Alopoglossidae is a family of Neotropical lizards composed of 23 species allocated in two genera (
- Award ID(s):
- 1655635
- NSF-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 Alopoglossus andPtychoglossus ). There is a lack of knowledge about the phylogenetic relationships and systematics of this family. Published phylogenies that include alopoglossid species have very low taxon coverage within the family, and are usually based on limited character sampling. Considering these shortcomings, we infer the phylogenetic relationships of Alopoglossidae—including all but one species in the family—based on the combined analyses of DNA sequences and morphological characters. We use four loci (the mitochondrial12S ,16S andND4 ; the nuclear C‐mos) and a matrix of 143 phenotypic characters from scutellation, tongue morphology, hemipenis morphology, and osteology. The dataset is analyzed with Maximum Parsimony, with four alternative weighting schemes: three under Extended Implied Weighting, and one with equal weighting. The respective resulting topologies are compared in a sensitivity analysis framework. Our analyses support the paraphyly ofPtychoglossus , withAlopoglossus nested within it. We provide an updated classification for the family, wherePtychoglossus Boulenger, 1890 is considered a junior synonym ofAlopoglossus Boulenger, 1885. -
Abstract We performed a molecular phylogenetic analysis on the family Euteliidae to clarify deep divergences and elucidate evolutionary relationships at the level of the subfamily, tribe, and genus. Our dataset consists of 6.3 kbp of one mitochondrial and seven nuclear DNA loci and was analysed using model‐based phylogenetic methods, that is, maximum likelihood and Bayesian inference. Based on the recovered topology, we recognize two subfamilies, Euteliinae and Stictopterinae, and the tribes Stictopterini and Odontini. We identify apomorphic morphological character states for Euteliidae and its component subfamilies and tribes. Several genera (e.g.,
Targalla, Paectes, Marathyssa, Eutelia ) were found polyphyletic and require taxonomic revision. Two new genera (Niklastelia Zahiri & Hollowaygen.nov. andPellinentelia Holloway & Zahirigen.nov. ) are described and a number of taxonomic changes (new combinations and new synonymies) are established. The Neotropical genusThyriodes , currently included in Euteliidae, is found to be associated with Erebinae (Erebidae). The divergence time estimate for the split between the Euteliidae and Noctuidae is at 53 Ma, and the Euteliidae subfamilies Euteliinae and Stictopterinae are estimated to have diverged at 42 Ma. In Stictopterinae, the tribes Stictopterini and Odontodini split at 31 Ma, while Euteliinae began diversifying at 34 Ma. Malpighiales are inferred to have been the ancestral larval hostplant order for Euteliidae. The ancestors of Stictopterinae also appear to have been Malpighiales feeders, but then diverged to Malvales specialists (Odontodini) and Malpighiales specialists (Stictopterini) hostplants. Larvae of Stictopterini appear to be restricted primarily to Clusiaceae, apart from a few records from Dipterocarpaceae. In Euteliinae, Anacardiaceae are predominant as larval hosts. Thus, all hosts in the family are lactiferous, possibly providing some degree of pre‐adaptation for exploiting Dipterocarpaceae. -
Abstract Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within data sets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade’s species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of the genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower-quality samples. Most instances of topological conflict and nonmonophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, the noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many data sets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology. [Historical DNA; machine learning; museomics; Psittaciformes; species tree.]
-
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.
-
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