DOI: 10.5061/dryad.v6wwpzh4w
title: Taxonomic, functional and phylogenetic beta diversity of upland forest birds in the Amazon: The relative importance of biogeographic regions, climate, and geographic distance

description: 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.
description: 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.
description: 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](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](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](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](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](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](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](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++).