Taxonomic, functional and phylogenetic beta diversity of upland forest birds in the Amazon: The relative importance of biogeographic regions, climate, and geographic distance

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 contribution..., 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 a..., , 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, liste...

研究目的：本研究旨在探讨生物地理分区（areas of endemism）、区域气候以及空间因子对亚马逊高地terra firme森林鸟类群落的分类、功能和系统发育β多样性的相对重要性。
研究区域：亚马逊生物群区
研究类群：鸟类
方法：我们收集了分布于亚马逊主要河流划定的9个生物地理分区内的115个鸟类群落的27,498条873种鸟类的出现记录。仅纳入采用标准采样方法且开展全面普查式采样的研究数据。我们分解了由气候、生物地理分区、空间因子及其间共享变异所解释的分类、功能和系统发育β多样性的组分。
研究结果：在整个亚马逊区域，我们发现总分类β多样性（0.68±0.10）高于系统发育β多样性（0.46±0.08），而功能β多样性较低（0.34±0.08）。生物地理分区展现出最高的独特贡献……
本研究共包含27,498条873个物种的出现记录，对应亚马逊流域内的115个鸟类群落。约80%的出现数据来自公开可获取的文献，剩余约20%来自我们的野外调查。本研究分析所用的全部出现数据已整理为电子表格并随文提供。
本研究的功能性状数据源自AVONET数据库（Tobias等，2022；https://onlinelibrary.wiley.com/doi/full/10.1111/ele.13898），涵盖每个物种的5项功能性状。针对其中3项性状——喙长、喙宽和跗跖长——我们通过将性状值除以对应物种体重的立方根，校正了物种体重差异带来的影响。系统发育分析采用Jetz等（2012）提出的鸟类系统发育树数据库（BirdTree，http://www.birdtree.org）。对于Jetz等（2012）未涵盖的55个近期拆分的物种，我们通过在该物种原所在分支处拆分的方式对系统发育树进行了编辑……
我们已提供本研究使用的鸟类物种出现数据（**ocurrence_data.csv**，原文存在拼写笔误，标准应为occurrence_data.csv），其中标注了每个样点的特有分布区；还提供了针对BirdTree未涵盖的近期拆分物种编辑后的系统发育树（**phylogeny.phy**），以及本研究涉及的873种鸟类的5项功能性状数据（**traits.csv**，数据源自Tobias等2022年的AVONET数据库）。
### 数据集说明
**ocurrence_data.csv**
该数据集整合了亚马逊生物群区115个样点森林中的鸟类物种组成数据，其中92个群落数据来自已发表文献的名录（包括期刊论文、学位论文及生物评估报告），剩余23个群落数据来自我们的野外采样。
* Location：每个样点（研究位点）的名称。
* Endemism：每个样点所在的特有分布区名称。本研究共涵盖8个特有分布区：圭亚那（Guiana）、伊梅里（Imeri）、纳波（Napo）、因班巴里（Inambari）、隆多尼亚（Rondônia）、塔帕若斯（Tapajós）、欣古（Xingu）和贝伦（Belém）。
* 各列名称为873种鸟类的学名，详见原文。