Cladistics最新文献

Proteocephalids are a cosmopolitan and diverse group of tapeworms (Cestoda) that have colonized vertebrate hosts in freshwater and terrestrial environments. Despite the ubiquity of the group, key macroevolutionary processes that have driven the group's evolution have yet to be identified. Here, we review the phylogenetic relationships of proteocephalid tapeworms using publicly available (671) and newly generated (91) nucleotide sequences of the nuclear RNA28S and the mitochondrial MT-CO1 for 537 terminals. The main tree search was carried out under the parsimony optimality criterion, analysing different gene alignments simultaneously. Interestingly, we were not able to recover monophyly of the Proteocephalidae. Additionally, it was difficult to reconcile the tree with host and biogeographical data using traditional character optimization strategies in two dimensions. Therefore, we investigated if host and biogeographical data can be correlated with the parasite clades in a multidimensional space–thus considering multiple layers of information simultaneously. To that end, we used random forests (a class of machine learning models) to test the predictive potential of combined (not individual) host and biogeographical data in the context of the proteocephalid tree. Our resulting models can correctly place 88.85% (on average) of the terminals into eight representative clades. Moreover, we interactively increased the levels of clade perturbation probability and confirmed the expectation that model accuracy negatively correlates with the degree of clade perturbation. Our results show that host and biogeographical data can accurately predict proteocephalid clades in multidimensional space, even though they are difficult to optimize in the parasite tree. These results agree with the assumption that the evolution of proteocephalids is not independent of host and biogeography, and both may provide external support for our tree.

The angiosperm tribe of Elsholtzieae (Lamiaceae) is characterized by complex inflorescences and has notable medicinal and economic significance. Relationships within Elsholtzieae, including the monophyly of Elsholtzia and Keiskea, and relationships among Mosla, Keiskea and Perilla, remain uncertain, hindering insights into inflorescence evolution within the tribe. Using hybridization capture sequencing and deep genome skimming data analysis, we reconstruct a phylogeny of Elsholtzieae using 279 orthologous nuclear loci from 56 species. We evaluated uncertainty among relationships using concatenation, coalescent and network approaches. Using a time-calibrated phylogeny, we reconstructed ancestral inflorescence traits to elucidate the patterns in their evolution within the tribe. Our analyses consistently support the paraphyly of the genus Elsholtzia. Phylogenetic network analyses, confirmed by PhyloNetworks and SplitsTree, showed reticulation events among the major lineages of Elsholtzieae. The unstable polyphyly of Keiskea observed in ASTRAL (accurate species tree algorithm), ML (maximum likelihood) and MP (maximum parsimony) analyses may be related to introgression from Perilla and Mosla. Based on the analyses of phylogenetic trees within Elsholtzieae, the evolutionary trajectory of inflorescences demonstrates a pattern of diversification, with specialization as one aspect of this process. Elsholtzieae support the hypothesis that compressed inflorescences evolved from larger and more complex ancestral forms through successive compressions of the inflorescence axis. Additionally, certain lineages within the tribe display a trend towards simplified inflorescences, characterized by a reduction in the number of florets. This highlights both the specialization and the diversity in the evolution of inflorescence structures within the tribe.

We are entering the sixth mass extinction with little data for “dark taxa”, although they comprise most species. Much of the neglect is due to the fact that conventional taxonomic methods struggle with handling thousands of specimens belonging to hundreds of species. We thus here propose a new strategy that we call “dark taxonomy”. It addresses (i) taxonomic impediments, (ii) the lack of biodiversity baselines and (iii) the low impact of revisionary research. Taxonomic impediments are reduced by carrying out revisions at small geographic scales to keep the number of specimens low. The risk of taxonomic error is reduced by delimiting species based on two types of data. We furthermore show that dark taxonomy can yield important biodiversity baseline data by using samples obtained with biomonitoring traps. Lastly, we argue that the impact of revisionary research can be improved by publishing two papers addressing different readerships. The principles of dark taxonomy are illustrated by our taxonomic treatment of Singapore's fungus gnats (Mycetophilidae) based only on Malaise trap samples. We show that a first batch of specimens (N = 1454) contains 120 species, of which 115 are new to science, thus reducing taxonomic impediments by increasing the number of described Oriental species by 25%. Species delimitation started with using DNA barcodes to estimate the number of Molecular Operational Taxonomic Units (MOTUs) before “LIT” (Large-scale Integrative Taxonomy) was used to obtain the species boundaries for the 120 species by integrating morphological and molecular data. To test the taxonomic completeness of the revision, we next analysed a second batch of 1493 specimens and found that >97% belonged to the 120 species delimited based on the first batch. Indeed, the second batch only contained 18 new and rare MOTUs, i.e. our study suggests that a single revision can simultaneously yield the names for all important species and relevant biodiversity baseline data. Overall, we believe that “dark taxonomy” can quickly ready a large unknown taxon for biomonitoring.

Phylogenetic minimum description length (PMDL) is proposed as an optimality criterion for phylogenetic analysis. PMDL is based on algorithmic (Kolmogorov) information and the minimum description length principle. This criterion generates natural weighting functions (i.e. not being externally specified) for a diversity of phylogenetic graph, data and model types. PMDL is a generalized criterion that converges on existing forms of inference (i.e. parsimony, likelihood, Bayesian) in specific circumstances. Furthermore, as opposed to existing criteria, PMDL includes graph complexity allowing for the competition of hypotheses with myriad types of phylogenetic graphs (e.g. trees, networks, forests). Owing to its compound nature, PMDL allows for analytical model choice along with phylogenetic graph hypothesis while avoiding over-parameterization. Although uncomputable, heuristic methods are presented for the calculation of upper bounds on the algorithmic information content of a phylogenetic hypothesis. Examples are presented demonstrating the approach.

Quantitative traits are a source of evolutionary information often difficult to handle in cladistics. Tools exist to analyse this kind of data without subjective discretization, avoiding biases in the delimitation of categorical states. Nonetheless, our ability to accurately infer relationships from continuous characters is incompletely understood, particularly under parsimony analysis. This study evaluates the accuracy of phylogenetic reconstructions from simulated matrices of continuous characters evolving under alternative evolutionary processes and analysed by parsimony. We sampled 100 empirical trees to simulate 9000 matrices, each containing between 25 and 50 taxa, and 50 and 150 continuous characters evolving under three evolutionary processes: Brownian motion, Ornstein–Uhlenbeck and early burst with variable parametrizations. Our cladogram comparisons revealed that continuous character matrices, when properly coded and analysed by parsimony in TNT, carry phylogenetic signals from which species relationships can be inferred, regardless of the evolutionary models and parameterization schemes. Interestingly, implementing equal weighting or implied weighting with varying penalization strengths against homoplasies did not affect cladogram reconstructions based on continuous characters. Finally, the accuracy of continuous characters in resolving species relationships is skewed towards apical nodes of the recovered trees. Our findings provide general insights of the utility of quantitative traits in cladistics and demonstrate that their effectiveness in estimating shallower nodes is independent of the underlying evolutionary model, parameters and weighting schemes.

We describe a protocol for estimating evolutionary rates from phylogenetic trees based on parsimony character optimization. The rate estimation is conducted through a TNT script and the results are analysed in a script for the software environment R. The TNT script allows analysing multiple optimal topologies, considering optimization ambiguity, and alternative time-calibrations or pre-calibrated trees. The R script summarizes estimated rates on a consensus tree and plots the variation of evolutionary rates through time, jointly with the phylogenetic diversity and a new metric (clade completeness index) that measures the distribution of missing data along the tree. We present results for simulated and empirical analyses, and evaluate the impact of missing data and alternative calibration methods in rate estimates. We found that while missing data can lower the nominal values of evolutionary rates, the overall pattern of rate variation through time remained robust. Empirical cases highlight different scenarios, such as datasets in which peaks of evolutionary rates can be coupled or decoupled from diversification dynamics (phylogenetic diversity) and cases in which missing data may influence the variation of estimated evolutionary rates. We conclude with recommendations for using this protocol and interpreting the results of parsimony-based rate estimates.

Since their origin, sauropodomorphs have undergone numerous anatomical changes from small and bipedal early sauropodomorphs towards massive-bodied and quadrupedal sauropods. However, the timing of these changes in the evolution of the group is unclear. Here, we describe the appendicular skeleton of the early diverging eusauropod Bagualia alba from the late Early Jurassic of Patagonia, Argentina, and conduct a morphological disparity analysis based on a phylogenetic dataset of Sauropoda. The results reveal a change in morphospace occupation between the pre-Toarcian and Toarcian–Middle Jurassic sauropodomorphs and between the latter and Late Jurassic forms. The first shift corresponds with the extinction of non-sauropodan sauropodomorphs and the diversification of sauropods, while the second corresponds with the diversification of Neosauropoda and closely related eusauropods (mamenchisaurids, turiasaurians) in the Late Jurassic, leading to a substantial shift and increase in morphological disparity. Finally, we found that body mass is significantly correlated with the first principal coordinate axis of the morphospace in two-thirds of a random sample of optimal trees, which suggests that body size played a role in shaping the evolution of sauropod morphology. In this context, Bagualia provides insights into the evolution of Sauropoda, particularly regarding changes that occurred during the Early to Middle Jurassic.

The royal ferns (Osmundales) are a morphologically diverse group of leptosporangiate ferns, the fossil record of which dates back to the Permian. Despite there being numerous described permineralized species, the phylogenetic relationships between extinct species remain contentious. Although several analytical approaches have been applied to infer well-resolved phylogenetic hypotheses—even methods that are arguably conceived to be better at dealing with data conflict and uncertainty, many taxa have not been assigned to specific taxonomic categories. Here, we evaluate the phylogenetic affinities in Osmundales by reanalysing a dataset comprising an extensive taxon sampling of fossil Osmundalean rhizomes. The impact of both character dependence and weighting characters against homoplasy on the inferred topologies is also evaluated. Our analyses cast doubts on the monophyly of Osmundaceae and Guaireaceae. Subfamily Itopsidemoideae was rendered monophyletic when inferences were conducted by considering character dependence and downweighting characters. The subfamily Osmundoideae was retrieved monophyletic only under one concavity value and using character dependence while the remaining subfamilies included fossils with uncertain affinities within Osmundales. The position of Osmundacaulis, for instance, was recovered as a sister taxon to guaireoid fossils. To recover the monophyly of the categories below the subfamily level, incorporating character dependence and/or weighting against homoplasy was necessary. Consistent with previous studies, multiple taxa were unstable, leaving their phylogenetic affinities unclear. Our analyses underline the impact of accounting for both character dependence and weighting against homoplasy, especially when considering the contribution of missing data to observed homoplasy. Ultimately, these considerations yield markedly different topologies that imply contrasting classification schemes, highlighting the complexity inherent in resolving the evolutionary history of royal ferns.

Each published phylogeny is a potential contribution to the synthesis of the Tree of Life and countless downstream projects. Steps are needed for fully synthesizable science, but only a minority of studies achieve these. We here review the range of phylogenetic presentation and note aspects that hinder further analysis. We provide simple suggestions on publication that would greatly enhance utilizability, and propose a formal grammar for phylogeny terminal format. We suggest that each published phylogeny should be accompanied by at minimum the single preferred result in machine readable tree (e.g. Newick) form in the supplement, a simple task fulfilled by fewer than half of studies. Further, the tree should be clear from the file name and extension; the orientation (rooted or unrooted) should match the figures; terminals labels should include genus and species IDs; underscores should separate strings within-field (instead of white spaces); and if other informational fields are added these should be separated by a unique delimiting character (we suggest multiple underscores or the vertical pipe character, |) and ordered consistently. These requirements are largely independent of phylogenetic study aims, while we note other requirements for synthesis (e.g. removal of species repeats and uninformative terminals) that are not necessarily the responsibility of authors. Machine readable trees show greater variation in terminal formatting than typical phylogeny images (owing presumably to greater scrutiny of the latter), and thus are complex and laborious to parse. Since the majority of existing studies have provided only images, we additionally review typical variation in plotting style, information that will be necessary for developing the automated phylogeny transcription tools needed for their eventual inclusion in the Tree of Life.

Some of the smallest examples of dinosaurian body size are from alvarezsaurians, an enigmatic group of maniraptoran coelurosaurians with a peculiar combination of anatomical features unique among theropods. Despite the large number of alvarezsaurian species described worldwide and the increased understanding this has provided, the body-size macroevolution of alvarezsaurians has received little attention. Here we reconstruct and analyse directional trends of alvarezsaurian body-size evolution through an integrated analysis of body mass, ontogenetic age, and morphological rate data enabled by a comprehensively revised phylogeny. Our analyses identify four periods of high morphological rate evolution (Bathonian–Callovian, Hauterivian–early Berriasian, early Cenomanian, and late Cenomanian–Turonian) that we link to the key effects of animal body-size changes for the first time, including morphological novelty, structural reduction and simplification, elevated homoplasy, and behavioral changes associated with miniaturization. In doing so, this study provides a holistic example of miniaturization in a Mesozoic vertebrate group that offers a framework for other detailed studies of animal body-size evolution, including in more disparate groups.