Spatial and temporal analysis of beta diversity in the Barro Colorado Island forest dynamics plot, Panama
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摘要
Background: Ecologists are interested in assessing the spatial and temporal variation in ecological surveys repeated over time. This paper compares the 1985 and 2015 surveys of the Barro Colorado Forest Dynamics plot(BCI), Panama,divided into 1250(20 m × 20 m) quadrats.Methods, spatial analysis: Total beta diversity was measured as the total variance of the Hellinger-transformed community data throughout the BCI plot. Total beta was partitioned into contributions of individual sites(LCBD indices), which were tested for significance and mapped.Results, spatial analysis: LCBD indices indicated the sites with exceptional community composition. In 1985,they were mostly found in the swamp habitat. In the 2015 survey, none of the swamp quadrats had significant LCBDs.What happened to the tree community in the interval?Methods, temporal analysis: The dissimilarity in community composition in each quadrat was measured between time 1(1985) and time 2(2015). Temporal Beta Indices(TBI) were computed from abundance and presence-absence data and tested for significance. TBI indices can be decomposed into B = species(or abundances-per-species) losses and C = species(or abundances-per-species) gains. B-C plots were produced; they display visually the relative importance of the loss and gain components, through time, across the sites.Results, temporal analysis: In BCI, quadrats with significant TBI indices were found in the swamp area, which is shrinking in importance due to changes to the local climate. A published habitat classification divided the BCI forest plot into six habitat zones. Graphs of the B and C components were produced for each habitat group. Group 4(the swamp) was dominated by species(and abundances-per-species) gains whereas the five other habitat groups were dominated by losses, some groups more than others.Conclusions: We identified the species that had changed the most in abundances in the swamp between T1 and T2.This analysis supported the hypothesis that the swamp is drying out and is invaded by species from the surrounding area. Analysis of the B and C components of temporal beta diversity bring us to the heart of the mechanisms of community change through time: losses(B) and gains(C) of species, losses and gains of individuals of various species. TBI analysis is especially interesting in species-rich communities where we cannot examine the changes in every species individually.
Background: Ecologists are interested in assessing the spatial and temporal variation in ecological surveys repeated over time. This paper compares the 1985 and 2015 surveys of the Barro Colorado Forest Dynamics plot(BCI), Panama,divided into 1250(20 m × 20 m) quadrats.Methods, spatial analysis: Total beta diversity was measured as the total variance of the Hellinger-transformed community data throughout the BCI plot. Total beta was partitioned into contributions of individual sites(LCBD indices), which were tested for significance and mapped.Results, spatial analysis: LCBD indices indicated the sites with exceptional community composition. In 1985,they were mostly found in the swamp habitat. In the 2015 survey, none of the swamp quadrats had significant LCBDs.What happened to the tree community in the interval?Methods, temporal analysis: The dissimilarity in community composition in each quadrat was measured between time 1(1985) and time 2(2015). Temporal Beta Indices(TBI) were computed from abundance and presence-absence data and tested for significance. TBI indices can be decomposed into B = species(or abundances-per-species) losses and C = species(or abundances-per-species) gains. B-C plots were produced; they display visually the relative importance of the loss and gain components, through time, across the sites.Results, temporal analysis: In BCI, quadrats with significant TBI indices were found in the swamp area, which is shrinking in importance due to changes to the local climate. A published habitat classification divided the BCI forest plot into six habitat zones. Graphs of the B and C components were produced for each habitat group. Group 4(the swamp) was dominated by species(and abundances-per-species) gains whereas the five other habitat groups were dominated by losses, some groups more than others.Conclusions: We identified the species that had changed the most in abundances in the swamp between T1 and T2.This analysis supported the hypothesis that the swamp is drying out and is invaded by species from the surrounding area. Analysis of the B and C components of temporal beta diversity bring us to the heart of the mechanisms of community change through time: losses(B) and gains(C) of species, losses and gains of individuals of various species. TBI analysis is especially interesting in species-rich communities where we cannot examine the changes in every species individually.
Background: Ecologists are interested in assessing the spatial and temporal variation in ecological surveys repeated over time. This paper compares the 1985 and 2015 surveys of the Barro Colorado Forest Dynamics plot(BCI), Panama,divided into 1250(20 m × 20 m) quadrats.Methods, spatial analysis: Total beta diversity was measured as the total variance of the Hellinger-transformed community data throughout the BCI plot. Total beta was partitioned into contributions of individual sites(LCBD indices), which were tested for significance and mapped.Results, spatial analysis: LCBD indices indicated the sites with exceptional community composition. In 1985,they were mostly found in the swamp habitat. In the 2015 survey, none of the swamp quadrats had significant LCBDs.What happened to the tree community in the interval?Methods, temporal analysis: The dissimilarity in community composition in each quadrat was measured between time 1(1985) and time 2(2015). Temporal Beta Indices(TBI) were computed from abundance and presence-absence data and tested for significance. TBI indices can be decomposed into B = species(or abundances-per-species) losses and C = species(or abundances-per-species) gains. B-C plots were produced; they display visually the relative importance of the loss and gain components, through time, across the sites.Results, temporal analysis: In BCI, quadrats with significant TBI indices were found in the swamp area, which is shrinking in importance due to changes to the local climate. A published habitat classification divided the BCI forest plot into six habitat zones. Graphs of the B and C components were produced for each habitat group. Group 4(the swamp) was dominated by species(and abundances-per-species) gains whereas the five other habitat groups were dominated by losses, some groups more than others.Conclusions: We identified the species that had changed the most in abundances in the swamp between T1 and T2.This analysis supported the hypothesis that the swamp is drying out and is invaded by species from the surrounding area. Analysis of the B and C components of temporal beta diversity bring us to the heart of the mechanisms of community change through time: losses(B) and gains(C) of species, losses and gains of individuals of various species. TBI analysis is especially interesting in species-rich communities where we cannot examine the changes in every species individually.
引文
Anderson MJ,Crist TO,Chase JM,Vellend M,Inouye BD,Freestone AL,Sanders NJ,Cornell HV,Comita LS,Davies KF,Harrison SP,Kraft NJB,Stegen JC,Swenson NG(2011)Navigating the multiple meanings ofβdiversity:a roadmap for the practicing ecologist.Ecol Lett 14:19-28.
Chisholm RA,Condit R,Rahman KA,Baker PJ,Bunyavejchewin S,Chen Y-Y,Chuyong G,Dattaraja HS,Davies S,Ewango CEN,Gunatilleke CVS,Nimal Gunatilleke IAU,Hubbell S,Kenfack D,Kiratiprayoon S,Lin Y,Makana J-R,Pongpattananurak N,Pulla S,Punchi-Manage R,Sukumar R,Su S-H,Sun I-F,Suresh HS,Tan S,Thomas D,Yap S(2014)Temporal variability of forest communities:empirical estimates of population change in 4000 tree species.Ecol Lett 17:855-865.
Condit R,Aguilar S,Pérez R,Lao S,Hubbell SP,Foster RB(2017a)BCI 50-ha plot taxonomy as of 2017.https://doi.org/10.25570/stri/10088/32990.
Condit R,Hubbell SP,Foster RB(1996)Changes in tree species abundance in a neotropical forest:impact of climate change.J Trop Ecol 12:231-256.
Condit R,Lao S,Pérez R,Dolins SB,Foster RB,Hubbell SP(2012)Barro Colorado Forest census plot data,2012 Version.https://doi.org/10.5479/data.bci.20130603.
Condit R,Pérez R,Lao S,Aguilar S,Hubbell SP(2017b)Demographic trends and climate over 35 years in the Barro Colorado 50 ha plot.For Ecosystems 4:17.
Dray S,Bauman D,Blanchet G,Borcard D,Clappe S,Guénard G,Jombart T,Larocque G,Legendre P,Madi M,Wagner HH(2019)adespatial:Multivariate multiscale spatial analysis.R package version 0.3-3.https://cran.r-project.org/package=adespatial.
Harms KE,Condit R,Hubble SP,Foster RB(2001)Habitat associations of trees and shrubs in a 50-ha neotropical forest plot.J Ecol 89:947-959.
Holm S(1979)A simple sequentially rejective multiple test procedure.Scand JStat 6:65-70.
Hubbell SP(2001)The unified neutral theory of biodiversity and biogeography.Princeton University Press,Princeton,New Jersey.
Hubbell SP,Foster RB(1983)Diversity of canopy trees in a neotropical forest and implications for conservation.In:Whitmore T,Chadwick A,Sutton A(eds)Tropical rain Forest:ecology and management.The British Ecological Society,Oxford,pp 25-41.
Koleff P,Gaston KJ,Lennon JJ(2003)Measuring beta diversity for presenceabsence data.J Anim Ecol 72:367-382.
Kuczynski L,Legendre P,Grenouillet G(2018)Concomitant impacts of climate change,fragmentation and non-native species have led to reorganization of fish communities since the 1980s.Glob Ecol Biogeogr 27:213-222.
Legendre P(2014)Interpreting the replacement and richness difference components of beta diversity.Glob Ecol Biogeogr 23:1324-1334.
Legendre P(2019)A temporal beta-diversity index to identify sites that have changed in exceptional ways in space-time surveys.Ecol Evol 2019;00:1-15.https://doi.org/10.1002/ece3.4984.
Legendre P,Borcard D(2018)Box-cox-chord transformations for community composition data prior to beta diversity analysis.Ecography 41:1-5.
Legendre P,Borcard D,Peres-Neto PR(2005)Analyzing beta diversity:partitioning the spatial variation of community composition data.Ecol Monogr 75:435-450.
Legendre P,De Cáceres M(2013)Beta diversity as the variance of community data:dissimilarity coefficients and partitioning.Ecol Lett 16:951-963.
Legendre P,De Cáceres M,Borcard D(2010)Community surveys through space and time:testing the space-time interaction in the absence of replication.Ecology 91:262-272.
Legendre P,Gallagher ED(2001)Ecologically meaningful transformations for ordination of species data.Oecologia 129:271-280.
Legendre P,Gauthier O(2014)Statistical methods for temporal and space-time analysis of community composition data.Proc R Soc B 281:20132728.
Legendre P,Legendre L(2012)Numerical ecology,3rd English edition.Elsevier Science BV,Amsterdam.
Legendre P,Salvat B(2015)Thirty-year recovery of mollusc communities after nuclear experimentations on Fangataufa atoll(Tuamotu,French Polynesia).Proc R Soc B 282:20150750.
Odum EP(1950)Bird populations of the highlands(North Carolina)plateau in relation to plant succession and avian invasion.Ecology 31:587-605.
Shimadzu H,Dornelas M,Magurran AE(2015)Measuring temporal turnover in ecological communities.Methods Ecol Evol 6:1384-1394.
Whittaker RH(1972)Evolution and measurement of species diversity.Taxon 21:213-251.
Winegardner K,Legendre P,Beisner BE,Gregory-Eaves I(2017)Diatom diversity patterns over the past~150 years across the conterminous United States:identifying mechanisms behind beta diversity.Glob Ecol Biogeogr 26:1303-1315.
Chisholm RA,Condit R,Rahman KA,Baker PJ,Bunyavejchewin S,Chen Y-Y,Chuyong G,Dattaraja HS,Davies S,Ewango CEN,Gunatilleke CVS,Nimal Gunatilleke IAU,Hubbell S,Kenfack D,Kiratiprayoon S,Lin Y,Makana J-R,Pongpattananurak N,Pulla S,Punchi-Manage R,Sukumar R,Su S-H,Sun I-F,Suresh HS,Tan S,Thomas D,Yap S(2014)Temporal variability of forest communities:empirical estimates of population change in 4000 tree species.Ecol Lett 17:855-865.
Condit R,Aguilar S,Pérez R,Lao S,Hubbell SP,Foster RB(2017a)BCI 50-ha plot taxonomy as of 2017.https://doi.org/10.25570/stri/10088/32990.
Condit R,Hubbell SP,Foster RB(1996)Changes in tree species abundance in a neotropical forest:impact of climate change.J Trop Ecol 12:231-256.
Condit R,Lao S,Pérez R,Dolins SB,Foster RB,Hubbell SP(2012)Barro Colorado Forest census plot data,2012 Version.https://doi.org/10.5479/data.bci.20130603.
Condit R,Pérez R,Lao S,Aguilar S,Hubbell SP(2017b)Demographic trends and climate over 35 years in the Barro Colorado 50 ha plot.For Ecosystems 4:17.
Dray S,Bauman D,Blanchet G,Borcard D,Clappe S,Guénard G,Jombart T,Larocque G,Legendre P,Madi M,Wagner HH(2019)adespatial:Multivariate multiscale spatial analysis.R package version 0.3-3.https://cran.r-project.org/package=adespatial.
Harms KE,Condit R,Hubble SP,Foster RB(2001)Habitat associations of trees and shrubs in a 50-ha neotropical forest plot.J Ecol 89:947-959.
Holm S(1979)A simple sequentially rejective multiple test procedure.Scand JStat 6:65-70.
Hubbell SP(2001)The unified neutral theory of biodiversity and biogeography.Princeton University Press,Princeton,New Jersey.
Hubbell SP,Foster RB(1983)Diversity of canopy trees in a neotropical forest and implications for conservation.In:Whitmore T,Chadwick A,Sutton A(eds)Tropical rain Forest:ecology and management.The British Ecological Society,Oxford,pp 25-41.
Koleff P,Gaston KJ,Lennon JJ(2003)Measuring beta diversity for presenceabsence data.J Anim Ecol 72:367-382.
Kuczynski L,Legendre P,Grenouillet G(2018)Concomitant impacts of climate change,fragmentation and non-native species have led to reorganization of fish communities since the 1980s.Glob Ecol Biogeogr 27:213-222.
Legendre P(2014)Interpreting the replacement and richness difference components of beta diversity.Glob Ecol Biogeogr 23:1324-1334.
Legendre P(2019)A temporal beta-diversity index to identify sites that have changed in exceptional ways in space-time surveys.Ecol Evol 2019;00:1-15.https://doi.org/10.1002/ece3.4984.
Legendre P,Borcard D(2018)Box-cox-chord transformations for community composition data prior to beta diversity analysis.Ecography 41:1-5.
Legendre P,Borcard D,Peres-Neto PR(2005)Analyzing beta diversity:partitioning the spatial variation of community composition data.Ecol Monogr 75:435-450.
Legendre P,De Cáceres M(2013)Beta diversity as the variance of community data:dissimilarity coefficients and partitioning.Ecol Lett 16:951-963.
Legendre P,De Cáceres M,Borcard D(2010)Community surveys through space and time:testing the space-time interaction in the absence of replication.Ecology 91:262-272.
Legendre P,Gallagher ED(2001)Ecologically meaningful transformations for ordination of species data.Oecologia 129:271-280.
Legendre P,Gauthier O(2014)Statistical methods for temporal and space-time analysis of community composition data.Proc R Soc B 281:20132728.
Legendre P,Legendre L(2012)Numerical ecology,3rd English edition.Elsevier Science BV,Amsterdam.
Legendre P,Salvat B(2015)Thirty-year recovery of mollusc communities after nuclear experimentations on Fangataufa atoll(Tuamotu,French Polynesia).Proc R Soc B 282:20150750.
Odum EP(1950)Bird populations of the highlands(North Carolina)plateau in relation to plant succession and avian invasion.Ecology 31:587-605.
Shimadzu H,Dornelas M,Magurran AE(2015)Measuring temporal turnover in ecological communities.Methods Ecol Evol 6:1384-1394.
Whittaker RH(1972)Evolution and measurement of species diversity.Taxon 21:213-251.
Winegardner K,Legendre P,Beisner BE,Gregory-Eaves I(2017)Diatom diversity patterns over the past~150 years across the conterminous United States:identifying mechanisms behind beta diversity.Glob Ecol Biogeogr 26:1303-1315.