Cladistics最新文献

Gene-tree-inference error can cause species-tree-inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene-tree branches, and subsampling gene trees based on their pairwise congruence. We tested the effect of collapsing gene-tree branches with 0% approximate-likelihood-ratio-test (SH-like aLRT) support in likelihood analyses and strict consensus trees for parsimony, and then subsampled those partially resolved trees based on congruence measures that do not penalize polytomies. For this purpose we developed a new TNT script for congruence sorting (congsort), and used it to calculate topological incongruence for eight phylogenomic datasets using three distance measures: standard Robinson–Foulds (RF) distances; overall success of resolution (OSR), which is based on counting both matching and contradicting clades; and RF contradictions, which only counts contradictory clades. As expected, we found that gene-tree incongruence was often concentrated in clades that are arbitrarily or dubiously resolved and that there was greater congruence between the partially collapsed gene trees and the coalescent and concatenation topologies inferred from those genes. Coalescent branch lengths typically increased as the most incongruent gene trees were excluded, although branch supports typically did not. We investigated two successful and complementary approaches to prioritizing genes for investigation of alignment or homology errors. Coalescent-tree clades that contradicted concatenation-tree clades were generally less robust to gene-tree subsampling than congruent clades. Our preferred approach to collapsing likelihood gene-tree clades (0% SH-like aLRT support) and subsampling those trees (OSR) generally outperformed competing approaches for a large fungal dataset with respect to branch lengths, support and congruence. We recommend widespread application of this approach (and strict consensus trees for parsimony-based analyses) for improving quantification of gene-tree congruence/conflict, estimating coalescent branch lengths, testing robustness of coalescent analyses to gene-tree-estimation error, and improving topological robustness of summary coalescent analyses. This approach is quick and easy to implement, even for huge datasets.

As it spread through time and into distinct areas of science—from comparative anatomy to evolutionary biology, cladistics, developmental and molecular biology—the homology concept has changed considerably, presenting various meanings. Despite many attempts at developing a comprehensive understanding of the concept, this context-sensitive notion of homology has been a subject of an ongoing debate. Inspired by that and following Kevin de Queiroz and Richard Mayden's view on species concept and delimitation, we presented in this article an attempt to systematize and advance the understanding of the homology problem. Our main goals were: (i) to present a comprehensive checklist of ‘concepts of homology’; (ii) to identify which are really concepts with ontological definitions (theoretically rooted in structural correspondence and common ancestry), and which are, in fact, not concepts, but epistemological (empirical and methodological) criteria of homology delimitation; (iii) to provide a synonymy of the concepts and criteria of homology delimitation; (iv) to present a hierarchy of homology concepts within Hennig's hologenetic system; and (v) to endorse the adoption of a unified view of homology by treating homology as a correspondence of spatio-temporal properties (genetic, epigenetic, developmental and positional) at the level of the individual, species or monophyletic group. We found 59 ‘concepts of homology’ in the literature, from which 34 were categorically treated as concepts, 17 as criteria of homology delimitation, Four were excluded from our treatment, and Müller’s five concepts were rather treated as approaches to homology. Homology concepts and criteria were synonymized based on structural correspondence, replicability, common ancestry, genetic and epigenetic developmental causes, position and optimization. Regarding the synonymy, we conclusively recognized 21 different concepts of homology, and five empirical and four methodological criteria. Hierarchical ontological aspects of homology were systematized under Hennig's hologenetic system, based on the existence of ontogenetic, tokogenetic and phylogenetic levels of homology. The delimitation of tokogenetic and phylogenetic homologies depends on optimization criteria. The unified view of homology is discussed in the context of the ancestral angiosperm flower.

The pantropical fern genus Didymochlaena (Didymochlaenaceae) has long been considered to contain one species only. Recent studies have resolved this genus/family as either sister to the rest of eupolypods I or as the second branching lineage of eupolypods I, and have shown that this genus is not monospecific, but the exact species diversity is unknown. In this study, a new phylogeny is reconstructed based on an expanded taxon sampling and six molecular markers. Our major results include: (i) Didymochlaena is moderately or weakly supported as sister to the rest of eupolypods I, highlighting the difficulty in resolving the relationships of this important fern lineage in the polypods; (ii) species in Didymochlaena are resolved into a New World clade and an Old World clade, and the latter further into an African clade and an Asian-Pacific clade; (iii) an unusual tripling of molecular, morphological and geographical differentiation in Didymochlaena is detected, suggesting single vicariance or dispersal events in individual regions and no evidence for reversals at all, followed by allopatric speciation at more or less homogeneous rates; (iv) evolution of 18 morphological characters is inferred and two morphological synapomorphies defining the family are recognized—the elliptical sori and fewer than 10 sori per pinnule, the latter never having been suggested before; (v) based on morphological and molecular variation, 22 species in the genus are recognized contrasting with earlier estimates of between one and a few; and (vi) our biogeographical analysis suggests an origin for Didymochlaena in the latest Jurassic–earliest Cretaceous and the initial diversification of the extant lineages in the Miocene—all but one species diverged from their sisters within the last 27 Myr, in most cases associated with allopatric speciation owing to geologic and climatic events, or dispersal.

Antrophyum is one of the largest genera of vittarioid ferns (Pteridaceae) and is most diverse in tropical Asia and the Pacific Islands, but also occurs in temperate Asia, Australia, tropical Africa and the Malagasy region. The only monographic study of Antrophyum was published more than a century ago and a modern assessment of its diversity is lacking. Here, we reconstructed a comprehensively sampled and robustly supported phylogeny for the genus based on four chloroplast markers using Bayesian inference, maximum likelihood and maximum parsimony analyses. We then explored the evolution of the genus from the perspectives of morphology, systematics and historical biogeography. We investigated nine critical morphological characters using a morphometric approach and reconstructed their evolution on the phylogeny. We describe four new species and provide new insight into species delimitation. We currently recognize 34 species for the genus and provide a key to identify them. The results of biogeographical analysis suggest that the distribution of extant species is largely shaped by both ancient and recent dispersal events.

Dance flies and relatives (Empidoidea) are a diverse and ecologically important group of Diptera in nearly all modern terrestrial ecosystems. Their fossil record, despite being scattered, attests to a long evolutionary history dating back to the early Mesozoic. Here, we describe seven new species of Empidoidea from Cretaceous Kachin amber inclusions, assigning them to the new genus Electrochoreutes gen.n. (type species: Electrochoreutes trisetigerus sp.n.) based on unique apomorphies among known Diptera. Like many extant dance flies, the males of Electrochoreutes are characterized by species-specific sexually dimorphic traits, which are likely to have played a role in courtship. The fine anatomy of the fossils was investigated through high-resolution X-ray phase-contrast microtomography to reconstruct their phylogenetic affinities within the empidoid clade, using cladistic reasoning. Morphology-based phylogenetic analyses including a selection of all extant family- and subfamily-ranked empidoid clades along with representatives of all extinct Mesozoic genera, were performed using a broad range of analytical methods (maximum parsimony, maximum-likelihood and Bayesian inference). These analyses converged in reconstructing Electrochoreutes as a stem-group representative of the Dolichopodidae, suggesting that complex mating rituals evolved in this lineage during the Cretaceous.

The superfamily Blaberoidea is a highly species-rich group of cockroaches. High-level blaberoidean phylogenetics are still under debate owing to variable taxon sampling and incongruence between mitochondrial and nuclear evolution, as well as different methods used in various phylogenetic studies. We here present a phylogenetic analysis of Blaberoidea based on a dataset combining the mitochondrial genome with two nuclear markers from representatives of all recognized families within the superfamily. Our results support the monophyly of Blaberiodea, which includes Ectobiidae s.s. (=Ectobiinae), Pseudophyllodromiidae, Nyctiboridae, Blattellidae s.s. (=Blattellinae) and Blaberidae. Ectobiidae s.s. was recovered as sister to the remaining Blaberoidea in all inferences. Pseudophyllodromiidae was paraphyletic with respect to Anaplectoidea + Malaccina. Blattellidae s.s. excluding Anaplectoidea + Malaccina formed a monophyletic group that was sister to Blaberidae. Based on our results, we propose a revised classification for Blaberoidea: Anaplectoidinae subfam.nov. and Episorineuchora gen.nov., and two new combinations at species level within Pseudophyllodromiidae; Rhabdoblattellinae subfam.nov., Calolamprodinae subfam.nov., Acutirhabdoblatta gen.nov., as well as new combinations for three species within Blaberidae. Ancestral state reconstructions based on four morphological characters allow us to infer that the common ancestor of blaberoid cockroaches is likely to be a species with characteristics similar to those found in Ectobiidae, that is, front femur Type B, arolium present, abdomen with a visible gland and male genital hook on the left side.

All Epiponini wasps are polygynic, with multiple queens alternating over the colony cycle. There are several potential queens in the early stages of this cycle, but as it progresses, the number of queens is reduced. Because most individuals remain reproductively totipotent, there is great potential for conflicts over reproduction. Workers could have an advantage in controlling queen production because they are much more numerous than queens. Nevertheless, the queen selection process is little known for Epiponini. For this reason, we aimed to study the behaviour of queens and workers during queen selection in multiple species of Epiponini, integrate information from previous behavioural studies, and perform a comparative analysis to interpret changes evolutionarily. We conducted observations on nine species belonging to five genera: Brachygastra, Chartergellus, Metapolybia, Polybia and Protopolybia. Females were individually marked to make direct and video observations. Queen production was artificially induced. A total of 28 behaviours related to queen selection were identified. The most aggressive interactions between castes, such as bite and dart, were lost in the major lineages of Epiponini. Bending display I is an ancient behaviour used as the main dominance display. Behaviours exhibited by workers to test queen status arose in the common ancestor of the Epiponini and are not shared by other polistine wasps. Consequently, the act of workers testing queen status probably was present in the Epiponini ancestor. Ritualized test display and dominance behaviours are used in Epiponini as honest signals of the queen's reproductive potential instead of aggressive behaviours. Caste flexibility had already been suggested as the ground plan for Epiponini and is herein discussed as decisive for colony survival of swarm wasps, because it allows colonies to respond efficiently to different situations that may eventually arise.

The morphology of paired fins is commonly overlooked in morphological studies, particularly the pelvic girdle and fins. Consequently, previous phylogenetic studies incorporating morphological data used few skeletal characters from this complex. In this paper, the phylogenetic significance of pelvic articular characters for elasmobranchs is discussed in light of the morphological variation observed in 130 species, the most comprehensive study exploring the morphology of the pelvic girdle done so far. The 10 morphological characters proposed herein for the pelvic articulation were incorporated into a molecular matrix of NADH2 sequences and submitted to an analysis of maximum parsimony employing extended implied weighting. The most stable tree was selected based on the distortion coefficients, SPR distances (subtree pruning and regrafting) and fit values. Some of the striking synapomorphies recovered within elasmobranchs include the presence of an articular surface for the first enlarged pelvic radial supporting Elasmobranchii and the pelvic articular region for the basipterygium extending from the posterolatral margin of the pelvic girdle over its lateral surface in Echinorhinus + Hexanchiformes. Additionally, the proposed characters and their distributions are discussed considering the relationships recovered and also compared with previous morphological and molecular phylogenetic hypotheses.

Figure 18 of Hennig's Phylogenetic Systematics (University of Illinois Press, Urbana, IL, 1966) shows a phylogenetic tree (a generative hierarchy) and what appear to be nested sets (an inclusive hierarchy) that he stated were two representations of the same pattern of relationships. This essay questions whether this is correct or not, explores the meanings of different hierarchical patterns, reviews various interpretations of Hennig's figure, and discusses the conceptual path from systematic evidence to phylogenetic explanation. The crux of the argument is that systematic hierarchies as we know them scientifically are nested sets that group theoretical entities based on patterns of synapomorphy. The notions of phylogeny and common ancestry reflect this hierarchical pattern.

In the field of phylogenetic systematics, the terms homology and homologue and their relationship to cladistic terms such as character, character state, synapomorphy and symplesiomorphy, as well as their relationships to each other, have been and are still discussed frequently. A recent re-emergence of concepts of homology/homologue free of any reference to explanatory hypotheses prompted us to explore these concepts and their relationships to each other as well as to the concept of morpheme, as introduced recently. All concepts are examined with regard to their ontological status and their bearing in the epistemological process in morphology and phylogenetic systematics. To us, morphemes, homologues and in partem character states refer to things (concrete objects in the ontological sense). However, although morphemes are exclusively descriptive, the latter two represent objects of causal explanations. Homologue always refers to the things themselves, yet a character state also can be a property or the absence of a thing. In this context, a character as a transformation series of character states does not represent a thing but a natural kind. Character states of one character are connected by homology relationships, i.e. common descent. Synapomorphy and symplesiomorphy represent different states of a single transformation series. A nonexplanatory, purely descriptive, concept of homologues is contradictory to its original as well as the post-Darwinian, evolutionary, concept which refers to causal relationships between parts of organisms and their correspondences in the archetype or ancestor, respectively. Character states, homologues and synapomorphies/symplesiomorphies can only be approximated in the form of hypotheses. We argue that the high value of the concept of homology and its related concepts for evolutionary biology should be maintained by acknowledging their explanatory nature and that dilution with nonexplanatory (even idealistic) definitions should be avoided.