhonti north" F N. brichardi F N. helianthus M N. marunguensis F N. marunguensis F N. olivaceous F N. longicaudatus M N. falcicula F N. falcicula F N. toae M N. pleuromaculatus F N. pleuromaculatus F L. ornatipinnis M L. profundicola M N. ventralis F N. ventralis F N. boulengeri M L. speciosus F L. speciosus F L. profundicola M N. similis F N. similis F C. sp. "ndobhoi" M N. longior F N. walteri F J. regani F N. niger F T. bifrenatus M N. boulengeri F J. sp. "marlieri south" F T. dhonti M N. leloupi F L. mimicus F N. sp. "furcifer ulwile" M N. sp. "furcifer ulwile" M N. sp. "caudopunctatus kipili" F N. longior M N. sp. "eseki" F N. sp. "eseki" M N. sp. "cygnus" M L. kamambae F L. kamambae F J. marksmithi F N. timidus F C. cyanophleps F N. petricola F L. sp. "meeli kipili" F T. sp. "dhonti twiyu" F N. bifasciatus F J. transcriptus M T. brachygnathus Fig. S2. Genotypes of GWAS F L. attenuatus F N. gracilis M L. mimicus outlier regions (approach 1). M T. temporalis F N. sp. "brevis magara" F N. calliurus Heatmaps show individual F L. cunningtoni F T. brachygnathus M N. chitamwebwai F N. sp. "cygnus" genotypes for outlier SNPs F L. kungweensis M L. kungweensis M N. niger (Haplochromini and Cyprichromini M N. helianthus M T. sp. "lufubu" M N. cylindricus 100 most significant SNPs, F N. crassus F N. furcifer F N. prochilus Lamprologini three outlier regions F N. modestus M N. bifasciatus M N. gracilis on LG15, LG20 and an unplaced F N. chitamwebwai M T. vittatus M L. ornatipinnis contig) of sex-linked regions M T. dhonti F J. dickfeldi F C. bifrenatus detected by GWAS shown in fig. M N. longicaudatus M N. obscurus 5 F N. nigriventris S1; purple: homozygous; green: M N. nigriventris M N. prochilus heterozygous. Bathybatini Haplochromini

Benthochromini Lamprologini

Cyphotilapiini Limnochromini

Ectodini Perissodini

Eretmodini Trematocarini

Fig. S3. Sex-specific SNP windows per tribe (approach 2). Gray dots show results for tests of overrepresentation of XY- (left Y-axis, positive scale) and ZW- (left Y-axis, negative scale) SNPs in windows of 10 kb with a slide of 2 kb. Repetitive sequence regions on LGs 02, 03a and 03b were excluded in the final call set of sex chromosomes and are plotted in lighter gray. Background shadings refer to LGs of the reference genome. Vertical lines indicate XY-ZW SNP difference per window normalized by the number of species (right Y-axis), windows with more XY-SNPs are plotted with blue lines, those with more ZW-SNPs with red lines. Dotted horizontal lines indicate the largest absolute XY-ZW difference normalized by species number obtained in each tribe over 100 permutations (right Y-axis). 6 Supplementary Figure 4

Benthochromini | LG10 Cyphotilapiini | LG09 Cyphotilapiini | LG16 M C. frontosa

F C. frontosa M C. gibberosa

F C. sp. "5-bar frontosa” F B. tricoti F C. sp. "5-bar frontosa” F C. gibberosa F B. melanoides F C. frontosa M B. tricoti M C. frontosa M C. sp. "5-bar frontosa” M B. melanoides M C. gibberosa F C. gibberosa

M C. sp. "5-bar frontosa” w

o F C. benthicola

55 F C. benthicola M C. benthicola M C. benthicola

50 w w o o erence per wind f 0 60 45

−10 40 40 erence per wind erence per wind f f XY−ZW SNP dif −20 20 icoti r

B. t 0 −30 B. melanoides XY−ZW SNP dif XY−ZW SNP dif berosa berosa b b C. frontosa C. frontosa C. gi C. gi C. benthicola C. benthicola . "5−bar frontosa" . "5−bar frontosa" p p s s C. C.

Trematocarini | LG04 Eretmodini | LG07 Eretmodini | LG10

F T. unimaculatum

F T. macrostoma F T. irsacae F S. marlieri F T. zebra F S. erythrodon F E. marksmithi M T. zebra F E. marksmithi F S. marlieri F T. marginatum F S. erythrodon F T. irsacae M T. marginatum F E. cyanostictus F E. cyanostictus

M S. marlieri M E. marksmithi M T. unimaculatum M E. marksmithi M S. marlieri M T. macrostoma M S. erythrodon M S. erythrodon

M T. nigrifrons M T. irsacae M T. irsacae M E. cyanostictus F T. nigrifrons M E. cyanostictus

0 w w o o 50 22

−50 20 40 18 −100 16 erence per wind erence per wind f f 30 14 −150 12 20

XY−ZW SNP difference per window 10 XY−ZW SNP dif XY−ZW SNP dif 10 i i r r lie lie T. zebra r r ksmithi ksmithi r r T. nigrifrons . irsacae . irsacae ythrodon ythrodon r r T T anostictus anostictus S. ma S. ma T. marginatum T. macrostoma y y T. unimaculatum S. e S. e E. ma E. ma E. c E. c

7 Supplementary Figure 4 (continued)

F T. vittatus M T. sp. "dhonti twiyu" Lamprologini | LG20 M T. sp. "dhonti north" M T. bifrenatus F T. brichardi M T. brichardi M T. sp. "shell" M C. sp. "ndobhoi" M C. cyanophleps M J. marksmithi M N. mondabu M J. dickfeldi M J. regani M J. sp. "marlieri south" M J. marlieri M J. sp. "regani south" M C. popelini M J. ornatus M J. sp. "kombe" M J. transcriptus M C. sp. "bifrenatus" M C. brichardi M N. olivaceous M V. moorii F L. sp. "ornatipinnis zambia" F N. sp. "brevis magara" F N. calliurus F N. brevis M N. brevis M N. sp. "brevis magara" M N. calliurus F L. ornatipinnis M L. ornatipinnis F L. kungweensis M L. kungweensis M L. sp. "ornatipinnis zambia" M N. sp. "ventralis stripe" F N. sp. "ventralis stripe" F A. sp. "compressiceps shell" M A. sp. "compressiceps shell" F N. ventralis M N. ventralis F L. laparogramma M L. laparogramma F L. signatus M L. signatus F N. similis M N. similis F N. multifasciatus M N. multifasciatus F N. fasciatus M N. fasciatus M L. lemairii F L. lemairii F A. compressiceps M A. compressiceps F A. calvus M A. calvus F L. speciosus M L. speciosus F L. ocellatus M L. ocellatus F N. leloupi M N. leloupi F N. sp. "caudopunctatus kipili" M N. sp. "caudopunctatus kipili" F N. caudopunctatus M N. caudopunctatus F L. callipterus M L. callipterus F N. meeli M N. meeli F L. sp. "meeli kipili" F L. attenuatus M L. attenuatus M L. sp. "meeli kipili" F L. profundicola M L. profundicola F N. boulengeri F N. pleuromaculatus M N. pleuromaculatus F L. kamambae M L. kamambae M L. mimicus M N. boulengeri F L. mimicus F L. kendalli M L. kendalli F L. elongatus M L. elongatus M T. dhonti F T. brachygnathus M T. vittatus F T. sp. "dhonti twiyu" F T. dhonti F T. sp. "dhonti north" F T. temporalis M T. brachygnathus M T. temporalis F T. bifrenatus F C. sp. "bifrenatus" F J. dickfeldi F J. marksmithi F J. ornatus F J. transcriptus F J. sp. "kombe" F N. buescheri M N. buescheri F N. longior M N. longior F C. cyanophleps M N. timidus M N. mustax F N. mustax F N. bifasciatus M N. bifasciatus F N. cylindricus M N. cylindricus F N. niger M N. niger F C. popelini F N. timidus F J. sp. "regani south" M N. obscurus F N. prochilus M N. prochilus F N. obscurus M N. sp. "furcifer ulwile" F N. sp. "furcifer ulwile" F N. furcifer M N. furcifer F C. sp. "ndobhoi" F C. brichardi M N. toae F T. sp. "shell" F N. tretocephalus M N. tretocephalus F N. sexfasciatus M N. sexfasciatus M N. walteri F N. walteri F N. chitamwebwai M N. chitamwebwai F N. falcicula M N. falcicula F N. tetracanthus M N. tetracanthus M L. cunningtoni F L. cunningtoni F N. toae F N. sp. "eseki" M N. sp. "eseki" M N. christyi F N. christyi F N. mondabu F N. petricola M N. petricola F N. modestus M N. modestus F N. sp. "cygnus" M N. sp. "cygnus" F N. marunguensis M N. marunguensis M N. crassus M N. helianthus F N. helianthus F N. crassus F N. sp. "kombe" F N. savoryi M N. savoryi F N. sp. "gracilis tanzania" M N. sp. "gracilis tanzania" M N. sp. "falcicula mahale" F N. sp. "falcicula mahale" M N. brichardi F N. brichardi F N. pulcher M N. pulcher F N. olivaceous M N. gracilis F N. gracilis M N. sp. "kombe" F V. moorii F J. sp. "marlieri south" F J. regani F J. marlieri F N. longicaudatus M N. longicaudatus M N. nigriventris F N. nigriventris 40

20

0

−20 XY−ZW SNP difference per window N. toae N. niger N. meeli J. regani N. brevis T. dhonti N. similis V. moorii A. calvus N. walteri N. leloupi L. lemairii T. vittatus sp. "shell" N. longior N. gracilis J. marlieri J. ornatus N. furcifer N. timidus N. christyi N. savoryi L. kendalli N. mustax sp. "eseki" N. pulcher N. crassus J. dickfeldi L. mimicus C. popelini L. signatus N. falcicula N. calliurus N. petricola T. brichardi L. ocellatus N. ventralis N. brichardi C. brichardi N. fasciatus N. prochilus sp. "kombe" sp. "kombe" N. obscurus L. elongatus N. mondabu sp. "cygnus" T. L. speciosus T. bifrenatus L. callipterus N. modestus N. buescheri T. temporalis L. attenuatus N. helianthus sp. "ndobhoi" N. N. cylindricus J. marksmithi N. boulengeri N. bifasciatus N. olivaceous L. kamambae N. nigriventris L. ornatipinnis J. transcriptus L. cunningtoni J. L. profundicola N. sp. "bifrenatus" N. N. tetracanthus N. sexfasciatus L. kungweensis C. cyanophleps sp. "meeli kipili" C. N. tretocephalus N. multifasciatus N. longicaudatus L. laparogramma N. marunguensis sp. "dhonti north" sp. "dhonti twiyu" N. chitamwebwai sp. "compr. shell" T. brachygnathus sp. "regani south" A. compressiceps C. L. sp. "caudop. kipili" sp. "furcifer ulwile" sp. "marlieri south" N. caudopunctatus N. pleuromaculatus sp. "brevis magara" sp. "ventralis stripe" T. T. J. A. sp. "ornatip. zambia" J. N. N. sp. "falcicula mahale" sp. "gracilis tanzania" N. N. L. N. N. Supplementary Figure 4 (continued)

Haplochromini/Tropheini | LG05

M O. indermauri F O. indermauri F A. burtoni M A. burtoni F H. sp. "chipwa" M H. sp. "chipwa" M P. trewavasae M P. sp. "red" M P. sp. "kipili brown" M P. horii M P. sp. "macrognathus rainbow" M P. sp. "polyodon texas" M P. sp. "giant" M I. loocki M P. sp. "orthognathus ikola" M P. fasciolatus M P. curvifrons F P. curvifrons M L. dardennii F L. dardennii F P. marginatus (North) F P. marginatus (South) F P. babaulti (North) F P. babaulti (South) F G. pfefferi M G. pfefferi F C. horei M C. horei F L. labiatus M L. labiatus F T. duboisi M T. duboisi F T. annectens M Tropheus annectens F T. sp. "brichardi kipili" M T. sp. "brichardi kipili" F T. sp. "lukuga" M T. sp. "lukuga" F T. sp. "lunatus" M T. sp. "lunatus" F T. brichardi M T. brichardi M T. sp. "kirschfleck" F T. sp. "kirschfleck" M T. sp. "black" F T. sp. "black" F T. sp. "mpimbwe" M T. sp. "mpimbwe" F T. sp. "murago" M T. sp. "murago" F T. polli M T. polli F T. moorii M T. moorii F T. sp. "red" M T. sp. "red" M P. famula F P. famula F P. fasciolatus F P. sp. "orthognathus ikola" M P. orthognathus F P. orthognathus F I. loocki F P. trewavasae F P. macrognathus M P. macrognathus F P. sp. "kipili brown" F P. sp. "red" F P. horii M P. sp. "kazumbae" F P. sp. "kazumbae" F P. sp. "macrognathus rainbow" F P. sp. "moshi yellow" M P. sp. "moshi yellow" M P. ephippium F P. ephippium F P. sp. "giant" F P. sp. "polyodon texas" F P. polyodon M P. polyodon M S. diagramma F S. diagramma M P. marginatus (North) M P. marginatus (South) M P. babaulti (North) M P. babaulti (South)

25 w o

20

15

10 erence per wind f 5

0

− XY−ZW SNP dif i i ii ii r r r r a" e" w" w" th) e ula f r w o o w wn" ola" toni xas" ago" r lack" m k o asae odon ef r . polli e f mau ell u v b . "red" . "red" y a amma u T r f vifrons ichardi y r b a (North) P. ho p p (South) r (South) . moo r (No . "giant" I. loocki ainb . " C. horei m s s . duboisi r T

w p

p P. . "lukuga" T . "chip A. G. p e s asciolatus . b . "lunatus" L. labiatus . " T. f p s p P. thognathus T p . p . annectens odon t s P. pol L. dardennii r s thogn. i s ichardi kipili" . "mpimb P. cu T s P. T y . r P. ephippium r . "kazumbae" . "kirschfleck" P. p . O. inde . "kipili br . S. diag P. tr T p p s T H. T p s s . "moshi . P. o s . "o . "b p . P. macrognathus T p p . "pol s T P. P. babaulti P. babaulti s s P. p . s . "macrogn. P. T P. P. marginatus p P. marginatus P. s P.

9 Supplementary Figure 4 (continued)

Haplochromini/Tropheini | start of LG19

M O. indermauri M T. polli M T. sp. "lunatus" M T. sp. "lukuga" M T. brichardi M T. sp. "kirschfleck" M T. sp. "black" F A. burtoni M A. burtoni F H. sp. "chipwa" M H. sp. "chipwa" F O. indermauri F G. pfefferi M G. pfefferi F C. horei M C. horei M L. dardennii F L. dardennii M P. famula F P. famula F P. sp. "orthogn. ikola" M P. sp. "orthogn. ikola" M P. orthognathus F P. orthognathus M I. loocki F I. loocki F P. fasciolatus M P. fasciolatus F T. duboisi M T. duboisi F T. annectens M T. annectens F T. sp. "mpimbwe" M T. sp. "mpimbwe" F T. sp. "lunatus" F T. sp. "brichardi kipili" M T. sp. "brichardi kipili" F T. sp. "lukuga" F T. brichardi F T. sp. "kirschfleck" F T. sp. "black" F T. polli F T. sp. "murago" M T. sp. "murago" F T. moorii M T. moorii F T. sp. "red" M T. sp. "red" F L. labiatus M L. labiatus F P. macrognathus M P. macrognathus F P. trewavasae M P. trewavasae F P. sp. "kipili brown" M P. sp. "kipili brown" F P. sp. "red" M P. sp. "red" F P. horii M P. horii F P. sp. "moshi yellow" M P. sp. "moshi yellow" M P. ephippium F P. ephippium M P. sp. "kazumbae" F P. sp. "kazumbae" F P. sp. "macrogn. rainbow" M P. sp. "macrogn. rainbow" F P. sp. "giant" M P. sp. "giant" F P. sp. "polyodon texas" M P. sp. "polyodon texas" F P. polyodon M P. polyodon M S. diagramma F S. diagramma M P. curvifrons F P. curvifrons F P. marginatus (North) M P. marginatus (North) F P. marginatus (South) M P. marginatus (South) F P. babaulti (North) M P. babaulti (North) F P. babaulti (South) M P. babaulti (South)

80

60

40

20

0 XY−ZW SNP difference per window (North) T. polli (North) P. horii (South) (South) I. loocki C. horei sp. "red" sp. "red" T. moorii P. famula A. burtoni T. duboisi G. pfefferi sp. "giant" L. labiatus sp. "black" T. P. T. brichardi sp. "lukuga" P. polyodon L. dardennii sp. "chipwa" sp. "lunatus" P. curvifrons P. sp. "murago" T. annectens T. P. ephippium P. fasciolatus O. indermauri S. diagramma P. trewavasae T. sp. "mpimbwe" H. T. T. sp. "kazumbae" sp. "kirschfleck" P. orthognathus sp. "kipili brown" P. macrognathus T. P. babaulti sp. "moshi yellow" P. T. P. babaulti sp. "orthogn. ikola" sp. "brichardi kipili" P. sp. "polyodon texas" P. P. T. P. marginatus P. marginatus sp. "macrogn. rainbow" P. P.

10 Supplementary Figure 4 (continued)

Haplochromini/Tropheini | middle of LG19

M O. indermauri M T. polli M T. sp. "lunatus" M T. sp. T. M Tropheus brichardi M T. sp. "kirschfleck" M T. sp. "black" F A. burtoni M A. burtoni F H. sp. "chipwa" M H. sp. "chipwa" F O. indermauri F G. pfefferi M G. pfefferi F C. horei M C. horei M L. dardennii F L. dardennii M P. orthognathus F P. orthognathus F P. sp. "orthogn. ikola" M P. sp. "orthogn. ikola" M I. loocki F I. loocki F P. fasciolatus M P. fasciolatus M S. diagramma F S. diagramma M P. famula F P. famula F L. labiatus M L. labiatus F T. duboisi M T. duboisi F T. sp. "mpimbwe" M T. sp. "mpimbwe" F T. annectens M T. annectens F T. sp. "lunatus" F T. sp. "brichardi kipili" M T. sp. "brichardi kipili" F T. sp. "lukuga" F T. brichardi F T. polli F T. sp. "kirschfleck" F T. sp. "black" F T. sp. "murago" M T. sp. "murago" F T. moorii M T. moorii F T. sp. "red" M T. sp. "red" F P. macrognathus M P. macrognathus F P. trewavasae M P. trewavasae F P. sp. "kipili brown" M P. sp. "kipili brown" F P. sp. "red" M P. sp. "red" F P. horii M P. horii F P. sp. "moshi yellow" M P. sp. "moshi yellow" M P. ephippium F P. ephippium M P. sp. "kazumbae" F P. sp. "kazumbae" F P. sp. "macrogn. rainbow" M P. sp. "macrogn. rainbow" F P. sp. "giant" M P. sp. "giant" F P. sp. "polyodon texas" M P. sp. "polyodon texas" F P. polyodon M P. polyodon M P. curvifrons F P. curvifrons F P. marginatus (North) M P. marginatus (North) F P. marginatus (South) M P. marginatus (South) F P. babaulti (North) M P. babaulti (North) F P. babaulti (South) M P. babaulti (South)

60

40

20

0 XY−ZW SNP difference per window (North) T. polli (North) (South) P. horii (South) I. loocki C. horei sp. "red" sp. "red" T. moorii P. famula A. burtoni T. duboisi G. pfefferi sp. "giant" L. labiatus sp. "black" T. P. T. brichardi sp. "lukuga" P. polyodon L. dardennii sp. "chipwa" sp. "lunatus" P. curvifrons sp. "murago" P. T. annectens T. P. ephippium P. fasciolatus O. indermauri S. diagramma P. trewavasae T. sp. "mpimbwe" H. T. T. sp. "kazumbae" sp. "kirschfleck" P. orthognathus sp. "kipili brown" P. macrognathus T. P. babaulti sp. "moshi yellow" T. P. P. babaulti sp. "orthogn. ikola" sp. "brichardi kipili" P. sp. "polyodon texas" P. T. P. P. marginatus P. marginatus sp. "macrogn. rainbow" P. P.

11 Haplochromini/Tropheini end of

M O. indermauri F O. indermauri M P. famula M P. curvifrons F P. curvifrons F A. burtoni M A. burtoni F H. sp. "chipwa" M H. sp. "chipwa" M P. trewavasae M P. sp. "kipili brown" M P. sp. "red" M P. horii M P. sp. "macrognathus rainbow" M P. sp. "polyodon texas" M P. sp. "giant" M P. sp. "orthognathus ikola" M I. loocki M P. fasciolatus F G. pfefferi M G. pfefferi M L. dardennii F L. dardennii F P. marginatus (North) F P. marginatus (South) F P. babaulti (North) F P. babaulti (South) F C. horei M C. horei F Petrochromis famula F T. duboisi M T. duboisi F T. sp. "mpimbwe" M T. sp. "mpimbwe" F T. sp. "brichardi kipili" M T. sp. "brichardi kipili" F T. sp. "kirschfleck" M T. sp. "kirschfleck" F T. sp. "lunatus" M T. sp. "lunatus" F T. sp. "lukuga" M T. sp. "lukuga" F T. brichardi M T. brichardi M T. sp. "black" F T. sp. "black" F T. annectens M T. annectens F T. polli M T. polli F T. sp. "murago" M T. sp. "murago" F T. moorii M T. moorii F T. sp. "red" M T. sp. "red" F L. labiatus M L. labiatus F P. macrognathus M P. macrognathus F P. trewavasae F P. sp. "kipili brown" F P. sp. "red" F P. horii F P. sp. "orthogn. ikola" M P. orthognathus F P. orthognathus F P. fasciolatus F I. loocki F P. sp. "moshi yellow" M P. sp. "moshi yellow" M P. ephippium F P. ephippium F P. sp. "macrogn. rainbow" M P. sp. "kazumbae" F P. sp. "kazumbae" F P. sp. "polyodon texas" F P. sp. "giant" F P. polyodon M P. polyodon M S. diagramma F S. diagramma M P. marginatus (North) M P. marginatus (South) M P. babaulti (North) M P. babaulti (South)

0

20

0

0

−0 XY−ZW SNP difference per window (North) T. polli P. horii I. loocki C. horei T. moorii P. famula A. burtoni T. duboisi G. pfefferi L. labiatus T. sp. "red" P. sp. "red" T. brichardi P. polyodon L. dardennii P. curvifrons P. sp. "giant" T. annectens T. sp. "black" P. ephippium P. fasciolatus O. indermauri S. diagramma P. trewavasae T. sp. "lukuga" H. sp. "chipwa" T. sp. "lunatus" T. sp. "murago" P. orthognathus P. macrognathus T. sp. "mpimbwe" P. babaulti (North) T. sp. "kirschfleck" P. sp. "kazumbae" P. babaulti (South) P. sp. "kipili brown" P. sp. "moshi yellow" T. sp. "brichardi kipili" P. marginatus P. marginatus (South) P. sp. "polyodon texas" P. sp. "macrogn. rainbow" P. sp. "orthognathus ikola"

Fig. S4. Species values of sex-specific outlier regions (approach 2). Dendograms of samples based on divisive hierarchical clustering of genotype values in outlier windows of approach 2 with individuals clustering by sex colored in blue for XY-systems and in red for ZW-systems and boxplots of per species XY-ZW difference in XY/ZW outlier windows (fig. S3) with color-coding based on the dendograms. Boxplot center lines represent the median, box limits the upper and lower quartiles, and whiskers the 1.5x interquartile range; points represent outliers.

12 Bathybates fasciatus Bathybates ferox

Bathybates graueri Bathybates minor

Bathybates vittatus Hemibates stenosoma

Perissodus microlepis Plecodus multidentatus

Plecodus paradoxus Xenochromis hecqui

Fig. S5. Chromosome-wide sex-specific alleles in Hemibates stenosoma and Plecodus paradoxus. Visualization of per species XY-ZW differences in windows of 10 kb with a slide of 2 kb overlaid on the tribe- wise test results for sex-specific SNPs for Bathybatini and Perissodini (fig. S3). 13 Supplementary Figure 6

Bathybatini Benthochromini Boulengerochromini Cyphotilapiini

Batgra Benhor Boumic Cphgib

6 4 4 2 4 2 2 2 1

0 0 0 0 Density −2 −1 −2 −2 −4 −2 −4 −4 −6 2 4 6 8 10 2 4 6 8 10 12 1.0 1.5 2.0 2.5 3.0 3.5 4.0 2 4 6 8 10 12 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

10 5 3

2 10

5 1 0 5 0 0 −1 0 −5 −2

(per window) −5 −5 −3

XY-ZW-patterned SNPs −10 −10 −4

10 5 10

5 0 5

0 0 −5 −5 −5 (per outlier window) XY-ZW-patterned SNPs −10 −10 LG02 LG04 LG05 LG08 LG09 LG11 LG14 LG16 LG17 LG19 LG20 LG23 LG02 LG17 LG20 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03b LG03b

3 P = 0.345 15 P = 0.034 P = 0.778 40 2 10 20 1 5

0 0 0

−1 −5 −20 (per outlier window) Sex-patterned SNPs −2 −10 −40 −3 −15 5 6 7 8 9 10 5 6 7 8 9 10 11 12 6 8 10 12 Number of SNPs Number of SNPs Number of SNPs

0.015

0.010

(normalised) 0.005 Sex-patterned SNPs

0.000 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b

14 Supplementary Figure 6 (continued)

Cyprichromini

Cypdwj Cyplep Cypmic PcybrN

2 1.0 6 4 4 1 0.5 2 2

0 0 0.0 0

Density −2 −2 −0.5 −4 −1 −4 −6 −2 −1.0 1.0 1.5 2.0 2.5 3.0 3.5 4.0 0 5 10 15 20 25 0 5 10 15 20 25 1.0 1.5 2.0 2.5 3.0 3.5 4.0 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

3 4 25 2 10 3 20 1 2 0 15 0 1 10 −1 0 −10 5 −2 −1

(per window) 0 −20 −3 −5 −2 XY-ZW-patterned SNPs −4 −10 −3

25 10 20

0 15 10

−10 5

0

(per outlier window) −20

XY-ZW-patterned SNPs −5

−10 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG03b LG03a LG03b

100 P = 0 P = 0 100 50 50

0 0

−50

(per outlier window) −50 Sex-patterned SNPs −100

−100 10 15 20 25 5 10 15 20 25 Number of SNPs Number of SNPs

1.5 1.5

1.0 1.0

(normalised) 0.5 0.5 Sex-patterned SNPs

0.0 0.0 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b LG03a LG03b

15 Supplementary Figure 6 (continued)

Cyprichromini Haplochromini/Tropheini

Pcynig Ctehor Gnapfe Intloo

4 2 2 3

2 2 1 1 1

0 0 0 0

Density −1 −1 −1 −2 −2

−2 −3 −2 −4 5 10 15 2 4 6 8 10 12 5 10 15 20 5 10 15 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

25 5 15 5 20 10 0 15 0 5 10 −5 5 0 −5 −10 0 (per window) −5 −5 −15

XY-ZW-patterned SNPs −10 −10 −10

25 5 15 5 20 10 0 15 0 5 10 −5 5 0 −5 −10 0

(per outlier window) −5

XY-ZW-patterned SNPs −5 −15 −10 −10 −10 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG02 LG04 LG05 LG07 LG08 LG09 LG10 LG11 LG13 LG14 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG04 LG09 LG11 LG14 LG15 LG17 LG19 LG20 LG23 LG02 LG07 LG12 LG15 LG23 LG03a LG03b LG03b LG03a LG03b LG03b

15 4 P = 0.003 P = 0.21 100 P = 0 P = 0.174 10 50 50 2 5

0 0 0 0

−5 −50

(per outlier window) −2

Sex-patterned SNPs −50 −10

−15 −100 −4 6 8 10 12 14 16 5 6 7 8 9 10 11 12 5 10 15 20 6 8 10 12 14 16 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

0.35 0.7

0.30 0.6

0.25 0.5

0.20 0.4

0.15 0.3

(normalised) 0.10 0.2 Sex-patterned SNPs 0.05 0.1

0.00 0.0 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b LG03a LG03b

16 Supplementary Figure 6 (continued)

Haplochromini/Tropheini

Loblab Peteph Petfam Petfas

3 2 1.5 2 2 1.0 1 1 1 0.5

0 0.0 0 0 Density −1 −0.5 −1 −1 −1.0 −2 −1.5 −2 −3 −2 2 4 6 8 2 4 6 8 10 12 14 5 10 15 5 10 15 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

20

15 15 5 10 10 10 5 5 0 5

0 0 0 (per window) −5 −5 −5 −5 XY-ZW-patterned SNPs −10

20

15 15 5 10 10 10 5 5 0 5

0 0 0

(per outlier window) −5 −5

XY-ZW-patterned SNPs −5 −5 −10 LG13 LG16 LG1 LG1 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG12 LG14 LG15 LG16 LG1 LG1 LG20 LG23 LG02 LG08 LG11 LG12 LG04 LG05 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG16 LG1 LG1 LG1 LG20 LG23 LG02 LG05 LG06 LG07 LG08 LG10 LG12 LG13 LG16 LG1 LG1 LG20 LG22 LG23 LG03b LG03a LG03a LG03b LG03a LG03b

6 P = 0.13 P = 0.05 60 P = 0.002 P = 0.002 10 40 4 40 5 20 2 20

0 0 0 0

−2 −20 −5 −20 (per outlier window)

Sex-patterned SNPs −40 −4 −10 −60 −40 −6 5 6 7 8 9 6 8 10 12 14 6 8 10 12 14 16 1 6 8 10 12 14 16 1 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

0.25 0.15 0.20

0.15 0.10

0.10 (normalised) 0.05

Sex-patterned SNPs 0.05

0.00 0.00 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG1 LG1 LG1 LG20 LG22 LG23 LG13 LG14 LG15 LG16 LG1 LG1 LG1 LG20 LG22 LG23 LG03a LG03b LG03a LG03b

17 Supplementary Figure 6 (continued)

Haplochromini/Tropheini

Petmac Petpol Pscbab Pscple

1.5 2 2 1.5 1.0 1.0 1 1 0.5 0.5

0.0 0 0 0.0 Density −0.5 −0.5 −1 −1 −1.0 −1.0 −2 −1.5 −1.5 −2 2 4 6 8 10 12 5 10 15 5 10 15 5 10 15 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

10 15 15 15 10 5 10 5 10

0 5 0 5

−5 −5 0

(per window) 0 −10 −10 −5 XY-ZW-patterned SNPs −5 −15

10 15 15 15 10 5 10 5 10

0 5 0 5

−5 −5 0 0 (per outlier window) −10 XY-ZW-patterned SNPs −10 −5 −5 −15 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG16 LG18 LG19 LG22 LG23 LG04 LG05 LG07 LG08 LG12 LG13 LG17 LG19 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG11 LG12 LG14 LG15 LG16 LG17 LG19 LG20 LG22 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG14 LG15 LG16 LG19 LG20 LG22 LG23 LG03b LG03a LG03b LG03b

P = 1 P = 0.5 P = 0.002 P = 0.002 10 40 50 5 5 20

0 0 0 0

−5 −20 (per outlier window)

Sex-patterned SNPs −5 −50 −10 −40

5 6 7 8 9 10 11 12 6 8 10 12 14 16 6 8 10 12 14 16 18 6 8 10 12 14 16 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

0.25 0.30 0.20 0.25

0.20 0.15

0.15 0.10

(normalised) 0.10

Sex-patterned SNPs 0.05 0.05

0.00 0.00 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b LG03a LG03b

18 Supplementary Figure 6 (continued)

Haplochromini/Tropheini Ectodini

Simdia Tromoo Tronig Auldew

4 4 1.5 2 1.0 2 2 1 0.5

0 0 0.0 0

Density −0.5 −1 −2 −2 −1.0 −2 −1.5 −4 −4 2 4 6 8 1 2 3 4 5 6 7 2 4 6 8 10 12 2 4 6 8 10 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

6 5 5 10 4

2 0 0 0 5

−2 −5 (per window) −5 −4 0

−6 XY-ZW-patterned SNPs

6 5 5 10 4

2 0 0 0 5

−2 −5 −5 −4 0 (per outlier window)

XY-ZW-patterned SNPs −6 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG02 LG04 LG06 LG10 LG12 LG13 LG14 LG15 LG16 LG18 LG23 LG02 LG04 LG05 LG06 LG08 LG09 LG10 LG11 LG12 LG15 LG16 LG17 LG18 LG22 LG23 LG01 LG02 LG05 LG07 LG08 LG11 LG13 LG17 LG18 LG19 LG20 LG22 LG03a LG03b LG03b LG03a LG03a LG03b

3 300 10 P = 0.174 10 P = 0.56 P = 0.344 P = 0.1 2 200 5 5 1 100

0 0 0 0

−1 −100 −5

(per outlier window) −5 Sex-patterned SNPs −2 −200 −10 −3 −300 −10 5 6 7 8 9 5.0 5.5 6.0 6.5 7.0 2 4 6 8 10 12 5 6 7 8 9 10 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

19 Supplementary Figure 6 (continued)

Ectodini

Calmac Calple Cyafur Enamel

3 3 2 2 2 2 1 1 1 1

0 0 0 0 Density −1 −1 −1 −1

−2 −2 −2 −2 −3 −3 2 4 6 8 10 12 5 10 15 2 4 6 8 10 12 14 5 10 15 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

15 10 5 10 5 5 0 5 0 0 −5 0 −5 −5 −5 −10 (per window) −10 −10 −10 −15 XY-ZW-patterned SNPs −15

15 10 5 10 5 5 0 5 0 0 −5 0 −5 −5 −5 −10

(per outlier window) −10 −10 XY-ZW-patterned SNPs −10 −15 −15 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG08 LG09 LG10 LG11 LG04 LG05 LG06 LG07 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG07 LG09 LG10 LG12 LG14 LG15 LG16 LG22 LG23 LG01 LG02 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG19 LG20 LG22 LG23 LG03b LG03a LG03b LG03b LG03a

P = 1 P = 0.007 P = 0.033 P = 0.002 40 30 40 50 20 20 20 10

0 0 0 0

−10 −20 −20 (per outlier window)

Sex-patterned SNPs −20 −50 −40 −40 −30

5 6 7 8 9 10 11 12 6 8 10 12 14 16 6 8 10 12 14 6 8 10 12 14 16 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

0.12 0.5 0.010 0.10 0.4 0.008 0.08 0.006 0.3 0.06

0.004 0.2

(normalised) 0.04

Sex-patterned SNPs 0.02 0.002 0.1

0.00 0.000 0.0 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b LG03a LG03b LG03a LG03b

20 Supplementary Figure 6 (continued)

Ectodini

Ophven Xenbou Xennas Xenspi

3 3 2 2 2 2 1 1 1 1

0 0 0 0

Density −1 −1 −1 −1 −2 −2 −2 −2 −3 −3 2 4 6 8 10 5 10 15 2 4 6 8 10 2 4 6 8 10 12 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

10 10 10 10 5 5 5 5 0 0 0 −5 0

−10 −5 (per window) −5 −5 −15 −10 XY-ZW-patterned SNPs −20

10 10 10 10 5 5 5 5 0 0 0 −5 0

−10 −5 −5 −5 (per outlier window) −15 XY-ZW-patterned SNPs −10 −20 LG01 LG02 LG04 LG06 LG07 LG10 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG01 LG02 LG04 LG06 LG07 LG08 LG10 LG12 LG14 LG15 LG17 LG19 LG20 LG22 LG23 LG02 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG16 LG17 LG18 LG20 LG22 LG23 LG02 LG04 LG07 LG16 LG19 LG22 LG03a LG03a LG03a LG03b LG03b

2 P = 0.75 20 P = 0.002 P = 0.584 P = NaN 10 5 1 10 5

0 0 0 0

−10 −5

(per outlier window) −1 Sex-patterned SNPs −5 −10 −20 −2 5 6 7 8 9 10 11 6 8 10 12 14 16 18 5 6 7 8 9 10 5 6 7 8 9 10 11 12 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

0.08

0.06

0.04 (normalised) 0.02 Sex-patterned SNPs

0.00 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b

21 Supplementary Figure 6 (continued)

Eretmodini

Erecya Eremar Spaery Tanirs

2 1.0 2 2

1 0.5 1 1

0 0 0.0 0 Density −1 −1 −0.5 −1

−2 −2 −1.0 −2 2 4 6 8 2 4 6 8 10 2 4 6 8 10 12 1 2 3 4 5 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

10 4 5 5

5 2 0 0 0 0 −5 (per window) −5 −5 −2 XY-ZW-patterned SNPs −10

7 10 5 5 6 5 0 0 5 0

−5 4

(per outlier window) −5 −5 XY-ZW-patterned SNPs −10 3 LG02 LG04 LG05 LG07 LG10 LG12 LG13 LG14 LG15 LG16 LG1 LG01 LG02 LG06 LG07 LG08 LG10 LG14 LG15 LG16 LG1 LG1 LG1 LG20 LG23 LG01 LG04 LG06 LG07 LG08 LG09 LG10 LG14 LG15 LG1 LG1 LG20 LG23 LG10

15 4 P = 0.684 P = 0.223 P = 0.03

5 10 2 5

0 0 0

−5

(per outlier window) −2 Sex-patterned SNPs −5 −10

−15 −4 5 6 7 8 9 5 6 7 8 9 10 5 6 7 8 9 10 11 12 Number of SNPs Number of SNPs Number of SNPs

0.007

0.006

0.005

0.004

0.003 (normalised) 0.002 Sex-patterned SNPs 0.001

0.000 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG1 LG1 LG1 LG20 LG22 LG23 LG03a LG03b

22 Supplementary Figure 6 (continued)

Lamprologini

Altcom Chabri Juldic Julorn

1.5 2 2 2 1.0

1 1 0.5 1

0 0.0 0 0 Density −0.5 −1 −1 −1 −1.0 −2 −2 −2 −1.5 5 10 15 5 10 15 2 4 6 8 10 12 2 4 6 8 10 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

10 15 15 10 10 5 10 5 5 5 0 0 0 0

(per window) −5 −5 −5 −5

XY-ZW-patterned SNPs −10 −10

10 15 15 10 10 5 10 5 5 5 0 0 0 0 −5 −5 (per outlier window) −5

XY-ZW-patterned SNPs −5 −10 −10 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG02 LG04 LG05 LG07 LG08 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG22 LG23 LG01 LG05 LG06 LG07 LG08 LG10 LG11 LG12 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG03a LG03a LG03b LG03a

40 15 P = 0.01 P = 0.013 10 P = 0.1 20 P = 1 10 20 5 10 5

0 0 0 0

−5 −5 −10

(per outlier window) −20 Sex-patterned SNPs −10 −10 −20 −40 −15 6 8 10 12 14 16 6 8 10 12 14 16 18 6 8 10 12 5 6 7 8 9 10 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

0.05

0.04

0.03

0.02 (normalised)

Sex-patterned SNPs 0.01

0.00 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b

23 Supplementary Figure 6 (continued)

Lamprologini

Julreg Lamkun Lamlem Lamoce

3 4 3 2 2 2 2 1 1

0 0 0 0 Density −1 −1 −2 −2 −2 −2 −3 −3 −4 2 4 6 8 10 1 2 3 4 5 6 2 4 6 8 10 12 1 2 3 4 5 6 7 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

6 4 5 5 4 2 2 0 0 0 0 −5 −2 −5 −2 (per window) −4 −10 −4 −6 XY-ZW-patterned SNPs −10

6 4 5 5 4 2 2 0 0 0 0 −5 −2 −5 −2 −4

(per outlier window) −10 XY-ZW-patterned SNPs −4 −6 −10 LG11 LG15 LG19 LG20 LG22 LG01 LG02 LG05 LG06 LG07 LG08 LG11 LG12 LG19 LG20 LG22 LG23 LG01 LG02 LG05 LG06 LG07 LG08 LG09 LG11 LG12 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG02 LG06 LG07 LG09 LG12 LG13 LG15 LG18 LG19 LG22 LG03a LG03b

3 10 15 P = 0.1 P = 1 P = 0.784 6 P = 0.25 2 10 4 5 5 1 2

0 0 0 0

−5 −1 −2

(per outlier window) −5

Sex-patterned SNPs −10 −4 −2 −15 −6 −3 −10 5 6 7 8 9 10 5.0 5.2 5.4 5.6 5. 6.0 6 8 10 12 5.0 5.5 6.0 6.5 7.0 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

24 Supplementary Figure 6 (continued)

Lamprologini

Lepatt Lepelo Neocyg Neocyl

3 2 2 1.0 2 1 1 0.5 1

0 0 0 0.0 Density −1 −1 −1 −0.5 −2 −2 −2 −1.0 −3 2 4 6 8 10 12 1 2 3 4 5 6 7 8 2 4 6 8 10 12 14 2 4 6 8 10 12 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

5 10 5 5

0 5 0 0 0 −5 −5 (per window) −5 −5 −10 −10 XY-ZW-patterned SNPs

5 10 5 5

0 5 0 0 0 −5 −5

−5 (per outlier window) −5 −10 −10 XY-ZW-patterned SNPs LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG04 LG06 LG07 LG13 LG14 LG15 LG18 LG02 LG04 LG05 LG06 LG07 LG08 LG10 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG01 LG04 LG05 LG06 LG07 LG08 LG10 LG11 LG13 LG14 LG16 LG17 LG19 LG20 LG03b LG03a

6 30 6 P = 0.5 P = 0.022 10 P = 0.021 P = 0.13 4 20 4 5 2 10 2

0 0 0 0

−2 −10 −2 −5 (per outlier window) Sex-patterned SNPs −4 −20 −4 −10 −6 −30 −6 6 8 10 12 5.0 5.5 6.0 6.5 7.0 .5 8.0 6 8 10 12 14 5 6 7 8 9 10 11 12 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

0.012 0.020 0.010 0.015 0.008

0.006 0.010

(normalised) 0.004 0.005 Sex-patterned SNPs 0.002

0.000 0.000 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b LG03a LG03b

25 Supplementary Figure 6 (continued)

Lamprologini

Neofas Neofur Neomod Neonig

4 2 2 2

2 1 1 1

0 0 0 0 Density

−1 −1 −2 −1

−2 −2 −4 −2 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 5 10 15 5 10 15 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

10 4 15 5 2 10 5

0 5 0 0 0 −2 −5 −5 (per window) −4 −5 −10 −6 −10 XY-ZW-patterned SNPs −15

10 4 15 5 2 10 5

0 5 0 0 0 −2 −5

−4 −5 −5 (per outlier window) −10

XY-ZW-patterned SNPs −6 −10 −15 LG01 LG02 LG06 LG11 LG13 LG14 LG17 LG18 LG19 LG22 LG23 LG02 LG04 LG07 LG10 LG17 LG19 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG12 LG13 LG14 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b LG03a LG03b LG03a

4 60 P = 0.089 P = 0.346 P = 0.036 P = 0.203 40 5 40 2 20 20

0 0 0 0

−20 −20

(per outlier window) −2 Sex-patterned SNPs −5 −40 −40 −4 −60 5.0 5.5 6.0 6.5 7.0 7.5 8.0 5.0 5.5 6.0 6.5 7.0 7.5 8.0 6 8 10 12 14 16 6 8 10 12 14 16 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

0.08

0.06

0.04 (normalised) 0.02 Sex-patterned SNPs

0.00 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b

26 Supplementary Figure 6 (continued)

Lamprologini

Neopul Neosav Neotet Neotoa

3 2 2 3 2 2 1 1 1 1

0 0 0 0 Density −1 −1 −1 −1 −2 −2 −3 −2 −2 −3 2 4 6 8 10 12 2 4 6 8 10 12 14 1 2 3 4 5 6 1 2 3 4 5 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

15 6

5 10 2 4 5 0 2 0 0 0 −5 −5 −2 −2 (per window) −10 −10 −4 −4 XY-ZW-patterned SNPs −15

15 6 −3

5 10 4 −4 5 0 2 0 −5 0 −5 −5 −2 −6 (per outlier window) −10 −10 XY-ZW-patterned SNPs −4 −15 − LG02 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG05 LG06 LG07 LG08 LG09 LG11 LG16 LG17 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03a

P = 0.05 P = 0.399 P = NaN 30 40 4 20 20 2 10

0 0 0

−10 −20 −2 (per outlier window)

Sex-patterned SNPs −20

−30 −40 −4

6 8 10 12 6 8 10 12 14 5.0 5.2 5.4 5.6 5. 6.0 Number of SNPs Number of SNPs Number of SNPs

27 Supplementary Figure 6 (continued)

Lamprologini

Neowal TeldhS TelteS Telvit

2 2 2 2

1 1 1 1

0 0 0 0 Density −1 −1 −1 −1

−2 −2 −2 −2

2 4 6 8 10 12 2 4 6 8 10 12 2 4 6 8 10 12 5 10 15 20 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

10 10 10 5

5 5 0 5 −5 0 0 0 −10 −5 −5 −15 (per window) −5 −10 −10 −20 XY-ZW-patterned SNPs −10 −25

10 10 10 5

5 5 0 5 −5 0 0 0 −10 −5 −5 −15 −5 (per outlier window) −20

XY-ZW-patterned SNPs −10 −10

−10 −25 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b LG03a LG03b LG03a LG03b LG03b

40 P = 0.903 P = 0.034 P = 0.017 P = 0.064 2000 50 20 20 1000

0 0 0 0

−1000

(per outlier window) −20 −20 Sex-patterned SNPs −50 −2000 −40 6 8 10 12 6 8 10 12 6 8 10 12 5 10 15 20 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

0.014 0.020

0.012 0.015 0.010

0.008 0.010 0.006

(normalised) 0.004 0.005 Sex-patterned SNPs 0.002

0.000 0.000 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b LG03a LG03b

28 Supplementary Figure 6 (continued)

Limnochromini Oreochromini Perissodini

Lchaur Oretan Plepar Plestr

3 3 2 2 2 2 1 1 1 1

0 0 0 0 Density −1 −1 −1 −1 −2 −2 −2 −3 −3 −2 2 4 6 8 10 2 4 6 8 0 5 10 15 20 25 5 10 15 20 Number of SNPs per window Number of SNPs per window Number of SNPs per window Number of SNPs per window

25 20 5 20 15 5 15 10 0 10 5 0 5 0 −5

(per window) 0 −5 −5

XY-ZW-patterned SNPs −5 −10 −10 −10

25 20 5 20 15 5 15 10 0 10 5 0 5 0 −5 0

(per outlier window) −5

XY-ZW-patterned SNPs −5 −5 −10 −10 −10 LG04 LG06 LG11 LG14 LG22 LG02 LG07 LG08 LG09 LG10 LG11 LG12 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG12 LG13 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG02 LG04 LG05 LG07 LG09 LG15 LG17 LG19 LG20 LG22 LG03b LG03b LG03a

4 10 P = 0.035 P = 0.71 100 P = 0 100 P = 0

5 2 50 50

0 0 0 0

−5 −50 −50

(per outlier window) −2 Sex-patterned SNPs

−10 −4 −100 −100 5 6 7 8 9 10 5 6 7 8 9 5 10 15 20 25 5 10 15 20 Number of SNPs Number of SNPs Number of SNPs Number of SNPs

0.010 0.8 0.8 0.008 0.6 0.6 0.006 0.4 0.004 0.4 (normalised)

0.2 0.2 Sex-patterned SNPs 0.002

0.000 0.0 0.0 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b LG03a LG03b LG03a LG03b

29 Supplementary Figure 6 (continued)

Trematocarini

Tremar Trenig

4

2 2 1

0 0

Density − −2 −2

− −

2 4 6 8 10 12 12 4 67 Number of SNPs per window Number of SNPs per window

4

2 0 0

− −2

(per window) −

−0 − XY-ZW-patterned SNPs

4

2 0 0

− −2

− (per outlier window)

XY-ZW-patterned SNPs −0 − LG01 LG02 LG04 0 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG14 LG16 LG17 LG18 LG19 LG20 LG22 2 LG02 LG09 2 0 0

2 P = 0.022 P 0

0 1

0 0

(per outlier window) − Sex-patterned SNPs −0

−2 6 7 8 9 10 11 12 0 6.0 7.0 Number of SNPs Number of SNPs

00

0.02 (normalised) 0.01 Sex-patterned SNPs

0.00 LG01 LG02 LG04 0 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG14 LG16 LG17 LG18 LG19 LG20 LG22 2 0 0

Fig. S6. Identification of sex chromosomes based on transcriptome data (approach 3). Per-species visualization of the results for tests of allele differences based on replicate male and female transcriptome data (approach 3). For each species, four to five plots are shown i) Density plot of the number of sex-specific SNPs per 10 kb non-overlapping window; the density of XY- windows is represented in blue (positive y-axis scale) and the density of ZW-windows in red (negative y-axis scale); ii) Boxplot of the difference between XY- and ZW-SNPs in 10 kb windows. Windows with a higher number of XY-SNPs are represented with positive values (>0) while windows with a higher number of ZW-SNPs are represented with negative values (<0). Boxplot center lines represent the median; box limits the upper and lower quartiles and whiskers the 1.5x interquartile ranges. The width of the boxes is proportional to the number of observations; iii) Boxplot of the difference in XY- and ZW-SNPs for outlier windows only and represented per LG. Boxplot center lines represent the median; box limits the upper and lower quartiles and whiskers the 1.5x interquartile ranges. The width of the boxes is proportional to the number of observations. vi) Histogram of the number of sex-specific SNPs per 10 kb outlier window, XY-windows are represented in blue (positive y-axis scale) and ZW-windows in red (negative y-axis scale). For species with a detected heterogametic system v) Visualization of the number of sex-specific (XY-system in blue and ZW-system in red) SNPs of outlier windows normalized by chromosome length with species-specific Y-axis scales. 30 Supplementary Figure 7 Posterior probability 0 1 estimated turnover event

LG 04 LG 05 LG 07 LG 10 Varmoo Varmoo Varmoo Varmoo Neotoa Neotoa Neotoa Neotoa Neotre Neotre Neotre Neotre Neosex Neosex Neosex Neosex TelteS TelteS TelteS TelteS TeldhN TeldhN TeldhN TeldhN Telshe Telshe Telshe Telshe Telbra Telbra Telbra Telbra TeldhT TeldhT TeldhT TeldhT TeldhS TeldhS TeldhS TeldhS Telluf Telluf Telluf Telluf Neodev Neodev Neodev Neodev Telbri Telbri Telbri Telbri Telbif Telbif Telbif Telbif Telvit Telvit Telvit Telvit Neoese Neoese Neoese Neoese Neochr Neochr Neochr Neochr Neomon Neomon Neomon Neomon Neopet Neopet Neopet Neopet Neomod Neomod Neomod Neomod Neotet Neotet Neotet Neotet Lepcun Lepcun Lepcun Lepcun Lamtig Lamtig Lamtig Lamtig Neopul Neopul Neopul Neopul Neooli Neooli Neooli Neooli Neosav Neosav Neosav Neosav Neokom Neokom Neokom Neokom Neospl Neospl Neospl Neospl Neohel Neohel Neohel Neohel Neobri Neobri Neobri Neobri Neomar Neomar Neomar Neomar Neocra Neocra Neocra Neocra NeofaM NeofaM NeofaM NeofaM Neogra Neogra Neogra Neogra NeogrM NeogrM NeogrM NeogrM Neocyg Neocyg Neocyg Neocyg Neowal Neowal Neowal Neowal Neochi Neochi Neochi Neochi Neofal Neofal Neofal Neofal Julorn Julorn Julorn Julorn Julkom Julkom Julkom Julkom Jultra Jultra Jultra Jultra Chapop Chapop Chapop Chapop Juldic Juldic Juldic Juldic Chabif Chabif Chabif Chabif Chando Chando Chando Chando Chabri Chabri Chabri Chabri JulmaS JulmaS JulmaS JulmaS JulmaN JulmaN JulmaN JulmaN Julreg Julreg Julreg Julreg JulreK JulreK JulreK JulreK Julmrk Julmrk Julmrk Julmrk Chacya Chacya Chacya Chacya Neofur Neofur Neofur Neofur NeofuU NeofuU NeofuU NeofuU Neotim Neotim Neotim Neotim Neoleu Neoleu Neoleu Neoleu Neocyl Neocyl Neocyl Neocyl Neomux Neomux Neomux Neomux Neobif Neobif Neobif Neobif Neopro Neopro Neopro Neopro Neoobs Neoobs Neoobs Neoobs Neobue Neobue Neobue Neobue Neonve Neonve Neonve Neonve Neolon Neolon Neolon Neolon Neonig Neonig Neonig Neonig Neople Neople Neople Neople Neobou Neobou Neobou Neobou Neohec Neohec Neohec Neohec LepmeK LepmeK LepmeK LepmeK Lepatt Lepatt Lepatt Lepatt Neomee Neomee Neomee Neomee Lepken Lepken Lepken Lepken Lepkam Lepkam Lepkam Lepkam Lepmim Lepmim Lepmim Lepmim Lepelo Lepelo Lepelo Lepelo Leppro Leppro Leppro Leppro Lamlem Lamlem Lamlem Lamlem Altshe Altshe Altshe Altshe Altcom Altcom Altcom Altcom Altcal Altcal Altcal Altcal Lamspe Lamspe Lamspe Lamspe Lamoce Lamoce Lamoce Lamoce Neolou Neolou Neolou Neolou NeocaK NeocaK NeocaK NeocaK Neocau Neocau Neocau Neocau Lamcal Lamcal Lamcal Lamcal Neofas Neofas Neofas Neofas Lamlap Lamlap Lamlap Lamlap Lamsig Lamsig Lamsig Lamsig Lamkun Lamkun Lamkun Lamkun Lamorn Lamorn Lamorn Lamorn LamorS LamorS LamorS LamorS NeoveS NeoveS NeoveS NeoveS NeoveB NeoveB NeoveB NeoveB Neosim Neosim Neosim Neosim Neomul Neomul Neomul Neomul Neocal Neocal Neocal Neocal Neobre Neobre Neobre Neobre NeobrM NeobrM NeobrM NeobrM Pscmrg Pscmrg Pscmrg Pscmrg Pscmar Pscmar Pscmar Pscmar Pscple Pscple Pscple Pscple Pscbab Pscbab Pscbab Pscbab Psccur Psccur Psccur Psccur Gnapfe Gnapfe Gnapfe Gnapfe Ctehor Ctehor Ctehor Ctehor Limdar Limdar Limdar Limdar Petfam Petfam Petfam Petfam Petort Petort Petort Petort Petiko Petiko Petiko Petiko Petfas Petfas Petfas Petfas Intloo Intloo Intloo Intloo Simdia Simdia Simdia Simdia Pettex Pettex Pettex Pettex Petpol Petpol Petpol Petpol Petgia Petgia Petgia Petgia Petrai Petrai Petrai Petrai Petkas Petkas Petkas Petkas Petmos Petmos Petmos Petmos Peteph Peteph Peteph Peteph Petred Petred Petred Petred Pethor Pethor Pethor Pethor Petkip Petkip Petkip Petkip Pettre Pettre Pettre Pettre Petmac Petmac Petmac Petmac Loblab Loblab Loblab Loblab Troluk Troluk Troluk Troluk Trobri Trobri Trobri Trobri TrobrK TrobrK TrobrK TrobrK Trolun Trolun Trolun Trolun Tronig Tronig Tronig Tronig Trokir Trokir Trokir Trokir Tromor Tromor Tromor Tromor Tromoo Tromoo Tromoo Tromoo Trored Trored Trored Trored Tropol Tropol Tropol Tropol Trompi Trompi Trompi Trompi Troann Troann Troann Troann Trodub Trodub Trodub Trodub Hplsta Hplsta Hplsta Hplsta HplspC HplspC HplspC HplspC Astpal Astpal Astpal Astpal Astfla Astfla Astfla Astfla Hplkil Hplkil Hplkil Hplkil Astbur Astbur Astbur Astbur Hplvan Hplvan Hplvan Hplvan Arcstr Arcstr Arcstr Arcstr Psephi Psephi Psephi Psephi Ortcho Ortcho Ortcho Ortcho Thobra Thobra Thobra Thobra Ctepol Ctepol Ctepol Ctepol Ortred Ortred Ortred Ortred Ortmaz Ortmaz Ortmaz Ortmaz Ortuvi Ortuvi Ortuvi Ortuvi Spamar Spamar Spamar Spamar Spaery Spaery Spaery Spaery Eremar Eremar Eremar Eremar Tanirs Tanirs Tanirs Tanirs Erecya Erecya Erecya Erecya Cypkan Cypkan Cypkan Cypkan Cypcol Cypcol Cypcol Cypcol Cypdwj Cypdwj Cypdwj Cypdwj Cyplep Cyplep Cyplep Cyplep Cypzon Cypzon Cypzon Cypzon Cypkib Cypkib Cypkib Cypkib Cypmic Cypmic Cypmic Cypmic Cyppav Cyppav Cyppav Cyppav Pcybri Pcybri Pcybri Pcybri PcybrN PcybrN PcybrN PcybrN Pcynig Pcynig Pcynig Pcynig Xchhec Xchhec Xchhec Xchhec Pleela Pleela Pleela Pleela Plemul Plemul Plemul Plemul Plestr Plestr Plestr Plestr Permic Permic Permic Permic Plepar Plepar Plepar Plepar Bentri Bentri Bentri Bentri Benmel Benmel Benmel Benmel Benhor Benhor Benhor Benhor Xenoch Xenoch Xenoch Xenoch Xenkil Xenkil Xenkil Xenkil Xensin Xensin Xensin Xensin Enamel Enamel Enamel Enamel Xensim Xensim Xensim Xensim Xenbou Xenbou Xenbou Xenbou Xenbat Xenbat Xenbat Xenbat Xenfla Xenfla Xenfla Xenfla Mdcten Mdcten Mdcten Mdcten Xenspi Xenspi Xenspi Xenspi XenspN XenspN XenspN XenspN Mdcrot Mdcrot Mdcrot Mdcrot Xenpap Xenpap Xenpap Xenpap XenpaK XenpaK XenpaK XenpaK Xensun Xensun Xensun Xensun Asplep Asplep Asplep Asplep Xennas Xennas Xennas Xennas Xenorn Xenorn Xenorn Xenorn XenniS XenniS XenniS XenniS Xenlon Xenlon Xenlon Xenlon Xencau Xencau Xencau Xencau Ophwhi Ophwhi Ophwhi Ophwhi Ophven Ophven Ophven Ophven Ophhet Ophhet Ophhet Ophhet Ophboo Ophboo Ophboo Ophboo Ophpar Ophpar Ophpar Ophpar Ophnas Ophnas Ophnas Ophnas Cunlon Cunlon Cunlon Cunlon Auldew Auldew Auldew Auldew Cyafur Cyafur Cyafur Cyafur Cyafoa Cyafoa Cyafoa Cyafoa Lessta Lessta Lessta Lessta Lesper Lesper Lesper Lesper EctspN EctspN EctspN EctspN Ectdes Ectdes Ectdes Ectdes Carsch Carsch Carsch Carsch Calmel Calmel Calmel Calmel Calmac Calmac Calmac Calmac Calple Calple Calple Calple Gralem Gralem Gralem Gralem Regcal Regcal Regcal Regcal Baicen Baicen Baicen Baicen Tchdha Tchdha Tchdha Tchdha Trioto Trioto Trioto Trioto Lchaur Lchaur Lchaur Lchaur Lchsta Lchsta Lchsta Lchsta Gwcchr Gwcchr Gwcchr Gwcchr Lchabe Lchabe Lchabe Lchabe Gnaper Gnaper Gnaper Gnaper Cphfro Cphfro Cphfro Cphfro Cphfr5 Cphfr5 Cphfr5 Cphfr5 Cphgib Cphgib Cphgib Cphgib Cteben Cteben Cteben Cteben Batvit Batvit Batvit Batvit Batfas Batfas Batfas Batfas Batfer Batfer Batfer Batfer Batgra Batgra Batgra Batgra Batmin Batmin Batmin Batmin Hemste Hemste Hemste Hemste Trenig Trenig Trenig Trenig Tremar Tremar Tremar Tremar Tremac Tremac Tremac Tremac Trezeb Trezeb Trezeb Trezeb Treuni Treuni Treuni Treuni Boumic Boumic Boumic Boumic Supplementary Figure 7 (continued) Posterior probability 0 1 estimated turnover event

LG 11 LG 13 LG 14 LG 15 Varmoo Varmoo Varmoo Varmoo Neotoa Neotoa Neotoa Neotoa Neotre Neotre Neotre Neotre Neosex Neosex Neosex Neosex TelteS TelteS TelteS TelteS TeldhN TeldhN TeldhN TeldhN Telshe Telshe Telshe Telshe Telbra Telbra Telbra Telbra TeldhT TeldhT TeldhT TeldhT TeldhS TeldhS TeldhS TeldhS Telluf Telluf Telluf Telluf Neodev Neodev Neodev Neodev Telbri Telbri Telbri Telbri Telbif Telbif Telbif Telbif Telvit Telvit Telvit Telvit Neoese Neoese Neoese Neoese Neochr Neochr Neochr Neochr Neomon Neomon Neomon Neomon Neopet Neopet Neopet Neopet Neomod Neomod Neomod Neomod Neotet Neotet Neotet Neotet Lepcun Lepcun Lepcun Lepcun Lamtig Lamtig Lamtig Lamtig Neopul Neopul Neopul Neopul Neooli Neooli Neooli Neooli Neosav Neosav Neosav Neosav Neokom Neokom Neokom Neokom Neospl Neospl Neospl Neospl Neohel Neohel Neohel Neohel Neobri Neobri Neobri Neobri Neomar Neomar Neomar Neomar Neocra Neocra Neocra Neocra NeofaM NeofaM NeofaM NeofaM Neogra Neogra Neogra Neogra NeogrM NeogrM NeogrM NeogrM Neocyg Neocyg Neocyg Neocyg Neowal Neowal Neowal Neowal Neochi Neochi Neochi Neochi Neofal Neofal Neofal Neofal Julorn Julorn Julorn Julorn Julkom Julkom Julkom Julkom Jultra Jultra Jultra Jultra Chapop Chapop Chapop Chapop Juldic Juldic Juldic Juldic Chabif Chabif Chabif Chabif Chando Chando Chando Chando Chabri Chabri Chabri Chabri JulmaS JulmaS JulmaS JulmaS JulmaN JulmaN JulmaN JulmaN Julreg Julreg Julreg Julreg JulreK JulreK JulreK JulreK Julmrk Julmrk Julmrk Julmrk Chacya Chacya Chacya Chacya Neofur Neofur Neofur Neofur NeofuU NeofuU NeofuU NeofuU Neotim Neotim Neotim Neotim Neoleu Neoleu Neoleu Neoleu Neocyl Neocyl Neocyl Neocyl Neomux Neomux Neomux Neomux Neobif Neobif Neobif Neobif Neopro Neopro Neopro Neopro Neoobs Neoobs Neoobs Neoobs Neobue Neobue Neobue Neobue Neonve Neonve Neonve Neonve Neolon Neolon Neolon Neolon Neonig Neonig Neonig Neonig Neople Neople Neople Neople Neobou Neobou Neobou Neobou Neohec Neohec Neohec Neohec LepmeK LepmeK LepmeK LepmeK Lepatt Lepatt Lepatt Lepatt Neomee Neomee Neomee Neomee Lepken Lepken Lepken Lepken Lepkam Lepkam Lepkam Lepkam Lepmim Lepmim Lepmim Lepmim Lepelo Lepelo Lepelo Lepelo Leppro Leppro Leppro Leppro Lamlem Lamlem Lamlem Lamlem Altshe Altshe Altshe Altshe Altcom Altcom Altcom Altcom Altcal Altcal Altcal Altcal Lamspe Lamspe Lamspe Lamspe Lamoce Lamoce Lamoce Lamoce Neolou Neolou Neolou Neolou NeocaK NeocaK NeocaK NeocaK Neocau Neocau Neocau Neocau Lamcal Lamcal Lamcal Lamcal Neofas Neofas Neofas Neofas Lamlap Lamlap Lamlap Lamlap Lamsig Lamsig Lamsig Lamsig Lamkun Lamkun Lamkun Lamkun Lamorn Lamorn Lamorn Lamorn LamorS LamorS LamorS LamorS NeoveS NeoveS NeoveS NeoveS NeoveB NeoveB NeoveB NeoveB Neosim Neosim Neosim Neosim Neomul Neomul Neomul Neomul Neocal Neocal Neocal Neocal Neobre Neobre Neobre Neobre NeobrM NeobrM NeobrM NeobrM Pscmrg Pscmrg Pscmrg Pscmrg Pscmar Pscmar Pscmar Pscmar Pscple Pscple Pscple Pscple Pscbab Pscbab Pscbab Pscbab Psccur Psccur Psccur Psccur Gnapfe Gnapfe Gnapfe Gnapfe Ctehor Ctehor Ctehor Ctehor Limdar Limdar Limdar Limdar Petfam Petfam Petfam Petfam Petort Petort Petort Petort Petiko Petiko Petiko Petiko Petfas Petfas Petfas Petfas Intloo Intloo Intloo Intloo Simdia Simdia Simdia Simdia Pettex Pettex Pettex Pettex Petpol Petpol Petpol Petpol Petgia Petgia Petgia Petgia Petrai Petrai Petrai Petrai Petkas Petkas Petkas Petkas Petmos Petmos Petmos Petmos Peteph Peteph Peteph Peteph Petred Petred Petred Petred Pethor Pethor Pethor Pethor Petkip Petkip Petkip Petkip Pettre Pettre Pettre Pettre Petmac Petmac Petmac Petmac Loblab Loblab Loblab Loblab Troluk Troluk Troluk Troluk Trobri Trobri Trobri Trobri TrobrK TrobrK TrobrK TrobrK Trolun Trolun Trolun Trolun Tronig Tronig Tronig Tronig Trokir Trokir Trokir Trokir Tromor Tromor Tromor Tromor Tromoo Tromoo Tromoo Tromoo Trored Trored Trored Trored Tropol Tropol Tropol Tropol Trompi Trompi Trompi Trompi Troann Troann Troann Troann Trodub Trodub Trodub Trodub Hplsta Hplsta Hplsta Hplsta HplspC HplspC HplspC HplspC Astpal Astpal Astpal Astpal Astfla Astfla Astfla Astfla Hplkil Hplkil Hplkil Hplkil Astbur Astbur Astbur Astbur Hplvan Hplvan Hplvan Hplvan Arcstr Arcstr Arcstr Arcstr Psephi Psephi Psephi Psephi Ortcho Ortcho Ortcho Ortcho Thobra Thobra Thobra Thobra Ctepol Ctepol Ctepol Ctepol Ortred Ortred Ortred Ortred Ortmaz Ortmaz Ortmaz Ortmaz Ortuvi Ortuvi Ortuvi Ortuvi Spamar Spamar Spamar Spamar Spaery Spaery Spaery Spaery Eremar Eremar Eremar Eremar Tanirs Tanirs Tanirs Tanirs Erecya Erecya Erecya Erecya Cypkan Cypkan Cypkan Cypkan Cypcol Cypcol Cypcol Cypcol Cypdwj Cypdwj Cypdwj Cypdwj Cyplep Cyplep Cyplep Cyplep Cypzon Cypzon Cypzon Cypzon Cypkib Cypkib Cypkib Cypkib Cypmic Cypmic Cypmic Cypmic Cyppav Cyppav Cyppav Cyppav Pcybri Pcybri Pcybri Pcybri PcybrN PcybrN PcybrN PcybrN Pcynig Pcynig Pcynig Pcynig Xchhec Xchhec Xchhec Xchhec Pleela Pleela Pleela Pleela Plemul Plemul Plemul Plemul Plestr Plestr Plestr Plestr Permic Permic Permic Permic Plepar Plepar Plepar Plepar Bentri Bentri Bentri Bentri Benmel Benmel Benmel Benmel Benhor Benhor Benhor Benhor Xenoch Xenoch Xenoch Xenoch Xenkil Xenkil Xenkil Xenkil Xensin Xensin Xensin Xensin Enamel Enamel Enamel Enamel Xensim Xensim Xensim Xensim Xenbou Xenbou Xenbou Xenbou Xenbat Xenbat Xenbat Xenbat Xenfla Xenfla Xenfla Xenfla Mdcten Mdcten Mdcten Mdcten Xenspi Xenspi Xenspi Xenspi XenspN XenspN XenspN XenspN Mdcrot Mdcrot Mdcrot Mdcrot Xenpap Xenpap Xenpap Xenpap XenpaK XenpaK XenpaK XenpaK Xensun Xensun Xensun Xensun Asplep Asplep Asplep Asplep Xennas Xennas Xennas Xennas Xenorn Xenorn Xenorn Xenorn XenniS XenniS XenniS XenniS Xenlon Xenlon Xenlon Xenlon Xencau Xencau Xencau Xencau Ophwhi Ophwhi Ophwhi Ophwhi Ophven Ophven Ophven Ophven Ophhet Ophhet Ophhet Ophhet Ophboo Ophboo Ophboo Ophboo Ophpar Ophpar Ophpar Ophpar Ophnas Ophnas Ophnas Ophnas Cunlon Cunlon Cunlon Cunlon Auldew Auldew Auldew Auldew Cyafur Cyafur Cyafur Cyafur Cyafoa Cyafoa Cyafoa Cyafoa Lessta Lessta Lessta Lessta Lesper Lesper Lesper Lesper EctspN EctspN EctspN EctspN Ectdes Ectdes Ectdes Ectdes Carsch Carsch Carsch Carsch Calmel Calmel Calmel Calmel Calmac Calmac Calmac Calmac Calple Calple Calple Calple Gralem Gralem Gralem Gralem Regcal Regcal Regcal Regcal Baicen Baicen Baicen Baicen Tchdha Tchdha Tchdha Tchdha Trioto Trioto Trioto Trioto Lchaur Lchaur Lchaur Lchaur Lchsta Lchsta Lchsta Lchsta Gwcchr Gwcchr Gwcchr Gwcchr Lchabe Lchabe Lchabe Lchabe Gnaper Gnaper Gnaper Gnaper Cphfro Cphfro Cphfro Cphfro Cphfr5 Cphfr5 Cphfr5 Cphfr5 Cphgib Cphgib Cphgib Cphgib Cteben Cteben Cteben Cteben Batvit Batvit Batvit Batvit Batfas Batfas Batfas Batfas Batfer Batfer Batfer Batfer Batgra Batgra Batgra Batgra Batmin Batmin Batmin Batmin Hemste Hemste Hemste Hemste Trenig Trenig Trenig Trenig Tremar Tremar Tremar Tremar Tremac Tremac Tremac Tremac Trezeb Trezeb Trezeb Trezeb Treuni Treuni Treuni Treuni Boumic Boumic Boumic Boumic Supplementary Figure 7 (continued) Posterior probability 0 1 estimated turnover event

LG 16 LG 17 LG 18 LG 19 Varmoo Varmoo Varmoo Varmoo Neotoa Neotoa Neotoa Neotoa Neotre Neotre Neotre Neotre Neosex Neosex Neosex Neosex TelteS TelteS TelteS TelteS TeldhN TeldhN TeldhN TeldhN Telshe Telshe Telshe Telshe Telbra Telbra Telbra Telbra TeldhT TeldhT TeldhT TeldhT TeldhS TeldhS TeldhS TeldhS Telluf Telluf Telluf Telluf Neodev Neodev Neodev Neodev Telbri Telbri Telbri Telbri Telbif Telbif Telbif Telbif Telvit Telvit Telvit Telvit Neoese Neoese Neoese Neoese Neochr Neochr Neochr Neochr Neomon Neomon Neomon Neomon Neopet Neopet Neopet Neopet Neomod Neomod Neomod Neomod Neotet Neotet Neotet Neotet Lepcun Lepcun Lepcun Lepcun Lamtig Lamtig Lamtig Lamtig Neopul Neopul Neopul Neopul Neooli Neooli Neooli Neooli Neosav Neosav Neosav Neosav Neokom Neokom Neokom Neokom Neospl Neospl Neospl Neospl Neohel Neohel Neohel Neohel Neobri Neobri Neobri Neobri Neomar Neomar Neomar Neomar Neocra Neocra Neocra Neocra NeofaM NeofaM NeofaM NeofaM Neogra Neogra Neogra Neogra NeogrM NeogrM NeogrM NeogrM Neocyg Neocyg Neocyg Neocyg Neowal Neowal Neowal Neowal Neochi Neochi Neochi Neochi Neofal Neofal Neofal Neofal Julorn Julorn Julorn Julorn Julkom Julkom Julkom Julkom Jultra Jultra Jultra Jultra Chapop Chapop Chapop Chapop Juldic Juldic Juldic Juldic Chabif Chabif Chabif Chabif Chando Chando Chando Chando Chabri Chabri Chabri Chabri JulmaS JulmaS JulmaS JulmaS JulmaN JulmaN JulmaN JulmaN Julreg Julreg Julreg Julreg JulreK JulreK JulreK JulreK Julmrk Julmrk Julmrk Julmrk Chacya Chacya Chacya Chacya Neofur Neofur Neofur Neofur NeofuU NeofuU NeofuU NeofuU Neotim Neotim Neotim Neotim Neoleu Neoleu Neoleu Neoleu Neocyl Neocyl Neocyl Neocyl Neomux Neomux Neomux Neomux Neobif Neobif Neobif Neobif Neopro Neopro Neopro Neopro Neoobs Neoobs Neoobs Neoobs Neobue Neobue Neobue Neobue Neonve Neonve Neonve Neonve Neolon Neolon Neolon Neolon Neonig Neonig Neonig Neonig Neople Neople Neople Neople Neobou Neobou Neobou Neobou Neohec Neohec Neohec Neohec LepmeK LepmeK LepmeK LepmeK Lepatt Lepatt Lepatt Lepatt Neomee Neomee Neomee Neomee Lepken Lepken Lepken Lepken Lepkam Lepkam Lepkam Lepkam Lepmim Lepmim Lepmim Lepmim Lepelo Lepelo Lepelo Lepelo Leppro Leppro Leppro Leppro Lamlem Lamlem Lamlem Lamlem Altshe Altshe Altshe Altshe Altcom Altcom Altcom Altcom Altcal Altcal Altcal Altcal Lamspe Lamspe Lamspe Lamspe Lamoce Lamoce Lamoce Lamoce Neolou Neolou Neolou Neolou NeocaK NeocaK NeocaK NeocaK Neocau Neocau Neocau Neocau Lamcal Lamcal Lamcal Lamcal Neofas Neofas Neofas Neofas Lamlap Lamlap Lamlap Lamlap Lamsig Lamsig Lamsig Lamsig Lamkun Lamkun Lamkun Lamkun Lamorn Lamorn Lamorn Lamorn LamorS LamorS LamorS LamorS NeoveS NeoveS NeoveS NeoveS NeoveB NeoveB NeoveB NeoveB Neosim Neosim Neosim Neosim Neomul Neomul Neomul Neomul Neocal Neocal Neocal Neocal Neobre Neobre Neobre Neobre NeobrM NeobrM NeobrM NeobrM Pscmrg Pscmrg Pscmrg Pscmrg Pscmar Pscmar Pscmar Pscmar Pscple Pscple Pscple Pscple Pscbab Pscbab Pscbab Pscbab Psccur Psccur Psccur Psccur Gnapfe Gnapfe Gnapfe Gnapfe Ctehor Ctehor Ctehor Ctehor Limdar Limdar Limdar Limdar Petfam Petfam Petfam Petfam Petort Petort Petort Petort Petiko Petiko Petiko Petiko Petfas Petfas Petfas Petfas Intloo Intloo Intloo Intloo Simdia Simdia Simdia Simdia Pettex Pettex Pettex Pettex Petpol Petpol Petpol Petpol Petgia Petgia Petgia Petgia Petrai Petrai Petrai Petrai Petkas Petkas Petkas Petkas Petmos Petmos Petmos Petmos Peteph Peteph Peteph Peteph Petred Petred Petred Petred Pethor Pethor Pethor Pethor Petkip Petkip Petkip Petkip Pettre Pettre Pettre Pettre Petmac Petmac Petmac Petmac Loblab Loblab Loblab Loblab Troluk Troluk Troluk Troluk Trobri Trobri Trobri Trobri TrobrK TrobrK TrobrK TrobrK Trolun Trolun Trolun Trolun Tronig Tronig Tronig Tronig Trokir Trokir Trokir Trokir Tromor Tromor Tromor Tromor Tromoo Tromoo Tromoo Tromoo Trored Trored Trored Trored Tropol Tropol Tropol Tropol Trompi Trompi Trompi Trompi Troann Troann Troann Troann Trodub Trodub Trodub Trodub Hplsta Hplsta Hplsta Hplsta HplspC HplspC HplspC HplspC Astpal Astpal Astpal Astpal Astfla Astfla Astfla Astfla Hplkil Hplkil Hplkil Hplkil Astbur Astbur Astbur Astbur Hplvan Hplvan Hplvan Hplvan Arcstr Arcstr Arcstr Arcstr Psephi Psephi Psephi Psephi Ortcho Ortcho Ortcho Ortcho Thobra Thobra Thobra Thobra Ctepol Ctepol Ctepol Ctepol Ortred Ortred Ortred Ortred Ortmaz Ortmaz Ortmaz Ortmaz Ortuvi Ortuvi Ortuvi Ortuvi Spamar Spamar Spamar Spamar Spaery Spaery Spaery Spaery Eremar Eremar Eremar Eremar Tanirs Tanirs Tanirs Tanirs Erecya Erecya Erecya Erecya Cypkan Cypkan Cypkan Cypkan Cypcol Cypcol Cypcol Cypcol Cypdwj Cypdwj Cypdwj Cypdwj Cyplep Cyplep Cyplep Cyplep Cypzon Cypzon Cypzon Cypzon Cypkib Cypkib Cypkib Cypkib Cypmic Cypmic Cypmic Cypmic Cyppav Cyppav Cyppav Cyppav Pcybri Pcybri Pcybri Pcybri PcybrN PcybrN PcybrN PcybrN Pcynig Pcynig Pcynig Pcynig Xchhec Xchhec Xchhec Xchhec Pleela Pleela Pleela Pleela Plemul Plemul Plemul Plemul Plestr Plestr Plestr Plestr Permic Permic Permic Permic Plepar Plepar Plepar Plepar Bentri Bentri Bentri Bentri Benmel Benmel Benmel Benmel Benhor Benhor Benhor Benhor Xenoch Xenoch Xenoch Xenoch Xenkil Xenkil Xenkil Xenkil Xensin Xensin Xensin Xensin Enamel Enamel Enamel Enamel Xensim Xensim Xensim Xensim Xenbou Xenbou Xenbou Xenbou Xenbat Xenbat Xenbat Xenbat Xenfla Xenfla Xenfla Xenfla Mdcten Mdcten Mdcten Mdcten Xenspi Xenspi Xenspi Xenspi XenspN XenspN XenspN XenspN Mdcrot Mdcrot Mdcrot Mdcrot Xenpap Xenpap Xenpap Xenpap XenpaK XenpaK XenpaK XenpaK Xensun Xensun Xensun Xensun Asplep Asplep Asplep Asplep Xennas Xennas Xennas Xennas Xenorn Xenorn Xenorn Xenorn XenniS XenniS XenniS XenniS Xenlon Xenlon Xenlon Xenlon Xencau Xencau Xencau Xencau Ophwhi Ophwhi Ophwhi Ophwhi Ophven Ophven Ophven Ophven Ophhet Ophhet Ophhet Ophhet Ophboo Ophboo Ophboo Ophboo Ophpar Ophpar Ophpar Ophpar Ophnas Ophnas Ophnas Ophnas Cunlon Cunlon Cunlon Cunlon Auldew Auldew Auldew Auldew Cyafur Cyafur Cyafur Cyafur Cyafoa Cyafoa Cyafoa Cyafoa Lessta Lessta Lessta Lessta Lesper Lesper Lesper Lesper EctspN EctspN EctspN EctspN Ectdes Ectdes Ectdes Ectdes Carsch Carsch Carsch Carsch Calmel Calmel Calmel Calmel Calmac Calmac Calmac Calmac Calple Calple Calple Calple Gralem Gralem Gralem Gralem Regcal Regcal Regcal Regcal Baicen Baicen Baicen Baicen Tchdha Tchdha Tchdha Tchdha Trioto Trioto Trioto Trioto Lchaur Lchaur Lchaur Lchaur Lchsta Lchsta Lchsta Lchsta Gwcchr Gwcchr Gwcchr Gwcchr Lchabe Lchabe Lchabe Lchabe Gnaper Gnaper Gnaper Gnaper Cphfro Cphfro Cphfro Cphfro Cphfr5 Cphfr5 Cphfr5 Cphfr5 Cphgib Cphgib Cphgib Cphgib Cteben Cteben Cteben Cteben Batvit Batvit Batvit Batvit Batfas Batfas Batfas Batfas Batfer Batfer Batfer Batfer Batgra Batgra Batgra Batgra Batmin Batmin Batmin Batmin Hemste Hemste Hemste Hemste Trenig Trenig Trenig Trenig Tremar Tremar Tremar Tremar Tremac Tremac Tremac Tremac Trezeb Trezeb Trezeb Trezeb Treuni Treuni Treuni Treuni Boumic Boumic Boumic Boumic Posterior probability 0 1 estimated turnover event

LG 20 LG 23 Varmoo Varmoo Neotoa Neotoa Neotre Neotre Neosex Neosex TelteS TelteS TeldhN TeldhN Telshe Telshe Telbra Telbra TeldhT TeldhT TeldhS TeldhS Telluf Telluf Neodev Neodev Telbri Telbri Telbif Telbif Telvit Telvit Neoese Neoese Neochr Neochr Neomon Neomon Neopet Neopet Neomod Neomod Neotet Neotet Lepcun Lepcun Lamtig Lamtig Neopul Neopul Neooli Neooli Neosav Neosav Neokom Neokom Neospl Neospl Neohel Neohel Neobri Neobri Neomar Neomar Neocra Neocra NeofaM NeofaM Neogra Neogra NeogrM NeogrM Neocyg Neocyg Neowal Neowal Neochi Neochi Neofal Neofal Julorn Julorn Julkom Julkom Jultra Jultra Chapop Chapop Juldic Juldic Chabif Chabif Chando Chando Chabri Chabri JulmaS JulmaS JulmaN JulmaN Julreg Julreg JulreK JulreK Julmrk Julmrk Chacya Chacya Neofur Neofur NeofuU NeofuU Neotim Neotim Neoleu Neoleu Neocyl Neocyl Neomux Neomux Neobif Neobif Neopro Neopro Neoobs Neoobs Neobue Neobue Neonve Neonve Neolon Neolon Neonig Neonig Neople Neople Neobou Neobou Neohec Neohec LepmeK LepmeK Lepatt Lepatt Neomee Neomee Lepken Lepken Lepkam Lepkam Lepmim Lepmim Lepelo Lepelo Leppro Leppro Lamlem Lamlem Altshe Altshe Altcom Altcom Altcal Altcal Lamspe Lamspe Lamoce Lamoce Neolou Neolou NeocaK NeocaK Neocau Neocau Lamcal Lamcal Neofas Neofas Lamlap Lamlap Lamsig Lamsig Lamkun Lamkun Lamorn Lamorn LamorS LamorS NeoveS NeoveS NeoveB NeoveB Neosim Neosim Neomul Neomul Neocal Neocal Neobre Neobre NeobrM NeobrM Pscmrg Pscmrg Pscmar Pscmar Pscple Pscple Pscbab Pscbab Psccur Psccur Gnapfe Gnapfe Ctehor Ctehor Limdar Limdar Petfam Petfam Petort Petort Petiko Petiko Petfas Petfas Intloo Intloo Simdia Simdia Pettex Pettex Petpol Petpol Petgia Petgia Petrai Petrai Petkas Petkas Petmos Petmos Peteph Peteph Petred Petred Pethor Pethor Petkip Petkip Pettre Pettre Petmac Petmac Loblab Loblab Troluk Troluk Trobri Trobri TrobrK TrobrK Trolun Trolun Tronig Tronig Trokir Trokir Tromor Tromor Tromoo Tromoo Trored Trored Tropol Tropol Trompi Trompi Troann Troann Trodub Trodub Hplsta Hplsta HplspC HplspC Astpal Astpal Astfla Astfla Hplkil Hplkil Astbur Astbur Hplvan Hplvan Arcstr Arcstr Psephi Psephi Ortcho Ortcho Thobra Thobra Ctepol Ctepol Ortred Ortred Ortmaz Ortmaz Ortuvi Ortuvi Spamar Spamar Spaery Spaery Eremar Eremar Tanirs Tanirs Erecya Erecya Cypkan Cypkan Cypcol Cypcol Cypdwj Cypdwj Cyplep Cyplep Cypzon Cypzon Cypkib Cypkib Cypmic Cypmic Cyppav Cyppav Pcybri Pcybri PcybrN PcybrN Pcynig Pcynig Xchhec Xchhec Pleela Pleela Plemul Plemul Plestr Plestr Permic Permic Plepar Plepar Bentri Bentri Benmel Benmel Benhor Benhor Xenoch Xenoch Xenkil Xenkil Xensin Xensin Enamel Enamel Xensim Xensim Xenbou Xenbou Xenbat Xenbat Xenfla Xenfla Mdcten Mdcten Xenspi Xenspi XenspN XenspN Mdcrot Mdcrot Xenpap Xenpap XenpaK XenpaK Xensun Xensun Asplep Asplep Xennas Xennas Xenorn Xenorn XenniS XenniS Xenlon Xenlon Xencau Xencau Ophwhi Ophwhi Ophven Ophven Ophhet Ophhet Ophboo Ophboo Ophpar Ophpar Ophnas Ophnas Cunlon Cunlon Auldew Auldew Cyafur Cyafur Cyafoa Cyafoa Lessta Lessta Lesper Lesper EctspN EctspN Ectdes Ectdes Carsch Carsch Calmel Calmel Calmac Calmac Fig. S7. Sex chromosome turnover points. Sex Calple Calple Gralem Gralem Regcal Regcal chromosome turnover points visuali ed per sex-linked Baicen Baicen z Tchdha Tchdha Trioto Trioto Lchaur Lchaur LG derived from ancestral state reconstructions based Lchsta Lchsta Gwcchr Gwcchr Lchabe Lchabe Gnaper Gnaper on stochastic character mappings (using the permissive Cphfro Cphfro Cphfr5 Cphfr5 Cphgib Cphgib Cteben Cteben dataset). Batvit Batvit Batfas Batfas Batfer Batfer Batgra Batgra Batmin Batmin Hemste Hemste Trenig Trenig Tremar Tremar Tremac Tremac Trezeb Trezeb Treuni Treuni Boumic Boumic A B

Sex-linkedHeterogamety LG Oryzias dancena Reference linkage group medaka LG1 LG8 LG16 Oryzias javanicus LG2 LG10 LG24 300

Oryzias hubbsi LG5 LG12

Oryzias sinensis Heterogamety 200 XY Adrianichthys oophorus ZW

Oryzias matanensis 100

Oryzias latipes (My) transition of Age

Oryzias luzonensis

Oryzias curvinotus 0 to XY to ZW Oryzias mekongensis

Oryzias carnaticus

Oryzias minutillus

Oryzias celebensis

Oryzias eversi

Oryzias sarasinorum

Oryzias marmoratus

Oryzias nigrimas

Oryzias profundicola

Oryzias hadiatyae

80 60 40 20 0 Ma

Fig. S8. Sex chromosome evolution in ricefishes. (A) Stochastic character mapping for sex chromosomes in ricefishes. Colored circles at tips represent sex-associated LGs with respect to the medaka (Oryzias latipes) genome. Pie charts at nodes represent the probability for an LG being a sex chromosome at this time. Heterogametic status is indicated at tips (triangle: ZW, circle: XY). (B) Age of heterogametic transitions in ray- finned fishes. Transitions to ZW-systems are younger than transitions to XY-systems (Kruskal-Wallis rank sum test P = 0.014). Boxplot center lines represent the median, box limits the upper and lower quartiles, and whiskers the 1.5x interquartile rang, points represent outliers. The size of boxes within a plot is proportional to the number of transition events.

35 Posterior probability 0 1 estimated turnover event ZW

Varmoo Neotoa Neotre Neosex TelteS TeldhN Telshe Telbra TeldhT TeldhS Telluf Neodev Telbri Telbif Telvit Neoese Neochr Neomon Neopet Neomod Neotet Lepcun Lamtig Neopul Neooli Neosav Neokom Neospl Neohel Neobri Neomar Neocra NeofaM Neogra NeogrM Neocyg Neowal Neochi Neofal Julorn Julkom Jultra Chapop Juldic Chabif Chando Chabri JulmaS JulmaN Julreg JulreK Julmrk Chacya Neofur NeofuU Neotim Neoleu Neocyl Neomux Neobif Neopro Neoobs Neobue Neonve Neolon Neonig Neople Neobou Neohec LepmeK Lepatt Neomee Lepken Lepkam Lepmim Lepelo Leppro Lamlem Altshe Altcom Altcal Lamspe Lamoce Neolou NeocaK Neocau Lamcal Neofas Lamlap Lamsig Lamkun Lamorn LamorS NeoveS NeoveB Neosim Neomul Neocal Neobre NeobrM Pscmrg Pscmar Pscple Pscbab Psccur Gnapfe Ctehor Limdar Petfam Petort Petiko Petfas Intloo Simdia Pettex Petpol Petgia Petrai Petkas Petmos Peteph Petred Pethor Petkip Pettre Petmac Loblab Troluk Trobri TrobrK Trolun Tronig Trokir Tromor Tromoo Trored Tropol Trompi Troann Trodub Hplsta HplspC Astpal Astfla Hplkil Astbur Hplvan Arcstr Psephi Ortcho Thobra Ctepol Ortred Ortmaz Ortuvi Spamar Spaery Eremar Tanirs Erecya Cypkan Cypcol Cypdwj Cyplep Cypzon Cypkib Cypmic Cyppav Pcybri PcybrN Pcynig Xchhec Pleela Plemul Plestr Permic Plepar Bentri Benmel Benhor Xenoch Xenkil Xensin Enamel Xensim Xenbou Xenbat Xenfla Mdcten Xenspi XenspN Mdcrot Xenpap XenpaK Xensun Asplep Xennas Xenorn XenniS Fig. S9. Stochastic character mapping for Xenlon Xencau Ophwhi Ophven heterogametic status and inference of Ophhet Ophboo Ophpar Ophnas heterogametic changes. Circles at the tips of the tree Cunlon Auldew Cyafur represent the identifed heterogametic status (blue: Cyafoa Lessta Lesper EctspN XY, red: ZW). For species without a symbol, no sex Ectdes Carsch Calmel Calmac chromosome could be identifed. Pie charts at internal Calple Gralem Regcal Baicen nodes represent the reconstructed heterogametic Tchdha Trioto Lchaur Lchsta state in 1,000 simulations. Black points represent Gwcchr Lchabe Gnaper Cphfro estimated heterogamety turnover points derived from Cphfr5 Cphgib Cteben ancestral state reconstructions based on stochastic Batvit Batfas Batfer Batgra character mappings. Batmin Hemste Trenig Tremar Tremac Trezeb Treuni Boumic Fig. S10. Distribution of sex-differentiated SNPs along the sex-associated LGs. Each plot represents one identified sex chromosomal system. In each plot, upper panels show the density of XY- or ZW-SNPs, lower panels show the distribution of the total number of SNPs called for each window along the LG. Colored bars represent the number of sex-linked SNPs along the linkage group with color-coding according to tribe.

37 All cichlids Cichlids with sexual color dimorphism Cichlids without sexual color dimorphism

6e+07

5e+07

4e+07

3e+07 Base pairs

2e+07

1e+07

0e+00 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG01 LG02 LG04 LG05 LG06 LG07 LG08 LG09 LG10 LG11 LG12 LG13 LG14 LG15 LG16 LG17 LG18 LG19 LG20 LG22 LG23 LG03a LG03b LG03a LG03b LG03a LG03b

candidate genes sex determination pigmentation genes ZW region XY region ZW/XY region

Fig. S11. Distribution of candidate genes for sex determination and pigmentation. Gray bars represent LGs and lines candidate genes for sex determination and pigmentation. Sex-differentiated regions are indicated with colored shadings.

38 Supplementary Tables

All supplementary tables are provided as excel file (Supplementary Material 2),

Table S1 contains information on the included species, the experimental set-up and sample sizes for all analyses.

Table S2 contains all obtained results concerning sex chromosome identification on the tribe- and subsequent species-level, including degree of sex chromosome differentiation, potential candidate genes in the sex-differentiated region, and source data for fig. S11.

Table S3 includes sequencing information for the used transcriptome data.

Table S4 includes information on sex chromosomal systems in ricefishes (source data for fig. S8A).

Table S5 includes information on sex chromosomal systems in ray-finned fishes (source data for fig. S8B).

Table S6 contains reference genome gene IDs (NCBI) for putative candidate genes involved in sex determination and pigmentation (source data for fig. S11).

39