Adaptive Evolution of Gamete-Recognition Proteins in Birds and Mammals

SUPPLEMENTARY MATERIAL

Adaptive evolution of gamete-recognition proteins in birds and mammals

Sofia Berlin, Qu Lujiang 1 and Hans Ellegren

Supplementary Table 1-3, Supplementary Figure 1 and 2 + some other information Supplementary Table 1. Avian Genbank accession numbers.

Gene Chicken Zebra finch Mallard Turkey Quail CD9 AB032767 EF191917 Acrosin XR_026893 ZP1 NM_204683 AB251639 AB253774 AB061520 ZP2 NM_00103909 ZP4 NM_204879 ZPAX NM_001045837

Trees that were used in the PAML4 analyses of the mammalian orthologues (topologies based on Murphy et al. (2001)):

CD9: ((((Homo_sapiens,Pan_troglodytes),Macaca_mulatta),Callithrix_jacchus),(Rattus_norvegicus,Mus_musculus),((Sus_scrofa,Bos_taurus),

(Felis_catus,Phoca_vitulina)))

ZP1: (((Homo_sapiens,Pan_troglodytes),Macaca_mulatta),Equus_caballus,(Mesocricetus_auratus,(Mus_musculus,Rattus_norvegicus)))

ZP2: (((Equus_caballus,(Felis_catus,(Canis_familiaris,Mustela_erminea))),(Bos_taurus,Sus_scrofa)),(Callithrix_jacchus,(Homo_sapiens,

Macaca_mulatta)),(Oryctolagus_cuniculus,(Mesocricetus_auratus,(Mus_musculus,Rattus_norvegicus))))

ZP4: ((Macaca_mulatta,(Homo_sapiens,Pan_troglodytes)),(Oryctolagus_cuniculus,(Mesocricetus_auratus,Rattus_norvegicus)),((Sus_scrofa,

Bos_taurus),(Mustela_erminea,Felis_catus)))

Supplementary Table 2. Primers combinations and tissue used for amplification of bird sequences.

CD9 Acrosin ZP1 ZP2 ZP4 ZPAX

(spleen) (testis) (ovary) (ovary) (ovary) (ovary) Mallard A/B C/D - C/D, K/L, M/N, C/D, E/F C/D

O/P Pigeon A/B - - A/B, C/D, E/F E/F, G/H Guineafowl A/B A/B C/D A/B, C/D, E/F, A/B, C/D A/B, C/D, E/F,

G/H, G/H, I/J Pheasant C/D C/D A/B, C/D, E/F C/D, I/J, K/L; A/B, C/D C/D, E/F, G/H, I/J

M/N Red grouse A/B - - - - - Turkey A/B - - A/B, C/D, E/F, A/B, C/D A/B, C/D, E/F,

G/H, G/H, I/J Quail A/B A/B - A/B, C/D, E/F, A/B, C/D A/B, E/F, G/H, I/J

Primer sequences: C: CD9-cons-for: AAGTGCATCAARTACTTGCTC (22) CD9 D: CD9-cons-rev: CTTTCTGCGGATAGCACAG A: CD9-for: ATGCCTGTCAAAGGAGGCAC (1) B: CD9-rev: CAGCTCTTAGACCATYTCTC (662) Acrosin F: ZP2c-rev: GGGTCATTGCGGTTCAGGAG A: Acro-for: GATGGTGCTGCTGCTGCCC G: ZP2d-for: ATCCTTCTAAGCTACCCAG B: Acro-rev: GGGCTGCCATTGGGCATTA H: ZP2d-rev: ACCACATTTGCCATCAAGG C: AcroN-for: GGCACGGGRCACATSTGTGG I: ZP2Na-for: GACCTGCCTGCAGGACAGGC D: AcroN-rev: AYATGCAGGAGCTCCTGGAGC J: ZP2Na-rev: GCATTCTTGACTCCACGGTC K: ZP2Nb-for: GCCTTCACTGCCACTGGAG ZP1 L: ZP2Nb-rev: GGTCCCACAYCCRCTCAGTG A: ZP1Na-for: AGCYGCTCCCTGCTGCTGC M: ZP2Nc-for: TAGCTGCTGTATGCACCCAGG B: ZP1Na-rev: GACCACTAGCGTGGGTCATCC N: ZP2Nc-rev: GCAGTGGAAGTAGACTAGGC C: ZP1Nd-for: CCCAAGCAGGTCTTTTTCAC O: ZP2Nd-for: GGCTGGAAGTGAAGGCTTTTG D: ZP1Nd-rev: CACTGTGTGACGGGAAAGTG P: ZP2Nd-rev: TCTTCTCTTCAGGCATTTAAG E: ZP1Ne-for: CAGCCCTACAACCTGGACA F: ZP1Ne-rev: CTGGTAGTGGCTGGGGAAG ZP4 A: ZP4a-for: TGTGGCCAAGGGAGCTTGC ZP2 B: ZP4a-rev: AAGTGCTGTCCCTAGTGACAG A: ZP2a-for: CTGTTCTTGGCCCCTGGTG C: ZP4b-for: CAGGTGACTGGAGACCAGG B: ZP2a-rev: GGTAGGCAACAGTCATGTGTG D: ZP4b-rev: GGGCCTTTGCTGGAAACAC C: ZP2b-for: TCTACACTGCGGCACTGAAGC E: ZP4Na-for: GGCTGGGAAGGGAATGCTTCC D: ZP2b-rev: GCTAGCCTGAACTCACTGTC F: ZP4Na-rev: CCCTGGATGCCACCAACTC E: ZP2c-for: CTAGTCCTGGACACGCTCAG ZPAX F: ZPAXb-rev: GGAAGGCACTGTATTAGCTCTG A: ZPAXa-for: TAGGAATACTCATCTCTGC F: ZPAXc-for: TCTCAATTTCCTGCAGATTTCC B: ZPAXa-rev: ATCATCCACTGCTGTTTGTA G: ZPAXc-rev: GCAGTTCAACTTCAAAGTACA C: ZPAXstar-for: TATGTGAAACCAACTACATGG H: ZPAXd-for: GAATACATGTGGAACAAGTAG D: ZPAXstar-rev: TGTTCCAAGAACAGGTTGAT I: ZPAXd-rev: CACTGCAGTGCAAATATAACT E: ZPAXb-for: TAGGTGCAGAAGGTGGCTCTT

Murphy, W. J., E. Eizirik, S. J. O'Brien, O. Madsen, M. Scally, C. J. Douady, E. Teeling, O. A. Ryder, M. J. Stanhope, W. W. de Jong, and M. S. Springer. 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351. Supplementary Table 3. Number of base pairs analysed for each species and gene.

Gene Chicken Zebra finch Mallard Pigeon Guinea fowl Pheasant Red grouse Turkey Quail CD9 672 672 641 637 641 576 640 640 641 Acrosin 1335 459 630 - 693 647 - - 894 ZP1 2802 915 2814 - 497 1167 - 2802 2802 ZP2 2061 1542 1350 - 1995 1667 - 1995 1998 ZP4 1629 1411 535 1280 1317 1285 - 1317 1320 ZPAX 2718 1926 614 1245 2468 1332 - 2468 1874 Supplementary Figure 1. Amino acid alignment of chicken and human Acrosin. Positively selected sites are indicated in bold.

Chicken ------Human ------VEMLPTAILLVLAVSVVAKDN

Chicken ------GTRVVGGTDAPQGAWPWIVSLQSTWYVGTG--H Human ATCDGPCGLRFRQNPQGGVRIVGGKAAQHGAWPWMVSLQIFT-YNSHRYH

Chicken ICGGSLITPQWVLTAAHCFDHATPDTPWHVVIGGHDLKR-----LGPEAV Human TCGGSLLNSRWVLTAAHCFVGKNNVHDWRLVFGAKEITYGNNKPVKAPLQ

Chicken VRNVIRIIPHEYYHRNNMANDIALLELDQPVQCSYYIQLACVPDASLRVS Human ERYVEKIIIHEKYNSATEGNDIALVEITPPISCGRFIGPGCLPHFKAGLP

Chicken ELTD-CYVSGWGHMGLRSLQEYVEPYRVLQEAKVQLIDLNICNSSNWYAG Human RGSQSCWVAGWGYIE----EKAPRPSSILMEARVDLIDLDLCNSTQWYNG

Chicken AVHIHNVCAGYPQGGIDTCQGDSGGPLMCKDKTADYFWLIGVTSWGKG?? Human RVQPTNVCAGYPVGKIDTCQGDSGGPLMCKDSKESAYVVVGITSWGVGCA

Chicken ???QPGVYASTQYFPLWILVQMGLLPAEAPTTTPYPVYISSSYQRPKPTY Human RAKRPGIYTATWPYLNWIASKIGSNALRMIQ------

Chicken SSPFRPCPFPRQKLLDFFNLLQELLQGLRGKKA Human ------

Supplementary Figure 2. Amino acid alignment of chicken and human ZP2. Positively selected sites are indicated in bold.

Chicken ------RGRLLLLLLFGFLLFLAPGASGEWDL Human ACRQRGGSWSPSGWFN--AGWSTYRSISLFFALVTSVNSIDVSQLVNPAF

Chicken SESMTCLQDRLELELPRELGNYTWHVRAVDVSGEEMMSCEHAVDYEKLLL Human PGTVTCDEREITVEFPSSPGTKKWHASVVDPLGLDMPNCTYILDPEKLTL

Chicken SALLVNCTSLEHGQYQLRLLLLLNGTAGEERNVTYSAHCSAAHGDEIIAP Human RATYDNCTRRVHGGHQMTIRVMNNSAALRHGAVMYQFFCPAMQVEE--TQ

Chicken LFVGETNCTKDSMAVTFP--GPSLSDEHLV---QVAVLTGTLTIDDGIKV Human GLSASTICQKDFMSFSLPRVFSGLADDSKG---TKVQMGWSIEVGDGARA

Chicken HQLSLGEAMQHGYSFLADG-HHLVFQAAFTATGVVSYKHNHKALYTAALK Human KTLTLPEAMKEGFSLLIDN-HRMTFHVPFNATGVTHYVQGNSHLYMVSLK

Chicken LMYGPPEHRLTVESRMLCVPGP-VFCNTTHMTVAIPAFPGTLMAVAVEDE Human LTFISPGQKVIFSSQAICAPDP-VTCNATHMTLTIPEFPGKLKSVSFENQ

Chicken TIPMDQLQDKGITLKTTVGVELHVSRRVLKSTLHGESCPRVQSYLSSLKL Human NIDVSQLHDNGIDLEATNGMKLHFSKTLLKTKL-SEKCLLHQFYLASLKL

Chicken TFHFHEETVAMVMHPQCPCDQLTPIA--AACTRDGYMDFEVLAGSTTPPL Human TFLLRPETVSMVIYPECLCESPVSIVTGELCTQDGFMDVEVYSYQTQPAL

Chicken VLDTLRLRDPTCKPASRSPLNDRAWFHVPLSGCGTRYWLEGEKIMYENEV Human DLGTLRVGNSSCQPVFEAQSQGLVRFHIPLNGCGTRYKFEDDKVVYENEI

Chicken RALRSDSVLHRISRDSEFRLAVLCSFSNGDASVSVRVDNPPPLAASTNQG Human HALWTDFPPSKISRDSEFRMTVKCSYSRNDMLLNINVESLTPPVASVKLG

Chicken PLSLILLSYPEDSYRQPYHDDQYPIVRYLQQPIFMEVQVLNRNDPNLYLQ Human PFTLILQSYPDNSYQQPYGENEYPLVRFLRQPIYMEVRVLNRDDPNIKLV

Chicken LDDCWATALEDPTSLPQWNIVVDGCEYEQDSYRTVFHPVGHGVSYPNYRQ Human LDDCWATSTMDPDSFPQWNVVVDGCAYDLDNYQTTFHPVGSSVTHPDHYQ

Chicken RLEVKAFAFVSGDKALPGLVYFHCSVLICSRFQLDSPLCTARCPRLPRRK Human RFDMKAFAFVSEAHVLSSLVYFHCSALICNRLSPDSPLCSVTCPVSSRHR

Chicken RGSGMLGA-SSVVSLQGPVLLVPHGWAAA------Human RATGATEAEKMTVSLPGPILLLSDDSSFRGVGSSD---LKASGSSGEKSR

Chicken ------RGGTLLSKVVWAA------VTATAVGVFSLTAIMLLFMDLL Human SETGEEVGSRGAMDTKGHKTAG-----DVGSKAVAAVAAFAGVVATLGFI

Chicken KCLKRR------Human YYLYEKRTVSNH-