scholarly journals The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding

Genome ◽  
2016 ◽  
Vol 59 (12) ◽  
pp. 1130-1140 ◽  
Author(s):  
Trevor T. Bringloe ◽  
Karl Cottenie ◽  
Gillian K. Martin ◽  
Sarah J. Adamowicz
Keyword(s):  
Dna Barcoding ◽  
Species Turnover ◽  
Spatial Scales ◽  
Species Level ◽  
Taxonomic Resolution ◽  
Diversity Partitioning ◽  
Spatial Design ◽  
Β Diversity ◽  
Caddisfly Larvae ◽  
Additive Measures

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.

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

2016 ◽  
Vol 61 (5) ◽  
pp. 646-657 ◽  
Author(s):  
Trevor T. Bringloe ◽  
Sarah J. Adamowicz ◽  
Vivian F. I. Harvey ◽  
John K. Jackson ◽  
Karl Cottenie
Keyword(s):  
Dna Barcoding ◽  
Observational Data ◽  
Spatial Scales ◽  
Combined Approach ◽  
Diversity Partitioning

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

2013 ◽  
Vol 10 (4) ◽  
pp. 2553-2568 ◽  
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.

scholarly journals Species turnover drives β-diversity patterns across multiple spatial scales of plant-galling interactions in mountaintop grasslands

PLoS ONE ◽  
2018 ◽  
Vol 13 (5) ◽  
pp. e0195565 ◽  
Author(s):  
Marcel Serra Coelho ◽  
Marco Antônio Alves Carneiro ◽  
Cristina Alves Branco ◽  
Rafael Augusto Xavier Borges ◽  
Geraldo Wilson Fernandes
Keyword(s):  
Species Turnover ◽  
Spatial Scales ◽  
Diversity Patterns ◽  
Multiple Spatial Scales ◽  
Β Diversity

scholarly journals Adding DNA barcoding to stream monitoring protocols – What’s the additional value and congruence between morphological and molecular identification approaches?

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0244598
Author(s):  
Simone Behrens-Chapuis ◽  
Fabian Herder ◽  
Matthias F. Geiger
Keyword(s):  
Dna Barcoding ◽  
Cost Benefit Analysis ◽  
Ecological Status ◽  
Species Level ◽  
Aquatic Macroinvertebrates ◽  
Taxonomic Resolution ◽  
Morphological Identification ◽  
Stream Monitoring ◽  
Monitoring Protocols ◽  
Additional Value

Although aquatic macroinvertebrates and freshwater fishes are important indicators for freshwater quality assessments, the morphological identification to species-level is often impossible and thus especially in many invertebrate taxa not mandatory during Water Framework Directive monitoring, a pragmatism that potentially leads to information loss. Here, we focus on the freshwater fauna of the River Sieg (Germany) to test congruence and additional value in taxa detection and taxonomic resolution of DNA barcoding vs. morphology-based identification in monitoring routines. Prior generated morphological identifications of juvenile fishes and aquatic macroinvertebrates were directly compared to species assignments using the identification engine of the Barcode of Life Data System. In 18% of the invertebrates morphology allowed only assignments to higher systematic entities, but DNA barcoding lead to species-level assignment. Dissimilarities between the two approaches occurred in 7% of the invertebrates and in 1% of the fishes. The 18 fish species were assigned to 20 molecular barcode index numbers, the 104 aquatic invertebrate taxa to 113 molecular entities. Although the cost-benefit analysis of both methods showed that DNA barcoding is still more expensive (5.30–8.60€ per sample) and time consuming (12.5h), the results emphasize the potential to increase taxonomic resolution and gain a more complete profile of biodiversity, especially in invertebrates. The provided reference DNA barcodes help building the foundation for metabarcoding approaches, which provide faster sample processing and more cost-efficient ecological status determination.

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

2012 ◽  
Vol 9 (12) ◽  
pp. 18331-18369 ◽  
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 assuring oceanographic connectivity with the Mediterranean Sea, Equatorial and Northern 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 ind. per 0.25 m2) but a number of species 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 indicated significant differences between Shallow and Deep MVs: The environmental conditions at the Shallow MVs makes 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 MVs 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 approximation 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 deeper 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.

scholarly journals On the importance of spatial scales on beta diversity of coral assemblages: a study from Venezuelan coral reefs

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9082
Author(s):  
Emy Miyazawa ◽  
Luis M. Montilla ◽  
Esteban Alejandro Agudo-Adriani ◽  
Alfredo Ascanio ◽  
Gloria Mariño-Briceño ◽  
...  
Keyword(s):  
Coral Reefs ◽  
Beta Diversity ◽  
Species Turnover ◽  
Spatial Scales ◽  
Assemblage Structure ◽  
Caribbean Region ◽  
Management Actions ◽  
Β Diversity ◽  
Coral Assemblage ◽  
The Caribbean

Estimating variability across spatial scales has been a major issue in ecology because the description of patterns in space is extremely valuable to propose specific hypotheses to unveil key processes behind these patterns. This paper aims to estimate the variability of the coral assemblage structure at different spatial scales in order to determine which scales explain the largest variability on β-diversity. For this, a fully-nested design including a series of hierarchical-random factors encompassing three spatial scales: (1) regions, (2) localities and (3) reefs sites across the Venezuelan territory. The variability among spatial scales was tested with a permutation-based analysis of variance (Permanova) based on Bray-Curtis index. Dispersion in species presence/absence across scales (i.e., β-diversity) was tested with a PermDisp analysis based on Jaccard’s index. We found the highest variability in the coral assemblage structure between sites within localities (Pseudo-F = 5.34; p-value = 0.001, CV = 35.10%). We also found that longitude (Canonical corr = 0.867, p = 0.001) is a better predictor of the coral assemblage structure in Venezuela, than latitude (Canonical corr = 0.552, p = 0.021). Largest changes in β-diversity of corals occurred within sites (F = 2.764, df1= 35, df2 = 107, p = 0.045) and within localities (F = 4.438, df1= 6, df2 = 29, p = 0.026). Our results suggest that processes operating at spatial scales of hundreds of meters and hundreds of kilometers might both be critical to shape coral assemblage structure in Venezuela, whereas smaller scales (i.e., hundreds of meters) showed to be highly- important for the species turnover component of β-diversity. This result highlights the importance of creating scale-adapted management actions in Venezuela and likely across the Caribbean region.

Diversity metrics, species turnovers and nestedness of bird assemblages in a deep karst sinkhole

2017 ◽  
Vol 63 (2) ◽  
pp. 8-16 ◽  
Author(s):  
Corrado Battisti ◽  
Marco Giardini ◽  
Francesca Marini ◽  
Lorena Di Rocco ◽  
Giuseppe Dodaro ◽  
...  
Keyword(s):  
Species Richness ◽  
Random Distribution ◽  
Diversity Index ◽  
Species Turnover ◽  
Floristic Composition ◽  
Bird Assemblages ◽  
Β Diversity ◽  
Stick Model ◽  
Karst Sinkhole

We reported a study on breeding birds occurring inside an 80 m-deep karst sinkhole, with the characterization of the assemblages recorded along its semi-vertical slopes from the upper edge until the bottom. The internal sides of the sinkhole have been vertically subdivided in four belts about 20 m high. The highest belt (at the upper edge of the cenote) showed the highest values in mean number of bird detections, mean and normalized species richness, and Shannon diversity index. The averaged values of number of detections and species richness significantly differ among belts. Species turnover (Cody’s β-diversity) was maximum between the highest belts. Whittaker plots showed a marked difference among assemblages shaping from broken-stick model to geometric series, and explicited a spatial progressive stress with a disruption in evenness towards the deepest belts. Bird assemblages evidenced a nested subset structure with deeper belts containing successive subsets of the species occurring in the upper belts. We hypothesize that, at least during the daytime in breeding season, the observed non-random distribution of species along the vertical stratification is likely due to (i) the progressive simplification both of the floristic composition and vegetation structure, and (ii) the paucity of sunlight as resources from the upper edge to the inner side of the cenote.

A quantitative null model of additive diversity partitioning: examining the response of beta diversity to extinction

Paleobiology ◽  
2007 ◽  
Vol 33 (1) ◽  
pp. 116-124 ◽  
Author(s):  
Karen M. Layou
Keyword(s):  
Null Model ◽  
Sampling Strategy ◽  
Diversity Partitioning ◽  
Opposite Pattern ◽  
Β Diversity ◽  
Α Diversity ◽  
Before And After ◽  
Four Levels ◽  
Total Diversity ◽  
Selective Extinction

Paleobiological diversity is often expressed as α (within-sample), β (among-sample), and γ (total) diversities. However, when studying the effects of extinction on diversity patterns, only variations in α and γ diversities are typically addressed. A null model that examines changes in β diversity as a function of percent extinction is presented here.The model examines diversity in the context of a hierarchical sampling strategy that allows for the additive partitioning of γ diversity into mean α and β diversities at varying scales. Here, the sampling hierarchy has four levels: samples, beds, facies, and region; thus, there are four levels of α diversity (α1, α2, α3, α4) and three levels of β diversity (β1, β2, and β3). Taxa are randomly assigned to samples within the hierarchy according to probability of occurrence, and initial mean α and β values are calculated. A regional extinction is imposed, and the hierarchy is resampled from the remaining extant taxa. Post-extinction mean α and β values are then calculated.Both non-selective and selective extinctions with respect to taxon abundance yield decreases in α, β, and γ diversities. Non-selective extinction with respect to taxon abundance shows little effect on diversity partitioning except at the highest extinction magnitudes (above 75% extinction), where the contribution of α1 to total γ increases at the expense of β3, with β1 and β2 varying little with increasing extinction magnitude. The pre-extinction contribution of α1 to total diversity increases with increased probabilities of taxon occurrence and the number of shared taxa between facies. Both β1 and β2 contribute equally to total diversity at low occurrence probabilities, but β2 is negligible at high probabilities, because individual samples preserve all the taxonomic variation present within a facies. Selective extinction with respect to rare taxa indicates a constant increase in α1 and constant decrease in β3 with increasing extinction magnitudes, whereas selective extinction with respect to abundant taxa yields the opposite pattern of an initial decrease in α1 and increase in β3. Both β1 and β2 remain constant with increasing extinction for both cases of selectivity. By comparing diversity partitioning before and after an extinction event, it may be possible to determine whether the extinction was selective with respect to taxon abundances, and if so, whether that selectivity was against rare or abundant taxa.Field data were collected across a Late Ordovician regional extinction in the Nashville Dome of Tennessee, with sampling hierarchy similar to that of the model. These data agree with the abundant-selective model, showing declines in α, β, and γ diversities, and a decrease in α1 and increase in β3, which suggests this extinction may have targeted abundant taxa.

scholarly journals The conservation value of South East Asia's highly degraded forests: evidence from leaf-litter ants

2011 ◽  
Vol 366 (1582) ◽  
pp. 3256-3264 ◽  
Author(s):  
Paul Woodcock ◽  
David P. Edwards ◽  
Tom M. Fayle ◽  
Rob J. Newton ◽  
Chey Vun Khen ◽  
...  
Keyword(s):  
Species Richness ◽  
Leaf Litter ◽  
Oil Palm ◽  
Species Turnover ◽  
Spatial Scales ◽  
Forest Conversion ◽  
Conservation Value ◽  
Natural Forests ◽  
Ant Communities ◽  
Logged Forest

South East Asia is widely regarded as a centre of threatened biodiversity owing to extensive logging and forest conversion to agriculture. In particular, forests degraded by repeated rounds of intensive logging are viewed as having little conservation value and are afforded meagre protection from conversion to oil palm. Here, we determine the biological value of such heavily degraded forests by comparing leaf-litter ant communities in unlogged (natural) and twice-logged forests in Sabah, Borneo. We accounted for impacts of logging on habitat heterogeneity by comparing species richness and composition at four nested spatial scales, and examining how species richness was partitioned across the landscape in each habitat. We found that twice-logged forest had fewer species occurrences, lower species richness at small spatial scales and altered species composition compared with natural forests. However, over 80 per cent of species found in unlogged forest were detected within twice-logged forest. Moreover, greater species turnover among sites in twice-logged forest resulted in identical species richness between habitats at the largest spatial scale. While two intensive logging cycles have negative impacts on ant communities, these degraded forests clearly provide important habitat for numerous species and preventing their conversion to oil palm and other crops should be a conservation priority.

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