An official website of the United States government
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
Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae?
For the past several centuries, millipede taxonomists have used the morphology of male copulatory structures (modified legs called gonopods), which are strongly variable and suggestive of species-level differences, as a source to understand taxon relationships. Millipedes in the family Xystodesmidae are blind, dispersal-limited and have narrow habitat requirements. Therefore, geographical proximity may instead be a better predictor of evolutionary relationship than morphology, especially since gonopodal anatomy is extremely divergent and similarities may be masked by evolutionary convergence. Here we provide a phylogenetics-based test of the power of morphological versus geographical character sets for resolving phylogenetic relationships in xystodesmid millipedes. Molecular data from 90 species-group taxa in the family were included in a six-gene phylogenetic analysis to provide the basis for comparing trees generated from these alternative character sets. The molecular phylogeny was compared to topologies representing three hypotheses: (1) a prior classification formulated using morphological and geographical data, (2) hierarchical groupings derived from Euclidean geographical distance, and (3) one based solely on morphological data. Euclidean geographical distance was not found to be a better predictor of evolutionary relationship than the prior classification, the latter of which was the most similar to the molecular topology. However, all three of the alternative topologies were highly divergent (Bayes factor >10) from the molecular topology, with the tree inferred exclusively from morphology being the most divergent. The results of this analysis show that a high degree of morphological convergence from substantial gonopod shape divergence generated spurious phylogenetic relationships. These results indicate the impact that a high degree of morphological homoplasy may have had on prior treatments of the family. Using the results of our phylogenetic analysis, we make several changes to the classification of the family, including transferring the rare state-threatened species Sigmoria whiteheadi Shelley, 1986 to the genus Apheloria Chamberlin, 1921—a relationship not readily apparent based on morphology alone. We show that while gonopod differences are a premier source of taxonomic characters to diagnose species pairwise, the traits should be viewed critically as taxonomic features uniting higher levels.
more »
« less
- Award ID(s):
- 1655635
- PAR ID:
- 10056811
- Date Published:
- Journal Name:
- PeerJ
- Volume:
- 5
- ISSN:
- 2167-8359
- Page Range / eLocation ID:
- e3854
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Speciation processes in plants can be difficult to evaluate, but are essential to understanding evolutionary processes that lead to diversification. Determining the juncture at which a genetically and/or morphologically divergent population can be reliably considered a separate species is often challenging. This is particularly so with respect to recent divergences amongst closely related taxa wherein factors such as incomplete lineage sorting may yield confounding results. Taxa in theCymopterus terebinthinus(Apiaceae) species complex have long puzzled botanists. Named entities in this group display similar, yet apparently distinct morphologies that have been classified as varieties under various generic names highlighting long‐standing nomenclatural instability. Previous phylogenetic studies have challenged the monophyly of this complex. This study aims to clarify taxonomic boundaries and infer evolutionary relationships among the fourC. terebinthinusvarieties andC. petraeusby applying phylogenetic inference and incorporating ecological, morphological, and geographical evidence. We sampled from populations of all varieties ofC. terebinthinusandC. petraeusfor target capture with the Angiosperms353 bait kit. We performed phylogenetic analyses with maximum likelihood (RAxML and IQ‐TREE) and coalescent‐based phylogenetic analysis (ASTRAL). We also conducted principal component analysis of soil samples and climatic variables. We find thatC. terebinthinusand its varietal infrataxa comprise a monophyletic clade that includesC. petraeus. Clade groupings correspond to previous taxonomic assignments and morphology. Clades are often closely associated with geographical variables and at times correlated with ecological variables. Exceptions to this are here attributed to various evolutionary factors that often confound other phylogenetic analyses such as incomplete lineage sorting, introgression, and paralogous loci. Our findings suggests that geographical factors might play a major role in genetic and morphological differentiation in this complex. Despite finding well‐supported clades that correspond to defined morphological characters; further sampling amongC. petraeuspopulations is required to make taxonomic decisions.more » « less
-
Abstract The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for all but one genus in the typical owl family. Our results reveal extensive paraphyly of taxonomic groups across phylogenies inferred using different analytical approaches and suggest the genera Athene, Otus, Asio, Megascops, Bubo, and Strix are paraphyletic, whereas Ninox and Glaucidium are polyphyletic. Secondary analyses of protein-coding mitochondrial genes harvested from off-target sequencing reads and mitochondrial genomes downloaded from GenBank generally support the extent of paraphyly we observe, although some disagreements exist at higher taxonomic levels between our nuclear and mitochondrial phylogenetic hypotheses. Overall, our results demonstrate the importance of taxon sampling for understanding and describing evolutionary relationships in this group, as well as the need for additional sampling, study, and taxonomic revision of typical owl species. Additionally, our findings highlight how both divergence and convergence in morphological characters have obscured our understanding of the evolutionary history of typical owls, particularly those with insular distributions.more » « less
-
null (Ed.)Abstract Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstractmore » « less
-
Bond, Jason (Ed.)Abstract Morphology has long been used to classify and identify living organisms. However, taxonomic descriptions are often limited to qualitative descriptions of size and shape, making identification difficult due to the subjective language used to describe complex shapes. Additionally, for some taxa, there are few reliable qualitative characters available for delimitation that have yet to be tested objectively in a phylogenetic context. Solifugae is one such example. The order, Solifugae, is recognized from the other arachnid orders by the possession of large, powerful jaws or chelicerae. Male cheliceral morphology is the leading diagnostic character system in solifuge systematics and is the basis for much of solifuge current taxonomy. Female chelicerae, on the other hand, are reportedly deeply conserved and much of the species identification is based on female operculum morphology. To elucidate patterns of chelicerae and opercula trait evolution within the solifuge family, Eremobatidae, we used a 2-dimenstional morphological analysis using an Elliptical Fourier approach for closed outlines, in addition to an analysis of traditionally used measures in a phylogenetic context. Using ancestral state reconstruction and ultra-conserved elements, we assessed the taxonomic utility of female cheliceral and opercular morphology, and we evaluated which male morphological characters reflect shared, derived ancestry. Investigation into ubiquitously used character sets, in addition to newly proposed characters herein, illustrates the complex evolution of traits with high levels of convergence. Our results provide taxonomic insight into future, higher level taxonomic revisions of Eremobatidae.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.7717/peerj.3854
