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

(spleen) /

Acrosin

(testis) /

ZP1

(ovary) /

ZP2

(ovary) /

ZP4

(ovary) /

ZPAX

(ovary)
Mallard / A/B / C/D / - / C/D, K/L, M/N, O/P / C/D, E/F / C/D
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, G/H, / A/B, C/D / A/B, C/D, E/F, G/H, I/J
Pheasant / C/D / C/D / A/B, C/D, E/F / C/D, I/J, K/L; M/N / A/B, C/D / C/D, E/F, G/H, I/J
Red grouse / A/B / - / - / - / - / -
Turkey / A/B / - / - / A/B, C/D, E/F, G/H, / A/B, C/D / A/B, C/D, E/F, G/H, I/J
Quail / A/B / A/B / - / A/B, C/D, E/F, G/H, / A/B, C/D / A/B, E/F, G/H, I/J

Primer sequences:

CD9

A: CD9-for: ATGCCTGTCAAAGGAGGCAC (1)

B: CD9-rev: CAGCTCTTAGACCATYTCTC (662)

C: CD9-cons-for: AAGTGCATCAARTACTTGCTC (22)

D: CD9-cons-rev: CTTTCTGCGGATAGCACAG

Acrosin

A: Acro-for: GATGGTGCTGCTGCTGCCC

B: Acro-rev: GGGCTGCCATTGGGCATTA

C: AcroN-for: GGCACGGGRCACATSTGTGG

D: AcroN-rev: AYATGCAGGAGCTCCTGGAGC

ZP1

A: ZP1Na-for: AGCYGCTCCCTGCTGCTGC

B: ZP1Na-rev: GACCACTAGCGTGGGTCATCC

C: ZP1Nd-for: CCCAAGCAGGTCTTTTTCAC

D: ZP1Nd-rev: CACTGTGTGACGGGAAAGTG

E: ZP1Ne-for: CAGCCCTACAACCTGGACA

F: ZP1Ne-rev: CTGGTAGTGGCTGGGGAAG

ZP2

A: ZP2a-for: CTGTTCTTGGCCCCTGGTG

B: ZP2a-rev: GGTAGGCAACAGTCATGTGTG

C: ZP2b-for: TCTACACTGCGGCACTGAAGC

D: ZP2b-rev: GCTAGCCTGAACTCACTGTC

E: ZP2c-for: CTAGTCCTGGACACGCTCAG

F: ZP2c-rev: GGGTCATTGCGGTTCAGGAG

G: ZP2d-for: ATCCTTCTAAGCTACCCAG

H: ZP2d-rev: ACCACATTTGCCATCAAGG

I: ZP2Na-for: GACCTGCCTGCAGGACAGGC

J: ZP2Na-rev: GCATTCTTGACTCCACGGTC

K: ZP2Nb-for: GCCTTCACTGCCACTGGAG

L: ZP2Nb-rev: GGTCCCACAYCCRCTCAGTG

M: ZP2Nc-for: TAGCTGCTGTATGCACCCAGG

N: ZP2Nc-rev: GCAGTGGAAGTAGACTAGGC

O: ZP2Nd-for: GGCTGGAAGTGAAGGCTTTTG

P: ZP2Nd-rev: TCTTCTCTTCAGGCATTTAAG

ZP4

A: ZP4a-for: TGTGGCCAAGGGAGCTTGC

B: ZP4a-rev: AAGTGCTGTCCCTAGTGACAG

C: ZP4b-for: CAGGTGACTGGAGACCAGG

D: ZP4b-rev: GGGCCTTTGCTGGAAACAC

E: ZP4Na-for: GGCTGGGAAGGGAATGCTTCC

F: ZP4Na-rev: CCCTGGATGCCACCAACTC

ZPAX

A: ZPAXa-for: TAGGAATACTCATCTCTGC

B: ZPAXa-rev: ATCATCCACTGCTGTTTGTA

C: ZPAXstar-for: TATGTGAAACCAACTACATGG

D: ZPAXstar-rev: TGTTCCAAGAACAGGTTGAT

E: ZPAXb-for: TAGGTGCAGAAGGTGGCTCTT

F: ZPAXb-rev: GGAAGGCACTGTATTAGCTCTG

F: ZPAXc-for: TCTCAATTTCCTGCAGATTTCC

G: ZPAXc-rev: GCAGTTCAACTTCAAAGTACA

H: ZPAXd-for: GAATACATGTGGAACAAGTAG

I: ZPAXd-rev: CACTGCAGTGCAAATATAACT

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-