Published March 24, 2026 | Version v1
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Genetic diversity and structure analysis of critically endangered Goniurosaurus yingdeensis (Squamata, Eublepharidae) based on SSR markers

  • 1. Sun Yat-sen University, Guangzhou, China
  • 2. Hainan Normal University, Haikou, China
  • 3. Guangdong Wildlife Rescue and Monitoring Center, Guangzhou, China

Description

The Yingde Leopard Gecko (Goniurosaurus yingdeensis) is a critically endangered reptile restricted to a narrow-fragmented karst region in China. Investigating the role of terrestrial islands in biodiversity generation by conducting genetic analyses of G. yingdeensis can offer insights into the ecological and evolutionary dynamics of inselbergs, while also providing theoretical and practical guidance for future conservation of this species. In this study, we employed 20 pairs of SSR primers to assess the genetic diversity and analyze the population structure of 86 individuals from 10 geographical populations of G. yingdeensis. The results revealed low genetic diversity in G. yingdeensis. Populations exhibited a high degree of genetic differentiation and a low level of gene flow, which may contribute to the loss of genetic diversity due to genetic drift. Clustering analyses indicated that the genetic differentiation between one population and the other nine was the most pronounced. Furthermore, the genetic distance among G. yingdeensis populations was found to be influenced by more than just spatial distance. This study demonstrates that for species with limited dispersal capability such as G. yingdeensis, karst inselbergs function similarly to aquatic islands in evolutionary processes: gene flow is restricted to a small range by geographic barriers, isolated populations evolve independently, and genetic differentiation increases over time. Among the factors contributing to population isolation in G. yingdeensis, rivers play the most significant role.

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References

  • Abdul-Muneer PM (2014) Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies. Genetics Research International 2014(1): 691759. https://doi.org/10.1155/2014/691759
  • Barbour T (1908) Some new reptiles and amphibians. Bulletin of the Museum of Comparative Zoology at Harvard College 51(12): 315–325.
  • Crall JP, Stewart CV, Berger-Wolf TY, Rubenstein DI, Sundaresan SR (2013) HotSpotter — Patterned species instance recognition. Proceedings of the IEEE Workshop on Applications of Computer Vision (WACV), 230–237. https://doi.org/10.1109/WACV.2013.6475023
  • Earl DA, VonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361. https://doi.org/10.1007/s12686-011-9548-7
  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14(8): 2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  • Grismer LL, Ngo HN, Qi S, Wang YY, Le MD, Ziegler T (2021) Phylogeny and evolution of habitat preference in Goniurosaurus (Squamata: Eublepharidae) and their correlation with karst and granite-stream-adapted ecomorphologies in species groups from Vietnam. Vertebrate Zoology 71: 335–352. https://doi.org/10.3897/vz.71.e65969
  • Honda M, Kurita T, Toda M, Ota H (2014) Phylogenetic relationships, genetic divergence, historical biogeography and conservation of an endangered gecko, Goniurosaurus kuroiwae (Squamata: Eublepharidae), from the Central Ryukyus, Japan. Zoological Science 31(5): 309–320. https://doi.org/10.2108/zs130201
  • IUCN (2024) The IUCN Red List of Threatened Species. Version 2024-1. https://www.iucnredlist.org [accessed 1 October 2025]
  • Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14): 1801–1806. https://doi.org/10.1093/bioinformatics/btm233
  • Kumar P, Banjarey P, Malik R, Tikle AN, Verma RPS (2020) Population structure and diversity assessment of barley (Hordeum vulgare L.) introduction from ICARDA. Journal of Genetics 99(1): 70. https://doi.org/10.1007/s12041-020-01226-6
  • Kurita T, Aoyama H, Saitoh S, Shinzato N, Honda M, Toda M (2014) Development and characterization of 24 microsatellite markers in a eublepharid gecko, Goniurosaurus kuroiwae. Conservation Genetics Resources 6(1): 247–249. https://doi.org/10.1007/s12686-013-0074-7
  • Kurita T, Honda M, Toda M (2018) Species delimitation and biogeography of the Ryukyu ground geckos, Goniurosaurus kuroiwae ssp. (Squamata: Eublepharidae), by use of mitochondrial and nuclear DNA analyses. Zoological Science 56(2): 209–222. https://doi.org/10.1111/jzs.12198
  • Kurita T, Toda M (2024) Genetic and Morphological Studies on Goniurosaurus kuroiwae (Squamata: Eublepharidae), with a Description of a New Species from the Northern Part of Okinawajima Island, Ryukyu Archipelago, Japan. Current Herpetology 43(1): 86–114. https://doi.org/10.5358/hsj.43.86
  • Nagylaki T (1998) Fixation indices in subdivided populations. Genetics 148(3): 1325–1332. https://doi.org/10.1093/genetics/148.3.1325
  • Ngo HN, Nguyen HQ, Tran HM, Ngo HT, Le MD, Gewiss LR, van Schingen-Khan M, Nguyen TQ, Ziegler T (2021) A morphological and molecular review of the genus Goniurosaurus, including an identification key. European Journal of Taxonomy 751: 38–67. https://doi.org/10.5852/ejt.2021.751.1379
  • Ngo HN, Nguyen HQ, Tran HM, Phan TQ, Tran TT, Gewiss LR, Rödder D, Nguyen TQ, Ziegler T (2022) Living under the risk of extinction: population status and conservation needs assessment of a micro–endemic tiger gecko in Vietnam. Nature Conservation 45(2): 175–188. https://doi.org/10.32800/abc.2022.45.0175
  • Ngo HN, Nguyen TQ, Phan TQ, van Schingen M, Ziegler T (2019) A case study on trade in threatened Tiger Geckos (Goniurosaurus) in Vietnam including updated information on the abundance of the Endangered G. catbaensis. Nature Conservation 33: 1–19. https://doi.org/10.3897/natureconservation.32.33590
  • Ngo HN, Rödder D, Grismer L, Nguyen TQ, Le MD, Qi S, Ziegler T (2023) Extraordinary diversity among allopatric species in the genus Goniurosaurus (Squamata: Eublepharidae): understanding niche evolution and the need of conservation measures. Biodiversity and Conservation 32(5): 1549–1571. https://doi.org/10.1007/s10531-023-02564-4
  • Oksanen J, Simpson G, Blanchet F, Kindt R, Legendre P, Minchin P, O'Hara R, Solymos P, Stevens M, Szoecs E, Wagner H, Barbour M, Bedward M, Bolker B, Borcard D, Carvalho G, Chirico M, De Caceres M, Durand S, Evangelista H, FitzJohn R, Friendly M, Furneaux B, Hannigan G, Hill M, Lahti L, McGlinn D, Ouellette M, Ribeiro Cunha E, Smith T, Stier A, Ter Braak C, Weedon J (2022) vegan: Community Ecology Package. R package version 2.6-4. https://doi.org/10.32614/cran.package.vegan
  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6(1): 288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x
  • Putman AI, Carbone I (2014) Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecology and Evolution 4(22): 4399–4428. https://doi.org/10.1002/ece3.1305
  • Ramesh P, Mallikarjuna G, Sameena S, Kumar A, Gurulakshmi K, Reddy BV, Reddy PCO, Sekhar AC (2020) Advancements in molecular marker technologies and their applications in diversity studies. Journal of Genetics 45: 1–15. https://doi.org/10.1007/s12038-020-00089-4
  • Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145(4): 1219–1228. https://doi.org/10.1093/genetics/145.4.1219
  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual (2nd edn.). Cold Spring Harbor Laboratory Press.
  • Senan S, Dhanya K, Sasikumar B, Sheeja TE (2014) Methods for development of microsatellite markers: an overview. Notulae Scientia Biologicae 6(1): 1–13. https://doi.org/10.15835/nsb619199
  • Slatkin M, Barton NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 43(7): 1349–1368. https://doi.org/10.1111/j.1558-5646.1989.tb02587.x
  • Song HM, Qi S, Wang HT, Gong YN, Liu Y, Wang YY (2025) Definition and taxonomic revision of the karst-associated Odorrana lipuensis group (Anura, Ranidae), with a new species from Guangdong, China. Zoosystematics and Evolution 101(3): 935–952. https://doi.org/10.3897/zse.101.142746
  • Sun CH, Liu HY, Xu P, Lu CH (2021) Genetic diversity of wild wintering red-crowned crane (Grus japonensis) by microsatellite markers and mitochondrial Cyt B gene sequence in the Yancheng reserve. Animal Biotechnology 32(5): 531–536. https://doi.org/10.1080/10495398.2020.1725538
  • Uetz P, Freed P, Aguilar R, Reyes F, Hošek J (2025) The Reptile Database. http://www.reptile-database.org [accessed 1 October 2025]
  • Vanschoenwinkel B, De Paula LFA, Snoeks JM, Van der Stocken T, Buschke FT, Porembski S, Silveira FAO (2024) The ecological and evolutionary dynamics of inselbergs. Biological Reviews 99(5): 1765–1787. https://doi.org/10.1111/brv.13150
  • Vieira MLC, Santini L, Diniz AL, Munhoz CF (2016) Microsatellite markers: what they mean and why they are so useful. Genetics and Molecular Biology 39(3): 312–328. https://doi.org/10.1590/1678-4685-GMB-2016-0027
  • Wang YY, Yang JH, Cui RF (2010) A new species of Goniurosaurus (Squamata: Eublepharidae) from Yingde, Guangdong Province, China. Herpetologica 66(2): 229–240. https://doi.org/10.1655/09-046R2.1
  • Zhang J, Qing N, Yi ZS, Wang YY, Jiang XS, Lu WH, Lazell J (2014) Validity of Goniurosaurus indet. and genetic relationships of Goniurosaurus (Squamata: Sauria: Eublepharidae) species in China. Journal of South China Normal University (Natural Science Edition) 46(2): 92–98.
  • Zhu XY, Liu YJ, Bai Y, Román Palacios C, Li Z, He ZQ (2021) Goniurosaurus chengzheng sp. nov., a new species of Leopard Gecko from Guangxi, China (Squamata: Eublepharidae). Zootaxa 4996(3): 540–554. https://doi.org/10.11646/zootaxa.4996.3.8
  • Zhu XY, Wu SY, Liu YJ, Bai Y, Román Palacios C, Li Z, He ZQ (2022) Goniurosaurus wangshu sp. nov., a new species of Tiger Gecko from Guangdong, China (Squamata: Eublepharidae). Zootaxa 5188(6): 544–558. https://doi.org/10.11646/zootaxa.5188.6.3