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).
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).
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.
Odum, W. E. Comparative ecology of tidal freshwater and salt marshes. Ann. Rev. Ecul. Sysl 19, 147–176 (1988).
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).
Reis, V. et al. A global assessment of inland wetland conservation status. Bioscience 67(6), 523. https://doi.org/10.1093/biosci/bix045 (2017).
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).
Kaplan, J. O. Wetlands at the last glacial maximum: Distribution and methane emissions. Geophys. Res. Lett. https://doi.org/10.1029/2001GL013366 (2002).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Sabater, S. et al. The Iberian rivers’. In Rivers of Europe 181–224 (Elsevier, 2022).
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).
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.
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).