REFERENCES
Abed, A., Légaré, G., Pomerleau, S., St-Cyr, J., Boyle, B., & Belzile, F. J. (2019). Genotyping-by-sequencing on the ion torrent platform in barley.  In: Harwood, W. (Eds) Barley. Methods in Molecular Biology , vol 1900. Humana Press, New York, NY. DOI: https://doi.org/10.1007/978-1-4939-8944-7_15
Aguilar, R., Quesada, M., Ashworth, L., Herrerias-Diego, Y., & Lobo, J. (2008). Genetic consequences of habitat fragmentation in plant populations: susceptible signals in plant traits and methodological approaches. Molecular Ecology, 17, 5177–5188.
Albert, J. S., Carnaval, A. C., Flantua, S. G. A., Lohmann, L. G., Ribas, C. C., Riff, D., Carrillo, J. D., Fan, Y., Figueiredo, J. J. P., Guayasamin, J. M., Hoorn, C., de Melo, G. H., Nascimento, N., Quesada, C. A., Ulloa Ulloa, C., Val, P., Arieira, J., Encalada, A. C., Nobre, C. A. (2023). Human impacts outpace natural processes in the Amazon.Science , 379, 6630. doi:10.1126/science.abo5003
Aldrich, P. R., Hamrick, J. L., Chavarriaga, P., Kochert, G. (1998). Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera .Molecular Ecology , 7, 933–944. /10.1046/j.1365-294x.1998.00396.x
Aleixo, I., Norris, D., Hemerik, L., Barbosa, A., Prata, E., Costa, F., & Poorter, L. (2019). Amazonian rainforest tree mortality driven by climate and functional traits. Nature Climate Change,  9, 384–388.
Alonso-García, M., Villarreal A., J. C., McFarland, K., & Goffinet, B. (2020). Population genomics and phylogeography of a clonal bryophyte with spatially separated sexes and extreme sex ratios. Frontiers in Plant Science , 11, 495. doi: 10.3389/fpls.2020.00495.
Alvarenga, L. D. P., Pôrto, K. C., & Silva, M. P. P. (2009). Relations between regional–local habitat loss and metapopulation properties of epiphyllous bryophytes in the Brazilian Atlantic Forest.Biotropica , 41, 682-691. https://doi.org/10.1111/j.1744-7429.2009.00532.x
Alvarenga, L. D. P., Pôrto, K. C., Coelho, M. L. P. & Zartman, C. E. (2016). How does reproductive strategy influence demography? A case study in the tropical, unisexual epiphyllous moss Crossomitrium patrisiae . American Journal of Botany , 103, 1921–1927. https://doi.org/10.3732/ajb.1600202
Andrews, S. (2010). FastQC:  A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Auffret, A. G., Rico, Y., Bullock, J. M., Hooftman, D. A. P., Pakeman, R. J., Soons, M. B., Suárez-Esteban, A., Traveset, A., Wagner, H. H., & Cousins S. A. O. (2017), Plant functional connectivity – integrating landscape structure and effective dispersal. Journal of Ecology , 105, 1648-1656. https://doi.org/10.1111/1365-2745.12742
Aycrigg, J. L., & Garton, E. O. (2014). Linking metapopulation structure to elk population management in Idaho: a genetic approach.Journal of Mammalogy, 95, 597–614. https://doi.org/10.1644/12-MAMM-A-300
Buza, L., Young, A., & Thrall, P. (2000). Genetic erosion, inbreeding and reduced fitness in fragmented populations of the endangered tetraploid pea Swainsona recta . Biological Conservation93, 177–186. https://doi.org/10.1016/S0006-3207(99)00150-0.
Campos, L. V., Stech, M., Mota de Oliveira, S., Muñoz-Ortiz, A., Ter Steege, H., & Uribe-M., J. (2022). Genetic population structure ofCheilolejeunea rigidula (Lejeuneaceae) in the Amazon region.Bryophyte Diversity and Evolution 45, 119–132. DOI: 10.11646/BDE.45.1.8
Carley, L. N., Morris, W. F., Walsh, R., Riebe, D., & Mitchell-Olds, T. (2022). Are genetic variation and demographic performance linked? Evolutionary Applications , 15, 1888–1906. https://doi.org/10.1111/eva.13487
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: an analysis tool set for population genomics. Molecular Ecology22 , 3124–3140. https://doi.org/10.1111/mec.12354
Chase, J. M., Blowes, S. A., Knight, T. M., Gerstner, K., & May, F.  (2020). Ecosystem decay exacerbates biodiversity loss with habitat loss. Nature,  584, 238–243 https://doi.org/10.1038/s41586-020-2531-2
Côrtes, M. C., Uriarte, M., Lemes, M. R., Gribel, R., Kress, W. J., Smouse, P. E., & Bruna, E. M. (2013). Low plant density enhances gene dispersal in the Amazonian understory herb Heliconia acuminata .Molecular Ecology, 22, 5716–5729. doi: 10.1111/mec.12495.
Costanzi, J.‐M., & Steifetten, Ø. (2019). Island biogeography theory explains the genetic diversity of a fragmented rock ptarmigan (Lagopus muta ) population. Ecology and Evolution 9, 3837–3849. https://doi.org/10.1002/ece3.5007
Curtis, P. G., Slay, C. M., Harris, N. L., Tyukavina, A., & Hansen, M. C. (2018). Classifying drivers of global forest loss. Science361, 1108–1111. doi:10.1126/science.aau3445
Daskalova, G. N., Myers-Smith, I. H., Bjorkman, A. D., Blowes, S. A., Supp, S. R., Magurran, A. E., & Dornelas, M. (2020). Landscape-scale forest loss as a catalyst of population and biodiversity change.Science 368, 1341–1347.
Diamond, J. M. (1975). The island dilemma: Lessons of modern biogeographic studies for the design of natural reserves.Biological Conservation , 7, 129–146.
Epskamp, S., Cramer, A. O., Waldorp, L. J., Schmittmann, V. D., & Borsboom, D. (2012). qgraph: Network Visualizations of Relationships in Psychometric Data. Journal of Statistical Software , 48, 1–18. https://doi.org/10.18637/jss.v048.i04
Escolástico-Ortiz, D. A., Hedenäs, L., Quandt, D., Harpke, D., Larraín, J., Stech, M., Villarreal A., J. C. (2023). Cryptic speciation shapes the biogeographic history of a northern distributed moss, Botanical Journal of the Linnean Society , 201, 114–134. https://doi.org/10.1093/botlinnean/boac027
Fahrig, L. (2019). Habitat fragmentation: A long and tangled tale.Global Ecology and Biogeography , 28, 33– 41. https://doi.org/10.1111/geb.12839
Fahrig, L., Arnillas, C., Arroyo-Rodríguez, V., J.rger-Hickfang, T., Müller, J., Pereira, H., Riva, F., Rösch, V., Seibold, S., Tscharntke, T.,Watling, J., & May, F. (2022). Resolving the SLOSS dilemma for biodiversity conservation: a research agenda. Biological Reviews , 97, 99–114.
Ferreira, S. J. F., Luizão F. J., & Dallarosa, R. L. G. (2005). Throughfall and rainfall interception by an upland forest submitted to selective logging in Central Amazonia. Acta Amazonica,  35, 55–62.
Fischer, R., Taubert, F., Müller, M. S., Groeneveld, J., Lehmann, S., Wiegand, T., & Huth, A. (2021). Accelerated forest fragmentation leads to critical increase in tropical forest edge area. Science advances7 , eabg7012. https://doi.org/10.1126/sciadv.abg7012
Figueiredo, L., Krauss, J., Steffan-Dewenter, I., & Cabral, J. S. (2019). Understanding extinction debts: spatio-temporal scales, mechanisms and a roadmap for future research. Ecography, 42, 1–18.
Gascon, C., & Bierregaard, R. O. Jr. (2001). The Biological Dynamics of Forest Fragments Project. In: Bierregaard, R. O., Gascon, C., Lovejoy, T. E. & Mesquita, R. (Eds.), Lessons from Amazonia (pp. 31–42). New Haven, CT: Yale University Press.
Gomes, V. H. F., Vieira, I. C. G., Salomão, R. P., & ter Steege, H. (2019). Amazonian tree species threatened by deforestation and climate change. Nature Climate Change, 9, 547–553.
Goudet, J., & Jombart, T. (2022). hierfstat: Estimation and Tests of Hierarchical F-Statistics. R package version 0.5-11. https://CRAN.R-project.org/package=hierfstat
Gruber, B., Unmack, P. J., Berry, O. F., & Georges, A. (2018). “dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing.” Molecular Ecology Resources , 18, 691–699. doi:10.1111/1755-0998.12745.
Haddad, N. M., Brudvig, L. A., Clobert, J., Davies, K. F., Gonzalez, A., Holt, R. D., Lovejoy, T. E., Sexton, J. O., Austin, M. P., Collins, C. D., Cook, W. M., Damschen, E. I., Ewers, R. M., Foster, B. L., Jenkins, C. N., King, A. J., Laurance, W. F., Levey, D. J., Margules, C. R., Melbourne, B. A., Nicholls, A. O., Orrock, J. L., Song, D. -X., & Townshend, J. R. (2015). Habitat fragmentation and its lasting impact on Earth’s ecosystems. Science Advance , 1, e1500052.
Hamabata, T., Kinoshita, G., Kurita, K., Cao, P. -L., Ito, M., Murata, J., Komaki, Y., Isagi, Y., & Makino, T. (2019). Endangered island endemic plants have vulnerable genomes. Communication Biology, 2, 244. https://doi.org/10.1038/s42003-019-0490-7
Hamilton, M. (1999). Tropical tree gene flow and seed dispersal.Nature , 401, 129–130. https://doi.org/10.1038/43597
Hanski, I. (2012). Eco-evolutionary dynamics in a changing world.Annals of the New York Academy of Sciences , 1249, 1–17. https://doi.org/10.1111/j.1749-6632.2011.06419.x
Hanski, I. (2015). Habitat fragmentation and species richness.Journal of Biogeography , 42, 989–993. https://doi.org/10.1111/jbi.12478
Hanski, I., & Gagiotti, O.E. (2004). Ecology, Genetics, and Evolution of Metapopulations. Elsevier, San Diego.
Hanski, I., Zurita, G. A., Bellocq, M. I., & Rybicki, J. (2013). Species-fragmented area relationship. Proccedings National Academy of Science USA , 110, 12715–12720. https://doi.org/10.1073/pnas.1311491110
Hanski, I., Schulz, T., Wong, S., Ahola, V., Roukolainen, A., & Ojanen, S. P. (2017). Ecological and genetic basis of metapopulation persistence of the Glanville fritillary butterfly in fragmented landscapes. Nature Communication,  8, 14504. https://doi.org/10.1038/ncomms14504
He O., & Zhu R-L. (2011). Spore output in selected species of Lejeuneaceae (Marchantiophyta) from China. Cryptogamie, Bryologie , 32, 107-112.
Hedenäs, L., Hylander, K., Lönnell, N., & Bisang, I. (2021). Genetic variation and reproductive patterns in wetland mosses suggest efficient initial colonization of disturbed sites. Ecology and Evolution , 11, 15846– 15859. https://doi.org/10.1002/ece3.8255
Hepenstrick, D., Zemp, N., Widmer, A., & Holderegger, R. (2022). Neither connectivity nor genetic diversity matter in the conservation of a rare fern and a moss on insular erratic boulders. Conservation Genetics,  23 , 193–209. https://doi.org/10.1007/s10592-021-01414-6
Hill, R., Loxterman, J. L., & Aho, K. (2017). Insular biogeography and population genetics of dwarf mistletoe (Arceuthobium americanum ) in the Central Rocky Mountains. Ecosphere , 8, e01810.
Holá, E., Košnar, J., & Kučera, J. (2015). Comparison of genetic structure of epixylic liverwort Crossocalyx Hellerianus  between central European and Fennoscandian populations. PLoS ONE , 10, e0133134. https://doi.org/10.1371/journal.pone.0133134
Honnay, O., Jacquemyn, H., Bossuyt, B., & Hermy, M. (2005). Forest fragmentation effects on patch occupancy and population viability of herbaceous plant species. New Phytologist , 166, 723–736. https://doi.org/10.1111/j.1469-8137.2005.01352.x
Honnay, O., & Bossuyt, B. (2005). Prolonged clonal growth: escape route or route to extinction? Oikos , 108, 427–432. https://doi.org/10.1111/j.0030-1299.2005.13569.x
Hufbauer, R. A., Szűcs, M., Kasyon, E., Youngberg, C., Koontz, M. J., Richards, C., Tuff, T., & Melbourne, B. A. (2015). Three types of rescue can avert extinction in a changing environment. Proccedings National Academy of Science USA, 112, 10557–10562.
Jombart, T., Devillard, S., & Balloux, F. (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics,  11, 94. https://doi.org/10.1186/1471-2156-11-94
Kamvar, Z. N., Tabima, J. F., & Grünwald, N. J. (2014). Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ, 2, e281. doi: 10.7717/peerj.281.
Kamvar, Z. N., Brooks J. C., & Grünwald, N. J. (2015). Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Frontiers in Genetics, 6, 208. doi: 10.3389/fgene.2015.00208
Keenan, K., McGinnity, P., Cross, T. F., Crozier, W.W., & Prodöhl, P. A. (2013). DiveRsity: An R package for the estimation of population genetics parameters and their associated errors. Methods in Ecology and Evolution, 4, 782–788. https://CRAN.R-project.org/package=genetics; DOI: 10.1111/2041-210X.12067
Kuussaari, M., Bommarco, R., Heikkinen, R. K., Helm, A., Krauss, J., Lindborg, R., Öckinger, E., Pärtel, M., Pino, J., Rodà, F., Stefanescu, C., Teder, T., Zobel, M., & Steffan-Dewenter, I. (2009). Extinction debt: a challenge for biodiversity conservation. Trends in Ecology and Evolution , 24, 564–571.
Laenen, B., Désamoré, A., Devos, N., Shaw, A. J., González-Mancebo, J. M., Carine, M. A., & Vanderpoorten, A. (2011). Macaronesia: a source of hidden genetic diversity for post-glacial recolonization of western Europe in the leafy liverwort Radula lindenbergiana .Journal of Biogeography , 38, 631–639. https://doi.org/10.1111/j.1365-2699.2010.02440.x
Laenen, B., Machac, A., Gradstein, S. R., Shaw, B., Patiño, J., Désamoré, A., Goffinet, B., Cox, C. J., Shaw, J., & Vanderpoorten, A. (2016). Geographical range in liverworts: does sex really matter?Journal of Biogeography , 43, 627–635. https://doi.org/10.1111/jbi.12661
Lang, A. S., Gehrmann, T., & Cronberg N. (2021). Genetic diversity and population structure in bryophyte with facultative nannandry.Frontiers in Plant Science, 12, 1664–462X. DOI 10.3389/fpls.2021.517547
Laurance, W. F., Camargo, J. L. C., Regina, C. C., Luizão, R. C. C., Laurance, S. G., Pimm, S. L., Bruna, E. M., Stouffer, P. C., Williamson, G. B., Benítez-Malvido, J., Vasconcelos, H. L., Van Houtan, K. S., Zartman, C. E., Boyle, S. A., Didham, R. K., Andrade, A., & Lovejoy, T. E. (2011). The fate of Amazonian forest fragments: A 32-year investigation. Biological Conservation , 144, 56–67.
Laurance, W. F., Camargo, J. L. C., Fearnside, P. M., Lovejoy, T. E., Williamson, G. B., Mesquita, R. C. G., Meyer, C. F. J., Bobrowiec, P. E. D., & Laurance, S. G. W. (2018). An Amazonian rainforest and its fragments as a laboratory of global change. Biological Reviews , 93, 223–247.
Lapola, D. M., Pinho, P., Barlow, J., Aragão, L. E. O. C., Berenguer, E., Carmenta, R., Liddy, H. M., Seixas, H., Silva, C. V. J., Silva-Junior, C. H. L., Alencar, A. A. C., Anderson, L. O., Armenteras, D., Brovkin, V., Calders, K., Chambers, J., Chini, L., Costa, M. H., Faria, B. L., Fearnside, P. M., Ferreira, J., Gatti, L., Gutierrez-Velez, V. H., Han, Z., Hibbard, K., Koven, C., Lawrence, P., Pongratz, J., Portela, B. T. T., Rounsevell, M., Ruane, A. C., Schaldach, R., da Silva, S. S., von Randow, C. & Walker, W. S. (2023). The drivers and impacts of Amazon forest degradation. Science,379, 6630. doi:10.1126/science.abp8622
Ledent, A., Gauthier, J., Pereira, M., Overson, R., Laenen, B., Mardulyn, P., Gradstein, S. R., de Haan, M., Ballings, P., Van der Beeten, I., Zartman, C. E., & Vanderpoorten, A. (2020). What do tropical cryptogams reveal? Strong genetic structure in Amazonian bryophytes. New Phytologist, 228, 640–650. https://doi.org/10.1111/nph.16720
Levins, R. A. 1969. Some demographic and genetic consequences of environmental heterogeneity for biological control. Bulletin of the Entomological Society of America , 15, 237–240. DOI: 10.1093/besa/15.3.237
Losos, J. B., & Ricklefs, R. E. (2009). The theory of island biogeography revisited. Princeton, NJ: Princeton University Press.
Lovejoy, T. E., Rankin, J. M., Bierregaard, R. O., Brown, K. S., Emmons, L. H., & Van der Voort, M. E. (1984). Ecosystem decay of Amazon forest fragments. In: Nitecki, M. H. (Ed.), Extinctions. University of Chicago Press, Chicago, pp. 295–325.
Lovejoy, T. E., & Nobre, C. (2019). Winds of will: Tipping change in the Amazon. Science Advance, 5, eaba2949.
Lowe, A. J., Boshier, D., Ward, M., Bacles, C. F. E., & Navarro, C. (2005). Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees. Heredity , 95, 255–273.
MacArthur, R. H., & Wilson, E. O. (1967). The theory of island biogeography. Princeton, NJ: Princeton University Press.
Maciel-Silva, A. S., Marques Valio, I. F., & Rydin, H. (2012). Altitude affects the reproductive performance in monoicous and dioicous bryophytes: examples from a Brazilian Atlantic rainforest. AoB PLANTS , pls016. doi:10.1093/aobpla/pls016
Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Research , 27, 209–220. PMID 6018555.
Matricardi, E. A. T., Skole, D. L., Costa, O. B., Pedlowski, M. A., Samek, J. H., & Miguel, E. P. (2020). Long-term forest degradation surpasses deforestation in the Brazilian Amazon. Science , 369, 1378–1382. doi:10.1126/science.abb3021
Mežaka, A., Bader, M. Y., Salazar Allen, N., & Mendieta-Leiva, G. (2020). Epiphyll specialization for leaf and forest successional stages in a tropical lowland rain forest. Journal of Vegetation Science,31, 118–128. https://doi.org/10.1111/jvs.12830
Morris, W. F., Pfister, C. A., Tuljapurkar, S., Haridas, C. V., Boggs, C. L., Boyce, M. S., Bruna, E. M., Church, D. R., Coulson, T., Doak, D. F., Forsyth, S., Gaillard, J. -M., Horvitz, C. C., Kalisz, S., Kendall, B. E., Knight, T. M., Lee, C. T., & Menges, E. S. (2008). Longevity can buffer plant and animal populations against changing climatic variability. Ecology , 89, 19–25. DOI: https://doi.org/10.1890/07-0774.1
Morris, R. J. (2010). Anthropogenic impacts on tropical forest biodiversity: a network structure and ecosystem functioning perspective.Philosophical Transaction of the Royal Society of London, 365, 3709–3718.
Mota de Oliveira, S., & ter Steege, H. (2015). Bryophyte communities in the Amazon forest are regulated by height on the host tree and site elevation. Journal of Ecology  102, 441–450. Doi: https://doi.org/10.1111/1365-2745.12359
Mota de Oliveira, S., Duijm, E., Stech, M., Ruijgrok, J., Polling, M., Barbosa, C. G. G., Cerqueira, G. R., Nascimento, A. H. M., Godoi, R. H. M., Taylor, P. E., Wolff, S., Weber, B., & Kesselmeier, J. (2022). Life is in the air: An expedition into the Amazonian atmosphere.Frontiers in Ecology and Evolution , 10, 789791. doi: 10.3389/fevo.2022.789791
Nazareno, A. G., Alzate-Marin, A. L., & Pereira, R. A. S. (2013). Dioicy, more than monoecy, affects plant spatial genetic structure: the case study of FicusEcology and Evolution,  3, 3495–3508. doi: 10.1002/ece3.739
Nazareno, A. G., Dick, C. W., & Lohmann, L. G. (2019). A biogeographic barrier test reveals a strong genetic structure for a canopy-emergent Amazon tree species. Scientific Reports  9, 18602.
Obbard, D. J., Harris, S. A., & Pannell, J. R. (2006). Sexual Systems and Population Genetic Structure in an Annual Plant: Testing the Metapopulation Model. The American Naturalist, 167, 354–366. DOI: 10.1086/499546
Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Simpson G. L., Solymos, P., Henry, M., Stevens, H., & Wagner, H. (2016). vegan: Community Ecology Package. R package version 2.3–5. https://CRAN.R-project.org/package=vegan.
Paradis, E. (2010). “pegas: an R package for population genetics with an integrated–modular approach.” Bioinformatics , 26, 419–420.
Patiño, J., Werner, O., & González-Mancebo, J. M. (2010). Impact of forest disturbance on the late successional moss Isothecium myosuroides : local-scale variations of genetic diversity and population structure. Journal of Bryology , 32, 220–231.
Patiño, J., Bisang, I., Hedenäs, L., Dirkse, G., Bjarnason, Á.H., Ah-Peng, C., & Vanderpoorten, A. (2013). Baker’s law and the island syndromes in bryophytes. Journal of Ecology , 101, 1245–1255. https://doi.org/10.1111/1365-2745.12136
Patiño, J., Carine, M., Mardulyn, P., Devos, N., Mateo, R. G., González-Mancebo, J. M., Shaw, A. J., & Vanderpoorten, A. (2015). Approximate Bayesian Computation Reveals the Crucial Role of Oceanic Islands for the Assembly of Continental Biodiversity. Systematic Biology , 64, 579–589. https://doi.org/10.1093/sysbio/syv013
Pharo, E. J., & Zartman, C. E. (2007). Bryophytes in a changing landscape: the hierarchical effects of habitat fragmentation on ecological and evolutionary processes. Biological Conservation , 135, 315–325.
Pohjamo, M., Korpelainen, H., & Kalinauskaitė, N. (2008). Restricted gene flow in the clonal hepatic Trichocolea tomentella in fragmented landscapes. Biological Conservation , 141, 1204–1217. https://doi.org/10.1016/j.biocon.2008.02.016.
R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Rochette, N. C., Rivera-Colón, A. G., & Catchen, J. M. (2019). Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Molecular Ecology , 28, 4737–4754. https://doi.org/10.1111/mec.15253
Rochette, N., & Catchen, J. (2017). Deriving genotypes from RAD-seq short-read data using Stacks. Nature Protocols , 12, 2640–2659.
Rosenzweig, M. L. (1995). Species Diversity in Space and Time (Cambridge Univ Press, Cambridge, UK.
Rousset, F. (1997). Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics , 145, 1219–1228. doi: 10.1093/genetics/145.4.1219.
Sala, O. E., Chapin, F. S., Armesto, J. J., Berlow, E., Bloomfield, J., Dirzo, R., Huber-Sanwald, E., Huenneke, L. F., Jackson, R. B., Kinzig, A., Leemans, R., Lodge, D. M., Mooney, H. A., Oesterheld, M., Poff, N. L., Sykes, M. T., Walker, B. H., Walker, M., & Wall, D. H. (2000). Global Biodiversity Scenarios for the Year 2100. Science , 287, 1770–1774.
Schuster R. M. (1983). Phytogeography of the bryophyta.In:  Schuster R. M. (Ed.) New manual of bryologyvol. 1 . Nichinan, Japan: The Hattori Botanical Laboratory, 463–626.
Scott, E. R., Uriarte, M., & Bruna, E. M. (2022). Delayed effects of climate on vital rates lead to demographic divergence in Amazonian forest fragments. Global Change Biology , 28, 463–479. https://doi.org/10.1111/ gcb.15900
Sierra, A. M., Toledo, J. J., Salazar Allen, N., & Zartman, C. E. (2019a). Reproductive traits as predictors of assembly chronosequence patterns in epiphyllous bryophyte metacommunities. Journal of Ecology, 107, 875–886.
Sierra, A. M., Toledo, J. J., Nascimento, H. E., Pereira, M. R., & Zartman, C. E. (2019b). Are extinction debts reflected in temporal changes of life history trait profiles? A fifteen-year reappraisal of bryophyte metacommunities in a fragmented landscape. Biological Conservation, 238, 108218.
Snäll, T., Fogelqvist, J., Ribeiro, P. J., & Lascoux, M. (2004). Spatial genetic structure in two congeneric epiphytes with different dispersal strategies analysed by three different methods. Molecular Ecology  13, 2109–2119.
Sonnleitner, M., Dullinger, S., Wanek, W., & Zechmeister, H. (2009). Microclimatic patterns correlate with the distribution of epiphyllous bryophytes in a tropical lowland rainforest in Costa Rica. Journal of Tropical Ecology , 25, 321–330. https://doi.org/10.1017/S0266467409006002.
Spagnuolo, V., Muscariello, L., Terracciano, S., & Giordano, S. (2007). Molecular biodiversity in the moss Leptodon smithii  (Neckeraceae) in relation to habitat disturbance and fragmentation. Journal of Plant Research,  120, 595–604. https:/10.1007/s10265-007-0097-9
Sundqvist, L., Keenan, K., Zackrisson, M., Prodöhl, P., & Kleinhans, D. (2016). Directional genetic differentiation and relative migration.Ecology and Evolution, 6, 3461–3475. doi: 10.1002/ece3.2096.
Stouffer, P. C. (2020). Birds in fragmented Amazonian rainforest: Lessons from 40 years at the Biological Dynamics of Forest Fragments Project. The Condor , 122, 3, 4 duaa005. https://doi.org/10.1093/condor/duaa005
Taubert, F., Fischer, R., Groeneveld, J., Lehmann, S., Müller, M. S., Rödig, E., Wiegand, T., & Huth, A. (2018). Global patterns of tropical forest fragmentation. Nature,  554, 519–522 https://doi.org/10.1038/nature25508
Thrall, P., Burdon, J., & Murray, B. (2000). The metapopulation paradigm: A fragmented view of conservation biology. In: Young, A. & Clarke, G. (Eds.), Genetics, Demography and Viability of Fragmented Populations (Conservation Biology, pp. 75-96). Cambridge: Cambridge University Press. doi:10.1017/CBO9780511623448.007
Tilman, D., May, R. M., Lehman, C. L., & Nowak, M. A. (1994). Habitat destruction and the extinction debt. Nature , 371, 65–66.
Tjørve, E. (2010). How to resolve the SLOSS debate: Lessons from species-diversity models. Journal of Theoretical Biology , 264, 604–612. https://doi.org/10.1016/j.jtbi.2010.02.009.
Tjørve, E., & Tjørve, K. M. (2017). Species–Area Relationship. In: eLS, John Wiley & Sons, Ltd (Ed.). https://doi-org.acces.bibl.ulaval.ca/10.1002/9780470015902.a0026330
Vanderpoorten, A., Patiño, J., Désamoré, A., Laenen, B., Górski, P., Papp, B., Holá, E., Korpelainen, H., & Hardy, O. (2019). To what extent are bryophytes efficient dispersers? Journal of Ecol ogy, 107, 2149–2154. DOI: https://doi.org/10.1111/1365-2745.13161
Vellend, M., Baeten, L., Becker-Scarpitta, V., McCune, J. L., Messier, J., Myers-Smith, I. H., & Sax, D. F. (2017). Plant Biodiversity Change Across Scales During the Anthropocene. Annual Review in Plant Biology 68, 563–86.
Vellend, M. (2003). Island biogeography of genes and species.American Naturalist, 162, 358–365.
Vellend, M., & Geber, M. A. (2005). Connections between species diversity and genetic diversity. Ecology Letters , 8, 767–781.
Vranckx, G., Jacquemyn, H., Muys, B., & Honnay, O. (2011). Meta-analysis of susceptibility of woody plants to loss of genetic diversity through habitat fragmentation. Conservation Biology , 26, 228–237. doi: 10.1111/j.1523-1739.2011.01778.x.
Wang, S., & Altermatt, F. (2019). Metapopulations revisited: the area-dependence of dispersal matters. Ecology,  100, e02792. 10.1002/ecy.2792
Wang, Y., Zhu, Y., & Wang, Y. (2012). Differences in spatial genetic structure and diversity in two mosses with different dispersal strategies in a fragmented landscape. Journal of Bryology, 34, 9–16. Doi: 10.1179/037366810X12735734836133
Watling, J. I., Arroyo-Rodríguez, V., Pfeifer, M., Baeten, L., Banks-Leite, C., Cisneros, L. M., Fang, R., Hamel-Leigue, A. C., Lachat, T., Leal, I. R., Lens, L., Possingham, H. P., Raheem, D. C., Ribeiro, D. B., Slade, E. M., Urbina-Cardona, J. N., Wood, E. M., & Fahrig, L. (2020). Support for the habitat amount hypothesis from a global synthesis of species density studies. Ecology Letters , 23, 674–681. https://doi.org/10.1111/ele.13471
Whittaker, R. J., Triantis, K. A., & Ladle, R. J. (2008). A general dynamic theory of oceanic island biogeography. Journal of Biogeography, 35, 977–994. DOI: 10.1111/j.1365-2699.2008.01892.x
Whittaker, R. J., Fernández-Palacios, J. M., Matthews, T. J., Borregaard, M. K., & Triantis, K. A. (2017). Island biogeography: Taking the long view of nature’s laboratories. Science, 357, eaam8326. DOI: 10.1126/science.aam8326
Weir, B. S., & Cockerham, C. C. (1984). Estimating F-Statistics, for the analysis of population structure. Evolution , 38, 1358–1370.
Young, A., Boyle, T. & Brown, T. (1996). The population genetic consequences of habitat fragmentation for plants. Trends in Ecology & Evolution, 11, 413–418. Doi : https://doi.org/10.1016/0169-5347(96)10045-8.
Zanatta, F., Engler, R., Collart, F., Broennimann, O., Mateo, R. G., Papp, B., Muñoz, J., Baurain, D., Guisan, A., & Vanderpoorten, A. (2020). Bryophytes are predicted to lag behind future climate change despite their high dispersal capacities. Nature Communication,  11, 5601. https://doi.org/10.1038/s41467-020-19410-8
Zartman, C. E. (2003). Forest fragmentation effects on epiphyllous bryophyte communities of central Amazonia. Ecology, 84, 948–954. https://doi.org/10.1890/0012-9658.
Zartman, C. E., & Nascimento H. E. (2006). Are patch-tracking metacommunites dispersal limited? Inferences from abundance-occupancy patterns of epiphylls in Amazonian forest fragments. Biological Conservation, 127, 46–54. https://doi.org/10.1016/j.biocon.2005.07.012.
Zartman, C. E., & Shaw, A. J. (2006). Metapopulation extinction thresholds in rainforest remnants. The American Naturalist, 167, 177–189. https://doi.org/10.1086/499376.
Zartman, C. E., McDaniel, S. F., & Shaw, A. J. (2006). Experimental habitat fragmentation increases linkage disequilibrium but does not affect genetic diversity or population structure in the Amazonian liverwort Radula flaccida . Molecular Ecology, 15, 2305–2315. https://doi.org/10.1111/j.1365-294X.2006.02929.x
Zartman, C. E., Nascimento, H. E. M., Cagani, K. G., Alvarenga, L. D. P., & Snäll, T. (2012). Finescale changes in connectivity affect the metapopulation dynamics of a bryophyte confined to ephemeral patches.Journal of Ecology , 100, 980–986. https://doi.org/10.1111/j.1365-2745.2012.01969.x.
Zartman, C. E., Amaral, J. A., Figueiredo, J. N., & Dambros, C. S. (2015). Drought impacts survivorship and reproductive strategies of an epiphyllous leafy liverwort in central Amazonia. Biotropica, 47, 172–178
Legends
Tables
Table 1. Summary statistics results of Wilcoxon rank sum exact test of differences in estimated number of colonies between categories considering 1- & 10-ha forest fragments as small patches and 100-ha & continuous forest as large patches and compared between the two years sampled (2000 and 2016). Significant differences with p-value <0.01 and <0.001 are highlighted in bold.
Table 2. Analysis of Molecular Variance (AMOVA) of epiphyllous population in forest fragment and continuous forest for the two filtered dataset by the minimum percentage of individuals across populations required to process a locus. Significant differences with p-value<0.01 and <0.001 are highlighted in bold.
Figures
Figure 1. Expected population genetic outcomes under different metapopulation structure models with variable degree of isolation (connectivity) and patch size. In the non-equilibrium metapopulation patches of equal size are highly isolated, that there is no exchange of migrants between populations. In the classical metapopulation model, patches of equal size present high probability of extinction, but have enough connectivity to allow (re)colonization of unoccupied patches allowing metapopulation persistence. The mainland-island metapopulation present small and large patches, where unidirectional migration to small patches is dependent of the mainland population where extinction rate is low (Island-Mainland). Distances from the mainland will determine the rate of migration represented by the arrow size. In patchy metapopulation, patches of variable size are highly connected (patchy) with high rate of migration among all populations. In the metapopulation models following a patch size and connectivity continuum, a high degree of genetic differentiation will be observed in highly isolated small patches, and in highly connected patches of varying size, the genetic differentiation will be lower (Aycrigg & Garton 2014). Figure is adapted from Aycrigg & Garton 2014.
Figure 2. Population size as the estimated number of epiphyllous bryophyte colonies of the species Radula flaccida andCololejeunea surinamensis per 1-ha study plot. Temporal variation in population size between the year 2000 and 2016 per 1-ha study plots in A. Small Forest patches (1- and 10-ha), and B. in large forests patches (100-ha and continuous forest). C. Population size density distribution comparison between small and large forests patches for the year 2000 and 2016. Mean population size are depicted as follow: orange solid line for 1-ha, orange dashed line for 10-ha, green solid line for 100-ha and green dashed line for continuous forests.
Figure 3. Fine-scale population genetic structure of the speciesRadula flaccida and Cololejeunea surinamensis in an experimental Amazonian fragmented landscape for: A. R. flaccida(Dataset n = 105, -R = 15); B. R. flaccida (Datasetn = 70, -R = 20); C. C. surinamensis (Dataset n = 108, -R = 15); and D. C. surinamensis (Dataset n = 71, -R = 20). Ordination plot of Discriminant Analysis of Principal Components (DAPC) and density plot depicting the two-ordination axis showing the genotype similarity of populations in different forest fragment size and continuous forest. Points represent individuals assigned to their respective size category and 95% ellipse showing confidence interval.
Figure 4. Population genetic differentiation of the species Radula flaccida and Cololejeunea surinamensis in an experimental Amazonian fragmented landscape with the two datasets. MeanF ST pairwise comparison of populations within small patches, between small and large patches, and within large patches for: A. R. flaccida (Dataset n = 105, -R = 15); B.R. flaccida (Dataset n = 70, -R = 20); C. C. surinamensis (Dataset n = 108, -R = 15); and D. C. surinamensis (Dataset n = 71, -R = 20).
Figure 5. Isolation by distance relationship (Fij )FST/1-FST of epiphyll populations and geographic distance (log-transformed) for A. R. flaccida(Dataset n = 105, -R = 15); and B. C. surinamensis(Dataset n = 108, -R = 15). Regression lines correspond to pairwise comparison among populations in small forest patches (1- and 10-ha), populations in large forest patches (100-ha and Continuous Forest), and between small and large forest patches for both species. Symmetrical relative migration network graph using the Nmparameter among small forest patches (1- and 10-ha), and large forest patches (100-ha and Continuous Forest) for C. R. flaccida(Dataset n = 105, -R = 15); and D. C. surinamensis(Dataset n = 108, -R = 15) in an experimental Amazonian fragmented landscape. Filter threshold for the asymmetric values was set to 0.35. Colors corresponds to the patch size as in Figure 3.