Is accurate taxon identification important for molecular studies? Several cases of faux pas in pentatomoid bugs (Hemiptera: Heteroptera: Pentatomoidea)

Zootaxa ◽  
2011 ◽  
Vol 2932 (1) ◽  
pp. 47 ◽  
Author(s):  
JERZY A. LIS ◽  
BARBARA LIS

Recently, DNA has become a major source for phylogenetic inference. Although, in entomology, morphology-based methods of taxon identification and the use of morphological data for phylogenetic analyses remain prevalent, the value of these types of studies (often called “traditional”) are depreciated from time to time. It is obvious, that wrong taxon identification may affect results of any taxonomic study. Here we examine evidence that not only the modern “molecular” taxonomists, but even the so-called “traditional” taxonomists, may be casual and irresponsible in taxa identification, when they do their phylogenomic research. We also argue that a researcher’s responsibility for proper taxon identification and its naming is actually much higher in molecular studies than in any others.

2019 ◽  
Author(s):  
Caio A. Leal-Dutra ◽  
Gareth W. Griffith ◽  
Maria Alice Neves ◽  
David J. McLaughlin ◽  
Esther G. McLaughlin ◽  
...  

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.


Zootaxa ◽  
2017 ◽  
Vol 4273 (2) ◽  
pp. 177 ◽  
Author(s):  
KLÁRA DÓZSA-FARKAS ◽  
TAMÁS FELFÖLDI

Five Achaeta species (A. affinis, A. bohemica sensu stricto, A. camerani, A. cf. danica, A. unibulba) and a new species, described here as A. tothi sp. n., were found during the investigation of the enchytraeid fauna of western Hungary (Őrség National Park and Kőszeg Mts.). Comparative morphological and molecular taxonomic investigations were performed with several individuals representing these six Achaeta species. A detailed description of the new species is given, and we also present some additional morphological data and photos about the other five Achaeta species. Such information could have importance in subsequent taxonomic studies and will aid the discrimination among the members of genus Achaeta. Furthermore, the obtained sequences could serve as references in forthcoming studies applying DNA-based taxon identification. 


Author(s):  
Duilio Iamonico

Background and Aims: Stellaria traditionally comprises 150-200 species, mainly distributed in the temperate regions of Eurasia and North America. Molecular studies demonstrated that Stellaria is polyphyletic and includes about 120 species. The genus has a high phenotypic variability which has led to nomenclatural disorders, making the identification of the various species difficult. A note is presented about a taxon currently accepted under the genus Stellaria -Stellaria obtusa- which should be recognized as a separate genus, here proposed as Engellaria gen. nov.Methods: This study is based on examination of specimens of American and European herbaria and analysis of relevant literature.Key results: Available molecular data show that Stellaria obtusa is not included in the Stellaria s.s. clade, but instead is basal to another clade comprising the genera Honckenya, Schiedea, and Wilhelmsia. Stellaria obtusa was, therefore, compared with these three groups and with morphologically similar apetalous members of Stellaria s.s. (S. crispa, S. media, S. pallida, and S. irrigua). The results obtained lead to the recognition of S. obtusa as a separate new North American monotypic genus. A diagnostic key of the apetalous members belonging to the American Caryophyllaceae genera is proposed. Finally, the names Stellaria obtusa and S. washingtoniana (= S. obtusa) are lectotypified based on specimens deposited, respectively, at UC (isolectotypes at GH, NY, and YU) and GH (isolectotypes at BM, CAN, CAS, CS, DOV, F, GH, K, MIN, MSC, NY, US, and VT). For the name Alsine viridula (= S. obtusa) the holotype was found at US (isotypes at CAS, F, GH, NY, OSC, RM, and UC).Conclusions: Stellaria obtusa does not belong to the genus Stellaria. The present study shows that the combined use of morphological data and phylogenetic analyses helped to clarify the taxonomic position of difficult plant groups, as in Stellaria.


2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.


2020 ◽  
Vol 94 ◽  
Author(s):  
J. Schwelm ◽  
O. Kudlai ◽  
N.J. Smit ◽  
C. Selbach ◽  
B. Sures

Abstract Bithynids snails are a widespread group of molluscs in European freshwater systems. However, not much information is available on trematode communities from molluscs of this family. Here, we investigate the trematode diversity of Bithynia tentaculata, based on molecular and morphological data. A total of 682 snails from the rivers Lippe and Rhine in North Rhine-Westphalia, Germany, and 121 B. tentaculata from Curonian Lagoon, Lithuania were screened for infections with digeneans. In total, B. tentaculata showed a trematode prevalence of 12.9% and 14%, respectively. The phylogenetic analyses based on 55 novel sequences for 36 isolates demonstrated a high diversity of digeneans. Analyses of the molecular and morphological data revealed a species-rich trematode fauna, comprising 20 species, belonging to ten families. Interestingly, the larval trematode community of B. tentaculata shows little overlap with the well-studied trematode fauna of lymnaeids and planorbids, and some of the detected species (Echinochasmus beleocephalus and E. coaxatus) constitute first records for B. tentaculata in Central Europe. Our study revealed an abundant, diverse and distinct trematode fauna in B. tentaculata, which highlights the need for further research on this so far understudied host–parasite system. Therefore, we might currently be underestimating the ecological roles of several parasite communities of non-pulmonate snail host families in European fresh waters.


2009 ◽  
Vol 34 (1) ◽  
pp. 102-114 ◽  
Author(s):  
M. A. Bello ◽  
A. Bruneau ◽  
F. Forest ◽  
J. A. Hawkins

The order Fabales, including Leguminosae, Polygalaceae, Quillajaceae and Surianaceae, represents a novel hypothesis emerging from angiosperm molecular phylogenies. Despite good support for the order, molecular studies to date have suggested contradictory, poorly supported interfamilial relationships. Our reappraisal of relationships within Fabales addresses past taxon sampling deficiencies, and employs parsimony and Bayesian approaches using sequences from the plastid regions rbcL (166 spp.) and matK (78 spp.). Five alternative hypotheses for interfamilial relationships within Fabales were recovered. The Shimodaira-Hasegawa test found the likelihood of a resolved topology significantly higher than the one calculated for a polytomy, but did not favour any of the alternative hypotheses of relationship within Fabales. In the light of the morphological evidence available and the comparative behavior of rbcL and matK, the topology recovering Polygalaceae as sister to the rest of the order Fabales with Leguminosae more closely related to Quillajaceae + Surianaceae, is considered the most likely hypothesis of interfamilial relationships of the order. Dating of selected crown clades in the Fabales phylogeny using penalized likelihood suggests rapid radiation of the Leguminosae, Polygalaceae, and (Quillajaceae + Surianaceae) crown clades.


2021 ◽  
Vol 8 ◽  
Author(s):  
MJosé Pérez-Alvarez ◽  
Sebastián Kraft ◽  
Nicolás I. Segovia ◽  
Carlos Olavarría ◽  
Sergio Nigenda-Morales ◽  
...  

Four fin whale sub-species are currently considered valid: Balaenoptera physalus physalus in the North Atlantic, B. p. velifera in the North Pacific, B. p. quoyi and B. p. patachonica in the Southern Hemisphere. The last, not genetically validated, was described as a pygmy-type sub-species, found in low to mid latitudes of the Southern Hemisphere. Genetic analyses across hemispheres show strong phylogeographic structure, yet low geographic coverage in middle latitudes of the Southern Hemisphere impeded an assessment within the area, as well as evaluating the validity of B. p. patachonica. New mtDNA sequences from the Southeastern Pacific allowed an improved coverage of the species’ distribution. Our phylogenetic analyses showed three main lineages and contrasting phylogeographic patterns between Northern and Southern Hemispheres. Absence of recurrent female mediated gene flow between hemispheres was found; however, rare dispersal events revealing old migrations were noted. The absence of genetic structure suggests the existence of one single taxa within the Southern Hemisphere. Thus, until further evidence supporting this subspecies can be produced, such as genetic, ecological, behavioral, or morphological data, we propose that all fin whales from the Southern Hemisphere, including those from middle latitudes of the Southeastern Pacific belong to B. p. quoyi subspecies. This information is important for the current assessment of fin whales, contributing to the evaluation of the taxonomic classification and the conservation of the species.


1995 ◽  
Vol 347 (1320) ◽  
pp. 213-234 ◽  

Phylogenedc reladonships of higher taxa of echinoids have been invesdgated using a 163 character morphological data base and molecular sequences from large and small subunit (LSU and SSU) ribosomal RNA (rRNA) genes. The complete ssu rRNA gene has been sequenced for 21 taxa, with representatives from nine of the 14 extant orders of Echinoidea. Partial LSU sequences, representing the first 400 base pairs (b.p.) from the 5' end were also sequenced for three taxa to complement an existing data base of ten taxa. The two molecular sequences provided a total of 371 variable sites, of which 143 were phylogenetically informative (compared to 145 phylogenetically informative sites from morphological data). Morphological, LSU and SSU data have been analysed separately and together. Morphological and ssu sequence data generate topologies that are not significantly in conflict (under Templeton’s test), but the strong signal pairing arbaciids with clypeasteroids in the LSU derived tree marks the LSU sequence data as anomalous for this taxon. A ‘ total evidence’ approach derived a tree very similar in topology to that derived from morphological data. Rooted on the stem group echinoid Archaeocidaris , our total evidence tree suggested relationships of higher taxa as follows: Gidaroida Phormosomatidae Echinothuriidae Diadematidae Spatangoida Clypeasteroida, Cassiduloida Calycina, Arbacioida Stomopneustidae Glyphocidaridae Temnopleuridae Echinometridae Echinidae, Strongylocentridae. Phylogenetic analyses run both with and without key fossil taxa yielded slightly different topologies. It is important to include fossil taxa in a phylogenetic analysis where there are long stem-group branches or where the crown group is highly derived.


Author(s):  
Benoit Morel ◽  
Pierre Barbera ◽  
Lucas Czech ◽  
Ben Bettisworth ◽  
Lukas Hübner ◽  
...  

Abstract Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8, 736 out of all 16, 453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into sub-classes using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.


Zootaxa ◽  
2012 ◽  
Vol 3241 (1) ◽  
pp. 1 ◽  
Author(s):  
WILLIAM T. WHITE

A taxonomic re-evaluation of the Carcharhinus sealei-dussumieri group using meristic and morphological data revealedthat this group consists of 5 species. Two species, Carcharhinus coatesi (Whitley, 1939) from northern Australia and prob-ably New Guinea and C. tjutjot (Bleeker, 1852) from Indonesian to Taiwan, are resurrected as valid species and togetherwith C. dussumieri and C. sealei are redescribed. Garrick’s lectotype designation of C. dussumieri and C. tjutjot areretained. A neotype for C. sealei, collected from the same locality as the holotype which was destroyed during World WarII, is designated. A fifth, possibly undescribed species (Carcharhinus sp.) is also noted from the Western Indian Oceanand its affinities briefly discussed. The four redescribed species are very similarly morphologically but can be distin-guished by a combination of meristic, morphological, dental and colour characters. The most important characters for dis-tinguishing these species are: vertebral counts, tooth counts, tooth morphology, shape of first dorsal and pectoral fins,second dorsal fin colouration, and mouth width. Two independent molecular studies have produced results which closely correlate with and support the findings of this study.


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