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Wiley Online Library : Cladistics
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August 23, 2015
A large-scale phylogeny of the lycophyte genus Selaginella (Selaginellaceae: Lycopodiopsida) based on plastid and nuclear loci
The lycophyte genus Selaginella alone constitutes the family Selaginellaceae, the largest of the lycophyte families. The genus is estimated to contain 700–800 species distributed on all continents except Antarctica, with highest species diversity in tropical and subtropical regions. The monophyly of Selaginella in this broad sense has rarely been doubted, whereas its intrageneric classification has been notoriously contentious. Previous molecular studies were based on very sparse sampling of Selaginella (up to 62 species) and often used DNA sequence data from one genome. In the present study, DNA sequences of one plastid (rbcL) and one nuclear (ITS) locus from 394 accessions representing approximately 200 species of Selaginella worldwide were used to infer a phylogeny using maximum likelihood, Bayesian inference and maximum parsimony methods. The study identifies strongly supported major clades and well resolves relationships among them. Major results include: (i) six deep-level clades are discovered representing the deep splits of Selaginella; and (ii) 20 major clades representing 20 major evolutionary lineages are identified, which differ from one another in molecular, macro-morphological, ecological and spore features, and/or geographical distribution.
Previous taxonomic schemes for the Cylindropuntieae were re-evaluated in the light of a molecular phylogeny derived from a Bayesian, maximum-likelihood and parsimony reconstructions with three plastid regions (atpB-rbcL, psbA-trnH and trnK/matK data sets). The reconstruction revealed that Corynopuntia and Grusonia as currently defined were polyphyletic. Quiabentia, Micropuntia, Pereskiopsis and Cylindropuntia were the only genera recovered as monophyletic. Grusonia s.s. (only including G. bradtiana) is nested in a polytomy with the rest of the species of Corynopuntia. Grusonia s.l. (G. bradtiana plus Corynopuntia) and Corynopuntia as currently defined are polyphyletic because G. pulchella is sister to Pereskiopsis. Some previous taxonomic proposals for Cylindropuntia and Grusonia recognized polyphyletic series and subgenera that do not conform to the strongly supported monophyletic groups here recovered. This study proposes redefining the polyphyletic Grusonia excluding G. pulchella in order to recognize a strongly supported monophyletic genus and the acceptance of a monotypic Micropuntia (G. pulchella) avoiding a new combination into Pereskiopsis. The infrageneric classification for Grusonia is discussed and the recognition of only four monophyletic strongly supported series (Bigelovianae, Imbricatae, Leptocaules and Ramosissimae) for Cylindropuntia is presented.
August 10, 2015
Coleoid cephalopod phylogeny is well studied via both molecular and morphological data, yet although some agreement has been reached (e.g. that extant Decapodiformes and Octopoda are monophyletic) many details remain poorly resolved. Fossil coleoids, for which much data exists, have hitherto not been incorporated into analyses. Their inclusion is highly desirable for the support of neontological phylogenies, to better reconstruct character-state histories, and to investigate the placement of the fossil groups themselves. In this study we present and analyse a morphological data matrix including both extinct and extant taxa. Homology assumptions in our data are discussed. Our results are presented both with and without the constraint of a monophyletic Decapodiformes imposed. When analysed with this constraint our results are strikingly congruent with those from molecular phylogeny, for instance placing Idiosepius in a basal position within Decapodiformes, and recovering Oegopsida and Bathyteuthoidea (although as grades). Our results support an Octopodiformes clade (“vampire squid” Vampyroteuthis as sister to Octopoda) and an octopodiform interpretation for most fossil coleoids. They suggest the fossil sister taxon to the octopods to be Plesioteuthididae. Most fossil higher taxa are supported, although many genera, especially within suborder Teudopseina, appear para- or polyphyletic.
July 30, 2015
Chinese Cretaceous larva exposes a southern Californian living fossil (Insecta, Coleoptera, Eucnemidae)
Palaeoxenus sinensis Chang, Muona & Teräväinen sp. nov. (Coleoptera, Eucnemidae) is described on the basis of a Cretaceous larva found from the Yixian Formation in Huangbanjigou, Liaoning Province, China. The only previously known member of this clade is a southern Californian endemic, Dohrn's elegant eucnemid beetle (Palaeoxenus dohrni), a species that develops in conifers, especially the incense cedar (Calocedrus decurrens). The new find proves that the highly specialized main eucnemid lineages had evolved 123 Mya, before the main radiation of the angiosperms and probably as an adaptation to development in gymnosperms.
July 19, 2015
Plesiomorphic character states cause systematic errors in molecular phylogenetic analyses: a simulation study
Analysis of sequence data using time-reversible substitution models and maximum likelihood (ML) algorithms is currently the most popular method to infer phylogenies, despite the fact that results often contradict each other. Searching for sources of error we focus on a hitherto neglected feature of these methods: character polarity is usually thought to be irrelevant in ML analyses. Mechanisms that lead to wrong tree topologies were analysed at the level of split-supporting site patterns. In simulations, plesiomorphic site patterns can be identified by comparison with known root sequences. These patterns cause some surprising effects: Using data sets generated with simulations of sequence evolution along a variety of topologies and inferring trees using the same (correct) model, we show for cases of branch-length heterogeneity that (i) as already known, ML analyses can fail to recover the correct tree even when the correct substitution model is used, but also that (ii) plesiomorphic character states cause substantial mistakes and therefore character polarity is relevant, and (iii) accumulating chance similarities on long branches are far less misleading than plesiomorphic states accumulating on shorter branches. The artefacts occur when branch lengths are heterogeneous. The systematic errors disappear for the most part when the sites with symplesiomorphies supporting false clades are deleted from the data set. We conclude that many of the phylogenies published during the past decades may be false due to the neglected effects of symplesiomorphies.
July 15, 2015
Despite its ubiquity in the natural world, polymorphism is commonly disregarded or poorly sampled in phylogenetic analyses due to deliberate sampling strategy, inadequate sampling effort and limited specimen availability. Poor sampling of intraspecific variation engenders differential sampling of morphs within polymorphic species, which could generate conflicting tree topologies by altering the character-based affinity among taxa. To assess the potential magnitude of this impact, Polymorphic Entry Replacement Data Analysis (PERDA) was developed as a new script for the TNT phylogenetic program. This script simulates poor sampling of polymorphic taxa on a matrix of discrete characters by iteratively replacing each polymorphic state (e.g. ) with a randomly selected single state included in the original polymorphic coding (e.g. 0 or 1). The trees recovered from these subsampled data sets provide a distribution of tree distances, which indicates the level of incongruent trees resulting from different combinations of single states. Performing PERDA on empirical data sets shows alarming frequencies and magnitudes of conflicting tree topologies, demonstrating that poor sampling within polymorphic taxa could yield highly incompatible trees in many data sets. This troubling outcome undermines phylogenetic inferences based on data with poor intraspecific sampling, which is typical for palaeontological studies. With trees obtained from subsampled data sets, PERDA also generates a metaconsensus tree revealing interspecific relationships that become ambiguous due to documented levels of intraspecific variation. These collapsed clades point to taxa for which evidence should be sought to justify their taxonomic classification.
July 14, 2015
A morphological supermatrix-based phylogeny for the Neotropical fish superfamily Anostomoidea (Ostariophysi: Characiformes): phylogeny, missing data and homoplasy
Although 11 studies have addressed the systematics of the four families and 281 fish species of the ecomorphologically diverse Anostomoidea, none has proposed a global hypothesis of relationships. We synthesized these studies to yield a supermatrix with 463 morphological characters among 174 ingroup species, and inferred phylogeny with parsimony and Bayesian optimization. We evaluated the applicability of the supermatrix approach to morphological datasets, tested its sensitivity to missing data, determined the impact of homoplastic characters on phylogenetic resolution, and determined the distribution of homologies and homoplasies on the topology. Despite more than 60% missing data, analyses supported the monophyly of all families, and phylogenetic structure degraded only with inclusion of species with high percentages of missing data and in analyses limited to homoplasies. The latter differs modestly from the full matrix indicating phylogenetic signal in homoplastic characters. Character distributions differ across the phylogeny, with a greater prevalence of homologies at deeper nodes and homoplasies nearer the tips than expected by chance. This may suggest early diversification into distinct bauplans with subsequent diversification of faster evolving character systems. The morphological supermatrix approach is powerful and allows integration of classical data with modern methods to examine the evolution of multiple character systems.
Laying the foundations of evolutionary and systematic studies in crickets (Insecta, Orthoptera): a multilocus phylogenetic analysis
Orthoptera have been used for decades for numerous evolutionary questions but several of its constituent groups, notably crickets, still suffer from a lack of a robust phylogenetic hypothesis. We propose the first phylogenetic hypothesis for the evolution of crickets sensu lato, based on analysis of 205 species, representing 88% of the subfamilies and 71% tribes currently listed in the database Orthoptera Species File (OSF). We reconstructed parsimony, maximum likelihood and Bayesian phylogenies using fragments of 18S, 28SA, 28SD, H3, 12S, 16S, and cytb (~3600 bp). Our results support the monophyly of the cricket clade, and its subdivision into two clades: mole crickets and ant-loving crickets on the one hand, and all the other crickets on the other (i.e. crickets sensu stricto). Crickets sensu stricto form seven monophyletic clades, which support part of the OSF families, “subfamily groups”, or subfamilies: the mole crickets (OSF Gryllotalpidae), the scaly crickets (OSF Mogoplistidae), and the true crickets (OSF Gryllidae) are recovered as monophyletic. Among the 22 sampled subfamilies, only six are monophyletic: Gryllotalpinae, Trigonidiinae, Pteroplistinae, Euscyrtinae, Oecanthinae, and Phaloriinae. Most of the 37 tribes sampled are para- or polyphyletic. We propose the best-supported clades as backbones for future definitions of familial groups, validating some taxonomic hypotheses proposed in the past. These clades fit variously with the morphological characters used today to identify crickets. Our study emphasizes the utility of a classificatory system that accommodates diagnostic characters and monophyletic units of evolution. Moreover, the phylogenetic hypotheses proposed by the present study open new perspectives for further evolutionary research, especially on acoustic communication and biogeography.
The phylogeny of the superfamily Pamphilioidea is reconstructed using morphology and DNA sequence data of living and fossil taxa by employing two phylogenetic methods (maximum parsimony and Bayesian inference). Based on our results, the monophyly of Pamphilioidea and Pamphiliidae are corroborated, whereas two extinct families, Xyelydidae and Praesiricidae, are not monophyletic. Because members of Praesiricidae together with Megalodontes form a monophyletic group, we propose that the paraphyletic Praesiricidae is synonymized under Megalodontesidae (syn. nov.). The origin of Pamphilioidea is hypothesized to be as early as the Early Jurassic. To better understand morphological evolution in the early lineages of Pamphilioidea, ancestral states of the first flagellomere and the first and second abdominal terga are reconstructed on the morphology-based tree. In addition, three new genera (Medilyda, Brevilyda, Strenolyda) with five new species (Medilyda procera, M. distorta, Brevilyda provecta, Strenolyda marginalis and S. retrorsa) are described based on well-preserved xyelydid fossils from the Middle Jurassic Jiulongshan Formation of north-eastern China.
Evolutionary analysis identifies multiple genome expansions and contractions in Sepsidae (Diptera) and suggests targets for future genomic research
We here argue that data from comparative studies of genome size and karyotypes provide important information for planning comparative research on genome evolution. We document for 39 species of sepsids that there is a four-fold difference in genome size (151–618 Mbp). Mapping genome sizes onto a phylogenetic hypothesis identifies that this range is the result of five genome expansions and four genome contractions that we here define as changes in genome size of more than 50 Mbp. We then generate karyotype data for 10 species and find no changes in chromosome number. The study reveals that the “Oriental” clade of sepsids is a promising system for studying genome evolution because it has experienced three genome expansion events. These events can be compared with an expansion in the “Neotropical” clade in order to reveal the mechanisms that underlie genome expansion in Sepsidae. A review of the literature on genome sizes and karyotypes reveals that they have been poorly documented in Metazoa. This means that researchers interested in the evolution of genome expansions and contractions are currently not being able to identify appropriate target taxa for genome sequencing. We thus argue for more comparative research on genome sizes and karyotypes and point out that historically species were chosen for genome sequencing for reasons not related to genome evolution (e.g. small genome size, model species status, phylogenetic position, interesting phenotypes). We believe that it is now time to use a more genome-centric selection criterion, where species for whole genome sequencing are selected based on their importance for understanding genome evolution.
June 24, 2015
The subfamily Dysponetinae (Annelida, Chrysopetalidae) was proposed by Aguado et al. (Cladistics 29, 610) based on a phylogenetic analysis including morphological and molecular information. However, as a differential diagnosis of the new subfamily, as required by the International Code of Zoological Nomenclature, was not included, the name was not made available. A diagnosis of the subfamily is proposed herein to correct this oversight.
June 21, 2015
A phylogenetic analysis of molecular and morphological characters of Herminium (Orchidaceae, Orchideae): evolutionary relationships, taxonomy, and patterns of character evolution
The first comprehensive phylogenetic study of the orchid genus Herminium and its allies is presented, based on seven molecular markers (nuclear internal transcribed spacer, Xdh, chloroplast matK, psaB, psbA-trnH, rbcL and trnL-F) and 37 morphological characters. Phylogenetic analyses indicate that Herminium as currently delimited is paraphyletic and that several genera are deeply nested within it. Based on parsimony analysis of total evidence, the generic circumscription of Herminium is expanded to include Androcorys, Bhutanthera, Frigidorchis and Porolabium. Apomorphic and plesiomorphic character states are identified for various clades recovered in this study. A few species currently wrongly assigned to Peristylus and Platanthera are here included in Herminium. All necessary new combinations are made.
June 14, 2015
Phylogenetic position of the house dust mite subfamily Guatemalichinae (Acariformes: Pyroglyphidae) based on integrated molecular and morphological analyses and different measures of support
Based on multilocus phylogenetic analyses (18S, 28S, EF1-α, SRP54, HSP70, CO1, 10 860 nt aligned), we show that the house dust mite subfamily Guatemalichinae is nested within non-onychalgine pyroglyphid mites and forms the sister group to the genus Sturnophagoides (bootstrap support 100, posterior probability 1.0). Because high bootstrap support values may be misleading in the presence of incongruence, we evaluate robustness of the Guatemalichinae+Sturnophagoides clade using: (1) internode certainty indices to estimate the frequency of conflicting bipartitions in maximum-likelihood bootstrap trees, (ii) consensus networks to investigate conflict among different loci; and (iii) statistical hypothesis testing based on information theory, both multi-scale and regular bootstrap. Results suggest that this grouping is very well supported given the data. The molecular analyses were integrated with detailed morphological study using scanning electron and light microscopy. We suggest that the subfamilial status of Guatemalichinae should be reconsidered, and this lineage should be placed within the subfamily Dermatophagoidinae. The latter subfamily is currently accepted in the literature as a monophyletic group but was here inferred as paraphyletic and was not supported by any morphological synapomorphy. The paraphyly involved the most species-rich and medically important genus, Dermatophagoides. Our findings suggest the need for a comprehensive revision of the higher-level relationships of pyroglyphid house dust mites using both DNA sequences and morphology coupled with a broad taxonomic sampling.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology