Showing papers by "Ralph Charles Mac Nally published in 2015"

How pervasive is biotic homogenization in human‐modified tropical forest landscapes?

Abstract: Land-cover change and ecosystem degradation may lead to biotic homogenization, yet our understanding of this phenomenon over large spatial scales and different biotic groups remains weak. We used a multi-taxa dataset from 335 sites and 36 heterogeneous landscapes in the Brazilian Amazon to examine the potential for landscape-scale processes to modulate the cumulative effects of local disturbances. Biotic homogenization was high in production areas but much less in disturbed and regenerating forests, where high levels of among-site and among-landscape β-diversity appeared to attenuate species loss at larger scales. We found consistently high levels of β-diversity among landscapes for all land cover classes, providing support for landscape-scale divergence in species composition. Our findings support concerns that β-diversity has been underestimated as a driver of biodiversity change and underscore the importance of maintaining a distributed network of reserves, including remaining areas of undisturbed primary forest, but also disturbed and regenerating forests, to conserve regional biota.

The effects of climate change and land-use change on demographic rates and population viability.

Abstract: Understanding the processes that lead to species extinctions is vital for lessening pressures on biodiversity. While species diversity, presence and abundance are most commonly used to measure the effects of human pressures, demographic responses give a more proximal indication of how pressures affect population viability and contribute to extinction risk. We reviewed how demographic rates are affected by the major anthropogenic pressures, changed landscape condition caused by human land use, and climate change. We synthesized the results of 147 empirical studies to compare the relative effect size of climate and landscape condition on birth, death, immigration and emigration rates in plant and animal populations. While changed landscape condition is recognized as the major driver of species declines and losses worldwide, we found that, on average, climate variables had equally strong effects on demographic rates in plant and animal populations. This is significant given that the pressures of climate change will continue to intensify in coming decades. The effects of climate change on some populations may be underestimated because changes in climate conditions during critical windows of species life cycles may have disproportionate effects on demographic rates. The combined pressures of land-use change and climate change may result in species declines and extinctions occurring faster than otherwise predicted, particularly if their effects are multiplicative.

Fast processing of diel oxygen curves: Estimating stream metabolism with BASE (BAyesian Single‐station Estimation)

Abstract: The measurement of stream metabolism (gross primary production and respiration) has become more feasible with the availability of more reliable dissolved oxygen (DO) probes. Such metabolic measurements offer important opportunities in fundamental and applied research, especially in relating stream metabolic responses to human and other pressures. The accurate determination of the reaeration coefficient is one challenge for making reliable ecological inferences from DO measurements made over many diel periods (i.e., months or years). We outline three methods for calculating atmospheric reaeration but concentrate on the use of statistical estimation to simultaneously estimate reaeration and metabolic rates using Bayesian model fitting. While there are existing programs (ModelMaker and Bayesian Metabolic Model [BaMM]), these are either slow or unable to be used easily for fitting multiple days of metabolic data (one to many months). Our implementation, BAyesian Single-station Estimation (BASE), uses freely available software (R and OpenBUGS), includes a batch mode that can fit data for many days, and provides visual and statistical measures of “goodness-of-fit.” We compare the results of the BASE, ModelMaker, and BaMM programs.

Reforestation with native mixed-species plantings in a temperate continental climate effectively sequesters and stabilizes carbon within decades

Abstract: Reforestation has large potential for mitigating climate change through carbon sequestration. Native mixed-species plantings have a higher potential to reverse biodiversity loss than do plantations of production species, but there are few data on their capacity to store carbon. A chronosequence (5-45 years) of 36 native mixed-species plantings, paired with adjacent pastures, was measured to investigate changes to stocks among C pools following reforestation of agricultural land in the medium rainfall zone (400-800 mm yr(-1)) of temperate Australia. These mixed-species plantings accumulated 3.09 ± 0.85 t C ha(-1) yr(-1) in aboveground biomass and 0.18 ± 0.05 t C ha(-1) yr(-1) in plant litter, reaching amounts comparable to those measured in remnant woodlands by 20 years and 36 years after reforestation respectively. Soil C was slower to increase, with increases seen only after 45 years, at which time stocks had not reached the amounts found in remnant woodlands. The amount of trees (tree density and basal area) was positively associated with the accumulation of carbon in aboveground biomass and litter. In contrast, changes to soil C were most strongly related to the productivity of the location (a forest productivity index and soil N content in the adjacent pasture). At 30 years, native mixed-species plantings had increased the stability of soil C stocks, with higher amounts of recalcitrant C and higher C:N ratios than their adjacent pastures. Reforestation with native mixed-species plantings did not significantly change the availability of macronutrients (N, K, Ca, Mg, P, and S) or micronutrients (Fe, B, Mn, Zn, and Cu), content of plant toxins (Al, Si), acidity, or salinity (Na, electrical conductivity) in the soil. In this medium rainfall area, native mixed-species plantings provided comparable rates of C sequestration to local production species, with the probable additional benefit of providing better quality habitat for native biota. These results demonstrate that reforestation using native mixed-species plantings is an effective alternative for carbon sequestration to standard monocultures of production species in medium rainfall areas of temperate continental climates, where they can effectively store C, convert C into stable pools and provide greater benefits for biodiversity.

Resistance and resilience of terrestrial birds in drying climates: do floodplains provide drought refugia?

Abstract: Aim Climate refugia will become increasingly important for biota as climate change causes an increased frequency and intensity of extreme events, such as drought. Floodplains are potential drought refugia because they have cooler and more mesic microclimates than adjacent areas, and greater water availability through shallower groundwater and flooding. We explored the role of floodplains as drought refugia by estimating the resistance and resilience of terrestrial birds over a 13-year drought (the ‘Big Dry’) and for 4 years following the break in the drought in floodplain and non-floodplain zones. Location Murray–Darling Basin, Australia. Methods We used Atlas of Australian Birds survey data from more than 39,000 surveys at over 28,000 sites to estimate trends in reporting rates in floodplain and non-floodplain zones for 144 bird species during extended drought (1998–2009) and in the post-drought period (2010–13). Results There was greater resistance to drought in floodplain zones: fewer species declined in floodplain zones (19%) than in non-floodplain zones (29%) during the Big Dry, and more species had elevated reporting rates (13% vs. 8%). More species showed a recovery in reporting rates in non-floodplain zones (40.3%) than in floodplain zones (15.3%) during the post-drought period, which was expected because declines during the Big Dry were more common in non-floodplain zones. There was some evidence for limitations in the resilience of floodplain avifauna, with only 17.9% of species that declined in floodplain zones during the drought subsequently recovering. Conclusions Floodplains appear to enhance resistance to drought for many bird species, and are likely to be particularly important as refugia in areas with an arid climate. However, their role in resilience is less clear. Floodplain ecosystems require long-term management to relieve pressures and to restore their ecological condition so that their role as drought refugia is maintained or enhanced.

Nitrogen loads explain primary productivity in estuaries at the ecosystem scale

Abstract: Increased nutrient loads stimulate estuary primary productivity and can alter the structure and function of biological communities within estuaries, particularly when producer groups respond differently to changes in nutrient availability. Here, the relative influence of riverine inputs of nitrogen and phosphorus were compared to determine their contribution to estuarine primary producers at large spatial scales. Indices of demersal (extent of macroalgae relative to other vegetation, total shallow water area vegetated) and planktonic (seasonally averaged chlorophyll concentration) primary producer communities were derived at whole-of-ecosystem scales in 14 estuaries dispersed across a longitudinal gradient using aerial imaging, underwater videography and in situ monitoring. A model selection framework was used to relate annual nutrient loads (total nitrogen [TN], dissolved inorganic nitrogen [DIN], total phosphorus [TP]), sediment loads (TSS), molar stoichiometric load ratios (TNM: TPM), and estuary water residence times to the demersal and planktonic indices. Dissolved inorganic nitrogen was the best predictor of the extent of macroalgae, total vegetation coverage, and the concentration of planktonic chlorophyll. Rapid increases in all three indices occurred at inorganic nitrogen loads of ∼ 5–10 Mg km−2 yr−1. There was some evidence that TNM: TPM, TP and TSS loads were informative model covariates. Relative to DIN loads, TP loads were a poor predictor of the macroalgal and planktonic indices. These findings underscore the critical role of catchment-derived nitrogen in contributing to producer communities at the whole-of-ecosystem scale and support the growing consensus that nitrogen loads (in addition to phosphorus) must be managed to effectively alleviate eutrophication in estuaries.

Avifaunal disarray: quantifying models of the occurrence and ecological effects of a despotic bird species.

Abstract: Aim Strongly interacting species have disproportionately large ecological effects relative to their abundances or biomass. We previously developed two conceptual models that described how one such strong interactor, the Australian bird the noisy miner Manorina melanocephala : (1) establishes resident high-density and hyperaggressive colonies and (2) in doing so, affects other biota and ecosystem processes. Here, we evaluate parts of those models relating to noisy miner habitat preferences and effects on bird assemblages using data from across the geographical range of the miner. Location Eastern Australia. Methods Avian-assemblage data were compiled for 2 128 survey transects (distributed over > 1.3 × 10 6 km 2 ) and were linked to variables reflecting productivity, local habitat structure and landscape context. Predictors were chosen based on the models, although detailed data for some variables were unavailable at such large scales. We used hierarchical Bayesian models that included observation models to account for different survey effort coupled with potentially nonlinear, spatially-explicit process models. Conclusions Noisy miner densities increased with proximity to forest edges (higher densities on forest edges and open sites), in low rainfall areas, and in vegetation dominated by trees with blade-shaped rather than needle-shaped leaves. The presence of noisy miners at even relatively small densities (> 0.6 individuals ha −1 ) depressed both species richness and the abundances of smaller ( 63 g) bird species. In areas with higher mean rainfall, the associations between noisy miners and small- and large-bird species were more negative and less positive, respectively.

Fragmentation, vegetation change and irruptive competitors affect recruitment of woodland birds

Abstract: Early View (EV): 1-EVAnthropogenic greenhouse gas emissions have been linked to increasing global temperatures, changes in the spatial patterns of precipitation, and increases in the severity and frequency of extreme climatic events, such as droughts and floods (IPCC 2007). Increases in extreme climatic events arising from global warming, including drought and heat stress, have led to widespread vegetation dieback (Allen et al. 2010) that may be amplified in fragmented sys-tems (Bennett et al. 2013).Vegetation change has many effects on biota, such as reduced survival and breeding, smaller population sizes, changed dispersal, and altered species composition (Mac Nally and Bennett 1997). Changes in assemblage composi-tion occur because species have different responses to habitat change (Ockinger et al. 2010). Different species composi-tion affects interspecific interactions, such as competition, predation, parasitism and pollination, which influence assemblage dynamics and ecosystem function (Ewers and Didham 2006). Some species that strongly interact with others have a disproportionate influence on assemblage structure (Mac Nally et al. 2012). Highly competitive spe-cies that are tolerant of, or benefit from, direct or indirect human disturbances may monopolize resources (nesting sites and food) and limit the survival and recruitment of distur-bance-sensitive species (Brown 2007). Despite extensive evi-dence that habitat attributes and interspecific interactions control species assemblages, biotic interactions are poorly integrated into biogeographical knowledge because of difficulties in measuring interaction strengths that vary in space and time (Brown 2007, Tylianakis et al. 2008).Studies on the effects of human pressures typically focus on impacts on species richness, assemblage composi-tion or, more less commonly, abundances, but these measures may not provide an indication of the population viabilities of the constituent taxa (Korfanta et al. 2012). Degraded habitat may act as an ‘ecological trap’ into which individuals of a species may be attracted but in which they are unable to breed successfully (Battin 2004). The ‘gold standard’ to address this would be to conduct a full demographic analysis at the appropriate spatial scale for the taxa of interest, including species-specific measurements of recruitment, mortality, emigration and immigration (Selwood et al. pers. comm.). This probably is infeasible for even one species let alone assemblages of dozens of taxa, so a compromise is to move to a subset of measures that relate to recruitment rather than point

A bust but no boom: responses of floodplain bird assemblages during and after prolonged drought

Abstract: © 2015 British Ecological Society.Climate change alters the frequency and severity of extreme events, such as drought. Such events will be increasingly important in shaping communities as climate change intensifies. The ability of species to withstand extreme events (resistance) and to recover once adverse conditions abate (resilience) will determine their persistence. We estimated the resistance and resilience of bird species during and after a 13-year drought (the 'Big Dry') in floodplain forests in south-eastern Australia. We conducted bird surveys at the beginning and end of the Big Dry, and after the abrupt end to the drought (the 'Big Wet'), to evaluate species-specific changes in reporting rates among the three periods. We assessed changes in bird-breeding activity before and after the Big Wet to estimate demographic resilience based on breeding. Between the start and the end of the Big Dry (1998 vs. 2009), 37 of 67 species declined substantially. Of those, only two had increased reporting rates after the Big Wet (2009 vs. 2013) that were equal to or larger than their declines, while three partially recovered. All other declining species showed low resilience: 25 showed no change in reporting rates and seven declined further. The number of breeding species and total breeding activity of all species declined after the Big Wet, and there was no change in the number of young produced. The Big Dry caused widespread declines in the floodplain avifauna. Despite the drought being broken by 2 years of well-above-average rainfall and subsequent near-average rainfall, most species showed low resilience and there was little indication that overall breeding had increased. The effects of drought appeared to be pervasive for much of the floodplain avifauna, regardless of species traits (species body mass, fecundity, mobility or diet). Ecosystems such as these are likely to require active management and restoration, including reinstatement of natural flooding regimes, to improve ecological condition, to enhance resistance and resilience to extreme climate events.

Function regression in ecology and evolution: FREE

Abstract: Summary Many questions in ecology and evolutionary biology consider response variables that are functions (e.g. species-abundance distributions) rather than a single scalar value (e.g. species richness). Although methods for analysing function-valued data have been available for several decades, ecological and evolutionary applications are rare. We outline methods for regression when the response variable is a function (‘function regression') and introduce the r package FREE, which focuses on straightforward implementation and interpretation of function regression analyses. Several computational methods are implemented, including machine learning and several Bayesian methods. We compare different methods using simulated data and real ecological data on individual-size distributions (ISDs) of fish and trees. No single method performed best overall, with several performing equally well for a given data set. Which method to use depends on sample sizes and the questions being considered; in many cases, a consensus approach should be used to combine or compare fitted models. Function regression allows the direct modelling of many function-valued data (e.g. species-abundance distributions) rather than having to reduce those functions to a single scalar response variable (e.g. species diversity or functional diversity indices). Our ecological examples using ISD data show that larger rivers support more-even fish-size distributions than smaller rivers and that low initial planting densities lead to more-even tree-size distributions than high initial planting densities. Function regression provided more informative and intuitive interpretations of these data than conventional non-function-valued approaches.

Climate drying amplifies the effects of land-use change and interspecific interactions on birds

Abstract: Climate change may amplify the effects of land-use change, including induced changes in interspecific interactions. To investigate whether an avifauna changed over a period of severe drought, and if changes in avifaunas were related to changes in vegetation characteristics and the irruption of a despotic native species, the noisy miner Manorina melanocephala. In the box–ironbark forests of south-eastern Australia, we resurveyed the avifaunas and remeasured vegetation characteristics in 120 forest transects in 2010–2011 that had previously been measured in 1995–1997. The avifauna changed markedly over the prolonged drought, and changes were more marked in smaller fragments of remnant vegetation in which more pronounced vegetation change had occurred. The noisy miner increased differentially in smaller remnants adding to the declines, especially for small-bodied birds. Long droughts interspersed with short wet periods are projected for the region, so the imposition of climate effects on an already much-modified region has profound implications for the avifauna. The noisy miner has (and continues) to benefit from both land-use and climate change, so future sequences of drought interspersed with short wet periods are likely to lead to further changes in the avifauna as the miner extends its occupancy. Differential reductions in small nectarivores and insectivores will affect ecosystem processes, including the control of defoliating insects, seed dispersal and pollination.

A commentary on 'Long-term ecological trends of flow-dependent ecosystems in a major regulated river basin', by Matthew J. Colloff, Peter Caley, Neil Saintilan, Carmel A. Pollino and Neville D. Crossman

Abstract: Colloff et al. in Marine and Freshwater Research (http:dx.doi.org/10.1071/MF14067) examined time-series data for flow-dependent vegetation, invertebrates, fish, frogs, reptiles and waterbirds in the Murray–Darling Basin, 1905–2013. They concluded that temporal patterns fluctuated, declining during droughts and recovering after floods. They suggested that major changes in land use in the late 19th century permanently modified these freshwater ecosystems, irretrievably degrading them before major water diversions. Restoring water to the environment might then be interpreted as not addressing biotic declines. We argue that their conclusions are inadequately supported, although data quality remains patchy and they neglected the influence of hydrology and the timing and extent of water resource development. We are critical of the lack of adequate model specification and the omission of statistical power analyses. We show that declines of native flow-dependent flora and fauna have continued through the 20th and early 21st centuries, in response to multiple factors, including long-term changes in flow regimes. We argue that flow-regime changes have been critical, but not in isolation. So, returning water to the environment is a prerequisite for sustained recovery but governments need to improve monitoring and analyses to adequately determine effectiveness of management of the rivers and wetlands of the Murray–Darling Basin.

How might cross-system subsidies in riverine networks be affected by altered flow variability?

Abstract: The cross-system exchange of energy and nutrients (subsidies) is a core attribute of landscapes that controls productivity and community dynamics in recipient systems. Such exchanges are likely to be disrupted by human influences. Inland waters receive significant subsidies from inflows from the surrounding landscape. Hydrologic modifications by water extraction, damming or altered precipitation patterns affect the magnitude and timing of flow extremes, which disrupts longitudinal, lateral and vertical connectivity in river networks. How subsidy transport responds to flow extremes has been little explored because watershed budgets usually do not consider the influence of floods. We measured the effects of storm-flows on organic carbon dynamics (concentration and standing stock) and projected how altered hydrologic variability might affect organic carbon accumulation and transport. We sampled dissolved and particulate organic carbon concentration at base- and storm-flow conditions in 19 stream sites over 2 years and modelled annual carbon fluxes. The highest flow events (5% of time) dominated the annual export of dissolved (39%) and fine particulate (59%) organic carbon. High flows increased the transport of particulate relative to dissolved organic carbon and reduced the accumulation of benthic coarse organic carbon. Minor changes to flow variability and storm-flow magnitude or frequency will strongly affect exchange among systems, with substantial consequences for ecosystem function. Shifts in the extremes of hydrological variability must be considered to ensure the longitudinal, lateral and vertical subsidy dynamics in freshwater systems.

Bird responses to riparian management of degraded lowland streams in southeastern Australia

Abstract: We assessed the degree to which fencing, livestock exclusion, and replanting of riparian zones affected avian assemblages in massively cleared landscapes. Measurements were made at three creeks in the southern Murray–Darling Basin in southeastern Australia, each of which had circa 1-km long treated sections and paired “untreated” circa 1-km sections, where no fencing, planting, or stock exclusion was done. We measured the change in vegetation characteristics and abundances of native birds for up to 8 years after works were completed. Prior to data collection, we developed expected responses of bird species based on the anticipated time-courses of change in vegetation structure. We used hierarchical Bayesian models to explore the effects of the management actions, and to account for within-site variation in vegetation characteristics. There were major changes in vegetation structure (reductions in bare ground and increases in shrubs and tree recruitment) but avian responses generally were small and not as expected. There are at least four possible reasons for the limited avian responses: (1) there has been a long-term decline in woodland birds across the region; (2) the study was conducted during the longest drought in the instrumental record in the study region; (3) the total amount of replanted vegetation was small in a massively denuded region; and (4) monitoring may have been over too short a term to detect responses to longer-term changes in structural vegetation.

Thermodynamics predicts density-dependent energy use in organisms and ecological communities

Abstract: Linking our knowledge of organisms to our knowledge of ecological communities and ecosystems is a key challenge for ecology. Individual size distributions (ISDs) link the size of individual organisms to the structure of ecological communities, so that studying ISDs might provide insight into how organism functioning affects ecosystems. Similarly shaped ISDs among ecosystems, coupled with allometric links between organism size and resource use, suggest the possibility of emergent resource-use patterns in ecological communities. We drew on thermodynamics to develop a maximization principle that predicted both organism and community energy use. These predictions highlighted the importance of density-dependent metabolic rates and were able to explain nonlinear relationships between community energy use and community biomass. We analyzed data on fish community energy use and biomass and found evidence of nonlinear scaling, which was predicted by the thermodynamic principle developed here and is not explained by other theories of ISDs. Detailed measurements of organism energy use will clarify the role of density dependence in driving metabolic rates and will further test our derived thermodynamic principle. Importantly, our study highlights the potential for fundamental links between ecology and thermodynamics.