DATA SET INCONGRUENCE, MISLEADING CHARACTERS, AND INSIGHTS FROM THE FOSSIL RECORD: THE CANID PHYLOGENY
Identifying and accounting for sources of significant, explicit phylogenetic conflicts among data sets is an issue that requires further study. In this paper I explore the usefulness of the known fossil record for assessing the accuracy of conflicting sister taxa hypotheses, and in identifying and a...
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| Format: | Article |
| Language: | English |
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Universidad Nacional de Colombia
2011-12-01
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| Series: | Caldasia |
| Online Access: | http://www.revistas.unal.edu.co/index.php/cal/article/view/36416 |
| _version_ | 1811241616602562560 |
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| author | Muñoz Joao |
| author_facet | Muñoz Joao |
| author_sort | Muñoz Joao |
| collection | DOAJ |
| description | Identifying and accounting for sources of significant, explicit phylogenetic conflicts among data sets is an issue that requires further study. In this paper I explore the usefulness of the known fossil record for assessing the accuracy of conflicting sister taxa hypotheses, and in identifying and accounting for misleading characters (MCs). The alternative I present begins with a parsimony analysis of each available data set. Bootstrap proportions >95% supporting conflicting clades among most parsimonious trees (MPTs) identify instances of "strong" data set incongruence. The accuracy of conflicting sister taxa hypotheses is assessed through a comparison of their temporal gaps (T). Conflicting clades, with a significantly longer than average T, are called into question. As exceptionally long Ts can result from incompleteness and/or biases in the fossil record, it is necessary to differentiate the effect of MCs from the effect of a fragmentary fossil record. For this, the effect that characters supporting questioned conflicting clades have on data set homoplasy is assessed. If resetting these characters to missing values reduces data set homoplasy in a manner that is significantly different from random, then conflicting clades with exceptionally long T must arise from the effect of MCs. If so, new MPTs are calculated for modified data sets and the testing process is repeated until no more well-supported, conflicting clades are found. Finally, data sets are combined and the MPT is calculated. I applied this approach to the phylogeny of the Caninae using morphological and mtDNA data sets. Among the MCs characters identified were some that cannot be accounted for by commonly used a priori weighting schemes. The phylogeny of canids is also briefly discussed. The resulting MPT suggests the colonization of South America by three canid lineages and that the trenchant heel, a trait associated with hypercarnivory and sociality, evolved only once within the Caninae. |
| first_indexed | 2024-04-12T13:38:48Z |
| format | Article |
| id | doaj.art-f43adc57baba47b5925ac2857bb32bf4 |
| institution | Directory Open Access Journal |
| issn | 0366-5232 |
| language | English |
| last_indexed | 2024-04-12T13:38:48Z |
| publishDate | 2011-12-01 |
| publisher | Universidad Nacional de Colombia |
| record_format | Article |
| series | Caldasia |
| spelling | doaj.art-f43adc57baba47b5925ac2857bb32bf42022-12-22T03:30:54ZengUniversidad Nacional de ColombiaCaldasia0366-52322011-12-01332DATA SET INCONGRUENCE, MISLEADING CHARACTERS, AND INSIGHTS FROM THE FOSSIL RECORD: THE CANID PHYLOGENYMuñoz JoaoIdentifying and accounting for sources of significant, explicit phylogenetic conflicts among data sets is an issue that requires further study. In this paper I explore the usefulness of the known fossil record for assessing the accuracy of conflicting sister taxa hypotheses, and in identifying and accounting for misleading characters (MCs). The alternative I present begins with a parsimony analysis of each available data set. Bootstrap proportions >95% supporting conflicting clades among most parsimonious trees (MPTs) identify instances of "strong" data set incongruence. The accuracy of conflicting sister taxa hypotheses is assessed through a comparison of their temporal gaps (T). Conflicting clades, with a significantly longer than average T, are called into question. As exceptionally long Ts can result from incompleteness and/or biases in the fossil record, it is necessary to differentiate the effect of MCs from the effect of a fragmentary fossil record. For this, the effect that characters supporting questioned conflicting clades have on data set homoplasy is assessed. If resetting these characters to missing values reduces data set homoplasy in a manner that is significantly different from random, then conflicting clades with exceptionally long T must arise from the effect of MCs. If so, new MPTs are calculated for modified data sets and the testing process is repeated until no more well-supported, conflicting clades are found. Finally, data sets are combined and the MPT is calculated. I applied this approach to the phylogeny of the Caninae using morphological and mtDNA data sets. Among the MCs characters identified were some that cannot be accounted for by commonly used a priori weighting schemes. The phylogeny of canids is also briefly discussed. The resulting MPT suggests the colonization of South America by three canid lineages and that the trenchant heel, a trait associated with hypercarnivory and sociality, evolved only once within the Caninae.http://www.revistas.unal.edu.co/index.php/cal/article/view/36416 |
| spellingShingle | Muñoz Joao DATA SET INCONGRUENCE, MISLEADING CHARACTERS, AND INSIGHTS FROM THE FOSSIL RECORD: THE CANID PHYLOGENY Caldasia |
| title | DATA SET INCONGRUENCE, MISLEADING CHARACTERS, AND INSIGHTS FROM THE FOSSIL RECORD: THE CANID PHYLOGENY |
| title_full | DATA SET INCONGRUENCE, MISLEADING CHARACTERS, AND INSIGHTS FROM THE FOSSIL RECORD: THE CANID PHYLOGENY |
| title_fullStr | DATA SET INCONGRUENCE, MISLEADING CHARACTERS, AND INSIGHTS FROM THE FOSSIL RECORD: THE CANID PHYLOGENY |
| title_full_unstemmed | DATA SET INCONGRUENCE, MISLEADING CHARACTERS, AND INSIGHTS FROM THE FOSSIL RECORD: THE CANID PHYLOGENY |
| title_short | DATA SET INCONGRUENCE, MISLEADING CHARACTERS, AND INSIGHTS FROM THE FOSSIL RECORD: THE CANID PHYLOGENY |
| title_sort | data set incongruence misleading characters and insights from the fossil record the canid phylogeny |
| url | http://www.revistas.unal.edu.co/index.php/cal/article/view/36416 |
| work_keys_str_mv | AT munozjoao datasetincongruencemisleadingcharactersandinsightsfromthefossilrecordthecanidphylogeny |