Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system‐level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi‐scalar community‐level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel‐2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.
Biodiversity is changing at an accelerating rate at both local and regional scales. Beta diversity, which quantifies species turnover between these two scales, is emerging as a key driver of ecosystem function that can inform spatial conservation. Yet measuring biodiversity remains a major challenge, especially in aquatic ecosystems. Decoding environmental DNA (eDNA) left behind by organisms offers the possibility of detecting species sans direct observation, a Rosetta Stone for biodiversity. While eDNA has proven useful to illuminate diversity in aquatic ecosystems, its utility for measuring beta diversity over spatial scales small enough to be relevant to conservation purposes is poorly known. Here we tested how eDNA performs relative to underwater visual census (UVC) to evaluate beta diversity of marine communities. We paired UVC with 12S eDNA metabarcoding and used a spatially structured hierarchical sampling design to assess key spatial metrics of fish communities on temperate rocky reefs in southern California. eDNA provided a more-detailed picture of the main sources of spatial variation in both taxonomic richness and community turnover, which primarily arose due to strong species filtering within and among rocky reefs. As expected, eDNA detected more taxa at the regional scale (69 vs. 38) which accumulated quickly with space and plateaued at only ~ 11 samples. Conversely, the discovery rate of new taxa was slower with no sign of saturation for UVC. Based on historical records in the region (2000–2018) we found that 6.9 times more UVC samples would be required to detect 50 taxa compared to eDNA. Our results show that eDNA metabarcoding can outperform diver counts to capture the spatial patterns in biodiversity at fine scales with less field effort and more power than traditional methods, supporting the notion that eDNA is a critical scientific tool for detecting biodiversity changes in aquatic ecosystems.
more » « less- Award ID(s):
- 1831937
- NSF-PAR ID:
- 10275239
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Scientific Reports
- Volume:
- 11
- Issue:
- 1
- ISSN:
- 2045-2322
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Aim Our aim was to uncover patterns of distribution of marine subtidal rocky reef communities across six taxonomic groups and decompose the relative roles of species loss and turnover in total community variation. Additionally, we propose an easily calculated index that can be used to highlight areas with unique species composition for conservation planning. We estimated the strengths of associations between environmental factors and species richness and rarity.
Location Ilha Grande Bay, Brazil, covering about 150,000 ha harbouring different marine habitats.
Methods We used the Marine Rapid Assessment Protocol at 42 sites to gather information on environmental variables and species in six subtidal marine groups. We determined “singular” sites as the regions harbouring higher numbers of rare species. Then, we estimated the roles of species loss and turnover on the observed total variation among sites. We used Generalized Linear Model to partition the relative importance of the selected environmental factors in driving variation in species richness and singularity.
Results The singularity index and richness showed that the bay could be divided into three subregions for subtidal communities. Richness and rarity were structured at different spatial scales and associated with environmental variables related to water productivity and nutrients but varied among taxonomic groups. Community variation over space was largely associated with turnover of species.
Main conclusions Higher singularity and richness on the western side of the bay and around the main island suggested that these regions should be conservation priorities, but high species turnover across the whole bay indicated that portions of the central channel should be included in conservation strategies. This draws attention to the importance of community variation rather than just species numbers in conservation and management planning. The high species turnover indicated that these rocky reefs have high beta diversity when compared to other studied biological systems.
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Abstract Urbanization can influence local richness (alpha diversity) and community composition (beta diversity) in numerous ways. For instance, reduced connectivity and land cover change may lead to the loss of native specialist taxa, decreasing alpha diversity. Alternatively, if urbanization facilitates nonnative species introductions and generalist taxa, alpha diversity may remain unchanged or increase, while beta diversity could decline due to the homogenization of community structure. Wetlands and ponds provide critical ecosystem services and support diverse communities, making them important systems in which to understand the consequences of urbanization. To determine how urban development shapes pond community structure, we surveyed 68 ponds around Madison, Wisconsin, USA, which were classified as urban, greenspace, or rural based on surrounding land use. We evaluated how landscape and local pond factors were correlated with the alpha diversity of aquatic plants, macroinvertebrates, and aquatic vertebrates. We also analyzed whether surrounding land use was associated with changes in community composition and the presence of specific taxa. We found a 23% decrease in mean richness (alpha diversity) from rural to urban pond sites and a 15% decrease from rural to greenspace pond sites. Among landscape factors, adjacent developed land, mowed lawn cover, and greater distances to other waterbodies were negatively correlated with observed pond richness. Among pond level factors, habitat complexity was associated with increased richness, while nonnative fishes were associated with decreased richness. Beta diversity was relatively high for all ponds due to turnover in composition between sites. Urban ponds supported more nonnative species, lacked a subset of native species found in rural ponds, and had slightly higher beta diversity than greenspace and rural ponds. Our results suggest that integrating ponds into connected greenspaces, maintaining riparian vegetation, preventing nonnative fish introductions, and promoting habitat complexity may mitigate the negative effects of urbanization on aquatic richness. While ponds are small in size and rarely incorporated into urban conservation planning, the high beta diversity of distinct pond communities emphasizes their importance for supporting urban biodiversity.
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1) Urbanization may lead to changes in local richness (alpha diversity) or in community composition (beta diversity), although the direction of change can be challenging to predict. For instance, introduced species may offset the loss of native specialist taxa, leading to no change in alpha diversity in urban areas, but decreased beta diversity (i.e., more homogenous community structure). Alternatively, because urban areas can have low connectivity and high environmental heterogeneity between sites, they may support distinct communities from one another over small geographic distances. 2) Wetlands and ponds provide critical ecosystem services and support diverse communities, making them important systems in which to understand consequences of urbanization. To determine how urban development shapes pond community structure, we surveyed 68 ponds around Madison, Wisconsin, USA, which were classified as urban, greenspace, or rural based on surrounding land use. We evaluated the influence of local abiotic factors, presence of nonnative fishes, and landscape characteristics on alpha diversity of aquatic plants, macroinvertebrates, and vertebrates. We also analyzed whether surrounding land cover was associated with changes in community composition and/or the presence of specific taxa. 3) We found a 23% decrease in mean richness (alpha diversity) from rural to urban pond sites, and a 15% decrease in richness from rural to urban greenspace pond sites. Among landscape factors, observed pond richness was negatively correlated with adjacent developed land and mowed lawns, as well as greater distances to other waterbodies. Among pond level factors, habitat complexity was associated with increased richness, while the presence of invasive fish was associated with decreased richness. 4) Beta diversity was relatively high for all ponds due to turnover in composition between sites. Urban ponds supported more introduced species, lacked a subset of native species found in rural ponds, and had slightly higher beta diversity than greenspace and rural ponds. 5) Synthesis and Applications: Integrating ponds into connected greenspaces comprised of native vegetation (rather than mowed grass), preventing nonnative fish introductions, and promoting habitat complexity may mitigate negative effects of urbanization on aquatic richness. The high beta diversity of distinct pond communities emphasizes their importance to biodiversity support in urban environments, despite being small in size and rarely incorporated into urban conservation planning.more » « less
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1) Urbanization may lead to changes in local richness (alpha diversity) or in community composition (beta diversity), although the direction of change can be challenging to predict. For instance, introduced species may offset the loss of native specialist taxa, leading to no change in alpha diversity in urban areas, but decreased beta diversity (i.e., more homogenous community structure). Alternatively, because urban areas can have low connectivity and high environmental heterogeneity between sites, they may support distinct communities from one another over small geographic distances. 2) Wetlands and ponds provide critical ecosystem services and support diverse communities, making them important systems in which to understand consequences of urbanization. To determine how urban development shapes pond community structure, we surveyed 68 ponds around Madison, Wisconsin, USA, which were classified as urban, greenspace, or rural based on surrounding land use. We evaluated the influence of local abiotic factors, presence of nonnative fishes, and landscape characteristics on alpha diversity of aquatic plants, macroinvertebrates, and vertebrates. We also analyzed whether surrounding land cover was associated with changes in community composition and/or the presence of specific taxa. 3) We found a 23% decrease in mean richness (alpha diversity) from rural to urban pond sites, and a 15% decrease in richness from rural to urban greenspace pond sites. Among landscape factors, observed pond richness was negatively correlated with adjacent developed land and mowed lawns, as well as greater distances to other waterbodies. Among pond level factors, habitat complexity was associated with increased richness, while the presence of invasive fish was associated with decreased richness. 4) Beta diversity was relatively high for all ponds due to turnover in composition between sites. Urban ponds supported more introduced species, lacked a subset of native species found in rural ponds, and had slightly higher beta diversity than greenspace and rural ponds. 5) Synthesis and Applications: Integrating ponds into connected greenspaces comprised of native vegetation (rather than mowed grass), preventing nonnative fish introductions, and promoting habitat complexity may mitigate negative effects of urbanization on aquatic richness. The high beta diversity of distinct pond communities emphasizes their importance to biodiversity support in urban environments, despite being small in size and rarely incorporated into urban conservation planning.more » « less
