Precipitation is the main axis of tropical phylogenetic turnover across space and time

Abstract

Early natural historians – Compte de Buffon, von Humboldt and De Candolle – established ecology and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, an iconic pantropical clade with 3,400 species, we show that the water availability gradient from deserts to rainforests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.

Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)

“…For full results of the sequencing, orthology assembly and phylogenetic inference, see Ringelberg et al (2022) . Here a brief overview is provided.…”

“…Library preparation, hybrid capture, enrichment and sequencing were performed by Arbor Biosciences (previously MYcroarray; Ann Arbor, USA). Full details about how the new Caesalpinioideae phylogeny was inferred are presented by Ringelberg et al (2022) , but briefly, HybPiper ( Johnson et al 2016 ) was used to assemble the loci and the pipeline of Yang and Smith (2014) was used for data cleaning and orthology assessment. Various phylogenetic methods, including the multi-species coalescent approach using individual gene trees with ASTRAL ( Zhang et al 2018 ), Maximum Likelihood based on concatenated alignments with RAxML ( Stamatakis 2014 ) and Bayesian gene jack-knifing with PhyloBayes ( Lartillot et al 2013 ), were used to infer ten nuclear species trees, which also differ in whether nucleotide or amino acid sequences were used and in the way orthology was assessed ( Ringelberg et al 2022 ).…”

“…Nielsen). The ecological versatility of the subfamily across the lowland tropical moisture availability spectrum is matched by its great diversity of life-history strategies, from massive canopy-emergent rainforest trees to small desert shrubs, and functionally-herbaceous savanna geoxyles to woody lianas and aquatic plants ( Lewis et al 2005 ; LPWG 2013 , 2017 ; Koenen et al 2020b ; Ringelberg et al 2022 ). Many species are economically important because of their highly-nutritious fruits, valuable wood, nitrogen-rich leaves and other products ( Lewis et al 2005 ) and are especially prominent as multipurpose trees in tropical silvo-pastoral and other agroforestry systems.…”

“…This new phylogeny provides the basis for testing the monophyly of genera (the main focus of this paper and of this Special Issue Advances in Legume Systematics (ALS) 14, Part 1), establishing a new higher-level classification of the subfamily (the focus of ALS 14, Part 2) and for downstream analyses of biogeography, trait evolution and diversification ( de Faria et al 2022 ; Ringelberg et al 2022 ). Caesalpinioideae provides an excellent clade for investigating evolutionary diversification and phylogenetic turnover across the lowland tropics ( Lavin et al 2004 ; Gagnon et al 2019 ; Ringelberg et al 2020 , 2022 ), as well as the evolution of several prominent plant functional traits including compound leaves, armature, extrafloral nectaries and ant associations ( Marazzi et al 2019 ), agglomeration of pollen into polyads, plant growth forms ( Gagnon et al 2019 ), floral morphology and pollination syndromes, fruit morphology and seed dispersal syndromes and the ability to form nitrogen-fixing root nodule symbiosis ( Sprent et al 2017 ; de Faria et al 2022 ). However, all of these opportunities require a robust and well-sampled subfamily-wide phylogeny of Caesalpinioideae .…”

The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes

“…The original 420‐taxon Caesalpinioideae phylogeny of Ringelberg et al . (2022) was time‐calibrated in Beast (Drummond & Rambaut, 2007), using a species tree topology estimated by Astral (Zhang et al ., 2018), a subset of 100 informative and clock‐like genes, and seven Caesalpinioideae fossil constraints (Ringelberg et al ., 2022). We pruned this chronogram until each genus was represented by just a single taxon, with two exceptions: first, the genus Chamaecrista , for which we retained four species due to known variation in nodule type within that genus (Naisbitt et al ., 1992; Santos et al ., 2017); and second, the dense sampling of 420 taxa in the original phylogeny allowed us to test the monophyly of genera, and for nonmonophyletic genera we retained representative taxa for each para‐/polyphyletic lineage.…”