scholarly journals Phylogenetic alpha and beta diversity in tropical tree assemblages along regional-scale environmental gradients in northwest South America

2014 ◽  
Vol 7 (2) ◽  
pp. 145-153 ◽  
Author(s):  
Sebastián González-Caro ◽  
María Natalia Umaña ◽  
Esteban Álvarez ◽  
Pablo R. Stevenson ◽  
Nathan G. Swenson
2016 ◽  
Vol 27 (6) ◽  
pp. 1117-1128 ◽  
Author(s):  
Meghna Krishnadas ◽  
Ajith Kumar ◽  
Liza S. Comita

Ecology ◽  
2012 ◽  
Vol 93 (sp8) ◽  
pp. S112-S125 ◽  
Author(s):  
Nathan G. Swenson ◽  
David L. Erickson ◽  
Xiangcheng Mi ◽  
Norman A. Bourg ◽  
Jimena Forero-Montaña ◽  
...  

2020 ◽  
Author(s):  
Felix Trotter ◽  
Caroline Lehmann ◽  

<p>Patterns of woody plant diversity in the tropical savanna biome has received little research attention but is relevant to understanding the complex vegetation dynamics of a biome that have remained contentious for almost a century. Tropical savannas of Africa and Australia are defined by the co-existence of woody plants and grasses, and the evolution and assembly of the savanna biome trace back 3-10 million years. Here, we explored patterns of local (alpha-) diversity and species turnover (beta-diversity) of woody plant species across African and Australian savannas. We aimed test the relative role of the environmental gradients of rainfall, temperature, fire and soil in shaping the relative abundance of all of woody species, genera, and families. Using generalized additive models (GAMs) and generalised dissimilarity models (GDMs) of field inventory data from vegetation plots across sub-Saharan Africa and Northern Australia we analysed changes in alpha- and beta-diversity. Environmental gradients were characterised as effective rainfall (ER), rainfall seasonality (coefficient of variation of monthly rainfall), mean annual temperature (MAT), temperature seasonality, fire frequency, and cation exchange capacity (CEC) in soils.</p><p>Savannas in Australia are on average drier and hotter than in Africa likely as a product of lower altitude. Crucially, diversity across all taxonomic levels is approximately two to three times greater in Africa compared with Australia. Within each continent, rainfall seasonality was the strongest environmental correlate of both alpha- and beta-diversity. In Africa, there is a strongly negative relationship between alpha-diversity at all taxonomic levels and rainfall seasonality. In contrast, in Australia, the relationship between alpha-diversity and rainfall seasonality while relevant is non-linear. Surprisingly within continents, rainfall, temperature, soils and fire had little bearing in these data on patterns of alpha diversity.</p><p>In terms of beta-diversity, and likely linked to the overall differences in diversity between continents, the geographic distance equalling total species turnover is greater in Australia than in Africa. Effective rainfall was the only additional significant correlate of woody species turnover in Australia, but only in arid regions. In Australia, at higher taxonomic levels the capacity of GDMs to explain variation in the data diminished substantially as a product of low diversity in genera and families. When compared to Australia, species turnover in Africa increases when geographic distance, rainfall seasonality and mean annual temperature are relatively low.</p><p>Our findings highlight that with ongoing climate change specifically with shifts in rainfall distribution that will also affect local drought regimes, rainfall seasonality could substantially alter patterns of diversity, specifically in Africa. There have been persistent attempts to explain ecosystem dynamics in savannas with respect to climate, soils and fire with emphasis often on total rainfall, but our findings suggest that rainfall seasonality can have strong effects on diversity that may interact with other environmental correlates such as fire.</p>


Ecosphere ◽  
2021 ◽  
Vol 12 (7) ◽  
Author(s):  
Samantha J. Worthy ◽  
Vanessa E. Rubio ◽  
Kirstin Staiger ◽  
Boris Ngouajio ◽  
Jie Yang ◽  
...  

Author(s):  
Maciej Chichlowski ◽  
Nicholas Bokulich ◽  
Cheryl L Harris ◽  
Jennifer L Wampler ◽  
Fei Li ◽  
...  

Abstract Background Milk fat globule membrane (MFGM) and lactoferrin (LF) are human milk bioactive components demonstrated to support gastrointestinal (GI) and immune development. Significantly fewer diarrhea and respiratory-associated adverse events through 18 months of age were previously reported in healthy term infants fed a cow's milk-based infant formula with added source of bovine MFGM and bovine LF through 12 months of age. Objectives To compare microbiota and metabolite profiles in a subset of study participants. Methods Stool samples were collected at Baseline (10–14 days of age) and Day 120 (MFGM + LF: 26, Control: 33). Bacterial community profiling was performed via16S rRNA gene sequencing (Illumina MiSeq) and alpha and beta diversity were analyzed (QIIME 2). Differentially abundant taxa were determined using Linear discriminant analysis effect size (LefSE) and visualized (Metacoder). Untargeted stool metabolites were analyzed (HPLC/mass spectroscopy) and expressed as the fold-change between group means (Control: MFGM + LF ratio). Results Alpha diversity increased significantly in both groups from baseline to 4 months. Subtle group differences in beta diversity were demonstrated at 4 months (Jaccard distance; R2 = 0.01, P = 0.042). Specifically, Bacteroides uniformis and Bacteroides plebeius were more abundant in the MFGM + LF group at 4 months. Metabolite profile differences for MFGM + LF vs Control included: lower fecal medium chain fatty acids, deoxycarnitine, and glycochenodeoxycholate, and some higher fecal carbohydrates and steroids (P < 0.05). After applying multiple test correction, the differences in stool metabolomics were not significant. Conclusions Addition of bovine MFGM and LF in infant formula was associated with subtle differences in stool microbiome and metabolome by four months of age, including increased prevalence of Bacteroides species. Stool metabolite profiles may be consistent with altered microbial metabolism. Trial registration:  https://clinicaltrials.gov/ct2/show/NCT02274883).


Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 745
Author(s):  
Michelle Martin de Bustamante ◽  
Diego Gomez ◽  
Jennifer MacNicol ◽  
Ralph Hamor ◽  
Caryn Plummer

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.


2021 ◽  
pp. 1-9
Author(s):  
Patrick F McKenzie ◽  
Gwenllian D Iacona ◽  
Eric R Larson ◽  
Paul R Armsworth

Summary The available tools and approaches to inform conservation decisions commonly assume detailed distribution data. We examine how well-established ecological concepts about patterns in local richness and community turnover can help overcome data limitations when planning future protected areas. To inform our analyses, we surveyed tree species in protected areas in the southern Appalachian Mountains in the eastern USA. We used the survey data to construct predictive models for alpha and beta diversity based on readily observed biophysical variables and combined them to create a heuristic that could predict among-site richness in trees (gamma diversity). The predictive models suggest that site elevation and latitude in this montane system explain much of the variation in alpha and beta diversity in tree species. We tested how well resulting protected areas would represent species if a conservation planner lacking detailed species inventories for candidate sites were to rely only on our alpha, beta and gamma diversity predictions. Our approach selected sites that, when aggregated, covered a large proportion of the overall species pool. The combined gamma diversity models performed even better when we also accounted for the cost of protecting sites. Our results demonstrate that classic community biogeography concepts remain highly relevant to conservation practice today.


Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 463
Author(s):  
Mariusz Sikora ◽  
Albert Stec ◽  
Magdalena Chrabaszcz ◽  
Aleksandra Knot ◽  
Anna Waskiel-Burnat ◽  
...  

(1) Background: A growing body of evidence highlights that intestinal dysbiosis is associated with the development of psoriasis. The gut–skin axis is the novel concept of the interaction between skin diseases and microbiome through inflammatory mediators, metabolites and the intestinal barrier. The objective of this study was to synthesize current data on the gut microbial composition in psoriasis. (2) Methods: We conducted a systematic review of studies investigating intestinal microbiome in psoriasis, using the PRISMA checklist. We searched MEDLINE, EMBASE, and Web of Science databases for relevant published articles (2000–2020). (3) Results: All of the 10 retrieved studies reported alterations in the gut microbiome in patients with psoriasis. Eight studies assessed alpha- and beta-diversity. Four of them reported a lack of change in alpha-diversity, but all confirmed significant changes in beta-diversity. At the phylum-level, at least two or more studies reported a lower relative abundance of Bacteroidetes, and higher Firmicutes in psoriasis patients versus healthy controls. (4) Conclusions: There is a significant association between alterations in gut microbial composition and psoriasis; however, there is high heterogeneity between studies. More unified methodological standards in large-scale studies are needed to understand microbiota’s contribution to psoriasis pathogenesis and its modulation as a potential therapeutic strategy.


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