scholarly journals The phylogeny and taxonomic status of the Chlorocystini (sensu stricto) (Homoptera, Tibicinidae)

1995 ◽  
Vol 65 (4) ◽  
pp. 201-231 ◽  
Author(s):  
A.J. de Boer
Keyword(s):  
Computer Program ◽  
Computer Analysis ◽  
Phylogenetic Reconstruction ◽  
Taxonomic Status ◽  
Sister Group ◽  
Sensu Stricto ◽  
Complete Data ◽  
Data Matrix ◽  
A Posteriori

The “Baeturia and related genera complex”, as defined earlier (De Boer, 1990) by shared aedeagal characters, is identified as the tribe Chlorocystini (sensu stricto). The Prasiini (sensu stricto) are identified as the sister group of the Chlorocystini (sensu stricto), while the genus Muda is recognized as the nearest outgroup. The phylogeny and biogeography of the sister group and outgroup is briefly discussed. Baeturia kuroiwae Matsumura is transferred to the genus Muda. A phylogenetic reconstruction of all 147 species of the Chlorocystini (sensu stricto) is presented, based on 154 characters and 409 character states. The computer program PAUP 3.1.1 (Swofford, 1993) was used for analysing the data; the genera Prasia and Muda were used as outgroups in this analysis. The results obtained from the computer analysis were slightly modified a posteriori, favouring some presumably phylogenetically important characters over strongly fluctuating ones. These final modifications were carried out with the aid of the computer program MacClade 3.0 (Maddison & Maddison, 1992). A complete data matrix and a list of characters and character states are given in an appendix; for descriptions and illustrations of these characters one is referred to previous publications.

scholarly journals Morphological and molecular differences between the Amphiamerican populations of Antillesoma (Sipuncula: Antillesomatidae), with the description of a new species

2019 ◽  
Vol 67 (S5) ◽  
pp. S101-S109
Author(s):  
Itzahí Silva-Morales ◽  
Mónica J. López-Aquino ◽  
Valentina Islas-Villanueva ◽  
Fernando Ruiz-Escobar ◽  
J. Rolando Bastida-Zavala
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Genetic Distances ◽  
Likelihood Method ◽  
Tropical Eastern Pacific ◽  
Mexican Pacific ◽  
The Caribbean

Introduction: The sipunculans are a group of marine invertebrates that have been little studied in the tropical eastern Pacific (TEP). Antillesoma antillarum is a species belonging to the monospecific family Antillesomatidae, considered widely distributed in tropical and subtropical localities across the globe. Objective: The main objective of this work was to examine the morphological and molecular differences between specimens from both coasts of tropical America to clarify the taxonomy of this species. Methods: We examined the morphology with material from the Mexican Caribbean and southern Mexican Pacific. To perform molecular analyses, two sequences of the COI molecular marker were obtained from specimens collected in Panteón Beach, Oaxaca, southern Mexican Pacific, and compared with four sequences identified as A. antillarum in GenBank, all of them from different localities. A phylogenetic reconstruction was performed with the maximum likelihood method and genetic distances were calculated with the Kimura 2P model and compared to reference values. Results: The phylogenetic analysis revealed three different lineages of Antillesoma that are well supported by bootstrap values: Antillesoma antillarum sensu stricto from the Caribbean Sea and Florida; a sister group to the one represented by our samples from the Mexican Pacific; and a third group from Thailand. Conclusion: Based on morphological traits and molecular data, Antillesoma mexicanum sp. nov. is described from the Mexican Pacific, differing from A. antillarum in the trunk papillae, color patterns and, additionally, the specimens from the Caribbean attain significantly bigger trunk sizes than the ones Pacific.

scholarly journals Low-Coverage Whole Genomes Reveal the Higher Phylogeny of Green Lacewings

Insects ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 857
Author(s):  
Yuyu Wang ◽  
Ruyue Zhang ◽  
Yunlong Ma ◽  
Jing Li ◽  
Fan Fan ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Sister Group ◽  
Data Matrix ◽  
Limited Sampling ◽  
Green Lacewings ◽  
Whole Genomes ◽  
History Of ◽  
Low Coverage ◽  
Cretaceous Period

Green lacewings are one of the largest families within Neuroptera and are widely distributed all over the world. Many species within this group are important natural predators that are widely used for the biological control of pests in agricultural ecosystems. Several proposed phylogenetic relationships among the three subfamilies of Chrysopidae have been extensively debated. To further understand the higher phylogeny as well as the evolutionary history of Chrysopidae, we newly sequenced and analyzed the low-coverage genomes of 5 species (Apochrysa matsumurae, Chrysopa pallens, Chrysoperla furcifera, Italochrysa pardalina, Nothochrysa sinica), representing 3 subfamilies of Chrysopidae. There are 2213 orthologs selected to reconstruct the phylogenetic tree. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches, based on different data matrices. All the results suggested that Chrysopinae were a monophyletic sister group to the branch Apochrysinae + Nothochrysinae. These results were completely supported, except by the concatenation analyses of the nt data matrix, which suggested that Apochrysinae were a sister group to Chrysopinae + Nothchrysinae. The different topology from the nt data matrix may have been caused by the limited sampling of Chrysopidae. The divergence time showed that Chrysopinae diverged from Apochrysinae + Nothochrysinae during the Early Cretaceous period (144–151 Ma), while Aporchrysinae diverged from Nothochrysinae around 117–133 Ma. These results will improve our understanding of the higher phylogeny of Chrysopidae and lay a foundation for the utilization of natural predators.

scholarly journals Less is more stable: arguing for few names in turtle’s taxonomy

2015 ◽  
Author(s):  
Pedro S. R. Romano
Keyword(s):  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Sensu Stricto ◽  
Botanical Nomenclature ◽  
Crown Group ◽  
Diagnostic Characters ◽  
Less Is More ◽  
Phylogenetic Reconstructions ◽  
Stem Species ◽  
Phylogenetic Nomenclature

Background. Beyond the International Codes of Zoological (ICZN) and Botanical Nomenclature and the PhyloCode, there is an alternative taxonomic system for phylogenetic systematics proposed. This phylogenetic nomenclature suggests the elimination of suprageneric names and the use of negative indexes instead of it. This system of nomenclature has a basic principle to identify clades: the presence of nominal heterobathmy, which is analogous to Hennig's "heterobathmy of characters", but applied to taxa names. Here I argue for an extensive use of heterobathmy as basic criteria to determinate “good” nodes to identify higher level taxa names. Methods. I used a previews published dataset (doi:10.5061/dryad.f2h6r) and ran several searches for Most Parsimonious Trees (MPT) using different search algorithms and assumptions in TNT. After that, I compared the results of different searches, mapped the characters transformations, and calculate the Bremer supports. The results were then compared with the current taxonomy proposed for Pelomedusoides, with emphasis on Bothremydidae. Results. The remarkable divergences with the current taxonomy of Bothremydidae are: (1) Kurmademydini and Bothremydini need to be redefined; (2) Cearachelyini and Galianemys lack diagnostic characters and, therefore, are not monophyletic; and (3) Bothremydidae do not possess common diagnostic characters in all MPT, thus, lacks a well supported heterobathmy with its sister-group, Podocnemidinura (=Pan-Podocnemididae). Moreover, the Infrafamily Bothremydodda has Bremer support of 3. However, given that all bothremydids are extinct, it is impossible to define a panstem clade based on a crown group. The result is an unstable nomenclature with more names than necessary. Discussion. The use of heterobathmy is a center point in Hennig's argumentation for phylogenetic reconstruction. Indeed, it implies the zero length collapsing rule applied to cladistic reconstruction (which is the TNT default option). Nonetheless, ambiguous characters or several equal MPT can imply on phylogenetic reconstructions that lack a consistent heterobathmy (i.e.: a common diagnostic character in the ancestor eidophoront of a given node in all MPT; as is the case of Bothremydidae). A possible solution is to use the suffix “formes” to designate extinct lineages with stem-species when some nodes are not well supported in a given phylogeny. In the example presented here, it would consist on naming ICZN’s Bothremydodda as “Bothremydidae” (sensu stricto) and ICZN’s Bothremydidae (sensu lato, i.e.: including stem-Bothremydidae) as “Bothremydidiformes” and avoid naming each node of the consensus tree unless it has high Bremer support. By taking into account this delimitation criterion, we can propose a more stable and clean taxonomy.

scholarly journals Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data

2019 ◽  
Vol 20 (5) ◽  
pp. 1072 ◽  
Author(s):  
Yuyu Wang ◽  
Xiaofan Zhou ◽  
Liming Wang ◽  
Xingyue Liu ◽  
Ding Yang ◽  
...  
Keyword(s):  
Large Scale ◽  
Gene Selection ◽  
Homogeneous Model ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Data Matrix ◽  
Bootstrap Support ◽  
Heterogeneous Model ◽  
Phylogenomic Analyses ◽  
A Site

Neuropterida is a super order of Holometabola that consists of the orders Megaloptera (dobsonflies, fishflies, and alderflies), Neuroptera (lacewings) and Raphidioptera (snakeflies). Several proposed higher-level relationships within Neuropterida, such as the relationships between the orders or between the families, have been extensively debated. To further understand the evolutionary history of Neuropterida, we conducted phylogenomic analyses of all 13 published transcriptomes of the neuropterid species, as well as of a new transcriptome of the fishfly species Ctenochauliodes similis of Liu and Yang, 2006 (Megaloptera: Corydalidae: Chauliodinae) that we sequenced. Our phylogenomic data matrix contained 1392 ortholog genes from 22 holometabolan species representing six families from Neuroptera, two families from Raphidioptera, and two families from Megaloptera as the ingroup taxa, and nine orders of Holometabola as outgroups. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches under a site-homogeneous model as well as under a site-heterogeneous model. Surprisingly, analyses using the site-homogeneous model strongly supported a paraphyletic Neuroptera, with Coniopterygidae assigned as the sister group of all other Neuropterida. In contrast, analyses using the site-heterogeneous model recovered Neuroptera as monophyletic. The monophyly of Neuroptera was also recovered in concatenation and coalescent-based analyses using genes with stronger phylogenetic signals [i.e., higher average bootstrap support (ABS) values and higher relative tree certainty including all conflicting bipartitions (RTCA) values] under the site-homogeneous model. The present study illustrated how both data selection and model selection influence phylogenomic analyses of large-scale data matrices comprehensively.

scholarly journals Using mitochondrial genomes to infer phylogenetic relationships among the oldest extant winged insects (Palaeoptera)

2017 ◽  
Author(s):  
Sereina Rutschmann ◽  
Ping Chen ◽  
Changfa Zhou ◽  
Michael T. Monaghan
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Data Matrix ◽  
Mitochondrial Genomes ◽  
Sampling Effort ◽  
Reconstruction Method ◽  
Marker Selection ◽  
Phylogenetic Resolution

AbstractPhylogenetic relationships among the basal orders of winged insects remain unclear, in particular the relationship of the Ephemeroptera (mayflies) and the Odonata (dragonflies and damselflies) with the Neoptera. Insect evolution is thought to have followed rapid divergence in the distant past and phylogenetic reconstruction may therefore be susceptible to problems of taxon sampling, choice of outgroup, marker selection, and tree reconstruction method. Here we newly sequenced three mitochondrial genomes representing the two most diverse families of the Ephemeroptera, one of which is a basal lineage of the order. We then used an additional 90 insect mitochondrial genomes to reconstruct their phylogeny using Bayesian and maximum likelihood approaches. Bayesian analysis supported a basal Odonata hypothesis, with Ephemeroptera as sister group to the remaining insects. This was only supported when using an optimized data matrix from which rogue taxa and terminals affected by long-branch attraction were removed. None of our analyses supported a basal Ephemeroptera hypothesis or Ephemeroptera + Odonata as monophyletic clade sister to other insects (i.e., the Palaeoptera hypothesis). Our newly sequenced mitochondrial genomes of Baetis rutilocylindratus, Cloeon dipterum, and Habrophlebiodes zijinensis had a complete set of protein coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. Increased mayfly sampling, removal of problematic taxa, and a Bayesian phylogenetic framework were needed to infer phylogenetic relationships within the three ancient insect lineages of Odonata, Ephemeroptera, and Neoptera. Pruning of rogue taxa improved the number of supported nodes in all phylogenetic trees. Our results add to previous evidence for the Odonata hypothesis and indicate that the phylogenetic resolution of the basal insects can be resolved with more data and sampling effort.

scholarly journals Less is more stable: arguing for few names in turtle’s taxonomy

2015 ◽  
Author(s):  
Pedro S. R. Romano
Keyword(s):  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Sensu Stricto ◽  
Botanical Nomenclature ◽  
Crown Group ◽  
Diagnostic Characters ◽  
Less Is More ◽  
Phylogenetic Reconstructions ◽  
Stem Species ◽  
Phylogenetic Nomenclature

Background. Beyond the International Codes of Zoological (ICZN) and Botanical Nomenclature and the PhyloCode, there is an alternative taxonomic system for phylogenetic systematics proposed. This phylogenetic nomenclature suggests the elimination of suprageneric names and the use of negative indexes instead of it. This system of nomenclature has a basic principle to identify clades: the presence of nominal heterobathmy, which is analogous to Hennig's "heterobathmy of characters", but applied to taxa names. Here I argue for an extensive use of heterobathmy as basic criteria to determinate “good” nodes to identify higher level taxa names. Methods. I used a previews published dataset (doi:10.5061/dryad.f2h6r) and ran several searches for Most Parsimonious Trees (MPT) using different search algorithms and assumptions in TNT. After that, I compared the results of different searches, mapped the characters transformations, and calculate the Bremer supports. The results were then compared with the current taxonomy proposed for Pelomedusoides, with emphasis on Bothremydidae. Results. The remarkable divergences with the current taxonomy of Bothremydidae are: (1) Kurmademydini and Bothremydini need to be redefined; (2) Cearachelyini and Galianemys lack diagnostic characters and, therefore, are not monophyletic; and (3) Bothremydidae do not possess common diagnostic characters in all MPT, thus, lacks a well supported heterobathmy with its sister-group, Podocnemidinura (=Pan-Podocnemididae). Moreover, the Infrafamily Bothremydodda has Bremer support of 3. However, given that all bothremydids are extinct, it is impossible to define a panstem clade based on a crown group. The result is an unstable nomenclature with more names than necessary. Discussion. The use of heterobathmy is a center point in Hennig's argumentation for phylogenetic reconstruction. Indeed, it implies the zero length collapsing rule applied to cladistic reconstruction (which is the TNT default option). Nonetheless, ambiguous characters or several equal MPT can imply on phylogenetic reconstructions that lack a consistent heterobathmy (i.e.: a common diagnostic character in the ancestor eidophoront of a given node in all MPT; as is the case of Bothremydidae). A possible solution is to use the suffix “formes” to designate extinct lineages with stem-species when some nodes are not well supported in a given phylogeny. In the example presented here, it would consist on naming ICZN’s Bothremydodda as “Bothremydidae” (sensu stricto) and ICZN’s Bothremydidae (sensu lato, i.e.: including stem-Bothremydidae) as “Bothremydidiformes” and avoid naming each node of the consensus tree unless it has high Bremer support. By taking into account this delimitation criterion, we can propose a more stable and clean taxonomy.

scholarly journals Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach

2016 ◽  
Vol 283 (1833) ◽  
pp. 20160857 ◽  
Author(s):  
Sarah Lemer ◽  
Vanessa L. González ◽  
Rüdiger Bieler ◽  
Gonzalo Giribet
Keyword(s):  
Phylogenetic Reconstruction ◽  
Strong Support ◽  
Sister Group ◽  
Data Matrix ◽  
Shell Microstructure ◽  
Bayesian Mixture Model ◽  
Bayesian Mixture ◽  
Exact Position ◽  
Adaptive Radiations ◽  
Basal Position

Mussels (Mytilida) are a group of bivalves with ancient origins and some of the most important commercial shellfish worldwide. Mytilida consists of approximately 400 species found in various littoral and deep-sea environments, and are part of the higher clade Pteriomorphia, but their exact position within the group has been unstable. The multiple adaptive radiations that occurred within Pteriomorphia have rendered phylogenetic classifications difficult and uncertainty remains regarding the relationships among most families. To address this phylogenetic uncertainty, novel transcriptomic data were generated to include all five orders of Pteriomorphia. Our results, derived from complex analyses of large datasets from 41 transcriptomes and evaluating possible pitfalls affecting phylogenetic reconstruction (matrix occupancy, heterogeneity, evolutionary rates, evolutionary models), consistently recover a well-supported phylogeny of Pteriomorphia, with the only exception of the most complete but smallest data matrix ( Matrix 3 : 51 genes, 90% gene occupancy). Maximum-likelihood and Bayesian mixture model analyses retrieve strong support for: (i) the monophyly of Pteriomorphia, (ii) Mytilida as a sister group to Ostreida, and (iii) Arcida as sister group to all other pteriomorphians. The basal position of Arcida is congruent with its shell microstructure (solely composed of aragonitic crystals), whereas Mytilida and Ostreida display a combination of a calcitic outer layer with an aragonitic inner layer composed of nacre tablets, the latter being secondarily lost in Ostreoidea.

Review of Eohiodon (Teleostei: Osteoglossomorpha) from western North America, with a phylogenetic reassessment of Hiodontidae

1997 ◽  
Vol 71 (6) ◽  
pp. 1109-1124 ◽  
Author(s):  
Li Guo-Qing ◽  
Mark V. H. Wilson ◽  
Lance Grande
Keyword(s):  
North America ◽  
Sister Group ◽  
Sensu Stricto ◽  
Valid Species ◽  
Western North America ◽  
Extant Species ◽  
The Family ◽  
Fossil Records ◽  
Fossil Genus ◽  
Freshwater Teleosts

Review of recently collected material of Eohiodon from North America suggests that there are two valid species, E. rosei (Hussakof) and E. woodroffi Wilson. Eohiodon falcatus Grande is identical to E. woodruffi in known skeletal features and nearly all meristic features and is treated as a junior synonym of the latter. The fossil genus Eohiodon Cavender differs from Hiodon Lesueur, which is known from both fossil and extant species, in numerous meristic and osteological features. The caudal skeleton in Eohiodon is nearly identical to that in Hiodon.The traditionally accepted Notopteroidei, containing Lycopteridae, Hiodontidae, and Notopteridae, is a polypheletic group. The Asian fossil family Lycopteridae is not more closely related to Hiodontidae than it is to other taxa in the Osteoglossomorpha, but is sister to all other Osteoglossomorpha. The Hiodontiformes sensu stricto, including only the family Hiodontidae, is the sister-group of the Osteoglossiformes. This family is not more closely related to notopterids than to other taxa in Osteoglossiformes. The Notopteridae are most closely related to the Mormyroidea; together they and the fossil family Ostariostomidae constitute the sister-group of the Osteoglossoidei.Fossil records of Hiodontiformes sensu stricto and Notopteroidei indicate a widespread pre-Neogene biogeographic range of these freshwater teleosts, suggesting that extinction must have been involved in the Cenozoic evolution of these two osteoglossomorph sublineages.

Disentangling the Sudanonautes granulatus (Balss, 1929) species complex (Potamoidea: Potamonautidae), with the description of two new freshwater crabs from Nigeria and Côte d’Ivoire, West Africa

Zootaxa ◽  
2021 ◽  
Vol 4948 (2) ◽  
pp. 201-220
Author(s):  
NEIL CUMBERLIDGE ◽  
PIERRE A. MVOGO NDONGO ◽  
PAUL F. CLARK
Keyword(s):  
Cote D'ivoire ◽  
Côte D’Ivoire ◽  
Central Africa ◽  
Taxonomic Status ◽  
Sensu Stricto ◽  
Morphological Evidence ◽  
Cote D’Ivoire ◽  
Distribution Maps ◽  
Freshwater Crabs ◽  
Côte D'ivoire

The taxonomic status of the widely distributed West and Central African freshwater crab Sudanonautes granulatus (Balss, 1929) sensu lato is revised in the light of improved morphological evidence which indicates that this taxon is a complex comprising at least 4 species: Sudanonautes granulatus (Balss, 1929) sensu stricto from Togo, S. koudougou n. sp. from Côte d’Ivoire, S. umaji n. sp. from Nigeria, and S. tiko from Cameroon, Nigeria, and Bioko. Diagnoses, illustrations and distribution maps are provided for these species and they are compared with congeners from West and Central Africa. 

Rediagnosis of the squat lobster genus Gastroptychus Caullery, 1896, with a new genus Sternostylus and a new family Sternostylidae (Crustacea: Decapoda: Anomura: Chirostyloidea)

Zootaxa ◽  
2018 ◽  
Vol 4524 (1) ◽  
pp. 77 ◽  
Author(s):  
KEIJI BABA ◽  
SHANE T. AHYONG ◽  
KAREEN E. SCHNABEL
Keyword(s):  
Type Species ◽  
Anterior Margin ◽  
New Genus ◽  
Sister Group ◽  
Sensu Stricto ◽  
The Other ◽  
Squat Lobster ◽  
Terminal Spine ◽  
New Family ◽  
Left And Right

The chirostyloidean squat lobster genus Gastroptychus Caullery, 1896 is revised and is split into two genera: Gastroptychus sensu stricto (type species, Ptychogaster spinifer A. Milne-Edwards, 1880) and Sternostylus new genus (type species, Ptychogaster formosus Filhol, 1884). Gastroptychus sensu stricto, is restricted to nine species with a sternal plastron, at sternite 3, abruptly demarcated from the preceding sternites (excavated sternum) by a distinct step forming a well-defined transverse or concave anterior margin at the articulation with maxillipeds 3, the maxillipeds 3 widely separated, with the distal parts accommodated in the excavated sternum between the left and right maxillipeds 3 when folded, and the P2–4 dactyli with the terminal spine demarcated by a suture. Sternostylus new genus, represented by 12 species, has the sternite 3 anteriorly bluntly produced medially and steeply sloping anterodorsally to the anterior sternite, with a pair of spines directly behind the anterior margin, the left and right maxillipeds 3 adjacent, and the P2–4 dactyli ending in an indistinctly demarcated corneous spine. The above-mentioned characters of Gastroptychus are consistent with Chirostylidae sensu stricto. Published molecular phylogenies indicate, however, that Sternostylus is the sister group to all the other Chirostylidae, and is designated the type genus of a new family, Sternostylidae. 

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