Functional and phylogenetic structure of forest bird assemblages along an Afrotropical elevational gradient
Data files
Aug 25, 2024 version files 24.84 KB
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Functional_traits.csv
18.45 KB
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Presence_absence_table.csv
5.33 KB
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README.md
1.06 KB
Sep 04, 2025 version files 184.88 KB
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All_traits.xlsx
33.13 KB
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Dietary_traits.xlsx
18.72 KB
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Morpho_traits_2.xlsx
19.50 KB
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Morpho_traits.xlsx
19.89 KB
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Phylo.zip
11.65 KB
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Presence_absence_table_2.xlsx
19.51 KB
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Presence_absence_table.xlsx
18.62 KB
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README.md
7.42 KB
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Strata_traits.xlsx
17.18 KB
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Tactics_traits.xlsx
19.25 KB
Abstract
Elevational gradients offer valuable opportunities to investigate biodiversity patterns and the ecological and evolutionary processes that shape them. Although tropical mountains are recognized as biodiversity hotspots, the various dimensions of biodiversity in these systems, particularly in equatorial Africa, remain poorly understood. In this study, we examined the functional (FD) and phylogenetic diversity (PD) of bird assemblages along a primary forest elevational gradient in Cameroon, West-Central Africa, spanning from lowland forests to the treeline (~2300 m a.s.l.). We analyzed how FD and PD vary with elevation and tested the roles of abiotic filtering and biotic interactions, such as competition, in community assembly. Additionally, we assessed whether taxonomic diversity (TD) increases through niche packing or expansion, based on morphological and resource-use traits. Using null models and bird occurrence data, we inferred the drivers of FD and PD patterns and evaluated whether species in more diverse assemblages occupied novel functional space compared to less diverse assemblages. Our results showed that both functional richness and TD declined with elevation, whereas functional nearest neighbor distance, functional evenness, and mean nearest taxon distance increased. Traits related to resource use suggested that bird species at higher elevations were functionally less similar than expected by chance, partially supporting the influence of competition consistent with the guild assembly rule. Phylogenetic clustering observed at both low and high elevations pointed to independent species radiations, likely shaped by historical forest dynamics. In species-rich lowland assemblages, we found evidence of niche packing, suggesting increased specialization or niche overlap. In contrast, niche expansion appeared to contribute to higher TD at elevated sites. Overall, our findings indicate that while abiotic filters along forested elevational gradients and competition in lowland forests play roles in shaping avian diversity, they are not the sole or dominant mechanisms. Nonetheless, partial support for competition aligns with theoretical expectations under the guild assembly framework.
Description
This study is the analysis of functional and phylogenetic structure of bird assemblages on Mt. Cameroon (west-central Africa). To infer community assembly process, we compared observed functional and phylogenetic metrics with null model expectations. We recorded bird occurrences of 212 species across the whole elevational forest gradient and collected their functional traits from published sources (Brown et al., 1982; Urban et al., 1986, 1997; Fry et al., 1988; Keith et al., 1992; Fry & Keith, 2000, 2004). For the phylogenetic metrics, we constructed a consensus phylogenetic tree for the species using 1000 random trees based on the ‘Ericson all species: a set of 10,000 trees with 9993 OTUs each’ backbone (Jetz et al., 2012) from the BirdTree.org (http://birdtree.org/) platform. We also estimated the contribution of niche packing/expansion to increments in species richness using the niche packing “flexible” metric created by Pigot et al. (2016).
File list and descriptions:
All_traits.xlsx
This file consists of all sets of functional traits data for 212 bird species. This sheet contains:
- A set of traits related to species diet (Invert, Fruits, Leaves, Nectar, Seeds, Vert), where each column represents the relative amount of time spent feeding on the given food item.
- A set of traits related to foraging strata (Ground, Low, Middle, Canopy), where each column represents the relative amount of time spent in particular strata while foraging.
- A set of traits related to foraging tactics (Foliage gleaning, Bark probing, Flycatching, Sit-and-wait, Ground search, Fruit taking, Nectar taking), where each column represents the relative amount of time spent using the given foraging strategy.
- A set of morphological traits (Wing length (mm), Tail length (mm), Culmen (mm), Tarsus length (mm), Weight (g)), where each column represents the mean of all measurements reported in literature for the given morphological attribute.
Dietary_traits.xlsx
This file consists of dietary traits data for 212 bird species. Each column represents the % of time spent feeding on the given food item.
Morpho_traits.xlsx
This file consists of morphological traits data for 212 bird species. Each column represents the mean of all measurements reported in the literature for the given morphological attribute.
Morpho_traits_2.xlsx
This file is the same as the Morpho_trait dataset, except for the taxonomy in the Species column that matches the one given by BirdTree.org. (Jetz et al., 2012). This is the file used for estimating phylogenetic metrics.
Phylo.zip
This zip contains a file for generating a consensus tree. The consensus tree was generated in Mesquite using 1000 random trees based on the 'Ericson all species: a set of 10000 trees with 9993 OTUs each' backbone from the BirdTree.org platform.
Presence_absence_table.xlsx
Presence of birds (value = 1) recorded through point counts, mist netting, or compiled from the published dataset of Chmel et al. (2021), at each elevational band (~200 m wide), from 350 to 2350 m a.s.l.
Presence_absence_table_2.xlsx
This file is identical to the Presence_absence_table.xlsx, except for the taxonomy in the Species column that matches the one given by BirdTree.org. (Jetz et al., 2012). This is the community table used for estimating phylogenetic metrics.
Strata_traits.xlsx
This file consists of traits data related to foraging strata for 212 bird species. Each column represents the % of time spent in particular strata while foraging.
Tactics_traits.xlsx
This file consists of traits data related to foraging strategies for 212 bird species. Each column represents the % of time spent while adopting particular strategies for foraging.
Analyses_script.R
This file provides R codes of analyses, containing all steps and sections of the total analysis procedure. The steps of analysis are commented, and the positions of the main sections are provided with the corresponding sequence number at the beginning of the script. The script consists of the following main contents:
- Calculating functional diversity metrics; generating null model distributions of corresponding functional diversity metrics; computing standard effect sizes of each functional diversity metric.
- Comparing the trait space created from the mFD R package (Magneville et al., 2022) with the trait space generated from the gawdis R package (de Bello et al., 2021).
- Calculating phylogenetic signal of morphological traits; calculating phylogenetic diversity metrics; generating null model distributions of corresponding phylogenetic diversity metrics; computing standard effect sizes of each phylogenetic diversity metric.
- Segmented regression models were used to explore the relationship between each functional and phylogenetic diversity metric, as the dependent variable, and elevation as the explanatory variable.
- Estimating the contribution of the niche packing/expansion model to increases in taxonomic diversity.
References
Brown, L., Urban, E. K., & Newman, K. B. (2020). The birds of Africa: Volume I. Bloomsbury Publishing.
Chmel, K., Kamga, S. M., Awa, T., Ewome, F. L., Uceda‐Gómez, G., Hořák, D., Mlíkovský, J., Molua, L. L., Riegert, J., & Janeček, Š. (2021). Vertical stratification and seasonal changes of the avian community in Mount Cameroon lowland rainforest. African Journal of Ecology, 59(3), 655–666.
de Bello, F., Botta-Dukát, Z., Lepš, J., & Fibich, P. (2021). Towards a more balanced combination of multiple traits when computing functional differences between species. Methods in Ecology and Evolution, 12(3), 443–448. https://doi.org/10.1111/2041-210X.13537.
Fry, C. H., & Keith, S. (2020). The birds of Africa: Volume VI. Bloomsbury Publishing.
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K., & Mooers, A. O. (2012). The global diversity of birds in space and time. Nature, 491(7424), 444–448.
Keith, S. (2020). The Birds of Africa: Volume VII. Bloomsbury Publishing.
Magneville, C., Loiseau, N., Albouy, C., Casajus, N., Claverie, T., Escalas, A., Leprieur, F., Maire, E., Mouillot, D., & Villéger, S. (2022). mFD: An R package to compute and illustrate the multiple facets of functional diversity. Ecography, 2022(1). https://doi.org/10.1111/ecog.05904.
Pigot, A. L., Trisos, C. H., & Tobias, J. A. (2016). Functional traits reveal the expansion and packing of ecological niche space underlying an elevational diversity gradient in passerine birds. Proceedings of the Royal Society B: Biological Sciences, 283(1822), 20152013.
Urban, E. K., Fry, C. H., & Keith, S. (2020). The Birds of Africa: Volume V. Bloomsbury Publishing.
Version changes
04-Sept-2025:
- Added the R script used for all analyses.
- Data files have been reorganized: instead of multiple sheets within the same Excel files (e.g., dietary traits, strategy traits in separate sheets), the data are now provided as separate Excel files for each category.
- Added Phylo.zip, which contains the consensus phylogenetic tree generated with Mesquite and required for the phylogenetic diversity analyses.