Taxonomic, functional and phylogenetic beta diversity of upland forest birds in the Amazon: The relative importance of biogeographic regions, climate, and geographic distance
Data files
Sep 13, 2024 version files 753.40 KB
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ocurrence_data.csv
221.08 KB
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phylogeny.phy
466.87 KB
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README.md
7.49 KB
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traits.csv
57.96 KB
Abstract
Aim: We address the relative importance of biogeographic regions (areas of endemism), regional climate, and spatial factors on taxonomic, functional, and phylogenetic β-diversity of bird assemblages in upland terra-firme forests in the Amazon.
Location: Amazon biome.
Taxon: Birds
Methods: We gathered 27,498 occurrence records of 873 bird species for 115 bird assemblages distributed in all nine biogeographic regions delimited by the major Amazonian rivers. Only data from studies surveying whole communities with standard sampling methods and exhaustive sampling effort were included. We partitioned the fractions of taxonomic, functional and phylogenetic beta diversity explained by climate, biogeographic regions, spatial factors, and the variation shared between them.
Results: Across the entire Amazon, we found higher total taxonomic (0.68±0.10) than phylogenetic (0.46±0.08) β-diversity, and low functional β-diversity (0.34±0.08). Biogeographic regions showed the highest unique contributions explaining taxonomic and phylogenetic β-total (7% and 5%, respectively) and turnover components (7% of β-jtu taxonomic, 7% of β-jtu phylogenetic), but accounted for only 2% of total functional β-diversity and trait turnover. Climatic variables explained slightly more trait nestedness (5%) compared to species and lineage turnover (3% each). Species composition was clearly distinct between biogeographical regions limited by the Amazon River, but support for the effect of other rivers was mixed.
Main conclusions: Our study highlights the significant influence of biogeographic regions and climate on species composition in the Amazon. However, our findings also suggest that the Amazon River exerts a more pronounced impact on species distribution compared to other major Amazonian rivers. Species turnover across biogeographical regions is particularly evident at the species level, with minor effects observed in functional traits, suggesting that taxonomic turnover is driven mainly by functionally redundant species. In addition, recent diversification events, predominantly occurring at the tips of the phylogeny without substantial turnover at deeper nodes, are likely responsible for the patchy distribution of species across Amazonia.
README
We have provided our bird species occurrence data (ocurrence_data.csv) indicating the area of endemism for each site, the edited phylogeny with species that were recently split and not considered by BirdTree (phylogeny.phy), and five traits (traits.csv) obtained from AVONET (Tobias et al. 2022) for each of the 873 bird species studied.
Descriptions
ocurrence_data.csv
This dataset is the result of compiled data on the bird species composition occurring at 115 sites in forests within the Amazon biome, of which 92 assemblages were obtained from checklists of published literature (articles, theses, and biological assessment reports) and 23 were based on our field sampling.
- Location: name of each location (site).
- Endemism: name of the area of endemism in which each site is located. Eight areas of endemism are presented: Guiana, Imeri, Napo, Inambari, Rondônia, Tapajós, Xingu, and Belém.
- The names in the columns are the scientific names of 873 bird species, listed alphabetically from left to right.
- The cells are filled with 0 (if there was no record of the species in the locality) and 1 indicating that the species was recorded in the respective locality.
phylogeny.phy
We used the phylogeny proposed by Jetz, Thomas, Joy, Hartmann, & Mooers (2012) (BirdTree, [http://www.birdtree.org]), which contains information on approximately 10,000 bird species around the world. From this phylogeny, were randomized 9,999 complete and dated phylogenies, and thus produced a maximum clade credibility tree (MCC), using the TreeAnnotator software v1.8.1 in BEAST (Drummond, Suchard, Xie, & Rambaut, 2012; Sobral, Lees, & Cianciaruso, 2016). Molecular phylogenetic analyzes have led to taxonomic revisions of many Amazonian birds, resulting in the splits and description of new species, many of them genetically structured and limited by major rivers. For example, the polytypic Dendrocolaptes certhia (Boddaert, 1783), formerly considered a single species, was divided into seven species by Batista et al. (2013): D. certhia, D. radiolatus, D. juruanus, D. concolor, D. ridgwayi, D. retentus, and D. medius. Similarly, D. transfasciatus was separated from the polytypic species D. picumnus based on genetic and morphological data (Santana et al., 2021). For the species that have been recently split or are new descriptions for science, not considered by Jetz et al. (2012), we edited the tree by dividing the branch where the species originally was and placing new species following the topology of the tree presented in the specialized literature published for each complex of species that became distinct species (for example, Campylorhamphus phylogeny by Portes et al., 2013).
The 55 species missing from BirdTree that we included in the phylogenetic tree presented in this paper are: Psophia napensis, Psophia interjecta, Psophia obscura, Psophia dextralis, Psophia ochroptera, Nystalus obamai, Nystalus torridus, Piculus paraensis, Celeus ochraceus, Piculus capistratus, Piculus laemostictus, Forpus sclateri, Pyrrhura roseifrons, Pyrrhura snethlageae, Pyrrhura amazonum, Pyrrhura lucianii, Pyrrhura anerythra, Aulacorhynchus atrogularis, Pteroglossus mariae, Megascops usta, Phaethornis aethopyga, Trogon ramonianus, Dendrocolaptes concolor, Dendrocolaptes medius, Dendrocolaptes retentus, Dendrocolaptes ridgwayi, Dendrocolaptes juruanus, Dendrocolaptes radiolatus, Xiphorhynchus chunchotambo, Campylorhamphus probatus, Campylorhamphus cardosoi, Campylorhamphus procurvoides, Lepidocolaptes layardi, Lepidocolaptes fatimalimae, Xiphocolaptes carajaensis, Sirystes albocinereus, Automolus cervicalis, Automolus paraensis, Hylopezus paraensis, Hylopezus witthakeri, Icterus chrysocephalus, Psarocolius yuracares, Myiothlypis mesoleuca, Machaeropterus striolatus, Polioptila paraensis, Herpsilochmus stotzi, Percnostola subcristata, Percnostola minor, Frederickena fulva, Epinecrophylla pyrrhonota, Epinecrophylla amazonica, Cercomacroides fuscicauda, Willisornis vidua, Schiffornis amazonum, Schiffornis olivacea.
traits.csv
We present a matrix containing five functional traits obtained for each of the 873 species from the AVONET database. The selected functional traits included: two beak measurements (beak length, beak width), tarsus length, body mass, and hand-wing index (HWI). We removed the influence of differences in species body mass on beak length, beak width and tarsus length, which cause allometry in these traits. To do this, we divided the trait value by the cube root of the body mass of the respective species (West, Brown, and Enquist 1997).
References
Batista, R., A. Aleixo, M. Vallinoto, et al. 2013. “Molecular Systematics and Taxonomic Revision of the Amazonian Barred Woodcreeper Complex (Dendrocolaptes certhia: Dendrocolaptidae), with Description of a New Species From the Xingu—Tocantins Interfluve.” In Handbook of the Birds of the World, Special Volume: New Species and Global Index, edited by J. del Hoyo, A. Elliott, J. Sargatal, and D. A. Christie, 245–247. Barcelona: Lynx Edicions.
Drummond, A. J., M. A. Suchard, D. Xie, and A. Rambaut. 2012. “Bayesian Phylogenetics With BEAUti and the BEAST 1.7.” Molecular Biology and Evolution 29, no. 8: 1969–1973. https://doi.org/10.1093/molbev/mss075.
Jetz, W., G. H. Thomas, J. B. Joy, K. Hartmann, and A. O. Mooers. 2012. “The Global Diversity of Birds in Space and Time.” Nature 491: 444–448. https://doi.org/10.1038/nature11631
Portes, C. E. B., A. Aleixo, K. J. Zimmer, et al. 2013. “A New Species of Campylorhamphus (Aves: Dendrocolaptidae) From the Tapajós Xingu Interfluve in Amazonian Brazil.” In Handbook of the Birds of the World, Special Volume: New Species and Global Index, edited by J. del Hoyo, A. Elliott, J. Sargatal, and D. A. Christie, 258–262. Barcelona: Lynx Edicions.
Santana, A., S. M. Silva, N. F. Do Nascimento, I. Sampaio, and A. Aleixo. 2021. “Phylogeography of the Dendrocolaptes picumnus (Aves: Dendrocolaptidae) Species Complex: New Insights on the Diversification of a Trans-American Lineage.” Journal of Avian Biology 52: 1–13. https://doi.org/10.1111/jav.02723
Sobral, F. L., Lees, A. C., & Cianciaruso, M. V. (2016). Introductions do not compensate for functional and phylogenetic losses following extinctions in insular bird assemblages. Ecology Letters, 19, 1091–1100. https://doi.org/10.1111/ele.12646
Tobias, J. A., C. Sheard, A. L. Pigot, et al. 2022. “AVONET: Morphological, Ecological and Geographical Data for all Birds.” Ecology Letters 25: 581–597. https://doi.org/10.1111/ele.13898.
West, G. B., J. H. Brown, and B. J. Enquist. 1997. “A General Model for the Origin of Allometric Scaling Laws in Biology.” Science 276, no. 5309: 122–126. https://doi.org/10.1126/science.276.5309.12.
Usage notes
Microsoft Excel can be used to view ocurrence_data.csv and traits.csv
phylogeny.phy can be open in any viewer of phylogenetic trees (e.g., iTOL, FigTree), in the R programming language, or any .txt reader (e.g., Notepad++).
Methods
This work contains 27,498 occurrence records of 873 species, compiled for 115 bird assemblages distributed in the Amazon basin. Approximately 80% of the occurrence data were obtained from freely available literature, while ~20% were obtained from our fieldwork. The spreadsheet containing all occurrence data used in the analyses is provided. The trait data included here contain information on five traits for each species, obtained from the AVONET database (Tobias et al., 2022; https://onlinelibrary.wiley.com/doi/full/10.1111/ele.13898). For three of these traits—beak length, beak width, and tarsus length—we adjusted for differences in species body mass by dividing the trait values by the cube root of the respective species' body mass. We used the phylogeny proposed by Jetz et al. 2012 (BirdTree, http://www.birdtree.org) for phylogenetic analyses. For 55 recently split species not included in Jetz et al. (2012), we edited the tree by splitting the branch where the species originally was and placing new species according to the topology of the tree presented in the published literature for each complex of species that became separate species.