Genomic data suggest parallel dental vestigialization within the xenarthran radiation
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<strong>Supplementary Material for:</strong> Emerling C.A., Gibb G.C., Tilak M.-K., Hughes J., Kuch M., Duggan A.T., Poinar H.N., Nachman M.W. & Delsuc F. Genomic data suggest parallel dental vestigialization within the xenarthran radiation. <em>Submitted to PCI Genomics</em>. <strong>DATASETS</strong> Dataset S1. Set of baits used in the exon capture experiments of the 11 tooth genes considered in Xenarthra. Dataset S2. ACPT genomic alignment used for characterizing inactivating mutations. Dataset S3. AMBN genomic alignment used for characterizing inactivating mutations. Dataset S4. AMELX genomic alignment used for characterizing inactivating mutations. Dataset S5. AMTN genomic alignment used for characterizing inactivating mutations. Dataset S6. DMP1 genomic alignment used for characterizing inactivating mutations. Dataset S7. DSPP genomic alignment used for characterizing inactivating mutations. Dataset S8. ENAM genomic alignment used for characterizing inactivating mutations. Dataset S9. MEPE genomic alignment used for characterizing inactivating mutations. Dataset S10. MMP20 genomic alignments used for characterizing inactivating mutations. Dataset S11. ODAM genomic alignments used for characterizing inactivating mutations. Dataset S12. ODAPH genomic alignments used for characterizing inactivating mutations. Dataset S13. ACPT codon alignment used in Coevol and PAML analyses. Dataset S14. AMBN codon alignment used in Coevol and PAML analyses. Dataset S15. AMELX codon alignment used in Coevol and PAML analyses. Dataset S16. AMTN codon alignment used in Coevol and PAML analyses. Dataset S17. DMP1 codon alignment used in Coevol and PAML analyses. Dataset S18. DSPP codon alignment used in Coevol and PAML analyses. Dataset S19. ENAM codon alignment used in Coevol and PAML analyses. Dataset S20. MEPE codon alignment used in Coevol and PAML analyses. Dataset S21. MMP20 codon alignment used in Coevol and PAML analyses. Dataset S22. ODAM codon alignment used in Coevol and PAML analyses. Dataset S23. ODAPH codon alignment used in Coevol and PAML analyses. Dataset S24. Draft DISCOVAR de novo genome assembly of the southern naked-tailed armadillo (<em>Cabassous unicinctus</em>) specimen MVZ 155190 from the Museum of Vertebrate Zoology (University of California Berkeley, USA). <strong>SUPPLEMENTARY TABLES (Supplementary_Tables_S1-S26.xlsx)</strong> Table S1. Specimen information for newly generated sequences. Table S2. Sources for DNA sequences listed for each gene, indicating methodology used. In some cases, sequences were generated via two or three methodologies. Accession numbers are associated with NCBI-derived sequences. Table S3. Primers used in PCR amplification experiments. Table S4. Results from PAML analyses (one ratio models) to determine the best codon frequency model fits. CF = codon frequency model; K = free parameters. Table S5. Inactivating mutations recorded in ACPT. The details in this caption also apply to Tables S6–S15. Taxa in bold are represented by whole genome assemblies. Exon colors code for the following: green = putatively functional; yellow = missing; pink = one or more inactivating mutations found. Abbreviations for mutations are as follows: del = deletion; ins = insertion; start = start codon mutation; stop = premature stop codon; ? = ambiguity whether the mutation is shared among all members of the clade; poly = polymorphism inferred by short reads. Abbreviations in brackets following an inactivating mutation indicate shared inactivating mutation. Key for each abbreviation follows: Bpyg = <em>Bradypus pygmaeus</em>; BRAD = <em>Bradypus</em>; Btri = <em>Bradypus tridactylus</em>; Bvar = <em>Bradypus variegatus</em>; CAB = <em>Cabassous</em>; Ccen = <em>Cabassous centralis</em>; Ccha = <em>Cabassous chacoensis</em>; CHAET = <em>Chaetophractus</em>; CHLAM = Chlamyphoridae; CHOL = <em>Choloepus</em>; Cnat = <em>Chaetophractus nationi</em>; Cuni = <em>Cabassous unicinctus</em>; Cvel = <em>Chaetophractus vellerosus</em>; Cvil = <em>Chaetophractus villosus</em>; DASY = Dasypodidae; Dkap = <em>Dasypus kappleri</em>; Dnov = <em>Dasypus novemcinctus</em>; Dpil = <em>Dasypus pilosus</em>; Dsab = <em>Dasypus sabanicola</em>; FOLI = Folivora; MYRM = Myrmecophagidae; PEUT = Tolypeutinae; PHOR = Chlamyphorinae; PHRAC = Euphractinae; PILO = Pilosa; Pmax = <em>Priodontes maximus</em>; TAM = <em>Tamandua</em>; TOLY = <em>Tolypeutes</em>; VERM = Vermilingua; XEN = Xenarthra; Zpic = <em>Zaedyus pichiy</em>. Table S6. Inactivating mutations recorded in AMBN. See additional details in Table S5 caption. Table S7. Inactivating mutations recorded in AMELX. See additional details in Table S5 caption. Table S8. Inactivating mutations recorded in AMTN. See additional details in Table S5 caption. Table S9. Inactivating mutations recorded in DMP1. See additional details in Table S5 caption. Table S10. Inactivating mutations recorded in DSPP. See additional details in Table S5 caption. Table S11. Inactivating mutations recorded in ENAM. See additional details in Table S5 caption. Table S12. Inactivating mutations recorded in MEPE. See additional details in Table S5 caption. Table S13. Inactivating mutations recorded in MMP20. See additional details in Table S5 caption. Table S14. Inactivating mutations recorded in ODAM. See additional details in Table S5 caption. Table S15. Inactivating mutations recorded in ODAPH. See additional details in Table S5 caption. Table S16. PAML results for ACPT. Model: BG = branch(es) grouped with background; fixed 1 = branch(es) fixed at 1. p-value: specific p-value only shown if lower than 0.05. Model Comparison: if model comparison yields statistically significant differences (p < 0.05), model comparison bolded and given green background. For most models, w only shown for branch(es) of interest. Table S17. PAML results for AMBN. See additional details in Table S16 caption. Table S18. PAML results for AMELX. See additional details in Table S16 caption. Table S19. PAML results for AMTN. See additional details in Table S16 caption. Table S20. PAML results for DMP1. See additional details in Table S16 caption. Table S21. PAML results for DSPP. See additional details in Table S16 caption. Table S22. PAML results for ENAM. See additional details in Table S16 caption. Table S23. PAML results for MEPE. See additional details in Table S16 caption. Table S24. PAML results for MMP20. See additional details in Table S16 caption. Table S25. PAML results for ODAM. See additional details in Table S16 caption. Table S26. PAML results for ODAPH. See additional details in Table S16 caption. <strong>SUPPLEMENTARY FIGURES</strong> Figure S1. Portion of ACPT exon 7 alignment showing two alternative alignments for a putative shared 2-bp inactivating mutation. See manuscript for details. Figure S2. Visualization of PAML results for ACPT. Phylogram branch lengths optimized for substitutions per codon. Red bars represent minimum dates for pseudogenization based on shared or unique inactivating mutations. Blue branches = w statistically lower than 1; blue branches with asterisk = w statistically lower than 1 and background; purple branches = statistically higher than background and lower than 1; red branches = w statistically higher than background ; red branches with asterisk = w statistically higher than background and 1; black branches that pre-date inactivating mutations = not statistically distinguishable from background or 1; black branches that post-date inactivating mutations = no statistically analyses performed on these branches. Figure S3. Visualization of PAML results for AMBN. See caption for Figure S2 for more details. Figure S4. Visualization of PAML results for AMELX. See caption for Figure S2 for more details. Figure S5. Visualization of PAML results for AMTN. See caption for Figure S2 for more details. Figure S6. Visualization of PAML results for DMP1. See caption for Figure S2 for more details. Figure S7. Visualization of PAML results for DSPP. See caption for Figure S2 for more details. Figure S8. Visualization of PAML results for ENAM. See caption for Figure S2 for more details. Figure S9. Visualization of PAML results for MEPE. See caption for Figure S2 for more details. Figure S10. Visualization of PAML results for MMP20. See caption for Figure S2 for more details. Figure S11. Visualization of PAML results for ODAM. See caption for Figure S2 for more details. Figure S12. Visualization of PAML results for ODAPH. See caption for Figure S2 for more details. Figure S13. Visualization of Coevol results for ACPT. The figure shows the Bayesian reconstruction of dN/dS across the placental phylogeny with focus on xenarthrans (armadillos, anteaters, and sloths). The variation of dN/dS was jointly reconstructed with divergence times while controlling the effect of three life-history traits (body mass, longevity, and sexual maturity). The tree is rooted with Afrotheria as the sister-group to all other placentals. Asterisks indicate non-functional sequences. Figure S14. Visualization of Coevol results for AMBN. See caption for Figure S13 for more details. Figure S15. Visualization of Coevol results for AMELX. See caption for Figure S13 for more details. Figure S16. Visualization of Coevol results for AMTN. See caption for Figure S13 for more details. Figure S17. Visualization of Coevol results for DMP1. See caption for Figure S13 for more details. Figure S18. Visualization of Coevol results for DSPP. See caption for Figure S13 for more details. Figure S19. Visualization of Coevol results for ENAM. See caption for Figure S13 for more details. Figure S20. Visualization of Coevol results for MEPE. See caption for Figure S13 for more details. Figure S21. Visualization of Coevol results for MMP20. See caption for Figure S13 for more details. Figure S22. Visualization of Coevol results for ODAM. See caption for Figure S13 for more details. Figure S23. Visualization of Coevol results for ODAPH. See caption for Figure S13 for more details.
**补充材料：** Emerling C.A.、Gibb G.C.、Tilak M.-K.、Hughes J.、Kuch M.、Duggan A.T.、Poinar H.N.、Nachman M.W. & Delsuc F.：基因组数据显示异关节类（Xenarthra）辐射演化中出现平行的牙齿结构退化。**已提交至PCI Genomics**。 **数据集** 数据集S1：本研究针对异关节类（Xenarthra）中11个牙齿基因开展外显子捕获实验（exon capture experiments）所用的诱饵探针集。 数据集S2：用于表征失活突变（inactivating mutations）的ACPT基因组比对文件。 数据集S3：用于表征失活突变的AMBN基因组比对文件。 数据集S4：用于表征失活突变的AMELX基因组比对文件。 数据集S5：用于表征失活突变的AMTN基因组比对文件。 数据集S6：用于表征失活突变的DMP1基因组比对文件。 数据集S7：用于表征失活突变的DSPP基因组比对文件。 数据集S8：用于表征失活突变的ENAM基因组比对文件。 数据集S9：用于表征失活突变的MEPE基因组比对文件。 数据集S10：用于表征失活突变的MMP20基因组比对文件。 数据集S11：用于表征失活突变的ODAM基因组比对文件。 数据集S12：用于表征失活突变的ODAPH基因组比对文件。 数据集S13：用于Coevol与PAML分析的ACPT密码子比对（codon alignment）文件。 数据集S14：用于Coevol与PAML分析的AMBN密码子比对文件。 数据集S15：用于Coevol与PAML分析的AMELX密码子比对文件。 数据集S16：用于Coevol与PAML分析的AMTN密码子比对文件。 数据集S17：用于Coevol与PAML分析的DMP1密码子比对文件。 数据集S18：用于Coevol与PAML分析的DSPP密码子比对文件。 数据集S19：用于Coevol与PAML分析的ENAM密码子比对文件。 数据集S20：用于Coevol与PAML分析的MEPE密码子比对文件。 数据集S21：用于Coevol与PAML分析的MMP20密码子比对文件。 数据集S22：用于Coevol与PAML分析的ODAM密码子比对文件。 数据集S23：用于Coevol与PAML分析的ODAPH密码子比对文件。 数据集S24：美国加州大学伯克利分校脊椎动物博物馆（Museum of Vertebrate Zoology）馆藏标本MVZ 155190的<em>Cabassous unicinctus</em>（南部裸尾犰狳）经DISCOVAR从头组装的草图基因组。 **补充附表（Supplementary_Tables_S1-S26.xlsx）** 表S1：新获得序列的标本信息。 表S2：各基因DNA序列的来源及所用实验方法说明。部分序列通过两种或三种方法获得。源自NCBI的序列均关联有登录号。 表S3：聚合酶链式反应（PCR）扩增实验所用引物。 表S4：PAML分析（单比率模型（one ratio models））结果，用于确定最优拟合的密码子频率模型（codon frequency model）。CF：密码子频率模型；K：自由参数数目。 表S5：ACPT中记录的失活突变。本说明同样适用于表S6至S15。加粗的类群代表其拥有全基因组组装数据（whole genome assemblies）。外显子颜色编码规则如下：绿色=推定具有功能；黄色=序列缺失；粉色=存在一个或多个失活突变。突变缩写说明如下：del=缺失（deletion）；ins=插入（insertion）；start=起始密码子突变；stop=提前终止密码子；?=无法确定该突变是否为该演化支所有成员所共享；poly=由短读长序列推断的多态性（polymorphism）。失活突变后的方括号内缩写代表该突变为共享失活突变（shared inactivating mutation）。各缩写的含义如下：Bpyg=<em>Bradypus pygmaeus</em>（侏三趾树懒）；BRAD=<em>Bradypus</em>（三趾树懒属）；Btri=<em>Bradypus tridactylus</em>（三趾树懒）；Bvar=<em>Bradypus variegatus</em>（褐喉三趾树懒）；CAB=<em>Cabassous</em>（裸尾犰狳属）；Ccen=<em>Cabassous centralis</em>（中美裸尾犰狳）；Ccha=<em>Cabassous chacoensis</em>（查科裸尾犰狳）；CHAET=<em>Chaetophractus</em>（倭犰狳属）；CHLAM=Chlamyphoridae（倭犰狳科）；CHOL=<em>Choloepus</em>（二趾树懒属）；Cnat=<em>Chaetophractus nationi</em>（纳氏倭犰狳）；Cuni=<em>Cabassous unicinctus</em>（南部裸尾犰狳）；Cvel=<em>Chaetophractus vellerosus</em>（长毛倭犰狳）；Cvil=<em>Chaetophractus villosus</em>（大倭犰狳）；DASY=Dasypodidae（犰狳科）；Dkap=<em>Dasypus kappleri</em>（大犰狳）；Dnov=<em>Dasypus novemcinctus</em>（九带犰狳）；Dpil=<em>Dasypus pilosus</em>（毛犰狳）；Dsab=<em>Dasypus sabanicola</em>（萨氏犰狳）；FOLI=Folivora（树懒亚目）；MYRM=Myrmecophagidae（食蚁兽科）；PEUT=Tolypeutinae（倭犰狳亚科）；PHOR=Chlamyphorinae（倭犰狳亚科）；PHRAC=Euphractinae（密毛犰狳亚科）；PILO=Pilosa（披毛亚目）；Pmax=<em>Priodontes maximus</em>（巨犰狳）；TAM=<em>Tamandua</em>（小食蚁兽属）；TOLY=<em>Tolypeutes</em>（三带犰狳属）；VERM=Vermilingua（食蚁兽亚目）；XEN=Xenarthra（异关节类）；Zpic=<em>Zaedyus pichiy</em>（巴塔哥尼亚犰狳）。 表S6：AMBN中记录的失活突变。详细说明参见表S5的注释。 表S7：AMELX中记录的失活突变。详细说明参见表S5的注释。 表S8：AMTN中记录的失活突变。详细说明参见表S5的注释。 表S9：DMP1中记录的失活突变。详细说明参见表S5的注释。 表S10：DSPP中记录的失活突变。详细说明参见表S5的注释。 表S11：ENAM中记录的失活突变。详细说明参见表S5的注释。 表S12：MEPE中记录的失活突变。详细说明参见表S5的注释。 表S13：MMP20中记录的失活突变。详细说明参见表S5的注释。 表S14：ODAM中记录的失活突变。详细说明参见表S5的注释。 表S15：ODAPH中记录的失活突变。详细说明参见表S5的注释。 表S16：PAML分析ACPT的结果。模型说明：BG=与背景类群归为一组的分支；fixed 1=分支的ω值固定为1。p值：仅当p值小于0.05时显示具体数值。模型比较：若模型比较结果存在统计学显著性差异（p<0.05），则将比较结果加粗并添加绿色背景。多数模型仅展示目标分支的ω值。 表S17：PAML分析AMBN的结果。详细说明参见表S16的注释。 表S18：PAML分析AMELX的结果。详细说明参见表S16的注释。 表S19：PAML分析AMTN的结果。详细说明参见表S16的注释。 表S20：PAML分析DMP1的结果。详细说明参见表S16的注释。 表S21：PAML分析DSPP的结果。详细说明参见表S16的注释。 表S22：PAML分析ENAM的结果。详细说明参见表S16的注释。 表S23：PAML分析MEPE的结果。详细说明参见表S16的注释。 表S24：PAML分析MMP20的结果。详细说明参见表S16的注释。 表S25：PAML分析ODAM的结果。详细说明参见表S16的注释。 表S26：PAML分析ODAPH的结果。详细说明参见表S16的注释。 **补充附图** 图S1：ACPT外显子7比对的部分序列，展示推定共享的2bp失活突变的两种比对方式，详细信息参见正文。 图S2：ACPT的PAML分析结果可视化。以每个密码子的替换数优化系统发育树分支长度。红色条代表基于共享或独特失活突变推断的假基因化（pseudogenization）最小时间。蓝色分支：ω值显著小于1；带星号的蓝色分支：ω值显著小于1且低于背景分支；紫色分支：ω值显著高于背景分支且小于1；红色分支：ω值显著高于背景分支；带星号的红色分支：ω值显著高于背景分支且大于1；早于失活突变的黑色分支：与背景或ω=1无统计学差异；晚于失活突变的黑色分支：未对这些分支开展统计学分析。 图S3：AMBN的PAML分析结果可视化。详细说明参见图S2的注释。 图S4：AMELX的PAML分析结果可视化。详细说明参见图S2的注释。 图S5：AMTN的PAML分析结果可视化。详细说明参见图S2的注释。 图S6：DMP1的PAML分析结果可视化。详细说明参见图S2的注释。 图S7：DSPP的PAML分析结果可视化。详细说明参见图S2的注释。 图S8：ENAM的PAML分析结果可视化。详细说明参见图S2的注释。 图S9：MEPE的PAML分析结果可视化。详细说明参见图S2的注释。 图S10：MMP20的PAML分析结果可视化。详细说明参见图S2的注释。 图S11：ODAM的PAML分析结果可视化。详细说明参见图S2的注释。 图S12：ODAPH的PAML分析结果可视化。详细说明参见图S2的注释。 图S13：ACPT的Coevol分析结果可视化。本图展示基于胎盘类哺乳动物系统发育树的dN/dS（非同义替换率与同义替换率之比）贝叶斯重建（Bayesian reconstruction），重点关注异关节类（犰狳、食蚁兽和树懒）。dN/dS的变异与分化时间（divergence times）联合重建，同时控制三种生活史性状（life-history traits）的影响：体重、寿命与性成熟年龄。以非洲兽总目作为其余胎盘类的姊妹群（sister-group）为树根。星号代表无功能序列。 图S14：AMBN的Coevol分析结果可视化。详细说明参见图S13的注释。 图S15：AMELX的Coevol分析结果可视化。详细说明参见图S13的注释。 图S16：AMTN的Coevol分析结果可视化。详细说明参见图S13的注释。 图S17：DMP1的Coevol分析结果可视化。详细说明参见图S13的注释。 图S18：DSPP的Coevol分析结果可视化。详细说明参见图S13的注释。 图S19：ENAM的Coevol分析结果可视化。详细说明参见图S13的注释。 图S20：MEPE的Coevol分析结果可视化。详细说明参见图S13的注释。 图S21：MMP20的Coevol分析结果可视化。详细说明参见图S13的注释。 图S22：ODAM的Coevol分析结果可视化。详细说明参见图S13的注释。 图S23：ODAPH的Coevol分析结果可视化。详细说明参见图S13的注释。
