Eumycetozoans and molecular systematics

1995 ◽  
Vol 73 (S1) ◽  
pp. 738-746 ◽  
Author(s):  
F. W. Spiegel ◽  
S. B. Lee ◽  
S. A. Rusk
Keyword(s):  
Morphological Characters ◽  
Small Subunit ◽  
Monophyletic Group ◽  
Morphological Data ◽  
Morphological Evidence ◽  
Slime Molds ◽  
Phylogenetic Reconstructions ◽  
History Of ◽  
Phylogenetic Hypotheses ◽  
Molecular Trees

Eumycetozoans, the myxomycetes, protostelids, and dictyostelids, were first hypothesized to be a monophyletic group by L.S. Olive, who suggested that the primitive members of the group were similar to some of the extant protostelids. A review of morphological evidence supporting some aspects of this hypothesis is presented along with explicit explanations of the shortcomings of morphological data as tests of other aspects. For the hypothesis to be supported, modified, or rejected, data from other areas such as the sequences of the nuclear ribosomal small subunit genes (SSrDNA) will have to be used. Presently, sequences for this gene are known only from Physarum polycephalum and Dictyostelium discoideum. These two slime molds are treated as separate, deep clades in the grand eukaryote phylogenies derived from the sequences of SSrDNA. That is, each species represents an independent lineage that diverged early in the history of the eukaryotes. Insufficient taxon sampling may account for the molecular trees which suggest that the dictyostelids and myxomycetes are not members of a monophyletic group. We have begun to examine the SSrDNA sequence in the protostelid Protostelium mycophaga. Preliminary phylogenetic reconstructions using 11 eukaryotic outgroups suggest that the protostelids, myxomycetes, and dictyostelids are members of a single monophyletic group which may be most closely related to the Chromista. It is interesting that these results coincide with earlier phylogenetic hypotheses based on the morphological characters of these slime molds. Key words: dictyostelids, myxomycetes, protostelids, ribosomal DNA, slime molds.

scholarly journals Towards a phylogeny of the Metazoa: evaluating alternative phylogenetic positions of Platyhelminthes, Nemertea, and Gnathostomulida, with a critical reappraisal of cladistic characters

2004 ◽  
Vol 73 (1-2) ◽  
pp. 3-163 ◽  
Author(s):  
Ronald A. Jenner
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Total Evidence ◽  
Morphological Data ◽  
Future Research ◽  
Sister Group Relationship ◽  
Cladistic Analyses ◽  
Phylogenetic Hypotheses ◽  
Data Matrices

This paper critically assesses all morphological cladistic analyses of the Metazoa that were published during the last one and a half decades. Molecular and total evidence analyses are also critically reviewed. This study focuses on evaluating alternative phylogenetic positions of the ‘acoelomate’ worms: Platyhelminthes, Nemertea, and Gnathostomulida. This paper consists of two parts. In Part I, all recently proposed sister group hypotheses and the supporting synapomorphies for these phyla are evaluated. Discrepancies in the treatment of corresponding characters in different cladistic analyses are identified, and where possible, resolved. In Part II, the overall phylogenetic significance across the Metazoa of all characters relevant for placing the ‘acoelomate’ worms is examined. The coding and scoring of these characters for other phyla are evaluated, and uncertainties in our understanding are pointed out in order to guide future research. The characters discussed in this paper are broadly categorized as follows: epidermis and cuticle, reproduction and sexual condition, development, larval forms, coeloms and mesoderm source, nervous system and sensory organs, nephridia, musculature, digestive system, and miscellaneous characters. Competing phylogenetic hypotheses are compared in terms of several criteria: 1) taxon sampling and the fulfillment of domain of definition for each character; 2) character sampling; 3) character coding; 4) character scoring and quality of primary homology; 5) quality of the proposed diagnostic synapomorphies as secondary homologies. On the basis of this study I conclude that a sister group for the Platyhelminthes has not yet been unambiguously established. A clade minimally composed of Neotrochozoa (Mollusca, Sipuncula, Echiura, Annelida) emerges as the most likely sister group of the Nemertea on the basis of morphological and total evidence analyses. Finally, morphological data currrently favor a sister group relationship of Gnathostomulida and Syndermata (probably plus Micrognathozoa). In contrast, molecular or total evidence analyses have not identified a reliable sister group of Gnathostomulida.Further progress in our understanding of metazoan phylogeny crucially depends on the improvement of the quality of currently adopted cladistic data matrices. A thorough reassessment of many of the more than 70 morphological characters discussed here is necessary. Despite the recent compilation of comprehensive data matrices, the power to test competing hypotheses of higher-level metazoan relationships is critically compromised due to uncritical data selection and poor character study in even the most recently published cladistic analyses.

Description of a new genus and two new species of killifish (Cyprinodontiformes: Nothobranchiidae) from West Africa, with a discussion of the taxonomic status of Aphyosemion maeseni Poll, 1941

Zootaxa ◽  
2009 ◽  
Vol 2294 (1) ◽  
pp. 1-22 ◽  
Author(s):  
RAINER SONNENBERG ◽  
ECKHARD BUSCH
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
New Genus ◽  
Nuclear Dna ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Color Pattern ◽  
Monophyletic Group ◽  
Morphological Data ◽  
Adult Males

The phylogeny of the West African genus Archiaphyosemion was studied with mitochondrial and nuclear DNA sequences. The results of the combined dataset presented here did not support a monophyletic group. After the exclusion of the type species of the genus, A. guineense, the remaining species form a well-supported monophyletic group. Based on these molecular results and supported by morphological data, we suggest a new name for this group, Nimbapanchax, new genus. Additionally, based on a recent collection in Guinea, two new Nimbapanchax species were described. The taxon Nimbapanchax leucopterygius, new species, is described for a nothobranchiid fish formerly misidentified as Archiaphyosemion maeseni (Poll, 1941). Nimbapanchax melanopterygius, new species, is described from the Mount Nimba region in southeastern Guinea. Both new Nimbapanchax species are clearly distinguished from their congeners by the coloration pattern of adult males. The results of the DNA data support the assumption based on color pattern and morphological characters that the new described species are sister taxa. The type of Aphyosemion maeseni Poll, 1941 was reexamined and transferred to the genus Epiplatys, a decision based on diagnostic morphological characters.

Phylogeny, Molecules Versus Morphology, and Rates of Character Evolution Among Fruitbats (Chiroptera: Megachiroptera)

1995 ◽  
Vol 43 (6) ◽  
pp. 557 ◽  
Author(s):  
MS Springer ◽  
LJ Hollar ◽  
JAW Kirsch
Keyword(s):  
Cladistic Analysis ◽  
Strong Support ◽  
Morphological Characters ◽  
Character Evolution ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Minimum Length ◽  
Data Set ◽  
Dna Hybridisation ◽  
Phylogenetic Hypotheses

Andersen's 1912 monograph on megachiropterans remains the definitive work on the systematics of this group. Andersen argued that the Macroglossinae, containing the eonycterine and notopterine sections, are a monophyletic sister-group to other fruitbats (i.e. Andersen's Rousettus, Cynopterus and Epomophorus sections). Two recent molecular studies (DNA hybridisation and restriction mapping of ribosomal cistrons), as well as an analysis of female reproductive characters, challenge the monophyly of the Macroglossinae and several of Andersen's other conclusions such as the phylogenetic position of Nyctimene. We performed a cladistic analysis on 36 morphological characters, including 33 that were gleaned from Andersen, to determine whether phylogenetic hypotheses based on modem phylogenetic methods are in agreement with Andersen's original conclusions and to compare morphological and molecular phylogenetic hypotheses. Minimum-length trees based on parsimony are largely consistent with Andersen and support (1) a monophyletic Macroglossinae, within which the eonycterine section is paraphyletic with respect to a monophyletic notopterine section, (2) a monophyletic Cynopterus section, excepting the exclusion of Myonycteris, (3) a monophyletic Epomophorus section, excepting the exclusion of Plerotes, and (4) a paraphyletic Rousettus section, with several of the Rousettus-like forms branching off near the base of the tree. Bootstrapping analyses on a reduced data-set that included taxa shared in common with the DNA hybridisation study did not provide strong support (greater than or equal to 95%) for any clades but did provide moderate support (greater than or equal to 70) for several clades, including a monophyletic Macroglossinae. These findings are in marked contrast to the DNA hybridisation phylogeny. A high index of between-data-set incongruence is further evidence for the clash between DNA hybridisation and morphology. A phylogenetic framework was constructed on the basis of morphological data and DNA hybridisation data using a criterion of moderate support and shows little resolution, whereas employing a criterion of strong support produced a framework resolving several additional nodes. One implication of this framework is that characteristic macroglossine features such as a long tongue with a thick carpet of filiform papillae have evolved independently on several occasions (or evolved once and were lost several times). Rates of character evolution for the morphological characters employed in our analysis were calculated using divergence times estimated from DNA hybridisation data. Rates have apparently been fastest in the interior branches, and slower along the external branches, which suggests an early adaptive radiation in the history of fruitbats.

scholarly journals The tribe Scrophularieae (Scrophulariaceae): A Review of Phylogenetic Studies

Hacquetia ◽  
2019 ◽  
Vol 18 (2) ◽  
pp. 337-347 ◽  
Author(s):  
Mehrshid Riahi ◽  
Farrokh Ghahremaninejad
Keyword(s):  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Morphological Data ◽  
Hybrid Speciation ◽  
The North ◽  
Phylogenetic Studies ◽  
Phylogenetic Reconstructions ◽  
Data Collection And Analysis ◽  
History Of ◽  
Review Reports

Abstract Molecular data have been increasingly used to study the phylogenetic relationships among many taxa, including scrophs. Sometimes they have provided phylogenetic reconstructions that are in conflict with morphological data leading to a re-evaluation of long-standing evolutionary hypotheses. In this paper, we review reports of the recent knowledge of the phylogenetic relationships within Scrophularieae (2011–2017). The results of these analyses led to the following conclusions. (1) Species of Scrophularia have undergone one or more Miocene migration events occurred from eastern Asia to the North America with subsequent long dispersal and diversification in three main directions. (2) Allopolyploid and aneuploid hybrid speciation between Scrophularia species can occur, so hybridization and polyploidy have an important role for history of diversification. (3) The ancestral staminode type for the genus Scrophularia seems to be a large staminode. (4) Monophyly of the genus Verbascum with respect to the genus Scrophularia is strongly supported. (5) Oreosolen, is not monophyletic, because all accessions of Oreosolen were nested within Scrophularia. We discuss methods of data collection and analysis, and we describe the areas of conflict and agreement between molecular phylogenies.

scholarly journals Phylogeny of the Anomura (Decapoda, Crustacea): Spermatozoa and spermatophore morphological evidence

1997 ◽  
Vol 67 (2) ◽  
pp. 125-141 ◽  
Author(s):  
Christopher C. Tudge
Keyword(s):  
Phylogenetic Analysis ◽  
Decapod Crustacean ◽  
Sister Group ◽  
Morphological Characters ◽  
The Other ◽  
Monophyletic Group ◽  
Morphological Evidence ◽  
Monophyletic Clade ◽  
The Family ◽  
Single Clade

A phylogenetic analysis of selected anomuran, thalassinidean, and other decapod crustacean taxa, based on spermatozoal ultrastructural characters and spermatophore morphological characters, was performed and the following relationships of the taxa are elucidated from the trees produced. The Anomura are not a monophyletic assemblage, with the lomoid Lomis being exclusive of the remainder of the anomuran taxa, and the thalassinid Thalassina included in the anomuran clade. The synapomorphy joining the majority of the conventional anomuran taxa (Lomis excluded) is the cytoplasmic origin of the microtubular arms. When the palinurid and thalassinoid representatives are separately designated as outgroups, the Astacidea and Brachyura jointly formed a sister group to the Anomura. The superfamilies Thalassinoidea, Paguroidea, and Galatheoidea are not monophyletic groups. In all analyses the anomuran families Coenobitidae and Porcellanidae each form a monophyletic group. The paguroid family Diogenidae is paraphyletic, with the genera Clibanarius and Cancellus separate from a single clade containing the remaining diogenid genera. The families Paguridae and Parapaguridae form a monophyletic clade with the exception of Porcellanopagurus. The two representatives of the family Chirostylidae (Eumunida and Uroptychus) fail to associate with the other species in the Galatheoidea. The taxa in the family Galatheidae are not a monophyletic assemblage. The only investigated hippoid Hippa is portrayed as the sister group to the remainder of the anomuran taxa (with the exception of Lomis).

Qualitative and quantitative morphological evidence for recognition of a new species within Ceratozamia (Zamiaceae) from Mexico

Phytotaxa ◽  
2017 ◽  
Vol 317 (1) ◽  
pp. 17 ◽  
Author(s):  
LILÍ MARTÍNEZ-DOMÍNGUEZ ◽  
FERNANDO NICOLALDE-MOREJÓN ◽  
DENNIS WM. STEVENSON
Keyword(s):  
New Species ◽  
Population Level ◽  
Morphological Characters ◽  
Morphological Evidence ◽  
Herbarium Specimens ◽  
Qualitative And Quantitative ◽  
Leaf Emergence ◽  
Taxonomic History ◽  
History Of ◽  
A New Species

Several Ceratozamia populations from the “Carso Huasteco” region in Mexico have a controversial circumscription and have been historically identified as Ceratozamia fuscoviridis. In this paper, we present a review of the taxonomic history of this species and provide taxa circumscriptions based on analyses of herbarium specimens from this region and supplemented with fieldwork. For this, we have studied qualitative and quantitative morphological variation at population level. We recognize two species in this group: C. fuscoviridis and a new species, C. chamberlainii. Here, we provide two lines of qualitative and quantitative morphological evidence showing that plants of C. chamberlainii from southern San Luis Potosí to northern Hidalgo are distinct from C. fuscoviridis of central Hidalgo east of Veracruz. These species can be identified by leaflet form, leaf emergence color, color of the ovulate strobilus, and form of the megasporophyll, along with a combination of quantitative morphological characters.

scholarly journals Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)

2020 ◽  
Author(s):  
Jean-Yves Rasplus ◽  
Lillian Jennifer Rodriguez ◽  
Laure Sauné ◽  
Yang-Qiong Peng ◽  
Anthony Bain ◽  
...  
Keyword(s):  
Gc Content ◽  
Indirect Evidence ◽  
Principal Component ◽  
Morphological Plasticity ◽  
Morphological Characters ◽  
Evolutionary Rates ◽  
Morphological Data ◽  
Morphological Evidence ◽  
Ancestral State ◽  
Fig Trees

ABSTRACTDespite their ecological and evolutionary importance as key components of tropical ecosystems, the phylogeny of fig trees is still unresolved. We use restriction-site-associated DNA (RAD) sequencing (ca 420kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus representing all known subgenera and sections and five outgroups. We compare morphological and molecular results to highlight discrepancies and reveal possible inference bias. We analyse marker and taxon properties that may bias molecular inferences, with existing softwares and a new approach based on iterative principal component analysis to reduce variance between clusters of samples. For the first time, with both molecular and morphological data, we recover a monophyletic subgenus Urostigma and a clade with all gynodioecious fig trees. However, our analyses show that it is not possible to homogenize evolutionary rates and GC content for all taxa prior to phylogenetic inference and that four competing positions for the root of the molecular tree are possible. The placement of the long-branched section Pharmacosycea as sister to all other fig trees is not supported by morphological data and considered as a result of a long branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides the genus Ficus into monoecious versus gynodioecious species appears most likely. Active pollination is inferred as the ancestral state for all topologies, ambiguity remains for ancestral breeding system including for the favored topology, and it appears most likely that the ancestor of fig trees was a freestanding tree. Increasing sampling may improve results and would be at least as relevant as maximizing the number of sequenced regions given the strong heterogeneity in evolutionary rates, and to a lesser extent, base composition among species. Despite morphological plasticity and frequent homoplasy of multiple characters, we advocate giving a central role to morphology in our understanding of the evolution of Ficus, especially as it can help detect insidious systematic errors that tend to become more pronounced with larger molecular data sets.

scholarly journals Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA bar-coding and molecular phylogenetic reconstruction

2021 ◽  
Author(s):  
Takehiro K Katoh ◽  
Ji-Min Chen ◽  
Jin-Hua Yang ◽  
Guang Zhang ◽  
Lu Wang ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Morphological Data ◽  
Sister Relationship ◽  
Mitochondrial Coi ◽  
Adaptive Diversification ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Cladistic Analyses ◽  
Species Groups

The genus Dichaetophora Duda is of 69 formally described, Old World species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. Most of these species were delimitated morphologically, with the within-genus relationship established largely via cladistic analyses of morphological characters. In the present study, we first conducted species-delimitation with aids of morphological data as well DNA barcodes (nucleotide sequences of the mitochondrial COI, i.e., cytochrome c oxidase subunit I, gene), for a huge sample of Dichaetophora and allied taxa (genus Mulgravea and subgenus Dudaica of Drosophila) collected from a wide geographical range. Then, multiple-locus phylogenetic reconstruction was conducted based on elaborate taxon sampling from the known and newly recognized species in the above taxa, with the maximum likelihood (ML) and Bayesian inference (BI) methods. As a result, 189 species (186 of Dichaetophora, 2 of Mulgravea, and 1 for Dudaica) were newly recognized. In our ML and BI trees, several well-supported species clusters equivalent to the species groups agbo (excluding of neocirricauda), tenuicauda, sinensis (inclusive of neocirricauda) and trilobita of Dichaetophora, were recovered, with the sister-relationship between the third and fourth proved. Other well-supported clusters include 1) a clade comprising of Di. acutissima group and Dudaica, with the former proved to be paraphyletic to the latter; 2) genus Mulgravea; 3) a clade comprising exclusively of newly recognized Dichaetophora species, and was placed as sister to Mulgravea. Three of the remaining five representatives of Dichaetophora species form a solid cluster, leaving the positions of the last two unresolved. The present study greatly renewed out knowledge about the species diversity in a pan-Dichaetophora clade, providing us with an unprecedented historical framework for further taxonomy revision of this clade, and valuable baseline knowledge for future reconstruction of the history of its adaptive diversification in the particular microhabitats.

World genera of Mastigitae: review of morphological structures and new ecological data (Coleoptera: Staphylinidae: Scydmaeninae)

Zootaxa ◽  
2018 ◽  
Vol 4453 (1) ◽  
pp. 1 ◽  
Author(s):  
PAWEŁ JAŁOSZYŃSKI
Keyword(s):  
Upper Cretaceous ◽  
Habitat Preferences ◽  
Morphological Characters ◽  
Ecological Data ◽  
Ecological Adaptations ◽  
History Of ◽  
Phylogenetic Hypotheses ◽  
First Time ◽  
Maxillary Palps

Mastigitae comprise most unusual ant-like stone beetles, showing intriguing morphological characters and ecological adaptations. The largest adults among Scydmaeninae can be found in this group; some reaching nearly 9 mm in length, but there are also adults as small as 1.10 mm. Members of Leptomastacini are microphthalmous and depigmented; Mastigini are often black or contrastingly bicolored and have diurnal life style, adults of some species climbing bushes and trees. Papusini inhabit the driest North American deserts and are active during the warmest time of the year; other taxa live in subtropical forests; some are known to enter caves. Adults of some genera have enigmatic modifications of maxillary palps, postgenae or antennae, whose functions still remain unknown. In one genus the male genitalia are enormously elongate, so that these beetles have evolved a method of copulation not known in any other Coleoptera. The evolutionary history of Mastigitae is documented by fossils since the Upper Cretaceous, and extinct forms are even more 'extreme' in their spiny antennae and unusually elongate appendages than their extant relatives. Although phylogenetic hypotheses have been proposed to clarify the relationships and classification of Mastigitae, morphological structures of most genera remain undescribed. They are reviewed in the present synopsis, with detailed descriptions and illustrations of adult structures of all extant genera (Ablepton, Leptomastax, Taurablepton, Mastigus, Palaeostigus, Stenomastigus, Leptochromus, Clidicus and Papusus), with a brief review of known larval forms and fossils. Novel ecological data are given, with emphasis on habitat preferences and feeding behavior. The 'springtail trap' hypothesis for the spiny antennae of Mastigini is rejected, based on field observations and laboratory experiments. For the first time, details of feeding for Palaeostigus and Leptomastax are described. A checklist of species is given, and the main problems related to the classification, phylogeny and ecology of Mastigitae are discussed. 

scholarly journals Hagfish from the Cretaceous Tethys Sea and a reconciliation of the morphological–molecular conflict in early vertebrate phylogeny

2019 ◽  
Vol 116 (6) ◽  
pp. 2146-2151 ◽  
Author(s):  
Tetsuto Miyashita ◽  
Michael I. Coates ◽  
Robert Farrar ◽  
Peter Larson ◽  
Phillip L. Manning ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Morphological Data ◽  
Vertebrate Lineage ◽  
Crown Group ◽  
Tethys Sea ◽  
History Of ◽  
Animal Phylogeny ◽  
Early Late

Hagfish depart so much from other fishes anatomically that they were sometimes considered not fully vertebrate. They may represent: (i) an anatomically primitive outgroup of vertebrates (the morphology-based craniate hypothesis); or (ii) an anatomically degenerate vertebrate lineage sister to lampreys (the molecular-based cyclostome hypothesis). This systematic conundrum has become a prominent case of conflict between morphology- and molecular-based phylogenies. To date, the fossil record has offered few insights to this long-branch problem or the evolutionary history of hagfish in general, because unequivocal fossil members of the group are unknown. Here, we report an unequivocal fossil hagfish from the early Late Cretaceous of Lebanon. The soft tissue anatomy includes key attributes of living hagfish: cartilages of barbels, postcranial position of branchial apparatus, and chemical traces of slime glands. This indicates that the suite of characters unique to living hagfish appeared well before Cretaceous times. This new hagfish prompted a reevaluation of morphological characters for interrelationships among jawless vertebrates. By addressing nonindependence of characters, our phylogenetic analyses recovered hagfish and lampreys in a clade of cyclostomes (congruent with the cyclostome hypothesis) using only morphological data. This new phylogeny places the fossil taxon within the hagfish crown group, and resolved other putative fossil cyclostomes to the stem of either hagfish or lamprey crown groups. These results potentially resolve the morphological–molecular conflict at the base of the Vertebrata. Thus, assessment of character nonindependence may help reconcile morphological and molecular inferences for other major discords in animal phylogeny.

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