A Berry-Esseen theorem for Pitman's α\alpha-diversity

This paper is concerned with the study of the random variable $K_n$ denoting the number of distinct elements in a random sample $(X_1, \dots, X_n)$ of exchangeable random variables driven by the two parameter Poisson-Dirichlet distribution, $PD(\alpha,\theta)$. For $\alpha\in(0,1)$, Theorem 3.8 in \cite{Pit(06)} shows that $\frac{K_n}{n^{\alpha}}\stackrel{\text{a.s.}}{\longrightarrow} S_{\alpha,\theta}$ as $n\rightarrow+\infty$. Here, $S_{\alpha,\theta}$ is a random variable distributed according to the so-called scaled Mittag-Leffler distribution. Our main result states that \sup_{x \geq 0} \Big| \ppsf\Big[\frac{K_n}{n^{\alpha}} \leq x \Big] - \ppsf[S_{\alpha,\theta} \leq x] \Big| \leq \frac{C(\alpha, \theta)}{n^{\alpha}} holds with an explicit constant $C(\alpha, \theta)$. The key ingredients of the proof are a novel probabilistic representation of $K_n$ as compound distribution and new, refined versions of certain quantitative bounds for the Poisson approximation and the compound Poisson distribution

Aroma Map in European Woodland Strawberry

Woodland strawberry (Fragaria vesca, 2x) is a wild, diploid ancestor of the cultivated strawberry (Fragaria ananassa, 8x), the most economically important berry crop. F. vesca is very appreciated for its intense fruity aroma, characterized by a unique combination of volatile compounds, which are absent, or accumulated at lower rates, in the commercial strawberry varieties. In addition, F. vesca presents a wide genetic diversity and it is naturally distributed across Europe. Our aim is to describe the genetic and organoleptic diversity of European woodland strawberry and decipher the genetic control of its characteristic volatile compounds. A collection of 199 accessions representing the European genetic diversity of F. vesca has been re-sequenced obtaining a set of 1.8M SNPs. In addition, the volatilome of ripe fruits was quantified in two independent harvests by GCMS providing a set of 100 unambiguously identified compounds. This study has revealed genetic and metabolic differences between subpopulations with different geographical origin. In addition, Genome-Wide Association Analysis has revealed genetic regions significantly associated to the accumulation of several metabolites that contribute to strawberry aroma, such as terpenes (alpha-farnesene, alpha-pinene, alpha-terpineol, linalool, myrtenol), lactones (g-decalactone), eugenol and mesifurane among others.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome.

Standardized conditions for collection, preservation and storage of urine for microbiome research have not been established. We aimed to identify the effects of the use of preservative AssayAssure® (AA), and the effects of storage time and temperatures on reproducibility of urine microbiome results. We sequenced the V3-4 segment of the 16S rRNA gene to characterize the bacterial community in the urine of a cohort of women. Each woman provided a single voided urine sample, which was divided into aliquots and stored with and without AA, at three different temperatures (room temperature [RT], 4 °C, or -20 °C), and for various time periods up to 4 days. There were significant microbiome differences in urine specimens stored with and without AA at all temperatures, but the most significant differences were observed in alpha diversity (estimated number of taxa) at RT. Specimens preserved at 4 °C and -20 °C for up to 4 days with or without AA had no significant alpha diversity differences. However, significant alpha diversity differences were observed in samples stored without AA at RT. Generally, there was greater microbiome preservation with AA than without AA at all time points and temperatures, although not all results were statistically significant. Addition of AA preservative, shorter storage times, and colder temperatures are most favorable for urinary microbiome reproducibility

Temporal dynamics of aquatic communities and implications for pond conservation

Conservation through the protection of particular habitats is predicated on the assumption that the conservation value of those habitats is stable. We test this assumption for ponds by investigating temporal variation in macroinvertebrate and macrophyte communities over a 10-year period in northwest England. We surveyed 51 ponds in northern England in 1995/6 and again in 2006, identifying all macrophytes (167 species) and all macroinvertebrates (221 species, excluding Diptera) to species. The alpha-diversity, beta-diversity and conservation value of these ponds were compared between surveys. We find that invertebrate species richness increased from an average of 29. 5 species to 39. 8 species between surveys. Invertebrate gamma-diversity also increased between the two surveys from 181 species to 201 species. However, this increase in diversity was accompanied by a decrease in beta-diversity. Plant alpha-, beta and gamma-diversity remained approximately constant between the two periods. However, increased proportions of grass species and a complete loss of charophytes suggests that the communities are undergoing succession. Conservation value was not correlated between sampling periods in either plants or invertebrates. This was confirmed by comparing ponds that had been disturbed with those that had no history of disturbance to demonstrate that levels of correlation between surveys were approximately equal in each group of ponds. This study has three important conservation implications: (i) a pond with high diversity or high conservation value may not remain that way and so it is unwise to base pond conservation measures upon protecting currently-speciose habitats; (ii) maximising pond gamma-diversity requires a combination of late and early succession ponds, especially for invertebrates; and (iii) invertebrate and plant communities in ponds may require different management strategies if succession occurs at varying rates in the two groups

Beta-diversity of Central European forests decreases along an elevational gradient due to the variation in local community assembly processes

Beta-diversity has been repeatedly shown to decline with increasing elevation, but the causes of this pattern remain unclear, partly because they are confounded by coincident variation in alpha- and gamma-diversity. We used 8,795 forest vegetation-plot records from the Czech National Phytosociological Database to compare the observed patterns of beta diversity to null-model expectations (beta-deviation) controlling for the effects of alpha- and gamma-diversity. We tested whether \b{eta}-diversity patterns along a 1,200 m elevation gradient exclusively depend on the effect of varying species pool size, or also on the variation of the magnitude of community assembly mechanisms determining the distribution of species across communities (e.g., environmental filtering, dispersal limitation). The null model we used is a novel extension of an existing null-model designed for presence/absence data and was specifically designed to disrupt the effect of community assembly mechanisms, while retaining some key features of observed communities such as average species richness and species abundance distribution. Analyses were replicated in ten subregions with comparable elevation ranges. Beta-diversity declined along the elevation gradient due to a decrease in gamma-diversity, which was steeper than the decrease in alpha-diversity. This pattern persisted after controlling for alpha- and gamma-diversity variation, and the results were robust when different resampling schemes and diversity metrics were used. We conclude that in temperate forests the pattern of decreasing beta-diversity with elevation does not exclusively depend on variation in species pool size, as has been hypothesized, but also on variation in community assembly mechanisms. The results were consistent across resampling schemes and diversity measures, thus supporting the use of vegetation plot databases for understanding...Comment: Accepted version 25 pages, 5 figures, 1 tabl