scholarly journals Decomposing phylogenetic entropy into α , β and γ components

2010 ◽  
Vol 7 (2) ◽  
pp. 205-209 ◽  
Author(s):  
Maud A. Mouchet ◽  
David Mouillot
Keyword(s):  
Species Richness ◽  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Biological Diversity ◽  
Diversity Indices ◽  
Species Loss ◽  
Full Understanding ◽  
Abundance Distribution ◽  
Additive Decomposition ◽  
Weak Monotonicity

Measuring the phylogenetic diversity of communities has become a key issue for biogeography and conservation. However, most diversity indices that rely on interspecies phylogenetic distances may increase with species loss and thus violate the principle of weak monotonicity. Moreover, most published phylogenetic diversity indices ignore the abundance distribution along phylogenetic trees, even though lineage abundances are crucial components of biodiversity. The recently introduced concept of phylogenetic entropy overcomes these limitations, but has not been decomposed across scales, i.e. into α , β and γ components. A full understanding of mechanisms sustaining biological diversity within and between communities needs such decomposition. Here, we propose an additive decomposition framework for estimating α , β and γ components of phylogenetic entropy. Based on simulated trees, we demonstrate its robustness to phylogenetic tree shape and species richness. Our decomposition fulfils the requirements of both independence between components and weak monotonicity. Finally, our decomposition can also be adapted to the partitioning of functional diversity across different scales with the same desirable properties.

scholarly journals Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals

2011 ◽  
Vol 366 (1576) ◽  
pp. 2414-2425 ◽  
Author(s):  
T. Jonathan Davies ◽  
Lauren B. Buckley
Keyword(s):  
Species Richness ◽  
Phylogenetic Diversity ◽  
Diversity Indices ◽  
Environmental Predictors ◽  
Terrestrial Mammals ◽  
Extinction Rates ◽  
Biogeographic History ◽  
Shared Ancestry ◽  
History Of ◽  
Dispersal Events

Phylogenetic diversity (PD) captures the shared ancestry of species, and is increasingly being recognized as a valuable conservation currency. Regionally, PD frequently covaries closely with species richness; however, variation in speciation and extinction rates and/or the biogeographic history of lineages can result in significant deviation. Locally, these differences may be pronounced. Rapid recent speciation or high temporal turnover of lineages can result in low PD but high richness. In contrast, rare dispersal events, for example, between biomes, can elevate PD but have only small impact on richness. To date, environmental predictors of species richness have been well studied but global models explaining variation in PD are lacking. Here, we contrast the global distribution of PD versus species richness for terrestrial mammals. We show that an environmental model of lineage diversification can predict well the discrepancy in the distribution of these two variables in some places, for example, South America and Africa but not others, such as Southeast Asia. When we have information on multiple diversity indices, conservation efforts directed towards maximizing one currency or another (e.g. species richness versus PD) should also consider the underlying processes that have shaped their distributions.

Assessment of the network of protected areas for birds in Taiwan with regard to functional and phylogenetic diversity

2016 ◽  
Vol 22 (1) ◽  
pp. 61 ◽  
Author(s):  
Hungyen Chen ◽  
Satoshi Nagai ◽  
Hirohisa Kishino
Keyword(s):  
Species Richness ◽  
Protected Areas ◽  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Bird Species ◽  
Elevational Gradient ◽  
Mountain Areas ◽  
Phylogenetic Constraint ◽  
Lower Elevation ◽  
Functional And Phylogenetic Diversity

In Taiwan, conserved areas represent more than 20% of the current jurisdiction, which is about twice that of the proportion of protected land worldwide. In this study, we explored the spatial distribution of bird assemblages in Taiwan. By analysing functional and phylogenetic diversity relative to elevational gradient, we assessed the network of bird protected areas. Hotspots of species richness were located at the coastal areas of northern and western Taiwan, although hotspots for protected bird species were located in the mountain areas. We found that phylogenetically close birds have similar trait values, and the protected species were evenly distributed in the functional and phylogenetic trees. The assemblages in higher-elevation areas were more phylogenetically clumped than those in lower-elevation areas, indicating that, in addition to elevational gradient, phylogenetic constraint may be a crucial factor that influences bird distribution in Taiwan. However, the current bird protected areas in Taiwan may overly depend on species richness and overlook the importance of the overall phylogenetic diversity.

scholarly journals Low Temperature Decreases the Phylogenetic Diversity of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofiltration Systems

2007 ◽  
Vol 74 (3) ◽  
pp. 894-900 ◽  
Author(s):  
Hidetoshi Urakawa ◽  
Yoshiyuki Tajima ◽  
Yoshiyuki Numata ◽  
Satoshi Tsuneda
Keyword(s):  
Population Structure ◽  
Species Richness ◽  
Low Temperature ◽  
Phylogenetic Diversity ◽  
Cold Water ◽  
Diversity Indices ◽  
Rarefaction Analysis ◽  
Ammonia Oxidizing Archaea ◽  
Key Factor

ABSTRACT The phylogenetic diversity and species richness of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were examined with aquarium biofiltration systems. Species richness, deduced from rarefaction analysis, and diversity indices indicated that the phylogenetic diversity and species richness of AOA are greater than those of AOB; the diversity of AOA and of AOB is minimized in cold-water aquaria. This finding implies that temperature is a key factor influencing the population structure and diversity of AOA and AOB in aquarium biofiltration systems.

scholarly journals Relative Reduction of the Biological and phylogenetic diversity of oral microbiome in diabetic and pre-diabetic subjects

2018 ◽  
Author(s):  
Amr T. M. Saeb ◽  
Khalid A. Al-Rubeaan ◽  
Khalid Aldosary ◽  
G. K. Udaya Raja ◽  
Balavenkatesh Mani ◽  
...  
Keyword(s):  
Oral Health ◽  
Phylogenetic Diversity ◽  
Biological Diversity ◽  
Systemic Disease ◽  
Diversity Indices ◽  
Oral Infection ◽  
Reciprocal Relationship ◽  
Oral Microbiome ◽  
Diabetic Group ◽  
Relative Reduction

AbstractBackgroundThere is a suggested reciprocal relationship between oral health and systemic disease such as type 2 diabetes. In this relationship, a systemic disease predisposing to oral infection, and when that infection is present, the oral infection aggravates the progression of the systemic disease. Several studies suggested that some oral microbiome constituents are linked to both diabetes, metabolic syndrome and obesity. This study aims to compare the microbial diversity and population structure of oral microbiome among normoglycemic, impaired glucose tolerance (IGT) and diabetic subjects.MethodologyThis study followed a case-control design (15 T2D patients, 10 IGTs and, 19 controls). Patient records were screened as per the inclusion and exclusion criteria. Assessment of periodontitis and oral health was performed to all subjects. DNA Isolation purification and quantification from collected Saliva samples were performed. 16SrRNA hypervariable regions were amplified and sequenced. Generated sequences were subjected to bioinformatics analysis. Statistical analysis and diversity indices were computed with the statistical software R, the vegan R-package, and Past318 software.ResultsA total observed number of 551 OTUs. A clear reduction of the number of species (OTUs) was observed in both IGT (412) and diabetic group (372) compared with the normoglycemic group (502). This was associated with a similar pattern of biological diversity among the three groups. Phylogenetic diversity (PD-SBL) value in the normoglycemic group was higher than the diabetic group. The diabetic group had the highest evenness value and the highest microbiome bacterial pathogenic content.ConclusionWe observed a clear reduction in the biological and phylogenetic diversity in the diabetic and pre-diabetic oral microbiome in comparison with the normoglycemic oral microbiome. However, this reduction was associated with an increase in the pathogenic content of the hyperglycemic microbiomes.

Temporal trends in biodiversity of the middle-slope assemblages in Sardinian seas (Central-Western Mediterranean)

2013 ◽  
Vol 93 (7) ◽  
pp. 1739-1752 ◽  
Author(s):  
Andrea Sabatini ◽  
Ivan Locci ◽  
Anna M. Deiana ◽  
Maria C. Follesa ◽  
Alice Gastoni ◽  
...  
Keyword(s):  
Species Richness ◽  
Biological Diversity ◽  
Temporal Trends ◽  
Diversity Indices ◽  
Fishing Effort ◽  
Western Mediterranean ◽  
Species Structure ◽  
Fishing Pressure ◽  
Ecological Diversity ◽  
Middle Slope

It has been amply demonstrated that trawl fishing affects overall biomass, size and species structure of demersal fish communities, and an increasing number of studies are proving that this could have even greater unexpected effects on biological diversity. The aims of this study are: (1) to examine the temporal trends of several ecological diversity indices for middle-slope communities in specific locations within the Sardinian seas, which have been recently subject to increasing fishing capacity; and (2) to simulate the Shannon's entropy (H′) temporal trend, using a multiple linear regression, in order to investigate about the relationships between fishing effort and species diversity. The data come from 11 MEDITS trawl surveys (1994 to 2004). Temporal trends in fishing effort were analysed and ecological diversity indices were measured. Analysis was conducted for four areas (NW, NE, SE, SSW). Significant variations over time in both fishing pressure and ecological diversity indices were found for the southern zones. More precisely, the SE zone showed an increase in fishing effort (+120% in 2004), and a decrease of Shannon–Weiner's diversity. The SSW zone exhibited a 22.6% increase of fishing effort and a decrease of species richness. The best model of H′ incorporates species richness and fishing effort expressed as number of boats per trawling area. Our results seem to indicate that fishing pressure affected the species richness and the abundance of middle-slope species and that variation in ecological diversity indices differed with different levels of fishing effort.

scholarly journals Impacts of species richness on productivity in a large-scale subtropical forest experiment

Science ◽  
2018 ◽  
Vol 362 (6410) ◽  
pp. 80-83 ◽  
Author(s):  
Yuanyuan Huang ◽  
Yuxin Chen ◽  
Nadia Castro-Izaguirre ◽  
Martin Baruffol ◽  
Matteo Brezzi ◽  
...  
Keyword(s):  
Species Richness ◽  
Primary Productivity ◽  
Ecosystem Functioning ◽  
Phylogenetic Diversity ◽  
Large Scale ◽  
Subtropical Forest ◽  
Species Loss ◽  
Shrub Species ◽  
Mitigate Climate Change ◽  
Functional And Phylogenetic Diversity

Biodiversity experiments have shown that species loss reduces ecosystem functioning in grassland. To test whether this result can be extrapolated to forests, the main contributors to terrestrial primary productivity, requires large-scale experiments. We manipulated tree species richness by planting more than 150,000 trees in plots with 1 to 16 species. Simulating multiple extinction scenarios, we found that richness strongly increased stand-level productivity. After 8 years, 16-species mixtures had accumulated over twice the amount of carbon found in average monocultures and similar amounts as those of two commercial monocultures. Species richness effects were strongly associated with functional and phylogenetic diversity. A shrub addition treatment reduced tree productivity, but this reduction was smaller at high shrub species richness. Our results encourage multispecies afforestation strategies to restore biodiversity and mitigate climate change.

Aquatic and semi aquatic Hemiptera community of Sonebeel, the largest wetland of Assam, northeastern India

2018 ◽  
Vol 10 (13) ◽  
pp. 12792-12799
Author(s):  
Anupama Saha ◽  
Susmita Gupta
Keyword(s):  
Species Richness ◽  
Pest Control ◽  
Relative Abundance ◽  
Species Distribution ◽  
Diversity Indices ◽  
Environmental Data ◽  
Northeastern India ◽  
Ecological Roles

Aquatic and semiaquatic Hemiptera bugs play significant ecological roles, and they are important indicators and pest control agents.  Little information is currently available concerning its populations in southern Assam.  This study assessed hemipterans in four sites of Sonebeel, the largest wetland in Assam (3458.12 ha at full storage level), situated in Karimganj District.  The major inflow and outflow of the wetland are the rivers Singla and Kachua, respectively (the Kachua drains into the Kushiyara River).  Samples were trapped with pond nets and were seasonally recorded.  This study recorded a total of 28 species of aquatic and semiaquatic hemipterans belonging to 20 genera under nine families.  Population, geographical and environmental data (e.g., rainfall) were used to assess the relative abundance of species, species richness and different diversity indices, and species distribution. 

Field Margin Weed-Species Diversity in Relation to Landscape Attributes and Adjacent Land Use

Weed Science ◽  
2007 ◽  
Vol 55 (2) ◽  
pp. 129-136 ◽  
Author(s):  
Lynn M. Sosnoskie ◽  
Edward C. Luschei ◽  
Mark A. Fanning
Keyword(s):  
Land Use ◽  
Species Richness ◽  
Agricultural Landscape ◽  
Elevation Gradient ◽  
Shape Index ◽  
Diversity Indices ◽  
Weed Species ◽  
Field Margin ◽  
Local Climate ◽  
Modeling Strategy

The importance of managing weeds in seminatural habitats that are adjacent to farm fields is unclear. Weedy-margin vegetation may harbor pests or pathogens and may ALSo serve as source populations for ongoing immigration of weeds into the field. It is ALSo possible, however, that margin vegetation provides habitat for organisms that consume weed seeds or suppress the likelihood of pest or pathogen outbreak. We examined the nature of margin habitat using spatial-scaling of Weed-Species richness as an ecological assay. In 2003, we recorded the occurrence of weedy species along the perimeters of 63 fields in Wisconsin. The fields were distributed within six counties that differed in topography, geological history, local climate, and soil type and which spanned the range of variability in the agricultural landscape. We identified seven habitats that differed in geology and land use. The relationship between species richness and margin class was estimated using an analog of the power law. Additionally, we investigated broadscale correlates of habitat heterogeneity at the field level, using a modeling strategy that included additional explanatory factors logically connected to plant diversity. Using a model-confrontation approach, the survey supported the inclusion of two topographical diversity indices, elevation gradient and a field-shape index, into our model. Our broadscale survey provides information on one of a suite of important considerations needed to make decisions about the importance of managing weeds in field margins.

scholarly journals Altitudinal Vascular Plant Richness and Climate Change in the Alpine Zone of the Lefka Ori, Crete

Diversity ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 22
Author(s):  
George Kazakis ◽  
Dany Ghosn ◽  
Ilektra Remoundou ◽  
Panagiotis Nyktas ◽  
Michael A. Talias ◽  
...  
Keyword(s):  
Climate Change ◽  
Species Richness ◽  
Spatial Scales ◽  
Vascular Plant ◽  
Monitoring Network ◽  
Mediterranean Area ◽  
Mean Annual Temperature ◽  
High Mountain ◽  
Species Loss ◽  
Total Species Richness

High mountain zones in the Mediterranean area are considered more vulnerable in comparison to lower altitudes zones. Lefka Ori massif, a global biodiversity hotspot on the island of Crete is part of the Global Observation Research Initiative in Alpine Environments (GLORIA) monitoring network. The paper examines species and vegetation changes with respect to climate and altitude over a seven-year period (2001–2008) at a range of spatial scales (10 m Summit Area Section-SAS, 5 m SAS, 1 m2) using the GLORIA protocol in a re-survey of four mountain summits (1664 m–2339 m). The absolute species loss between 2001–2008 was 4, among which were 2 endemics. At the scale of individual summits, the highest changes were recorded at the lower summits with absolute species loss 4 in both cases. Paired t-tests for the total species richness at 1 m2 between 2001–2008, showed no significant differences. No significant differences were found at the individual summit level neither at the 5 m SAS or the 10 m SAS. Time series analysis reveals that soil mean annual temperature is increasing at all summits. Linear regressions with the climatic variables show a positive effect on species richness at the 5 m and 10 m SAS as well as species changes at the 5 m SAS. In particular, June mean temperature has the highest predictive power for species changes at the 5 m SAS. Recorded changes in species richness point more towards fluctuations within a plant community’s normal range, although there seem to be more significant diversity changes in higher summits related to aspects. Our work provides additional evidence to assess the effects of climate change on plant diversity in Mediterranean mountains and particularly those of islands which remain understudied.

scholarly journals Flower‐visitor communities of an arcto‐alpine plant—Global patterns in species richness, phylogenetic diversity and ecological functioning

2018 ◽  
Vol 28 (2) ◽  
pp. 318-335 ◽  
Author(s):  
Mikko Tiusanen ◽  
Tea Huotari ◽  
Paul D. N. Hebert ◽  
Tommi Andersson ◽  
Ashley Asmus ◽  
...  
Keyword(s):  
Species Richness ◽  
Phylogenetic Diversity ◽  
Alpine Plant ◽  
Flower Visitor ◽  
Global Patterns ◽  
Ecological Functioning
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