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Something is not quite right: Effects of two land uses on anuran diversity in subtropical grasslands
Abstract
Although habitat modification is considered one of the main causes of biodiversity loss, the relative contribution of different rural land uses to biodiversity conservation is far less known. Additionally, the realization of the multidimensionality of biodiversity demands studies integrating variation of functional traits and phylogenetic information as complements to address the effects of land use on the structure of animal communities. Herein, we investigated the effects of land use (i.e., intensive agricultural and extensive livestock rearing) on functional and phylogenetic diversity of anuran communities in farmland ponds from the Uruguayan savanna ecoregion, while considering the effects of local factors (i.e., water depth) on species composition. We surveyed adults and tadpoles in 22 ponds and quantified five traits related to tadpole feeding, habitat use, and predator avoidance. Tadpole identification was corroborated by DNA barcoding based on a fragment of the mitochondrial 16S rRNA gene. We observed a decline in phylogenetic mean nearest taxon distance associated with increase of surrounding agricultural land use. While land use intensification did not affect richness (functional or phylogenetic), ponds in livestock ranches hosted about four times more tadpoles than agricultural ponds. Functional evenness decreased with water depth, although such relationship disappeared when considering phylogenetic non‐independence. Our results indicated that specific anuran clades were more sensitive to intensification in land use, reinforcing a recent view of phylogenetic homogenization following habitat conversion. Additionally, our study suggests that extensive cattle grazing over wide native pastures may provide an alternative more compatible with conservation than short‐term crops in subtropical grasslands.
Abstract in Portuguese is available with online material.
... Ignoring such phylogenetic relationships might distort inferences of assembly mechanisms because of biological and methodological reasons (Cadotte et al., 2017). For example, functional evenness (FEve) decreases with water depth, but such association seems to be a statistical artefact generated by phylogenetic non-independency among tadpole species (Moreira et al., 2020). As such, combining functional and phylogenetic metrics enables insights into evolutionary and ecological dynamics (Lipinski et al., 2020;Ribeiro et al., 2017). ...
... In addition, human land uses affect habitat suitability for amphibian species and eventually affect tadpole morphology, depending on adult reproductive mode and tadpole plasticity. Evidence from southern Brazil has shown that crop areas (Moreira et al., 2020;Saccol et al., 2022) and exotic reforestation (Machado et al., 2012;Saccol et al., 2017) promote amphibian biodiversity erosion in its different dimensions (e.g., taxonomic, functional, and phylogenetic). ...
... We cannot rule out the possibility that land use might affect other tadpole traits. Traits associated with food acquisition are effect traits and, therefore, more likely to affect ecosystem services, such as nutrient cycling (e.g., Moreira et al., 2020;Sun et al., 2023). Sadly, the feeding ecology of Neotropical tadpoles is relatively poorly known . ...
Land use changes are considered a significant cause of amphibian declines worldwide. However, little is known regarding which land uses have more pervasive impacts and which help to supplement the biodiversity conserved in protected areas. In addition, amphibian species respond to a broad array of geographical constraints, which may blur responses to disturbance, depending on the species' natural history.
Here, we explored whether functional diversity patterns of amphibian assemblages are linked to human land use while considering spatial autocorrelation and phylogenetic relatedness among species. We surveyed tadpoles along 500 km in coastal wetlands in southern Brazil and quantified four traits related to tadpole habitat use and predator avoidance.
Spatial components influenced functional richness to a greater extent than land use. Functional evenness was higher in ponds surrounded by more exotic reforestation, and to a lesser extent an effect of crop area. Functional divergence was also associated with reforestation areas.
Our results showed that some land uses (reforestation with exotic species and temporary crops) have more pervasive impacts on tadpole communities. Such changes in amphibian communities occurred even at low levels of landscape change. Our findings highlight that conversion to human land use requires complementary approaches (i.e., tadpole and adult responses) to provide early warning signals about habitat modification effects.
... Evidence already shows that the conversion of natural grasslands into shortterm crops promotes biodiversity erosion in its different dimensions (i.e., species richness, functional and phylogenetic diversity). Such erosion is consistent across primary producers, terrestrial consumers, and key consumers in wetlands (Staude et al. 2018;Moreira et al. 2020;Saccol et al. 2022). In a closer look at amphibians, phylogenetic relatedness and reproductive modes mediate most responses to land use intensification Saccol et al. 2022). ...
... Species that deposit eggs directly in the water, without the protection of foam nests, are the most sensible to grassland modification ( Fig. 13.2a). Currently, there is growing consensus that extensive cattle grazing over large native pastures may provide an alternative more compatible with conservation than short-term crops in wetlands of Campos Sulinos (e.g., Fontana et al. 2016;Staude et al. 2018;Moreira et al. 2020). After the conversion of natural ecosystems around wetlands to croplands, alterations of hydrological regimes and vegetation homogenization are the immediate impacts on freshwater communities. ...
Wetlands are among the most productive ecosystems on the earth, with enormous ecological and social importance. Here, we cover most of the recent knowledge produced in relation to the wetland ecosystems of Pampa and South Brazilian highland grasslands (Campos Sulinos). We review the main drivers of the biodiversity of small wetlands; the contribution of specific land-management practices to wetland-dependent wildlife; the importance of dispersal processes to the biodiversity of isolated wetlands; the occurrence of endemic and endangered annual fish species; and the importance of restoration initiatives in impacted wetlands. Finally, we provide some suggestions that provide relevant information to wetland conservation and management in the Campos Sulinos. The wetlands of the Campos Sulinos present high biological diversity for different groups of organisms (invertebrates and vertebrates). The conservation of the wetlands will guarantee the maintenance of a large part of the region’s biological and genetic diversity and will provide natural resources to local human population. In addition, the conservation of wetlands will provide leisure and recreation areas for the urban population, and minimize the negative impacts that floods bring to large- and medium-sized cities.
... Differences in land cover were recognized as the main drivers of patterns of compositional dissimilarity in communities of different taxa, including birds (Lee & Martin, 2017), amphibians (Iop et al., 2020;Moreira et al., 2020) and reptiles (Wanger et al., 2010). In general, the presence of soils with some type of vegetation cover is an essential condition for the maintenance of species, especially in the southern region of Brazil, where the conversion of natural habitats to human activities is intense (Iop et al., 2020;Moreira et al., 2020). ...
... Differences in land cover were recognized as the main drivers of patterns of compositional dissimilarity in communities of different taxa, including birds (Lee & Martin, 2017), amphibians (Iop et al., 2020;Moreira et al., 2020) and reptiles (Wanger et al., 2010). In general, the presence of soils with some type of vegetation cover is an essential condition for the maintenance of species, especially in the southern region of Brazil, where the conversion of natural habitats to human activities is intense (Iop et al., 2020;Moreira et al., 2020). More precisely, habitats composed of different types of vegetation are structurally more complex and, a priori, add a greater set of ecological niches that can be occupied by species with different ecological requirements (Valério et al., 2016;Dalmolin et al., 2020). ...
We studied the species composition of frogs in two phytophysiognomies within Pampa biome (grassland and forest) of a Ramsar site in southern Brazil to assess the distribution of species and dissimilarities in community composition on a small spatial scale. We tested the hypothesis that the vegetation structure and the types of land cover present in each physiognomy influence species distribution and the compositional dissimilarity patterns between locations. We sampled individuals using pitfall traps and active search in the areas around the traps. We evaluated the existence of these differences by using permutational multivariate analysis of variance and multivariate dispersion. We found that the compositional dissimilarity was higher between the sampling sites from different phytophysiognomies than within the same phytophysiognomy. Also, the difference in anuran species composition between the sampling sites within the forest was considerably high. These differences were mainly due to the type of land cover present in each sampled site. Based on our results, we could assume that the phytophysiognomies evaluated here offer quite different colonization opportunities for anurans, especially those related to microhabitat characteristics, such as microclimate variables. Still, the presence of different types of land cover seems to be a decisive factor for the maintenance of some anuran species, since these can serve as an important source for obtaining food resources, in addition to facilitating the dispersion of individuals within and between locals, serve as sites for the regulation of physiological functions and also refuges against predators.
KEYWORDS
Beta diversity; Dissimilarity; forest; south Brazil; Taim
... In a community dynamic viewpoint, β-diversity increases (greater heterogenization) when common species do not co-occur among all sites, or when new species arrive at some sites; and β-diversity decreases (homogenization) when rare or non-common species become extinct, or when formerly rare or absent species become widespread (Socolar et al. 2016 Functional and phylogenetic β-diversity have been relatively less investigated in fragmented landscapes when compared to traditional taxonomic metrics (Moreno et al. 2018), but despite being less used, some studies show that a decrease in such dimensions of β-diversity are associated with land-use intensi cation (Pereira et al. 2018; Moreira et al. 2020). Thus, decomposition of biodiversity into different dimensions may allow greater understanding of how communities are affected by forest conversion and fragmentation (Cisneros et al. 2015). ...
Diversity can be partitioned into several components and dimensions that are affected in different ways by habitat loss and fragmentation. However, these partitions and dimensions are rarely investigated in human-modified landscapes. In this study, we investigated different partitions (Hill numbers) and dimensions (taxonomic [TβD], functional [FβD] and phylogenetic [PβD]) of small mammal β-diversity in a fragmented landscape of central Brazil using a multi-scale approach. TβD was estimated considering rare, common and abundant species. Tolerance to disturbed habitat, assessed via the traits “habitat use”, “tail length” and “use of vertical strata”, and trophic guild, defined by “diet”, were used to estimate FβD. PβD was based on phylogenetic relatedness of the sampled species. The association between different partitions and dimensions of β-diversity and habitat and landscape attributes was investigated using Mantel tests. We found a significant positive effect of geographical distance on all partitions and dimensions of β-diversity. Canopy cover were positively associated with abundance-based TβD, FβD and PβD. While, forest area and normalized difference vegetation index (NDVI) were associated with PβD and FβD, respectively. Our findings support the hypothesis that even in a highly modified landscape, small mammal’s β-diversity is determined by different environmental factors and geographical distance of forest patches. However, the relatively higher importance of distance appears to be related to dispersal limitation of this group.
... The conversion of pristine habitats into agricultural areas is one of the main ways of intensifying land use worldwide (Ellis et al., 2010). This often negatively impacts biodiversity (Moreira et al., 2020;Susi & Laine, 2021) through changes in conditions, resources, and interactions between organisms (Valladares et al., 2015). After use and consecutive land abandonment, it is expected that the regeneration of native vegetation will gradually recover the diversity and functioning of the environment, depending on factors such as previous land use and the type of native vegetation (Latawiec et al., 2016;Warring et al., 2016). ...
Anthropogenic changes in habitats are one of the main threats to biodiversity.
Understanding how species diversity and their functions are affected by these
changes is crucial to assess environmental impacts. In this work, we aim to
understand how lizard composition, taxonomic and functional diversity respond
to differences in native vegetation regeneration stages (conserved vegetation
and open secondary vegetation) and agricultural land use in different vegetation
types (Caatinga sensu stricto, Cerrado sensu stricto and Relictual Humid Forest)
in Caatinga domain, Brazil. In more degraded areas (open secondary vegetation and agricultural areas), we found a decline in species evenness, shown
by greater dominance of few species. Moreover, we found a lower functional
evenness in agricultural areas than in areas of conserved vegetation, which suggests that a smaller portion of functional traits present greater dominance in
more anthropized areas. We did not detect any significant differences in species
richness, but we did registered differences in species composition in Relictual
Humid Forest. Contrary to our expectations, lizard abundance was also greater
in more degraded areas, probably as a result of the increased abundance of
species benefited by anthropization. In this work, we advance the knowledge of
how anthropogenic changes influence lizard diversity and emphasize the importance of analysing different facets of diversity and different habitat environments
to understand how anthropization affects patterns in community ecology.
... In a community dynamic viewpoint, β-diversity increases (greater heterogenization) when common species do not co-occur among all sites, or when new species arrive at some sites; and β-diversity decreases (homogenization) when rare or non-common species become extinct, or when formerly rare or absent species become widespread (Socolar et al. 2016 Functional and phylogenetic β-diversity have been relatively less investigated in fragmented landscapes when compared to traditional taxonomic metrics (Moreno et al. 2018), but despite being less used, some studies show that a decrease in such dimensions of β-diversity are associated with land-use intensi cation (Pereira et al. 2018; Moreira et al. 2020). Thus, decomposition of biodiversity into different dimensions may allow greater understanding of how communities are affected by forest conversion and fragmentation (Cisneros et al. 2015). ...
Diversity can be partitioned in several components and dimensions that are affected in different ways by habitat loss and fragmentation. However, these partitions and dimensions are rarely investigated on human-modified landscapes. In this study, we investigated different partitions (Hill numbers) and dimensions (taxonomic [TβD], functional [FβD] and phylogenetic [PβD]) of small mammal β-diversity in a fragmented landscape of central Brazil using a multi-scale approach. TβD was estimated considering rare, common and abundant species. Tolerance to disturbed habitat, assessed via the traits “habitat use”, “tail length” and “use of vertical strata”, and trophic guild, defined by the “diet”, were used to estimate FβD. PβD was based on phylogenetic relatedness of the sampled species. The association between different partitions and dimensions of β-diversity with habitat and landscape attributes were investigated using Mantel tests. We found a significant positive effect of geographical distance on all partitions and dimensions of β-diversity. NDVI was the second most important variable affecting abundance based TβD, and all phylogenetic and functional β-diversity dimensions. Habitat characteristics, such as fallen logs and canopy cover were positively associated with all β-diversity dimensions. Our findings support the hypothesis that even in a highly modified landscape, small mammal’s β-diversity is determined by different environmental factors and spatial disposition of forest patches. However, the relatively higher importance of space appears to be related to dispersal limitation of this group.
... Thus, we made comparisons on patterns of species richness, abundance, taxonomic composition, prevalence and intensity of parasitic infection, as well as how multiple-scale descriptors change among two contrasting land uses. The extensive livestock on native grasslands is considered a less impactful land-use type in this region (Pillar & Vélez-Martin, 2010), and it was recently highlighted as more compatible with anuran conservation than crops (see Santos et al., 2014;Iop et al., 2020;Moreira et al., 2020). Our hypotheses are: ...
Degradation and habitat loss of natural grasslands in Southern Brazil has a negative impact on native organisms, potentially including the composition of anuran helminth communities. Here, we characterized the richness, abundance, taxonomic composition, prevalence and intensity of helminth infection in four anuran species. Host anurans were collected in 34 ponds (19 in native grasslands with livestock and 15 in agricultural cultivation) from the highland grasslands in the Brazilian states of Santa Catarina and Paraná. Our results showed a significant difference between native grasslands with livestock and agricultural cultivation regarding the structure of helminth communities for the hosts Aplastodiscus perviridis and Pseudis cardosoi. We also found a greater prevalence and intensity of infection in anurans in areas of agricultural cultivation than in native grasslands with livestock. We found that the environmental descriptors (local and landscape) seem to explain most of the differences in anuran parasitism recorded between native grasslands with livestock and agricultural areas. Thus, we emphasized that the loss of grassy habitat due to conversion to agricultural cultivation can alter helminth communities in anurans, with further work needed to understand the mechanisms involved.
The degradation of natural ecosystems due to land use changes has been increasing, altering ecosystem composition, structure and processes, which negatively affects biodiversity. Herein, we explored how the diversity patterns of anurans respond to the scenario of extensive replacement of grasslands with agriculture in southernmost Brazil. We determined possible changes in the species richness, taxonomic composition, and structure of pond-breeding anuran communities in the grassland ecosystems of the South Brazilian Grasslands (SBG). Using the survey at breeding sites method, we sampled a total of 238 ponds, 153 from extensive livestock grazing on grasslands and 85 from agricultural areas. The higher species richness was found in the livestock areas on grasslands. There was a significant nestedness pattern associated with agricultural areas, indicating a non-random process of community simplification by species loss. Seven anuran species were considered land use indicators, of which five were considered indicators of grasslands with livestock, and two as indicators of agricultural areas. Generalist species were persistent and dominant in agricultural areas, while habitat specialists disappeared from these areas. Land use was a significant factor explaining the community structure segregation between land uses regardless of the natural variation reported at the local and regional levels. We highlight the importance of grasslands for the conservation of pond-breeding anurans in non-forest landscapes of the subtropical region, and we discuss the view that extensive livestock production needs strategic incentives to help the conservation of SBG biodiversity, such as multi-institutional measures.
Fauna inventories are important for the knowledge of local diversity; however, most ecosystems are underestimated, which is the case of grasslands. We conducted an inventory of the anuran species from the Biological Reserve of São Donato and summarized species richness along conservation units (CUs) in the Brazilian Pampa biome. This is one of the few CUs in the Brazilian Pampa, located in the southwest of Rio Grande do Sul state. We complemented the qualitative inventory with visual and auditive sampling surveys, and pitfall traps. We also searched for anuran records in scientific collections to complement the checklist. In addition, we performed an extensive literature review of published articles in academic databases to include further knowledge on the species richness. We found 19 species, distributed in five families, with confirmed occurrence in the Biological Reserve of São Donato. We recorded 18 species during field activities and one species was exclusively confirmed based on scientific collection data. We recorded at least other six species in the surrounding areas. To date, only five from 31 CUs along the Brazilian Pampa (16%) have published inventories of anuran species. We hope that our findings will stimulate future studies on anuran diversity in the remaining CUs of the Brazilian Pampa biome. Finally, we highlight that the Biological Reserve of São Donato is in real danger of disappearing within the next years due to a series of neglections, which have been encouraging rapid agricultural expansion on natural ecosystems.
Keywords. Anura, Species List, Grassland Ecosystems, Uruguayan Savanna, Southern Brazil
Pastureland currently occupies 26% of Earth's ice‐free land surface. As the global human population continues to increase and developing countries consume more protein‐rich diets, the amount of land devoted to livestock grazing will only continue to rise. To mitigate the loss of global biodiversity as a consequence of the ever‐expanding amount of land converted from native habitat into pastureland for livestock grazing, an understanding of how livestock impact wildlife is critical. While previous reviews have examined the impact of livestock on a wide variety of taxa, there have been no reviews examining how global livestock grazing affects amphibians. We conducted both an empirical study in south‐central Florida examining the impact of cattle on amphibian communities and a quantitative literature review of similar studies on five continents. Our empirical study analyzed amphibian community responses to cattle as both a binary (presence/absence) variable, and as a continuous variable based on cow pie density. Across all analyses, we were unable to find any evidence that cattle affected the amphibian community at our study site. The literature review returned 46 papers that met our criteria for inclusion. Of these studies, 15 found positive effects of livestock on amphibians, 21 found neutral/mixed effects, and 10 found negative effects. Our quantitative analysis of these data indicates that amphibian species that historically occurred in closed‐canopy habitats are generally negatively affected by livestock presence. In contrast, open‐canopy amphibians are likely to experience positive effects from the presence of livestock, and these positive effects are most likely to occur in locations with cooler climates and/or greater precipitation seasonality. Collectively, our empirical work and literature review demonstrate that under the correct conditions well‐managed rangelands are able to support diverse assemblages of amphibians. These rangeland ecosystems may play a critical role in protecting future amphibian biodiversity by serving as an “off‐reserve” system to supplement the biodiversity conserved within traditional protected areas.
Microhabitat use by tadpoles has been little documented, especially for neotropical anuran species. Here we describe microhabitat use by tadpoles in two different aquatic systems, lentic and lotic, in the Atlantic Rainforest. We sampled tadpoles in 98 sites within lentic habitats, and 187 sites within lotic habitats. We categorized each of the sites sampled according to its environmental features, such as aquatic vegetation cover, substrate type, and depth. To describe the tadpoles’ preferences in microhabitat use according to the environmental features, we performed a Canonical Correspondence Analysis for lentic and lotic water bodies separately. We noticed that in ponds, groups of tadpoles belonging to different species occurred in similar microhabitat types, determined especially by vegetation cover, depth, and organic matter. In contrast, stream-dwelling species showed particular preferences for specific microhabitat types, determined mostly by the kind of substrate (e.g., leaf litter, rock cover). Thus, in streams, the use of particular environmental features leads to differences in microhabitat use among species, driving the segregation of species within streams according to each microhabitat type. Therefore, pond-dwelling tadpoles tend to occur in similar environmental microhabitat, resulting in a greater number of species using the same type of microhabitat, than stream-dwelling tadpoles.
Significance
Widespread conversion of natural habitats to human land use creates evolutionarily novel environments and causes declines of native species. Stemming biodiversity loss requires an understanding of why some species persist while others decline in these novel habitats. We analyzed survey data of amphibian species from around the globe to determine whether closely related species respond similarly to habitat conversion. We find that species that persist in converted habitats tend to come from the same clades within the amphibian tree of life and that by favoring these widely distributed clades, habitat conversion leads to nonrandom extirpations and loss of evolutionary history. Our results show that the identity of winners and losers during the Anthropocene can be tightly linked to their evolutionary history.
Functional traits are increasingly being used to understand the response of species to environmental change and their effects on ecosystem functioning. However, some ecologically important traits, such as plant height, influence the probability of species detection during field surveys. Imperfect detection of species could therefore bias measures of functional trait composition and diversity, leading to incorrect estimates of trait–environment relationships due to a process of “detection filtering.” The importance of detection filtering for functional ecological studies remains unknown.
We used hierarchical models that account for detection filtering to analyse data on 1,296 vascular plant species sampled in 362 1‐km ² plots, distributed along a 2,460‐m elevational gradient in Central Europe. We examined how detection filtering altered measures of functional diversity (multivariate functional richness and packing) and composition (community means of three traits). We also determined whether the strength of detection filtering varied over the gradient, to determine whether detection filtering biased trait–environment relationships.
Species detectability was correlated with all three functional traits tested in this study, meaning that short species with small seeds and high specific leaf area values were less likely to be detected. This suggests that imperfect detection has the potential to bias measures of functional composition. Generally, measures of functional composition were not strongly affected by detection filtering, but functional packing was underestimated when detection filtering was not accounted for. In addition to the traits, distributional characteristics were important; rare species and species occurring mainly at low elevations tended to have lower detection probabilities.
Overall, detection filtering did not strongly bias trait–environment relationships because the effects of the environment on functional composition and diversity were larger than the effects of detection.
Our results suggest that many measures of functional composition and diversity are robust to detection filtering, but some are likely biased. Functional ecologists should consider correcting for imperfect detection, and our approach provides a simple method to do so for a wide range of datasets.
1. Habitat loss is one of the greatest threats to biodiversity, exerting negative effects on the ecological viability of natural vegetation remnants. The South Brazilian grasslands belong to one of the largest temperate grassland regions in the world, but have lost 50% of their natural extent in the past 35 years. To date, there is no empirical evidence for the effects of habitat loss on these grasslands' biological diversity, undermining their conservation.
2. Using data from a large-scale biodiversity survey, we asked if local plant communities respond to levels of habitat loss representative of the entire region (≤50%). Vegetation in grassland remnants was sampled in 24 landscapes at three localities each, using 9 plots per locality. To investigate whether species losses were a consequence of stochastic or nonrandom local extinctions and whether plant communities became more homogenized, we evaluated species richness, beta-diversity components (spatial turnover and nestedness), and phylogenetic diversity, in respect to landscape change. In part of the landscapes, arthropods were sampled to investigate if loss of plant diversity had a cascading effect on other trophic levels. We evaluated generic richness of ants, an omnivore group with high levels of plant associations, in respect to a plant community’s phylogenetic diversity.
3. Local plant communities in landscapes with less grassland cover had fewer species, less spatial turnover, increased nestedness and lower phylogenetic diversity. Our results suggest that the observed species loss can be linked to taxonomic homogenization and is nonrandom, decreasing evolutionary diversity within the community. Furthermore, ant richness declined by 50% in plant communities with the lowest phylogenetic diversity, suggesting that effects of habitat loss propagate to higher trophic levels.
4. Policy implications. We conclude that the biological diversity of South Brazilian grasslands, at the producer and consumer level, is at risk under the current rate of land use conversion, even at habitat losses below 50%. To avoid substantial biodiversity loss, conservation and more restrictive policies for conversion of native grasslands to different land uses in South Brazil are urgent.
Including threats in spatial conservation prioritization helps identify areas for conservation actions where biodiversity is at imminent risk of extinction. At the global level, an important limitation when identifying spatial priorities for conservation actions is the lack of information on the spatial distribution of threats. Here, we identify spatial conservation priorities under three prominent threats to biodiversity (residential and commercial development, agricultural expansion, and forest loss), which are primary drivers of habitat loss and threaten the persistence of the highest number of species in the International Union for the Conservation of Nature (IUCN) Red List, and for which spatial data is available. We first explore how global priority areas for the conservation of vertebrate (mammals, birds, and amphibians) species coded in the Red List as vulnerable to each threat differ spatially. We then identify spatial conservation priorities for all species vulnerable to all threats. Finally, we identify the potentially most threatened areas by overlapping the identified priority areas for conservation with maps for each threat. We repeat the same with four other well-known global conservation priority area schemes, namely Key Biodiversity Areas, Biodiversity Hotspots, the global Protected Area Network, and Wilderness Areas. We find that residential and commercial development directly threatens only about 4% of the global top 17% priority areas for species vulnerable under this threat. However, 50% of the high priority areas for species vulnerable to forest loss overlap with areas that have already experienced some forest loss. Agricultural expansion overlapped with ~20% of high priority areas. Biodiversity Hotspots had the greatest proportion of their total area under direct threat from all threats, while expansion of low intensity agriculture was found to pose an imminent threat to Wilderness Areas under future agricultural expansion. Our results identify areas where limited resources should be allocated to mitigate risks to vertebrate species from habitat loss.
Key innovations are organismal traits that trigger adaptive radiation and lineage diversification. The wide range of anuran reproductive strategies from aquatic to terrestrial modes are potential key innovations. One such strategy is the foam nest, a structure with multiple functions that originated independently several times in different continents. Here, we explore several evolutionary aspects associated with the foam nest in multiple lineages to test the hypothesis that this trait is phylogenetically conserved and has influenced diversification. We used the most inclusive anuran phylogeny to date to reconstruct ancestral states, measure phylogenetic signal and evaluate models of trait-dependent diversification. Our results show that the foam nest appeared during the Paleocene–Eocene transition (c. 55 Myr) in three major groups (Leptodactylidae, Limnodynastidae and Rhacophoridae) and has been highly conserved ever since. The foam nest probably originated from an ancestor with aquatic reproduction, except in Rhacophoridae (in which it evolved from an ancestor with jelly nests). Despite possessing several ecological functions, we found evidence of the influence of foam nests on diversification rates only in the South American lineage Leptodactylidae. We suggest that the foam nest was an important adaptation to historical climatic changes, enabling reproduction in dry open areas.
Agricultural expansion is a major driver of biodiversity loss, especially in the megadiverse tropics. Rice is among the world’s most important food crops, invariably affecting biodiversity worldwide. Although the effects of habitat conversion to rice crops on biodiversity are not completely understood, landscape modification often creates conditions that benefit some species and excludes others. We conducted an integrative evaluation of the effects that habitat conversion to irrigated rice crops has on anuran communities from a Cerrado-Amazon ecotone. We adopted a multidimensional approach to compare anuran communities from agricultural and pristine environments considering (i) taxonomic metrics; (ii) functional and phylogenetic diversity; (iii) selected and excluded traits and (iv) body condition indices. When compared to their pristine counterparts, agricultural waterbodies showed increased functional divergence and decreased species diversity and functional richness. Furthermore, agricultural anuran communities exhibited lower phylogenetic diversity. Nonetheless, taxonomic diversity did not vary significantly, suggesting that it should not be used without complementary metrics. Species with small range, habitat specialization, small clutches and large body size were excluded from rice crops. Furthermore, frogs showed lower body condition in crops than in pristine areas. Understanding how species traits correlate with specific responses to agriculture will allow better predictions of the functional effects of anthropogenic land-use. Maintaining high diversity in anthropogenic environments is important for ecosystem resilience because diverse communities are more likely to hold multiple species capable of contributing to ecological functions. Our results show that converting natural vegetation to irrigated rice crops drives many species to local extinction, and resilient species to exhibit lower body condition.
Because ecosystems throughout the globe are contaminated with pesticides, there is a need to understand how natural populations cope with pesticides and the implications for ecological interactions. From an evolutionary perspective, there is evidence that pesticide tolerance can be achieved via two mechanisms: selection for constitutive tolerance over multiple generations or by inducing tolerance within a single generation via phenotypic plasticity. While both mechanisms can allow organisms to persist in contaminated environments, they might result in different performance trade-offs including population susceptibility to parasites. We have identified 15 wood frog populations that exist along a gradient from close to agriculture and high, constitutive pesticide tolerance to far from agriculture and inducible pesticide tolerance. Using these populations, we investigated the relationship between evolutionary responses to the common insecticide carbaryl and host susceptibility to the trematode Echinoparyphium lineage 3 and ranavirus using laboratory exposure assays. For Echinoparyphium, we discovered that wood frog populations living closer to agriculture with high, constitutive tolerance experienced lower loads than populations living far from agriculture with inducible pesticide tolerance. For ranavirus, we found no relationship between the mechanism of evolved pesticide tolerance and survival, but populations living closer to agriculture with high, constitutive tolerance experienced higher viral loads than populations far from agriculture with inducible tolerance. Land use and mechanisms of evolved pesticide tolerance were associated with susceptibility to parasites, but the direction of the relationship is dependent on the type of parasite, underscoring the complexity between land use and disease outcomes. Collectively, our results demonstrate that evolved pesticide tolerance can indirectly influence host–parasite interactions and underscores the importance of including evolutionary processes in ecotoxicological studies.
Land-use change is one of the greatest threats to biodiversity, especially in the tropics where secondary and plantation forests are expanding while primary forest is declining. Understanding how well these disturbed habitats maintain biodiversity is therefore important—specifically how the maturity of secondary forest and the management intensity of plantation forest affect levels of biodiversity. Previous studies have shown that the biotas of different continents respond differently to land use. Any continental differences in the response could be due to differences in land-use intensity and maturity of secondary vegetation or to differences among species in their sensitivity to disturbances. We tested these hypotheses using an extensive dataset collated from published biodiversity comparisons within four tropical regions—Asia, Africa, Central America and South America—and a wide range of animal and plant taxa. We analysed responses to land use of several aspects of biodiversity—species richness, species composition and endemicity—allowing a more detailed comparison than in previous syntheses. Within each continent, assemblages from secondary vegetation of all successional stages retained species richness comparable to those in primary vegetation, but community composition was distinct, especially in younger secondary vegetation. Plantation forests, particularly the most intensively managed, supported a smaller—and very distinct—set of species from sites in primary vegetation. Responses to land use did vary significantly among continents, with the biggest difference in richness between plantation and primary forests in Asia. Responses of individual taxonomic groups did not differ strongly among continents, giving little indication that species were inherently more sensitive in Asia than elsewhere. We show that oil palm plantations support particularly low species richness, indicating that continental differences in the response of biodiversity to land use are perhaps more likely explained by Asia’s high prevalence of oil palm plantations.
Tropical forest restoration is increasingly seen as an activity that may counteract or reduce biodiversity loss. However, few studies monitor fauna or consider measures of functional diversity to assess restoration success. We assessed the effect of a tropical montane forest restoration program on species and functional diversity, using amphibians as the target group. We compared amphibian assemblages in three types of land use: restoration areas, tropical montane cloud forest (TMCF; reference ecosystem) and cattle pastures (degraded ecosystem) in southern Mexico. We also described microclimate, microhabitat heterogeneity, woody vegetation structure and diversity for each type of land use, and their relationship to amphibian species and functional diversity. Compared to TMCF, restoration areas had similar environmental conditions. However, amphibian species richness was similar in the three types of land use and abundance was lower in the restoration areas. In TMCF, the amphibian assemblage was dominated by forest-specialist species, the pastures by generalist species, and the restoration areas by a combination of both species types. Interestingly, functional richness, functional evenness and functional divergence did not vary with land use, though the number of functional groups in restoration areas and TMCF was slightly higher. Overall, the results suggest that after seven years, active restoration provided habitat heterogeneity and recovered woody vegetation capable of maintaining amphibian species and functional groups similar to those inhabiting TMCF. Forest fragments adjacent to restoration areas seem to facilitate fauna
recolonization and this emphasizes the importance of the conservation of the reference ecosystems to achieving restoration success.
Tree cultivation is widely stimulated due to the provision of environmental services by sequestering atmospheric carbon, but forestry is a potential danger to biodiversity, mainly when cultivation replaces originally non-forested landscapes. Due to the rapid expansion of afforestation in grassland ecosystems, we used environmental descriptors and structure of amphibian and reptile communities as a tool to assess the possible effects of forestry on wildlife. We used pitfall traps with drift fences in Eucalyptus afforestation and native grasslands of the Pampa biome from southern Brazil. Amphibians and reptile species richness was lower in afforestation than in native grasslands. Furthermore, the reptile community found in afforestation was a poor subset of the community recorded in native grasslands. Indeed, the structure of communities for both amphibians and reptiles in afforestation was highly dissimilar from the native grasslands, with major environmental descriptors that influenced this difference being related to the structure of undergrowth vegetation, incident light, and sodium concentration in soil. Amphibians and reptiles proved to be an efficient tool to assess the potential impacts effects of afforestation/forestation since the replacement of natural grassland ecosystems by eucalypt afforestation caused detectable negative effects on the diversity of herpetofauna. Biodiversity conservation strategies in non-forest ecosystems are urgently needed and should encompass policies to restrict the expansion of forestry on the remaining native grasslands.
Anthropogenic habitat alterations cause biodiversity loss, which in turn negatively affects ecosystem functioning and services, and thus human well-being. To be able to consider ecosystem functioning in conservation actions, analyzing the effects of habitat alteration on functional diversity is essential. Some altered habitats can maintain a significant part of regional biodiversity, however, functional diversity information in altered habitats is so far mostly lacking. We compared functional richness and functional β-diversity based on resource-use traits of frogs between three land-use categories in a rainforest ecosystem in Madagascar. Land-use categories represent a habitat alteration gradient ranging from continuous forest over forest fragments to matrix habitats including different agricultures. Our study revealed distinct changes in resource-use trait composition and complex patterns in the relationship between species richness and functional richness. Thus, the functional structure of frog assemblages changed due to habitat alterations. However, altered habitats likely provide different, rather than fewer functions compared to intact forest. Streams in all land-use categories were the functionally richest habitats, and thus important for ecosystem functioning. Species richness was one, but not the only driver of functional richness in our system. Functional clustering, potentially due to environmental filters depending on resource availability, was caused by anthropogenic and natural drivers. Our study shows that, even in systems where fragmented landscapes still maintain high species diversity, functional diversity can be altered in human altered habitats, which may affect ecosystem processes like productivity, nutrient cycling, and energy flows.
While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010–2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon’s landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non-significant effects on functional diversity. Our results also indicate that effectiveness of CP38 in conserving avian diversity, particularly, taxonomic diversity, could be limited without the consideration of landscape heterogeneity.
New livestock production models need to simultaneously meet the increasing global demand for meat and preserve biodiversity and ecosystem services. Since the 16th century beef cattle has been produced on the Pampas and Campos native grasslands in southern South America, with only small amounts of external inputs. We synthesised 242 references from peer-reviewed and grey literature published between 1945 and mid-2015 and analysed secondary data to examine the evidence on the ecosystem services provided by this grassland biodiversity hotspot and the way they are affected by land use changes and their drivers. The analysis followed the requirements of systematic review from the PRISMA statement (Moher et al 2009 Acad. Clin. Ann. Intern. Med. 151 264–9). The Pampas and Campos provide feed for 43 million heads of cattle and 14 million sheep. The biome is habitat of 4000 native plant species, 300 species of birds, 29 species of mammals, 49 species of reptiles and 35 species of amphibians. The soils of the region stock 5% of the soil organic carbon of Latin America on 3% of its area. Driven by high prices of soybean, the soybean area increased by 210% between 2000 and 2010, at the expense of 2 million ha (5%) of native grassland, mostly in the Pampas. Intensification of livestock production was apparent in two spatially distinct forms. In subregions where cropping increased, intensification of livestock production was reflected in an increased use of grains for feed as part of feedlots. In subregions dominated by native grasslands, stocking rates increased. The review showed that land use change and grazing regimes with low forage allowances were predominantly associated with negative effects on ecosystem service provision by reducing soil organic carbon stocks and the diversity of plants, birds and mammals, and by increasing soil erosion. We found little quantitative information on changes in the ecosystem services water provision, nutrient cycling and erosion control. We discuss how changing grazing regimes to higher forage allowance can contribute to greater meat production and enhancing ecosystem services from native grasslands. This would require working with farmers on changing their management strategies and creating enabling economic conditions.
More than a quarter of earth's land surface is used for grazing domestic livestock. Livestock grazing is generally assumed to negatively affect wildlife, however, a number of studies have found positive impacts as well. We conducted an evidence-based review of the existing literature using a series of livestock- and wildlife-related search words to systematically query Google Scholar and Web of Science. A total of 807 sources were included in the final list, including 646 primary sources which reported original data. The majority of studies were conducted in North America (338) or Europe (123), with many fewer from Africa (57), Australia (54), Central/South America (43), or Asia (31). Most studies examined birds (330) and mammals (262), with fewer including reptiles (91) or amphibians (58). We extracted further information from studies that included mammals on positive, negative, and neutral effects of livestock grazing on mammals. We found that livestock change vegetation structure and cover in ways important to small mammals, while ungulates may be affected more by interference competition and changes in forage quantity and quality. Community-level total abundance of small mammals typically declines with grazing. Species richness of small mammals either declines or stays the same, as many studies found a change in species composition from ungrazed to grazed sites while the number of species remained similar. Individual species responses of small mammals vary. Voles, harvest mice, cotton rats, and shrews show consistently negative responses to grazing while deer mice, kangaroo rats, ground squirrels, and lagomorphs show positive or variable responses. In general, species adapted to open habitats are often positively affected by grazing, while species needing denser cover are negatively affected. Studies of wild ungulates are more variable in methodology and quality than those for small mammals. We found more negative (n = 86) than positive (n = 34) ungulate responses overall, however, most studies have been on browsers and mixed feeders, namely deer and elk, and there is little available data for other groups. Although data is limited, several of the grazing species in Africa may show a trend toward positive responses, suggesting possible facilitation. For a number of species, responses varied by season. We find a strong need for additional research on ungulates of varying diets and body sizes, especially in the developing world, and across longer time scales to examine possible tradeoffs between competition and facilitation from livestock.
Subtropical dry forests are among the most vulnerable biomes to land transformation at a global scale. Among them, the Dry Chaco suffers an accelerated change due to agriculture expansion and intensification. The Dry Chaco ecoregion is characterized by high levels of endemisms and species diversity, which are the result of a variety of climates and reliefs, allowing a wide variety of environments. The amphibian group exhibits a high richness in the Dry Chaco, which has been barely studied in relation to land cover changes. We used ecological niche models (ENMs) to assess the potential geographic distribution of 10 Leptodactylus species (Anura, Leptodactylidae), which are mainly distributed within the Dry Chaco. We characterized these distributions environmentally, analyzed their overlap with land cover classes, and assessed their diversity of ecoregions. Also, we evaluated how these species potential distribution is affected by the transformation of land, and quantified the proportional area of the potential distribution in protected areas. We found that temperature seasonality is the main constraint to the occurrence of the species studied, whose main habitats are savannas, grasslands and croplands. The main threats to these species are the effects of climate change over spatial patterns of seasonality, which could affect their breeding and reproduction mode; the loss of their natural habitat; the exposure to contaminants used by intensive agriculture and their underrepresentation in protected areas.
The process of adaptive radiation—the proliferation of species from a single ancestor and diversification into many ecologically different forms—has been of great interest to evolutionary biologists since Darwin. From the middle of the last century, ecological opportunity has been invoked as a potential key to understanding when and how adaptive radiation occurs. Interest in the topic of ecological opportunity has accelerated as research on adaptive radiation has experienced a resurgence, fueled in part by advances in phylogenetic approaches to studying evolutionary diversification. Nonetheless, what the term actually means, much less how it mechanistically leads to adaptive diversification, is currently debated; whether the term has any predictive
value or is a heuristic useful only for post hoc explanation also remains unclear. Recent recognition that evolutionary change can occur rapidly and on a timescale commensurate with ecological processes suggests that it is time to synthesize ecological and evolutionary approaches to the study of community assembly and evolutionary diversification.
Although several studies have examined the functional diversity of freshwater macroinvertebrates, the variety of methodologies combined with the absence of a synthetic review make our understanding of this field incomplete. Therefore, we reviewed the current methodology for assessing functional diversity in freshwater macroinvertebrate research. Our review showed that most papers quantified functional diversity using biological traits, among which feeding habits were the most common traits probably due to the assumed links between feeding and ecosystem functions. A large number of diversity measures have been applied for quantifying functional diversity of freshwater macroinvertebrate assemblages, among which Rao’s quadratic entropy looks like the most frequent. In most papers, functional diversity was positively related to taxon richness, and functional redundancy was a key concept in explaining this correlation. Most studies detected strong influence of the environmental factors as well as human impact on functional diversity. Finally, our review revealed that functional diversity research is biased towards European running waters and is hindered by yet insufficient information on the autecology of macroinvertebrates.
Hill numbers (or the effective number of species) have been increasingly used to quantify the species/taxonomic diversity of an assemblage. The sample‐size‐ and coverage‐based integrations of rarefaction (interpolation) and extrapolation (prediction) of H ill numbers represent a unified standardization method for quantifying and comparing species diversity across multiple assemblages.
We briefly review the conceptual background of H ill numbers along with two approaches to standardization. We present an R package iNEXT (i N terpolation/ EXT rapolation) which provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the H ill number family (species richness, S hannon diversity and S impson diversity). Two types of biodiversity data are allowed: individual‐based abundance data and sampling‐unit‐based incidence data.
Several applications of the iNEXT packages are reviewed: (i) Non‐asymptotic analysis: comparison of diversity estimates for equally large or equally complete samples. (ii) Asymptotic analysis: comparison of estimated asymptotic or true diversities. (iii) Assessment of sample completeness (sample coverage) across multiple samples. (iv) Comparison of estimated point diversities for a specified sample size or a specified level of sample coverage.
Two examples are demonstrated, using the data (one for abundance data and the other for incidence data) included in the package, to illustrate all R functions and graphical displays.
Grassy biomes occupy about 20% of the earth's surface, and are characteristic of northern Australia, Africa and South America, being biodiversity in these environments poorly understood. The Área de Proteção Ambiental (APA) do Ibirapuitã includes areas with the best-preserved grassland areas in the Pampa biome in Rio Grande do Sul state, Brazil. This study aimed to determine anuran species richness, abundance, constancy of occurrence, and reproductive modes, and to compare the taxonomic composition in the APA with other localities within the grassland areas of the southernmost of South America. We collected frogs from September to November 2012 and in November 2013 by sampling of reproductive sites. We also examined specimens deposited in herpetological collections. In total, 32 frog species were identified from the combination of larval and adult sampling and analysis of specimens deposited in scientific collections. The registered anurofauna is typical of grassland areas, with at least 10% restricted to the subtropical region of South America and at least two species considered endangered in state and global scales. The most abundant species was Pseudopaludicola falcipes and Hypsiboas pulchellus was the species most frequently found among sites. Five reproductive modes were recorded, and the most common mode consists of development of exotrophic tadpole and deposition in to lentic bodies of water (57.5%). Cluster analysis of 16 communities representing grassland locations presented five groups with more than 50% similarity, whose structure was influenced by geographic distance but can be partially interpreted by regional peculiarities (e.g. height and phytophysiognomies). Our results consist of initial knowledge base on the anurofauna of APA do Ibirapuitã, supporting recommendations for future conservation actions to APA and also for the grassland biomes, which are increasingly threatened by human activities.
Human alteration of the global environment is leading to a pervasive loss of biodiversity. Most studies evaluating human impacts on biodiversity occur after the disturbance has taken place using spatially distinct sites to determine the undisturbed reference condition. This approach is known as a space‐for‐time ( SFT ) substitution. However, SFT substitution could be underestimating biodiversity loss if spatial controls fail to provide adequate inferences about pre‐disturbance conditions.
We compare the SFT substitution with a before–after control–impact ( BACI ) approach by assessing dung beetles before and after a logging exploration in the Brazilian Amazon. We sampled 34 logging management units, of which 29 were selectively logged with different intensities after our first collection. We used dung beetle species richness, species composition and biomass as our biodiversity response metrics and the gradient of selective logging intensity as our explanatory metric.
Only the BACI approach consistently demonstrated the negative impacts of logging intensification on all dung beetle community metrics. Moreover, the BACI approach explained significantly more of the variance in all the relationships and it doubled the estimates of species loss along the gradient of logging intensity when compared to SFT .
Synthesis and applications . Our results suggest that space‐for‐time ( SFT ) substitution may greatly underestimate the consequences on local species diversity and community turnover. These results have important implications for researchers investigating human impacts on biodiversity. Incentivizing before–after control–impact ( BACI ) approaches will require longer‐term funding to gather the data and stronger links between researchers and landowners. However, BACI approaches are accompanied by many logistical constraints, making the continued use of SFT studies inevitable in many cases. We highlight that non‐significant results and weak effects should be viewed with caution.
Trait selection is a critical step of functional diversity (FD) studies and is often hampered by the limited availability of trait data for large sets of species. Thus, most studies examine FD using traits determined primarily by the availability of data rather than a specific function. This practice implicitly assumes that the subset of functional traits available will be representative of the trait data of interest. Here, we test whether the different functional trait groups (FTGs-distinct axes of ecological niches of the species e.g. morphological, reproductive, physiological) show congruent FD spatial patterns and if one FTG could act as a surrogate for another FTG. We used data on the 85 amphibian species of Europe and 12 traits to estimate three aspects of FD (richness, evenness and dispersion) for three different FTGs (Morphological, Reproductive and Habitat-related) and the complete set of traits. Our results challenge the surrogacy value of one set of FTGs for another set of FTGs. We further found that this has an impact on identifying hotspots (different functions will have different hotspots). So the argument that FD is easier to preserve in less area due to the redundancy of traits may hold true for a specific function, but will not necessarily be the same for different functions. Finally, our results reveal that, for any given community, FD is not characterized by a single spatial pattern, but by many depending on the function analyzed.
Considered an endangered biome, the Pampa has one of the lowest percentages of legally protected areas. Furthermore, knowledge on anuran communities in this biome is still scarce. In this context, the aim of this study was to determine the composition of frogs in an area of Pampa in southern Brazil. Between January 2009 and February 2010 an inventory was conducted at the Fundação Estadual de Pesquisa Agropecuária in São Gabriel, Rio Grande do Sul. The search for specimens was held in permanent, semi-permanent and temporary ponds by survey method in breeding site. We recorded 21 species belonging to five families, which corresponds to approximately 20% of the species found in the state and 42% of the species cited for the Uruguayan Savanna ecoregion. Ten species were frequent, seven were considered common and four of them were considered rare. Three different reproductive modes were recorded, with 57% of the species using the first mode that appears to be related to the homogeneity of the area. Cluster analysis comparing the composition of anurans of four separate locations showed a greatest similarity with the municipality of Candiota (region of Campanha). These species are associated to grasslands in the state and neighbor countries, and might be considered typical from the Pampa biome. © 2014 Fundacao Zoobotanica do Rio Grande do Sul. All rights reserved.
There is a great need to understand the effects of man-made land transformation on freshwater biodiversity, because agricultural landscapes provide habitat for many aquatic and semi-aquatic organisms. However, not all forms of land use are equal in their capacity to support wildlife. Cattle grazing leads to a change in pasture vegetation structure, whereas conversion to commercial crop-based agriculture promotes structural and chemical degradation of the ecosystem. From 2010 to 2012, in the Pampa biome, southern Brazil, we modelled anuran occupancy for 39 farmland ponds. Specifically, we determined detection probabilities associated with survey- and pond-specific variables and examined tadpole occupancy in relation to land use in southern Brazil. We recorded eleven anuran species, but only five were detected at levels suitable for occupancy modelling. Species detectability varied with water temperature, extent of floating macrophyte cover, and sampling date. For three species, detection-adjusted occupancy models indicated a relationship between occupancy and agricultural activities and/or livestock management. Agriculture areas negatively affected occupancy by Odontophrynus americanus and Physalaemus gracilis. The presence of livestock within a 500 m radius positively affected pond occupancy by Hypsiboas pulchellus. Other species were negatively associated with pond area or fish presence. Our results demonstrate that traditional extensive livestock farming can provide a buffer that protects freshwater environments, because it did not greatly modify the grassland matrix. We argue that further species-based approaches will be critical for developing effective conservation strategies for anurans, particularly in the context of the expanding rice production/exotic forests in southern Brazil.
One of the most important goals of biodiversity studies is to identify which characteristics of local habitats act as filters that determine the diversity of functional traits along environmental gradients. In this study, we investigated the relationship between the environmental variables of ponds and the functional trait diversity distribution of anuran tadpoles in an agricultural area in southeastern Brazil. Our results show that the functional trait diversity of frog tadpoles has a bell-curve-shaped relationship with the depths of ponds inserted in a pasture matrix. Because we are witnessing increasing human pressure on land use, simple acts (e.g. maintaining reproductive habitats with medium depth) can be the first steps towards preserving the diversity of Neotropical frog tadpole traits in agricultural landscapes.
Recent advances in the implementation of spatial econometrics model estimation techniques have made it desirable to compare results, which should correspond between implementations across software applications for the same data. These model estimation techniques are associated with methods for estimating impacts (emanating effects), which are also presented and compared. This review constitutes an up-to-date comparison of generalized method of moments and maximum likelihood implementations now available. The comparison uses the cross-sectional US county data set provided by Drukker, Prucha, and Raciborski (2013d). The comparisons will be cast in the context of alternatives using the MATLAB Spatial Econometrics toolbox, Stata's user-written sppack commands, Python with PySAL and R packages including spdep, sphet and McSpatial.
AimLand-use change is the single biggest cause of biodiversity loss. With a rising demand for resources, understanding how and where agriculture threatens biodiversity is of increasing importance. Agricultural expansion has received much attention, but where high agricultural land-use intensity (LUI) threatens biodiversity remains unclear. We address this knowledge gap with two main research questions: (1) Where do global patterns of LUI coincide with the spatial distribution of biodiversity? (2) Where are regions of potential conflict between different aspects of high LUI and high biodiversity?LocationGlobal.Methods
We overlaid thirteen LUI metrics with endemism richness, a range size-weighted species richness indicator, for mammals, birds and amphibians. We then used local indicators of spatial association to delineate statistically significant (P < 0.05) areas of high and low LUI associated with biodiversity.ResultsPatterns of LUI are heterogeneously distributed in areas of high endemism richness, thus discouraging the use of a single metric to represent LUI. Many regions where high LUI and high endemism richness coincide, for example in South America, China and Eastern Africa, are not within currently recognized biodiversity hotspots. Regions of currently low LUI and high endemism richness, found in many parts of Mesoamerica, Eastern Africa and Southeast Asia, may be at risk as intensification accelerates.Main conclusionsWe provide a global view of the geographic patterns of LUI and its concordance with endemism richness, shedding light on regions where highly intensive agriculture and unique biodiversity coincide. Past assessments of land-use impacts on biodiversity have either disregarded LUI or included a single metric to measure it. This study demonstrates that such omission can substantially underestimate biodiversity threat. A wider spectrum of relevant LUI metrics needs to be considered when balancing agricultural production and biodiversity.
The environmental benefits of a broad scale adoption of biofuels are critically contingent on what current land uses will be converted for feedstock expansion and how converted land will be managed. We assessed the consequences of land use and land management for the agroindustrial production of sugarcane to the physical, chemical and biological properties of freshwater systems. We surveyed 16 environmental variables and algae, tadpoles, predatory invertebrates and fish in lentic water bodies distributed across a gradient in land use intensity ranging from seasonal Atlantic Forest and cerrado to pastures to sugarcane plantations in SE Brazil, the most important sugarcane-producing region in the world. The gradient in land use intensity was not only an axis of native habitat loss but also of ecosystem productivity, as indicated by increased conductivity, turbidity, and phytoplankton biomass. Land use had a clear signal on community and metacommunity organization, with converted land being impoverished in biodiversity relative to native habitats. However, frequency of occurrence, density, biomass and alpha diversity of tadpoles and their predators were not affected by land use. These results suggest that sugarcane fields function as habitat to a fraction of aquatic biodiversity. Within sugarcane fields, larger wetlands surrounded by buffer strips as required by law appeared comparatively buffered against land management practices and housed a disproportional fraction of animal biomass, likely acting as sources of migrants to other water bodies in the landscape. Conversion of pastures to sugarcane fields, suggested as a strategy to reduce competition for land with food production and biodiversity conservation, does not appear to have strong consequences to lentic freshwater systems, provided that wetlands and surrounding buffer strips are preserved. These observations emphasize the importance of enforcement of legislation regulating land use (i.e. the ′Forest Code′) and certification systems rewarding the voluntary adoption of better land management practices.This article is protected by copyright. All rights reserved.
Amphibian populations are dramatically declining, while their inventory is far from being achieved. Tadpoles are usually overlooked from biodiversity survey, whereas their consideration will optimize species counts and knowledge of their ecological and developmental requirements is essential in conservation planning. Two mitochondrial markers, 16S (397 new sequences obtained) and COI (343 new sequences obtained), are used to test DNA barcoding on a set of larval and adult Asian amphibians represented by 83 recognized species from 65 sites. The advantages and drawbacks of each marker are assessed, COI barcoding being advocated for global DNA barcoding, whereas 16S suits for taxonomically or geographically restricted DNA barcoding. About half of the collected tadpoles were badly identified or incompletely named in the field. All tadpole sequences (except one case of probable introgressive hybridization) were correctly assigned to their respective species. Finally six clusters of tadpole sequences without conspecific adults were revealed, stressing the importance of collecting and taking into account tadpoles in biodiversity survey and conservation planning.
Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.
The subdiscipline of ‘community phylogenetics’ is rapidly growing and influencing thinking regarding community assembly. In particular, phylogenetic dispersion of co‐occurring species within a community is commonly used as a proxy to identify which community assembly processes may have structured a particular community: phylogenetic clustering as a proxy for abiotic assembly, that is habitat filtering, and phylogenetic overdispersion as a proxy for biotic assembly, notably competition.
We challenge this approach by highlighting (typically) implicit assumptions that are, in reality, only weakly supported, including (i) phylogenetic dispersion reflects trait dispersion; (ii) a given ecological function can be performed only by a single trait state or combination of trait states; (iii) trait similarity causes enhanced competition; (iv) competition causes species exclusion; (v) communities are at equilibrium with processes of assembly having been completed; (vi) assembly through habitat filtering decreases in importance if assembly through competition increases, such that the relative balance of the two can be thus quantified by a single parameter; and (vii) observed phylogenetic dispersion is driven predominantly by local and present‐day processes.
Moreover, technical sophistication of the phylogenetic‐patterns‐as‐proxy approach trades off against sophistication in alternative, potentially more pertinent approaches to directly observe or manipulate assembly processes.
Despite concerns about using phylogenetic dispersion as a proxy for community assembly processes, we suggest there are underappreciated benefits of quantifying the phylogenetic structure of communities, including (i) understanding how coexistence leads to the macroevolutionary diversification of habitat lineage‐pools (i.e. phylogenetic‐patterns‐as‐result approach); and (ii) understanding the macroevolutionary contingency of habitat lineage‐pools and how it affects present‐day species coexistence in local communities (i.e. phylogenetic‐patterns‐as‐cause approach).
We conclude that phylogenetic patterns may be little useful as proxy of community assembly. However, such patterns can prove useful to identify and test novel hypotheses on (i) how local coexistence may control macroevolution of the habitat lineage‐pool, for example through competition among close relatives triggering displacement and diversification of characters, and (ii) how macroevolution within the habitat lineage‐pool may control local coexistence of related species, for example through origin of close relatives that can potentially enter in competition.
Quantifying and assessing changes in biological diversity are central aspects of many ecological studies, yet accurate methods of estimating biological diversity from sampling data have been elusive. Hill numbers, or the effective number of species, are increasingly used to characterize the taxonomic, phylogenetic, or functional diversity of an assemblage. However, empirical estimates of Hill numbers, including species richness, tend to be an increasing function of sampling effort and, thus, tend to increase with sample completeness. Integrated curves based on sampling theory that smoothly link rarefaction (interpolation) and prediction (extrapolation) standardize samples on the basis of sample size or sample completeness and facilitate the comparison of biodiversity data. Here we extended previous rarefaction and extrapolation models for species richness (Hill number qD, where q = 0) to measures of taxon diversity incorporating relative abundance (i.e., for any Hill number qD, q > 0) and present a unified approach for both individual-based (abundance) data and samplebased (incidence) data. Using this unified sampling framework, we derive both theoretical formulas and analytic estimators for seamless rarefaction and extrapolation based on Hill numbers. Detailed examples are provided for the first three Hill numbers: q = 0 (species richness), q = 1 (the exponential of Shannon's entropy index), and q = 2 (the inverse of Simpson's concentration index). We developed a bootstrap method for constructing confidence intervals around Hill numbers, facilitating the comparison of multiple assemblages of both rarefied and extrapolated samples. The proposed estimators are accurate for both rarefaction and short-range extrapolation. For long-range extrapolation, the performance of the estimators depends on both the value of q and on the extrapolation range. We tested our methods on simulated data generated from species abundance models and on data from large species inventories. We also illustrate the formulas and estimators using empirical data sets from biodiversity surveys of temperate forest spiders and tropical ants.
Structure and spatial organization of two anuran communities of the Pampa biome. The Pampa is the smallest Brazilian biome and is one of the most endangered, due to the expansion of the agropastoril cultures and the silviculture; is one of the Brazilian biomes with the lowest representation on the conservation unities system. In this study are presented information about the structure and spatial organization of anuran communities of two physiographic regions, from the four in which the biome is divided. Were sampled ten waterbodies in each region between the months of September 2011 and August 2012. Were registered 24 species characterized as generalist, with wide distribution and typical of the open areas. The species accumulation curve showed an assintota after the 12° month of sampling. The similarity analysis showed a segregation in the structure of both communities that were influenced by the environmental landscape descriptors.
Trait‐based approaches and functional diversity have been previously used to enlighten our knowledge on the structure of community assemblages which are driven by species interactions or abiotic factors. We assess what amphibian functional diversity implies for the community assembly of amphibians of Europe and whether the use of different Functional Trait Groups (FTGs) affects the results. We used presence/absence atlas with 50 km × 50 km grain size and three functional diversity indices (FRic, RaoQ and FDiv) which reflect functional richness and divergence to estimate functional diversity patterns calculated for three FTGs: Morphological, Habitat‐related, Reproductive and the complete set of traits. To identify the two key processes (environmental filtering and limiting similarity) that may shape amphibian communities and how the relative importance of these processes could change using different FTGs, we used null models to test for non‐random patterns of functional diversity accounting or not for the difference in regional species pool. We show that for the same grid cell, for one FTG we might observe lower than randomly expected functional diversity (i.e., trait convergence or environmental filtering as the dominant community assembly process) while for another FTG or for the complete set of traits, higher than randomly expected functional diversity (i.e., trait divergence or limiting similarity as the dominant community assembly process). This highlights the role of trait selection on the inference drawn regarding community assembly. Furthermore, the number of traits (complete set vs. FTGs) used to quantify functional diversity also affects the conclusions regarding community assembly.
Functional traits mediate ecological responses of organisms to the environment, determining community structure. Community-weighted trait means (CWM) are often used to characterize communities by combining information on species traits and distribution. Relating CWM variation to environmental gradients allows for evaluating species sorting across the metacommunity, either based on correlation tests or ordinary least squares (OLS) models. Yet, it is not clear if phylogenetic signal in both traits and species distribution affect
those analyses. On one hand, phylogenetic signal might indicate niche conservatism along
clade evolution, reinforcing the environmental signal in trait assembly patterns. On the
other hand, it might introduce phylogenetic autocorrelation to mean trait variation among
communities. Under this latter scenario, phylogenetic signal might inflate type I error in
analysis relating CWM variation to environmental gradients. We explore multiple ways
phylogenetic history may influence analysis relating CWM to environmental gradients. We
propose the concept of neutral trait diffusion, which predicts that for a functional trait x,
CWM variation among local communities does not deviate from the expectation that x
evolved according to a neutral evolutionary process. Based on this framework we introduce
a graphical tool called neutral trait diffusion representation (NTDR) that allows for the
evaluation of whether it is necessary to carry out phylogenetic correction in the trait prior to
analyzing the association between CWM and environmental gradients. We illustrate the
NTDR approach using simulated traits, phylogenies and metacommunities. We show that
even under moderate phylogenetic signal in both the trait used to define CWM and species
distribution across communities, OLS models relating CWM variation to environmental
gradients lead to inflated type I error when testing the null hypothesis of no association
between CWM and environmental gradient. To overcome this issue, we propose a
phylogenetic correction for OLS models and evaluate its statistical performance (type I error
and power). Phylogeny-corrected OLS models successfully control for type I error in analysis
relating CWM variation to environmental gradients but may show decreased power.
Combining the exploratory tool of NTDR and phylogenetic correction in traits, when
necessary, guarantees more precise inferences about the environmental forces driving traitmediated
species sorting across metacommunities.
The merger of phylogenies with ecology has given rise to the field of “community phylogenetics” predicated on the assumption that ecological differences among species can be estimated from phylogenetic relationships (the phylogenetic distance/ecological difference, PDED, hypothesis). A number of studies have failed to find strong support for this assumption, thus challenging the utility of phylogenetic approaches. This gap might highlight the fact that the PDED relationship is not useful for community assembly, but it is difficult to know because the lack of a relationship might also be due to a number of biological or methodological reasons, including inappropriate phylogenies, skewed distributions of phylogenetic distances, the lack of consideration of models of trait evolution, or the absence of sufficient niche space in experimental and observational venues. Each of these limitations, separately or combined, may confound recent experimental or observational results that examine relationships between phylogenetic distance and ecological differences. Notably, common evolutionary models can support alternative conclusions about the relationship between evolutionary distances and ecological differences than typically assumed and can change interpretations of community-based phylogenetic analyses. Here we review a number of issues that may lead to confounded effects in community phylogenetic analyses. In light of these potential pitfalls, we provide a number of guidelines for researchers to follow and stress that they need to address methodological shortcomings before concluding that ecological differences are unrelated to phylogenetic distances. This article is protected by copyright. All rights reserved.
This manuscript analyzes the land use changes and its conjectural drivers in the Brazilian Pampa Biome. Therefore, land use changes in the municipalities of this biome were collected from the Brazilian Agricultural Censuses of 1975, 1985, 1995/1996 and 2006. To analyze the changes in the land use for natural pastures, pampa’s microregions were compared in 10-year by a relative growth rate. There has been a 26% decrease in natural pastures in the Brazilian Pampa Biome since 1975, with a negative growth of −12.5% between 1975 and 1985. The activities with the highest growth were cultivated forests and temporary crops (1985–2005), and the increment of the area dedicated for those agricultural activities was related to the decrease in the area of natural pastures in the Pampa. Temporary crops (soy) and cultivated forests (forestry) began to integrate Pampa’s landscape mainly between 1995 and 2005, changing the native configuration of the biome. Finally, sharing information on the Brazilian Pampa Biome phenomena will facilitate future dialogue among all stakeholders, and this manuscript is expected to contribute to the global debate on the conservation of natural landscapes, especially natural grasslands.
Recent studies have explored feeding kinematics in tadpoles with intact labial teeth; however, it is unknown how missing teeth impacts foraging. We explored the impact of missing labial teeth on the feeding mechanics and foraging performance of Southern leopard frog (Lithobates sphenocephalus [= Rana sphenocephala]) tadpoles by controlling the pattern of labial tooth loss; that is, by surgically removing one row of labial teeth. We then used high-speed (500 frames/second) videography to test the hypothesis that tooth loss reduces the time that tadpoles attach to and graze upon an algal-covered substrate. We next conducted trials of foraging efficiency and foraging activity to test the hypothesis that tadpoles with fewer teeth forage less effectively than control tadpoles. The teeth of tadpoles from the surgery treatment slipped while closing and were in contact with an algal-covered substrate for a shorter duration compared to control tadpoles. Surprisingly, tadpoles with missing labial teeth obtained similar amounts of food and were as active as tadpoles with intact mouthparts. However, tadpoles with missing teeth completed about 25% more gape cycles per unit time than control tadpoles. Our data suggest that tadpoles with missing teeth compensate for inferior feeding kinematics during mouth closing in each gape cycle by increasing the number of gape cycles per unit time.
Land use change has been identified as a major driver of amphibian decline around the world. Yet we generally lack an understanding of how conversion to exotic pastures affects freshwater communities. This study examined tadpole assemblages in areas converted to exotic pastures and native wooded grasslands in northern Pantanal wetland, Midwestern Brazil. We tested the differences in site occupancy probability and assemblage composition during a flood season. We registered thirteen tadpole species, but only five were detected at levels suitable for occupancy modelling. For most species, tadpole occupancy was higher at the beginning of the flood season. Only Scinax fuscomarginatus occupancy was related with vegetation cover. Occupancy probability for three species (Dendropsophus nanus, Physalaemus centralis, and Physalaemus cuvieri) was associated positively with species richness of fish. Multivariate analyses demonstrated that exotic pastures hosted a different tadpole assemblage than native areas. The assemblage composition gradient was associated with species richness of fish, vegetation cover and volume of herbaceous vegetation and leaf litter. These differences likely relate to specific traits of individual anuran species (dietary plasticity, reproductive mode, and habitat preference). The study showed that some generalist species were able to cope with replacement of native vegetation by exotic species. However, management practices have maintained many areas in the Pantanal at a stage of a near-pristine wetland ecosystem and replacement of native vegetation by exotic pastures should be done with caution.
Competitive exclusion and habitat filtering influence community assembly, but ecologists and evolutionary biologists have not reached consensus on how to quantify patterns that would reveal the action of these processes. Currently, at least 22 α-diversity and 10 β-diversity metrics of community phylogenetic structure can be combined with nine null models (eight for β-diversity metrics), providing 278 potentially distinct approaches to test for phylogenetic clustering and overdispersion. Selecting the appropriate approach for a study is daunting. First, we describe similarities among metrics and null models across variance in phylogeny size and shape, species abundance, and species richness. Second, we develop spatially explicit, individual-based simulations of neutral, competitive exclusion, or habitat filtering community assembly, and quantify the performance (type I and II error rates) of all 278 approaches against each assembly process. Many α-diversity metrics and null models are at least functionally equivalent, reducing the number of truly unique metrics to 12, and the number of unique α-diversity approaches to 72. An even smaller subset of metric and null model combinations showed robust statistical performance. Of α-diversity metrics, phylogenetic diversity and mean nearest taxon distance were best able to detect habitat filtering, while mean pairwise phylogenetic distance-based metrics were best able to detect competitive exclusion. Overall, β-diversity metrics tended to outperform α-diversity metrics, showing greater power and fewer false positives, although some α-diversity metrics exhibited nearly comparably performance. Null model selection affected type I error rates more than metric selection. A new null model that maintains species richness, and approximately maintains occurrence frequency and abundance across plots, exhibited low type I and II error rates. This regional null model simulates neutral dispersal of individuals into local communities by sampling from a regional species pool. We introduce a flexible new R package, metricTester, to facilitate robust analyses of method performance. This article is protected by copyright. All rights reserved.
Looked at globally, agriculture is the greatest source of threat to biodiversity, through both ongoing conversion of natural habitat and intensification of existing farmland. Land sparing and land sharing have been suggested as alternative approaches to reconcile this threat with the need for land to produce food. To examine which approach holds most promise for grassland species, we examined how bird population densities changed with farm yield (production per unit area) in the Campos of Brazil and Uruguay. Information on biodiversity and yields were obtained from 24 sites which varied in agricultural production. Density-yield functions were fitted for 121 bird species to describe the response of population densities to increasing farm yield, measured in terms of both food energy and profit. Individual species were categorised according to how their population changed across the yield gradient as 'losers' or 'winners' from farming, and also according to whether the species' total population size would be greater under land sparing, land sharing or an intermediate strategy. Irrespective of the yield currency used, most species were losers; increasing yields reduced densities of around 80% of bird species. Land sparing would result in larger populations than other sorts of strategies for 67% (energy) to 70% (profit) of the loser species, given current production levels, including three threatened species. This suggests that increasing yields in some areas while reducing grazing to low levels elsewhere would be the best option for bird conservation in these grasslands. Implementing such an approach would require conservation and production policies to be explicitly linked, to (1) support yield increases in farmed areas; and (2) concurrently guarantee that larger areas of lightly-grazed natural grasslands are set aside for conservation. This article is protected by copyright. All rights reserved.
J.M. Diamond's assembly rules model predicts that competitive interactions between species lead to nonrandom co-occurrence patterns. We conducted a meta-analysis of 96 published presence-absence matrices and used a realistic "null model" to generate patterns expected in the absence of species interactions. Published matrices were highly nonrandom and matched the predictions of Diamond's model: there were fewer species combinations, more checkerboard species pairs, and less co-occurrence in real matrices than expected by chance. Moreover, nonrandom structure was greater in homeotherm vs. poikilotherm matrices. Although these analyses do not confirm the mechanisms of Diamond's controversial assembly rules model, they do establish that observed co-occurrence in most natural communities is usually less than expected by chance. These results contrast with previous analyses of species co-occurrence patterns and bridge the apparent gap between experimental and correlative studies in community ecology.
An ongoing controversy involves the debate about the effects of man-made land transformation on freshwater biodiversity. It has been suggested that agricultural areas provide habitats for many species of amphibians, but crop age may affect richness and community structure. In such modified landscapes, a nested structure has been commonly detected, although community structure may be season specific and guild specific. Here, we determined detectability associated with site-specific and survey-specific variables and examined nestedness patterns in anuran communities in natural areas and rice fields with different crop ages (10 and 20 years) in southern Brazil. We studied whether nestedness was associated with time since cultivation and whether these patterns were similar across guilds in these areas. Anuran detectability was related only with time after sunset. Community composition varied between crop ages. Aquatic and arboreal species were associated with native areas and showed a nested pattern. Fossorial species did not show significant nestedness. Our results showed that factors associated with crop age may affect guilds in different ways. These effects seem to be related to individual traits of species (habitat preferences, reproductive modes, plasticity). Incorporating species traits may enhance conservation strategies in agroecosystems.