02916nas a2200229 4500008004100000245008900041210006900130300001100199490000700210520219900217100001702416700001602433700002402449700002602473700001802499700001702517700001802534700002602552700001602578700001702594856007502611 2019 eng d00aA comprehensive approach to analyzing community dynamics using rank abundance curves0 acomprehensive approach to analyzing community dynamics using ran ae028810 v103 a

Univariate and multivariate methods are commonly used to explore the spatial and temporaldynamics of ecological communities, but each has limitations, including oversimplification or abstractionof communities. Rank abundance curves (RACs) potentially integrate these existing methodologies bydetailing species-level community changes. Here, we had three goals:first, to simplify analysis of commu-nity dynamics by developing a coordinated set of R functions, and second, to demystify the relationshipsamong univariate, multivariate, and RACs measures, and examine how each is influenced by the commu-nity parameters as well as data collection methods. We developed new functions for studying temporalchanges and spatial differences in RACs in an update to the R package library(“codyn”), alongside othernew functions to calculate univariate and multivariate measures of community dynamics. We also devel-oped a new approach to studying changes in the shape of RAC curves. The R package update presentedhere increases the accessibility of univariate and multivariate measures of community change over timeand difference over space. Next, we use simulated and real data to assess the RAC and multivariate mea-sures that are output from our new functions, studying (1) if they are influenced by species richness andevenness, temporal turnover, and spatial variability and (2) how the measures are related to each other.Lastly, we explore the use of the measures with an example from a long-term nutrient addition experiment.Wefind that the RAC and multivariate measures are not sensitive to species richness and evenness andthat all the measures detail unique aspects of temporal change or spatial differences. We alsofind that spe-cies reordering is the strongest correlate of a multivariate measure of compositional change and explainsmost community change observed in long-term nutrient addition experiment. Overall, we show that spe-cies reordering is potentially an understudied determinant of community changes over time or differencesbetween treatments. The functions developed here should enhance the use of RACs to further explore thedynamics of ecological communities.

1 aAvolio, M.L.1 aCarroll, I.1 aCollins, Scott., L.1 aHouseman, Gregory, R.1 aHallett, L.M.1 aIsbell, F.L.1 aKoerner, S.E.1 aKomatsu, Kimberly, J.1 aSmith, M.D.1 aWilcox, K.R. uhttps://esajournals.onlinelibrary.wiley.com/doi/epdf/10.1002/ecs2.288104634nas a2201021 4500008004100000245011700041210006900158300001600227490000800243520186900251100002602120700001702146700002402163700001902187700001702206700002602223700002302249700001802272700001702290700002202307700001902329700001402348700001502362700002402377700001402401700002202415700001702437700002002454700001802474700001702492700002102509700002802530700001702558700002402575700002202599700002602621700002102647700001802668700002402686700002402710700001102734700001902745700001902764700001502783700001402798700001402812700001802826700001202844700001602856700001902872700001902891700001602910700001902926700002002945700002002965700002202985700001103007700001403018700001903032700002403051700002303075700001703098700002503115700001903140700001803159700002003177700001603197700002403213700001803237700001503255700001903270700001603289700003203305700001603337700001703353700001703370700001603387700001803403700001703421700001903438700001403457700001503471700001703486700001103503700001903514700001803533856006103551 2019 eng d00aGlobal change effects on plant communities are magnified by time and the number of global change factors imposed0 aGlobal change effects on plant communities are magnified by time a17867-178730 v1163 a

Global change drivers (GCDs) are expected to alter community structure and consequently, the services that ecosystems provide. Yet, few experimental investigations have examined effects of GCDs on plant community structure across multiple ecosystem types, and those that do exist present conflicting patterns. In an unprecedented global synthesis of over 100 experiments that manipulated factors linked to GCDs, we show that herbaceous plant community responses depend on experimental manipulation length and number of factors manipulated. We found that plant communities are fairly resistant to experimentally manipulated GCDs in the short term (<10 y). In contrast, long-term (≥10 y) experiments show increasing community divergence of treatments from control conditions. Surprisingly, these community responses occurred with similar frequency across the GCD types manipulated in our database. However, community responses were more common when 3 or more GCDs were simultaneously manipulated, suggesting the emergence of additive or synergistic effects of multiple drivers, particularly over long time periods. In half of the cases, GCD manipulations caused a difference in community composition without a corresponding species richness difference, indicating that species reordering or replacement is an important mechanism of community responses to GCDs and should be given greater consideration when examining consequences of GCDs for the biodiversity–ecosystem function relationship. Human activities are currently driving unparalleled global changes worldwide. Our analyses provide the most comprehensive evidence to date that these human activities may have widespread impacts on plant community composition globally, which will increase in frequency over time and be greater in areas where communities face multiple GCDs simultaneously.

1 aKomatsu, Kimberly, J.1 aAvolio, M.L.1 aLemoine, Nathan, P.1 aIsbell, Forest1 aGrman, Emily1 aHouseman, Gregory, R.1 aKoerner, Sally, E.1 aJohnson, D.S.1 aWilcox, K.R.1 aAlatalo, Juha, M.1 aAnderson, J.P.1 aAerts, R.1 aBaer, S.G.1 aBaldwin, Andrew, H.1 aBates, J.1 aBeierkuhnlein, C.1 aBelote, R.T.1 aBlair, John, M.1 aBloor, J.M.G.1 aBohlen, P.J.1 aBork, Edward, W.1 aBoughton, Elizabeth, H.1 aBowman, W.D.1 aBritton, Andrea, J.1 aCahill, James, F.1 aChaneton, Enrique, J.1 aChiariello, N.R.1 aCheng, Jimin.1 aCollins, Scott., L.1 aCornelissen, J.H.C.1 aDu, G.1 aEskelinen, Anu1 aFirn, Jennifer1 aFoster, B.1 aGough, L.1 aGross, K.1 aHallett, L.M.1 aHan, X.1 aHarmens, H.1 aHovenden, M.J.1 aJagerbrand, A.1 aJentsch, A.1 aKern, Christel1 aKlanderud, Kari1 aKnapp, Alan, K.1 aKreyling, Juergen1 aLi, W.1 aLuo, Yiqi1 aMcCulley, R.L.1 aMcLaren, Jennie, R.1 aMegonigal, Patrick1 aMorgan, J.W.1 aOnipchenko, Vladimir1 aPennings, S.C.1 aPrevéy, J.S.1 aPrice, Jodi, N.1 aReich, P.B.1 aRobinson, Clare, H.1 aRussell, L.F.1 aSala, O.E.1 aSeabloom, E.W.1 aSmith, M.D.1 aSoudzilovskaia, Nadejda, A.1 aSouza, Lara1 aSuding, K.N.1 aSuttle, B.K.1 aSvejcar, T.1 aTilman, David1 aTognetti, P.1 aTurkington, R.1 aWhite, S.1 aXu, Zhuwen1 aYahdjian, L.1 aYu, Q.1 aZhang, Pengfei1 aZhang, Yunhai uhttps://www.pnas.org/content/early/2019/08/14/181902711601811nas a2200217 4500008004100000245005400041210005300095300001600148490000600164520117700170100001801347700001601365700002201381700001601403700001801419700001901437700001801456700001401474700002401488856008101512 2016 eng d00acodyn: An R package of community dynamics metrics0 acodyn An R package of community dynamics metrics a1146–11510 v73 a
  1. New analytical tools applied to long-term data demonstrate that ecological communities are highly dynamic over time. We developed an r package, library(“codyn”), to help ecologists easily implement these metrics and gain broader insights into ecological community dynamics.
  2. library(“codyn”) provides temporal diversity indices and community stability metrics. All functions are designed to be easily implemented over multiple replicates.
  3. Temporal diversity indices include species turnover, mean rank shifts and rate of community change over time. Community stability metrics calculate overall stability and patterns of species covariance and synchrony over time, and include a null-modelling method to test significance.
  4. Finally, library(“codyn”) contains vignettes that describe methods and reproduce figures from published papers to help users contextualize and apply functions to their own data.
1 aHallett, L.M.1 aJones, S.K.1 aMacDonald, A.A.M.1 aJones, M.B.1 aFlynn, D.F.B.1 aRipplinger, J.1 aSlaughter, P.1 aGries, C.1 aCollins, Scott., L. uhttps://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.1256902081nas a2200241 4500008004100000245008200041210006900123300001500192490000700207520135700214100001801571700001401589700001801603700002401621700001801645700001701663700001901680700001601699700001601715700001701731700001701748856007401765 2014 eng d00aBiotic mechanisms of community stability shift along a precipitation gradient0 aBiotic mechanisms of community stability shift along a precipita a1693 -17000 v953 a

Understanding how biotic mechanisms confer stability in variable environments is a fundamental quest in ecology, and one that is becoming increasingly urgent with global change. Several mechanisms, notably a portfolio effect associated with species richness, compensatory dynamics generated by negative species covariance and selection for stable dominant species populations can increase the stability of the overall community. While the importance of these mechanisms is debated, few studies have contrasted their importance in an environmental context. We analyzed nine long-term data sets of grassland species composition to investigate how two key environmental factors, precipitation amount and variability, may directly influence community stability and how they may indirectly influence stability via biotic mechanisms. We found that the importance of stability mechanisms varied along the environmental gradient: strong negative species covariance occurred in sites characterized by high precipitation variability, whereas portfolio effects increased in sites with high mean annual precipitation. Instead of questioning whether compensatory dynamics are important in nature, our findings suggest that debate should widen to include several stability mechanisms and how these mechanisms vary in importance across environmental gradients.

1 aHallett, L.M.1 aHsu, J.S.1 aCleland, E.E.1 aCollins, Scott., L.1 aDickson, T.L.1 aFarrer, E.C.1 aGherardi, L.A.1 aGross, K.L.1 aHobbs, R.J.1 aTurnbull, L.1 aSuding, K.N. uhttps://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/13-0895.103196nas a2200241 4500008004100000245010800041210006900149300001500218490000700233520244600240100001802686700002402704700001802728700001702746700001602763700001902779700001802798700001602816700001402832700001702846700001702863856007402880 2013 eng d00aSensitivity of grassland plant community composition to spatial vs. temporal variation in precipitation0 aSensitivity of grassland plant community composition to spatial  a1687 -16960 v943 a

Climate gradients shape spatial variation in the richness and composition of plant communities. Given future predicted changes in climate means and variability, and likely regional variation in the magnitudes of these changes, it is important to determine how temporal variation in climate influences temporal variation in plant community structure. Here, we evaluated how species richness, turnover, and composition of grassland plant communities responded to interannual variation in precipitation by synthesizing long-term data from grasslands across the United States. We found that mean annual precipitation (MAP) was a positive predictor of species richness across sites, but a positive temporal relationship between annual precipitation and richness was only evident within two sites with low MAP. We also found higher average rates of species turnover in dry sites that in turn had a high proportion of annual species, although interannual rates of species turnover were surprisingly high across all locations. Annual species were less abundant than perennial species at nearly all sites, and our analysis showed that the probability of a species being lost or gained from one year to the next increased with decreasing species abundance. Bray-Curtis dissimilarity from one year to the next, a measure of species composition change that is influenced mainly by abundant species, was insensitive to precipitation at all sites. These results suggest that the richness and turnover patterns we observed were driven primarily by rare species, which comprise the majority of the local species pools at these grassland sites. These findings are consistent with the idea that short-lived and less abundant species are more sensitive to interannual climate variability than longer-lived and more abundant species. We conclude that, among grassland ecosystems, xeric grasslands are likely to exhibit the greatest responsiveness of community composition (richness and turnover) to predicted future increases in interannual precipitation variability. Over the long term, species composition may shift to reflect spatial patterns of mean precipitation; however, perennial-dominated systems will be buffered against rising interannual variation, while systems that have a large number of rare, annual species will show the greatest temporal variability in species composition in response to rising interannual variability in precipitation.

1 aCleland, E.E.1 aCollins, Scott., L.1 aDickson, T.L.1 aFarrer, E.C.1 aGross, K.L.1 aGherardi, L.A.1 aHallett, L.M.1 aHobbs, R.J.1 aHsu, J.S.1 aSuding, K.N.1 aTurnbull, L. uhttps://esajournals.onlinelibrary.wiley.com/doi/abs/10.1890/12-1006.102725nas a2200193 4500008004100000245011900041210006900160300001500229490000700244520206400251100002802315700001502343700001602358700001702374700001802391700001602409700001602425856009002441 2011 eng d00aExplaining temporal variation in above-ground productivity in a mesic grassland: the role of climate and flowering0 aExplaining temporal variation in aboveground productivity in a m a1250 -12620 v993 a

1. Annual above-ground net primary productivity (ANPP) in mesic grasslands is known to be highly temporally variable. While yearly precipitation or average yearly temperature can explain some of this temporal variability, much of the variation in ANPP remains unexplained. 2. Here we address the heretofore unexplained variation in 25 years of productivity data from a mesic grassland at Konza Prairie (north-eastern Kansas) by examining the effects of precipitation and temperature during periods relevant to the phenology and growth cycle of the dominant C4 grasses and the flowering stalk production of these species. We assessed both the direct effects and indirect effects via flowering of phenologically relevant climate periods on ANPP using structural equation modelling (SEM). 3. We found ANPP to be strongly positively influenced by flowering stalk production of the dominant C4 grasses, precipitation during periods relevant to vegetative growth (15 April–14 July) and flowering stalk elongation (15 July–14 August) of the dominant grasses, and fire. In addition, flowering stalk production was negatively influenced by high temperatures during the flowering stalk elongation period, which therefore resulted in a negative indirect effect on ANPP. We found little evidence for the effects of the previous year’s total annual precipitation or mean annual temperature on ANPP. 4. By including flowering stalk production and separating climate variables into phenologically relevant periods we were able to increase the percentage of observed variance in ANPP explained by six models, relating to different topographic positions and burn regimes, from an average of 22% to 48%, with the best model explaining 61% of variation in ANPP. 5.Synthesis. The link between climatic periods relevant to the phenology and growth of dominant C4 grasses, flowering stalk production of these grasses and ANPP shown here improves our ability to predict productivity in mesic grasslands, an ecologically and economically important ecosystem.

1 aLa Pierre, Kimberly, J.1 aYuan, S.H.1 aChang, C.C.1 aAvolio, M.L.1 aHallett, L.M.1 aSchreck, T.1 aSmith, M.D. uhttps://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2745.2011.01844.x