1. The extent to which historical dispersal, environmental features and geographic barriers shape the phylogenetic structure and turnover of tree communities in northwestern Amazonia at multiple spatial scales remains poorly understood. 

2. We used 85 floristically standardized 0.1-ha plots (DBH ³ 2.5 cm) distributed in three subregions of northwestern (NW) Amazonia across three main habitat types (floodplain, swamp, terra firme forests), to hypothesize that: i) historical dispersal overcome geographical barriers, which meant low local phylogenetic relatedness and low phylogenetic turnover. ii) Geographical barriers triggered dispersal limitation, causing high local and subregional phylogenetic clustering and high regional phylogenetic turnover. iii) Edaphic properties and flooding were negatively associated to stem size and determined the tree phylogenetic structure and turnover at local and regional scales in Amazon forests.

3. We found that the extent to which environmental or evolutionary features shaped the phylogenetic structure and phylogenetic similarity of tree communities in NW Amazonia was scale dependent. Specifically, we show that the relative importance of environmental factors increases as spatial scale and species pool decreases. Further, we find that these results are generally robust for both adult and juvenile trees. 

Synthesis: Our analysis at the regional (NW Amazon) scale lends support to the idea of Amazonian forests as a large metacommunity primarily structured by historical dispersal at large spatial scales with an increasing importance of environmental factors at finer spatial scales. The convergence of ancestral lineages across habitat types may have been due to the relatively recent formation of geographical barriers that promoted local isolation and allopatric speciation.

Vegetation sampling and identification of botanical vouchers

A total of 85 0.1-ha plots were established: 35 in Metá-Chiribiquete (Duque et al., 2001; Duque, 2004) and 25 in both Yasuní (Romero-Saltos, Valencia, & Macía, 2001) and Ampiyacu (Grández et al., 2001) (Fig. 1). Plots were rectangular (20 x 50 m) and delimited by compass, tape and stakes from a random starting point respect to topographic conditions (i.e. elevation and slope), with the restriction that the long side of the plot was parallel to the contour line. The plots were located in areas with relatively homogeneous soils and physiognomically uniform forest stands. In each plot, all shrubs, treelets, and trees with DBH ≥ 2.5 cm were numbered and measured with tape. Plots were located in forest that lacked signs of human intervention, except in some swamp plots in the floodplain of the Ampiyacu River in Peru, where few palms had been cut recently to harvest fruits from Mauritia flexuosa L.f. Plots were established at a minimum between-plot distance of 500 m and were mapped with GPS.

In each plot, at least one botanical collection of each morpho-species was collected. The nomenclature of families and genera followed Angiosperm Phylogeny Group version 4 (Chase et al., 2016). Within families or groups of closely allied families, specimens that could not be identified to species because of lack of sufficient diagnostic characteristics, were treated as morpho-species on the basis of simultaneous morphological comparisons with all other specimens in herbarium. Hereafter, we will mostly refer as to species for both morpho-species and species. Botanical identification took place at the herbaria COAH, QCA, QCNE, AMAZ, US MO, NY, and AAU. Vouchers of around 90% of the species and morpho-species described by each independent group were pooled together and compared in MO and AAU between 2000 and 2002.