A Biodiversity Composition Map of California Derived from Environmental DNA Metabarcoding and Earth Observation

AbstractUnique 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. We offer a way to use environmental DNA, community science and remote sensing together as methods to reduce the discrepancy between the magnitude of change and historical approaches to measure it. Taking advantages of modern ecological models, we integrate environmental DNA and Earth observations to evaluate regional biodiversity patterns for a snapshot of time, and provide critical community-level characterization. We collected 278 samples in Spring 2017 from coastal, shrub and lowland forest sites in California, a large-scale biodiversity hotspot. We applied gradient forest to model 915 family occurrences and community composition together with environmental variables and multi-scalar habitat classifications to produce a statewide biodiversity-based map. 16,118 taxonomic entries recovered were associated with environmental variables to test their predictive strength on alpha, beta, and zeta diversity. Local habitat classification was diagnostic of community composition, illuminating a characteristic of biodiversity hotspots. Using gradient forest models, environmental variables predicted 35% of the variance in eDNA patterns at the family level, with elevation, sand percentage, and greenness (NDVI32) as the top predictors. This predictive power was higher than we found in published literature at global scale. In addition to this indication of substantial environmental filtering, we also found a positive relationship between environmentally predicted families and their numbers of biotic interactions. In aggregate, these analyses showed that strong eDNA community-environment correlation is a general characteristic of temperate ecosystems, and may explain why communities easily destabilize under disturbances. Our study provides the first example of integrating citizen science based eDNA with biodiversity mapping across the tree of life, with promises to produce large scale, high resolution assessments that promote a more comprehensive and predictive understanding of the factors that influence biodiversity and enhance its maintenance.

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Climatic effects on turnover of lowland forest bird communities across a precipitation gradient

10.1101/251264 ◽

2018 ◽

Author(s):

Juan Pablo Gomez ◽

José Miguel Ponciano ◽

Scott K. Robinson

Keyword(s):

Community Composition ◽

Species Abundance ◽

Environmental Filtering ◽

Bird Species ◽

Biotic Interactions ◽

Dry Forest ◽

Precipitation Gradient ◽

Climatic Effects ◽

Lowland Forest ◽

Abundance And Distribution

AbstractOne of the main goals of community ecology is to understand the influence of the abiotic environment on the abundance and distribution of species. It has been hypothesized that dry forests are harsher environments than wet forests, which leads to the prediction that environmental filtering should be a more important determinant of patterns of species abundance and composition than in wet forest, where biotic interactions or random assembly should be more important. We attempt to understand the influence of rainfall on the abundance and distribution of bird species along a steep precipitation gradient in an inter-Andean valley in Colombia. We gathered data on species distributions, abundance, morphological traits and phylogenetic relationships to determine the influence of rainfall on the taxonomic, functional and phylogenetic turnover of species along the Magdalena Valley. We demonstrate that there is a strong turnover of community composition at the limit of the dry forest. The taxonomic turnover is steeper than the phylogenetic turnover, suggesting that replacement of closely related species accounts for a disproportionate number of changes along the gradient. We found evidence for environmental filtering in dry forest as species tend to be more tolerant of higher temperature ranges, stronger rainfall seasonality and lower minimum rainfall. On the other hand, wet forest species tend to compete actively for nest space but not for the resources associated with the axes we measured. Our results suggest that rainfall is a strong determinant of community composition when comparing localities above and below the 2400 mm rainfall isocline.

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Diatoms Are Selective Segregators in Global Ocean Planktonic Communities

mSystems ◽

10.1128/msystems.00444-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 3

Author(s):

Flora Vincent ◽

Chris Bowler

Keyword(s):

Open Access ◽

Large Scale ◽

Abiotic Factors ◽

Biotic Interactions ◽

Distribution Patterns ◽

Global Scale ◽

Global Ocean ◽

Extensive Literature ◽

Microbial Association ◽

Species Specific

ABSTRACT Diatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of plankton. Through analyses of cooccurrence networks derived from the Tara Oceans expedition that take into account both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions; the vast majority are independent of abiotic factors. In contrast to most other plankton groups, on a global scale, diatoms display a much higher proportion of negative correlations with other organisms, particularly toward potential predators and parasites, suggesting that their biogeography is constrained by top-down pressure. Genus-level analyses indicate that abundant diatoms are not necessarily the most connected and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of cooccurrence networks, an open-access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best-known organismal groups. IMPORTANCE Diatoms are key phytoplankton in the modern ocean that are involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open-access database, we propose an ecosystems approach for exploring diatom interactions in the ocean.

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A large-scale ecological assessment of Swiss rivers using environmental DNA for the monitoring of macroinvertebrates

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65307 ◽

2021 ◽

Vol 4 ◽

Author(s):

Jeanine Brantschen ◽

Rosetta Blackman ◽

Jean-Claude Walser ◽

Florian Altermatt

Keyword(s):

Random Forest ◽

Community Composition ◽

Large Scale ◽

Anthropogenic Activities ◽

Ecological Status ◽

Environmental Dna ◽

Biotic Index ◽

Reference Database ◽

Macroinvertebrate Communities ◽

Monitoring Methods

Anthropogenic activities are changing the state of ecosystems worldwide, affecting community composition and often resulting in loss of biodiversity. Riverine ecosystems are among the most impacted ecosystems. Recording their current state with regular biomonitoring is important to assess the future trajectory of biodiversity. However, traditional monitoring methods for ecological assessments are costly and time-intense. Here, we compare environmental DNA (eDNA) to traditional kick-net sampling in a standardized framework of surface water quality assessment. We use surveys of macroinvertebrate communities to assess biodiversity and the biological state of riverine systems. Both methods were employed to monitor aquatic macroinvertebrate indicator groups at 92 sites across major Swiss river catchments. The eDNA data were taxonomically assigned using a customised reference database. All zero-radius Operational Taxonomic Units (zOTUs) mapping to one of the 142 traditionally used indicator taxon levels were used for subsequent diversity analyses (n = 205). At the site level, eDNA detected less indicator taxa than the kick-net method and alpha diversity correlated only weakly between the methods. However, the methods showed a strong congruence in the overall community composition (gamma diversity), as the same indicator groups were commonly detected. In order to set the community composition in relation to the biotic index, the ecological states of the sampling sites were predicted by a random forest approach. Using all zOTUs mapping to macroinvertebrate indicator groups (n = 693) as predictive features, the random forest models successfully predicted the ecological status of the sampled sites. The majority of the predictions (71%) resulted in the same classification like the kick-net based scores. Thus, the sampling of eDNA enabled the detection of indicator communities and provided valuable classifications of the ecological state, when combined with machine learning. Overall, eDNA based sampling has the potential to complement traditional surveys of macroinvertebrate communities in routine large-scale assessments in a non-invasive and scalable approach.

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Diatoms structure the plankton community based on selective segregation in the world’s ocean

10.1101/704353 ◽

2019 ◽

Author(s):

Flora Vincent ◽

Chris Bowler

Keyword(s):

Open Access ◽

Large Scale ◽

Abiotic Factors ◽

Biotic Interactions ◽

Distribution Patterns ◽

Global Scale ◽

Extensive Literature ◽

Microbial Association ◽

Biological Interpretation ◽

Species Specific

ABSTRACTDiatoms are a major component of phytoplankton, believed to be responsible for around 20% of the annual primary production on Earth. As abundant and ubiquitous organisms, they are known to establish biotic interactions with many other members of the plankton. Through analysis of co-occurrence networks derived from the Tara Oceans expedition that take into account the importance of both biotic and abiotic factors in shaping the spatial distributions of species, we show that only 13% of diatom pairwise associations are driven by environmental conditions, whereas the vast majority are independent of abiotic factors. In contrast to most other plankton groups, at a global scale diatoms display a much higher proportion of negative correlations with other organisms, particularly towards potential predators and parasites, suggesting that their biogeography is constrained by top down pressure. Genus level analyses indicate that abundant diatoms are not necessarily the most connected, and that species-specific abundance distribution patterns lead to negative associations with other organisms. In order to move forward in the biological interpretation of co-occurrence networks, an open access extensive literature survey of diatom biotic interactions was compiled, of which 18.5% were recovered in the computed network. This result reveals the extent of what likely remains to be discovered in the field of planktonic biotic interactions, even for one of the best known organismal groups.ImportanceDiatoms are key phytoplankton in the modern ocean involved in numerous biotic interactions, ranging from symbiosis to predation and viral infection, which have considerable effects on global biogeochemical cycles. However, despite recent large-scale studies of plankton, we are still lacking a comprehensive picture of the diversity of diatom biotic interactions in the marine microbial community. Through the ecological interpretation of both inferred microbial association networks and available knowledge on diatom interactions compiled in an open access database, we propose an eco-systems level understanding of diatom interactions in the ocean.

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The roles of mass extinction and biotic interaction in large-scale replacements: a reexamination using the fossil record of stromboidean gastropods

Paleobiology ◽

10.1017/s0094837300016389 ◽

1996 ◽

Vol 22 (3) ◽

pp. 436-452 ◽

Cited By ~ 47

Author(s):

Kaustuv Roy

Keyword(s):

Mass Extinction ◽

Large Scale ◽

Biotic Interactions ◽

Taxonomic Diversity ◽

Global Scale ◽

General Nature ◽

Biotic Interaction ◽

Geographic Scale ◽

Climatic Fluctuations ◽

Extinction Rates

The macroevolutionary processes underlying large-scale biotic replacements are still poorly understood. Opinion remains divided regarding the roles of mass extinction, biotic interaction, and environmental perturbations in these replacement events. Previous attempts to test replacement hypotheses have largely focused on taxonomic diversity patterns. Taxonomic data alone, however, provide little insight about ecological interactions and hence other approaches are needed to understand mechanics of biotic replacements. Here I propose a conceptual model of replacement based on predation-mediated biotic interactions, and attempt a test using analysis of the Cenozoic replacement of the gastropod family Aporrhaidae by a closely related group, the Strombidae.Taxonomic, morphologic, and geographic data analyzed in this study all suggest a replacement of aporrhaids by strombids following the end-Cretaceous mass extinction. While most of the taxonomic replacement was associated with a mass extinction, some replacement also occurred during background times and was mediated by higher origination rates in strombids rather than by higher extinction rates in aporrhaids. Morphologically, the replacement was largely confined to the portion of the morphospace unaffected by the end-Cretaceous extinction. At a global scale, the geographic overlap between the two groups declined through the Cenozoic, reflecting increasing restriction of aporrhaids to colder, temperate waters while strombids flourished in the tropics. However, at a finer geographic scale a more mosaic pattern of replacement is evident and coincides with Eocene and Oligocene climatic fluctuations.The results of this study suggest that mass extinction, long-term biotic interaction, and environmental change can all play significant roles in biotic replacements. Since the relative importance of each factor would vary from one event to another, an understanding of the general nature of large-scale biotic replacements requires a knowledge of the relative intensities of each of these processes.

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Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment

PLoS ONE ◽

10.1371/journal.pone.0257510 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257510

Author(s):

Jeanine Brantschen ◽

Rosetta C. Blackman ◽

Jean-Claude Walser ◽

Florian Altermatt

Keyword(s):

Machine Learning ◽

Random Forest ◽

Community Composition ◽

Large Scale ◽

Anthropogenic Activities ◽

Environmental Dna ◽

Biotic Index ◽

Ecological Classification ◽

Indicator Taxa

Anthropogenic activities are changing the state of ecosystems worldwide, affecting community composition and often resulting in loss of biodiversity. Rivers are among the most impacted ecosystems. Recording their current state with regular biomonitoring is important to assess the future trajectory of biodiversity. Traditional monitoring methods for ecological assessments are costly and time-intensive. Here, we compared monitoring of macroinvertebrates based on environmental DNA (eDNA) sampling with monitoring based on traditional kick-net sampling to assess biodiversity patterns at 92 river sites covering all major Swiss river catchments. From the kick-net community data, a biotic index (IBCH) based on 145 indicator taxa had been established. The index was matched by the taxonomically annotated eDNA data by using a machine learning approach. Our comparison of diversity patterns only uses the zero-radius Operational Taxonomic Units assigned to the indicator taxa. Overall, we found a strong congruence between both methods for the assessment of the total indicator community composition (gamma diversity). However, when assessing biodiversity at the site level (alpha diversity), the methods were less consistent and gave complementary data on composition. Specifically, environmental DNA retrieved significantly fewer indicator taxa per site than the kick-net approach. Importantly, however, the subsequent ecological classification of rivers based on the detected indicators resulted in similar biotic index scores for the kick-net and the eDNA data that was classified using a random forest approach. The majority of the predictions (72%) from the random forest classification resulted in the same river status categories as the kick-net approach. Thus, environmental DNA validly detected indicator communities and, combined with machine learning, provided reliable classifications of the ecological state of rivers. Overall, while environmental DNA gives complementary data on the macroinvertebrate community composition compared to the kick-net approach, the subsequently calculated indices for the ecological classification of river sites are nevertheless directly comparable and consistent.

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Building a Culture of Ethical, Comparable, Authentic Assessment

The Oxford Handbook of Philosophical and Qualitative Assessment in Music Education ◽

10.1093/oxfordhb/9780190265182.013.35 ◽

2019 ◽

pp. 463-481

Author(s):

Andrew Reid ◽

Julie Ballantyne

Keyword(s):

Teaching And Learning ◽

Large Scale ◽

Authentic Assessment ◽

Subject Area ◽

Music Educators ◽

System Level ◽

Diverse Range ◽

Effective Learning ◽

School Based ◽

The Subject

In an ideal world, assessment should be synonymous with effective learning and reflect the intricacies of the subject area. It should also be aligned with the ideals of education: to provide equitable opportunities for all students to achieve and to allow both appropriate differentiation for varied contexts and students and comparability across various contexts and students. This challenge is made more difficult in circumstances in which the contexts are highly heterogeneous, for example in the state of Queensland, Australia. Assessment in music challenges schooling systems in unique ways because teaching and learning in music are often naturally differentiated and diverse, yet assessment often calls for standardization. While each student and teacher has individual, evolving musical pathways in life, the syllabus and the system require consistency and uniformity. The challenge, then, is to provide diverse, equitable, and quality opportunities for all children to learn and achieve to the best of their abilities. This chapter discusses the designing and implementation of large-scale curriculum as experienced in secondary schools in Queensland, Australia. The experiences detailed explore the possibilities offered through externally moderated school-based assessment. Also discussed is the centrality of system-level clarity of purpose, principles and processes, and the provision of supportive networks and mechanisms to foster autonomy for a diverse range of music educators and contexts. Implications for education systems that desire diversity, equity, and quality are discussed, and the conclusion provokes further conceptualization and action on behalf of students, teachers, and the subject area of music.

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Collection of Environmental Variables and Bacterial Community Compositions in Marian Cove, Antarctica, during Summer 2018

Data ◽

10.3390/data6030027 ◽

2021 ◽

Vol 6 (3) ◽

pp. 27

Author(s):

Hyo-Ryeon Kim ◽

Jae-Hyun Lim ◽

Ju-Hyoung Kim ◽

Il-Nam Kim

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Marine Bacteria ◽

Environmental Variables ◽

Environmental Changes ◽

Bacterial Community Composition ◽

Composition Data ◽

Decomposition Of Organic Matter ◽

Class Level ◽

Earth’S Climate

Marine bacteria, which are known as key drivers for marine biogeochemical cycles and Earth’s climate system, are mainly responsible for the decomposition of organic matter and production of climate-relevant gases (i.e., CO₂, N₂O, and CH₄). However, research is still required to fully understand the correlation between environmental variables and bacteria community composition. Marine bacteria living in the Marian Cove, where the inflow of freshwater has been rapidly increasing due to substantial glacial retreat, must be undergoing significant environmental changes. During the summer of 2018, we conducted a hydrographic survey to collect environmental variables and bacterial community composition data at three different layers (i.e., the seawater surface, middle, and bottom layers) from 15 stations. Of all the bacterial data, 17 different phylum level bacteria and 21 different class level bacteria were found and Proteobacteria occupy 50.3% at phylum level following Bacteroidetes. Gammaproteobacteria and Alphaproteobacteria, which belong to Proteobacteria, are the highest proportion at the class level. Gammaproteobacteria showed the highest relative abundance in all three seawater layers. The collection of environmental variables and bacterial composition data contributes to improving our understanding of the significant relationships between marine Antarctic regions and marine bacteria that lives in the Antarctic.

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Remote Sensing Methods for the Biophysical Characterization of Protected Areas Globally: Challenges and Opportunities

ISPRS International Journal of Geo-Information ◽

10.3390/ijgi10060384 ◽

2021 ◽

Vol 10 (6) ◽

pp. 384

Author(s):

Javier Martínez-López ◽

Bastian Bertzky ◽

Simon Willcock ◽

Marine Robuchon ◽

María Almagro ◽

...

Keyword(s):

Remote Sensing ◽

Protected Areas ◽

Large Scale ◽

Anthropogenic Activities ◽

Global Scale ◽

Area Network ◽

Biophysical Characterization ◽

Challenges And Opportunities ◽

Scale Characterization

Protected areas (PAs) are a key strategy to reverse global biodiversity declines, but they are under increasing pressure from anthropogenic activities and concomitant effects. Thus, the heterogeneous landscapes within PAs, containing a number of different habitats and ecosystem types, are in various degrees of disturbance. Characterizing habitats and ecosystems within the global protected area network requires large-scale monitoring over long time scales. This study reviews methods for the biophysical characterization of terrestrial PAs at a global scale by means of remote sensing (RS) and provides further recommendations. To this end, we first discuss the importance of taking into account the structural and functional attributes, as well as integrating a broad spectrum of variables, to account for the different ecosystem and habitat types within PAs, considering examples at local and regional scales. We then discuss potential variables, challenges and limitations of existing global environmental stratifications, as well as the biophysical characterization of PAs, and finally offer some recommendations. Computational and interoperability issues are also discussed, as well as the potential of cloud-based platforms linked to earth observations to support large-scale characterization of PAs. Using RS to characterize PAs globally is a crucial approach to help ensure sustainable development, but it requires further work before such studies are able to inform large-scale conservation actions. This study proposes 14 recommendations in order to improve existing initiatives to biophysically characterize PAs at a global scale.

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Drug Prescription Profiles in Patients with Polypharmacy in Spain: A Large-Scale Pharmacoepidemiologic Study Using Real-World Data

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18094754 ◽

2021 ◽

Vol 18 (9) ◽

pp. 4754

Author(s):

Miguel Ángel Hernández-Rodríguez ◽

Ermengol Sempere-Verdú ◽

Caterina Vicens-Caldentey ◽

Francisca González-Rubio ◽

Félix Miguel-García ◽

...

Keyword(s):

Psychotropic Drugs ◽

Large Scale ◽

Anatomical Therapeutic Chemical ◽

Drug Prescription ◽

Age Groups ◽

System Level ◽

Real World Data ◽

Converting Enzyme Inhibitors ◽

Cross Sectional ◽

Β Blockers

We aimed to identify and compare medication profiles in populations with polypharmacy between 2005 and 2015. We conducted a cross-sectional study using information from the Computerized Database for Pharmacoepidemiologic Studies in Primary Care (BIFAP, Spain). We estimated the prevalence of therapeutic subgroups in all individuals 15 years of age and older with polypharmacy (≥5 drugs during ≥6 months) using the Anatomical Therapeutic Chemical classification system level 4, by sex and age group, for both calendar years. The most prescribed drugs were proton-pump inhibitors (PPIs), statins, antiplatelet agents, benzodiazepine derivatives, and angiotensin-converting enzyme inhibitors. The greatest increases between 2005 and 2015 were observed in PPIs, statins, other antidepressants, and β-blockers, while the prevalence of antiepileptics was almost tripled. We observed increases in psychotropic drugs in women and cardiovascular medications in men. By patient´s age groups, there were notable increases in antipsychotics, antidepressants, and antiepileptics (15–44 years); antidepressants, PPIs, and selective β-blockers (45–64 years); selective β-blockers, biguanides, PPIs, and statins (65–79 years); and in statins, selective β-blockers, and PPIs (80 years and older). Our results revealed important increases in the use of specific therapeutic subgroups, like PPIs, statins, and psychotropic drugs, highlighting opportunities to design and implement strategies to analyze such prescriptions’ appropriateness.

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