Funk, W. C., McKay, J. K., Hohenlohe, P. A. & Allendorf, F. W. Harnessing genomics for delineating conservation units. Trends Ecol. Evol. 27, 489–496. https://doi.org/10.1016/j.tree.2012.05.012 (2012).
Google Scholar
Hohenlohe, P. A., Funk, W. C. & Rajora, O. P. Population genomics for wildlife conservation and management. Mol. Ecol. 30, 62–82. https://doi.org/10.1111/mec.15720 (2020).
Google Scholar
Helyar, S. J. et al. Application of SNPs for population genetics of nonmodel organisms: New opportunities and challenges. Mol. Ecol. Resour. 11, 123–136. https://doi.org/10.1111/j.1755-0998.2010.02943.x (2011).
Google Scholar
Allendorf, F. W. Genetics and the conservation of natural populations: Allozymes to genomes. Mol. Ecol. 26, 420–430. https://doi.org/10.1111/mec.13948 (2017).
Google Scholar
Zimmerman, S. J., Aldridge, C. L. & Oyler-McCance, S. J. An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern. BMC Genomics 21, 38. https://doi.org/10.1186/s12864-020-06783-9 (2020).
Google Scholar
Lemopoulos, A. et al. Comparing RADseq and microsatellites for estimating genetic diversity and relatedness—implications for brown trout conservation. Ecol. Evol. 9, 2106–2120. https://doi.org/10.1002/ece3.4905 (2019).
Google Scholar
Kleinman-Ruiz, D. et al. Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx. BMC Genomics 18, 556. https://doi.org/10.1186/s12864-017-3946-5 (2017).
Google Scholar
Geist, J. Strategies for the conservation of endangered freshwater pearl mussels (Margaritifera margaritifera L.): A synthesis of conservation genetics and ecology. Hydrobiologia 644, 69–88. https://doi.org/10.1007/s10750-010-0190-2 (2010).
Lopes-Lima, M. et al. Conservation status of freshwater mussels in Europe: State of the art and future challenges. Biol. Rev. 92, 572–607. https://doi.org/10.1111/brv.12244 (2017).
Google Scholar
Outeiro, A., Ondina, P., Fernández, C., Amaro, R. & Miguel, E. S. Population density and age structure of the freshwater Pearl mussel, Margaritifera margaritifera, in two Iberian rivers. Freshw. Biol. 53, 485–496. https://doi.org/10.1111/j.1365-2427.2007.01913.x (2008).
Google Scholar
Clements, E. A., Thomas, R. & Adams, C. E. An investigation of salmonid host utilisation by the endangered freshwater pearl mussel (Margaritifera margaritifera) in north-west Scotland. Aquat. Conserv.: Mar. Freshw. Ecosyst. 28, 764–768. https://doi.org/10.1002/aqc.2900 (2018).
Taeubert, J-E. & Geist, J. The relationship between the Freshwater Pearl Mussel (Margaritifera margaritifera) and its hosts. Biol. Bull. 44, 67–73. https://doi.org/10.1134/S1062359017010149 (2017).
Sousa, R. et al. Conservation status of the freshwater pearl mussel Margaritifera margaritifera in Portugal. Limnologica 50, 4–10. https://doi.org/10.1016/j.limno.2014.07.004 (2015).
Google Scholar
Almodóvar, A., Nicola, G. G., Ayllón, D. & Elvira, B. Global warming threatens the persistence of Mediterranean brown trout. Glob. Change Biol. 18, 1549–1560. https://doi.org/10.1111/j.1365-2486.2011.02608.x (2012).
Google Scholar
Nicola, G. G., Elvira, B., Johnson, B., Ayllón, D. & Almodóvar, A. Local and global climatic drivers of Atlantic salmon decline in southern Europe. Fish. Res. 198, 78–85. https://doi.org/10.1016/j.fishres.2017.10.012 (2018).
Google Scholar
da Silva, J. P. et al. Predicting climatic threats to an endangered freshwater mussel in Europe: The need to account for fish hosts. Freshw. Biol. 00, 1–15. https://doi.org/10.1111/fwb.13885 (2022).
Google Scholar
Strayer, D. L., Geist, J., Haag, W. R., Jackson, J. K. & Newbold, J. D. Essay: Making the most of recent advances in freshwater mussel propagation and restoration. Conserv. Sci. Pract. 43, e53. https://doi.org/10.1111/csp2.53 (2009).
Google Scholar
Geist, J., Bayerl, H., Stoeckle, B. C. & Kuehn, R. Securing genetic integrity in freshwater pearl mussel propagation and captive breeding. Sci. Rep. 11, 16019. https://doi.org/10.1038/s41598-021-95614-2 (2021).
Google Scholar
Gomes dos Santos, A. et al. The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). DNA Res. 28, dsab002. https://doi.org/10.1093/dnares/dsab002 (2021).
Bouza, C. et al. Threatened freshwater pearl mussel Margaritifera margaritifera L. in NW Spain: low and very structured genetic variation in southern peripheral assessed using microsatellite markers. Conserv. Genet. 8: 937–948. https://doi.org/10.1007/s10592-006-9248-0 (2007).
Stoeckle, B. C. et al. Strong genetic differentiation and low genetic diversity of the freshwater pearl mussel (Margaritifera margaritifera L.) in the southwestern European distribution range. Conserv. Genet. 18, 147–157. https://doi.org/10.1007/s10592-016-0889-3 (2017).
Geist, J., Söderberg, H., Karllberg, A. & Kuehn, R. Drainage-independent genetic structure and high genetic diversity of endangered freshwater pearl mussels (Margaritifera margaritifera) in northern Europe. Conserv. Genet. 11, 1339–1350. https://doi.org/10.1007/s10592-009-9963-4 (2010).
Google Scholar
implications for conservation and management. Geist, J. & Kuehn, R. Genetic diversity and differentiation of central European freshwater pearl mussel (Margaritifera margaritifera L.) populations. Mol. Ecol. 14, 239–425. https://doi.org/10.1111/j.1365-294X.2004.02420.x (2005).
Google Scholar
Farrington, S. J., King, R. W., Baker, J. A. & Gibbons, J. G. Population genetics of freshwater pearl mussel (Margaritifera margaritifera) in central Massachusetts and implications for conservation. Aquat. Conserv.: Mar. Freshw. Ecosyst. 30, 1945–1958. https://doi.org/10.1002/aqc.3439 (2020).
Zanatta, D. T. et al. High genetic diversity and low differentiation in North American Margaritifera margaritifera (Bivalvia: Unionida: Margaritiferidae). Biol. J. Linn. Soc. Lond., 123, 850–863. https://doi.org/10.1093/biolinnean/bly010. (2018)
Garrison, N. L., Johnson, P. D. & Whelan, N. V. Conservation genomics reveals low genetic diversity and multiple parentage in the threatened freshwater mussel Margaritifera hembeli. Conser. Genet. 22, 217–231. https://doi.org/10.1007/s10592-020-01329-8 (2021).
Google Scholar
Roe, K. & Kim, K. S. Genome-wide SNPs redefine species-boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America. Sci. Rep. 11, 10752. https://doi.org/10.1038/s41598-021-90325-0 (2021).
Google Scholar
Wingett, S. W. & Andrews, S. FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res 7, 1338. https://doi.org/10.12688/f1000research.15931.2 (2018).
Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048. https://doi.org/10.1093/bioinformatics/btw354 (2016).
Google Scholar
Rochette, N. C., Rivera-Colón, A. G. & Catchen, J. M. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol. Ecol. 28, 4737–4754. https://doi.org/10.1111/mec.15253 (2019).
Google Scholar
Paris, R. J., Stevens, J. R. & Catchen, J. M. Lost in parameter space: A road map for STACKS. Methods Ecol. Evol. 8, 1360–1373. https://doi.org/10.1111/2041-210X.12775 (2017).
Google Scholar
Limin, F., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: Accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152. https://doi.org/10.1093/bioinformatics/bts565 (2012).
Google Scholar
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2. https://doi.org/10.48550/arXiv.1303.3997 (2013).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079. https://doi.org/10.1093/bioinformatics/btp352 (2009).
Google Scholar
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv:1207.3907v2. https://doi.org/10.48550/arXiv.1207.3907 (2012)
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158. https://doi.org/10.1093/bioinformatics/btr330 (2011).
Google Scholar
Excoffier, L. & Lischer, H. E. L. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x (2010).
Weir, B. S. & Cockerham, C. Estimating F-statistics for the analysis of population structure. Evol. 38, 1358–1370. https://doi.org/10.2307/2408641 (1984).
Google Scholar
Frichot, E. & François, O. LEA: An R package for landscape and ecological association studies. Methods Ecol. Evol. 6, 925–929. https://doi.org/10.1111/2041-210X.12382 (2015).
Google Scholar
Alexander, D. H, Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664. https://doi.org/10.1101/gr.094052.109 (2009).
Jakobsson, M. & Rosenberg, N. A. CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801–1806. https://doi.org/10.1093/bioinformatics/btm233 (2007).
Google Scholar
Frankham, R. et al. A practical guide for genetic management of fragmented animal and plant populations. Oxford University Press, New York. 174. https://doi.org/10.1093/oso/9780198783411.001.0001 (2019).
Wacker, S., Larson, B., Jakobsen, P. & Karlssona, S. Multiple paternity promotes genetic diversity in captive breeding of a freshwater mussel. Glob. Ecol. Cons. 17, e00564. https://doi.org/10.1016/j.gecco.2019.e00564 (2019).
Google Scholar
Cao, R. et al. Genetic structure and diversity of Australian freshwater crocodiles (Crocodylus johnstoni) from the Kimberley Western Australia. Conserv. Genet. 21, 421–429. https://doi.org/10.1007/s10592-020-01259-5 (2020).
Google Scholar
Escalante, M. A. et al. Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican Golden trout (Oncorhynchus chrysogaster). Conserv. Genet. 21, 907–926. https://doi.org/10.1371/journal.pone.0141775 (2020).
Google Scholar
Bauer, G. Reproductive strategy of the freshwater pearl mussel Margaritifera margaritifera. J. Anim. Ecol. 56, 691–704. https://doi.org/10.2307/5077 (1987).
Google Scholar
Machordom, A., Araujo, R., Erpenbeck, D. & Ramos, M. A. Phylogeography and conservation genetics of endangered European Margaritiferidae (Bibalvia: Unionoidae). Biol. J. Linn. Soc. 78, 235–252. https://doi.org/10.1046/j.1095-8312.2003.00158.x (2003).
Google Scholar
Viveen, W., Schoorl, J. M., Veldkamp, A., van Balen, R. T. & Vidal-Romani, J. R. Fluvial terraces of the northwest Iberian lower Miño River. J. Maps 9, 513–522. https://doi.org/10.1080/17445647.2013.821096 (2013).
Google Scholar
Pérez-Granados, C., López-Iborra, G. & Seoane, J. A multi-scale analysis of habitat selection in peripheral populations of the endangered Dupont’s Lark Chersophilus duponti. Bird Conserv. Intern. 27, 398–413. https://doi.org/10.1017/S0959270916000356 (2017).
Google Scholar
Sanz Ball-Llosera, N., Garcìa-Marìn, J. & Pla, C. Managing fish populations under mosaic relationships. The case of brown trout (Salmo trutta) in peripheral Mediterranean populations. Conserv. Genet. 3, 385–400. https://doi.org/10.1023/A:1020527420654 (2002).
Vila, M. et al. Phylogeography and Conservation Genetics of the Ibero-Balearic Three-Spined Stickleback (Gasterosteus aculeatus). PLoS One 12, e0170685. https://doi.org/10.1371/journal.pone.0170685 (2017)
Hamed, Y. et al. Climate impacto n Surface and groundwater in North Africa: A global synthesis of findings and recommendations. Euro-Mediterr. J. Environ. Integr. 3, 25. https://doi.org/10.1007/s41207-018-0067-8 (2018).
Google Scholar
Krijgsman, W. et al. The Gibraltar Corridor: Watergate of the Messinian Salinity Crisis. Mar. Geol. 403, 238–246. https://doi.org/10.1016/j.margeo.2018.06.008 (2018).
Google Scholar
Zanatta, D. T. & Wilson, C. C. Testing congruency of geographic and genetic population structure for a freshwater mussel Bivalvia: Unionoida) and its host fish. Biol. J. Linn. Soc. 102, 669–685. https://doi.org/10.1111/j.1095-8312.2010.01596.x (2011).
Google Scholar
Österling, E. M., Ferm, J. & Piccolo, J.J. Parasitic freshwater pearl mussel larvae (Margaritifera margaritifera L.) reduce the drift-feeding rate of juvenile brown trout (Salmo trutta L.). Environ. Biol. Fish. 97, 543–549. https://doi.org/10.1007/s10641-014-0251-x (2014).
Geist, J. et al. Genetic structure of Irish freshwater pearl mussels (Margaritifera margaritifera and Margaritifera durrovensis): Validity of subspecies, roles of host fish, and conservation implications. Aquat. Conserv. Mar. Freshw. Ecosyst. 28, 923–933. https://doi.org/10.1002/aqc.2913 (2018)
Wacker, S., Larsen, B. M., Karlsson, S. & Hindar, K. Host specificity drives genetic structure in a freshwater mussel. Sci. Rep. 9, 10409 (2019).
Machordom, A., Suárez, J., Almodóvar, A. & Bautista, J. Mitochondrial haplotype variation and phylogeography of Iberian brown trout populations. Mol. Ecol. 9, 1325–1338. https://doi.org/10.1046/j.1365-294x.2000.01015.x (2000).
Google Scholar
Suárez, J., Bautista, J. M., Almodóvar, A. & Machordom, A. Evolution of the mitocondrial control region in Paleartic brown trout (Salmo trutta) populations: The biogeographical role of the Iberian Peninsula. Heredity 87, 198–206. https://doi.org/10.1046/j.1365-2540.2001.00905.x (2001).
Google Scholar
Velasco, J. C. et al. Descubiertos algunos ejemplares de Margaritifera margaritifera (L.) (Bivalvia, Unionoida) en el alto Duero (Soria, España). Iberus 32(2), 97–104 (2014).
Geist, J. & Kuehn, R. Host-parasite interactions in oligotrophic stream ecosystems: the roles of life history strategy and ecological niche. Mol. Ecol. 17, 997–1008. https://doi.org/10.1111/j.1365-294X.2007.03636.x. (2008)
Ledoux, J.-B., et al. Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: Patterns, processes and conservation implications. Divers. Distrib. 27, 2104–2123 https://doi.org/10.1111/ddi.13382 (2021).
Hervella F, & Caballero P. Inventario piscícola dos ríos galegos. Consellería de Medio Ambiente. Xunta de Galicia. Santiago de Compostela (1999).
Saura, M., Caballero, P. & Morán, P. Are there Atlantic salmon in the River Tambre?. J. Fish Biol. 72, 1223–1229. https://doi.org/10.1111/j.1095-8649.2007.01782.x (2008).
Google Scholar
Hoban, S. et al. Genetic diversity targets and indicators in the CBD post-2020 global biodiversity framework must be improved. Biol. Conserv. 248, 108654. https://doi.org/10.1016/j.biocon.2020.108654 (2020).
Google Scholar
Rilov, G. et al. Adaptive marine conservation planning in the face of climate change: What can we learn from physiological, ecological and genetic studies?. Glob. Ecol. Conserv. 17, e00566. https://doi.org/10.1016/j.gecco.2019.e00566 (2019).
Google Scholar
Muniz, F. L. et al. Delimitation of evolutionary units in Cuvier’s dwarf caiman, Paleosuchus palpebrosus (Cuvier, 1807): Insights from conservation of a broadly distributed species. Conserv. Genet. 19, 599–610. https://doi.org/10.1007/s10592-017-1035-6 (2018).
Google Scholar
Gum, B., Lange, M. & Geist, J. A critical reflection on the success of rearing and culturing of juvenile freshwater mussels with a focus on the endangered freshwater pearl mussel (Margaritifera margaritifera L.). Aquat. Conserv. 21, 743–751. https://doi.org/10.1002/aqc.1222 (2011).
Thomas, G. R., Taylor, J. & García de Leaniz, C. Captive breeding of the endangered freshwater Pearl mussel Margaritifera margaritifera. Endanger. Species Res. 12, 1–9. https://doi.org/10.3354/esr00286 (2010).
Wilson, C. D. et al. The importance of population genetic information in formulating ex situ conservation strategies for the freshwater pearl mussel (Margaritifera margaritifera L.) in Northern Ireland. Anim. Conserv. 15, 595–602. https://doi.org/10.1111/j.1469-1795.2012.00553.x (2012).
Pires, D., Reis, J., Benites, L. & Rodrigues, P. Minimizing dams impacts on biodiversity by way of translocations: the case of freshwater mussels. Impact Assess. Proj. Apprais. 39, 110–117. https://doi.org/10.1080/14615517.2020.1836710. (2021)
Source: Ecology - nature.com
