An Initial Genetic Assessment of the Emblematic Pumas of the Torres del Paine UNESCO Biosphere Reserve
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Area
2.2. Phenotypic Variation: Observable Cowlicks
2.3. Genetic Sampling
2.4. Genetic Diversity and Inbreeding
2.5. Population Structure
3. Results
3.1. Cowlicks
3.2. Samples and Population Structure
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Gustafson, K.D.; Vickers, W.T.; Boyce, W.M.; Holly, E.B. A single migrant enhances the genetic diversity of an inbred puma population. R. Soc. Open Sci. 2017, 4, 170115. [Google Scholar] [CrossRef]
- Poirier, M.A.; Coltman, D.W.; Pelletier, F.; Jorgenson, J.; Festa-Bianchet, M. Genetic decline, restoration and rescue of an isolated ungulate population. Evol. Appl. 2018, 12, 1318–1328. [Google Scholar] [CrossRef]
- Roelke, M.E.; Martenson, J.S.; O’Brien, S.J. The consequences of demographic reduction and genetic depletion in the endangered Florida panther. Curr. Biol. 1993, 3, 340–350. [Google Scholar] [CrossRef] [PubMed]
- Raikkonen, J.; Vucetich, J.A.; Peterson, R.O.; Nelson, M.P. Congenital bone deformities and the inbred wolves (Canis lupus) of Isle Royale. Biol. Conserv. 2009, 142, 1025–1031. [Google Scholar] [CrossRef]
- Hogg, J.T.; Forbes, S.H.; Steele, B.M.; Luikart, G. Genetic rescue of an insular population of large mammals. Proc. R. Soc. B 2006, 273, 1491–1499. [Google Scholar] [CrossRef] [PubMed]
- Weeks, A.R.; Sgro, C.M.; Young, A.G.; Frankham, R.; Mitchell, N.J.; Miller, K.A.; Byrne, M.; Coates, D.J.; Eldridge, M.D.B.; Sunnucks, P.; et al. Assessing the benefits and risks of translocations in changing environments: A genetic perspective. Evol. Appl. 2011, 4, 709–725. [Google Scholar] [CrossRef] [PubMed]
- Whiteley, A.R.; Fitzpatrick, S.W.; Funk, W.C.; Tallmon, D.A. Genetic rescue to the rescue. Trends Ecol. Evol. 2015, 30, 42–49. [Google Scholar] [CrossRef]
- Hedrick, P.W.; Fredrickson, R. Genetic rescue guidelines with examples from Mexican wolves and Florida panthers. Conserv. Genet. 2010, 11, 615–626. [Google Scholar] [CrossRef]
- Tallmon, D.A.; Luikart, G.; Waples, R.S. The alluring simplicity and complex reality of genetic rescue. Trends Ecol. Evol. 2004, 19, 489–496. [Google Scholar] [CrossRef]
- Ochoa, A.; Onorato, D.P.; Roelke-Parker, M.E.; Culver, M.; Fitak, R.R. Give and take: Effects of genetic admixture on mutation load in endangered Florida panthers. J. Hered. 2022, 113, 491–499. [Google Scholar] [CrossRef]
- Johnson, W.E.; Onorato, D.P.; Roelke, M.E.; Land, E.D.; Cunningham, M.; Belden, R.C.; McBride, R.; Jansen, D.; Lotz, M.; Shindle, D.; et al. Genetic restoration of the Florida panther. Science 2010, 329, 1641–1645. [Google Scholar] [CrossRef] [PubMed]
- Van de Kerk, M.; Onorato, D.P.; Hostetler, J.A.; Bolker, B.M.; Oli, M.K. Dynamics, Persistence, and Genetic Management of the Endangered Florida Panther Population. Wildl. Monogr. 2019, 203, 3–35. [Google Scholar] [CrossRef]
- Huffmeyer, A.A.; Sikich, J.A.; Vickers, T.W.; Riley, S.P.D.; Wayne, R.K. First reproductive signs of inbreeding depression in Southern California male mountain lions (Puma concolor). Theriogenology 2022, 177, 157–164. [Google Scholar] [CrossRef]
- Gallo, O.; Castillo, D.F.; Godinho, R.; Mac Allister, M.E.; Fernàndez, G.P.; Failla, M.; Casanave, E.B. Molecular data reveal a structured puma (Puma concolor) population in northern Patagonia, Argentina. Mamm. Biol. 2021, 101, 653–663. [Google Scholar] [CrossRef]
- Novaro, A.J.; Walker, R.S. Lessons of 15,000 Years of Human–Wildlife Interaction for Conservation in Patagonia in the 21st Century. Diversity 2021, 13, 633. [Google Scholar] [CrossRef]
- Culver, M.; Johnson, W.E.; Pecon-Slattery, J.; O’Brien, S.J. Genomic ancestry of the American puma (Puma concolor). J. Hered. 2000, 91, 186–197. [Google Scholar] [CrossRef]
- Saremi, N.F.; Supple, M.A.; Byrne, A.; Cahill, J.A.; Coutinho, L.L.; Dalén, L.; Figueiró, H.V.; Johnson, W.E.; Milne, H.J.; O’Brien, S.J.; et al. Puma genomes from North and South America provide insights into the genomic consequences of inbreeding. Nature Comm. 2019, 10, 5276. [Google Scholar] [CrossRef]
- Allen, W.L.; Cuthill, I.C.; Scott-Samuel, N.E.; Baddeley, R. Why the leopard got its spots: Relating pattern development to ecology in felids. Proc. Biol. Sci. 2011, 278, 1373–1380. [Google Scholar] [CrossRef] [PubMed]
- Walker, S.; Novaro, A. The world´s southernmost pumas in Patagonia and the southern Andes. In Cougar: Ecology and Conservation; Hornocker, M., Negri, S., Eds.; University of Chicago Press: Chicago, IL, USA, 2010; pp. 91–102. [Google Scholar]
- Guerisoli, M.D.L.M.; Luengos Vidal, E.; Franchini, M.; Caruso, N.; Casanave, E.B.; Lucherini, M. Characterization of puma–livestock conflicts in rangelands of central Argentina. R. Soc. Open Sci. 2017, 4, 170852. [Google Scholar] [CrossRef]
- Ojeda, M.; Pérez, H. La Caza Del Puma. Master’s Thesis, University of Magallanes, Punta Arenas, Chile, 2009. [Google Scholar]
- Ohrens, O.; Tortato, F.R.; Hoogesteijn, R.; Sarno, R.J.; Quigley, H.; Goic, D.; Elbroch, L.M. Predator tourism improves tolerance for puma, but may increase future conflict among ranchers in Chile. Biol. Conserv. 2021, 258, 109150. [Google Scholar] [CrossRef]
- Ruiz-García, M.; Castellanos, A.; Arias-Vásquez, J.Y.; Shostell, J.M. Genetics of the Andean bear (Tremarctos ornatus; Ursidae, Carnivora) in Ecuador: When the Andean Cordilleras are not an Obstacle. Mitochondrial DNA Part A 2020, 31, 190–208. [Google Scholar] [CrossRef] [PubMed]
- Lorenzana, G.; Heidtmann, L.; Haag, T.; Ramalho, E.; Dias, G.; Hrbek, T.; Farias, I.; Eizirik, E. Large-scale assessment of genetic diversity and population connectivity of Amazonian jaguars (Panthera onca) provides a baseline for their conservation and monitoring in fragmented landscapes. Biol. Conserv. 2020, 242, 108417. [Google Scholar] [CrossRef]
- Pisano, E. Estudio ecológico de la region continental sur del área andino-patagónica, II. Contribución a la fitogeografía de la zona del Parque Nacional Torres del Paine. Ans. Inst. Pat. 1974, 5, 59–104. [Google Scholar]
- Tortato, F.R.; Hoogesteijn, R.; Elbroch, L.M. Have natural disasters created opportunities to initiate big cat tourism in South America? Biotropica 2020, 52, 400–403. [Google Scholar] [CrossRef]
- Elbroch, L.M.; Lagos, N.; Cárdenas, J.; Goic, D.; Moraga, R.; Ohrens, O. Tourism and human computers offer new tools to monitor Patagonia’s top carnivore. Sci. Total Environ. 2023, 877, 162916. [Google Scholar] [CrossRef]
- Hoelzel, A.R.; Green, A. Analysis of population-level variation by sequencing PCR-amplified DNA. In Molecular Genetic Analysis Of Populations: A Practical Approach; Hoelzel, A.R., Ed.; IRL Press: Oxford, UK, 1992; pp. 159–187. [Google Scholar]
- Farrell, L.E.; Roman, J.; Sunquist, M.E. Dietary separation of sympatric carnivores identified by molecular analysis of scats. Mol. Ecol. 2000, 9, 1583–1590. [Google Scholar] [CrossRef]
- Menotti-Raymond, M.; David, V.A.; Agarwala, R.; Schäffer, A.A.; Stephens, R.; O’Brien, S.J.; Murphy, W.J. Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome. Cytogenetic Genome Res. 2003, 102, 272–276. [Google Scholar] [CrossRef] [PubMed]
- Kurushima, J.D.; Collins, J.A.; Well, J.A.; Ernest, H.B. Development of 21 microsatellite loci for puma (Puma concolor) ecology and forensics. Mol. Ecol. Notes 2006, 6, 1260–1262. [Google Scholar] [CrossRef]
- Pilgrim, K.L.; McKelvey, K.S.; Riddle, A.E.; Schwartz, M.K. Felid sex identification based on noninvasive genetic samples. Mol. Ecol. Notes 2005, 5, 60–61. [Google Scholar] [CrossRef]
- McKelvey, K.S.; Schwartz, M.K. Dropout: A program to identify problem loci and samples for noninvasive genetic samples in a capture-mark-recapture framework. Mol. Ecol. Notes 2005, 5, 716–718. [Google Scholar] [CrossRef]
- Van Oosterhout, C.; Hutchinson, W.F.; Wills, D.P.; Shipley, P. MICRO-CHECKER: Software for identifying and correcting genotyping erros in microsatellite data. Mol. Ecol. Notes 2004, 4, 535–538. [Google Scholar] [CrossRef]
- Peakall, R.; Smous, P.E. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinforma Appl. 2012, 28, 2537–2539. [Google Scholar] [CrossRef] [PubMed]
- DeWoody, J.; Nason, J.D.; Hipkins, V.D. Mitigating scoring errors in microsatellite data from wild populations. Mol. Ecol. Notes 2006, 6, 951–957. [Google Scholar] [CrossRef]
- Schwartz, M.K.; Cushman, S.A.; McKelvey, K.S.; Hayden, J.; Engkjer, C. Detecting genotyping errors and describing American black bear movement in northern Idaho. Ursus 2006, 1, 138–148. [Google Scholar] [CrossRef]
- Raymond, M.; Rousset, F. GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism. J. Hered. 1995, 86, 248–249. [Google Scholar] [CrossRef]
- Piry, S.; Luikart, G.; Cornuet, J.M. BOTTLENECK: A computer program for detecting recent reductions in the effective population size using allele frequency data. J. Hered. 1999, 90, 502–503. [Google Scholar] [CrossRef]
- Cornuet, J.M.; Luikart, G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 1996, 144, 2001–2014. [Google Scholar] [CrossRef]
- Di Rienzo, A.; Peterson, A.C.; Garza, J.C.; Valdes, A.M.; Slatkin, M.; Freimer, N.B. Mutational processes of simple-sequence repeat loci in human populations. Proc. Natl. Acad. Sci. USA 1994, 91, 3166–3170. [Google Scholar] [CrossRef]
- Luikart, G.; Sherwin, W.B.; Steele, B.M.; Allendorf, F.W. Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Mol. Ecol. 1998, 7, 963–974. [Google Scholar] [CrossRef]
- Pritchard, J.K.; Stephens, M.; Donnelly, P. Inference of Population Structure Using Multilocus Genotype Data. Genetics 2000, 155, 945–959. [Google Scholar] [CrossRef]
- Earl, D.A.; VonHoldt, B.M. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. 2012, 4, 359–361. [Google Scholar] [CrossRef]
- Evanno, G.; Regnaut, S.; Goudet, J. Detecting the number of clusters of individuals using the software structure: A simulation study. Mol. Ecol. 2005, 14, 2611–2620. [Google Scholar] [CrossRef] [PubMed]
- Paetkau, D.; Strobeck, C. Microsatellite analysis of genetic variation in black bear populations. Mol. Ecol. 1994, 3, 489–495. [Google Scholar] [CrossRef]
- Evett, I.W.; Weir, B.S. Interpreting DNA Evidence: Statistical Genetics for Forensic Scientists; Sinauer Associates: Sunderland, MA, USA, 1998. [Google Scholar]
- Waits, L.P.; Luikart, G.; Taberlet, P. Estimating the probability of identityamong genotypes in natural populations: Cautions and guidelines. Mol. Ecol. 2001, 10, 249–256. [Google Scholar] [CrossRef]
- Wilkins, L.; Arias-Reveron, J.M.; Stith, B.; Roelke, M.E.; Belden, R.C. The Florida panther Puma concolor coryi: A morphological investigation of the subspecies with a comparison to other North and South American cougars. Bull. Florida Mus. Nat. Hist. 1997, 40, 221–269. [Google Scholar] [CrossRef]
- Castilho, C.S.; Marins-Sá, L.G.; Benedet, R.C.; Freitas, T.R. Genetic structure and conservation of mountain lions in the South-Brazilian Atlantic Rain Forest. Genet. Mol. Ecol. 2012, 35, 65–73. [Google Scholar] [CrossRef]
- Pereira, J.A.; Thompson, J.; di Bitetti, M.S.; Fracassi, N.G.; Paviolo, A.; Fameli, A.F.; Novaro, A.J. A small protected area facilitates persistence of a large carnivore in a ranching landscape. J. Nat. Conserv. 2020, 56, 125846. [Google Scholar] [CrossRef]
- Gutman, D. Ranchers push back as pumas fill Patagonian void. EcoAméricas 2021, October. Available online: https://www.ecoamericas.com/issues/article/2021/10/F0448F61-16C1-4537-8F14-99A2A5C409A8 (accessed on 15 December 2023).
- Novembre, J. Pritchard, Stephens, and Donnelly on population structure. Genetics 2016, 204, 391–393. [Google Scholar] [CrossRef]
- Lawson, D.J.; van Dorp, L.; Falush, D. A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. Nature Comm. 2018, 9, 3258. [Google Scholar] [CrossRef]
- Gustafson, K.D.; Gagne, R.B.; Buchalski, M.R.; Vickers, T.W.; Riley, S.P.; Sikich, J.A.; Rudd, J.L.; Dellinger, J.A.; LaCava, M.E.; Ernest, H.B. Multi-population puma connectivity could restore genomic diversity to at-risk coastal populations in California. Evol. Appl. 2022, 15, 286–299. [Google Scholar] [CrossRef]
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Elbroch, L.M.; Weckworth, B.V.; Pilgrim, K.; Ohrens, O.; Lagos, N.; Arroyo-Arce, S.; Montt, M.; Goic, D.; Schwartz, M.K. An Initial Genetic Assessment of the Emblematic Pumas of the Torres del Paine UNESCO Biosphere Reserve. Diversity 2024, 16, 581. https://doi.org/10.3390/d16090581
Elbroch LM, Weckworth BV, Pilgrim K, Ohrens O, Lagos N, Arroyo-Arce S, Montt M, Goic D, Schwartz MK. An Initial Genetic Assessment of the Emblematic Pumas of the Torres del Paine UNESCO Biosphere Reserve. Diversity. 2024; 16(9):581. https://doi.org/10.3390/d16090581
Chicago/Turabian StyleElbroch, L. Mark, Byron V. Weckworth, Kristine Pilgrim, Omar Ohrens, Nicolás Lagos, Stephanny Arroyo-Arce, Mauricio Montt, Dania Goic, and Michael K. Schwartz. 2024. "An Initial Genetic Assessment of the Emblematic Pumas of the Torres del Paine UNESCO Biosphere Reserve" Diversity 16, no. 9: 581. https://doi.org/10.3390/d16090581
APA StyleElbroch, L. M., Weckworth, B. V., Pilgrim, K., Ohrens, O., Lagos, N., Arroyo-Arce, S., Montt, M., Goic, D., & Schwartz, M. K. (2024). An Initial Genetic Assessment of the Emblematic Pumas of the Torres del Paine UNESCO Biosphere Reserve. Diversity, 16(9), 581. https://doi.org/10.3390/d16090581