References
Alahuhta, J., Toivanen, M. and Hjort, J., 2020.
Geodiversity-biodiversity relationship needs more empirical evidence.
Nature Ecology and Evolution 4, pp.2–3.
Anderson, C.B., 2018. Biodiversity monitoring, earth observations and
the ecology of scale. Ecology letters, 21(10), pp.1572-1585.
Anderson, S.C., Elsen, P.R., Hughes, B.B., Tonietto, R.K., Bletz, M.C.,
Gill, D.A., Holgerson, M.A., Kuebbing, S.E., McDonough MacKenzie, C.,
Meek, M.H. and Veríssimo, D., 2021. Trends in ecology and conservation
over eight decades. Frontiers in Ecology and the Environment; doi:
10.1002/fee.2320
Araújo, M.B., Anderson, R.P., Márcia Barbosa, A., Beale, C.M., Dormann,
C.F., Early, R., Garcia, R.A., Guisan, A., Maiorano, L., Naimi, B. and
O’Hara, R.B., 2019. Standards for distribution models in biodiversity
assessments. Sci. Adv. 5, pp.1–12.
Austin, M.P., 2013. Vegetation and environment: discontinuities and
continuities. In: van der Maarel, E. and Franklin, Vegetation Ecology,
Second Edition. John Wiley and Sons, Ltd.
Baveye, P.C., Chalhoub, M., Choquet, P., and Montagne, D., 2018. Is the
focus on “ecosystems” a liability in the research on nature’s
services? Front. Ecol. Evol. 6:226. doi: 10.3389/fevo.2018.00226
Blew, R.D., 1996. On the definition of ecosystem. Ecological Society of
America Bulletin 77, pp.171–173.
Bonan, G.B. and Doney, S.C., 2018. Climate, ecosystems, and planetary
futures: The challenge to predict life in Earth system models. Science
359, eaam8328.
Brodie, S.J., Thorson, J.T., Carroll, G., Hazen, E.L., Bograd, S.,
Haltuch, M.A., Holsman, K.K., Kotwicki, S., Samhouri, J.F.,
Willis‐Norton, E and Selden, R.L., 2020. Trade‐offs in covariate
selection for species distribution models: a methodological comparison.
Ecography, 43(1), pp.11-24.
Bryn, A., Bekkby, T., Rinde, E., Gundersen, H. and Halvorsen, R., 2021.
Reliability in distribution modeling—A synthesis and step-by-step
guidelines for improved practice. Frontiers in Ecology and Evolution,
pp.830.
Bullock, J.M.,
Fuentes‐Montemayor, E., McCarthy, B., Park, K., Hails, R.S., Woodcock,
B.A., Watts, K., Corstanje, R. and Harris, J., 2022. Future restoration
should enhance ecological complexity and emergent properties at multiple
scales. Ecography, doi: 10.1111/ecog.05780.
Cadenasso, M.L., Pickett, S.T., Weathers, K.C. and Jones, C.G., 2003. A
framework for a theory of ecological boundaries. BioScience, 53(8),
pp.750-758.
Caron-Lormier, G., Bohan, D.A., Hawes, C., Raybould, A., Haughton, A.J.,
Humphry, R.W., 2009. How might we model an ecosystem? Ecol. Model. 220,
pp.1935–1949.
Convention on Biological Diversity, 2021. First draft of the post-2020
global biodiversity framework. United Nations Convention on Biological
Diversity.
Chao, A. and Jost, L., 2012. Coverage‐based rarefaction and
extrapolation: standardizing samples by completeness rather than size.
Ecology, 93(12), pp.2533-2547.
Cogbill, C.V., Thurman, A.L., Williams, J.W., Zhu, J., Mladenoff, D.J.
and Goring, S.J., 2018. A retrospective on the accuracy and precision of
plotless forest density estimators in ecological studies. Ecosphere,
9(4), p.e02187.
Currie, W.S., 2011. Units of nature or processes across scales? The
ecosystem concept at age 75. New Phytol. 190, pp.21 –34.
D’Amen, M.D., Rahbek, C., Zimmerman, N.E., Guisan, A. 2017. Spatial
predictions at the community level: from current approaches to future
frameworks. Biol. Rev., 92, pp.169 – 187.
Dansereau, G., Legendre, P. and Poisot, T., 2022. Evaluating ecological
uniqueness over broad spatial extents using species distribution
modelling. Oikos, 2022(5), p.e09063.
DeAngelis, D. L., and Yurek, S. 2016. Spatially explicit modeling in
ecology: A review. Ecosystems, 20, pp.284–300.
Dietze, M., 2017. Ecological Forecasting. Princeton Univ Press,
Princeton.
Di Minin, E., Correia, R.A. and Toivonen, T., 2021. Quantitative
conservation geography. Trends in Ecology & Evolution 37, pp.42–52.
Dor-Haim, S., Orenstein, D.E. and Shachak, M., 2019. Web of interactions
among diversity approaches to identify ecosystem essential variables:
Negev Highlands case study. Ecosphere 10(11):e02906. 10.1002/ecs2.2906
D’Urban Jackson, T., Williams, G.J., Walker-Springett, G. and Davies,
A.J., 2020. Three-dimensional digital mapping of ecosystems: a new era
in spatial ecology. Proceedings of the Royal Society B, 287(1920),
p.20192383.
Evans, M. R., 2012. Modelling ecological systems in a changing world.
Phil. Trans. R. Soc. B 367, pp181–190.
Ferrier, S. and Guisan, A., 2006. Spatial modelling of biodiversity at
the community level. J. Appl. Ecol. 43, pp.393–404.
Frazier, A.E., 2022. Scope and its role in advancing a science of
scaling in landscape ecology. Landscape Ecology, pp.1-7.
Fulton, E.A., Blanchard, J.L., Melbourne-Thomas, J., Plagányi, É.E. and
Tulloch, V.J., 2019. Where the Ecological Gaps Remain, a Modelers’
Perspective. Front. Ecol. Evol. 7, pp.44–56
Gallagher, C.A., Chudzinska, M., Larsen‐Gray, A., Pollock, C.J., Sells,
S.N., White, P.J. and Berger, U., 2021. From theory to practice in
pattern‐oriented modelling: identifying and using empirical patterns in
predictive models. Biological Reviews, 96(5), pp.1868-1888.
Geary, W.L., Bode, M., Doherty,
T.S., Fulton, E.A., Nimmo, D.G., Tulloch, A.I., Tulloch, V.J. and
Ritchie, E.G., 2020. A guide to ecosystem models and their environmental
applications. Nat. Ecol. Evol. 4, pp.1459–1471
Gignoux, J., Davies, I., Flint, S., Zucker, J-D., 2011. The ecosystem in
practice: Interest and problems of an old definition for constructing
ecological models. Ecosystems 14(7), pp.1039–1054.
Gounand, I., Harvey, E., Little, C.J. and Altermatt, F., 2018.
Meta-ecosystems 2.0: rooting the theory into the field. Trends in
Ecology & Evolution, 33(1), pp.36-46. Guisan, A., Thuiller, W.,
Zimmermann, N.E., 2017. Habitat Suitability and Distribution Models:
With Applications in R. Cambridge University Press.
Guillera‐Arroita, G., Lahoz‐Monfort, J.J., Elith, J., Gordon, A.,
Kujala, H., Lentini, P.E., McCarthy, M.A., Tingley, R. and Wintle, B.A.,
2015. Is my species distribution model fit for purpose? Matching data
and models to applications. Global Ecology and Biogeography, 24(3),
pp.276-292.
Guisan, A., Thuiller, W., Zimmermann, N.E. 2017. Habitat Suitability and
Distribution Models: With Applications in R. Cambridge University Press.
Halvorsen, R., Skarpaas, O., Bryn, A., Bratli, H., Erikstad, L.,
Simensen, T. and Eriksen, E.L., 2020. Towards a systematics of
ecodiversity: the EcoSyst framework. Global Ecol. Biogeogr.
10.1111/geb.13164
Harris, D. J., 2015. Generating realistic assemblages with a joint
species distribution model. Methods in Ecology and Evolution 6,
pp.465–473.
Harvey, E., Marleau, J.N.,
Gounand, I., Leroux, S.J., Firkowski, C.R., Altermatt, F., Blanchet,
F.G., Cazelles, K., Chu, C., d’Aloia, C. and Donelle, L., 2021. A
general meta-ecosystem model to predict ecosystem function at landscape
extents. hal-03407501
Hill, N., Woolley, S.N., Foster, S., Dunstan, P.K., McKinlay, J.,
Ovaskainen, O. and Johnson, C., 2020. Determining marine bioregions: A
comparison of quantitative approaches. Methods in Ecology and
Evolution , 11 (10), pp.1258-1272.
Hjort, J., Tukiainen, H., Salminen, H., Kemppinen, J., Kiilunen, P.,
Snåre, H., Alahuhta, J. and Maliniemi, T., 2022. A methodological guide
to observe local‐scale geodiversity for biodiversity research and
management. Journal of Applied Ecology. 00: pp.1-13.
Holling, C.S., 1992. Cross-scale morphology, geometry and dynamics of
ecosystems. Ecological Monographs 62, 447–502.
Houlahan, J., McKinney S., Anderson T., McGill B. 2017. The priority of
prediction in ecological understanding. Oikos 126: pp.1–7.
Hui, F.K.C., Taskinen, S., Pledger, S., Foster, S.D. and Warton, D.I.,
2015. Model-based approaches to unconstrained ordination. Methods in
Ecology and Evolution, 6, pp.399–411.
Johnson, E.A. and Martin, Y.E. (eds.), 2016. A Biogeoscience Approach to
Ecosystems, Cambridge Univ. Press, UK, 2016.
Jørgensen, S.E., 2016. Ecological Model Types. Developments in
Environmental Modelling, 28. Elsevier
Keith, D.A., Rodríguez, J.P., Rodríguez-Clark, K.M., Nicholson, E.,
Aapala, K., Alonso, A., Asmussen, M., Bachman, S., Basset, A., Barrow,
E.G. and Benson, J.S., 2013. Scientific Foundations for an IUCN Red List
of Ecosystems. PLoS ONE 8(5): e62111. doi:10.1371/ journal.pone. 0062111
Keith, D.A., Ferrer-Paris, J.R.,
Nicholson, E., Bishop, M.J., Polidoro, B.A., Ramirez-Llodra, E., Tozer,
M.G., Nel, J.L., Mac Nally, R., Gregr, E.J. and Watermeyer, K.E., 2022.
A function-based typology for Earth’s ecosystems. Nature, pp.1-6.
Kissling, W.D., Walls, R., Bowser, A., Jones, M.O., Kattge, J., Agosti,
D., Amengual, J., Basset, A., Van Bodegom, P.M., Cornelissen, J.H. and
Denny, E.G., 2018. Towards global data products of Essential
Biodiversity Variables on species traits. Nature ecology and evolution,
2(10), pp.1531-1540.
König, C., Weigelt, P., Schrader, J., Taylor, A., Kattge, J. and Kreft,
H., 2019. Biodiversity data integration—the significance of data
resolution and domain. PLoS biology, 17(3), p.e3000183.
König, C., Wüest, R.O., Graham, C.H., Karger, D.N., Sattler, T.,
Zimmermann, N.E. and Zurell, D., 2021. Scale dependency of joint species
distribution models challenges interpretation of biotic interactions.
Journal of Biogeography, 48(7), pp.1541-1551.
Levin, S.A., 1992. The problem of pattern and scale in ecology. Ecology,
73(6), pp.1943–1967.
Leroux, S.J., and Loreau, M., 2012. Dynamics of reciprocal pulsed
subsidies in local and meta-ecosystems. Ecosystems 15, pp.48-59.
Leroux, S.J., Wal, E.V., Wiersma, Y.F., Charron, L., Ebel, J.D., Ellis,
N.M., Hart, C., Kissler, E., Saunders, P.W., Moudrá, L. and Tanner,
A.L., 2017. Stoichiometric distribution models: Ecological stoichiometry
at the landscape extent. Ecol. Lett. 20, 1495–1506. doi:
10.1111/ele.12859
Loreau, M., 2010. Linking biodiversity and ecosystems: towards a
unifying ecological theory. Philos. Trans. R. Soc. B: Biol. Sci.365,
pp.49–60.
Loreau, M., 2020. Ecosystem. In: Dobson, A. Tilman, D. and Holt, R. D.
(Eds.), Unsolved Problems in Ecology. Princeton University Press,
Princeton, USA.
Loreau, M., Mouquet, N. and Holt, R.D., 2003. Meta-ecosystems: a
theoretical framework for a spatial ecosystem ecology. Ecol. Lett., 6,
pp.673–679.
Lyons, M.B., Foster, S.D. and Keith, D.A., 2017. Simultaneous vegetation
classification and mapping at large spatial scales. Journal of
Biogeography, 44(12), pp.2891-2902.
Massol, F., Gravel, D., Mouquet, N., Cadotte, M., Fukami, T. and
Leibold, M., 2011. Linking community and ecosystem dynamics through
spatial ecology. Ecology Letters,14, pp.313–323.
McIntire, E.J., Chubaty, A.M., Cumming, S.G., Andison, D., Barros, C.,
Boisvenue, C., Haché, S., Luo, Y., Micheletti, T. and Stewart, F.E.,
2022. PERFICT: A Re‐imagined foundation for predictive ecology. Ecology
Letters.
Metzger, M.J., Brus, D.J., Bunce, R.G.H., Carey, P.D., Gonçalves, J.,
Honrado, J.P., Jongman, R.H.G., Trabucco, A. and Zomer, R., 2013.
Environmental stratifications as the basis for national, European and
global ecological monitoring. Ecological Indicators, 33, pp.26-35.
Meyer, H. and Pebesma, E., 2021. Predicting into unknown space?
Estimating the area of applicability of spatial prediction models.
Methods in Ecology and Evolution, 12(9), pp.1620-1633.
Miller, J.R., Turner, M.G., Smithwick, E.A., Dent, C.L. and Stanley,
E.H., 2004. Spatial extrapolation: the science of predicting ecological
patterns and processes. BioScience, 54(4), pp.310-320.
Mod, H.K., Chevalier, M., Luoto, M. and Guisan, A., 2020. Scale
dependence of ecological assembly rules: Insights from empirical
datasets and joint species distribution modelling. Journal of Ecology,
108(5), pp.1967-1977.
Mokany, K., Ferrier, S., Connolly, S.R., Dunstan, P.K., Fulton, E.A.,
Harfoot, M.B., Harwood, T.D., Richardson, A.J., Roxburgh, S.H.,
Scharlemann, J.P. and Tittensor, D.P., 2016. Integrating modelling of
biodiversity composition and ecosystem function. Oikos 125, pp.10–19
Mokany, K., Ware, C., Woolley, S.N., Ferrier, S. and Fitzpatrick, M.C.,
2022. A working guide to harnessing generalized dissimilarity modelling
for biodiversity analysis and conservation assessment. Global Ecology
and Biogeography 00: pp.1-20.
Mouquet, N., Lagadeuc, Y., Devictor, V., Doyen, L., Duputié, A.,
Eveillard, D., Faure, D., Garnier, E., Gimenez, O., Huneman, P. and
Jabot, F., 2015. Predictive ecology in a changing world. Journal of
Applied Ecology 52: pp.1293-1310.
Nash, K.L., Allen, C.R., Angeler, D.G., Barichievy, C., Eason, T.,
Garmestani, A.S., Graham, N.A., Granholm, D., Knutson, M., Nelson, R.J.
and Nyström, M., 2014. Discontinuities, cross-scale patterns, and the
organization of ecosystems. Ecology, 95, pp.654–667.
Newman, E.A., Kennedy, M.C., Falk, D.A. and McKenzie, D., 2019. Scaling
and complexity in landscape ecology. Frontiers in Ecology and Evolution,
7, pp.293.
Nieto-Lugilde, D., Maguire, K. C., Blois, J. L., Williams, J. W., and
Fitzpatrick, M. C. 2018. Multiresponse algorithms for community-level
modelling: Review of theory, applications, and comparison to species
distribution models. Methods in Ecology and Evolution, 9, pp.834 – 848.
Norberg, A., Abrego, N., Blanchet, F. G., Adler, F. R., Anderson, B. J.,
Anttila, J., Ovaskainen, O., 2019. A comprehensive evaluation of
predictive performance of 33 species distribution models at species and
community levels. Ecological Monographs, 89(3), e01370.
https://doi.org/10.1002/ecm.1370
O’Neill, R.V. 2001. Is it time to bury the ecosystem concept? (with full
military honors, of course!). Ecology 82, pp.3275–84.
Ovaskainen, O., Tikhonov, G., Norberg, A., Blanchet, F.G., Duan, L.,
Dunson, D., Roslin, T., Abrego, N., 2017. How to make more out of
community data? A conceptual framework and its implementation as models
and software. Ecol. Lett. 20, pp.561–576. (doi:10. 1111/ele.12757)
Ovaskainen, O. and Abrego, N., 2020. Joint Species Distribution
Modelling – With Applications in R. Cambridge University Press.
Pasetto, D., Arenas‐Castro, S., Bustamante, J., Casagrandi, R.,
Chrysoulakis, N., Cord, A.F., Dittrich, A., Domingo‐Marimon, C., El
Serafy, G., Karnieli, A. and Kordelas, G.A., 2018. Integration of
satellite remote sensing data in ecosystem modelling at local scales:
Practices and trends. Methods in Ecology and Evolution, 9(8),
pp.1810-1821.
Perino, A., Pereira, H.M., Felipe‐Lucia, M., Kim, H., Kühl, H.S.,
Marselle, M.R., Meya, J.N., Meyer, C., Navarro, L.M., van Klink, R. and
Albert, G., 2022. Biodiversity post-2020: Closing the gap between global
targets and national-level implementation. Conservation Letters. 2022;
e12848. https://doi.org/10.1111/conl.12848
Peterson, G.D. 2002. Contagious disturbance, ecological memory, and the
emergence of landscape pattern. Ecosystems 5, 329–338
Pickett, S.T.A. and Cadenasso, M.L., 1995. Landscape ecology: Spatial
heterogeneity in ecological systems. Science 269. pp.331–334.
Pickett, S.T.A. and Cadenasso, M.L., 2002. The ecosystem as a
multidimensional concept: meaning, model, and metaphor. Ecosystems 5,
pp.1-10.
Pinto-Ledezma, J.N. and Cavender-Bares, J., 2021. Predicting species
distributions and community composition using satellite remote sensing
predictors. Scientific Reports, 11(1), pp.1-12.
Poggiato, G., Münkemüller, T., Bystrova, D., Arbel, J., Clark, J.S. and
Thuiller, W., 2021. On the interpretations of joint modeling in
community ecology. Trends in Ecology & Evolution, 36(5), pp.391-401.
Pollock, L.J., O’connor, L.M., Mokany, K., Rosauer, D.F., Talluto, M.V.
and Thuiller, W., 2020. Protecting Biodiversity (in all its Complexity):
New Models and Methods. Trends in Ecology & Evolution 35(12),
pp.1119–1128
Regos, A., Gagne, L., Alcaraz-Segura, D., Honrado, J.P. and Domínguez,
J., 2019. Effects of species traits and environmental predictors on
performance and transferability of ecological niche models. Scientific
reports, 9(1), pp.1-14.
Richter, D.B., and Billings, S.A., 2015. “One physical system”:
Tansley’s ecosystem as Earth’s critical zone. New Phytol 206,
pp.900–912. https://doi.org/10.1111/nph.13338.
Rowe, J.S., 1961. The level of integration concept and ecology. Ecology
42, pp.420-427.
Rowe, J.S., and Barnes, B. V., 1994. Geo-ecosystems and bio-ecosystems.
Bulletin of the Ecological Society of America, Vol. 75, No. 1, pp.
40-41.
Sayre, R., Comer, P, Warner H, Cress, J. 2009. A new map of standardized
terrestrial ecosystems of the conterminous United States. US Geological
Survey Professional Paper 1768
Shea, T., Woodley, A., Lindsay, K., Lounds, J., Worbets, B., St.
Hilaire, A., Sumner, J., 2018. Canada’s conservation vision: A report of
the national advisory panel. Ottawa, ON: Government of Canada.
Simensen, T., Horvath, P., Vollering, J., Erikstad, L., Halvorsen, R.,
and Bryn, A., 2020. Composite landscape predictors improve distribution
models of ecosystem types. Diversity and Distributions. 26(8),
pp.928–943. doi: 10.1111/ddi.13060
Sonnewald, M., Dutkiewicz, S., Hill, C. and Forget, G., 2020.
Elucidating ecological complexity: Unsupervised learning determines
global marine eco-provinces. Science Advances, 6(22), p.eaay4740.
Soranno, P.A., Wagner, T., Collins, S.M., Lapierre, J.F., Lottig, N.R.
and Oliver, S.K., 2019. Spatial and temporal variation of ecosystem
properties at macroscales. Ecology Letters, 22(10), pp.1587-1598.
Svirezhev, Y.M., Krysanova, V.P., Voinov, A.A., 1984. Mathematical
modelling of a fishpond ecosystem. Ecol. Model. 21, pp.315 – 337.
Svirezhev, Y.M., Krysanova, V.P. and Voinov, A.A., 1984. Mathematical
modelling of a fish pond ecosystem. Ecological modelling ,21 (4), pp.315-337.
Taranu, Z.E., Pinel‐Alloul, B. and Legendre, P., 2021. Large‐scale
multi‐trophic co‐response models and environmental control of pelagic
food webs in Québec lakes. Oikos, 130(3), pp.377-395.
Tikhonov, G., Duan, L., Abrego, N., Newell, G., White, M., Dunson, D.
and Ovaskainen, O., 2020. Computationally efficient joint species
distribution modelling of big spatial data. Ecology, e02929.
https://doi.org/10.1002/ecy.2929
van der Plas, F., 2019. Biodiversity and ecosystem functioning in
naturally assembled communities. Biological Reviews, 94(4),
pp.1220-1245.
Warton, D.I., Blanchet, F.G., O’Hara, R.B., Ovaskainen, O., Taskinen,
S., Walker, S.C. and Hui, F.K., 2015. So many variables: joint modeling
in community ecology. Trends in Ecology & Evolution, 30(12),
pp.766-779.
Watson, J.E., Keith, D.A.,
Strassburg, B.B., Venter, O., Williams, B. and Nicholson, E., 2020. Set
a global target for ecosystems. Nature 578, pp.360–362.
Wilkinson, D. P., Golding, N., Guillera-Arroita, G., Tingley, R. and
McCarthy, M.A., 2021. Defining and evaluating predictions of joint
species distribution models. Methods Ecol. Evol. 12, pp.394–404.
Xia, J., McGuire, A.D., Lawrence, D., Burke, E., Chen, G., Chen, X.,
Delire, C., Koven, C., MacDougall, A., Peng, S. and Rinke, A., 2017.
Terrestrial ecosystem model performance in simulating productivity and
its vulnerability to climate change in the northern permafrost region.
Journal of Geophysical Research: Biogeosciences, 122(2), pp.430-446.
Yang, Q., F.-R. Meng, C. P.-A. Bourque and Z. Zhao., 2017. Production of
high-resolution forest-ecosite maps based on model predictions of soil
moisture and nutrient regimes over a large forested area. Sci. Rep.
7(1), pp1–13. doi:10.1038/s41598-017-11381-z.
Zarnetske, P.L., Read, Q.D., Record, S., Gaddis, K.D., Pau, S., Hobi,
M.L., Malone, S.L., Costanza, J., M. Dahlin, K., Latimer, A.M. and
Wilson, A.M., 2019. Towards connecting biodiversity and geodiversity
across scales with satellite remote sensing. Global Ecology and
Biogeography, 28(5), pp.548-556.
Zhang, C., Chen, Y., Xu, B., Xue, Y. and Ren, Y., 2018. Comparing the
prediction of joint species distribution models with respect to
characteristics of sampling data. Ecography, 41(11), pp.1876-1887.
Zhao, Q., Basher, Z. and Costello, M.J., 2020. Mapping near surface
global marine ecosystems through cluster analysis of environmental data.
Ecological Research, 35(2), pp.327-342.
Zurell, D., Franklin, J., König, C., Bouchet, P.J., Dormann, C.F.,
Elith, J., Fandos, G., Feng, X., Guillera‐Arroita, G., Guisan, A. and
Lahoz‐Monfort, J.J., 2020. A standard protocol for reporting species
distribution models. Ecography, 43(9), pp.1261-1277.
Zurell, D., König, C., Malchow, A.K., Kapitza, S., Bocedi, G., Travis,
J. and Fandos, G., 2022. Spatially explicit models for decision‐making
in animal conservation and restoration. Ecography, 2022(4). doi:
10.1111/ecog.05787.