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...,