An official website of the United States government
Insights from a general, full‐likelihood Bayesian approach to inferring shared evolutionary events from genomic data: Inferring shared demographic events is challenging*
- Award ID(s):
- 1656004
- PAR ID:
- 10397046
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Evolution
- Volume:
- 74
- Issue:
- 10
- ISSN:
- 0014-3820
- Format(s):
- Medium: X Size: p. 2184-2206
- Size(s):
- p. 2184-2206
- Sponsoring Org:
- National Science Foundation
More Like this
-
Abstract Unlike temporally symmetric inferences about simple sequences, inferences about our own lives are asymmetric: we are better able to infer the past than the future, since we remember our past but not our future. Here we explore whether there are asymmetries in inferences about the unobserved pasts and futures of other people’s lives. In two experiments (analyses of the replication experiment were pre-registered), our participants view segments of two character-driven television dramas and write out what they think happens just before or after each just-watched segment. Participants are better at inferring unseen past (versus future) events. This asymmetry is driven by participants’ reliance on characters’ conversational references in the narrative, which tend to favor the past. This tendency is also replicated in a large-scale analysis of conversational references in natural conversations. Our work reveals a temporal asymmetry in how observations of other people’s behaviors can inform inferences about the past and future.more » « less
-
Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. 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. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. 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. 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. 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. 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. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. 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.more » « less
