PMC

Speciation modes. a) The symmetric speciation mode captures the notion of allopatric speciation. All daughter lineages descending from a speciation event start with age 0. b) The asymmetric speciation mode is inspired by peripatric speciation and the two daughter lineages are not treated equally. On every split, one descendant has its age set to 0whereas the other keeps the ancestral “mother” age.

Model simulation for symmetric (a) and asymmetric (b) speciation modes. Speciation and extinction events are based on drawn waiting times from the distribution specified in the input. Drawn waiting times until speciation (green dashed lines) and extinction (red dashed lines) are plotted for each lineage, exemplifying the model mechanics. (a) Symmetric mode, where both descendants of a speciation event are new species with age 0. (b) Asymmetric mode, where one descendant of a speciation event is a new species and the second descendant is the mother species

Illustration of ProSSE algorithms. a) Shows the true lineage-level tree and true history of speciation completion events on the tree, with each letter representing a distinct species. Each extant lineage is labeled by its species identity. The letter on the LHS and the RHS of the arrow for each speciation completion event indicates the LHS species becomes the RHS species. Assuming no error in tree estimation, we can get some information on the history of speciation (a) from both lineage-level tree (b) and species-level tree (c), even though we do not know exactly where speciation completion events occurred on the tree. From lineage-level tree (b), we know which lineages belong to the same species (dashed edges) and what state certain nodes have (circles). We are also sure that the speciation completion event that leads to an extant species must occur along an edge with ancestral node in incipient state and descendent node in representative state. For species-level tree (c), we only sample one lineage of each extant species from lineage-level tree (b). Lineages 2 and 3 of species A, lineages 4 and 6 of species B, lineage 8 of species D in tree (b) are not in tree (c). Without these lineages, we do not know how many lineages each extant species has. We also do not know that, for example, along the edge connecting Nodes 1 and 6 in tree (c), there are unsampled descendants that lead to two extant lineages of species A and one extant lineage of species B in tree (b). As a result, we cannot be sure if Node 6 in tree (c) is species A, B, C, or some species that does not belong to any extant species. The only thing we know for sure is that, given the location of the speciation completion event of an extant species, edges after the speciation completion event should not leave any lineage of any other extant species in the tree, otherwise, the lineage-level tree will include at least two extant species that are paraphyletic to each, which cannot be generated from protracted speciation and extinction process alone (e.g., it would require gene flow after the completion of speciation). Because the location of the speciation completion event on the tree is uncertain, equations (–) are used to account for this uncertainty.

a) Speciation models predict repeated subdivision of a broad ancestral niche with decreased strength of disruptive selection after each speciation event and decreasing speciation rates. b) Rapid radiations observed in nature often exhibit an early burst of diversification greatly exceeding niche width and niche diversity in the ancestral population. Fitness functions (dotted lines) based on a) frequency dependent dynamics expected under models of speciation with repeated subdivision of ancestral niche and decreased strength of disruptive selection after each speciation event versus b) static and complex adaptive landscape underlying a burst of diversification that greatly exceeds ancestral niche width.