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Large‐scale environmental gradients have been invaluable for unraveling the processes shaping the evolution and maintenance of biodiversity. Environmental gradients provide a natural setting to test theories about species diversity and distributions within a landscape with changing biotic and abiotic interactions. Elevational gradients are particularly useful because they often encompass a large climatic range within a small geographical extent. Here, we analyzed tree communities in plots located throughout Arunachal Pradesh, a province in northeast India located on the southern face of the Eastern Himalayas, representing one of the largest elevational gradients in the world. Using indices of species and phylogenetic diversity, we described shifts in community structure across the landscape and explored the putative biotic and abiotic forces influencing species assembly. As expected, species richness and phylogenetic diversity decreased with increasing elevation; however, contrary to predictions of environmental filtering, species relatedness did not show any clear trend. Nonetheless, patterns of beta diversity (both taxonomic and phylogenetic) strongly suggest lineage filtering along the elevational gradient. Our results may be explained if filtering is driving the assembly of species from distinct evolutionary lineages. New metrics exploring community contributions to regional taxonomic and phylogenetic beta diversity provided additional evidence for the persistence of unique communities at high elevations. We suggest that these patterns may be consistent with filtering on glacial relicts, part of once more diverse clades with convergent traits suited to climates at the last glacial maximum, resulting in random or over‐dispersed community assemblages at high elevations. We propose that these high‐elevation sites with evolutionarily distinct species represent possible regions for conservation priority that may provide refugia for species threatened by current warming trends. [ABSTRACT FROM AUTHOR]