Pseudogenes document protracted parallel regression of oral anatomy in myrmecophagous mammals

Supplementary Data for: Pseudogenes Document Protracted Parallel Regression of Oral Anatomy in Myrmecophagous Mammals Christopher A. Emerling*, Sophie Teullet, Rémi Allio, John Gatesy, Mark S. Springer and Frédéric Delsuc* *Correspondence to [e-mail] and [e-mail] Description of available files: Supplementary Dataset S1: Complete DNA sequence alignments for all focal genes and taxa. Supplementary Dataset S2: Reference phylogeny and DNA sequence alignments for PAML analyses. Supplementary Figure S1: RAxML gene trees based on alignments after cleaning in preparation for PAML analyses. Supplementary Figure S2: DNA sequence alignments for ostentorian (Carnivora + Pholidota) genes ACP4, AMBN, AMELX, and AMTN. Supplementary Figure S3: DNA sequence alignments for ostentorian (Carnivora + Pholidota) genes DSPP, ENAM, KLK4, and MMP20. Supplementary Figure S4: DNA sequence alignments for ostentorian (Carnivora + Pholidota) genes ODAM, ODAPH, TAS1R3, MYH16, and PKD2L1. Supplementary Figure S5: DNA sequence alignments for ostentorian (Carnivora + Pholidota) TAS1R1. Supplementary Figure S6: DNA sequence alignments for ostentorian (Carnivora + Pholidota) TAS1R2. Supplementary Figure S7: DNA sequence alignments for xenarthran TAS1R genes. Supplementary Figure S8: DNA sequence alignments for xenarthran MYH16 and PKD2L1. Supplementary Figure S9: DNA sequence alignments for aardvark genes. Supplementary Figure S10: DNA sequence alignments for numbat ACP4 and TAS1R2. Supplementary Figure S11: DNA sequence alignments for numbat TAS1R1. Supplementary Figure S12: DNA sequence alignments for monotreme genes. Supplementary Table S1: Information on genome assemblies used in this study. Supplementary Table S2: Species used as outgroups for PAML analyses. Supplementary Table S3: PAML and pseudogene dating analysis results for ACP4. Supplementary Table S4: PAML and pseudogene dating analysis results for AMBN. Supplementary Table S5: PAML and pseudogene dating analysis results for AMELX. Supplementary Table S6: PAML and pseudogene dating analysis results for AMTN. Supplementary Table S7: PAML and pseudogene dating analysis results for DSPP. Supplementary Table S8: PAML and pseudogene dating analysis results for ENAM. Supplementary Table S9: PAML and pseudogene dating analysis results for KLK4. Supplementary Table S10: PAML and pseudogene dating analysis results for MMP20. Supplementary Table S11: PAML and pseudogene dating analysis results for MYH16. Supplementary Table S12: PAML and pseudogene dating analysis results for ODAM. Supplementary Table S13: PAML and pseudogene dating analysis results for ODAPH. Supplementary Table S14: PAML and pseudogene dating analysis results for PKD2L1. Supplementary Table S15: PAML and pseudogene dating analysis results for TAS1R1. Supplementary Table S16: PAML and pseudogene dating analysis results for TAS1R2. Supplementary Table S17: PAML and pseudogene dating analysis results for TAS1R3.补充数据：假基因证实食蚁哺乳动物口腔解剖结构的长期平行退化 克里斯托弗·A·埃默林*, 索菲·特勒莱, 雷米·阿利奥, 约翰·加茨, 马克·S·斯普林格, 弗雷德里克·德尔苏* *通讯作者：[e-mail] 与 [e-mail] 可用文件说明： 补充数据集S1：所有目标基因与类群的完整DNA序列比对结果。 补充数据集S2：用于PAML分析的参考系统发育树与DNA序列联配结果。 补充图S1：基于经清洗预处理以用于PAML分析的序列联配构建的RAxML基因树。 补充图S2：ostentorian类群（食肉目（Carnivora）+鳞甲目（Pholidota）基因ACP4、AMBN、AMELX及AMTN的DNA序列联配结果。 补充图S3：ostentorian类群（食肉目（Carnivora）+鳞甲目（Pholidota）基因DSPP、ENAM、KLK4及MMP20的DNA序列联配结果。 补充图S4：ostentorian类群（食肉目（Carnivora）+鳞甲目（Pholidota）基因ODAM、ODAPH、TAS1R3、MYH16及PKD2L1的DNA序列联配结果。 补充图S5：ostentorian类群（食肉目（Carnivora）+鳞甲目（Pholidota））TAS1R1的DNA序列联配结果。 补充图S6：ostentorian类群（食肉目（Carnivora）+鳞甲目（Pholidota））TAS1R2的DNA序列联配结果。 补充图S7：贫齿类（xenarthran）TAS1R基因的DNA序列联配结果。 补充图S8：贫齿类MYH16与PKD2L1的DNA序列联配结果。 补充图S9：土豚基因的DNA序列联配结果。 补充图S10：袋食蚁兽ACP4与TAS1R2的DNA序列联配结果。 补充图S11：袋食蚁兽TAS1R1的DNA序列联配结果。 补充图S12：单孔目基因的DNA序列联配结果。 补充表S1：本研究使用的基因组组装信息。 补充表S2：PAML分析所用的外类群物种。 补充表S3：ACP4基因的PAML与假基因定年分析结果。 补充表S4：AMBN基因的PAML与假基因定年分析结果。 补充表S5：AMELX基因的PAML与假基因定年分析结果。 补充表S6：AMTN基因的PAML与假基因定年分析结果。 补充表S7：DSPP基因的PAML与假基因定年分析结果。 补充表S8：ENAM基因的PAML与假基因定年分析结果。 补充表S9：KLK4基因的PAML与假基因定年分析结果。 补充表S10：MMP20基因的PAML与假基因定年分析结果。 补充表S11：MYH16基因的PAML与假基因定年分析结果。 补充表S12：ODAM基因的PAML与假基因定年分析结果。 补充表S13：ODAPH基因的PAML与假基因定年分析结果。 补充表S14：PKD2L1基因的PAML与假基因定年分析结果。 补充表S15：TAS1R1基因的PAML与假基因定年分析结果。 补充表S16：TAS1R2基因的PAML与假基因定年分析结果。 补充表S17：TAS1R3基因的PAML与假基因定年分析结果。