Registering the evolutionary history in individual-based models of speciation

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 th...

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Autores principales:	Costa, Carolina L. N., Marquitti, Flavia M. D., Pérez, Sergio Iván, Schneider, David Marcelo, Ramos, Marlon F., Aguiar, Marcus A. M. de
Formato:	Articulo Preprint
Lenguaje:	Inglés
Publicado:	2018
Materias:	Física Ciencias Naturales Distance-based trees Genealogies of individuals Macroevolutionary patterns Phylogenies of species Tree statistics
Acceso en línea:	http://sedici.unlp.edu.ar/handle/10915/97452 https://ri.conicet.gov.ar/11336/83130
Aporte de:	SEDICI (UNLP) de Universidad Nacional de La Plata

id	I19-R120-10915-97452
record_format	dspace
institution	Universidad Nacional de La Plata
institution_str	I-19
repository_str	R-120
collection	SEDICI (UNLP)
language	Inglés
topic	Física Ciencias Naturales Distance-based trees Genealogies of individuals Macroevolutionary patterns Phylogenies of species Tree statistics
spellingShingle	Física Ciencias Naturales Distance-based trees Genealogies of individuals Macroevolutionary patterns Phylogenies of species Tree statistics Costa, Carolina L. N. Marquitti, Flavia M. D. Pérez, Sergio Iván Schneider, David Marcelo Ramos, Marlon F. Aguiar, Marcus A. M. de Registering the evolutionary history in individual-based models of speciation
topic_facet	Física Ciencias Naturales Distance-based trees Genealogies of individuals Macroevolutionary patterns Phylogenies of species Tree statistics
description	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.
format	Articulo Preprint
author	Costa, Carolina L. N. Marquitti, Flavia M. D. Pérez, Sergio Iván Schneider, David Marcelo Ramos, Marlon F. Aguiar, Marcus A. M. de
author_facet	Costa, Carolina L. N. Marquitti, Flavia M. D. Pérez, Sergio Iván Schneider, David Marcelo Ramos, Marlon F. Aguiar, Marcus A. M. de
author_sort	Costa, Carolina L. N.
title	Registering the evolutionary history in individual-based models of speciation
title_short	Registering the evolutionary history in individual-based models of speciation
title_full	Registering the evolutionary history in individual-based models of speciation
title_fullStr	Registering the evolutionary history in individual-based models of speciation
title_full_unstemmed	Registering the evolutionary history in individual-based models of speciation
title_sort	registering the evolutionary history in individual-based models of speciation
publishDate	2018
url	http://sedici.unlp.edu.ar/handle/10915/97452 https://ri.conicet.gov.ar/11336/83130
work_keys_str_mv	AT costacarolinaln registeringtheevolutionaryhistoryinindividualbasedmodelsofspeciation AT marquittiflaviamd registeringtheevolutionaryhistoryinindividualbasedmodelsofspeciation AT perezsergioivan registeringtheevolutionaryhistoryinindividualbasedmodelsofspeciation AT schneiderdavidmarcelo registeringtheevolutionaryhistoryinindividualbasedmodelsofspeciation AT ramosmarlonf registeringtheevolutionaryhistoryinindividualbasedmodelsofspeciation AT aguiarmarcusamde registeringtheevolutionaryhistoryinindividualbasedmodelsofspeciation
bdutipo_str	Repositorios
_version_	1764820492788695040

Registering the evolutionary history in individual-based models of speciation

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