skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


  • NSF Public Access
  • Search Results
  • Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data
Title: Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data
Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in data sets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become “inapplicable” across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological data sets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded data set on palaeognathid birds. We find that in small, simulated data sets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger data sets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures—a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a data set, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space.  more » « less
Award ID(s):
2113425
PAR ID:
10410342
Author(s) / Creator(s):
; ;
Editor(s):
Liliana Davalos
Date Published:
Journal Name:
Systematic biology
ISSN:
1063-5157
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; (, Systematic Biology)
    Wright, April (Ed.)
    Abstract Popular optimality criteria for phylogenetic trees focus on sequences of characters that are applicable to all the taxa. As studies grow in breadth, it can be the case that some characters are applicable for a portion of the taxa and inapplicable for others. Past work has explored the limitations of treating inapplicable characters as missing data, noting that this strategy may favor trees where internal nodes are assigned impossible states, where the arrangement of taxa within subclades is unduly influenced by variation in distant parts of the tree, and/or where taxa that otherwise share most primary characters are grouped distantly. Approaches that avoid the first two problems have recently been proposed. Here, we propose an alternative approach which avoids all three problems. We focus on data matrices that use reductive coding of traits, that is, explicitly incorporate the innate hierarchy induced by inapplicability, and as such our approach extend to hierarchical characters, in general. In the spirit of maximum parsimony, the proposed criterion seeks the phylogenetic tree with the minimal changes across any tree branch, but where changes are defined in terms of dissimilarity metrics that weigh the effects of inapplicable characters. The approach can accommodate binary, multistate, ordered, unordered, and polymorphic characters. We give a polynomial-time algorithm, inspired by Fitch’s algorithm, to score trees under a family of dissimilarity metrics, and prove its correctness. We show that the resulting optimality criteria is computationally hard, by reduction to the NP-hardness of the maximum parsimony optimality criteria. We demonstrate our approach using synthetic and empirical data sets and compare the results with other recently proposed methods for choosing optimal phylogenetic trees when the data includes hierarchical characters. [Character optimization, dissimilarity metrics, hierarchical characters, inapplicable data, phylogenetic tree search.] 
    more » « less
  2. ; ; ; ; (, Journal of Vertebrate Paleontology, Abstracts and Program)
    It is now well established that the end-Cretaceous mass extinction had enormous repercussions for mammalian evolution. Following the extinction, during the Paleocene, mammals started to radiate, occupying new and diverse ecological niches. However, the phylogenetic relationships between the socalled “archaic” mammals of this time, and their position within Placentalia, remain contentious. The Periptychidae are a clade of distinctive “archaic” ungulates, composed of ~17 genera of small to large bodied, highly bunodont, terrestrial herbivores that were among the first placental mammals to appear after the end-Cretaceous mass extinction. Although the Periptychidae has been historically considered a distinctive “condylarth” subgroup, their higherlevel relationships have been rarely tested. Here, we present an inclusive cladistic analysis to determine and test the phylogenetic affinities of Periptychidae and other key Paleocene groups within Placentalia under different cladistic optimality criteria. We scored 140 taxa for 503 dental, cranial and postcranial characters, incorporating new morphological and taxonomic data. The data were then subject to parsimony and Bayesian tree of morphological evolution, running 5000000 generations with samples every 200 generations and discarding 25% of the samples as burn-in. Stationarity was achieved and a 50 percent majority rule consensus tree from the sampled trees was obtained. The parsimony analysis recovered 48 most parsimonious trees. The two consensus trees derived from the different analyses are largely congruent and recover a monophyletic Periptychidae, although the parsimony consensus tree is better resolved. These results are consistent with simulation studies showing that parsimony tends to be more precise (more nodes reconstructed) than Bayesian analyses, although less accurate. The main topological differences between the results relate to the position of poorly known Puercan (earliest Paleocene) species. Our results affirm the monophyly of Periptychidae and its nesting within a group of “condylarths” positioned at the base of Laurasiatheria and closely related to Artiodactyla. Within Periptychidae we found support for the three major subfamilial divisions in both analyses. These results highlight the importance of using different optimality criteria when resolving a phylogeny and provide a new insight into how placental mammals were evolving after the end-Cretaceous extinction. Grant Information: CONICYT PFCHA/DOCTORADO BECAS CHILE/2018, European Research Council Starting Grant (ERC StG 2017, 756226, PalM), National Science Foundation (NSF EAR 1654952, DEB 1654949) 
    more » « less
  3. ; ; ; ; ; (, Systematic Biology)
    Klopfstein, Seraina (Ed.)
    Abstract Reconstructing the evolutionary history of different groups of organisms provides insight into how life originated and diversified on Earth. Phylogenetic trees are commonly used to estimate this evolutionary history. Within Bayesian phylogenetics a major step in estimating a tree is in choosing an appropriate model of character evolution. While the most common character data used is molecular sequence data, morphological data remains a vital source of information. The use of morphological characters allows for the incorporation fossil taxa, and despite advances in molecular sequencing, continues to play a significant role in neontology. Moreover, it is the main data source that allows us to unite extinct and extant taxa directly under the same generating process. We therefore require suitable models of morphological character evolution, the most common being the Mk Lewis model. While it is frequently used in both palaeobiology and neontology, it is not known whether the simple Mk substitution model, or any extensions to it, provide a sufficiently good description of the process of morphological evolution. In this study we investigate the impact of different morphological models on empirical tetrapod datasets. Specifically, we compare unpartitioned Mk models with those where characters are partitioned by the number of observed states, both with and without allowing for rate variation across sites and accounting for ascertainment bias. We show that the choice of substitution model has an impact on both topology and branch lengths, highlighting the importance of model choice. Through simulations, we validate the use of the model adequacy approach, posterior predictive simulations, for choosing an appropriate model. Additionally, we compare the performance of model adequacy with Bayesian model selection. We demonstrate how model selection approaches based on marginal likelihoods are not appropriate for choosing between models with partition schemes that vary in character state space (i.e., that vary in Q-matrix state size). Using posterior predictive simulations, we found that current variations of the Mk model are often performing adequately in capturing the evolutionary dynamics that generated our data. We do not find any preference for a particular model extension across multiple datasets, indicating that there is no “one size fits all” when it comes to morphological data and that careful consideration should be given to choosing models of discrete character evolution. By using suitable models of character evolution, we can increase our confidence in our phylogenetic estimates, which should in turn allow us to gain more accurate insights into the evolutionary history of both extinct and extant taxa. 
    more » « less
  4. ; ; (, Systematic Biology)
    Abstract It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here we investigate patterns of discordance among 282 morphological characters, which we scored for 50 bee species particularly targeting corbiculate bees, a group that includes the well-known eusocial honeybees and bumblebees. As a starting point for selecting the most meaningful partitions in the data, we grouped characters as morphological modules, highly integrated trait complexes that as a result of developmental constraints or coordinated selection we expect to share an evolutionary history and trajectory. In order to assess conflict and coherence across and within these morphological modules, we used recently developed approaches for computing Bayesian phylogenetic information allied with model comparisons using Bayes factors. We found that despite considerable conflict among morphological complexes, accounting for among-character and among-partition rate variation with individual gamma distributions, rate multipliers, and linked branch lengths can lead to coherent phylogenetic inference using morphological data. We suggest that evaluating information content and dissonance among partitions is useful step in estimating phylogenies from morphological data, just as it is with molecular data. Furthermore, we argue that adopting emerging approaches for investigating dissonance in genomic datasets may provide new insights into the integration and evolution of anatomical complexes. 
    more » « less
  5. ; ; ; ; (, American Journal of Botany)
    Abstract PremiseTo date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target‐enriched nuclear data to improve our understanding of phylogenetic relationships in the family. MethodsWe used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species inBrunellia, and several outgroup taxa. We removed loci that indicated biased inference of relationships and applied concatenated and coalescent methods to inferBrunelliaphylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage sorting events and assessed their impact on phylogenetic inference. Finally, we performed ancestral‐state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections inBrunellia. ResultsBrunelliacomprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses. ConclusionsPhylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene‐tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character‐state reconstructions. While target enrichment data allows us to broaden our understanding of diversification inBrunellia, the relationships among subclades remain incompletely understood. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email