DOI: 10.5061/dryad.tdz08kq79
title: Functional and phylogenetic structure of forest bird assemblages along an Afrotropical elevational gradient

description: 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: # Functional and phylogenetic structure of forest bird assemblages along
 an Afrotropical elevational gradient ## 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/](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](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](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.