Genetic identification and reiterated captures suggest that the <i>Astyanax mexicanus</i> El Pachón cavefish population is closed and declining

Laurent Legendre; Julie Rode; Isabelle Germon; Marie Pavie; Carla Quiviger; Maxime Policarpo; Julien Leclercq; Stéphane Père; Julien Fumey; Carole Hyacinthe; Patricia Ornelas-García; Luis Espinasa; Sylvie Rétaux; Didier Casane

doi:10.24272/j.issn.2095-8137.2022.481

Volume 44 Issue 4

Jul. 2023

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Article Navigation > Zoological Research > 2023 > 44(4): 701-711

Laurent Legendre, Julie Rode, Isabelle Germon, Marie Pavie, Carla Quiviger, Maxime Policarpo, Julien Leclercq, Stéphane Père, Julien Fumey, Carole Hyacinthe, Patricia Ornelas-García, Luis Espinasa, Sylvie Rétaux, Didier Casane. Genetic identification and reiterated captures suggest that the Astyanax mexicanus El Pachón cavefish population is closed and declining. Zoological Research, 2023, 44(4): 701-711. doi: 10.24272/j.issn.2095-8137.2022.481

Citation:

Laurent Legendre, Julie Rode, Isabelle Germon, Marie Pavie, Carla Quiviger, Maxime Policarpo, Julien Leclercq, Stéphane Père, Julien Fumey, Carole Hyacinthe, Patricia Ornelas-García, Luis Espinasa, Sylvie Rétaux, Didier Casane. Genetic identification and reiterated captures suggest that the Astyanax mexicanus El Pachón cavefish population is closed and declining. Zoological Research, 2023, 44(4): 701-711. doi: 10.24272/j.issn.2095-8137.2022.481

Citation:

Laurent Legendre, Julie Rode, Isabelle Germon, Marie Pavie, Carla Quiviger, Maxime Policarpo, Julien Leclercq, Stéphane Père, Julien Fumey, Carole Hyacinthe, Patricia Ornelas-García, Luis Espinasa, Sylvie Rétaux, Didier Casane. Genetic identification and reiterated captures suggest that the Astyanax mexicanus El Pachón cavefish population is closed and declining. Zoological Research, 2023, 44(4): 701-711. doi: 10.24272/j.issn.2095-8137.2022.481

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Genetic identification and reiterated captures suggest that the Astyanax mexicanus El Pachón cavefish population is closed and declining

doi: 10.24272/j.issn.2095-8137.2022.481

1.
Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette 91190, France
2.
Objectif Sciences International NGO, OSI-Panthera Program, Geneva 99140, Switzerland
3.
Institut de Neuroscience Paris-Saclay, Université Paris-Saclay and CNRS, Saclay 91400, France
4.
Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Microbial Paleogenomics Unit, Paris 75015, France
5.
Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris 75015, France
6.
Department of Genetics, Harvard Medical School, Blavatnik Institute, Boston MA 02115, USA
7.
Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, México DF CP 04510, México
8.
School of Science, Marist College, Poughkeepsie, New York 12601, USA
9.
Université Paris Cité, UFR Sciences du Vivant, Paris 75013, France

Astyanax mexicanus: fin clips from surface and cave morphs of A. mexicanus were sampled during field expeditions, under the field permits SGPA/DGVS/02438/16, SGPA/DGVS/1893/19, and SGPA/DGVS/03334/22 provided to P.O.G and S.R. by the Secretaría de Medio Ambiente y Recursos Naturales of Mexico (SEMARNAT).
The R script “GenerateIndividual.r” can be found in GitHub “jmorode/Genetics”.
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
L.L., S.R., and D.C. conceived and designed the research; L.L., J.R., M.P., M.P., J.L., S.P., J.F., C.H., P.O.G., L.E., S.R., and D.C. conducted field surveys and collected samples; I.G., M.P., and C.Q. performed the molecular work; J.R., M.P., J.F., S.R., and D.C. analyzed the data; L.L., J.R., P.O.G., L.E., S.R., and D.C. wrote the manuscript. All authors read and approved the final version of the manuscript.
^$Current affiliation: Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
#Authors contributed equally to this work

Funds: This work was supported by a CNRS MITI (Mission pour les Initiatives Transverses et Interdisciplinaires) grant “Expérimentation en Milieux Extrêmes” to S.R. and collaborative grants from Agence Nationale de la Recherche (BLINDTEST) and Institut Diversité Ecologie et Evolution du Vivant to S.R. and D.C.

More Information

Corresponding author: E-mail: sylvie.retaux@cnrs.fr; didier.casane@universite-paris-saclay.fr
Received Date: 2023-01-27
Accepted Date: 2023-05-19

Published Online: 2023-05-24

Publish Date: 2023-07-18

Abstract

Abstract

The sizes of Astyanax mexicanus blind cavefish populations of North-East Mexico are demographic parameters of great importance for investigating a variety of ecological, evolutionary, and conservation issues. However, few estimates have been obtained. For these mobile animals living in an environment difficult to explore as a whole, methods based on capture-mark-recapture are appropriate, but their feasibility and interpretation of results depend on several assumptions that must be carefully examined. Here, we provide evidence that minimally invasive genetic identification from captures at different time intervals (three days and three years) can give insights into cavefish population size dynamics as well as other important demographic parameters of interest. We also provide tools to calibrate sampling and genotyping efforts necessary to reach a given level of precision. Our results suggest that the El Pachón cave population is currently very small, of an order of magnitude of a few hundreds of individuals, and is distributed in a relatively isolated area. The probable decline in population size in the El Pachón cave since the last census in 1971 raises serious conservation issues.
- Cavefish,
- Population size,
- Conservation,
- Swabbing,
- Genetic identification

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References(23)

References

[1]	Avise JC, Selander RK. 1972. Evolutionary genetics of cave-dwelling fishes of the genus Astyanax. Evolution, 26(1): 1–19.
[2]	Bailey NTJ. 1951. On estimating the size of mobile populations from recapture data. Biometrika, 38(3/4): 293−306. doi: 10.2307/2332575
[3]	Bichuette ME, Trajano E. 2021. Monitoring Brazilian cavefish: ecology and conservation of four threatened catfish of genus Ituglanis (Siluriformes: Trichomycteridae) from Central Brazil. Diversity, 13(2): 91. doi: 10.3390/d13020091
[4]	Bradic M, Beerli P, García-de León FJ, et al. 2012. Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus). BMC Evolutionary Biology, 12: 9. doi: 10.1186/1471-2148-12-9
[5]	Casane D, Rétaux S. 2016. Evolutionary genetics of the cavefish Astyanax mexicanus. Advances in Genetics, 95: 117–159.
[6]	Charlesworth B. 2009. Effective population size and patterns of molecular evolution and variation. Nature Reviews Genetics, 10(3): 195−205. doi: 10.1038/nrg2526
[7]	Elliott W. 2018. The Astyanax caves of Mexico. Cavefishes of Tamaulipas, San Luis Potosi, and Guerrero. Association for Mexican Cave Studies. Bulletin, 26: 1−325.
[8]	Espinasa L, Legendre L, Fumey J, et al. 2018. A new cave locality for Astyanax cavefish in Sierra de El Abra, Mexico. Subterranean Biology, 26: 39−53. doi: 10.3897/subtbiol.26.26643
[9]	Espinasa L, Ornelas-García CP, Legendre L, et al. 2020. Discovery of two new astyanax cavefish localities leads to further understanding of the species biogeography. Diversity, 12(10): 368. doi: 10.3390/d12100368
[10]	Fumey J, Hinaux H, Noirot C, et al. 2018. Evidence for late Pleistocene origin of Astyanax mexicanus cavefish. BMC Evolutionary Biology, 18(1): 43. doi: 10.1186/s12862-018-1156-7
[11]	Hedgecock D. 1994. Does variance in reproductive success limit effective population sizes of marine organisms? In: Beaumont AR. Genetics and Evolution of Aquatic Organisms. London: Chapman & Hall, 122–134.
[12]	Herman A, Brandvain Y, Weagley J, et al. 2018. The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra. Astyanax mexicanus. Molecular Ecology, 27(22): 4397−4416. doi: 10.1111/mec.14877
[13]	Kalinowski ST, Wagner AP, Taper ML. 2006. ML-RELATE: a computer program for maximum likelihood estimation of relatedness and relationship. Molecular Ecology Notes, 6(2): 576−579. doi: 10.1111/j.1471-8286.2006.01256.x
[14]	Keene AC, Yoshizawa M, McGaugh SE. 2016. Biology and Evolution of the Mexican Cavefish. San Diego: Academic Press.
[15]	Langecker TG, Wilkens H, Junge P. 1991. Introgressive hybridization in the Pachon Cave population of Astyanax fasciatus (Teleostei: Characidae). Ichthyological Exploration of Freshwaters, 2(3): 209−212.
[16]	Mitchell RW, Russell WH, Elliott WR. 1977. Mexican eyeless characin fishes, genus Astyanax: environment, distribution, and evolution. Special Publications, the Museum Texas Tech University, 12: 1−89.
[17]	Policarpo M, Fumey J, Lafargeas P, et al. 2021. Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals. Molecular Biology and Evolution, 38(2): 589−605. doi: 10.1093/molbev/msaa249
[18]	Protas ME, Hersey C, Kochanek D, et al. 2006. Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism. Nature Genetics, 38(1): 107−111. doi: 10.1038/ng1700
[19]	Prunier J, Kaufmann B, Grolet O, et al. 2012. Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt (Ichthyosaura alpestris). Molecular Ecology Resources, 12(3): 524−531. doi: 10.1111/j.1755-0998.2012.03116.x
[20]	R Core Team. 2021. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.
[21]	Simon V, Elleboode R, Mahé K, et al. 2017. Comparing growth in surface and cave morphs of the species Astyanax mexicanus: insights from scales. EvoDevo, 8(1): 23. doi: 10.1186/s13227-017-0086-6
[22]	Tilley CA, Carreño Gutierrez H, Sebire M, et al. 2020. Skin swabbing is a refined technique to collect DNA from model fish species. Scientific Reports, 10(1): 18212. doi: 10.1038/s41598-020-75304-1
[23]	Trontelj P, Zakšek V. 2016. Genetic monitoring of Proteus populations. Natura Sloveniae, 18(1): 53−54.