The many forms of beta diversity: a comment on McGill et al. and some notational suggestions

10.7287/peerj.preprints.3157v1 ◽

2017 ◽

Author(s):

Tobias Jeppsson

Keyword(s):

Spatial Patterns ◽

Beta Diversity ◽

Temporal Trend ◽

Species Turnover ◽

Temporal Trends ◽

Β Diversity ◽

Different Types ◽

Biodiversity Change ◽

The Many

Fundamentally, beta diversity is a measure of species turnover across time or space. In practice, it is sometimes unclear exactly what aspect of beta diversity that is implied in studies. For instance, a trend in ’spatial beta diversity’ can be used to refer to both differences in spatial beta diversity between sites, as well as a temporal trend in spatial beta diversity (at the same site). In a recent review, McGill et al. [1] provide a useful and much needed overview of different aspects of biodiversity change, and show areas where we lack knowledge. Even so, McGill et al. ignore some aspects of beta diversity and sometimes pool different types of beta diversity under the same heading. However, their review mainly focused on temporal trends in diversity, while I here want to highlight spatial patterns in temporal β -diversity (species turnover) as an important but somewhat overlooked component of biodiversity change. Furthermore, I propose a slightly modified classification and nomenclature of metrics of biodiversity change, with the aim of complementing their review. The notation used here can hopefully be useful to other authors as well.

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Geographical patterns and partition of turnover and richness components of beta-diversity in faunas from Tocantins river valley

Brazilian Journal of Biology ◽

10.1590/s1519-69842012000300012 ◽

2012 ◽

Vol 72 (3) ◽

pp. 497-504 ◽

Cited By ~ 10

Author(s):

MLS. Tonial ◽

HLR. Silva ◽

IJ. Tonial ◽

MC. Costa ◽

NJ. Silva Júnior ◽

...

Keyword(s):

Spatial Patterns ◽

Species Turnover ◽

Regional Scale ◽

Northeastern Brazil ◽

Amphibian Species ◽

Geographical Patterns ◽

Β Diversity ◽

Mantel Tests ◽

Dispersal Abilities ◽

Broad Scale

There has been a resurging interest in patterns of β-diversity, especially by the mechanisms driving broad-scale, continental and global patterns, and how partitioning β-diversity into richness (or nestedness) and turnover components can be linked with such mechanisms. Here we compared two recent methodologies to find richness and turnover components of β-diversity, using a large regional scale dataset of mammal, bird, reptiles and amphibian species found in seven regions of Central, North and Northeastern Brazil. As well as a simple comparison of the metrics available, we analyzed spatial patterns (i.e., distance-decay similarity) and the effects of biome type in these components using raw and partial Mantel tests. Our analyses revealed that turnover estimated using Baselga's (2010) approach is slightly higher than the estimate using Carvalho's et al. (2012) approach, but all analyses show consistent spatial patterns in species turnover using both methods. Spatial patterns in β-diversity revealed by Mantel tests are also consistent with expectations based on differential dispersal abilities. Our results also reinforce that spatial patterns in β-diversity, mainly in the turnover components expressing faunal differentiation, are determined by a mix or broad scale environmental effects and short distance spatially-structured dispersal.

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Ecological boundaries in estuaries: macrobenthic β-diversity in the Río de la Plata system (34–36°S)

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315407050126 ◽

2007 ◽

Vol 87 (2) ◽

pp. 377-381 ◽

Cited By ~ 19

Author(s):

D.A. Giberto ◽

C.S. Bremec ◽

A. Cortelezzi ◽

A. Rodrigues Capitulo ◽

A. Brazeiro

Keyword(s):

Beta Diversity ◽

Environmental Gradients ◽

Species Turnover ◽

Benthic Communities ◽

Rio De La Plata ◽

Río De La Plata ◽

La Plata ◽

Β Diversity ◽

Ecological Boundaries ◽

Taxonomic Groups

In this study, we analyse spatial patterns of macrobenthic communities of the Río de la Plata system, and assess the species turnover or beta diversity and its relationship with environmental gradients. Macrobenthic samples and physico-chemical parameters were collected from 20 sampling sites along a transect of 560 km, including the freshwater (FW), estuarine (ES) and marine (MA) sectors. Three main assemblages corresponding to the above mentioned sectors were defined with multivariate analysis (cluster, MDS). In total 134 taxa were recorded, 81 in MA, 33 in FW and 38 in ES, represented mainly by polychaete, mollusc and crustacean species. Depth, salinity and %clay showed the strongest correlation with the observed faunal patterns (ρw=0.62; BIO-ENV analysis). Beta diversity varied between dominant taxonomic groups and was positively correlated with changes in salinity. The high variability in the composition of assemblages was reflected in beta diversity, reaching its highest values at the boundaries between the defined sectors. This study suggests that beta diversity represents a useful tool to define ecological boundaries for benthic communities in the Río de la Plata.

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Biodiversity trends are stronger in marine than terrestrial assemblages

10.1101/457424 ◽

2018 ◽

Cited By ~ 3

Author(s):

Shane Blowes ◽

Sarah Supp ◽

Laura Antão ◽

Amanda Bates ◽

Helge Bruelheide ◽

...

Keyword(s):

Time Series ◽

Temporal Change ◽

Species Turnover ◽

Temporal Trends ◽

Compositional Change ◽

Taxa Richness ◽

Rates Of Change ◽

Extinction Rates ◽

Consistent Change ◽

Biodiversity Change

SummaryHuman activities have fundamentally altered biodiversity. Extinction rates are elevated and model projections suggest drastic biodiversity declines. Yet, observed temporal trends in recent decades are highly variable, despite consistent change in species composition. Here, we uncover clear spatial patterns within this variation. We estimated trends in the richness and composition of assemblages in over 50,000 time-series, to provide the most comprehensive assessment of temporal change in biodiversity across the planet to date. The strongest, most consistent pattern shows compositional change dominated by species turnover, with marine taxa experiencing up to fourfold the variation in rates of change of terrestrial taxa. Richness change ranged from no change to richness gains or losses of ~10% per year, with tropical marine biomes experiencing the most extreme changes. Earth is undergoing a process of spatial reorganisation of species and, while few areas are unaffected, biodiversity change is consistently strongest in the oceans.

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

PeerJ ◽

10.7717/peerj.9082 ◽

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.

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Sam Domains in Multiple Diseases

Current Medicinal Chemistry ◽

10.2174/0929867325666181009114445 ◽

2020 ◽

Vol 27 (3) ◽

pp. 450-476 ◽

Cited By ~ 1

Author(s):

Marian Vincenzi ◽

Flavia Anna Mercurio ◽

Marilisa Leone

Keyword(s):

Disease Onset ◽

Protein Domain ◽

Sam Domain ◽

Different Types ◽

Protein Functions ◽

Helical Protein ◽

The Many ◽

Novel Therapeutic Strategies ◽

Novel Drug ◽

Pathological Event

Background: The sterile alpha motif (Sam) domain is a small helical protein module, able to undergo homo- and hetero-oligomerization, as well as polymerization, thus forming different types of protein architectures. A few Sam domains are involved in pathological processes and consequently, they represent valuable targets for the development of new potential therapeutic routes. This study intends to collect state-of-the-art knowledge on the different modes by which Sam domains can favor disease onset and progression. Methods: This review was build up by searching throughout the literature, for: a) the structural properties of Sam domains, b) interactions mediated by a Sam module, c) presence of a Sam domain in proteins relevant for a specific disease. Results: Sam domains appear crucial in many diseases including cancer, renal disorders, cataracts. Often pathologies are linked to mutations directly positioned in the Sam domains that alter their stability and/or affect interactions that are crucial for proper protein functions. In only a few diseases, the Sam motif plays a kind of "side role" and cooperates to the pathological event by enhancing the action of a different protein domain. Conclusion: Considering the many roles of the Sam domain into a significant variety of diseases, more efforts and novel drug discovery campaigns need to be engaged to find out small molecules and/or peptides targeting Sam domains. Such compounds may represent the pillars on which to build novel therapeutic strategies to cure different pathologies.

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Are local losses of biodiversity causing degraded ecosystem function?

10.1093/oso/9780198808978.003.0004 ◽

2017 ◽

Author(s):

Mark Vellend

Keyword(s):

Ecosystem Function ◽

Species Interactions ◽

Regional Scale ◽

Temporal Trends ◽

Biodiversity Loss ◽

Large Degree ◽

Global Scale ◽

Degraded Ecosystem ◽

Biodiversity Change ◽

Local Extirpation

This chapter highlights the scale dependence of biodiversity change over time and its consequences for arguments about the instrumental value of biodiversity. While biodiversity is in decline on a global scale, the temporal trends on regional and local scales include cases of biodiversity increase, no change, and decline. Environmental change, anthropogenic or otherwise, causes both local extirpation and colonization of species, and thus turnover in species composition, but not necessarily declines in biodiversity. In some situations, such as plants at the regional scale, human-mediated colonizations have greatly outnumbered extinctions, thus causing a marked increase in species richness. Since the potential influence of biodiversity on ecosystem function and services is mediated to a large degree by local or neighborhood species interactions, these results challenge the generality of the argument that biodiversity loss is putting at risk the ecosystem service benefits people receive from nature.

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Effects of Polyphenols in Tea (Camellia sinensis sp.) on the Modulation of Gut Microbiota in Human Trials and Animal Studies

Gastroenterology Insights ◽

10.3390/gastroent12020018 ◽

2021 ◽

Vol 12 (2) ◽

pp. 202-216

Author(s):

Mus Azza Suhana Khairudin ◽

Abbe Maleyki Mhd Jalil ◽

Napisah Hussin

Keyword(s):

Gut Microbiota ◽

Beta Diversity ◽

Animal Studies ◽

Tea Polyphenols ◽

Microbiota Composition ◽

Polyphenol Compounds ◽

Human Trials ◽

Diet Induced Obesity ◽

Different Types ◽

Meta Analyses

A diet high in polyphenols is associated with a diversified gut microbiome. Tea is the second most consumed beverage in the world, after water. The health benefits of tea might be attributed to the presence of polyphenol compounds such as flavonoids (e.g., catechins and epicatechins), theaflavins, and tannins. Although many studies have been conducted on tea, little is known of its effects on the trillions of gut microbiota. Hence, this review aimed to systematically study the effect of tea polyphenols on the stimulation or suppression of gut microbiota in humans and animals. It was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol. Articles were retrieved from PubMed and Scopus databases, and data were extracted from 6 human trials and 15 animal studies. Overall, large variations were observed in terms of microbiota composition between humans and animals. A more consistent pattern of diversified microbiota was observed in animal studies. Tea alleviated the gut microbiota imbalance caused by high-fat diet-induced obesity, diabetes, and ultraviolet-induced damage. The overall changes in microbiota composition measured by beta diversity analysis showed that tea had shifted the microbiota from the pattern seen in animals that received tea-free intervention. In humans, a prebiotic-like effect was observed toward the gut microbiota, but these results appeared in lower-quality studies. The beta diversity in human microbiota remains intact despite tea intervention; supplementation with different teas affects different types of bacterial taxa in the gut. These studies suggest that tea polyphenols may have a prebiotic effect in disease-induced animals and in a limited number of human interventions. Further intervention is needed to identify the mechanisms of action underlying the effects of tea on gut microbiota.

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The Nanosystems Involved in Treating Lung Cancer

Life ◽

10.3390/life11070682 ◽

2021 ◽

Vol 11 (7) ◽

pp. 682

Author(s):

Andreea Crintea ◽

Alina Gabriela Dutu ◽

Gabriel Samasca ◽

Ioan Alexandru Florian ◽

Iulia Lupan ◽

...

Keyword(s):

Lung Cancer ◽

Side Effects ◽

Chromosomal Rearrangements ◽

Sirna Delivery ◽

Delivery Systems ◽

Inorganic Nanoparticles ◽

New Methods ◽

Different Types ◽

Or Gene ◽

The Many

Even though there are various types of cancer, this pathology as a whole is considered the principal cause of death worldwide. Lung cancer is known as a heterogeneous condition, and it is apparent that genome modification presents a significant role in the occurrence of this disorder. There are conventional procedures that can be utilized against diverse cancer types, such as chemotherapy or radiotherapy, but they are hampered by the numerous side effects. Owing to the many adverse events observed in these therapies, it is imperative to continuously develop new and improved strategies for managing individuals with cancer. Nanomedicine plays an important role in establishing new methods for detecting chromosomal rearrangements and mutations for targeted chemotherapeutics or the local delivery of drugs via different types of nano-particle carriers to the lungs or other organs or areas of interest. Because of the complex signaling pathways involved in developing different types of cancer, the need to discover new methods for prevention and detection is crucial in producing gene delivery materials that exhibit the desired roles. Scientists have confirmed that nanotechnology-based procedures are more effective than conventional chemotherapy or radiotherapy, with minor side effects. Several nanoparticles, nanomaterials, and nanosystems have been studied, including liposomes, dendrimers, polymers, micelles, inorganic nanoparticles, such as gold nanoparticles or carbon nanotubes, and even siRNA delivery systems. The cytotoxicity of such nanosystems is a debatable concern, and nanotechnology-based delivery systems must be improved to increase the bioavailability, biocompatibility, and safety profiles, since these nanosystems boast a remarkable potential in many biomedical applications, including anti-tumor activity or gene therapy. In this review, the nanosystems involved in treating lung cancer and its associated challenges are discussed.

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

Israel Journal of Ecology and Evolution ◽

10.1163/22244662-06301009 ◽

2017 ◽

Vol 63 (2) ◽

pp. 8-16 ◽

Cited By ~ 1

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.

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