Soule, V. | Search bioRxiv

bioRxiv2025

Synchronous Miocene radiations and geographic-dependent diversification of pantropical Xylopia (Annonaceae)

AimThe evolutionary drivers of hyperdiversity in tropical rain forests are complex and multifaceted. We used the pantropical Xylopia (Annonaceae) genus to address the diversification of rain forest lineages through time, across different regions, and into novel non-rain forest habitats with a comparative phylogenetic approach. LocationGlobal (pantropical) MethodsWe generated a time-calibrated phylogeny of Xylopia using hybrid capture sequence data, including 88% (168/191 spp.) of species within the genus. Diversification analyses were conducted to test for the presence of rate heterogeneity (BAMM, ClaDS, CoMET) and environmental-dependent (RPANDA), geographic-dependent, and habitat dependent (GeoHiSSE) diversification in Xylopia. ResultsSignificant diversification rate heterogeneity was detected along the backbone of the core Xylopia clade, leading to near synchronous radiations across tropical regions globally in the Miocene, with higher diversification rates in Africa, Central America, and Madagascar, and lower rates in Australia + New Guinea. Transitions from rain forest to subhumid habitats led to lower diversification rates, whereas transitions to ultramafic habitats lead to higher rates. Regional diversification models indicate sea-level changes as an important driver for Asian, Australian, Pacific, and Neotropical clades and regional temperature changes as the main diversification driver for an African clade of Xylopia. Main conclusionsOur study shows that despite synchronous radiations across regions, different regional environmental drivers have affected the diversification of Xylopia across tropical regions globally. A noteworthy example includes radiations of all five Malagasy clades c. 7 Ma coinciding with the establishment of heavy seasonal rainfall linked with the Indian monsoon. The diversification dynamics of rain forests are complex and heterogenous, with different clade-dependent and region-dependent environmental drivers.

evolutionary biology↗

bioRxiv2023

Truly the best of both worlds: merging lineage-specific and universal baiting kits to maximize phylogenomic inference

PREMISEThe development of RNA baiting kits for reduced representation approaches of genomic sequencing is popularized, with universal and clade-specific kits for flowering plants available. Here, we provided an updated version of the Annonaceae bait kit targeting 799 low copy genes, known as Annonaceae799. METHODSThis new version of the kit combines the original 469 genes from the previous version of the Annonaceae kit with 334 genes from the universal Angiosperms353 kit. We also compared the results obtained using the Original Angiosperms353 kit with our custom approach. Parsimony informative sites (pis) were evaluated for all genes and combined matrices. RESULTSThe new version of the kit has extremely high rates of gene recovery. On average, 796 genes were recovered per sample, and 777.5 genes recovered with at least 50% of their size. Off-target reads were also obtained. Evaluating size, the proportion of on- and off-target regions, and the number of pis, the genes from the Angiosperms353 usually outperform the genes from the original Annonaceae bait kit. DISCUSSIONThe results obtained show that the new sequences from the Angiosperms353 aggregate variable and putative relevant bases for future studies on species-level phylogenomics, and within species studies. The merging of kits also creates a link between projects and makes available new genes for phylogenetic and populational studies.

evolutionary biology↗