3d clock models1/4/2024 This would make current phylogenetic models with N − 1 independent divergence times overparameterized, introducing unnecessary error ( Fig. If, in the history leading to the tips we are studying, diversification processes affected multiple lineages simultaneously or caused them to diverge into more than two descendants, the true tree could have shared or multifurcating divergences. 34 for multifurcations in unrooted trees). Current methods for estimating rooted phylogenies with N tips only consider tree models with N − 1 bifurcating divergences and assume that these divergences are independent, conditional on the topology (see ref. To formalize this assumption of independent divergences and develop ways to relax it, it is instructive to view phylogenetic inference as an exercise of statistical model selection, where each topology is a separate model ( 31– 33). We are limited in our ability to infer patterns of divergences predicted by such processes because phylogenetic methods assume that lineages diverge independently. This model predicts that recently diverged taxa across the islands should have (potentially multifurcating) divergence times clustered around the beginning of interglacial periods. For example, the repeated fragmentation of the Philippines by interglacial rises in sea level since the late Pliocene ( 15– 19) has been an important model to help explain remarkably high levels of microendemism and biodiversity across the archipelago ( 20– 30). 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. Many processes of biological diversification can simultaneously affect multiple evolutionary lineages.
0 Comments
Leave a Reply.AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |