Registering the evolutionary history in individual-based models of speciation

Author(s)

Costa, Carolina L. N. ^[1] ; Marquitti, Flavia M. D. ^[2] ; Ivan Perez, S. ^{[2, 3]} ; Schneider, David M. ^[2] ; Ramos, Marlon F. ^[2] ; de Aguiar, Marcus A. M. ^{[2, 1]}

Affiliation

^[1] Univ Estadual Campinas, Inst Biol, BR-13083859 Campinas, SP - Brazil

^[2] Univ Estadual Campinas, UNICAMP, Inst Fis Gleb Wataghin, BR-13083859 Campinas, SP - Brazil

^[3] Univ Nacl La Plata, Museo La Plata, Div Antropol, Paseo Bosque S-N, RA-1900 La Plata, Buenos Aires - Argentina

• Document type: Journal article
• Source: PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS; v. 510, p. 1-14, NOV 15 2018.
• Web of Science Citations: 1

Abstract

Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been done to connect microevolutionary processes with macroevolutionary patterns. Knowledge of the evolutionary history allows the study of patterns underlying the processes being modeled, revealing their signatures and the role of speciation and extinction in shaping macroevolutionary patterns. In this paper we introduce two algorithms to record the evolutionary history of populations and species in individual-based models of speciation, from which genealogies and phylogenies can be constructed. The first algorithm relies on saving ancestor-descendant relationships, generating a matrix that contains the times to the most recent common ancestor between all pairs of individuals at every generation (the Most Recent Common Ancestor Time matrix, MRCAT). The second algorithm directly records all speciation and extinction events throughout the evolutionary process, generating a matrix with the true phylogeny of species (the Sequential Speciation and Extinction Events, SSEE). We illustrate the use of these algorithms in a spatially explicit individual-based model of speciation. We compare the trees generated via MRCAT and SSEE algorithms with trees inferred by methods that use only genetic distance between individuals of extant species, commonly used in empirical studies and applied here to simulated genetic data. Comparisons between trees are performed with metrics describing the overall topology, branch length distribution and imbalance degree. We observe that both MRCAT and distance-based trees differ from the true phylogeny, with the first being closer to the true tree than the second. (C) 2018 Elsevier B.V. All rights reserved. (AU)

• FAPESP's process: 16/01343-7 - ICTP South American Institute for Fundamental Research: a regional center for theoretical physics
• Grantee: Nathan Jacob Berkovits
• Support Opportunities: Special Projects
• FAPESP's process: 15/11985-3 - Evolution of cooperation among different species
• Grantee: Flávia Maria Darcie Marquitti
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 16/06054-3 - Spatially distributed population dynamics: speciation and coevolution
• Grantee: Marcus Aloizio Martinez de Aguiar
• Support Opportunities: Regular Research Grants