Spatio‐temporal scaling of biodiversity and the species–time relationship in a stream fish assemblage

1. The increase of species richness with the area of the habitat sampled, that is the species–area relationship, and its temporal analogue, the species–time relationship (STR), are among the few general laws in ecology with strong conservation implications. However, these two scale‐dependent phenomena have rarely been considered together in biodiversity assessment, especially in freshwater systems. 2. We examined how the spatial scale of sampling influences STRs for a Central‐European stream fish assemblage (second‐order Bernecei stream, Hungary) using field survey data in two simulation‐based experiments. 3. In experiment one, we examined how increasing the number of channel units, such as riffles and pools (13 altogether), and the number of field surveys involved in the analyses (12 sampling occasions during 3 years), influence species richness. Complete nested curves were constructed to quantify how many species one observes in the community on average for a given number of sampling occasions at a given spatial scale. 4. In experiment two, we examined STRs for the Bernecei fish assemblage from a landscape perspective. Here, we evaluated a 10‐year reach level data set (2000–09) for the Bernecei stream and its recipient watercourse (third‐order Kemence stream) to complement results on experiment one and to explore the mechanisms behind the observed patterns in more detail. 5. Experiment one indicated the strong influence of the spatial scale of sampling on the accumulation of species richness, although time clearly had an additional effect. The simulation methodology advocated here helped to estimate the number of species in a diverse combination of spatial and temporal scale and, therefore, to determine how different scale combinations influence sampling sufficiency. 6. Experiment two revealed differences in STRs between the upstream (Bernecei) and downstream (Kemence) sites, with steeper curves for the downstream site. Equations of STR curves were within the range observed in other studies, predominantly from terrestrial systems. Assemblage composition data suggested that extinction–colonisation dynamics of rare, non‐resident (i.e. satellite) species influenced patterns in STRs. 7. Our results highlight that the determination of species richness can benefit from the joint consideration of spatial and temporal scales in biodiversity inventory surveys. Additionally, we reveal how our randomisation‐based methodology may help to quantify the scale dependency of diversity components (α, β, γ) in both space and time, which have critical importance in the applied context.     

Species–area relationships and biodiversity loss in fragmented landscapes

To estimate species loss from habitat destruction, ecologists typically use species–area relationships, but this approach neglects the spatial pattern of habitat fragmentation. Here, we provide new, easily applied, analytical methods that place upper and lower bounds on immediate species loss at any spatial scale and for any spatial pattern of habitat loss. Our formulas are expressed in terms of what we name the ‘Preston function’, which describes triphasic species–area relationships for contiguous regions. We apply our method to case studies of deforestation and tropical tree species loss at three different scales: a 50 ha forest plot in Panama, the tropical city‐state of Singapore and the Brazilian Amazon. Our results show that immediate species loss is somewhat insensitive to fragmentation pattern at small scales but highly sensitive at larger scales: predicted species loss in the Amazon varies by a factor of 16 across different spatial structures of habitat loss.     

Global macroecology of bird assemblages in urbanized and semi‐natural ecosystems

Aim Despite the increasing pace of urbanization, little is known about how this process affects biodiversity globally. We investigate macroecological patterns of bird assemblages in urbanized areas relative to semi‐natural ecosystems. Location World‐wide. Methods We use a database of quantitative bird surveys to compare key assemblage structure parameters for plots in urbanized and semi‐natural ecosystems controlling for spatial autocorrelation and survey methodology. We use the term ‘urbanized’ instead of ‘urban’ ecosystems as many of the plots were not located in the centre of towns but in remnant habitat patches within conurbations. Results Some macroecological relationships were conserved in urbanized landscapes. Species–area, species–abundance and species–biomass relationships did not differ significantly between urbanized and non‐urbanized environments. However, there were differences in the relationships between productivity and assemblage structure. In forests, species richness increased with productivity; in both forests and open habitats, the evenness of species abundances declined as productivity increased. Among urbanized plots, instead, both species richness and the evenness of species abundances were independent of variation in productivity. Main conclusions Remnant habitats within urbanized areas are subject to many ecological alterations, yet key macroecological patterns differ remarkably little in urbanized versus non‐urbanized plots. Our results support the need for increased conservation activities in urbanized landscapes, particularly given the additional benefits of local experiences of biodiversity for the human population. With increasing urbanization world‐wide, broad‐scale efforts are needed to understand and manage the effects of this driver of change on biodiversity.     

Spatio‐temporal scaling of biodiversity in acoustic tropical bird communities

Automated analysis of acoustic communities is a rapidly emerging approach for the characterization and monitoring of biodiversity. To evaluate its utility, we should verify that such ‘bioacoustics’ can accurately detect ecological signal in spatiotemporal acoustic data. Targeting the ‘Biological Dynamics of Forest Fragments Project’ sites in Brazil, we ask: What is the relative contribution of the spatial, temporal and habitat dimension to variation in bird acoustic communities in a previously fragmented tropical rainforest? Does the functional diversity of bird communities scale similarly to space and time as does species diversity, when both are recorded by bioacoustics means? Overall, is the imprint of landscape fragmentation 30 years ago still audible in the present‐day soundscape? We sampled forty‐four sites in secondary forest and 107 sites in old‐growth forest, resulting in 11 000 h of audio recordings. We detected 60 bird species with satisfactory precision and recovered a linear log–log relation between sampling time and species diversity. Sites in primary forest host more species than sites in secondary forest, but the difference decreased with sampling time, as the slope was slightly higher in secondary than primary forests. Functional diversity, as exposed by vocalizing birds, accumulates faster than does species diversity. The similarity among local communities decreases with distance in both time and space, but stability in time is remarkably high: two acoustic samples from the same site one year (or more) apart prove more similar than two samples taken at the same time but from sites situated just a few hundred meters apart. These findings suggest that habitat modification can be heard as a long‐lasting imprint on the soundscape of regenerating habitats and identify soundscape–area and soundscape–time relations as a promising tool for biodiversity research, applied biomonitoring and restoration ecology.     

The response of stream fish to local and reach‐scale variation in the occurrence of a benthic aquatic macrophyte

1. The aquatic macrophyte Podostemum ceratophyllum has been shown to increase stream productivity, abundance and biomass of benthic invertebrates, and local occurrences of some stream fishes. However, experimental evidence that fishes preferentially associate with Podostemum is lacking, and the value of Podostemum as a predictor of stream fish assemblage composition has not been studied. 2. We conducted two short‐term (2 week), small‐scale (36 m²) experimental manipulations of Podostemum cover in the Conasauga River (Georgia and Tennessee, U.S.), and found higher abundances of benthic insectivorous fishes in patches with augmented (>80%) compared to reduced (7%) Podostemum cover. In an observational study, we quantified associations among percent cover of Podostemum, fish species richness, land cover, shoal length and base‐flow turbidity at 20 randomly selected shoals from a 39‐km reach that spanned a gradient of decreasing forest land cover. 3. Richness of all fish species and of lotic fishes peaked in the centre of the study reach, and richness was weakly correlated with predictor variables. Occupancy models for individual species also indicated that longitudinal position was a strong covariate for 13 of 19 species examined, with little support that Podostemum cover influenced occupancy. 4. Local associations may reflect choices by benthic fishes to utilise Podostemum, whereas downstream decline in fish species richness and Podostemum cover may reflect altered capacity of the system to support native species.     

Colonization and extinction of ant communities in a fragmented landscape

Abstract In this paper we tested the assumption that smaller and more isolated remnants receive fewer ant colonizers and lose more species. We also tested hypotheses to explain such a pattern. We sampled ants in Brazil for 3 years in 18 forest remnants and in 10 grasslands between them. We tested the influence of remnant area and isolation on colonization rate, as well as the effect of remnant area on extinction rate. We tested the correlation between remnant area and isolation to verify the landscape design. Colonization rate was not affected by remnant area or isolation. Extinction rate, however, was smaller in larger remnants. Remnant area and isolation were negatively correlated. We tested two hypotheses related to the decrease in ant species extinction rate with increased remnant area: (i) small remnants support smaller and more extinction‐prone populations; and (ii) small remnants are more often invaded by generalist species, which suffer higher extinction inside remnants. The density of ant populations significantly increased with area. Generalist species presented a lower colonization rate in larger remnants, contrary to the pattern observed in forest species. Generalist species suffered more extinction than expected inside remnants. The lack of response of colonization rate to remnant area can be explained by the differential colonization by generalist and forest species. The decrease of ant population density in smaller remnants could be related to loss of habitat quality or quantity. The higher colonization by generalist ant species in the smaller remnants could be related to landscape design, because smaller remnants are more similar to the matrix than larger ones. Our results have important implications for conservation strategies because small remnants seem to be more affected by secondary effects of fragmentation, losing more forest species and being invaded more often by generalist species. Studies that compare only species richness between remnants cannot detect such patterns in species composition.     

Plants on small islands revisited: the effects of spatial scale and habitat quality on the species–area relationship

Understanding how species diversity is related to sampling area and spatial scale is central to ecology and biogeography. Small islands and small sampling units support fewer species than larger ones. However, the factors influencing species richness may not be consistent across scales. Richness at local scales is primarily affected by small‐scale environmental factors, stochasticity and the richness at the island scale. Richness at whole‐island scale, however, is usually strongly related to island area, isolation and habitat diversity. Despite these contrasting drivers at local and island scales, island species–area relationships (SARs) are often constructed based on richness sampled at the local scale. Whether local scale samples adequately predict richness at the island scale and how local scale samples influence the island SAR remains poorly understood. We investigated the effects of different sampling scales on the SAR of trees on 60 small islands in the Raja Ampat archipelago (Indonesia) using standardised transects and a hierarchically nested sampling design. We compared species richness at different grain sizes ranging from single (sub)transects to whole islands and tested whether the shape of the SAR changed with sampling scale. We then determined the importance of island area, isolation, shape and habitat quality at each scale on species richness. We found strong support for scale dependency of the SAR. The SAR changed from exponential shape at local sampling scales to sigmoidal shape at the island scale indicating variation of species richness independent of area for small islands and hence the presence of a small‐island effect. Island area was the most important variable explaining species richness at all scales, but habitat quality was also important at local scales. We conclude that the SAR and drivers of species richness are influenced by sampling scale, and that the sampling design for assessing the island SARs therefore requires careful consideration.     

Multiple facets of biodiversity are threatened by mining-induced land-use change in the Brazilian Amazon

Aim

Mining is increasingly pressuring areas of critical importance for biodiversity conservation, such as the Brazilian Amazon. Biodiversity data are limited in the tropics, restricting the scope for risks to be appropriately estimated before mineral licensing decisions are made. As the distributions and range sizes of other taxa differ markedly from those of vertebrates—the common proxy for analysis of risk to biodiversity from mining—whether mining threatens lesser-studied taxonomic groups differentially at a regional scale is unclear.

Location

Brazilian Amazon.

Methods

We assess risks to several facets of biodiversity from industrial mining by comparing mining areas (within 70 km of an active mining lease) and areas unaffected by mining, employing species richness, species endemism, phylogenetic diversity and phylogenetic endemism metrics calculated for angiosperms, arthropods and vertebrates.

Results

Mining areas contained higher densities of species occurrence records than the unaffected landscape, and we accounted for this sampling bias in our analyses. None of the four biodiversity metrics differed between mining and nonmining areas for vertebrates. For arthropods, species endemism was greater in mined areas. Mined areas also had greater angiosperm species richness, phylogenetic diversity and phylogenetic endemism, although less species endemism than unmined areas.

Main Conclusions

Unlike for vertebrates, facets of angiosperm and arthropod diversity are relatively higher in areas of mining activity, underscoring the need to consider multiple taxonomic groups and biodiversity facets when assessing risk and evaluating management options for mining threats. Particularly concerning is the proximity of mining to areas supporting deep evolutionary history, which may be impossible to recover or replace. As pressures to expand mining in the Amazon grow, impact assessments with broader taxonomic reach and metric focus will be vital to conserving biodiversity in mining regions.     

Richness and composition of plants and birds on land‐bridge islands: effects of island attributes and differential responses of species groups

Aim To test relationships between the richness and composition of vascular plants and birds and attributes of habitat fragments using a model land‐bridge island system, and to investigate whether the effects of fragmentation differ depending on species natural history traits. Location Thousand Island Lake, China. Methods We compiled presence/absence data of vascular plant and bird species through exhaustive surveys of 41 islands. Plant species were assigned to two categories: shade‐intolerant and shade‐tolerant species; bird species were assigned to three categories: edge, interior, and generalist species. We analysed the relationships between island attributes (area, isolation, elevation, shape complexity, and perimeter to area ratio) and species richness using generalized linear models (GLMs). We also investigated patterns of composition in relation to island attributes using ordination (redundancy analysis). Results We found that island area explained a high degree of variation in the species richness of all species groups. The slope of the species–area relationship (z) was 0.16 for all plant species and 0.11 for all bird species. The lowest z‐value was for generalist birds (0.04). The species richness of the three plant species groups was associated with island area per se, while that of all, generalist, and interior birds was explained mainly by elevation, and that of edge bird species was associated primarily with island shape. Patterns of species composition were most strongly related to elevation, island shape complexity, and perimeter to area ratio rather than to island area per se. Species richness had no significant relationship with isolation, but species composition did. We also found differential responses among the species groups to changes in island attributes. Main conclusions Within the Thousand Island Lake system, the effects of fragmentation on both bird and plant species appear to be scale‐dependent and taxon‐specific. The number of plant species occurring on an island is strongly correlated with island area, and the richness of birds and the species composition of plants and birds are associated with variables related to habitat heterogeneity. We conclude that the effects of fragmentation on species diversity and composition depend not only on the degree of habitat loss but also on the specific patterns of habitat fragmentation.     

Biodiversity–ecosystem function experiments reveal the mechanisms underlying the consequences of biodiversity change in real world ecosystems

In a recent Forum paper, Wardle (Journal of Vegetation Science, 2016) questions the value of biodiversity–ecosystem function (BEF) experiments with respect to their implications for biodiversity changes in real world communities. The main criticism is that the previous focus of BEF experiments on random species assemblages within each level of diversity has ‘limited the understanding of how natural communities respond to biodiversity loss.’ He concludes that a broader spectrum of approaches considering both non‐random gains and losses of diversity is essential to advance this field of research. Wardle's paper is timely because of recent observations of frequent local and regional biodiversity changes across ecosystems. While we appreciate that new and complementary experimental approaches are required for advancing the field, we question criticisms regarding the validity of BEF experiments. Therefore, we respond by briefly reiterating previous arguments emphasizing the reasoning behind random species composition in BEF experiments. We describe how BEF experiments have identified important mechanisms that play a role in real world ecosystems, advancing our understanding of ecosystem responses to species gains and losses. We discuss recent examples where theory derived from BEF experiments enriched our understanding of the consequences of biodiversity changes in real world ecosystems and where comprehensive analyses and integrative modelling approaches confirmed patterns found in BEF experiments. Finally, we provide some promising directions in BEF research.     

Fine‐scale movements and habitat use of juvenile southern flounder Paralichthys lethostigma in an estuarine seascape

Habitat use of juvenile southern flounder Paralichthys lethostigma was examined within a shallow estuarine seascape during June and July 2011 using acoustic telemetry. Fine‐scale movement and habitat use of P. lethostigma was investigated with an acoustic positioning system placed in a seascape that varied in habitat type, physicochemical conditions and bathymetry. The use of different habitat types was examined with Euclidean distance‐based analyses, and generalized additive models were used to determine the relative importance of habitat type relative to physicochemical conditions and bathymetry. Tracks of P. lethostigma ranged in distance between 1477 and 8582 m and speed was 4·2 ± 1·1 m min^?1 (mean ± s.e .) for all P. lethostigma combined. Depth, slope and habitat type had the most influence on P. lethostigma occurrence and deep sandy areas with shallow slopes were used most frequently. In addition, depth use by P. lethostigma was influenced by tidal cycles, indicating habitat use varies temporally and is dynamic. Finally, temperatures <30·5° C were used more than warmer waters within the study area. The results successfully identify movements by juvenile P. lethostigma, and indicate that definitions of essential habitats need to account for dynamics in habitat use.