Detecting signatures of competition from observational data: a combined approach using DNA barcoding, diversity partitioning and checkerboards at small spatial scales

Additive diversity partitioning (α, β, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (β) diversity. Caddisfly larvae were sampled using a hierarchical spatial design in two regions (subarctic Churchill, Manitoba, Canada; temperate Pennsylvania, USA) and then additively partitioned according to Barcode Index Numbers (molecular clusters that serve as a proxy for species), genus, and family levels; diversity components were expressed as proportional species turnover. We screened 114 articles of additive diversity partitioning and found that a third reported difficulties with achieving species-level identifications, with a clear taxonomic tendency towards challenges identifying invertebrate taxa. Regarding our own study, caddisfly BINs appeared to show greater subregional turnover (e.g., proportional additive β) compared to genus or family levels. Diversity component studies failing to achieve species resolution due to morphological identifications may therefore be underestimating diversity turnover at larger spatial scales.

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Additive Diversity Partitioning of Reef Fishes across Multiple Spatial Scales

Caribbean Journal of Science ◽

10.18475/cjos.v44i1.a10 ◽

2008 ◽

Vol 44 (1) ◽

pp. 90-101 ◽

Cited By ~ 17

Author(s):

Fabián A. Rodríguez-Zaragoza ◽

Jesús E. Arias-González

Keyword(s):

Spatial Scales ◽

Reef Fishes ◽

Diversity Partitioning ◽

Multiple Spatial Scales

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Ant diversity partitioning across spatial scales: Ecological processes and implications for conserving Tropical Dry Forests

Austral Ecology ◽

10.1111/aec.12046 ◽

2013 ◽

Vol 39 (1) ◽

pp. 72-82 ◽

Cited By ~ 10

Author(s):

Tatianne Marques ◽

José H. Schoereder

Keyword(s):

Spatial Scales ◽

Tropical Dry Forests ◽

Diversity Partitioning ◽

Dry Forests ◽

Ecological Processes ◽

Ant Diversity

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Macrofaunal assemblages from mud volcanoes in the Gulf of Cadiz: abundance, biodiversity and diversity partitioning across spatial scales

Biogeosciences ◽

10.5194/bg-10-2553-2013 ◽

2013 ◽

Vol 10 (4) ◽

pp. 2553-2568 ◽

Cited By ~ 28

Author(s):

M. R. Cunha ◽

C. F. Rodrigues ◽

L. Génio ◽

A. Hilário ◽

A. Ravara ◽

...

Keyword(s):

Spatial Scales ◽

Cold Seeps ◽

Mud Volcanoes ◽

Gulf Of Cadiz ◽

Reference Sites ◽

Geologic History ◽

Diversity Partitioning ◽

Number Of Species ◽

Β Diversity ◽

Gulf Of Cádiz

Abstract. The Gulf of Cadiz is an extensive seepage area in the south Iberian margin (NE Atlantic) encompassing over 40 mud volcanoes (MVs) at depths ranging from 200 to 4000 m. The area has a long geologic history and a central biogeographic location with a complex circulation ensuring oceanographic connectivity with the Mediterranean Sea, equatorial and North Atlantic regions. The geodynamics of the region promotes a notorious diversity in the seep regime despite the relatively low fluxes of hydrocarbon-rich gases. We analyse quantitative samples taken during the cruises TTR14, TTR15 and MSM01-03 in seven mud volcanoes grouped into Shallow MVs (Mercator: 350 m, Kidd: 500 m, Meknès: 700 m) and Deep MVs (Captain Arutyunov: 1300 m, Carlos Ribeiro: 2200 m, Bonjardim: 3000 m, Porto: 3900 m) and two additional Reference sites (ca. 550 m). Macrofauna (retained by a 500 μm sieve) was identified to species level whenever possible. The samples yielded modest abundances (70–1567 individuals per 0.25 m2), but the local and regional number of species is among the highest ever reported for cold seeps. Among the 366 recorded species, 22 were symbiont-hosting bivalves (Thyasiridae, Vesicomyidae, Solemyidae) and tubeworms (Siboglinidae). The multivariate analyses supported the significant differences between Shallow and Deep MVs: The environmental conditions at the Shallow MVs make them highly permeable to the penetration of background fauna leading to high diversity of the attendant assemblages (H′: 2.92–3.94; ES(100): 28.3–45.0; J′: 0.685–0.881). The Deep MV assemblages showed, in general, contrasting features but were more heterogeneous (H′: 1.41–3.06; ES(100): 10.5–30.5; J′: 0.340–0.852) and often dominated by one or more siboglinid species. The rarefaction curves confirmed the differences in biodiversity of Deep and Shallow MVs as well as the convergence of the latter to the Reference sites. The Bray–Curtis dissimilarity demonstrated the high β-diversity of the assemblages, especially in pairwise comparisons involving samples from the Deep MVs. Diversity partitioning assessed for species richness, Hurlbert's expected number of species and Shannon–Wiener index confirmed the high β-diversity across different spatial scales (within MVs, between MVs, between Deep and Shallow MVs). We suggest that historical and contemporary factors with differential synergies at different depths contribute to the high α-, β- and γ-diversity of the mud volcano faunal assemblages in the Gulf of Cadiz.

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Carbon dioxide emissions in Northern China based on atmospheric observations from 2005 to 2009

10.5194/acp-2019-677 ◽

2019 ◽

Author(s):

Archana Dayalu ◽

J. William Munger ◽

Yuxuan Wang ◽

Steven C. Wofsy ◽

Yu Zhao ◽

...

Keyword(s):

Carbon Dioxide ◽

Observational Data ◽

Co2 Emissions ◽

Carbon Dioxide Emissions ◽

Spatial Scales ◽

Northern China ◽

High Temporal Resolution ◽

Anthropogenic Co2 ◽

Time Period ◽

Data Limitations

Abstract. China has pledged reduction of carbon dioxide emissions per unit GDP by 60–65 % relative to 2005 levels, and to peak carbon emissions overall by 2030. However, disagreement among available inventories makes it difficult for China to track progress toward these goals and evaluate the efficacy of control measures. In this study, we demonstrate an approach based on a long time series of surface CO2 observations to evaluate regional CO2 emissions rates in northern China estimated by three anthropogenic CO2 inventories – two of which are subsets from global inventories, and one of which is China-specific. Comparison of CO2 observations to CO2 predicted from accounting for global background concentration and atmospheric mixing of emissions suggests potential biases in the inventories. The period analyzed focuses on the key commitment period for the Paris accords (2005) and the Beijing Olympics (2008). Model-observation mismatch in concentration units is translated to mass units and is displayed against the original inventories in the measurement influence region, largely corresponding to northern China. Owing to limitations from having a single site, addressing the significant uncertainty stemming from transport error and error in spatial allocation of the emissions remains a challenge. Our analysis uses observations to support and justify increased use and development of China-specific inventories in tracking China's progress as a whole towards reducing emissions. Here we are restricted to a single measurement site; effectively evaluating and constraining inventories at relevant spatial scales requires multiple stations of high-temporal resolution observations. At this stage and with observational data limitations, we emphasize that this work is intended to be a comparison of a subset of anthropogenic CO2 emissions rates from inventories that were readily available at the time this research began. For this study's analysis time period, there was not enough spatially distinct observational data to conduct an optimization of the inventories. Rather, our analysis provides an important quantification of model-observation mismatch. In the northern China evaluation region, emission rates from the China-specific inventory produce the lowest model-observation mismatch at all timescales from daily to annual. Additionally, we note that averaged over the study time period, the unscaled China-specific inventory has substantially larger annual emissions for China as a whole (20 % higher) and the northern China evaluation region (30 %) than the unscaled global inventories. Our results lend support the rates and geographic distribution in the China-specific inventory. However, exploring this discrepancy for China as a whole requires a denser observational network in future efforts to measure and verify CO2 emissions for China both regionally and nationally. This study provides a baseline analysis for a small but import region within China, as well a guide for determining optimal locations for future ground-based measurement sites.

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Overview: On the transport and transformation of pollutants in the outflow of major population centres – observational data from the EMeRGe European intensive operational period in summer 2017

10.5194/acp-2021-500 ◽

2021 ◽

Author(s):

M. Dolores Andrés Hernández ◽

Andreas Hilboll ◽

Helmut Ziereis ◽

Eric Förster ◽

Ovid O. Krüger ◽

...

Keyword(s):

Observational Data ◽

Long Range ◽

Atmospheric Chemistry ◽

Field Experiments ◽

Spatial Scales ◽

Aerosol Particles ◽

Mitigation Strategies ◽

Transport And Transformation ◽

Airborne Measurements ◽

Fire Emissions

Abstract. EMeRGe (Effect of Megacities on the transport and transformation of pollutants on the Regional to Global scales) is an international project focusing on atmospheric chemistry, dynamics and transport of local and regional pollution originating in megacities and other major population centres (MPCs). Airborne measurements, taking advantage of the long range capabilities of the HALO research platform (High Altitude and Long range research aircraft, www.halo-spp.de), are a central part of the research project. In order to provide an adequate set of measurements at different spatial scales, two field experiments were positioned in time and space to contrast situations when the photochemical transformation of plumes emerging from MPCs is large. These experiments were conducted in summer 2017 over Europe and in the inter-monsoon period over Asia in spring 2018. The intensive observational periods (IOP) involved HALO airborne measurements of ozone and its precursors, volatile organic compounds, aerosol particles and related species as well as coordinated ground-based ancillary observations at different sites. Perfluorocarbon (PFC) tracer releases and model forecasts supported the flight planning and the identification of pollution plumes. This paper describes the experimental deployment of the IOP in Europe, which comprised 7 HALO research flights with aircraft base in Oberpfaffenhofen (Germany) for a total of 53 flight hours. The MPC targets London (Great Britain), Benelux/Ruhr area (Belgium, The Netherlands, Luxembourg and Germany), Paris (France), Rome and Po Valley (Italy), Madrid and Barcelona (Spain) were investigated. An in-flight comparison of HALO with the collaborating UK-airborne platform FAAM took place to assure accuracy and comparability of the instrumentation on-board. Generally, significant enhancement of trace gases and aerosol particles are attributed to emissions originating in MPCs at distances of hundreds of kilometres from the sources. The proximity of different MPCs over Europe favours the mixing of plumes of different origin and level of processing and hampers the unambiguous attribution of the MPC sources. Similarly, urban plumes mix efficiently with natural sources as desert dust and with biomass burning emissions from vegetation and forest fires. This confirms the importance of wildland fire emissions in Europe and indicates an important but discontinuous contribution to the European emission budget that might be of relevance in the design of efficient mitigation strategies. The synergistic use and consistent interpretation of observational data sets of different spatial and temporal resolution (e.g. from ground-based networks, airborne campaigns, and satellite measurements) supported by modelling within EMeRGe, provides a unique insight to test the current understanding of MPC pollution outflows. The present work provides an overview of the most salient results and scientific questions in the European context, these being addressed in more detail within additional dedicated EMeRGe studies. The deployment and results obtained in Asia will be the subject of separate publications.

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DNA Barcoding Reveals Hidden Diversity of Sand Flies (Diptera: Psychodidae) at Fine and Broad Spatial Scales in Brazilian Endemic Regions for Leishmaniasis

Journal of Medical Entomology ◽

10.1093/jme/tjy032 ◽

2018 ◽

Vol 55 (4) ◽

pp. 893-901 ◽

Cited By ~ 5

Author(s):

Bruno Leite Rodrigues ◽

Luís Fernando Carvalho-Costa ◽

Israel de Souza Pinto ◽

José Manuel Macário Rebêlo

Keyword(s):

Dna Barcoding ◽

Spatial Scales ◽

Sand Flies

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Hidden biodiversity in Neotropical streams: DNA barcoding uncovers high endemicity of freshwater macroinvertebrates at small spatial scales

10.1101/2020.03.31.018457 ◽

2020 ◽

Author(s):

Luis F. De León ◽

Aydeé Cornejo ◽

Ronnie G. Gavilán ◽

Celestino Aguilar

Keyword(s):

Spatial Scale ◽

Dna Barcoding ◽

Spatial Scales ◽

Freshwater Ecosystems ◽

Panama Canal ◽

Freshwater Macroinvertebrates ◽

Isthmus Of Panama ◽

Neotropical Streams ◽

Continental Islands ◽

Lineage Diversity

AbstractAquatic macroinvertebrates play a crucial role in freshwater ecosystems, but their diversity remains poorly known, particularly in the tropics. This “taxonomic void” represents limits our understanding of biodiversity patterns and processes in freshwater ecosystems, and the scale at which they operate. We used DNA barcoding to estimate lineage diversity (and the diversity of unique haplotypes) in 224 specimens of freshwater macroinvertebrates at a small spatial scale within the Panama Canal Watershed (PCW). In addition, we compiled available barcoding data to assess macroinvertebrate diversity at a broader spatial scale spanning the Isthmus of Panama. Consistently across two species delimitation algorithms (i.e., ABGD and GMYC), we found high lineage diversity within the PCW, with ~ 100-106 molecular operational taxonomic units (MOTUs at 2% sequence divergence) across 168 unique haplotypes. We also found a high lineage diversity along the Isthmus of Panama, but this diversity peaked within the PCW. However, our rarefaction/extrapolation approach showed that this diversity remains under sampled. As expected, these results indicate that the diversity of Neotropical freshwater macroinvertebrates is higher than previously thought, with the possibility of high endemicity even at narrow spatial scales. Geographic isolation is likely a main factor shaping these patterns of diversity. However, local disturbances such as the rupture of the continental divide due to the construction of the Panama Canal might be reshaping these patterns of diversity at a local scale. Although further work is needed to better understand the processes driving diversification in freshwater macroinvertebrates, we suggest that Neotropical streams represent continental islands of diversity. Understanding these islands of diversity is crucial in the face of increasing human disturbance.

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