Allopatric speciation and interspecific gene flow driven by niche conservatism of Diploderma tree lizards in Taiwan

Allopatric speciation is a widely accepted hypothesis for species distributed across geographic barriers. Meanwhile, niche conservatism, the tendency of species to retain their ancestral ecological traits, helps reinforce genetic differentiation by stabilizing species distributions over time and reducing the role of competition in shaping range boundaries. In contrast, hybridization can occur at the edges of distribution after secondary contact following climatic or geological events, leading to a reduction in genetic divergence between divergent lineages. In this study, we investigated the role of geographic barriers, niche conservatism, and gene flow in the speciation history of Diploderma species in Taiwan, where geographically distinct taxa share similar environmental preferences. By using ddRAD-seq data, seven distinct genetic clusters were identified with two putatively new cryptic species in D. brevipes and D. polygonatum. Most sister species pairs share similar climatic niches b..., Sampling and molecular data preparation The collection surveys were conducted across distribution range of each species (n = 227) and combined with samples from an earlier study (Yang et al., 2018, n = 19), with a total of 246 Diploderma samples implemented in the phylogenetic analysis (Fig. 1a). Genomic DNA was extracted using muscle tissues following the protocol of EasyPure Genomic DNA mini Kit (Bioman, New Taipei). To preliminarily investigate the phylogeny by multi-locus data, four pairs of primers were selected for following polymerase chain amplification process (PCR), including one mitochondrial (NADH dehydrogenase subunit 2, ND2) and three nuclear genes (brain-derived neurotrophic factor gene, BDNF; oocyte maturation factor Mos gene, CMOS; RNA fingerprint protein 35 gene, R35) (Table 1). The PCR cycles consisted of an initial cycle at 94 °C for 3 minutes, followed by 35 cycles at 94 °C for 30 seconds, suitable annealing temperature for 45 seconds, and 72 °C for 120 seconds, and..., , # Allopatric speciation and interspecific gene flow driven by niche conservatism of Diploderma tree lizards in Taiwan This reposity contains information for data used in the article: Authors: Tzong-Han Lin, Zong-Yu Shen, Ming-Hsun Chou, Pei-Wei Sun, Chin-Chia Shan, Jen-Pan Huang, Si-Min Lin Title: Allopatric speciation and interspecific gene flow driven by niche conservatism of Diploderma tree lizards in Taiwan 01 ND2_1136b: Sequence file for mitochondrial ND2 sequences 02 BDNF_480bp: Sequence file for nuclear BDNF sequences 03 CMOS_327bp: Sequence file for nuclear CMOS sequences 04 R35_561bp: Sequence file for nuclear R35 sequences 05 Diploderma.p.snps: SNPs file for ddRAD sequences from nuclear genome 06 Diploder_ddRAD_seq.fasta: fasta file for ddRAD sequences from nuclear genome 07 Diploderma_SNAP_tree.newick: Tree file using ddRAD-seq 08 BPP.zip: Input files for BPP analysis, including population file 'bpp.Imap.txt', sequence file 'BPP_new.phy', and control file 'msci_sin...,异域成种（Allopatric speciation）是解释跨地理屏障分布物种类群的广为接受的科学假说。生态位保守性（niche conservatism）指物种保留其祖先生态特征的倾向，该特性可通过长期稳定物种分布范围、削弱竞争对分布边界的塑造作用，强化种群间的遗传分化。与之相对，在气候或地质事件引发二次接触后，杂交可发生于物种分布的边缘地带，导致分歧支系间的遗传分化程度降低。 本研究聚焦台湾地区攀蜥属（Diploderma）物种的成种历史，探究地理屏障、生态位保守性与基因流的作用机制；该区域内地理分化的类群具有相似的环境偏好。我们通过双酶切简化基因组测序（ddRAD-seq）数据，鉴定出7个独立的遗传聚类簇，其中短肢攀蜥（D. brevipes）与多棱攀蜥（D. polygonatum）各存在1个疑似新的隐存物种（cryptic species）。多数姊妹物种类群具有相似的气候生态位…… 采样与分子数据制备 我们针对各物种的分布范围开展采集调查（有效样本量n=227），并结合前期研究（Yang等，2018，n=19）的样本，最终共获得246份攀蜥属样本用于系统发育分析（Fig. 1a）。基因组DNA提取采用肌肉组织，严格遵循EasyPure Genomic DNA mini Kit（Bioman，新北市）的操作流程。为通过多位点数据初步解析系统发育关系，我们选取4对引物开展聚合酶链式扩增（PCR），包括1个线粒体基因：烟酰胺腺嘌呤二核苷酸脱氢酶亚基2（ND2），以及3个核基因：脑源性神经营养因子基因（BDNF）、卵母细胞成熟因子Mos基因（CMOS）、RNA指纹蛋白35基因（R35）（详见表1）。PCR循环程序为：94℃预变性3分钟，随后35个循环：94℃变性30秒，适宜退火温度下退火45秒，72℃延伸120秒…… # 台湾地区攀蜥属树蜥生态位保守性驱动的异域成种与种间基因流 本数据集仓库包含本文研究所用的全部数据信息： 作者：林宗翰、沈宗宇、周明勋、孙佩玮、单钦嘉、黄仁磐、林思民 论文标题：台湾地区攀蜥属树蜥生态位保守性驱动的异域成种与种间基因流 01 ND2_1136b：线粒体ND2基因序列文件 02 BDNF_480bp：核基因BDNF序列文件 03 CMOS_327bp：核基因CMOS序列文件 04 R35_561bp：核基因R35序列文件 05 Diploderma.p.snps：核基因组ddRAD测序得到的单核苷酸多态性（SNPs）文件 06 Diploder_ddRAD_seq.fasta：核基因组ddRAD测序得到的FASTA格式序列文件 07 Diploderma_SNAP_tree.newick：基于ddRAD-seq数据构建的系统发育树文件 08 BPP.zip：BPP分析的输入文件压缩包，包含种群映射文件bpp.Imap.txt、序列文件BPP_new.phy与控制文件msci_sin……