Genetic structure and historical demography of inland wetland fish using the endangered Lisbon arched-mouth nase as a case-study


  • Keddy, P. A. et al. Wet and wonderful: The world’s largest wetlands are conservation priorities. Bioscience 59(1), 39–51. https://doi.org/10.1525/BIO.2009.59.1.8 (2009).

    Article 

    Google Scholar
     

  • Davidson, N. C. & Finlayson, C. M. Extent, regional distribution and changes in area of different classes of wetland. Mar. Freshw. Res. 69(10), 1525–1533. https://doi.org/10.1071/MF17377 (2018).

    Article 

    Google Scholar
     

  • De Groot, R., Stuip, M., Finlayson, C. & Davidson, N. Valuing wetlands: Guidance for valuing the benefits derived from wetland ecosystem services, Ramsar Technical Report No. 3/CBD Technical Series No. 27. ’, Montreal, Canada (2006).

  • Finlayson, C., D’Cruz, R. & Davidson, N. Ecosystems and human well-being: Wetlands and water. Synthesis. Millennium Ecosystem Assessment (2005).

  • Azevêdo, T. M. et al. Floodplain sediments of the tagus river, portugal: Assessing avulsion, channel migration and human impact. In Sedimentary Processes Environments and Basins 535–554 (Wiley, 2007). https://doi.org/10.1002/9781444304411.ch21.

    Chapter 

    Google Scholar
     

  • Odum, W. E. Comparative ecology of tidal freshwater and salt marshes. Ann. Rev. Ecul. Sysl 19, 147–176 (1988).

    Article 

    Google Scholar
     

  • Davidson, N. C., Fluet-Chouinard, E. & Finlayson, C. M. Global extent and distribution of wetlands: Trends and issues. Mar. Freshw. Res. 69(4), 620–627. https://doi.org/10.1071/MF17019 (2018).

    Article 

    Google Scholar
     

  • Reis, V. et al. A global assessment of inland wetland conservation status. Bioscience 67(6), 523. https://doi.org/10.1093/biosci/bix045 (2017).

    Article 

    Google Scholar
     

  • Ward, J. V. & Stanford, J. A. The serial discontinuity concept: Extending the model to floodplain rivers. Regul. Rivers Res. Manag. 10(2–4), 159–168. https://doi.org/10.1002/RRR.3450100211 (1995).

    Article 

    Google Scholar
     

  • Kaplan, J. O. Wetlands at the last glacial maximum: Distribution and methane emissions. Geophys. Res. Lett. https://doi.org/10.1029/2001GL013366 (2002).

    Article 

    Google Scholar
     

  • Davidson, N. C. How much wetland has the world lost? Long-term and recent trends in global wetland area. Mar. Freshw. Res. 65, 934–941. https://doi.org/10.1071/MF14173 (2014).

    Article 

    Google Scholar
     

  • Fluet-Chouinard, E. et al. Extensive global wetland loss over the past three centuries. Kees Klein Goldewijk 614, 26. https://doi.org/10.1038/s41586-022-05572-6 (2023).

    Article 
    CAS 

    Google Scholar
     

  • Čížková, H. et al. Actual state of European wetlands and their possible future in the context of global climate change. Aquat. Sci. 75(1), 3–26. https://doi.org/10.1007/S00027-011-0233-4/TABLES/2 (2013).

    Article 

    Google Scholar
     

  • Baldwin, A. H., Barendregt, A. & Whigham, D. F. Tidal Freshwater Wetlands—An Introduction to the Ecosystem (2009).

  • Baerwald, M., Bien, V., Feyrer, F. & May, B. Genetic analysis reveals two distinct Sacramento splittail (Pogonichthys macrolepidotus) populations. Conserv. Genet. 8, 159–167 (2007).

    Article 
    CAS 

    Google Scholar
     

  • Feyrer, F. et al. Metapopulation structure of a semi-anadromous fish in a dynamic environment. Can. J. Fish. Aquat. Sci. 72(5), 709–721. https://doi.org/10.1139/cjfas-2014-0433 (2015).

    Article 

    Google Scholar
     

  • Verissimo, A. et al. Distribution and demography of the critically endangered Lisbon arched-mouth nase, Iberochondrostoma olisiponense. Fish. Mediterr. Environ. 2018, 1–13. https://doi.org/10.29094/fishmed.2018.002 (2018).

    Article 

    Google Scholar
     

  • Magalhães, M. et al. Livro Vermelho dos Peixes Dulciaquícolas e Diádromos de Portugal Continental. (2023).

  • Ribeiro, D. ‘Inland Wetlands in the Lower Tagus: Land Uses, Habitat Condition and Fish Communities (University of Lisbon, 2023).


    Google Scholar
     

  • Gante, H. F., Santos, C. D. & Alves, M. J. A new species of Chondrostoma Agassiz, 1832 (Cypriniformes: Cyprinidae) with sexual dimorphism from the lower Rio Tejo Basin, Portugal. Zootaxa 1616, 23–35 (2007).

    Article 

    Google Scholar
     

  • Cabral, H. N., Costa, M. J. & Salgado, J. P. Does the Tagus estuary fish community reflect environmental changes?. Clim. Res. 18(1–2), 119–126. https://doi.org/10.3354/CR018119 (2001).

    Article 

    Google Scholar
     

  • Costa, M. J., Vasconcelos, R., Costa, J. L. & Cabral, H. N. River flow influence on the fish community of the Tagus estuary (Portugal). Hydrobiologia 587(1), 113–123. https://doi.org/10.1007/S10750-007-0690-X/FIGURES/6 (2007).

    Article 

    Google Scholar
     

  • Feyrer, F., Hobbs, J. & Sommer, T. Salinity inhabited by age-0 splittail (Pogonichthys macrolepidotus) as determined by direct field observation and retrospective analyses with otolith chemistry. San Franc. Estuary Watershed Sci. https://doi.org/10.15447/SFEWS.2010V8ISS2ART2 (2010).

    Article 

    Google Scholar
     

  • Ostrand, K. G. & Wilde, G. R. Temperature, dissolved oxygen, and salinity tolerances of five prairie stream fishes and their role in explaining fish assemblage patterns. Trans. Am. Fish. Soc. 130, 742–749. https://doi.org/10.1577/1548-8659(2001)130%3c0742:TDOAST%3e2.0.CO;2 (2001).

    Article 

    Google Scholar
     

  • Whiterod, N. R. & Walker, K. F. Will rising salinity in the Murray-Darling Basin affect common carp (Cyprinus carpio L.)?. Mar. Freshwater Res. 57, 817–823. https://doi.org/10.1071/MF06021 (2006).

    Article 
    CAS 

    Google Scholar
     

  • Bianco, P. G. & Nordlie, F. The salinity tolerance of Pseudophoxinus stymphalicus (Cyprinidae) and Valencia letourneuxi (Valenciidae) from western Greece suggests a revision of the ecological categories of freshwater fishes. Ital. J. Zool. 3(75), 285–293. https://doi.org/10.1080/11250000801931753 (2008).

    Article 

    Google Scholar
     

  • Benito, G., Sopeña, A., Sánchez-Moya, Y., Machado, M. J. & Pérez-González, A. Palaeoflood record of the Tagus River (Central Spain) during the Late Pleistocene and Holocene. Quat. Sci. Rev. 22, 1737–1756. https://doi.org/10.1016/S0277-3791(03)00133-1 (2003).

    Article 
    ADS 

    Google Scholar
     

  • Gante, H. F., Santos, C. D. & Alves, M. J. Phylogenetic relationships of the newly described species Chondrostoma olisiponensis (Teleostei: Cyprinidae). J. Fish. Biol. 76(4), 965–974. https://doi.org/10.1111/J.1095-8649.2010.02536.X (2010).

    Article 
    CAS 

    Google Scholar
     

  • Pais, J. The neogene of the lower Tagus Basin (Portugal). Span. J. Palaeontol. 19(2), 229. https://doi.org/10.7203/sjp.19.2.20534 (2004).

    Article 

    Google Scholar
     

  • Van Der Schriek, T., Passmore, D. G., Rolaõ, J. & Stevenson, A. C. Estuarine-fluvial floodplain formation in the Holocene Lower Tagus valley (Central Portugal) and implications for Quaternary fluvial system evolution. Quat. Sci. Rev. 26, 2937–2957. https://doi.org/10.1016/j.quascirev.2007.07.020 (2007).

    Article 
    ADS 

    Google Scholar
     

  • Almeida, I. M. et al. Holocene paleoenvironmental evolution of the Lisbon downtown area as recorded in the Esteiro da Baixa sediments—First results. J. Coast. Res. 56, 574–578 (2009).


    Google Scholar
     

  • Vis, G. J., Kasse, C. & Vandenberghe, J. Late Pleistocene and Holocene palaeogeography of the Lower Tagus Valley (Portugal): Effects of relative sea level, valley morphology and sediment supply. Quat. Sci. Rev. 27(17–18), 1682–1709. https://doi.org/10.1016/j.quascirev.2008.07.003 (2008).

    Article 
    ADS 

    Google Scholar
     

  • Vis, G. J. & Kasse, C. Late Quaternary valley-fill succession of the Lower Tagus Valley, Portugal. Sediment. Geol. 221(1–4), 19–39. https://doi.org/10.1016/j.sedgeo.2009.07.010 (2009).

    Article 
    ADS 

    Google Scholar
     

  • Azevêdo, T. M. & Gonçalves, M. A. Geochemistry of core sediments from the Middle Tagus alluvial plain (Portugal) since the last glacial: using background determination methods to outline environmental changes. Environ. Earth Sci. 59(1), 191–204. https://doi.org/10.1007/s12665-009-0016-6 (2009).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Lentacker, A. Fish remains from Portugal: Preliminary analysis of the Mesolithic shell-midden sites of Cabeço da Amoreira and Cabeço da Arruda. Annales du Musée Royal de l’Afrique Centrale, Sciences Zoologiques 274, 263–271 (1994).


    Google Scholar
     

  • Lentacker, A. Preliminary results of the fauna of Cabeço de Amoreira and Cabeço de Arruda (Muge, Portugal). Trabalhos de Antropologia e Etnologia 26(1–4), 9–26 (1986).


    Google Scholar
     

  • Rodrigues, A. O Rio Tejo, Clube do Colecionador dos Correios. (CTT—Correios de Portugal, 2018).

  • Fernandes, M. R., Aguiar, F. C., Martins, M. J., Rivaes, R. & Ferreira, M. T. Long-term human-generated alterations of Tagus River: Effects of hydrological regulation and land-use changes in distinct river zones. Catena (Amst) 188, 104466. https://doi.org/10.1016/J.CATENA.2020.104466 (2020).

    Article 

    Google Scholar
     

  • Sabater, S. et al. The Iberian rivers’. In Rivers of Europe 181–224 (Elsevier, 2022).

    Chapter 

    Google Scholar
     

  • Gonçalves, V. S., Sousa, A. C., Texugo, A. & Ramos-Pereira, A. In the Sorraia river valley (Coruche, Portugal): Settlement dynamics of ancient peasant societies on the left bank of the Lower Tagus river (5500 to 1800 B.C.E.). Cuadernos de Prehistoria y Arqueologia de la Universidad de Granada 31, 95–158. https://doi.org/10.30827/CPAG.v31i0.21118 (2021).

    Article 

    Google Scholar
     

  • Simberloff, D. The proximate causes of extinction. In Patterns and Processes in the History of Life 259–276 (Springer, 1986). https://doi.org/10.1007/978-3-642-70831-2_14.

    Chapter 

    Google Scholar
     

  • Crisfield, V. E., Guillaume Blanchet, F., Raudsepp-Hearne, C. & Gravel, D. How and why species are rare: Towards an understanding of the ecological causes of rarity. Ecography 2024(2), e07037. https://doi.org/10.1111/ECOG.07037 (2024).

    Article 
    ADS 

    Google Scholar
     

  • Purvis, A., Gittleman, J. L., Cowlishaw, G. & Mace, G. M. Predicting extinction risk in declining species. Proc. R Soc. Lond. B Biol. Sci. 267(1456), 1947–1952. https://doi.org/10.1098/RSPB.2000.1234 (2000).

    Article 
    CAS 

    Google Scholar
     

  • Guerreiro, S. B., Kilsby, C. G. & Fowler, H. J. Rainfall in Iberian transnational basins: A drier future for the Douro, Tagus and Guadiana?. Clim. Change 135(3–4), 467–480. https://doi.org/10.1007/S10584-015-1575-Z/FIGURES/5 (2016).

    Article 
    ADS 

    Google Scholar
     

  • Pambianchi, G., Gentilucci, M., Sondermann, M. N. & Proença De Oliveira, R. Climate Adaptation Needs to Reduce Water Scarcity Vulnerability in the Tagus River Basin (2022). https://doi.org/10.3390/w14162527.

  • Anastácio, P. M. et al. Non-native freshwater fauna in Portugal: A review. Sci. Total Environ. 650, 1923–1934. https://doi.org/10.1016/j.scitotenv.2018.09.251 (2019).

    Article 
    ADS 
    CAS 

    Google Scholar
     

  • Šmejkal, M. et al. Wetland fish in peril: A synergy between habitat loss and biological invasions drives the extinction of neglected native fauna. Biol. Conserv. 302(August), 2025. https://doi.org/10.1016/j.biocon.2024.110948 (2024).

    Article 

    Google Scholar
     

  • Sousa-Santos, C. et al. Evolutionary history and population genetics of a cyprinid fish (Iberochondrostoma olisiponensis) endangered by introgression from a more abundant relative. Conserv. Genet. 15(3), 665–677. https://doi.org/10.1007/S10592-014-0568-1/METRICS (2014).

    Article 

    Google Scholar
     

  • Boileau, N. et al. A complex mode of aggressive mimicry in a scale-eating cichlid fish. Biol. Lett. https://doi.org/10.1098/rsbl.2015.0521 (2015).

    Article 
    PubMed Central 

    Google Scholar
     

  • Gruber, B., Unmack, P. J., Berry, O. F. & Georges, A. dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Mol. Ecol. Resour. 18(3), 691–699. https://doi.org/10.1111/1755-0998.12745 (2018).

    Article 

    Google Scholar
     

  • Rousset, F. genepop’007: A complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8(1), 103–106. https://doi.org/10.1111/J.1471-8286.2007.01931.X (2008).

    Article 

    Google Scholar
     

  • Goudet, J. HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5(1), 184–186. https://doi.org/10.1111/j.1471-8286.2004.00828.x (2005).

    Article 

    Google Scholar
     

  • Lischer, H. E. L. & Excoffier, L. PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28(2), 298–299. https://doi.org/10.1093/BIOINFORMATICS/BTR642 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155(2), 945–959. https://doi.org/10.1111/j.1471-8286.2007.01758.x (2000).

    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • Hubisz, M. J., Falush, D., Stephens, M. & Pritchard, J. K. Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Resour. 9(5), 1322–1332. https://doi.org/10.1111/J.1755-0998.2009.02591.X (2009).

    Article 
    PubMed Central 

    Google Scholar
     

  • Falush, D., Stephens, M. & Pritchard, J. K. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164(4), 1567–1587. https://doi.org/10.1111/j.1471-8286.2007.01758.x (2003).

    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14(8), 2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x (2005).

    Article 
    CAS 

    Google Scholar
     

  • 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(14), 1801–1806. https://doi.org/10.1093/BIOINFORMATICS/BTM233 (2007).

    Article 
    CAS 

    Google Scholar
     

  • Rosenberg, N. A. distruct: A program for the graphical display of population structure. Mol. Ecol. Notes 4(1), 137–138. https://doi.org/10.1046/J.1471-8286.2003.00566.X (2004).

    Article 

    Google Scholar
     

  • Guillot, G., Mortier, F. & Estoup, A. GENELAND: A computer package for landscape genetics. Mol. Ecol. Notes 5(3), 712–715. https://doi.org/10.1111/j.1471-8286.2005.01031.x (2005).

    Article 
    CAS 

    Google Scholar
     

  • Manel, S. et al. A new individual-based spatial approach for identifying genetic discontinuities in natural populations. Mol. Ecol. 16(10), 2031–2043. https://doi.org/10.1111/J.1365-294X.2007.03293.X (2007).

    Article 
    CAS 

    Google Scholar
     

  • Balding, D. J. Likelihood-based inference for genetic correlation coefficients. Theor. Popul. Biol. 63(3), 221–230. https://doi.org/10.1016/S0040-5809(03)00007-8 (2003).

    Article 

    Google Scholar
     

  • Malinsky, M., Trucchi, E., Lawson, D. J. & Falush, D. RADpainter and fineRADstructure: Population Inference from RADseq Data. Mol. Biol. Evol. 35(5), 1284–1290. https://doi.org/10.1093/MOLBEV/MSY023 (2018).

    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • Lawson, D. J., Hellenthal, G., Myers, S. & Falush, D. Inference of population structure using dense haplotype data. PLoS Genet. 8(1), 1002453. https://doi.org/10.1371/journal.pgen.1002453 (2012).

    Article 
    CAS 

    Google Scholar
     

  • Foll, M. & Gaggiotti, O. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective. Genetics 180(2), 977–993. https://doi.org/10.1534/genetics.108.092221 (2008).

    Article 
    PubMed Central 

    Google Scholar
     

  • Foll, M., Fischer, M. C., Heckel, G. & Excoffier, L. Estimating population structure from AFLP amplification intensity. Mol. Ecol. 19(21), 4638–4647. https://doi.org/10.1111/J.1365-294X.2010.04820.X (2010).

    Article 
    CAS 

    Google Scholar
     

  • Fischer, M. C., Foll, M., Excoffier, L. & Heckel, G. Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis). Mol. Ecol. 20(7), 1450–1462. https://doi.org/10.1111/J.1365-294X.2011.05015.X (2011).

    Article 

    Google Scholar
     

  • Plummer, M., Best, N., Cowles, K. & Vines, K. ‘CODA: Convergence Diagnosis and Output Analysis for MCMC’, R News. Accessed 08 October 08 2024. Available: https://journal.r-project.org/articles/RN-2006-002/RN-2006-002.pdf

  • Do, C. et al. NeEstimator v2: Re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol. Ecol. Resour. 14(1), 209–214. https://doi.org/10.1111/1755-0998.12157 (2014).

    Article 
    CAS 

    Google Scholar
     

  • Hill, W. G. Estimation of effective population size from data on linkage disequilibrium1. Genet. Res. (Camb.) 38(3), 209–216. https://doi.org/10.1017/S0016672300020553 (1981).

    Article 

    Google Scholar
     

  • Gilbert, K. J. & Whitlock, M. C. Evaluating methods for estimating local effective population size with and without migration. Evolution (N Y) 69(8), 2154–2166. https://doi.org/10.1111/EVO.12713 (2015).

    Article 

    Google Scholar
     

  • Noskova, E., Ulyantsev, V., Koepfli, K. P., Obrien, S. J. & Dobrynin, P. GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data’. Gigascience https://doi.org/10.1093/gigascience/giaa005 (2020).

    Article 
    PubMed Central 

    Google Scholar
     

  • Recknagel, H., Elmer, K. R. & Meyer, A. A hybrid genetic linkage map of two ecologically and morphologically divergent midas cichlid fishes (Amphilophus spp.) obtained by massively parallel DNA sequencing (ddRADSeq). G3 Genes Genomes Genet. 3(1), 65–74. https://doi.org/10.1534/G3.112.003897/-/DC1 (2013).

    Article 
    CAS 

    Google Scholar
     

  • Jouganous, J., Long, W., Ragsdale, A. P. & Gravel, S. Inferring the joint demographic history of multiple populations: Beyond the diffusion approximation. Genetics 206(3), 1549–1567. https://doi.org/10.1534/GENETICS.117.200493 (2017).

    Article 
    PubMed Central 

    Google Scholar
     



  • Source link

    More From Forest Beat

    Biodiversity modeling to manage urban ecosystems for people and nature

    Elmqvist, T. et al. Sustainability and resilience for transformation in the urban century. Nat. Sustain. 2, 267–273 (2019).Article  ...
    Biodiversity
    10
    minutes

    Multiple floods interactions shape riparian plant communities and diversity

    Study areaThe survey was conducted in the riparian area of the Akigawa River (Fig. 4), covering a regulated section spanning 33.57 km with a...
    Biodiversity
    7
    minutes

    First detection and entomological characterisation of invasive malaria vector Anopheles stephensi...

    Study site and samplingOur team from the Ecology, Health, and Environment (ECOSEN) group, Université André Salifou, Zinder, embarked on a study of biodiversity...
    Biodiversity
    4
    minutes

    Morphological and molecular assessment of muscle metacercariae infecting tench Tinca tinca...

    Waikagul, J. & Thaenkham, U. Approaches To Research on the Systematics of Fish Borne Trematodes1–16 (Academic, 2014).Chai, J. & Jung, B. Epidemiology of...
    Biodiversity
    11
    minutes
    spot_imgspot_img