Another one bites the dust: taxonomic sampling of a key genus in phylogenomic datasets reveals more non-monophyletic groups in traditional scorpion classification

2020 ◽  
Vol 34 (2) ◽  
pp. 133
Author(s):  
Carlos E. Santibáñez-López ◽  
Andrés A. Ojanguren-Affilastro ◽  
Prashant P. Sharma
Keyword(s):  
Gene Tree ◽  
Sister Group ◽  
Morphological Characters ◽  
Incertae Sedis ◽  
Transcriptomic Sequencing ◽  
The Family ◽  
The Status ◽  
Significant Gene ◽  
Phylogenomic Analyses ◽  
Likelihood Mapping

Historically, morphological characters have been used to support the monophyly, composition, and phylogenetic relationships of scorpion families. Although recent phylogenomic analyses have recovered most of these traditional higher-level relationships as non-monophyletic, certain key taxa have yet to be sampled using a phylogenomic approach. Salient among these is the monotypic genus Caraboctonus Pocock,1893, the type species of the family Caraboctonidae Kraepelin, 1905. Here, we examined the putative monophyly and phylogenetic placement of this family, sampling the library of C. keyserlingi Pocock, 1893 using high throughput transcriptomic sequencing. Our phylogenomic analyses recovered Caraboctonidae as polyphyletic due to the distant placement of the genera Caraboctonus and Hadrurus Thorell, 1876. Caraboctonus was stably recovered as the sister-group of the monotypic family Superstitioniidae Stahnke, 1940, whereas Hadrurus formed an unstable relationship with Uroctonus Thorell, 1876and Belisarius Simon, 1879. Four-cluster likelihood mapping revealed that the instability inherent to the placement of Hadrurus, Uroctonus and Belisarius was attributable to significant gene tree conflict in the internodes corresponding to their divergences. To redress the polyphyly of Caraboctonidae, the following systematic actions have been taken: (1) the family Caraboctonidae has been delimited to consist of 23 species in the genera Caraboctonus and Hadruroides Pocock, 1893; (2) Caraboctonidae, previously included in the superfamily Iuroidea Thorell, 1876 or as incertae sedis, is transferred to the superfamily Caraboctonoidea (new rank); (3) the superfamily Hadruroidea (new rank) is established and the status of Hadrurinae Stahnke, 1973 is elevated to family (Hadruridae new status) including 9 species in the genera Hadrurus and Hoffmannihadrurus Fet & Soleglad, 2004 and (4) we treat Uroctonus and Belisarius as insertae sedis with respect to superfamilial placement. Our systematic actions engender the monophyly of both Iuroidea and Caraboctonidae. Future phylogenomic investigations should target similar taxon-poor and understudied lineages of potential phylogenetic significance, which are anticipated to reveal additional non-monophyletic groups.

The morphology, higher-level phylogeny and classification of the Empidoidea (Diptera)

Zootaxa ◽  
2006 ◽  
Vol 1180 (1) ◽  
pp. 1 ◽  
Author(s):  
BRADLEY J. SINCLAIR ◽  
JEFFREY M. CUMMING
Keyword(s):  
Feeding Habits ◽  
Cladistic Analysis ◽  
Sister Group ◽  
Morphological Characters ◽  
Male And Female ◽  
Ground Plan ◽  
Incertae Sedis ◽  
Higher Taxa ◽  
The Family

A cladistic analysis of the Empidoidea and basal lineages of the Cyclorrhapha, based on morphological characters, confirms the monophyly of both groups as well as that of the                    Eremoneura. The resulting final trees are used to revise the classification of the Empidoidea to include the following five families: Empididae, Hybotidae, Atelestidae (including Nemedininae n. subfam.), Brachystomatidae rev. stat. (comprising the subfamilies Brachystomatinae, Ceratomerinae and Trichopezinae), and Dolichopodidae s.lat. The family Microphoridae is not recognized, and the Microphorinae and Parathalassiinae are assigned to the Dolichopodidae s.lat. The Dolichopodidae s.str. includes 15 subfamilies that were previously recognized within the family. Within the Empidoidea we found support for Atelestidae as the sister group to the Hybotidae and for the monophyly of Parathalassiinae + Dolichopodidae s.str. The Empididae remains poorly defined and the genera Homalocnemis Philippi, Iteaphila Zetterstedt, Anthepiscopus Becker, and Oreogeton Schiner are classified as incertae sedis within the                   Empidoidea. In addition, the following higher taxa are proposed: Symballophthalmini n. tribe, Bicellariini n. tribe, Oedaleinae rev. stat., and Trichininae rev. stat., which are all assigned to the Hybotidae. The genus Sematopoda Collin is tentatively assigned to Trichopezinae, and Xanthodromia Saigusa is transferred from Hemerodromiinae to Brachystomatinae.        All morphological characters are extensively discussed and illustrated, including details of the antennae, mouthparts, internal thoracic structures, wings, and male and female terminalia. In addition, a key to families and unplaced genus groups of the Empidoidea is provided. Feeding habits are also discussed in terms of the empidoid ground plan condition.

scholarly journals Flourishing in subterranean ecosystems: Euro-Mediterranean Plusiocampinae and tachycampoids (Diplura, Campodeidae)

2020 ◽  
Author(s):  
Alberto Sendra ◽  
Dragan Antić ◽  
Pablo Barranco ◽  
Špela Borko ◽  
Erhard Christian ◽  
...  
Keyword(s):  
Organic Matter ◽  
Mediterranean Region ◽  
Body Shape ◽  
Taxonomic Revision ◽  
Terrestrial Ecosystems ◽  
Mediterranean Area ◽  
Sister Group ◽  
Morphological Characters ◽  
Incertae Sedis ◽  
The Family

Diplura is a group of entognathous hexapods, often considered a sister group to insects. They play an important role in recycling organic matter in soil and subterranean terrestrial ecosystems. The Campodeidae is the most diverse family, divided into four subfamilies. The subfamily Plusiocampinae has a subterranean life-style with many species distributed in the Euro-Mediterranean area. The incertae sedis tachycampoids (“lignée Tachycampoïde”) is a group within the family Campodeidae that share with the Plusiocampinae a strong preference for subterranean habitats and several morphological characters, such as slender body shape, elongated appendages, considerable increment in the number of antennomeres and cercal articles, and complexity of sensorial structures. The present monograph provides a taxonomic revision of the subfamily Plusiocampinae and the genera belonging to the tachycampoid lineage from Europe and the Mediterranean region. It comprises detailed morphological descriptions and illustrations together with data on the habitats and distributions of 87 species, 10 subspecies and 11 affinis forms. Seven new species are described among those, namely: Plusiocampa (Plusiocampa) apollo Sendra, Giachino & Vailati sp. nov., P. (P.) chiosensis Sendra & Gasparo sp. nov., P. (P.) dublanskii Sendra & Turbanov sp. nov., P. (P.) hoffmanni Sendra & Paragamian sp. nov., P. (P.) rhea Sendra sp. nov., P. (P.) ternovensis Sendra & Borko sp. nov. and P. (Venetocampa) ferrani Sendra & Delić sp. nov.

The millipede family Nemasomatidae. With the description of a new genus, and a revision of Orinisobates (Diplopoda: Julida)

1985 ◽  
Vol 16 (1) ◽  
pp. 27-67 ◽  
Author(s):  
Henrik Enghoff
Keyword(s):  
United States ◽  
New Genus ◽  
Sister Group ◽  
Eastern United States ◽  
Altai Region ◽  
Separate Genus ◽  
Incertae Sedis ◽  
The Family ◽  
Group Relationships ◽  
Doubtful Species

AbstractThe family Nemasomatidae is redefined to include onty genera with all sterna secondarily free from pleurotergites. Comments are given on the included genera, viz., Antrokoreana, Basoncopus gen. n. (type-species B. filiformis sp. n.) (Kazakhstan), Dasynemasoma, Thalassisobates, Sinostemmiulus, Nemasoma, and Orinisobates. Isobates coiffaiti Demange, 1961 is synonymized with Thalassisobates littoralis (Silvestri, 1903). Orinisobates is revised and shown to include O. soror sp. n. (Kuril Islands), O. microthylax sp. n. (Kamchatka and Siberia), O. gracilis (Verhoeff, 1933) (NW China), O. sibiricus (Gulicka, 1963) (Altai region, Kazakhstan), O. kasakstanus (Lohmander, 1933) (Kazahkstan), O. nigrior (Chamberlin, 1943) (eastern United States), O. utus (Chamberlin, 1912) (northwestern United States), and O. expressus (Chamberlin, 1941) (northwestern United States and adjacent Canada). Mimolene oregona Chambertin, 1941 and M. sectile Loomis & Schmitt, 1971 are synonymized with O. expressus. A possible case of parthenogenesis in O. microthylax is recorded. Evidence is presented for the following sister-group relationships: Antrokoreana + (Basoncopus + (Dasynemasoma + (Thalassisobates + (Sinostemmiulus + (Orinisobates + Nemasoma))))). The position of Basoncopus is uncertain, and O. soror may belong in a separate genus and constitute the sister-group of Orinisohates + Nemasoma. If soror does belong in Orinisobates, it is the sister-group of all its congeners. The American species of Orinisobates are shown probably to constitute a monophyietic group. The family is suggested to have originated in the eastern Palearctic region, Orinisobates having invaded North America via the Bering Bridge. Doubtful species and species erroneously assoiciated with the Nemasomatidae are listed. The genera Okeanobates and Yosidaiulus are excluded from the family and referred to Okeanobatidae stat. n. in superfamily Blaniuloidea. The genera Trichonemasoma, Telsonemasoma, and Chelojulus are also excluded from the Nemasomatidae and relegated to Julida incertae sedis.

scholarly journals A taxonomic revision of the family Harrimaniidae (Hemichordata: Enteropneusta) with descriptions of seven species from the Eastern Pacific

Zootaxa ◽  
2010 ◽  
Vol 2408 (1) ◽  
pp. 1 ◽  
Author(s):  
C. DELAND ◽  
C. B. CAMERON ◽  
K. P. RAO ◽  
W. E. RITTER ◽  
T. H. BULLOCK
Keyword(s):  
New Species ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Eastern Pacific ◽  
Nomen Nudum ◽  
Phylogenetic Hypothesis ◽  
Number Of Species ◽  
Dichotomous Key ◽  
The Family ◽  
The Status

The family Harrimaniidae (Hemichordata: Enteropneusta) is revised on the basis of morphological characters. The number of harrimaniid genera is increased to nine by the addition of Horstia n. gen., Mesoglossus n. gen., Ritteria n. gen. and Saxipendium, a genus previously assigned to the monospecific family Saxipendiidae. The number of species is increased to 34, resulting from the description of five new species from the eastern Pacific — Horstia kincaidi, Mesoglossus intermedius, M. macginitiei, Protoglossus mackiei and Ritteria ambigua. A description is supplied for a sixth harrimaniid species, Stereobalanus willeyi Ritter & Davis, 1904, which previously had the status of a nomen nudum. Four harrimaniids previously assigned to the genus Saccoglossus are transfered to the genus Mesoglossus — M. bournei, M. caraibicus, M. gurneyi and M. pygmaeus, while Saccoglossus borealis is reassigned to the genus Harrimania. Notes on habitat and zoogeography are included for the seven foregoing species and a table of diagnostic characters for existing and new species and a dichotomous key to the enteropneust families and harrimaniid genera are provided. Finally, a phylogenetic hypothesis concerning the Harrimaniidae is postulated, with discussion on the evolution of the group.

scholarly journals Cretaceous origin and repeated tertiary diversification of the redefined butterflies

2011 ◽  
Vol 279 (1731) ◽  
pp. 1093-1099 ◽  
Author(s):  
Maria Heikkilä ◽  
Lauri Kaila ◽  
Marko Mutanen ◽  
Carlos Peña ◽  
Niklas Wahlberg
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Bayesian Approaches ◽  
The Family ◽  
Family Level ◽  
Morphological And Molecular Data

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous–Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis , a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.

scholarly journals Phylogeny of the family Characidae (Teleostei: Characiformes): from characters to taxonomy

2010 ◽  
Vol 8 (3) ◽  
pp. 385-568 ◽  
Author(s):  
Juan Marcos Mirande
Keyword(s):  
Phylogenetic Analysis ◽  
Morphological Characters ◽  
Phylogenetic Hypothesis ◽  
Phylogenetic Information ◽  
Neotropical Fishes ◽  
Incertae Sedis ◽  
The Family ◽  
Taxonomic Implications

The family Characidae is the most diverse among Neotropical fishes. Systematics of this family are mainly based on pre-cladistic papers, and only recently a phylogenetic hypothesis for Characidae was proposed by the author. That phylogeny was based on 360 morphological characters studied for 160 species, including representatives of families related to Characidae. This paper is based on that phylogenetic analysis, with the analyzed characters described herein and documented, accompanied by comparisons of their definition and coding in previous papers. Synapomorphies of each node of the proposed phylogeny are listed, comparisons with previous classifications provided, and autapomorphies of the analyzed species listed. Taxonomic implications of the proposed classification and the position of the incertae sedis genera within Characidae are discussed. A discussion of the phylogenetic information of the characters used in the classical systematics of the Characidae is provided.

The Idoteidae (Crustacea: Isopoda: Valvifera) of the shallow waters of the northeastern North Pacific Ocean

1990 ◽  
Vol 68 (12) ◽  
pp. 2649-2687 ◽  
Author(s):  
F. Rafi ◽  
Diana R. Laubitz
Keyword(s):  
North Pacific ◽  
North Pacific Ocean ◽  
Morphological Characters ◽  
Generic Level ◽  
Additional Species ◽  
The Family ◽  
Juan De Fuca ◽  
The Status ◽  
Juan De Fuca Strait ◽  
Systematic Importance

The distribution of the northeastern North Pacific Idoteidae reflects the general eurytopy in the shallow marine environment of the component species. The family is represented by four genera and 20 species in the region between Juan de Fuca Strait, Washington, and Prince William Sound, Alaska. Collections studied from this area contained 16 species of idoteids, of which 3 (Idotea (Pentidotea) recta, Synidotea cornuta, and S. minuta) are new; the new species are fully illustrated and described. The status of nine additional species recorded in the literature from the area is discussed, and four of them are diagnosed and included in the keys. The morphological characters of the four genera were examined in detail and their systematic importance is discussed. All the appendages surveyed showed differences at least at the generic level.

scholarly journals Restructuring the Ancorabolidae Sars (Copepoda, Harpacticoida) and Cletodidae T. Scott, with a new phylogenetic hypothesis regarding the relationships of the Laophontoidea T. Scott, Ancorabolidae and Cletodidae

2020 ◽  
Vol 96 (2) ◽  
pp. 455-498
Author(s):  
Kai Horst George
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Morphological Characteristics ◽  
Sister Group ◽  
Morphological Characters ◽  
Sister Group Relationship ◽  
Phylogenetic Hypothesis ◽  
The Family ◽  
Swimming Leg

Uncovering the systematics of CopepodaHarpacticoida, the second-most abundant component of the meiobenthos after Nematoda, is of major importance for any further research dedicated especially to ecological and biogeographical approaches. Based on the evolution of the podogennontan first swimming leg, a new phylogenetic concept of the Ancorabolidae Sars and Cletodidae T. Scott sensu Por (Copepoda, Harpacticoida) is presented, using morphological characteristics. It confirms the polyphyletic status of the Ancorabolidae and its subfamily Ancorabolinae Sars and the paraphyletic status of the subfamily Laophontodinae Lang. Moreover, it clarifies the phylogenetic relationships of the so far assigned members of the family. An exhaustive phylogenetic analysis was undertaken using 150 morphological characters, resulting in the establishment of a now well-justified monophylum Ancorabolidae. In that context, the Ancorabolus-lineage sensu Conroy-Dalton and Huys is elevated to sub-family rank. Furthermore, the membership of Ancorabolina George in a rearranged monophylum Laophontodinae is confirmed. Conversely, the Ceratonotus-group sensu Conroy-Dalton is transferred from the hitherto Ancorabolinae to the Cletodidae. Within these, the Ceratonotus-group and its hypothesised sister-group Cletodes Brady are combined to form a monophyletic subfamily Cletodinae T. Scott, subfam. nov. Consequently, it was necessary to restructure the Ancorabolidae, Ancorabolinae and Laophontodinae and extend the Cletodidae to include the displacement and exclusion of certain taxa. Moreover, comparison of the Ancorabolidae, Cletodidae, Laophontoidea and other Podogennonta shows that the Ancorabolidae and Cletodidae form sister-groups in a monophylum Cletodoidea Bowman and Abele, which similarly has a sister-group-relationship with the Laophontoidea T. Scott. According to the present study, both taxa constitute a derived monophylum within the Podogennonta Lang.

scholarly journals A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

2021 ◽  
Author(s):  
Simon Crameri ◽  
Simone Fior ◽  
Stefan Zoller ◽  
Alex Widmer
Keyword(s):  
Biological Diversity ◽  
Gene Tree ◽  
General Purpose ◽  
Ecological Genetics ◽  
Bioinformatics Pipeline ◽  
Genetic Changes ◽  
Tropical Biodiversity ◽  
Target Capture ◽  
The Family ◽  
Phylogenomic Analyses

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macro-evolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots, ii) scaling the numbers of individuals analyzed and loci sequenced, and iii) building tools for reproducible bioinformatic analyses of such datasets. To address these challenges, we developed a set of target capture probes for phylogenomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built a general-purpose bioinformatics pipeline. Phylogenomic analyses of Dalbergia species from Madagascar yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatics resources will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

scholarly journals The phylogeny of the Schistosomatidae based on three genes with emphasis on the interrelationships of Schistosoma Weinland, 1858

Parasitology ◽  
2003 ◽  
Vol 126 (3) ◽  
pp. 203-224 ◽  
Author(s):  
A. E. LOCKYER ◽  
P. D. OLSON ◽  
P. ØSTERGAARD ◽  
D. ROLLINSON ◽  
D. A. JOHNSTON ◽  
...  
Keyword(s):  
Ribosomal Subunit ◽  
Good Deal ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Small Subunit ◽  
Small Subunit Rrna ◽  
Asian Origin ◽  
The Family ◽  
Veterinary Importance

Schistosomes are digenean flukes, parasitic of birds, mammals and crocodiles. The family Schistosomatidae contains species of considerable medical and veterinary importance, which cause the disease schistosomiasis. Previous studies, both morphological and molecular, which have provided a good deal of information on the phylogenetics of this group, have been limited in the number of species investigated or the type or extent of molecular data used. This paper presents the most comprehensive phylogeny to date, based on the sequences of 3 genes, complete ribosomal small subunit rRNA and large ribosomal subunit rRNA, and mitochondrial cytochrome oxidase 1, sequenced from 30 taxa including at least 1 representative from 10 of the 13 known genera of the Schistosomatidae and 17 of the 20 recognized Schistosoma species. The phylogeny is examined using morphological characters, intermediate and definitive host associations and biogeography. Theories as to the origins and spread of Schistosoma are also explored. The principal findings are that Ornithobilharzia and Austrobilharzia form a sister group to the Schistosoma; mammalian schistosomes appear paraphyletic and 2 Trichobilharzia species, T. ocellata and T. szidati, seem to be synonymous. The position of Orientobilharzia within the Schistosoma is confirmed, as is an Asian origin for the Schistosoma, followed by subsequent dispersal through India and Africa.

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