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dc.contributor.author
Goloboff, Pablo Augusto
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dc.contributor.author
De Laet, Jan
dc.date.available
2024-06-28T10:34:46Z
dc.date.issued
2023-11
dc.identifier.citation
Goloboff, Pablo Augusto; De Laet, Jan; Farewell to the requirement for character independence: phylogenetic methods to incorporate different types of dependence between characters; Wiley Blackwell Publishing, Inc; Cladistics; 40; 3; 11-2023; 209-241
dc.identifier.issn
0748-3007
dc.identifier.uri
http://hdl.handle.net/11336/238556
dc.description.abstract
This paper discusses methods to take into account interactions between characters, in the context of parsimony analysis. These interactions can be in the form of some characters becoming inapplicable given certain states of other, primary characters; in the form of only certain states being allowed in some characters when a given state or set of states occurs for other characters; or in the form of transformation costs in some character being higher or lower when other characters have certain states or transformations between states. Character–state reconstructions and evaluation of trees under the assumption of independence may easily lead to ancestral assignments that violate elementary rules of biomechanics, well-established theories relating form and function or ideas about character co-variation. An obvious example is reconstructing an ancestral bird as wingless and flying at the same time; another is reconstructing a protein-coding gene as having a stop codon in some ancestors. If the characters are optimized independently, such chimeric ancestral reconstructions can occur even when no terminal displays the impossible combination of states. A set of conventions (implemented via new TNT commands and options) allows the definition of complex rules of interaction. By recoding groups of characters with proper step–matrix costs (and excluding impossible combinations from the set of permissible states), it is possible to find the ancestral reconstructions that maximize homology (and thus the degree to which similarities can be explained by common ancestry), within the constraints imposed by the rules specified by the user. We expect that considerations of biomechanics, functional morphology and natural history will be a source of many theories on possible character dependences, and that the present implementation will encourage users to take the possibility of character dependences into account in their phylogenetic analyses.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Wiley Blackwell Publishing, Inc
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dc.rights
info:eu-repo/semantics/restrictedAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
phylogeny
dc.subject
parsimony
dc.subject
character dependences
dc.subject
inapplicable characters
dc.subject.classification
Biología
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dc.subject.classification
Ciencias Biológicas
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dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
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dc.title
Farewell to the requirement for character independence: phylogenetic methods to incorporate different types of dependence between characters
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2024-06-24T16:00:05Z
dc.journal.volume
40
dc.journal.number
3
dc.journal.pagination
209-241
dc.journal.pais
Reino Unido
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dc.journal.ciudad
Londres
dc.description.fil
Fil: Goloboff, Pablo Augusto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; Argentina
dc.description.fil
Fil: De Laet, Jan. Meise Botanical Garden; Bélgica
dc.journal.title
Cladistics
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dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1111/cla.12564
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1111/cla.12564
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