LATERAL TRANSFER IN STOCHASTIC DOLLO MODELS

• 成果类型: Article
• 署名作者: Kelly, Luke J.; Nicholls, Geoff K.
• 署名单位: University of Oxford
• 刊物名称: ANNALS OF APPLIED STATISTICS
• ISSN/ISSBN: 1932-6157
• DOI: 10.1214/17-AOAS1040
• 发表日期: 2017
• 页码: 1146-1168
• 关键词: binary trait data; phylogenetic analysis; evolutionary trees; divergence times; dna-sequences; gene-transfer; colonization; reconstruct; Coalescence; expansion

摘要

Lateral transfer, a process whereby species exchange evolutionary traits through nonancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the data as the histories of affected traits are mosaics of the overall phylogeny. We control for the effect of lateral transfer in a Stochastic Dollo model and a Bayesian setting. Our likelihood is highly intractable, as the parameters are the solution of a sequence of large systems of differential equations representing the expected evolution of traits along a tree. We illustrate our method on a data set of lexical traits in Eastern Polynesian languages, and obtain an improved fit over the corresponding model without lateral transfer.