Supplementary Material for: Genetic Content of the Neo-Sex Chromosomes in Ctenonotus and Norops (Squamata, Dactyloidae) and Degeneration of the Y Chromosome as Revealed by High-Throughput Sequencing of Individual Chromosomes

Pleurodont lizards are characterized by an ancient system of sex chromosomes. Along with stability of the central component of the system (homologous to the X chromosome of <i>Anolis carolinensis </i>[Dactyloidae], ACAX), in some genera the ancestral sex chromosomes are fused with microautosomes, forming neo-sex chromosomes. The genus <i>Ctenonotus </i>(Dactyloidae) is characterized by multiple X₁X₁X₂X₂/X₁X₂Y sex chromosomes. According to cytogenetic data, the large neo-Y chromosome is formed by fusion of the ancestral Y chromosome with 2 microautosomes (homologous to ACA10 or ACA11 and ACA12), the X₁ chromosome is formed by fusion of the ancestral X chromosome with the autosome homologous to ACA10 or ACA11, and the X₂ chromosome is homologous to autosome ACA12. To determine more precisely the content and evolution of the <i>Ctenonotus</i> sex chromosomes, we sequenced flow-sorted chromosomes (both sex chromosomes and microautosomes as control) of 2 species with a similar system: <i>C. pogus</i> and <i>C. sabanus</i>. Our results indicate that the translocated part of the X₁ is homologous to ACA11, X₂ is homologous to ACA12, and the Y contains segments homologous to both ACA11 and ACA12. Molecular divergence estimates suggest that the ancestral X-derived part has completely degenerated in the Y of <i>Ctenonotus</i>, similar to the degeneration of the <i>Norops sagrei </i>Y chromosome (Dactyloidae). The newly added regions show loss of DNA content, but without degeneration of the conserved regions. We hypothesize that the translocation of autosomal blocks onto sex chromosomes facilitated rapid degeneration of the pseudoautosomal region on the ancestral Y.

侧齿蜥蜴（Pleurodont lizards）以拥有一套古老的性染色体系统为特征。该系统的核心组分（与安乐蜥科（Dactyloidae）*Anolis carolinensis*的X染色体同源，即ACAX）保持稳定，部分类群的祖先性染色体与微型常染色体发生融合，形成新性染色体（neo-sex chromosomes）。隶属于安乐蜥科的栉趾蜥属（Ctenonotus），以X₁X₁X₂X₂/X₁X₂Y型多体性染色体为特征。根据细胞遗传学数据，大型新Y染色体由祖先Y染色体与两条微型常染色体（分别对应ACAX的AC10或AC11、AC12）融合形成；X₁染色体由祖先X染色体与对应AC10或AC11的常染色体融合而来；X₂染色体则与AC12号常染色体同源。为更精准地解析栉趾蜥属性染色体的组成与演化历程，本研究对该属两个拥有类似性染色体系统的物种——波古斯栉趾蜥（C. pogus）和萨巴栉趾蜥（C. sabanus）的流式分选染色体（flow-sorted chromosomes，包括性染色体及作为对照的微型常染色体）进行了测序。研究结果显示，X₁染色体的易位区段与AC11同源，X₂染色体与AC12同源，而Y染色体则包含与AC11和AC12均同源的染色体区段。分子分歧估算结果表明，栉趾蜥属Y染色体中源自祖先X染色体的区段已完全退化，这与安乐蜥科*Norops sagrei* Y染色体的退化模式一致。新并入的染色体区段呈现DNA含量丢失的特征，但保守区段并未发生退化。我们据此提出假说：常染色体区段易位至性染色体的过程，加速了祖先Y染色体上假常染色体区域（pseudoautosomal region）的快速退化。