If the landscape is fragmented into three or more regions, this can also cause multifurcations ( 14). At regional or global scales, when biogeographic processes fragment communities, this can cause shared divergences across multiple affected species ( 8– 13). If one of these individuals infects two or more others, this will create a multifurcation (a lineage diverging into three or more descendants) in the transmission tree. In epidemiology, when a pathogen is spread by multiple infected individuals at a social gathering, this will create shared divergences across the pathogen’s “transmission tree” ( 5– 7). At the scale of genome evolution, the duplication of a chromosome segment harboring multiple members of a gene family causes multiple, simultaneous (or “shared”) divergences across the phylogenetic history of the gene family ( 1– 4). Understanding such processes of diversification has important implications across many fields and scales of biology. There are many processes of biological diversification that affect multiple evolutionary lineages, generating patterns of temporally clustered divergences across the tree of life. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences.
Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands’ landscape caused bursts of speciation. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species.
★ Watch face configurations are accessible via Icon Launcher, Wear OS (Android Wear) Application on the phone or directly on the watch.Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. ★ You can have a beautiful seconds animation running
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