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Characterizing the phylogenetic tree community structure of a protected tropical rain forest area in Cameroon.

Manel S, Couvreur TL, Munoz F, Couteron P, Hardy OJ, Sonké B - PLoS ONE (2014)

Bottom Line: We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types.To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects.Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure.

View Article: PubMed Central - PubMed

Affiliation: Aix Marseille Université, IRD, LPED UMR 151, Marseille, France; Centre de coopération internationale en recherche agronomique pour le développement, UMR AMAP, Montpellier, France.

ABSTRACT
Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world.

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Related in: MedlinePlus

Schema of the 3 types of randomization used to test taxonomic and phylogenetic structure.In model 1-3x, individuals were randomized among transects or species within each habitat type (a). In model 2–3x, individuals or species were randomized among habitats (c). These models of permutation aimed to test for taxonomic turnover using IST. Phylogenetic structure (BST and ΠST) was tested using a model 1 s which randomized the observed species across the tips of the phylogenetic tree (b, d, e). Randomization were respectively done for the whole dataset (a,b), for the habitat data set (c, e) and for TPF only (d).
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pone-0098920-g001: Schema of the 3 types of randomization used to test taxonomic and phylogenetic structure.In model 1-3x, individuals were randomized among transects or species within each habitat type (a). In model 2–3x, individuals or species were randomized among habitats (c). These models of permutation aimed to test for taxonomic turnover using IST. Phylogenetic structure (BST and ΠST) was tested using a model 1 s which randomized the observed species across the tips of the phylogenetic tree (b, d, e). Randomization were respectively done for the whole dataset (a,b), for the habitat data set (c, e) and for TPF only (d).

Mentions: To address the four hypotheses above, we therefore partitioned taxonomic and phylogenetic diversity within and between transects, as well as within and between habitat types. For this we applied the statistical framework developed by Hardy and Senterre [20] for characterizing and testing the phylogenetic structure of transects and habitats types using appropriate randomization procedures [28] (Table 1, Figure 1).


Characterizing the phylogenetic tree community structure of a protected tropical rain forest area in Cameroon.

Manel S, Couvreur TL, Munoz F, Couteron P, Hardy OJ, Sonké B - PLoS ONE (2014)

Schema of the 3 types of randomization used to test taxonomic and phylogenetic structure.In model 1-3x, individuals were randomized among transects or species within each habitat type (a). In model 2–3x, individuals or species were randomized among habitats (c). These models of permutation aimed to test for taxonomic turnover using IST. Phylogenetic structure (BST and ΠST) was tested using a model 1 s which randomized the observed species across the tips of the phylogenetic tree (b, d, e). Randomization were respectively done for the whole dataset (a,b), for the habitat data set (c, e) and for TPF only (d).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4061019&req=5

pone-0098920-g001: Schema of the 3 types of randomization used to test taxonomic and phylogenetic structure.In model 1-3x, individuals were randomized among transects or species within each habitat type (a). In model 2–3x, individuals or species were randomized among habitats (c). These models of permutation aimed to test for taxonomic turnover using IST. Phylogenetic structure (BST and ΠST) was tested using a model 1 s which randomized the observed species across the tips of the phylogenetic tree (b, d, e). Randomization were respectively done for the whole dataset (a,b), for the habitat data set (c, e) and for TPF only (d).
Mentions: To address the four hypotheses above, we therefore partitioned taxonomic and phylogenetic diversity within and between transects, as well as within and between habitat types. For this we applied the statistical framework developed by Hardy and Senterre [20] for characterizing and testing the phylogenetic structure of transects and habitats types using appropriate randomization procedures [28] (Table 1, Figure 1).

Bottom Line: We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types.To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects.Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure.

View Article: PubMed Central - PubMed

Affiliation: Aix Marseille Université, IRD, LPED UMR 151, Marseille, France; Centre de coopération internationale en recherche agronomique pour le développement, UMR AMAP, Montpellier, France.

ABSTRACT
Tropical rain forests, the richest terrestrial ecosystems in biodiversity on Earth are highly threatened by global changes. This paper aims to infer the mechanisms governing species tree assemblages by characterizing the phylogenetic structure of a tropical rain forest in a protected area of the Congo Basin, the Dja Faunal Reserve (Cameroon). We re-analyzed a dataset of 11538 individuals belonging to 372 taxa found along nine transects spanning five habitat types. We generated a dated phylogenetic tree including all sampled taxa to partition the phylogenetic diversity of the nine transects into alpha and beta components at the level of the transects and of the habitat types. The variation in phylogenetic composition among transects did not deviate from a random pattern at the scale of the Dja Faunal Reserve, probably due to a common history and weak environmental variation across the park. This lack of phylogenetic structure combined with an isolation-by-distance pattern of taxonomic diversity suggests that neutral dispersal limitation is a major driver of community assembly in the Dja. To assess any lack of sensitivity to the variation in habitat types, we restricted the analyses of transects to the terra firme primary forest and found results consistent with those of the whole dataset at the level of the transects. Additionally to previous analyses, we detected a weak but significant phylogenetic turnover among habitat types, suggesting that species sort in varying environments, even though it is not predominating on the overall phylogenetic structure. Finer analyses of clades indicated a signal of clustering for species from the Annonaceae family, while species from the Apocynaceae family indicated overdispersion. These results can contribute to the conservation of the park by improving our understanding of the processes dictating community assembly in these hyperdiverse but threatened regions of the world.

Show MeSH
Related in: MedlinePlus