Molecular evidence for non-monophyly of the pinnotheroid crabs (Crustacea : Brachyura : Pinnotheroidea), warranting taxonomic reappraisal

2016 ◽  
Vol 30 (1) ◽  
pp. 1 ◽  
Author(s):  
Emma Palacios Theil ◽  
José A. Cuesta ◽  
Darryl L. Felder
Keyword(s):  
Molecular Phylogeny ◽  
Genetic Markers ◽  
Molecular Genetic ◽  
The Other ◽  
Molecular Evidence ◽  
Generic Level ◽  
Molecular Analyses ◽  
Histone 3 ◽  
The Family ◽  
Molecular Studies

The crabs of the family Pinnotheridae are well known as commensals or parasites, mainly of molluscs and tubeworms. The phylogeny of the group, however, is poorly understood, with preliminary morphological and molecular studies questioning its monophyly. Here we used molecular genetic markers (16S, 12S mitochondrial; histone 3 nuclear) to infer a phylogeny for the family Pinnotheridae De Haan, 1833 to reevaluate the phylogeny and systematics at the level of its subfamilies and genera. Our molecular phylogeny indicated that Parapinnixa cortesi Thoma, Heard, & Vargas, 2005, Parapinnixa hendersoni Rathbun, 1918, Pinnotherelia laevigata H. Milne Edwards & Lucas, 1844, Sakaina yokoyai (Glassell, 1933), Tetrias fischerii (A. Milne-Edwards, 1867) and Tetrias scabripes Rathbun, 1898 should be removed from the family Pinnotheridae, while composition of the present subfamilies, Pinnotherinae De Haan, 1833 and Pinnothereliinae Alcock, 1900, must be revised. At generic level, Clypeasterophilus Campos, 1990, Dissodactylus Smith, 1870, Fabia Dana, 1851, Nepinnotheres Manning, 1993 and Pinnixa White, 1846 were not monophyletic in our analyses. With the exclusion of Pinnotherelia from Pinnotheridae, remaining species of Pinnothereliinae are assigned to Pinnixinae Števčić, 2005, a new subfamily based upon revision and elevation of rank for the tribe Pinnixini Števčić, 2005. In addition, we restructure membership of the subfamily Pinnotherinae and propose Pinnixulalinae, subfam. nov. to accommodate species that were excluded by molecular analyses from the other two subfamilies. These have a firm, wider-than-long carapace with clearly defined regions, strong legs that are usually tuberculate and very setose, and a third maxilliped with an elongate ischiomerus in which the ischium and merus may or may not be indistinguishably fused. Our analyses included 169 pinnotherid exemplars, representing almost half of the genera and about a quarter of the species presently recognised for the family. The relationships within and among some taxa are resolved to greater or lesser extent and the phylogenetic biodiversity of pinnotherid crabs is revealed. However, future publications will most likely result in a further increase in the number of taxa.

A REVISED GENERIC SYNOPSIS OF HYACINTHACEAE IN SUB-SAHARAN AFRICA, BASED ON MOLECULAR EVIDENCE, INCLUDING NEW COMBINATIONS AND THE NEW TRIBE PSEUDOPROSPEREAE

2003 ◽  
Vol 60 (3) ◽  
pp. 533-568 ◽  
Author(s):  
J. C. MANNING ◽  
P. GOLDBLATT ◽  
M. F. FAY
Keyword(s):  
Phylogenetic Analysis ◽  
Sub Saharan Africa ◽  
Molecular Evidence ◽  
New Combinations ◽  
Generic Level ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Single Genus ◽  
New Tribe ◽  
Sub Saharan

A revised generic synopsis of sub-Saharan Hyacinthaceae is presented, based on a molecular phylogenetic analysis of the family. Generic rank is accorded only to reciprocally monophyletic clades that can be distinguished by recognizable morphological discontinuities, thereby permitting an appropriate generic assignment of species not included in the analysis. Three subfamilies are recognized within the region. Subfamily Ornithogaloideae, characterized by flattened or angular seeds with tightly adhering testa, is considered to include the single genus Ornithogalum, which is expanded to include the genera Albuca, Dipcadi, Galtonia, Neopatersonia and Pseudogaltonia. Recognizing any of these segregates at generic level renders the genus Ornithogalum polyphyletic, while subdivision of Ornithogalum into smaller, morphologically distinguishable segregates in order to preserve the monophyly of each is not possible. Subfamily Urgineoideae, characterized by flattened or winged seeds with brittle, loosely adhering testa, comprises the two mainland African genera Bowiea and Drimia. The latter is well circumscribed by its deciduous, short-lived perianth and includes the previously recognized genera Litanthus, Rhadamanthus, Schizobasis and Tenicroa. The monotypic Madagascan Igidia is provisionally included in the subfamily as a third genus on the basis of its seeds, pending molecular confirmation of its relationships. Subfamily Hyacinthoideae resolves into three clades, distinguished as tribes Hyacintheae (strictly northern hemisphere and not treated further), Massonieae and Pseudoprospereae tribus nov. Full descriptions and a key to their identification are provided for all genera. New combinations reflecting the generic circumscriptions adopted here are made for most African and all Indian and Madagascan species.

scholarly journals Sixty Years with the Chrysobalanaceae

2020 ◽  
Author(s):  
Ghillean T. Prance
Keyword(s):  
Economic Botany ◽  
Field Studies ◽  
Molecular Evidence ◽  
New Techniques ◽  
Conservation Ecology ◽  
The Past ◽  
New Findings ◽  
The Family ◽  
Molecular Studies ◽  
Economic Use

AbstractA review is given of the studies of Ghillean Prance and associates on the Chrysobalanaceae over the past sixty years. This has focussed on defining the generic boundaries in the family and on monographic work with a worldwide approach to this pantropical family. The importance of field studies for work on monographs and Floras is emphasized. Monographs are still the basis for much work on conservation, ecology and economic botany and are needed as a foundation for molecular studies. The importance of being open to experimenting with new techniques and as a result being willing to change the taxonomy in accordance with new findings is demonstrated and emphasized. The twelve genera of the Chrysobalanaceae at the beginning of this career-long study have now increased to twenty-eight in order to present a much better monophyletic and evolutionary arrangement based on recent molecular evidence. In particular it was necessary to divide and rearrange the originally large genera Parinari and Licania into a number of smaller segregate genera. All known species were included in a worldwide monograph published in 2003. A brief review of the economic use for the family is given.

scholarly journals Debating phylogenetic relationships of the scleractinian Psammocora: molecular and morphological evidences

2007 ◽  
Vol 76 (1) ◽  
pp. 35-54 ◽  
Author(s):  
Francesca Benzoni ◽  
Fabrizio Stefani ◽  
Jaroslaw Stolarski ◽  
Michel Pichon ◽  
Guillaume Mitta ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Genetic Distances ◽  
The Other ◽  
Congeneric Species ◽  
Genetic Affinity ◽  
Phylogenetic Structure ◽  
Skeletal Structures ◽  
The Family

The phylogenetic relationships of the scleractinian genus Psammocora with the other genera traditionally included in the family Siderastreidae and some Fungiidae are assessed based on combined skeletal and molecular data. P. explanulata differs from the other examined congeneric species (P. contigua, P. digitata, P. nierstraszi , P. profundacella, P. superficialis, and P. stellata) in possessing interstomatous septa between adult corallites, costae, and in having continuous buttress-like structures joining septal faces (i.e., fulturae) which typically occur in fungiids. These characters are shared with Coscinaraea wellsi but not with the remainder of the examined siderastreids (the congeneric C. columna, and Anomastraea irregularis, Horastrea indica, Pseudosiderastrea tayamai, Siderastrea savignyana) whose septa are interconnected by typical synapticulae. Most of the examined species form septa with distinct transverse groups of centers of calcification, a biomineralization pattern typical of the Robusta clade. The observations on skeletal structures corroborate the results of the ITS2 and 5.8S molecular phylogeny. C. wellsi and P. explanulata are phylogenetically very close to each other and show closer genetic affinity with the examined Fungiidae (Halomitra pileus, Herpolitha limax, Fungia paumotensis, and Podabacia crustacea) than with the other species in the genera Psammocora and Coscinaraea, or with any other siderastreid. Our results show that neither Psammocora nor Coscinaraea are monophyletic genera. The high genetic distances between the species of Siderastreidae, especially between Pseudosiderastrea tayamai and Siderastrea savignyana on one side and the other genera on the other, suggest a deep divergence in the phylogenetic structure of the family.

On the nomenclature of Bathyergidae and Fukomys n. gen. (Mammalia: Rodentia)

Zootaxa ◽  
2006 ◽  
Vol 1142 (1) ◽  
pp. 51-55 ◽  
Author(s):  
DIETER KOCK ◽  
COLLEEN M. INGRAM ◽  
LAURENCE J. FRABOTTA ◽  
RODNEY L. HONEYCUTT ◽  
HYNEK BURDA
Keyword(s):  
Literature Review ◽  
Phylogenetic Relationships ◽  
Species Group ◽  
Junior Synonym ◽  
Molecular Evidence ◽  
Generic Level ◽  
The Family ◽  
Taxonomic History ◽  
History Of ◽  
Subsequent Literature

Recently, in an examination of the phylogenetic relationships among the mole-rats of the family Bathyergidae (Mammalia: Rodentia), Ingram et al. (2004) documented molecular evidence for the recognition of the Cryptomys mechowii species group at the generic level and resurrected the name Coetomys Gray, 1864 for this group. Subsequent literature review revealed that Coetomys is not available to this species group, being a junior synonym of Cryptomys Gray, 1864. Here, we describe and diagnose Fukomys genus novum. In addition, we discuss the taxonomic history of this group in an attempt to reduce the nomenclatural confusion that has plagued studies of the Bathyergidae for over a century.

scholarly journals Molecular evidence and marine snake origins

2005 ◽  
Vol 1 (2) ◽  
pp. 227-230 ◽  
Author(s):  
Michael S.Y Lee
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Morphological Data ◽  
Molecular Evidence ◽  
Gene Sequences ◽  
Molecular Analyses ◽  
Marine Origin ◽  
Molecular Tree

A molecular phylogeny was used to refute the marine scenario for snake origins. Nuclear gene sequences suggested that snakes are not closely related to living varanid lizards, thus also apparently contradicting proposed relationships between snakes and marine mosasaurs (usually considered to be varanoids). However, mosasaurs share derived similarities with both snakes and living varanids. A reanalysis of the morphological data suggests that, if the relationships between living taxa are constrained to the proposed molecular tree, with fossil forms allowed to insert in their optimal positions within this framework, mosasaurs cluster with snakes rather than with varanids. Combined morphological and molecular analyses also still unite marine lizards with snakes. Thus, the molecular data do not refute the phylogenetic evidence for a marine origin of snakes.

Molecular evidence for the assignment of the Cameroonian freshwater crab genus Louisea Cumberlidge, 1994, to the Afrotropical subfamily Potamonautinae Bott, 1970 (Crustacea: Potamoidea: Potamonautidae)

Zootaxa ◽  
2017 ◽  
Vol 4286 (3) ◽  
pp. 439 ◽  
Author(s):  
PIERRE A. MVOGO NDONGO ◽  
NEIL CUMBERLIDGE ◽  
THEODOR S. POETTINGER ◽  
THOMAS VON RINTELEN ◽  
JOSEPH L. TAMESSE ◽  
...  
Keyword(s):  
East Africa ◽  
Arabian Peninsula ◽  
Sub Saharan Africa ◽  
Molecular Evidence ◽  
Freshwater Crab ◽  
Continental Islands ◽  
The Family ◽  
Molecular Studies ◽  
Sub Saharan ◽  
Zoogeographical Region

The family Potamonautidae Bott, 1970, currently comprises 19 genera assigned to two subfamilies (Potamonautinae Bott, 1970, and Deckeniinae Hilgendorf, 1869) based on morphological and molecular studies (Cumberlidge 1999; Daniels et al. 2006a, 2015; Cumberlidge et al. 2008; Cumberlidge & Ng 2009). All members of this family are endemic to the Afrotropical zoogeographical region that includes most of continental Africa plus the continental islands of Madagascar, the granitic Seychelles, Socotra, and the southern Arabian Peninsula. Seven genera from sub-Saharan Africa are presently assigned to Potamonautinae (see Cumberlidge et al. 2008; Daniels et al. 2015): Erimetopus Rathbun, 1894, Liberonautes Bott, 1955, Louisea Cumberlidge, 1994, Potamonautes Bott, 1970, Potamonemus Cumberlidge & Clark, 1992, Sudanonautes Bott, 1955, and Platythelphusa A. Milne-Edwards, 1887. Twelve genera from West and East Africa, Seychelles, and Madagascar are assigned to Deckeniinae (see Cumberlidge et al. 2008; Meyer et al. 2014; Daniels et al. 2015): Deckenia Hilgendorf, 1869, Seychellum Ng, Števčić & Pretzmann, 1995, Globonautes Bott, 1959, Afrithelphusa Bott, 1969, Boreas Cumberlidge & Sternberg, 2002, Foza Reed & Cumberlidge, 2006a, Hydrothelphusa A. Milne-Edwards, 1872, Madagapotamon Bott, 1965, Malagasya Cumberlidge & Sternberg, 2002, Marojejy Cumberlidge, Boyko & Harvey, 2000, Skelosophusa Ng & Takeda, 1994, and Glabrithelphusa Meyer, Cumberlidge & Koppin, 2014. 

Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses

Phytotaxa ◽  
2022 ◽  
Vol 531 (1) ◽  
pp. 1-17
Author(s):  
WICHARUJ TONGKHAM ◽  
SUPALAK PUMIKONG ◽  
NUTTHA POTAPOHN ◽  
WEENUN BUNDITHYA
Keyword(s):  
Rough Surface ◽  
Molecular Analysis ◽  
Molecular Evidence ◽  
Northern Thailand ◽  
Molecular Analyses ◽  
Yellow Color ◽  
The Family ◽  
Slipper Orchid ◽  
Aflp Technique

A new endemic slipper orchid in the family Orchidaceae from Northern Thailand was described according to morphological and molecular analyses. Morphological information specifies the new slipper orchid Paphiopedilum charlesworthii var. lannaense to be similar to Paphiopedilum charlesworthii (Rolfe) Pfitzer 1895, with the exception of its staminode being obovate-obcordate with yellow color, glittery and rough surface. Molecular analysis by AFLP technique indicates that Paphiopedilum charlesworthii var. lannaense can be included as a member of section Paphiopedilum and is closely related to Paphiopedilum coccineum Perner, H. & Herrmann, R. (2000) (syn. Paphiopedilum barbigerum var. coccineum), from which it differs morphologically by dorsal sepal and petal characters. The morphological and molecular evidence supported that Paphiopedilum charlesworthii var. lannaense is a new slipper orchid in the genus Paphiopedilum (Cypripedioideae, Orchidaceae).

scholarly journals Reclassification of Pterulaceae Corner (Basidiomycota: Agaricales) introducing the ant-associated genus Myrmecopterula gen. nov., Phaeopterula Henn. and the corticioid Radulomycetaceae fam. nov.

2019 ◽  
Author(s):  
Caio A. Leal-Dutra ◽  
Gareth W. Griffith ◽  
Maria Alice Neves ◽  
David J. McLaughlin ◽  
Esther G. McLaughlin ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Type Specimen ◽  
The Other ◽  
Morphological Data ◽  
New Combinations ◽  
Ant Nests ◽  
The Family ◽  
Molecular Studies ◽  
Molecular Investigation ◽  
The Relationship

ABSTRACTPterulaceae was formally proposed to group six coralloid and dimitic genera [Actiniceps (=Dimorphocystis), Allantula, Deflexula, Parapterulicium, Pterula and Pterulicium]. Recent molecular studies have shown that some of the characters currently used in Pterulaceae Corner do not distinguish the genera. Actiniceps and Parapterulicium have been removed and a few other resupinate genera were added to the family. However, none of these studies intended to investigate the relationship between Pterulaceae genera. In this study, we generated 278 sequences from both newly collected and fungarium samples. Phylogenetic analyses support by morphological data allowed a reclassification of Pterulaceae where we propose the introduction of Myrmecopterula gen. nov. and Radulomycetaceae fam. nov., the reintroduction of Phaeopterula, the synonymisation of Deflexula in Pterulicium and 51 new combinations. Pterula is rendered polyphyletic requiring a reclassification; thus, it is split into Pterula, Myrmecopterula gen. nov., Pterulicium and Phaeopterula. Deflexula is recovered as paraphyletic alongside several Pterula species and Pterulicium, and is sunk into the latter genus. Phaeopterula is reintroduced to accommodate species with darker basidiomes. The neotropical Myrmecopterula gen. nov. forms a distinct clade adjacent to Pterula, and most members of this clade are associated with active or inactive attine ant nests. The resupinate genera Coronicium and Merulicium are recovered in a strongly supported clade close to Pterulicium. The other resupinate genera previously included in Pterulaceae, and which form basidiomes lacking cystidia and with monomitic hyphal structure (Radulomyces, Radulotubus and Aphanobasidium), are reclassified into Radulomycetaceae fam. nov. Allantula is still an enigmatic piece in this puzzle known only from the type specimen that requires molecular investigation. A key for the genera of Pterulaceae and Radulomycetaceae fam. nov. is provided here.

scholarly journals New Data Define the Molecular Phylogeny and Taxonomy of Four Freshwater Suctorian Ciliates With Redefinition of Two Families Heliophryidae and Cyclophryidae (Ciliophora, Phyllopharyngea, Suctoria)

2021 ◽  
Vol 12 ◽  
Author(s):  
Mingzhen Ma ◽  
Yuqing Li ◽  
Qingxiang Yuan ◽  
Xuetong Zhao ◽  
Khaled A. S. Al-Rasheid ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
Freshwater Lake ◽  
The Other ◽  
Sufficient Evidence ◽  
Rdna Sequences ◽  
The Family ◽  
Molecular Phylogenetic

Four suctorian ciliates, Cyclophrya magna Gönnert, 1935, Peridiscophrya florea (Kormos & Kormos, 1958) Dovgal, 2002, Heliophrya rotunda (Hentschel, 1916) Matthes, 1954 and Dendrosoma radians Ehrenberg, 1838, were collected from a freshwater lake in Ningbo, China. The morphological redescription and molecular phylogenetic analyses of these ciliates were investigated. Phylogenetic analyses inferred from SSU rDNA sequences show that all three suctorian orders, Endogenida, Evaginogenida, and Exogenida, are monophyletic and that the latter two clusters as sister clades. The newly sequenced P. florea forms sister branches with C. magna, while sequences of D. radians group with those from H. rotunda within Endogenida. The family Heliophryidae, which is comprised of only two genera, Heliophrya and Cyclophrya, was previously assigned to Evaginogenida. There is now sufficient evidence, however, that the type genus Heliophrya reproduces by endogenous budding, which corresponds to the definitive feature of Endogenida. In line with this and with the support of molecular phylogenetic analyses, we therefore transfer the family Heliophryidae with the type genus Heliophrya to Endogenida. The other genus, Cyclophrya, still remains in Evaginogenida because of its evaginative budding. Therefore, combined with morphological and phylogenetic analysis, Cyclophyidae are reactivated, and it belongs to Evaginogenida.

An updated generic circumscription for Cryptangieae (Cyperaceae, Poales) based on a molecular phylogeny and a morphological character reconstruction

Phytotaxa ◽  
2021 ◽  
Vol 483 (3) ◽  
pp. 211-228
Author(s):  
SUZANA M. COSTA ◽  
FABIO A. VITTA ◽  
WILLIAM W. THOMAS ◽  
A. MUTHAMA MUASYA ◽  
ROSEMERI MOROKAWA ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
Morphological Character ◽  
Morphological Characters ◽  
New Combinations ◽  
Phylogenetic Significance ◽  
Generic Level ◽  
Molecular Analyses ◽  
Character Reconstruction ◽  
The Relationship

Cryptangieae is a monophyletic tribe, as asserted in a recent molecular hypothesis, but there are questions about the circumscription and relationships of its genera. We enlarged the sampling of the tribe diversity, including about 80% of known species, and provide new analyses using single and combined matrices from two chloroplast (rbcL and trnL-F) and three nuclear ribosomal (ITS, ETS and 5S-NTS) regions with Bayesian Inference to clarify these questions. We also performed character reconstruction analyses with diagnostic morphological characters, including some traditionally applied in Cryptangieae taxonomy, using parsimony methods. The molecular analyses show Lagenocarpus in the current circumscription as polyphyletic, and the need to merge Cephalocarpus and Everardia to avoid paraphyletic genera. We propose an updated circumscription following the phylogeny, including a new name to a group at generic level (Krenakia); and discuss the phylogenetic significance of the morphological characters in Cryptangieae taxonomy. Though the relationship among some genera still needs more research, the genera we propose are strongly supported clades with clear morphological synapomorphies. Additionally, we provide an identification key, a brief description of genera and a list of accepted species including the required new combinations.

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