An official website of the United States government
Abstract Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent “parts”, but instead a set of dependent and hierarchically nested entities resulting from ontogeny and phylogeny. How do we make sense of these dependent and at times redundant characters? One promising approach is using ontologies—structured controlled vocabularies that summarize knowledge about different properties of anatomical entities, including developmental and structural dependencies. Here, we assess whether evolutionary patterns can explain the proximity of ontology-annotated characters within an ontology. To do so, we measure phylogenetic information across characters and evaluate if it matches the hierarchical structure given by ontological knowledge—in much the same way as across-species diversity structure is given by phylogeny. We implement an approach to evaluate the Bayesian phylogenetic information (BPI) content and phylogenetic dissonance among ontology-annotated anatomical data subsets. We applied this to data sets representing two disparate animal groups: bees (Hexapoda: Hymenoptera: Apoidea, 209 chars) and characiform fishes (Actinopterygii: Ostariophysi: Characiformes, 463 chars). For bees, we find that BPI is not substantially explained by anatomy since dissonance is often high among morphologically related anatomical entities. For fishes, we find substantial information for two clusters of anatomical entities instantiating concepts from the jaws and branchial arch bones, but among-subset information decreases and dissonance increases substantially moving to higher-level subsets in the ontology. We further applied our approach to address particular evolutionary hypotheses with an example of morphological evolution in miniature fishes. While we show that phylogenetic information does match ontology structure for some anatomical entities, additional relationships and processes, such as convergence, likely play a substantial role in explaining BPI and dissonance, and merit future investigation. Our work demonstrates how complex morphological data sets can be interrogated with ontologies by allowing one to access how information is spread hierarchically across anatomical concepts, how congruent this information is, and what sorts of processes may play a role in explaining it: phylogeny, development, or convergence. [Apidae; Bayesian phylogenetic information; Ostariophysi; Phenoscape; phylogenetic dissonance; semantic similarity.]
more »
« less
Redescription of three basal anomodonts: a phylogenetic reassessment of the holotype of Eodicynodon oelofseni (NMQR 2913)
The Dicynodontia (Therapsida: Anomodontia) is one of the most successful Permo-Triassic terrestrial tetrapod clades and the oldest specimens are recorded from the middle PermianEodicynodonAssemblage Zone of South Africa. Their fossil record is abundant and species-rich across Pangea. By contrast, the fossil record of the basal-most anomodonts, which includes non-dicynodont anomodonts and early forms of dicynodonts, is patchy and their morphology and phylogeny are deduced from relatively few specimens. Discovered in 1982 and described in 1990, the holotype ofEodicynodon oelofseni(NMQR 2913) is one of the better-preserved early anomodont specimens. However, it has been suggested thatE. oelofsenidoes not belong to the genusEodicynodon. Here, using CT-scanning and 3D modeling, the skull ofEodicynodon oelofseni,Patranomodon nyaphuliiandEodicynodon oosthuizeniare redescribed. In the framework of this study, the application of 3D scanning technology to describe anatomical structures which were previously inaccessible in these fossils has enabled detailed redescription of the cranial morphology of the basal anomodontsPatranomodon,Eodicynodon oelofseniandE. oosthuizeniand led to a greater understanding of their cranial morphology and phylogenetic relationships. Based on an anatomical comparison and phylogenetic analyses (Bayesian and cladistics) the phylogenetic relationships of basal anomodonts are reassessed and it is suggested that NMQR 2913 does not belong to the genusEodicynodonbut likely represents a separate genus basal to other dicynodonts. A new genus is erected for NMQR 2913. This presents one of the first applications of Bayesian Inference of phylogeny on Therapsida.
more »
« less
- Award ID(s):
- 2045842
- PAR ID:
- 10600325
- Publisher / Repository:
- Frontiers
- Date Published:
- Journal Name:
- Frontiers in Earth Science
- Volume:
- 11
- ISSN:
- 2296-6463
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract The phylogenetic relationships within crown Crocodylia remain contentious due to conflicts between molecular and morphological hypotheses. However, morphology‐based datasets are mostly constructed on external characters, overlooking internal structures. Here, we use 3D geometric morphometrics to study the shape of the intertympanic sinus system in crown crocodylians during ontogeny, in order to assess its significance in a taxonomic context. Intertympanic sinus shape was found to be highly correlated with size and modulated by cranial shape during development. Still, adult sinus morphology distinguishes specimens at the family, genus and species level. We observe a clear distinction between Alligatoridae and Longirostres, a separation of differentCrocodylusspecies and the subfossil Malagasy genusVoay, and a distinction between theTomistomaandGavialislineages. Our approach is independent of molecular methods but concurs with the molecular topologies. Therefore, sinus characters could add significantly to morphological datasets, offering an alternative viewpoint to resolve problems in crocodylian relationships.more » « less
-
Summary The Cycadales are an ancient and charismatic group of seed plants. However, their morphological evolution in deep time is poorly understood. While molecular divergence time analyses estimate a Cretaceous origin for most major living cycad clades, much of the extant diversity is inferred to be a result of Neogene diversifications. This leads to long branches throughout the cycadalean phylogeny that, with few exceptions, have yet to be rectified by unequivocal fossil cycads.We report a permineralized pollen cone from the Campanian Holz Shale located in Silverado Canyon, CA, USA (c.80 million yr ago). This fossil was studied via serial sectioning, SEM, 3D reconstruction and phylogenetic analyses.Microsporophyll and pollen morphology indicate this cone is assignable toSkyttegaardia, a recently described genus based on disarticulated lignitized microsporophylls from the Early Cretaceous of Denmark. Data from this new species, including a simple cone architecture, anatomical details and vasculature organization, indicate cycadalean affinities forSkyttegaardia. Phylogenetic analyses support this assignment and recoverSkyttegaardiaas crown‐group Cycadales, nested within Zamiaceae.Our findings support a Cretaceous diversification for crown‐group Zamiaceae, which included the evolution of morphological divergent extinct taxa with unique traits that have yet to be widely identified in the fossil record.more » « less
-
Modern papionin monkeys are a diverse group that encompasses a broad range of morphologies, behaviors, and ecologies. A fossil genus known from African Plio-Pleistocene deposits, Parapapio, is widely regarded as a candidate ancestor to later African papionins. However, despite general agreement that this genus sits at or near the base of the African papionin clade, the taxonomy within Parapapio remains highly contentious. This project evaluates the species-level taxonomy of Parapapio with an explicit hypothesis-based approach to interpreting morphological variation in this sample of fossils. We tested two hypotheses: (H1) the craniodental variation within Parapapio does not cluster into three groups that reflect the three known species, and (H2) all the Parapapio fossils can be accommodated within the craniodental shape and size variation observed for a single extant species of papionin. To test the first hypothesis, we assessed a subset of relatively complete and well-preserved Parapapio crania (n=16), intentionally without reference to previous taxonomic identifications. Specimens were sorted by similarity in cranial features and results were then compared with published taxonomic classifications. Our results demonstrate that morphological traits do not cluster consistently according to the current species categories within Parapapio, failing to reject our first hypothesis. To test our second hypothesis, we examined variation in cranial and dental metrics within Parapapio (n=64) relative to three extant papionin samples (n=310). Our results fail to reject the hypothesis that all Parapapio specimens could belong to a single species and suggest that the three-species paradigm does not reflect the anatomical variation of this genus. We recommend subsuming all Parapapio specimens within Parapapio broomi, the species name with taxonomic priority. The results of this hypothesis-testing approach to taxonomy carry substantial implications for the taxonomy of Parapapio, as well as for biochronological and paleoecological studies more generally, including the taxonomy and paleobiology of hominids recovered from these same deposits.more » « less
-
Abstract The genusLiriomyzaMik (Diptera: Agromyzidae) is a diverse and globally distributed group of acalyptrate flies. Phylogenetic relationships amongLiriomyzaspecies have remained incompletely investigated and have never been fully addressed using molecular data. Here, we reconstruct the phylogeny of the genusLiriomyzausing various phylogenetic methods (maximum likelihood, Bayesian inference, and gene tree coalescence) on target‐capture‐based phylogenomic datasets (nucleotides and amino acids) obtained from anchored hybrid enrichment (AHE). We have recovered tree topologies that are nearly congruent across all data types and methods, and individual clade support is strong across all phylogenetic analyses. Moreover, defined morphological species groups and clades are well‐supported in our best estimates of the molecular phylogeny.Liriomyza violivora(Spencer) is a sister group to all remaining sampledLiriomyzaspecies, and the well‐known polyphagous vegetable pests [L. huidobrensis(Blanchard),L. langeiFrick,L. bryoniae.(Kaltenbach),L. trifolii(Burgess),L. sativaeBlanchard, andL. brassicae(Riley)]. belong to multiple clades that are not particularly closely related on the trees. Often, closely relatedLiriomyzaspecies feed on distantly related host plants. We reject the hypothesis that cophylogenetic processes betweenLiriomyzaspecies and their host plants drive diversification in this genus. Instead,Liriomyzaexhibits a widespread pattern of major host shifts across plant taxa. Our new phylogenetic estimate forLiriomyzaspecies provides considerable new information on the evolution of host‐use patterns in this genus. In addition, it provides a framework for further study of the morphology, ecology, and diversification of these important flies.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/feart.2023.1220341
