patrickbdevaney/mia9 · Datasets at Hugging Face

text stringlengths 0 6.44k
Coronado, C.; et al. The ecological–societal underpinnings of Everglades restoration. Front. Ecol. Environ.
2005, 3, 161–169.
25. Dorcas, M.E.; Willson, J.D.; Reed, R.N.; Snow, R.W.; Rochford, M.R.; Miller, M.A.; Meshaka, W.E., Jr.;
Andreadis, P.T.; Mazzotti, F.J.; Romagosa, C.M.; et al. Severe mammal declines coincide with proliferation of
invasive Burmese pythons in Everglades National Park. Proc. Natl. Acad. Sci. USA 2012, 109, 2418–2422.
[CrossRef] [PubMed]
26. Van der Valk, A.; Volin, J.; Labisky, R. Ecological effects of extreme hydrological events on the Greater
Everglades. In Independent Scientific Review Panel Report to RECOVER; Bepress: Berkeley, CA, USA, 2012.
27. Frohring, P.C.; Voorhees, D.P.; Kushlan, J.A. History of Wading Bird Populations in the Florida Everglades:
A Lesson in the Use of Historical Information. Colon. Waterbirds 1988, 11, 328. [CrossRef]
28. Wetzel, P.R.; van der Valk, A.G.; Newman, S.; Gawlik, D.E.; Gann, T.T.; Coronado-Molina, C.A.;
Childers, D.L.; Sklar, F.H. Maintaining tree islands in the Florida Everglades: Nutrient redistribution
is the key. Front. Ecol. Environ. 2005, 3, 370–376. [CrossRef]
29. Meshaka, W.E.; Snow, R.; Bass, O.L.; Robertson, W.B. Occurrence of Wildlife on Tree Islands in the Southern
Everglades. In Tree Islands of the Everglades; Springer: Berlin/Heidelberg, Germany, 2002; pp. 391–427.
30. Wetzel, P.R.; Sah, J.P.; Ross, M.S. Tree islands: The bellwether of Everglades ecosystem function and restoration
success. Restor. Ecol. 2017, 25, S71–S85. [CrossRef]
31. Wetzel, P.R.; van der Valk, A.G.; Newman, S.; Coronado, C.A.; Troxler-Gann, T.G.; Childers, D.L.; Orem, W.H.;
Sklar, F.H. Heterogeneity of phosphorus distribution in a patterned landscape, the Florida Everglades.
Plant Ecol. 2009, 200, 83–90. [CrossRef]
32. Sklar, F.H.; van der Valk, A. Tree Islands of the Everglades: An Overview. In Tree Islands of the Everglades;
Springer: Berlin/Heidelberg, Germany, 2002; pp. 1–18.
33. Doren, R.F.; Armentano, T.V.; Whiteaker, L.D.; Jones, R.D. Marsh vegetation patterns and soil phosphorus
gradients in the Everglades ecosystem. Aquat. Bot. 1997, 56, 145–163. [CrossRef]
34. Jones, D.T.; Sah, J.P.; Ross, M.S.; Oberbauer, S.F.; Hwang, B.; Jayachandran, K. Responses of twelve tree
species common in Everglades tree islands to simulated hydrologic regimes. Wetlands 2006, 26, 830–844.
[CrossRef]
35. Leifheit, E.F.; Veresoglou, S.D.; Lehmann, A.; Kathryn Morris, E.; Rillig, M.C. Multiple factors influence the
role of arbuscular mycorrhizal fungi in soil aggregation—A meta-analysis. Plant Soil 2014, 374, 523–537.
[CrossRef]
36. Grinhut, T.; Hadar, Y.; Chen, Y. Degradation and transformation of humic substances by saprotrophic fungi:
Processes and mechanisms. Fungal Biol. Rev. 2007, 21, 179–189. [CrossRef]
37. Dobson, A.; Crawley, M. Pathogens and the structure of plant communities. Trends Ecol. Evol. 1994, 9, 393–398.
[CrossRef]
Diversity 2020, 12, 0324 15 of 17
38. Gottlieb, A.D.; Richards, J.H.; Gaiser, E.E. Comparative study of periphyton community structure in long
and short-hydroperiod Everglades marshes. Hydrobiologia 2006, 569, 195–207. [CrossRef]
39. Pisani, O.; Gao, M.; Maie, N.; Miyoshi, T.; Childers, D.L.; Jaffé, R. Compositional aspects of herbaceous litter
decomposition in the freshwater marshes of the Florida Everglades. Plant Soil 2018, 423, 87–98. [CrossRef]
40. Wallace, B.; Dickinson, C.H. Peat Microfungi in Three Habitats in the Florida Everglades. Mycologia 1978, 70, 1151.
[CrossRef]
41. Aich, S.; Ewe, S.M.L.; Gu, B.; Dreschel, T.W. An evaluation of peat loss from an Everglades tree island,
Florida, USA. Mires Peat 2014, 14, 1–15.
42. Stoffella, S.L.; Ross, M.S.; Sah, J.P.; Price, R.M.; Sullivan, P.L.; Cline, E.A.; Scinto, L.J. Survival and growth
responses of eight Everglades tree species along an experimental hydrological gradient on two tree island
types. Appl. Veg. Sci. 2010, 13, 439–449. [CrossRef]
43. Sah, P.J.; Richards, J.H.; Ross, M.S.; Stoffella, S.L.; Cline, E.; Dreschel, T.W.; Sklar, F.H. Understory Vegetation
Composition and Biomass on the Tree Islands in the Loxahatchee Impoundment Landscape Assessment
(LILA) Experimental Site. in preparation.
44. Frazer, G.W.; Canham, C.D.; Lertzman, K.P. Gap Light Analyzer (Gla), Version 2.0: Imaging Software to Extract
Canopy Structure and Gap Light Transmission Indices from True-Colour Fisheye Photographs, Users Manual and
Program Documentation; Simon Fraser University: Burnaby, BC, Canada; Institute of Ecosystem Studies:
New York, NY, USA, 1999; 36p.
45. Gohl, D.M.; Vangay, P.; Garbe, J.; MacLean, A.; Hauge, A.; Becker, A.; Gould, T.J.; Clayton, J.B.; Johnson, T.J.;
Hunter, R.; et al. Systematic improvement of amplicon marker gene methods for increased accuracy in
microbiome studies. Nat. Biotechnol. 2016, 34, 942–949. [CrossRef]
46. Bolyen, E.; Rideout, J.R.; Dillon, M.R.; Bokulich, N.A.; Abnet, C.C.; Al-Ghalith, G.A.; Alexander, H.; Alm, E.J.;
Arumugam, M.; Asnicar, F.; et al. Reproducible, interactive, scalable and extensible microbiome data science
using QIIME 2. Nat. Biotechnol. 2019, 37, 852–857. [CrossRef]
47. Nilsson, R.H.; Larsson, K.-H.; Taylor, A.F.S.; Bengtsson-Palme, J.; Jeppesen, T.S.; Schigel, D.; Kennedy, P.;
Picard, K.; Glöckner, F.O.; Tedersoo, L.; et al. The UNITE database for molecular identification of fungi:
Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 2019, 47, D259–D264. [CrossRef]
[PubMed]
48. Glassman, S.I.; Martiny, J.B.H. Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants
versus Operational Taxonomic Units. mSphere 2018, 3. [CrossRef] [PubMed]
49. Barton, K. MuMIn: Multi-Model Inference, R Package Version 0.12.0. Available online: http://r-forge.rproject.org/projects/mumin/ (accessed on 29 June 2020).
50. Oksanen, J.; Blanchet, F.G.; Kindt, R.; Legendre, P.; O’hara, R.B.; Simpson, G.L.; Wagner, H. Vegan: Community
Ecology Package. R Package Version 1.17-4. Available online: http://CRAN.R-project.org/package=vegan
(accessed on 29 June 2020).
51. De Caceres, M.; Jansen, F.; Dell, N. Indicspecies: Studying the Statistical Relationship between Species and
Groups of Sites. R Package Version 1. Available online: https://cran.r-project.org/web/packages/indicspecies/
index.html (accessed on 29 June 2020).
52. Dufrene, M.; Legendre, P. Species Assemblages and Indicator Species: The Need for a Flexible Asymmetrical
Approach. Ecol. Monogr. 1997, 67, 345. [CrossRef]
53. Nguyen, N.H.; Song, Z.; Bates, S.T.; Branco, S.; Tedersoo, L.; Menke, J.; Schilling, J.S.; Kennedy, P.G.
FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol.
2016, 20, 241–248. [CrossRef]
54. Prinzing, A.; Durka, W.; Klotz, S.; Brandl, R. Geographic variability of ecological niches of plant species:
Are competition and stress relevant? Ecography 2002, 25, 721–729. [CrossRef]
55. Agrawal, A.A.; Ackerly, D.D.; Adler, F.; Elizabeth Arnold, A.; Cáceres, C.; Doak, D.F.; Post, E.; Hudson, P.J.;
Maron, J.; Mooney, K.A.; et al. Filling key gaps in population and community ecology. Front. Ecol. Environ.
2007, 5, 145–152. [CrossRef]
56. Brandt, L.A.; Ecker, D.; Rivera, I.G.; Traut, A.; Mazzotti, F.J. Wildlife and vegetation of bayhead islands in the
A.R.M. Loxahatchee National Wildlife Refuge. Southeast. Nat. 2003, 2, 179–194. [CrossRef]
57. Gann, T.T.; Childers, D.L. Relationships between Hydrology and Soils Describe Vegetation Patterns in
Seasonally Flooded Tree Islands of the Southern Everglades, Florida. Plant Soil 2006, 279, 271–286. [CrossRef]
Diversity 2020, 12, 0324 16 of 17
58. Wang, Y.; Huang, Y.; Qiu, Q.; Xin, G.; Yang, Z.; Shi, S. Flooding greatly affects the diversity of arbuscular
mycorrhizal fungi communities in the roots of wetland plants. PLoS ONE 2011, 6, e24512. [CrossRef]
59. Yang, H.; Koide, R.T.; Zhang, Q. Short-term waterlogging increases arbuscular mycorrhizal fungal species
richness and shifts community composition. Plant Soil 2016, 404, 373–384. [CrossRef]
60. Dobbs, C.G. On the primary dispersal and isolation of fungal spores. New Phytol. 1942, 41, 63–69. [CrossRef]
61. Light, S.S.; Dineen, J.W. Water control in the Everglades: A historical perspective. In The Ecosystem and Its
Restoration; St. Lucie Press: Boca Raton, FL, USA, 1994; Volume 5, pp. 47–84.
62. Willard, D.A.; Bernhardt, C.E.; Holmes, C.W.; Landacre, B.; Marot, M. Response of Everglades tree islands to
environmental change. Ecol. Monogr. 2006, 76, 565–583. [CrossRef]
63. Van Nuland, M.E.; Peay, K.G. Symbiotic niche mapping reveals functional specialization by two
ectomycorrhizal fungi that expands the host plant niche. Fungal Ecol. 2020, 46, 100960. [CrossRef]
64. Bougher, N.L.; Matheny, P.B. Two species of Inocybe (fungi) introduced into Western Australia. Nuytsia
2011, 3, 139–148.

Coronado, C.; et al. The ecological–societal underpinnings of Everglades restoration. Front. Ecol. Environ.

2005, 3, 161–169.

25. Dorcas, M.E.; Willson, J.D.; Reed, R.N.; Snow, R.W.; Rochford, M.R.; Miller, M.A.; Meshaka, W.E., Jr.;

Andreadis, P.T.; Mazzotti, F.J.; Romagosa, C.M.; et al. Severe mammal declines coincide with proliferation of

invasive Burmese pythons in Everglades National Park. Proc. Natl. Acad. Sci. USA 2012, 109, 2418–2422.

[CrossRef] [PubMed]

26. Van der Valk, A.; Volin, J.; Labisky, R. Ecological effects of extreme hydrological events on the Greater

Everglades. In Independent Scientific Review Panel Report to RECOVER; Bepress: Berkeley, CA, USA, 2012.

27. Frohring, P.C.; Voorhees, D.P.; Kushlan, J.A. History of Wading Bird Populations in the Florida Everglades:

A Lesson in the Use of Historical Information. Colon. Waterbirds 1988, 11, 328. [CrossRef]

28. Wetzel, P.R.; van der Valk, A.G.; Newman, S.; Gawlik, D.E.; Gann, T.T.; Coronado-Molina, C.A.;

Childers, D.L.; Sklar, F.H. Maintaining tree islands in the Florida Everglades: Nutrient redistribution

is the key. Front. Ecol. Environ. 2005, 3, 370–376. [CrossRef]

29. Meshaka, W.E.; Snow, R.; Bass, O.L.; Robertson, W.B. Occurrence of Wildlife on Tree Islands in the Southern

Everglades. In Tree Islands of the Everglades; Springer: Berlin/Heidelberg, Germany, 2002; pp. 391–427.

30. Wetzel, P.R.; Sah, J.P.; Ross, M.S. Tree islands: The bellwether of Everglades ecosystem function and restoration

success. Restor. Ecol. 2017, 25, S71–S85. [CrossRef]

31. Wetzel, P.R.; van der Valk, A.G.; Newman, S.; Coronado, C.A.; Troxler-Gann, T.G.; Childers, D.L.; Orem, W.H.;

Sklar, F.H. Heterogeneity of phosphorus distribution in a patterned landscape, the Florida Everglades.

Plant Ecol. 2009, 200, 83–90. [CrossRef]

32. Sklar, F.H.; van der Valk, A. Tree Islands of the Everglades: An Overview. In Tree Islands of the Everglades;

Springer: Berlin/Heidelberg, Germany, 2002; pp. 1–18.

33. Doren, R.F.; Armentano, T.V.; Whiteaker, L.D.; Jones, R.D. Marsh vegetation patterns and soil phosphorus

gradients in the Everglades ecosystem. Aquat. Bot. 1997, 56, 145–163. [CrossRef]

34. Jones, D.T.; Sah, J.P.; Ross, M.S.; Oberbauer, S.F.; Hwang, B.; Jayachandran, K. Responses of twelve tree

species common in Everglades tree islands to simulated hydrologic regimes. Wetlands 2006, 26, 830–844.

[CrossRef]

35. Leifheit, E.F.; Veresoglou, S.D.; Lehmann, A.; Kathryn Morris, E.; Rillig, M.C. Multiple factors influence the

role of arbuscular mycorrhizal fungi in soil aggregation—A meta-analysis. Plant Soil 2014, 374, 523–537.

[CrossRef]

36. Grinhut, T.; Hadar, Y.; Chen, Y. Degradation and transformation of humic substances by saprotrophic fungi:

Processes and mechanisms. Fungal Biol. Rev. 2007, 21, 179–189. [CrossRef]

37. Dobson, A.; Crawley, M. Pathogens and the structure of plant communities. Trends Ecol. Evol. 1994, 9, 393–398.

[CrossRef]

Diversity 2020, 12, 0324 15 of 17

38. Gottlieb, A.D.; Richards, J.H.; Gaiser, E.E. Comparative study of periphyton community structure in long

and short-hydroperiod Everglades marshes. Hydrobiologia 2006, 569, 195–207. [CrossRef]

39. Pisani, O.; Gao, M.; Maie, N.; Miyoshi, T.; Childers, D.L.; Jaffé, R. Compositional aspects of herbaceous litter

decomposition in the freshwater marshes of the Florida Everglades. Plant Soil 2018, 423, 87–98. [CrossRef]

40. Wallace, B.; Dickinson, C.H. Peat Microfungi in Three Habitats in the Florida Everglades. Mycologia 1978, 70, 1151.

[CrossRef]

41. Aich, S.; Ewe, S.M.L.; Gu, B.; Dreschel, T.W. An evaluation of peat loss from an Everglades tree island,

Florida, USA. Mires Peat 2014, 14, 1–15.

42. Stoffella, S.L.; Ross, M.S.; Sah, J.P.; Price, R.M.; Sullivan, P.L.; Cline, E.A.; Scinto, L.J. Survival and growth

responses of eight Everglades tree species along an experimental hydrological gradient on two tree island

types. Appl. Veg. Sci. 2010, 13, 439–449. [CrossRef]

43. Sah, P.J.; Richards, J.H.; Ross, M.S.; Stoffella, S.L.; Cline, E.; Dreschel, T.W.; Sklar, F.H. Understory Vegetation

Composition and Biomass on the Tree Islands in the Loxahatchee Impoundment Landscape Assessment

(LILA) Experimental Site. in preparation.

44. Frazer, G.W.; Canham, C.D.; Lertzman, K.P. Gap Light Analyzer (Gla), Version 2.0: Imaging Software to Extract

Canopy Structure and Gap Light Transmission Indices from True-Colour Fisheye Photographs, Users Manual and

Program Documentation; Simon Fraser University: Burnaby, BC, Canada; Institute of Ecosystem Studies:

New York, NY, USA, 1999; 36p.

45. Gohl, D.M.; Vangay, P.; Garbe, J.; MacLean, A.; Hauge, A.; Becker, A.; Gould, T.J.; Clayton, J.B.; Johnson, T.J.;

Hunter, R.; et al. Systematic improvement of amplicon marker gene methods for increased accuracy in

microbiome studies. Nat. Biotechnol. 2016, 34, 942–949. [CrossRef]

46. Bolyen, E.; Rideout, J.R.; Dillon, M.R.; Bokulich, N.A.; Abnet, C.C.; Al-Ghalith, G.A.; Alexander, H.; Alm, E.J.;

Arumugam, M.; Asnicar, F.; et al. Reproducible, interactive, scalable and extensible microbiome data science

using QIIME 2. Nat. Biotechnol. 2019, 37, 852–857. [CrossRef]

47. Nilsson, R.H.; Larsson, K.-H.; Taylor, A.F.S.; Bengtsson-Palme, J.; Jeppesen, T.S.; Schigel, D.; Kennedy, P.;

Picard, K.; Glöckner, F.O.; Tedersoo, L.; et al. The UNITE database for molecular identification of fungi:

Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 2019, 47, D259–D264. [CrossRef]

[PubMed]

48. Glassman, S.I.; Martiny, J.B.H. Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants

versus Operational Taxonomic Units. mSphere 2018, 3. [CrossRef] [PubMed]

49. Barton, K. MuMIn: Multi-Model Inference, R Package Version 0.12.0. Available online: http://r-forge.rproject.org/projects/mumin/ (accessed on 29 June 2020).

50. Oksanen, J.; Blanchet, F.G.; Kindt, R.; Legendre, P.; O’hara, R.B.; Simpson, G.L.; Wagner, H. Vegan: Community

Ecology Package. R Package Version 1.17-4. Available online: http://CRAN.R-project.org/package=vegan

(accessed on 29 June 2020).

51. De Caceres, M.; Jansen, F.; Dell, N. Indicspecies: Studying the Statistical Relationship between Species and

Groups of Sites. R Package Version 1. Available online: https://cran.r-project.org/web/packages/indicspecies/

index.html (accessed on 29 June 2020).

52. Dufrene, M.; Legendre, P. Species Assemblages and Indicator Species: The Need for a Flexible Asymmetrical

Approach. Ecol. Monogr. 1997, 67, 345. [CrossRef]

53. Nguyen, N.H.; Song, Z.; Bates, S.T.; Branco, S.; Tedersoo, L.; Menke, J.; Schilling, J.S.; Kennedy, P.G.

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol.

2016, 20, 241–248. [CrossRef]

54. Prinzing, A.; Durka, W.; Klotz, S.; Brandl, R. Geographic variability of ecological niches of plant species:

Are competition and stress relevant? Ecography 2002, 25, 721–729. [CrossRef]

55. Agrawal, A.A.; Ackerly, D.D.; Adler, F.; Elizabeth Arnold, A.; Cáceres, C.; Doak, D.F.; Post, E.; Hudson, P.J.;

Maron, J.; Mooney, K.A.; et al. Filling key gaps in population and community ecology. Front. Ecol. Environ.

2007, 5, 145–152. [CrossRef]

56. Brandt, L.A.; Ecker, D.; Rivera, I.G.; Traut, A.; Mazzotti, F.J. Wildlife and vegetation of bayhead islands in the

A.R.M. Loxahatchee National Wildlife Refuge. Southeast. Nat. 2003, 2, 179–194. [CrossRef]

57. Gann, T.T.; Childers, D.L. Relationships between Hydrology and Soils Describe Vegetation Patterns in

Seasonally Flooded Tree Islands of the Southern Everglades, Florida. Plant Soil 2006, 279, 271–286. [CrossRef]

Diversity 2020, 12, 0324 16 of 17

58. Wang, Y.; Huang, Y.; Qiu, Q.; Xin, G.; Yang, Z.; Shi, S. Flooding greatly affects the diversity of arbuscular

mycorrhizal fungi communities in the roots of wetland plants. PLoS ONE 2011, 6, e24512. [CrossRef]

59. Yang, H.; Koide, R.T.; Zhang, Q. Short-term waterlogging increases arbuscular mycorrhizal fungal species

richness and shifts community composition. Plant Soil 2016, 404, 373–384. [CrossRef]

60. Dobbs, C.G. On the primary dispersal and isolation of fungal spores. New Phytol. 1942, 41, 63–69. [CrossRef]

61. Light, S.S.; Dineen, J.W. Water control in the Everglades: A historical perspective. In The Ecosystem and Its

Restoration; St. Lucie Press: Boca Raton, FL, USA, 1994; Volume 5, pp. 47–84.

62. Willard, D.A.; Bernhardt, C.E.; Holmes, C.W.; Landacre, B.; Marot, M. Response of Everglades tree islands to

environmental change. Ecol. Monogr. 2006, 76, 565–583. [CrossRef]

63. Van Nuland, M.E.; Peay, K.G. Symbiotic niche mapping reveals functional specialization by two

ectomycorrhizal fungi that expands the host plant niche. Fungal Ecol. 2020, 46, 100960. [CrossRef]

64. Bougher, N.L.; Matheny, P.B. Two species of Inocybe (fungi) introduced into Western Australia. Nuytsia

2011, 3, 139–148.