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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.


Morphological structures of Scarabaeinae.a, Zonocopris gibbicollis; b, Onthophagus vinctus Erichson, 1843; c, Endroedyolus paradoxus; d, Gymnopleurus leei; e, Aphengium cupreum; f, Coprophanaeus telamon; g, Zonocopris gibbicollis; h, Onthophagus muticifrons Endrödi, 1973 a, pterothorax, ventral view; b, abdomen, ventral view; c, pygidium; d, abdomen, dorsal view; e, apex of metepisternum, lateral view; f, metanotum; g, mesotarsus; h, pterothorax, lateral view.
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pone.0116671.g047: Morphological structures of Scarabaeinae.a, Zonocopris gibbicollis; b, Onthophagus vinctus Erichson, 1843; c, Endroedyolus paradoxus; d, Gymnopleurus leei; e, Aphengium cupreum; f, Coprophanaeus telamon; g, Zonocopris gibbicollis; h, Onthophagus muticifrons Endrödi, 1973 a, pterothorax, ventral view; b, abdomen, ventral view; c, pygidium; d, abdomen, dorsal view; e, apex of metepisternum, lateral view; f, metanotum; g, mesotarsus; h, pterothorax, lateral view.

Mentions: The notes for the illustrations of the somatic characters (Figs. 34–47) are provided in their legends.


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)

Morphological structures of Scarabaeinae.a, Zonocopris gibbicollis; b, Onthophagus vinctus Erichson, 1843; c, Endroedyolus paradoxus; d, Gymnopleurus leei; e, Aphengium cupreum; f, Coprophanaeus telamon; g, Zonocopris gibbicollis; h, Onthophagus muticifrons Endrödi, 1973 a, pterothorax, ventral view; b, abdomen, ventral view; c, pygidium; d, abdomen, dorsal view; e, apex of metepisternum, lateral view; f, metanotum; g, mesotarsus; h, pterothorax, lateral view.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0116671.g047: Morphological structures of Scarabaeinae.a, Zonocopris gibbicollis; b, Onthophagus vinctus Erichson, 1843; c, Endroedyolus paradoxus; d, Gymnopleurus leei; e, Aphengium cupreum; f, Coprophanaeus telamon; g, Zonocopris gibbicollis; h, Onthophagus muticifrons Endrödi, 1973 a, pterothorax, ventral view; b, abdomen, ventral view; c, pygidium; d, abdomen, dorsal view; e, apex of metepisternum, lateral view; f, metanotum; g, mesotarsus; h, pterothorax, lateral view.
Mentions: The notes for the illustrations of the somatic characters (Figs. 34–47) are provided in their legends.

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.