Deforestation is the turning point for the spreading of a weedy epiphyte: an IBM approach
1.de Wet, J. M. J. & Harlan, J. R. Weeds and domesticates: Evolution in the man-made habitat. Econ. Bot. 29(2), 99–108. https://doi.org/10.1007/BF02863309 (1975).Article
Google Scholar
2.Ceballos, G. et al. Accelerated modern human—Induced species losses: Entering the sixth mass extinction. Sci. Adv. 1(June), 1–6. https://doi.org/10.1126/sciadv.1400253 (2015).Article
Google Scholar
3.Wilcove, D. S. Nest predation in forest tracts and the decline of migratory songbirds. Ecology 66(4), 1211–1214 (1985).Article
Google Scholar
4.Airoldi, L. & Bulleri, F. Anthropogenic disturbance can determine the magnitude of opportunistic species responses on marine urban infrastructures. PLoS ONE https://doi.org/10.1371/journal.pone.0022985 (2011).Article
PubMed
PubMed Central
Google Scholar
5.Baker, H. G. The evolution of weeds. Annu. Rev. Ecol. Syst. 5, 1–24. https://doi.org/10.2307/2096877 (1974).ADS
Article
Google Scholar
6.Richardson, D. M. et al. Naturalization and invasion of alien plants: Concepts and definitions. Divers. Distrib. 6, 93–107 (2008).Article
Google Scholar
7.van Etten, M. L., Conner, J. K., Chang, S. M. & Baucom, R. S. Not all weeds are created equal: A database approach uncovers differences in the sexual system of native and introduced weeds. Ecol. Evol. 7(8), 2636–2642. https://doi.org/10.1002/ece3.2820 (2017).Article
PubMed
PubMed Central
Google Scholar
8.Booth, B. D. & Swanton, C. J. Assembly theory applied to weed communities 50th Anniversary—Invited Article Assembly theory applied to weed communities. Weed Sci. 50(3), 2–13. https://doi.org/10.1614/0043-1745(2002)050 (2002).CAS
Article
Google Scholar
9.Kuester, A., Conner, J. K., Culley, T. & Baucom, R. S. How weeds emerge: A taxonomic and trait-based examination using United States data. New Phytol. 202(3), 1055–1068. https://doi.org/10.1111/nph.12698 (2014).Article
PubMed
PubMed Central
Google Scholar
10.van Kleunen, M. et al. The ecology and evolution of alien plants. Annu. Rev. Ecol. Evol. Syst. https://doi.org/10.1146/annurev-ecolsys-110617-062654 (2018).Article
Google Scholar
11.de Bona, S. et al. Spatio-temporal dynamics of density-dependent dispersal during a population colonisation. Ecol. Lett. 22, 634–644 (2019).PubMed
Article
Google Scholar
12.Baker, H. G. Self-compatibility and establishment after “long-distance” dispersal. Evolution 9(3), 347. https://doi.org/10.2307/2405656 (1955).Article
Google Scholar
13.Razanajatovo, M. et al. Plants capable of selfing are more likely to become naturalized. Nat. Commun. 7, 13313. https://doi.org/10.1038/ncomms13313 (2016).ADS
CAS
Article
PubMed
PubMed Central
Google Scholar
14.Vallejo-Marín, M., Dorken, M. E. & Barrett, S. C. H. The ecological and evolutionary consequences of clonality for plant mating. Annu. Rev. Ecol. Evol. Syst. 41(1), 193–213. https://doi.org/10.1146/annurev.ecolsys.110308.120258 (2010).Article
Google Scholar
15.Rodger, J. G., Van Kleunen, M. & Johnson, S. D. Pollinators, mates and Allee effects: The importance of self-pollination for fecundity in an invasive lily. Funct. Ecol. 27(4), 1023–1033. https://doi.org/10.1111/1365-2435.12093 (2013).Article
Google Scholar
16.Barrett, S. C. H. & Harder, L. D. The ecology of mating and its evolutionary consequences in seed plants. Annu. Rev. Ecol. Evol. Syst. https://doi.org/10.1146/annurev-ecolsys-110316-023021 (2017).Article
Google Scholar
17.Klimeš, L., Klimešová, J., Hendriks, R. & van Groenendael, J. Clonal plant architecture: A comparative analysis of form and function. In The Ecology and Evolution of Clonal Plants (eds De Kroon, H. & Van Groenendael, J. M.) 1–29 (Backhuys, 1997).
Google Scholar
18.Barrett, S. C. H. Influences of clonality on plant sexual reproduction. Proc. Natl. Acad. Sci. 112(29), 8859–8866. https://doi.org/10.1073/pnas.1501712112 (2015).ADS
CAS
Article
PubMed
PubMed Central
Google Scholar
19.Heywood, J. S. Spatial analysis of genetic variation in plant populations. Annu. Rev. Ecol. Syst. 22, 335–355 (1991).Article
Google Scholar
20.Barrett, S. C. H. Evolution of mating systems: Outcrossing versus selfing. In The Princeton Guide to Evolution (ed. Losos, J. B.) 356–362 (Princeton University Press, 2013).
Google Scholar
21.Barrett, S. C. H., Arunkumar, R. & Wright, S. I. The demography and population genomics of evolutionary transitions to self-fertilization in plants. Philos. Trans. R. Soc. B Biol. Sci. 369(1648), 20130344 (2014).Article
Google Scholar
22.Picó, F. X., Quintana-Ascencio, P. F., Mildén, M., Ehrlén, J. & Pfingsten, I. Modelling the effects of genetics and habitat on the demography of a grassland herb. Basic Appl. Ecol. 10(2), 122–130. https://doi.org/10.1016/j.baae.2008.02.006 (2009).Article
Google Scholar
23.Ellstrand, N. C. & Roose, M. L. Patterns of genotypic diversity in clonal plant species. Am. J. Bot. 74, 123–131 (1987).Article
Google Scholar
24.Loh, R., Scarano, F. R., Alves-Ferreira, M. & Salgueiro, F. Implications of clonality to population genetic structure of the nurse species Aechmea nuducaulis (L.) Griseb. (Bromeliaceae). Bot. J. Linn. Soc. 178, 329–341 (2015).Article
Google Scholar
25.Hedrick, P. W. Purging inbreeding depression and the probability of extinction: Full-sib mating. Heredity 73, 363–372. https://doi.org/10.1038/hdy.1994.183 (1994).Article
PubMed
Google Scholar
26.Arunkumar, R., Ness, R. W., Wright, S. I. & Barrett, S. C. H. The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations. Genetics 199(3), 817–829. https://doi.org/10.1534/genetics.114.172809 (2015).Article
PubMed
Google Scholar
27.Pannell, J. R. & Barrett, S. C. H. Baker’s law revisited: Reproductive assurance in a metapopulation. Evolution 52(3), 657–668. https://doi.org/10.2307/2411261 (1998).Article
PubMed
Google Scholar
28.Hamrick, J. L. & Trapnell, D. W. Using population genetic analyses to understand seed dispersal patterns. Acta Oecologica 37, 641–649 (2011).ADS
Article
Google Scholar
29.Côrtes, M. C. et al. Low plant density enhances gene dispersal in the Amazonian understory herb Heliconia acuminata. Mol. Ecol. 22, 5716–5729 (2013).PubMed
Article
CAS
Google Scholar
30.Trapnell, D. W., Hamrick, J. L., Ishibashi, C. D. & Kartzinel, T. R. Genetic inference of epiphytic orchid colonization; it may only take one. Mol. Ecol. 22, 3680–3692. https://doi.org/10.1111/mec.12338 (2013).Article
PubMed
Google Scholar
31.Chung, M. Y. et al. Fine-scale genetic structure in populations of the spring ephemeral herb Megaleranthis saniculifolia (Ranunculaceae). Flora Morphol. Distrib. Funct. Ecol. Plants 240, 16–24 (2018).
Google Scholar
32.Roberts, N. R., Dalton, P. J. & Jordan, G. J. Epiphytic ferns and bryophytes of Tasmanian tree-ferns: A comparison of diversity and composition between two host species. Austral Ecol. 30(2), 146–154. https://doi.org/10.1111/j.1442-9993.2005.01440.x (2005).Article
Google Scholar
33.Cardelús, C. L. & Chazdon, R. L. Inner-crown microenvironments of two emergent tree species in a lowland wet forest. Biotropica 37(2), 238–244. https://doi.org/10.1111/j.1744-7429.2005.00032.x (2005).Article
Google Scholar
34.Quaresma, A. C., Piedade, M. T. F., Wittmann, F. & ter Steege, H. Species richness, composition, and spatial distribution of vascular epiphytes in Amazonian black-water floodplain forests. Biodivers. Conserv. 27(8), 1981–2002. https://doi.org/10.1007/s10531-018-1520-3 (2018).Article
Google Scholar
35.Claver, F. K., Alaniz, J. R. & Caldíz, D. O. Tillandsia spp.: Epiphytic weeds of trees and bushes. For. Ecol. Manag. 6(4), 367–372. https://doi.org/10.1016/0378-1127(83)90044-0 (1983).Article
Google Scholar
36.Bartoli, C. G., Beltrano, J., Fernández, L. V. & Caldíz, D. O. Control of the epiphytic weeds Tillandsia recurvata and Tillandsia aeranthos with different herbicides. For. Ecol. Manage. 59, 289–294 (1993).Article
Google Scholar
37.Flores-Palacios, A., García-Franco, J. G. & Capistrán-Barradas, A. Biomass, phorophyte specificity and distribution of Tillandsia recurvata in a tropical semi-desert environment (Chihuahuan Desert, Mexico). Plant Ecology and Evolution 148(1), 68–75 (2015).Article
Google Scholar
38.Birge, W. I. The anatomy and some biological aspects of the “ball moss”, Tillandsia recurvata, 1–24. L. Bull. Univ. Tex. 194(20) (1911).39.Smith, L. B. & Downs, R. J. Tillandsioideae (Bromeliaceae). In Flora Neotropica Monograph 14(2), 663–1492 (1977).40.Hewitt, G. M. (1996). Some genetic consequences of ice ages, and their role in speciation. Biological Journal of the Linnaean Society, 58(July), 247–276. Retrieved from papers3://publication/uuid/B9DB7D5E-D6AE-404C-BFFC-9F813345329441.McWilliams, E. Chronology of the Natural Range Expansion of Tillandsia recurvata (Bromeliaceae) in Texas. Contributions to Botany 15(2), 343–346 (1992).42.Flores-Palacios, A., Barbosa-Duchateau, C. L., Valencia-Díaz, S., Capistrán-Barradas, A. & García-Franco, J. G. Direct and indirect effects of Tillandsia recurvata on Prosopis laevigata in the Chihuahua desert scrubland of San Luis Potosi, Mexico. J. Arid Environ. 104, 88–95. https://doi.org/10.1016/j.jaridenv.2014.02.010 (2014).ADS
Article
Google Scholar
43.Benzing, D. H. Bromeliaceae: Profile of an Adaptive Radiation (Cambridge University Press, 2000).Book
Google Scholar
44.Benzing, D. H. Air Plants: Epiphytes and Aerial Gardens (Cornell University Press, 2012).Book
Google Scholar
45.Foster, M. D. Blueprint of the jungle as depicted by the altitude of growth of the Bromeliadswith notes on the culture of certain tropical epiphytes. Bull. N. Y. Bot. Garden 46, 9–16 (1945).
Google Scholar
46.Soltis, D. E., Gilmartin, A. J., Rieseberg, L. & Gardner, S. Genetic variation in the epiphytes Tillandsia ionantha and T. recurvata (Bromeliaceae). Am. J. Bot. 74(4), 531–537 (1987).CAS
Article
Google Scholar
47.Orozco-Ibarrola, O. A., Flores-Hernández, P. S., Victoriano-Romero, E., Corona-López, A. M. & Flores-Palacios, A. Are breeding system and florivory associated with the abundance of Tillandsia species (Bromeliaceae)?. Bot. J. Linn. Soc. 177(1), 50–65. https://doi.org/10.1111/boj.12225 (2015).Article
Google Scholar
48.Chilpa-Galván, N. et al. Seed traits favouring dispersal and establishment of six epiphytic Tillandsia (Bromeliaceae) species. Seed Sci. Res. https://doi.org/10.1017/S0960258518000247 (2018).Article
Google Scholar
49.Southwood, T. & Kennedy, C. Trees as islands. Oikos 41(3), 359–371. https://doi.org/10.2307/3544094 (1983).Article
Google Scholar
50.Burns, K. C. Network properties of an epiphyte metacommunity. J. Ecol. 95(5), 1142–1151 (2007).Article
Google Scholar
51.Trapnell, D. W., Hamrick, J. L. & Nason, J. D. Three-dimensional fine-scale genetic structure of the neotropical epiphytic orchid, Laelia rubescens. Mol. Ecol. 13, 1111–1118 (2004).CAS
PubMed
Article
Google Scholar
52.Torres, E., Riofrío, M.-L. & Iriondo, J. M. Complex fine-scale spatial genetic structure in Epidendrum rhopalostele: an epiphytic orchid. Heredity https://doi.org/10.1038/s41437-018-0139-1 (2018).Article
PubMed
PubMed Central
Google Scholar
53.Victoriano-Romero, E., Valencia-Díaz, A., Toledo-Hernández, V. H. & Flores-Palacios, A. Dispersal limitation of Tillandsia species correlates with rain and host structure in a central Mexican tropical dry forest. PLoS ONE 12(2), e0171614 (2017).PubMed
PubMed Central
Article
CAS
Google Scholar
54.Martins, S. E. (2009). Flora fanerogâmica do estado de São Paulo. FAPESP: Instituto de Botânica.55.Chaves, C. J. N., Dyonisio, J. C. J. C. & Rossatto, D. R. D. R. Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages. AoB Plants 8(October 2015), plw010. https://doi.org/10.1093/aobpla/plw010 (2016).Article
PubMed
PubMed Central
Google Scholar
56.Epps, C. W. & Keyghobadi, N. Landscape genetics in a changing world: Disentangling historical and contemporary influences and inferring change. Mol. Ecol. 24(24), 6021–6040. https://doi.org/10.1111/mec.13454 (2015).Article
PubMed
Google Scholar
57.Cushman, S. A., Shirk, A. & Landguth, E. L. Separating the effects of habitat area, fragmentation and matrix resistance on genetic differentiation in complex landscapes. Landsc. Ecol. 27(3), 369–380. https://doi.org/10.1007/s10980-011-9693-0 (2012).Article
Google Scholar
58.Jackson, N. D. & Fahrig, L. Habitat amount, not habitat configuration, best predicts population genetic structure in fragmented landscapes. Landsc. Ecol. 31(5), 951–968. https://doi.org/10.1007/s10980-015-0313-2 (2016).Article
Google Scholar
59.Grimm, V. & Railsback, S. F. Individual-Based Modelling and Ecology (Princeton University Press, 2005).MATH
Book
Google Scholar
60.Csilléry, K., Blum, M. G. B., Gaggiotti, O. E. & François, O. Approximate Bayesian Computation (ABC) in practice. Trends Ecol. Evol. 25(7), 410–418. https://doi.org/10.1016/j.tree.2010.04.001 (2010).Article
PubMed
Google Scholar
61.Udupa, S. M. & Baum, M. High mutation rate and mutational bias at (TAA)n microsatellite loci in chickpea (Cicer arietinum L.). Mol. Genet. Genom. 265(6), 1097–1103. https://doi.org/10.1007/s004380100508 (2001).CAS
Article
Google Scholar
62.Anmarkrud, J. A., Kleven, O., Bachmann, L. & Lifjeld, J. T. Microsatellite evolution: Mutations, sequence variation, and homoplasy in the hypervariable avian microsatellite locus HrU10. BMC Evol. Biol. 8(1), 1–10. https://doi.org/10.1186/1471-2148-8-138 (2008).CAS
Article
Google Scholar
63.Marriage, T. N. et al. Direct estimation of the mutation rate at dinucleotide microsatellite loci in Arabidopsis thaliana (Brassicaceae). Heredity 103(4), 310–317. https://doi.org/10.1038/hdy.2009.67 (2009).CAS
Article
PubMed
Google Scholar
64.Bernal, R., Valverde, T. & Hernández-Rosas, L. Habitat preference of the epiphyte Tillandsia recurvata (Bromeliaceae) in a semi-desert environment in Central Mexico. Can. J. Bot. 83(10), 1238–1247 (2005).Article
Google Scholar
65.Chaves, C. J. & Rossatto, D. R. Unravelling intricate interactions among atmospheric bromeliads with highly overlapping niches in seasonal systems. Plant Biol. 22(2), 243–251 (2020).CAS
PubMed
Article
Google Scholar
66.Vekemans, X. & Hardy, O. J. New insights from fine-scale spatial genetic structure analyses in plant populations. Mol. Ecol. 13(4), 921–935. https://doi.org/10.1046/j.1365-294X.2004.02076.x (2004).CAS
Article
PubMed
Google Scholar
67.Ward, S. Genetic analysis of invasive plant populations at different spatial scales. Biol. Invasions 8(3), 541–552. https://doi.org/10.1007/s10530-005-6443-8 (2006).Article
Google Scholar
68.Pettengill, J. B., Briscoe Runquist, R. D. & Moeller, D. A. Mating system divergence affects the distribution of sequence diversity within and among populations of recently diverged subspecies of Clarkia xantiana (Onagraceae). Am. J. Bot. 103(1), 99–109. https://doi.org/10.3732/ajb.1500147 (2016).CAS
Article
PubMed
Google Scholar
69.Atwater, D. Z., Fletcher, R. A., Dickinson, C. C., Paterson, A. H. & Barney, J. N. Evidence for fine-scale habitat specialization in an invasive weed. J. Plant Ecol. 11(2), 189–199. https://doi.org/10.1093/jpe/rtw124 (2018).Article
Google Scholar
70.Li, J. & Dong, M. Fine-scale clonal structure and diversity of invasive plant Mikania micrantha H.B.K. and its plant parasite Cuscuta campestris Yunker. Biol. Invasions 11(3), 687–695. https://doi.org/10.1007/s10530-008-9283-5 (2009).MathSciNet
Article
Google Scholar
71.Ren, M. X., Cafasso, D., Cozzolino, S. & Pinheiro, F. Extensive genetic differentiation at a small geographical scale: Reduced seed dispersal in a narrow endemic marsh orchid, Anacamptis robusta. Bot. J. Linn. Soc. 183(3), 429–438. https://doi.org/10.1093/botlinnean/bow017 (2017).Article
Google Scholar
72.Barluenga, M. et al. Fine-scale spatial genetic structure and gene dispersal in Silene latifolia. Heredity 106(1), 13–24. https://doi.org/10.1038/hdy.2010.38 (2011).CAS
Article
PubMed
Google Scholar
73.Charbonneau, A. et al. Weed evolution: Genetic differentiation among wild, weedy, and crop radish. Evol. Appl. https://doi.org/10.1111/eva.12699 (2018).Article
PubMed
PubMed Central
Google Scholar
74.Sagnard, F., Oddou-Muratorio, S., Pichot, C., Vendramin, G. G. & Fady, B. Effects of seed dispersal, adult tree and seedling density on the spatial genetic structure of regeneration at fine temporal and spatial scales. Tree Genet. Genomes 7(1), 37–48. https://doi.org/10.1007/s11295-010-0313-y (2011).Article
Google Scholar
75.Counsens, R. & Mortimer, M. Dynamics of Weed Populations (Cambridge University Press, 1995).Book
Google Scholar
76.Loreau, M. et al. Unifying sources and sinks in ecology and Earth sciences. Biol. Rev. 88, 365–379 (2013).PubMed
Article
Google Scholar
77.dos Santos, L. S. et al. Generalized Allee effect model. Theory Biosci. 133, 117–124 (2014).PubMed
Google Scholar
78.Spruch, L. et al. Modeling community assembly on growing habitat “islands”: A case study on trees and their vascular epiphyte communities. Theor. Ecol. 12, 1–17 (2019).Article
Google Scholar
79.Einzmann, H. J. R. & Zotz, G. “No signs of saturation”: long-term dynamics of vascular epiphyte communities in a human-modified landscape. Biodivers. Conserv. 26, 1393–1410 (2017).Article
Google Scholar
80.Belinchón, R., Harrison, P. J., Mair, L., Várkonyi, G. & Snäll, T. Local epiphyte establishment and future metapopulation dynamics in landscapes with different spatiotemporal properties. Ecology 98(3), 741–750. https://doi.org/10.1002/ecy.1686 (2017).Article
PubMed
Google Scholar
81.Vergara-Torres, C. A., Pacheco-Álvarez, M. C. & Flores-Palacios, A. Host preference and host limitation of vascular epiphytes in a tropical dry forest of central Mexico. J. Trop. Ecol. 26(6), 563–570. https://doi.org/10.1017/S0266467410000349 (2010).Article
Google Scholar
82.Barrett, S. C. H. & Kohn, J. R. Genetic and evolutionary consequences of small population size in plants: Implications for conservation. In Genetics and Conservation of Rare Plants (eds Falk, D. A. & Holsinge, K. E.) 3–30 (Oxford University Press, 1991).
Google Scholar
83.Nathan, R., Horn, H. S., Chave, J. & Levin, S. A. Mechanistic models for tree seed dispersal by wind in dense forests and open landscapes. In Seed Dispersal and Frugivory-Ecologie, Evolution, Conservation 69–82 (2002). https://doi.org/10.1079/9780851995250.006984.Cousens, R. et al. Dispersal in Plants. A Population Perspective (Oxford University Press, 2008).Book
Google Scholar
85.Snäll, T., Ehrlén, J. & Rydin, H. Colonization-extinction dynamics of an epiphyte metapopulation in a dynamic landscape. Ecology 86(1), 106–115 (2005).Article
Google Scholar
86.Ruiz-Cordova, J. P., Toledo-Hernández, V. H. & Flores-Palacios, A. The effect of substrate abundance in the vertical stratification of bromeliad epiphytes in a tropical dry forest (Mexico). Flora Morphol. Distrib. Funct. Ecol. Plants 209(8), 375–384. https://doi.org/10.1016/j.flora.2014.06.003 (2014).Article
Google Scholar
87.Flores-Palacios, A., Bustamante-Molina, A. B., Corona-López, A. M. & Valencia-Díaz, S. Seed number, germination and longevity in wild dry forest Tillandsia species of horticultural value. Scientia Hortic. 187, 72–79 (2015).Article
Google Scholar
88.Goodman, R., & Herold, M. (2014). Why maintaining tropical forests is essential and urgent for a stable climate. Center for Global Development Working Paper, (385).89.Seymour, F. & Busch, J. Why Forests? Why Now?: The Science, Economics, and Politics of Tropical Forests and Climate Change (Brookings Institution Press, 2016).
Google Scholar
90.Stephenson, N. L. et al. Rate of tree carbon accumulation increases continuously with tree size. Nature 507(7490), 90–93 (2014).ADS
CAS
PubMed
Article
Google Scholar
91.Tel-Zur, N., Abbo, S., Myslabodsky, D. & Mizrahi, Y. Modified CTAB procedure for DNA isolation from epiphytic cacti of genera Hylocereus and Selenicereus (Cactaceae). Plant Mol. Biol. Rep. 17, 249–254 (1999).CAS
Article
Google Scholar
92.Chaves, C. J. N., Aoki-Gonçalves, F., Leal, B. S. S., Rossatto, D. R. & Palma-Silva, C. Transferability of nuclear microsatellite markers to the atmospheric bromeliads Tillandsia recurvata and T. aeranthos (Bromeliaceae). Braz. J. Bot. 41, 931–935. https://doi.org/10.1007/s40415-018-0494-4 (2018).Article
Google Scholar
93.Keenan, K., Mcginnity, P., Cross, T. F., Crozier, W. W. & Prodöhl, P. A. DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors. Methods Ecol. Evol. https://doi.org/10.1111/2041-210X.12067 (2013).Article
Google Scholar
94.Slatkin, M. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139, 457–462 (1995).CAS
PubMed
PubMed Central
Article
Google Scholar
95.Nei, M. Genetic distances between populations. Am. Nat. 106, 283–292 (1972).Article
Google Scholar
96.Edwards, A. W. F. Distance between populations on the basis of gene frequencies. Biometrics 27, 873–881 (1971).CAS
PubMed
Article
Google Scholar
97.Reynolds, J. B., Weir, B. S. & Cockerham, C. C. Estimation of the coancestry coefficient: Basis for a short-term genetic distance. Genetics 105, 767–779 (1983).CAS
PubMed
PubMed Central
Article
Google Scholar
98.Kamvar, Z. N., Tabima, J. F. & Grünwald, N. J. Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ https://doi.org/10.7717/peerj.281 (2014).Article
PubMed
PubMed Central
Google Scholar
99.Paradis, E. pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26, 419–420 (2010).CAS
PubMed
Article
Google Scholar
100.Excoffier, L., Smouse, P. E. & Quattro, J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131, 479–491. https://doi.org/10.1007/s00424-009-0730-7 (1992).CAS
Article
PubMed
PubMed Central
Google Scholar
101.Loiselle, B. A., Sork, V. L., Nason, J. & Graham, C. Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am. J. Bot. 82(11), 1420–1425 (1995).Article
Google Scholar
102.Bailleul, D., Stoeckel, S. & Arnaud-Haond, S. RClone: A package to identify MultiLocus Clonal Lineages and handle clonal data sets in r. Methods Ecol. Evol. 7(8), 966–970. https://doi.org/10.1111/2041-210X.12550 (2016).Article
Google Scholar
103.Harrison, S. et al. Beta diversity on geographic gradients in Britain. J. Anim. Ecol. 61(1), 151–158 (1992).Article
Google Scholar
104.Jost, L. Partitioning diversity into independent alpha and beta components. Ecology 88(10), 2427–2439. https://doi.org/10.1890/07-1861.1 (2007).Article
PubMed
Google Scholar
105.Charney, N. & Record, S. Vegetarian: Jost diversity measures for community data. https://cran.r-project.org/web/packages/vegetarian/index.html (2012). Accessed Jul 2018.106.Wilensky, U. NetLogo (Northwestern University, Center for Connected Learning and Computer-Based Modeling, 1999).
Google Scholar
107.Grimm, V. et al. A standard protocol for describing individual-based and agent-based models. Ecol. Model. 198(1–2), 115–126. https://doi.org/10.1016/j.ecolmodel.2006.04.023 (2006).Article
Google Scholar
108.Grimm, V. et al. The ODD protocol: A review and first update. Ecol. Model. 221(23), 2760–2768. https://doi.org/10.1016/j.ecolmodel.2010.08.019 (2010).Article
Google Scholar
109.Kooijman, B. & Kooijman, S. A. L. M. Dynamic Energy Budget Theory for Metabolic Organisation (Cambridge University Press, 2010).
Google Scholar
110.Sibly, R. M. et al. Representing the acquisition and use of energy by individuals in agent-based models of animal populations. Methods Ecol. Evol. 4(2), 151–161 (2013).Article
Google Scholar
111.Johnston, A. S. A., Hodson, M. E., Thorbek, P., Alvarez, T. & Sibly, R. M. An energy budget agent-based model of earthworm populations and its application to study the effects of pesticides. Ecol. Model. 280, 5–17 (2014).CAS
Article
Google Scholar
112.van der Vaart, E., Johnston, A. S. A. & Sibly, R. M. Predicting how many animals will be where: How to build, calibrate and evaluate individual-based models. Ecol. Model. 326, 113–123 (2016).Article
Google Scholar
113.Garza, J. C. & Williamson, E. G. Detection of reduction in population size using data from microsatellite loci. Mol. Ecol. 10, 305–318 (2001).CAS
PubMed
Article
Google Scholar
114.Excoffier, L., Laval, G. & Schneider, S. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evol. Bioinform. Online 1, 47–50 (2005).CAS
Article
Google Scholar
115.Csilléry, K., François, O. & Blum, M. G. abc: An R package for approximate Bayesian computation (ABC). Methods Ecol. Evol. 3(3), 475–479 (2012).Article
Google Scholar
116.Pastur, G. M., Lencinas, M. V., Cellini, J. M. & Mundo, I. Diameter growth: Can live trees decrease?. Forestry 80(1), 83–88. https://doi.org/10.1093/forestry/cpl047 (2007).Article
Google Scholar More