DOI: 10.5061/dryad.wstqjq2rs
title: Data from: Contrasting nidification behaviors facilitate diversification and colonization of the Music frogs under a changing paleoclimate

description: In order to cope with the complexity and variability of the terrestrial
 environment, amphibians have developed a wide range of reproductive and
 parental behaviors. Nest building occurs in some anuran species as
 parental care. Species of the Music frog genus Nidirana are known for
 their unique courtship behavior and mud nesting in several congeners.
 However, the evolution of these frogs and their nidification behavior has
 yet to be studied. With phylogenomic and phylogeographic analyses based on
 a wide sampling of the genus, we find that Nidirana originated from
 central-southwestern China and the nidification behavior initially evolved
 at ca 19.3 Ma but subsequently lost in several descendants. Further
 population genomic analyses suggest that the nidification species have an
 older diversification and colonization history, while N. adenopleura
 complex congeners that do not exhibit nidification behavior have
 experienced a recent rapid radiation. The presence and loss of the
 nidification behavior in the Music frogs may be associated with
 paleoclimatic factors such as temperature and precipitation. This study
 highlights the nidification behavior as a key evolutionary innovation that
 has contributed to the diversification of an amphibian group under past
 climate changes.
description: # Data from: Contrasting nidification behaviors facilitate diversification
 and colonization of the Music frogs under a changing paleoclimate ---
 Alignments for phylogeny and supplementary tables and figures for the
 Article "**Contrasting nidification behaviors facilitate
 diversification and colonization of the Music frogs under a changing
 paleoclimate**", published by Lyu et al. on Communications Biology.
 [https://doi.org/10.1038/s42003-024-06347-7](https://doi.org/10.1038/s42003-024-06347-7) ## Description of the data and file structure **196samples_for_snp_phylogeny.fas** Aligned sequences of SNPs data used for phylogenetic analysis. **261samples_for_mt_phylogeny_1684bp.fas** Aligned sequences of mitochondrial genes used for phylogenetic analysis. **Figure_1.pdf** Uncompressed file for Figure 1. **Contrasting nidification behaviors of *Nidirana* and the sampling localities in this work.** **a** A male *N. guangxiensis* built a mud-based burrow as its nest and was calling inside it. **b** Eggs of *N. daunchina* in a mud nest. **c** A male *N. mangveni* called at the standing water surface. **d **Eggs of *N. guangdongensis* in the standing water surface. **e** Map showing sampling localities in this work. Numbers for localities are corresponding to the information in Supplementary Table S1. Locality circles for species exhibiting nidification behavior, lacking nidification behavior, and nidification behavior remaining unknown, are colored with red, blue, and white, respectively. **Figure_2.pdf** Uncompressed file for Figure 2. **Phylogeny and PCA relationship for genus *Nidirana* based on SNPs data.** **a** Phylogeny of the genus *Nidirana*, using maximum likelihood based on SNPs data. Values of bootstrap supports (BS) larger than 90 are shown. Within the *N. adenopleura* complex, different populations are labelled with solid circles of different colors: *N. mangveni*, the Poyang population, *N. guangdongensis*, and four populations of *N. adenopleura*: Taiwan, north, center, and west. **b** Two-dimensional PCA plot for genetic variation in the genus *Nidirana*. **Figure_3.pdf** Uncompressed file for Figure 3. **Spatiotemporal reconstruction of *Nidirana*.** **a** Ten geographical areas delineated for the genus *Nidirana*. Characters for geographical areas and dashed lines for barriers are corresponding to the information in Supplementary Table S2. **b** Ancestral distributions reconstructed by Dispersal-Extinction-Cladogenesis model. Areas with the highest probabilities at nodes are shown with the same characters in Figure 3a. Within the *N. adenopleura* complex, populations are labelled with solid circles of different colors: *N. mangveni* (MV), the Poyang population (PY), *N. guangdongensis* (GD), and four populations of *N. adenopleura*: Taiwan (At), north (An), center (Ac), and west (Aw). **c** Dispersal events along branches through time.**d** Cladogenetic change events through time.**e** Development of East Asian Monsoon from Miocene with the fluctuations of fluvial mass accumulation rate representing level of precipitation and carbon isotopes representing level of temperature **Figure_4.pdf** Uncompressed file for Figure 4. **Population structure and differentiation.** **a** PCA plot of PC1 and PC2 for nidification species. **b** PCA plot of PC1 and PC2 for the *Nidirana adenopleura* complex. **c** Admixture plot for nidification species with K = 6. **d** Admixture plot for the *N. adenopleura *complex with K = 4. **e** Demographic trajectories for different populations for five nidification species. *Nidirana okinavana* was not included in this analysis due to a limited sample size. **f** Demographic trajectories for different populations for seven populations of the *N. adenopleura complex. Labels for different populations: N. chapaensis* (CP), *N. hainanensis* (HN), *N. yaoica* (Y), *N. daunchina* (D), *N. nankunensis* (N), *N. okinavana* (OK), N. mangveni (MV), the Poyang population (PY), *N. guangdongensis* (GD), and four populations of *N. adenopleura*: Taiwan (At), north (An), center (Ac), and west (Aw). **Figure_5.pdf** Uncompressed file for Figure 5. **Environmental Correlation of Nidification Behavior.** **a** Boxplots showing the correlation for absence/presence of nidification behavior with Bio 7 (annual temperature range), Bio 4 (temperature seasonality), Bio 6 (minimum temperature of coldest month), Bio 18 (precipitation of warmest quarter), Bio 15 (precipitation seasonality), and Bio19 (precipitation of coldest quarter). **b** Scatterplot showing the associations for absence/presence of nidification behavior with Bio 7 and Bio 18, with Bio4 and Bio15, and with Bio6 and Bio19. **Figure_S1_mtDNA_vs_SNPs.pdf** Uncompressed file for Supplementary Figure S1. **Figure_S2_Divergence_time.pdf** Uncompressed file for Supplementary Figure S2. **Figure_S3_Ancestral_distribution.pdf** Uncompressed file for Supplementary Figure S3. **Figure_S4_Pop_disribution_Fst_dxy.pdf** Uncompressed file for Supplementary Figure S4. **Supplementary_information.pdf** Supplemental Information for the original article, including four supplementary figures and four supplementary tables. **Supplementary Figure S1** Phylogeny of *Nidirana*, using maximum likelihood based on mitochondrial genes of 16S and COI **(a)** and based on SNPs data **(b)**, respectively. Bootstrap supports (BS) larger than 80 are shown, and asterisks represent BS = 100. **Supplementary Figure S2** Estimated divergence time for the genus *Nidirana*. Samples are labeled as “sample ID_species name_Population_Locaility ID”, which are corresponding to the information in Supplementary Table S1. **Supplementary Figure S3** Ancestral distributions for the genus *Nidirana* with pie charts for the proportional likelihoods of ancestral area states. Samples are labeled as “species name_Locaility ID”, which are corresponding to the information in Supplementary Table S1. Characters for geographical areas are defined in Supplementary Table S2. **Supplementary Figure S4** **(a)** Map showing collected locality for the nidification species. **(b)** Map showing collected locality for the *N. adenopleura* complex. Numbers for localities are corresponding to the information in Supplementary Table S1. **(c)** Wright’s fixation index (Fst) and absolute genetic divergences (dxy) statistics among the six nidification species. **(d)** Wright’s fixation index (Fst) and absolute genetic divergences (dxy) statistics among the seven population of the *N. adenopleura* complex. Labels for different populations: *N. chapaensis* (CP), *N. hainanensis* (HN), *N. yaoica* (Y), *N. daunchina* (D), *N. nankunensis* (N), *N. okinavana* (OK), *N. mangveni* (MV), the Poyang population (PY), *N. guangdongensis* (GD), and four populations of *N. adenopleura*: Taiwan (At), north (An), center (Ac), west (Aw). **Supplementary Table S1** Localities, vouchers, and GenBank numbers for all samples used in this study. Population labels are majorly abbreviated from species nomenclatures, except for: At – Taiwan population of *Nidirana adenopleura*, Ac – central population of *N. adenopleura*, An – northern population of *N. adenopleura*, Aw – western population of *N. adenopleura*, Au – samples of N. adenopleura that could not be assigned to a population due to deficient data, Pe – eastern population of *N. pleuraden*, and Pw – western population of *N. pleuraden*. **Supplementary Table S2** Adjacent geographical areas allowed for ancestral ranges estimating. **Supplementary Table S3** The four scenarios modeled for three pairs of *Nidirana* populations using fastsimcoal2. The best scenario model for each populations pair is highlighted in bold. **Supplementary Table S4** Correlation of nidification behavior with the 19 bioclimatic variables. Rank by *P* value from lowest to highest. * *P* values &lt; 0.05, ** *P* values &lt; 0.01. ## Sharing/Access information Link to the article: [https://doi.org/10.1038/s42003-024-06347-7](https://doi.org/10.1038/s42003-024-06347-7) ## Code/Software The SNPs data was generated using the ddRAD-seq with restriction enzymes EcoRI and NlaIII, and then analyses using Stacks v2.53, VCFtools v0.1.16, and vcf2phylip. Phylogenetic analyses were used RAxML v8.0, MrBayes 3.2.4, and RAxML-NG. Divergence time was estimated in PAML v4.8. Ancestral distributions was reconstrcted in RevBayes. Population and demographic analyses were performed in PLINK 1.9, Admixture 1.3, easySFS, Stairway Plot 2, and fastsimcoal v2.7. Environmental correlation analysis was made by lme4 package in R 4.2.1. **Detailed methods were addressed in the related article [https://doi.org/10.1038/s42003-024-06347-7](https://doi.org/10.1038/s42003-024-06347-7)**