Dataset Information

Decomposing changes in phylogenetic and functional diversity over space and time.

ABSTRACT: The ?, ?, ? diversity decomposition methodology is commonly used to investigate changes in diversity over space or time but rarely conjointly. However, with the ever-increasing availability of large-scale biodiversity monitoring data, there is a need for a sound methodology capable of simultaneously accounting for spatial and temporal changes in diversity.Using the properties of Chao's index, we adapted Rao's framework of diversity decomposition between orthogonal dimensions to a multiplicative ?, ?, ? decomposition of functional or phylogenetic diversity over space and time, thereby combining their respective properties. We also developed guidelines for interpreting both temporal and spatial ?-diversities and their interaction.We characterised the range of ?-diversity estimates and their relationship to the nested decomposition of diversity. Using simulations, we empirically demonstrated that temporal and spatial ?-diversities are independent from each other and from ? and ?-diversities when the study design is balanced, but not otherwise. Furthermore, we showed that the interaction term between the temporal and the spatial ?-diversities lacked such properties.We illustrated our methodology with a case study of the spatio-temporal dynamics of functional diversity in bird assemblages in four regions of France. Based on these data, our method makes it possible to discriminate between regions experiencing different diversity changes in time. Our methodology may therefore be valuable for comparing diversity changes over space and time using large-scale datasets of repeated surveys.

SUBMITTER: Chalmandrier L

PROVIDER: S-EPMC4326675 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

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Decomposing changes in phylogenetic and functional diversity over space and time.

Chalmandrier Loïc L Münkemüller Tamara T Devictor Vincent V Lavergne Sébastien S Thuiller Wilfried W

Methods in ecology and evolution 20150101 1

The α, β, γ diversity decomposition methodology is commonly used to investigate changes in diversity over space or time but rarely conjointly. However, with the ever-increasing availability of large-scale biodiversity monitoring data, there is a need for a sound methodology capable of simultaneously accounting for spatial and temporal changes in diversity.Using the properties of Chao's index, we adapted Rao's framework of diversity decomposition between orthogonal dimensions to a multiplicative ...[more]

PMID: 25685310

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Project description:BackgroundThe nasopharynx is a reservoir for pathogens associated with respiratory illnesses such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome of infants and adults during health and disease; less is known, however, about the composition and temporal dynamics (i.e., longitudinal variation) of microbiotas from children and adolescents. Here we use NGS technology to characterize the nasopharyngeal microbiomes of asthmatic children and adolescents (6 to 18 years) and determine their stability over time.MethodsTwo nasopharyngeal washes collected 5.5 to 6.5 months apart were taken from 40 children and adolescents with asthma living in the Washington D.C. area. Sequence data from the 16S-V4 rRNA gene region (~250 bp) were collected from the samples using the MiSeq platform. Raw data were processed in mothur (SILVA123 reference database) and Operational Taxonomic Units (OTU)-based alpha- and beta-diversity metrics were estimated. Relatedness among samples was assessed using PCoA ordination and Procrustes analyses. Differences in microbial diversity and taxon mean relative proportions were assessed using linear mixed effects models. Core microbiome analyses were also performed to identify stable and consistent microbes of the nasopharynx.Results and discussionA total of 2,096,584 clean 16S sequences corresponding to an average of 167 OTUs per sample were generated. Representatives of Moraxella*, Staphylococcus*, Dolosigranulum, Corynebacterium, Prevotella, Streptococcus*, Haemophilus*, Fusobacterium* and a Neisseriaceae genus accounted for 86% of the total reads. These nine genera have been previously found in the nasopharynxes of both infants and adults, but in different proportions. OTUs from the five genera highlighted (*) above defined the nasopharyngeal core microbiome at the 95% level. No significant differences in alpha- and beta-diversity were observed between seasons, but bacterial mean relative proportions of Haemophilus, Moraxella, Staphylococcus and Corynebacterium varied significantly between summer-fall and age groups (inter-patient variation). Additionally, OTUs varied significantly within patients between time points in 35 of the 40 patients analyzed. Future cross-sectional studies should be mindful of the temporal dynamics of the nasopharyngeal microbiota.

Project description:Polyhedrons, spheroids and bolas (PSBs) are present in lithic series from the Lower Palaeolithic onwards and are found in several regions of the world. Nevertheless, very little is known about them. We propose here to summarise, illustrate and discuss the current state of our knowledge about these artefacts. Based on the available data in the literature and on our observations of several collections, we set up a database comprising 169 Palaeolithic assemblages with PSBs. Thanks to the statistical analysis of these data, we aim to highlight potential relationships between PSB characteristics (e.g., quantity, raw material) and assemblage composition and context, according to regions and chrono-cultural attributions. We also aim to discuss the question of artefacts from possible independent local histories, especially in Northwest Europe, where these objects are scarce. Our study concludes that hard stones (stones with high resistance to a physical constraint) available locally were generally selected to produce PSBs. Soft sedimentary rocks are suitable for their manufacture, and were selected too, whereas siliceous materials were left aside. We hypothesise that the scarcity of PSBs in Northwest Europe could result from a combination of cultural and environmental factors: it could be part of a regional tradition, influenced by the abundance of siliceous materials in the environment. In this region where the lithic production is widely made of flint, even though other materials were available, objects made from hard stones are scarce, resulting in a toolkit with only rare PSBs and cleavers. Was flint too brittle for the functions of PSBs? Raw materials of PSBs are often similar to those of heavy-duty tools in assemblages, which could provide other clues about their functions (e.g., tasks requiring a resistance to shocks). It is possible that their raw materials partly conditioned their final shape. PSBs can comprise a wide variety of artefacts, that for some could have change of status (e.g., from cores to percussive tools), diffused, adapted but also reinvented over two million years.

Dataset Information

Decomposing changes in phylogenetic and functional diversity over space and time.

Publications

Decomposing changes in phylogenetic and functional diversity over space and time.

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