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Innovative Bayesian and parsimony phylogeny of dung beetles (coleoptera, scarabaeidae, scarabaeinae) enhanced by ontology-based partitioning of morphological characters.

Tarasov S, Génier F - PLoS ONE (2015)

Bottom Line: We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined.Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described.Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a Cenozoic origin.

View Article: PubMed Central - PubMed

Affiliation: Department of Research and Collections, National Center for Biosystematics, Natural History Museum University of Oslo, P.O. Box 1172 Blindern NO-0318, Oslo, Norway.

ABSTRACT
Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a Cenozoic origin.

No MeSH data available.


Phylogenetic tree of Scarabaeinae from parsimony analysis #5 with implied weights (same tree as in Fig. 6, see that figure for description).Branches of the tree are colored according to the area of endemism of the genus. The scheme of biogeographic regions is provided on the top of the figure (note: the Palearctic and Oriental Regions are combined for clarity). The photographs of beetles correspond to the taxa used in the analyses.
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pone.0116671.g007: Phylogenetic tree of Scarabaeinae from parsimony analysis #5 with implied weights (same tree as in Fig. 6, see that figure for description).Branches of the tree are colored according to the area of endemism of the genus. The scheme of biogeographic regions is provided on the top of the figure (note: the Palearctic and Oriental Regions are combined for clarity). The photographs of beetles correspond to the taxa used in the analyses.

Mentions: The statistics of trees for analyses #5 and 6 is provided in Table 6. The majority rule and strict consensus of analysis #5 is shown in Figs. 5b, 4b. The majority consensus is similar to that of analysis # 6 (S4 Fig.) but differs by the position and support of some clades. Under implied weights analysis #5 yielded trees of the same length as the unweighted parsimony analysis when concavity factor was ranging from 30 to 100. Noteworthy, implied weight analyses with k = 40–100 always uncovered the same set of the three most parsimonious trees (Fig. 6, 7). The analysis #6 with implied weights also yielded parsimonious trees of the same length as unweighted parsimony analysis when the concavity factor was varying from 20 to 100. The number of inferred trees in this range of concavity factor varied from 50 to 200.


Innovative Bayesian and parsimony phylogeny of dung beetles (coleoptera, scarabaeidae, scarabaeinae) enhanced by ontology-based partitioning of morphological characters.

Tarasov S, Génier F - PLoS ONE (2015)

Phylogenetic tree of Scarabaeinae from parsimony analysis #5 with implied weights (same tree as in Fig. 6, see that figure for description).Branches of the tree are colored according to the area of endemism of the genus. The scheme of biogeographic regions is provided on the top of the figure (note: the Palearctic and Oriental Regions are combined for clarity). The photographs of beetles correspond to the taxa used in the analyses.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4363793&req=5

pone.0116671.g007: Phylogenetic tree of Scarabaeinae from parsimony analysis #5 with implied weights (same tree as in Fig. 6, see that figure for description).Branches of the tree are colored according to the area of endemism of the genus. The scheme of biogeographic regions is provided on the top of the figure (note: the Palearctic and Oriental Regions are combined for clarity). The photographs of beetles correspond to the taxa used in the analyses.
Mentions: The statistics of trees for analyses #5 and 6 is provided in Table 6. The majority rule and strict consensus of analysis #5 is shown in Figs. 5b, 4b. The majority consensus is similar to that of analysis # 6 (S4 Fig.) but differs by the position and support of some clades. Under implied weights analysis #5 yielded trees of the same length as the unweighted parsimony analysis when concavity factor was ranging from 30 to 100. Noteworthy, implied weight analyses with k = 40–100 always uncovered the same set of the three most parsimonious trees (Fig. 6, 7). The analysis #6 with implied weights also yielded parsimonious trees of the same length as unweighted parsimony analysis when the concavity factor was varying from 20 to 100. The number of inferred trees in this range of concavity factor varied from 50 to 200.

Bottom Line: We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined.Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described.Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a Cenozoic origin.

View Article: PubMed Central - PubMed

Affiliation: Department of Research and Collections, National Center for Biosystematics, Natural History Museum University of Oslo, P.O. Box 1172 Blindern NO-0318, Oslo, Norway.

ABSTRACT
Scarabaeine dung beetles are the dominant dung feeding group of insects and are widely used as model organisms in conservation, ecology and developmental biology. Due to the conflicts among 13 recently published phylogenies dealing with the higher-level relationships of dung beetles, the phylogeny of this lineage remains largely unresolved. In this study, we conduct rigorous phylogenetic analyses of dung beetles, based on an unprecedented taxon sample (110 taxa) and detailed investigation of morphology (205 characters). We provide the description of morphology and thoroughly illustrate the used characters. Along with parsimony, traditionally used in the analysis of morphological data, we also apply the Bayesian method with a novel approach that uses anatomy ontology for matrix partitioning. This approach allows for heterogeneity in evolutionary rates among characters from different anatomical regions. Anatomy ontology generates a number of parameter-partition schemes which we compare using Bayes factor. We also test the effect of inclusion of autapomorphies in the morphological analysis, which hitherto has not been examined. Generally, schemes with more parameters were favored in the Bayesian comparison suggesting that characters located on different body regions evolve at different rates and that partitioning of the data matrix using anatomy ontology is reasonable; however, trees from the parsimony and all the Bayesian analyses were quite consistent. The hypothesized phylogeny reveals many novel clades and provides additional support for some clades recovered in previous analyses. Our results provide a solid basis for a new classification of dung beetles, in which the taxonomic limits of the tribes Dichotomiini, Deltochilini and Coprini are restricted and many new tribes must be described. Based on the consistency of the phylogeny with biogeography, we speculate that dung beetles may have originated in the Mesozoic contrary to the traditional view pointing to a Cenozoic origin.

No MeSH data available.