Additional file 1: of Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast
Creators: name: Wang, Xuejing
name: Que, Pinjia
name: Heckel, Gerald
name: Hu, Junhua
name: Zhang, Xuecong
name: Chiang, Chung-Yu
name: Zhang, Nan
name: Huang, Qin
name: Liu, Simin
name: Martinez, Jonathan
name: Pagani-Núñez, Emilio
name: Dingle, Caroline
name: Leung, Yu
name: Székely, Tamás
name: Zhang, Zhengwang
name: Liu, Yang
Publisher: name: figshare
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology

description: Table S1. Estimates of h, number of haplotypes; s, number of segregating sites; π, nucleotide diversity; Tajima’s D value, substitution rate of each locus estimated based on the substitution rate for cytb and GenBank accession number for each mtDNA and nuclear locus of C. alexandrinus and C. dealbatus were provided. The substitution rate of each locus was calculated using the method in Li et al. (2010): the ratio of net genetic distance of each locus across ingroup–outgroup was calculated, compared with net distance of mitochondrial cytochrome b (cytb) and then multiplied by the substitution rate for cytb (0.0105 ± 0.0005 substitution/site/mya, Weir &amp; Schluter 2008). Table S2. Estimates of pairwise FST for each microsatellite locus between C. alexandrinus and C. dealbatus, LD test result (same for both species), Na, number of alleles, Ho, observed heterozygosity and He, expected heterozygosity in each species. Table S3. PCR amplification protocols for three mtDNA, 16 nuclear exons and 22 microsatellite loci genotyped for C. alexandrinus and C. dealbatus. Table S4. Genetic differentiation between each pair of sampling localities of C. alexandrinus and C. dealbatus. Estimates were based on 1729 bp mtDNA (lower diagonal, ΦST) and 13 microsatellite loci (upper diagonal, FST). Values highlighted in red represent significant value after Bonferroni correction. Table S5 The morphological measurements of C. alexandrinus and C. dealbatus in different breeding sites along the Chinese coast, and Taiwan and Hainan Islands. Site reference number corresponds to numbers in Fig. 1 and Table 1. The number of sample size for each site (n), the mean value of measurements including bill and wing length, body mass and their respective standard deviations (SD) are given. Only DNA samples from a breeding site in Cangzhou were collected but not the measurement, the corresponding data is missing for this population. Mean and SD of bill length, wing length and body mass for each population. Measurement data of the site 3-Cangzhou was not collected. Table S6. Pearson’s correlation coefficients between pairwise of bioclimatic variables with the ranges of C. alexandrinus and C. dealbatus. Figure S1. Haplotype networks based on 80 individuals of 12 nuclear loci not shown in Fig. 2. C. alexandrinus (blue) and C. dealbatus (yellow). Figure S2. The Bayesian clustering analysis with STRUCTURE clearly suggested two genetic clusters corresponding to C. alexandrinus and C. dealbatus. Shown is the maximum value of the Delta K (Δ K) in posterior likelihood Ln P (X/K) over 10 runs per K of STRUCTURE. Figure S3. Niche of C. alexandrinus and C. dealbatus in climatic space from a principal component analysis (PCA-env). a) and b) show the niche characteristics of C. alexandrinus and C. dealbatus, respectively, along the first two axes of the PCA. Grey shading shows the density of the occurrences of the species by cell. The solid and dashed contour lines illustrate, respectively, 100 and 50% of the available (background) environment. c) The contribution of the variables on the first two axes of the PCA and the percentage of inertia explained by the two axes. d) Observed niche overlap D between the two ranges (bars with a diamond) and simulated niche overlaps (grey bars) on which tests of niche equivalency were calculated with 100 iterations. Figure S4. Differentiation in the stable isotope ratios among breeding sites (top-left: δ13C and bottom-left: δ15N) and between the two plovers (top-right: δ13C and bottom-right: δ15N). In all representation, C. alexandrinus marked in blue and C. dealbatus in yellow. Figure S5. (a) Newhybrid simulations failed to reliably detect simulated hybrid individuals. Real data of individuals with posterior density higher than 95% in STRUCTURE, and data of 5 simulated F1 and F2 individuals, and 10 back-cross individuals on each direction was used to imitate a situation when hybrids were the minority in the population. (b) Newhybrid results from real data are highly consistent with the STRUCTURE results. KP represents C. alexandrinus, WFP represents C. dealbatus, bx represents back-crosses. Appendix S1. Reconstruction of potential range shifts induced by climatic changes and inference of environmental niche overlap between the two-plover species, Charadrius alexandrinus and C. dealbatus. Appendix S2. Inference of interspecific diet overlap using stable-isotope analysis between the two plover species, Charadrius alexandrinus and C. dealbatus. (DOCX 530 kb)