Phylogenomic Diversity in Tropical Invertebrates

Abstract

Tropical invertebrates -- comprising the vast majority of animal species globally, with insects alone estimated at 5.5-10 million species of which fewer than 20% are formally described -- represent the most phylogenetically diverse and conservation-neglected animal group, concentrated in tropical forests where rapid habitat loss is driving accelerating extinction rates among taxa that have not yet been named, let alone assessed for conservation status. This study applied shotgun metagenomics and targeted phylogenomic capture (ultraconserved elements; UCE baits for Hymenoptera, Coleoptera, Diptera, and Arachnida) to 2,840 bulk arthropod samples from 42 tropical forest sites across three regions (Amazon basin: 14 sites; Congo basin: 14; Borneo: 14; 2019-2022) to characterise phylogenomic diversity without prior species identification, enabling comparison of arthropod evolutionary heritage across forest sites at different deforestation intensities (intact primary forest, selectively logged, secondary forest, oil palm plantation). Phylogenomic diversity (total phylogenetic branch length from de novo metagenome-assembled genomes and UCE phylogenies) was 2.84-fold higher in intact primary forest than oil palm plantation across all three regions. Secondary forests (10-30 years post-clearing) recovered 48.4% of primary forest phylogenomic diversity -- substantially less than the species richness recovery (64.4%) -- confirming that evolutionary heritage recovers more slowly than species richness after deforestation. A Phylogenomic Diversity Loss Index (PDLI) predicted arthropod community function (decomposition rate, pollination visits) with r = +0.84 and identified oil palm landscapes with PDLI > 0.70 as priority restoration targets.