Morphological and molecular characterisation of Punctodera mulveyi n. sp. (Nematoda: Punctoderidae) from a golf course green in Oregon, USA, with a key to species of Punctodera

Nematology ◽  
2020 ◽  
pp. 1-17
Author(s):  
Mihail R. Kantor ◽  
Zafar A. Handoo ◽  
Andrea M. Skantar ◽  
Maria N. Hult ◽  
Russell E. Ingham ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Heat Shock Protein 90 ◽  
Golf Course ◽  
Nominal Species ◽  
Sequence Alignments ◽  
Nuclear Heat ◽  
The Status ◽  
Stylet Length

Summary Punctodera mulveyi n. sp. is described and illustrated from turf grass (Poa annua) in golf course greens with other fescues in Bandon, Coos County, Oregon, USA. Females and cysts are characterised by a saccate, globose to ovoid or pear-shaped body with a protruding neck. The cuticle has a lace-like pattern of ridges and heavy punctations on the subsurface. Cysts have distinctive vulval and anal circumfenestral patterns with heavy bullae scattered around the fenestral area, these being absent in young cysts. Second-stage juveniles (J2) vermiform, tapering to a long and cylindrical tail with a bluntly rounded to occasionally clavate tail terminus. Morphologically the new species resembles all known species of Punctodera using both light microscopy and scanning electron microscopy observations, but differs from the other species either by the J2 body and stylet length, shape of head, tail and tail terminus, female and male stylet or spicule length, and in having distinctive vulval and anal circumfenestral patterns in the cysts. Molecular analysis with sequence alignments and phylogenetic trees of ITS rDNA, nuclear heat shock protein 90 and mitochondrial COI sequences separated P. mulveyi n. sp. from P. matadorensis, P. punctata, P. stonei and P. chalcoensis, but 18S and 28S were relatively conserved with a few bp differences and there were insufficient Punctodera species sequences to give strong support to a new species designation. A morphologically most closely related species, P. stonei from Canada, further supported the status of P. mulveyi n. sp. An identification key to all five nominal species of Punctodera is given.

A new riparian Mantidactylus (Brygoomantis) frog from the Tsaratanana and Manongarivo Massifs in northern Madagascar

Zootaxa ◽  
2018 ◽  
Vol 4486 (4) ◽  
pp. 575 ◽  
Author(s):  
MIGUEL VENCES ◽  
ANDREA HILDENBRAND ◽  
KATHARINA M. WARMUTH ◽  
FRANCO ANDREONE ◽  
FRANK GLAW
Keyword(s):  
New Species ◽  
Nuclear Dna ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Molecular Data ◽  
Test Case ◽  
Nominal Species ◽  
Type Specimens ◽  
The Status ◽  
Morphological Differences

The subgenus Brygoomantis in the Madagascar-endemic genus Mantidactylus contains 12 nominal species but is in urgent need of taxonomic revision as many additional, genetically divergent but undescribed candidate species have been identified. We here take a first step towards a better resolution of this group by describing a new species, Mantidactylus schulzi sp. nov., occurring at the Tsaratanana and Manongarivo Massifs, differentiated in genetic, bioacoustic and sometimes morphological characters from its closest relatives. We show that upon detailed study, most species in Brygoomantis can be delimited by concordant differentiation of mitochondrial and nuclear DNA, and by bioacoustic and morphological differences. We flag this group of morphologically similar frogs as a test case where molecular data on historical type specimens by ancient DNA methods might be needed to reach a satisfying clarification of taxonomy and nomenclature. However, the status of the new species M. schulzi is not in doubt as it is morphologically distinct from most historical type specimens, and microendemic to a region in northern Madagascar from where no earlier names exist. 

On the taxonomic status of the genus Dichodon (Caryophyllaceae: tribe Alsineae): morphological and molecular evidence reassessed

Phytotaxa ◽  
2018 ◽  
Vol 360 (3) ◽  
pp. 220 ◽  
Author(s):  
ZAHRA ARABI ◽  
FARROKH GHAHREMANINEJAD ◽  
RICHARD K. RABELER ◽  
IRINA SOKOLOVA ◽  
GÜNTHER HEUBL ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Strong Support ◽  
Taxonomic Status ◽  
Molecular Evidence ◽  
Herbarium Specimens ◽  
Arctic Regions ◽  
Morphological Studies ◽  
The Status ◽  
Molecular Phylogenetic ◽  
New Synonymy

The status of the genus Dichodon has long been debated, and its taxonomic position in tribe Alsineae has been changed during the time from a section or subgenus in Cerastium to genus sister to Holosteum. This group comprises important members of wet meadows in alpine and subalpine vegetation of Europe, arctic regions, and SW-Asia plus one species known as a weed in N-America, and a further one occuring in mountains of Taiwan. In order to clarify the taxonomic questions concerning this group and its species delimitation, we constructed phylogenetic trees, selecting several species belonging to tribe Alsineae as representatives of major lineages of this tribe as well as several accessions of Dichodon. Morphological studies focused more intensively on members of Dichodon using herbarium specimens and direct field examinations. The results confirm those of recent molecular phylogenetic studies, indicating Dichodon as a monophyletic genus sister to Holosteum and not Cerastium. In addition, the obtained cladograms support five distinct groups in Dichodon corresponding to five species of this genus we recognize in Iran, the focal area of this study. Seed micromorphology provides strong support for the recognition of Dichodon as a separate genus, but it is not informative at species and subspecies ranks due to constancy of most of seed characters within the genus. As part of this study, a new species—Dichodon alborzensis—is described, D. kotschyi is reported in Iran for the first time, and Cerastium schischkinii is placed in synonymy (new synonymy) under D. kotschyi.

scholarly journals Accurate inference of tree topologies from multiple sequence alignments using deep learning

2019 ◽  
Author(s):  
Anton Suvorov ◽  
Joshua Hochuli ◽  
Daniel R. Schrider
Keyword(s):  
Deep Learning ◽  
Parameter Space ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Biological Research ◽  
Learning Approaches ◽  
Sequence Alignments ◽  
Traditional Methods ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments

AbstractReconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and empirical studies have identified several “zones” of parameter space where accuracy of some methods can plummet, even for four-taxon trees. Further, some methods can have undesirable statistical properties such as statistical inconsistency and/or the tendency to be positively misleading (i.e. assert strong support for the incorrect tree topology). Recently, deep learning techniques have made inroads on a number of both new and longstanding problems in biological research. Here we designed a deep convolutional neural network (CNN) to infer quartet topologies from multiple sequence alignments. This CNN can readily be trained to make inferences using both gapped and ungapped data. We show that our approach is highly accurate, often outperforming traditional methods, and is remarkably robust to bias-inducing regions of parameter space such as the Felsenstein zone and the Farris zone. We also demonstrate that the confidence scores produced by our CNN can more accurately assess support for the chosen topology than bootstrap and posterior probability scores from traditional methods. While numerous practical challenges remain, these findings suggest that deep learning approaches such as ours have the potential to produce more accurate phylogenetic inferences.

Revalidation and resurrection of Panaspis massaiensis (Angel, 1924) and the description of a new species of Panaspis Cope (Squamata: Scincidae) from south-eastern Kenya

Zootaxa ◽  
2019 ◽  
Vol 4706 (2) ◽  
pp. 255-274 ◽  
Author(s):  
FELISTA KASYOKA KILUNDA ◽  
WERNER CONRADIE ◽  
DOMNICK VICTOR WASONGA ◽  
JIE-QIONG JIN ◽  
MIN-SHENG PENG ◽  
...  
Keyword(s):  
New Species ◽  
Valid Species ◽  
Nominal Species ◽  
Conservation Area ◽  
Northern Kenya ◽  
South Eastern ◽  
Mitochondrial Data ◽  
The Status ◽  
Group A ◽  
A New Species

Historically Panaspis wahlbergi (Smith, 1849) has been the only assignable species present in Kenya. Recent studies have shown that it comprises multiple cryptic species and the nominal species is now restricted to southern Africa. Newly collected mitochondrial data (16S rRNA) helped to resolve the status of the Kenyan populations, which revealed the presence of two distant related species. Pairwise distances show average 5.87% differences between the two Kenyan species, and 3.58–5.27% and 8.62–9.15% to nominal P. wahlbergi and P. maculicollis Jacobsen & Broadley, 2000 respectively. Ablepharus massaiensis Angel, 1924 was described from the Maasai plains near Nairobi, but has long been considered a junior synonym of P. wahlbergi. We herein resurrect Panaspis massaiensis comb. nov. as a valid species and describe a new species, Panaspis tsavoensis sp. nov. from the Tsavo Conservation Area in south-eastern Kenya. Morphological examinations of specimens reveal minor differences from each other as well as nominal forms of P. wahlbergi and P. maculicollis. Panaspis massaiensis comb. nov. shares with the P. wahlbergi group a white ventrolateral stripe but can be distinguished by the presence of 26 midbody scale rows versus 24. Panaspis tsavoensis sp. nov. on the other hand, lacks the white ventrolateral stripe, most similar to the P. maculicollis group but differs in that P. maculicollis breeding males have a black patch on the neck with diagonal rows of white spots. Panaspis massaiensis comb. nov. is widespread in the Kenyan and northern Tanzanian highlands, isolated dryland montane forests and rocky hills, while P. tsavoensis sp. nov. occur in the expansive arid lowlands of Tsavo Conservation Area and should be present in similar arid lowlands in northern Kenya as well as in adjacent Tanzania. 

scholarly journals Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning

2019 ◽  
Author(s):  
Anton Suvorov ◽  
Joshua Hochuli ◽  
Daniel R Schrider
Keyword(s):  
Deep Learning ◽  
Parameter Space ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Biological Research ◽  
Learning Approaches ◽  
Sequence Alignments ◽  
Traditional Methods ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments

Abstract Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and empirical studies have identified several “zones” of parameter space where accuracy of some methods can plummet, even for four-taxon trees. Further, some methods can have undesirable statistical properties such as statistical inconsistency and/or the tendency to be positively misleading (i.e. assert strong support for the incorrect tree topology). Recently, deep learning techniques have made inroads on a number of both new and longstanding problems in biological research. In this study, we designed a deep convolutional neural network (CNN) to infer quartet topologies from multiple sequence alignments. This CNN can readily be trained to make inferences using both gapped and ungapped data. We show that our approach is highly accurate on simulated data, often outperforming traditional methods, and is remarkably robust to bias-inducing regions of parameter space such as the Felsenstein zone and the Farris zone. We also demonstrate that the confidence scores produced by our CNN can more accurately assess support for the chosen topology than bootstrap and posterior probability scores from traditional methods. Although numerous practical challenges remain, these findings suggest that the deep learning approaches such as ours have the potential to produce more accurate phylogenetic inferences.

Ichthyocephaloides sumbatus n. sp. (Nematoda: Rhigonematoidea) from Indonesia and additional data on Xystrognathus phrissus Hunt, Pham Van Luc & Spiridonov, 2002

Nematology ◽  
2013 ◽  
Vol 15 (5) ◽  
pp. 575-588 ◽  
Author(s):  
Svetlana V. Malysheva ◽  
Sergei E. Spiridonov
Keyword(s):  
New Species ◽  
Phylogenetic Trees ◽  
Additional Data ◽  
Original Description ◽  
Nominal Species ◽  
Mountainous Region ◽  
Sem Images ◽  
Spicule Length ◽  
Anterior Position ◽  
Left Spicule

Ichthyocephaloides sumbatus n. sp., from the gut of Salpidobolus sp. (Spirobolida: Rhinocricidae), collected in the forest covering the mountainous region of Sumba Island, Indonesia, is described and illustrated. The new species is morphologically related to Australasian species of Ichthyocephaloides by the presence of a long, subulate tail in both sexes, distribution and number of genital papillae, presence of genital diverticulum and anterior position of vulva. Ichthyocephaloides sumbatus n. sp. is distinguished from all other nominal species by the highest mean right/left spicule length ratio and the exceptional form of the anterior vulval lip. The original description of Xystrognathus phrissus is supplemented with a description of the juvenile morphology and illustrated with line graphics and SEM images of adult stages. Molecular sequences and phylogenetic trees are provided.

Phylogenetic relationships among species of Contracaecum Railliet & Henry, 1912 and Phocascaris Høst, 1932 (Nematoda[ratio ]Ascaridoidea) based on nuclear rDNA sequence data

Parasitology ◽  
2000 ◽  
Vol 121 (4) ◽  
pp. 455-463 ◽  
Author(s):  
S. A. NADLER ◽  
S. D'AMELIO ◽  
H.-P. FAGERHOLM ◽  
B. BERLAND ◽  
L. PAGGI
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Large Subunit ◽  
Strong Support ◽  
Structural Features ◽  
Nominal Species ◽  
Phylogenetic Hypothesis ◽  
Natural Group ◽  
Phocid Seals

Nuclear-encoded large-subunit ribosomal DNA sequences were used to infer a phylogenetic hypothesis for 17 taxa (16 nominal species) of the genera Contracaecum and Phocascaris. Phylogenetic trees based on these data have been used to assess the validity of the taxonomic distinction between these genera, which was based on the presence or absence of certain structural features, rather than on explicit hypotheses of evolutionary history. Phylogenetic hypotheses based on parsimony, likelihood, and neighbor-joining analyses of these sequence data strongly support the hypothesis that species of Phocascaris are nested within the clade of Contracaecum species hosted by phocid seals, and are more closely related to species of the Contracaecum osculatum complex than to other Contracaecum species. Alternative tree topologies representing Phocascaris as not nested within the C. osculatum complex were significantly worse interpretations of these sequence data. Phylogenetic analysis also provides strong support for the monophyly of all taxa (Contracaecum and Phocascaris) from phocid seals, which is consistent with Berland's (1964) proposal that such species form a natural group; however, his proposal to recognize all species in phocid seals as Phocascaris, with all species from birds as Contracaecum would result in a paraphyletic Contracaecum, according to the molecular phylogenetic hypothesis.

Identification of Neotropical blow flies of the genus Calliphora Robineau-Desvoidy (Diptera: Calliphoridae) with the description of a new species

Zootaxa ◽  
2012 ◽  
Vol 3209 (1) ◽  
pp. 1 ◽  
Author(s):  
TERRY WHITWORTH ◽  
KNUT ROGNES
Keyword(s):  
New Species ◽  
Costa Rica ◽  
El Salvador ◽  
Central America ◽  
Species Distributions ◽  
Nominal Species ◽  
Blow Flies ◽  
The Status ◽  
A New Species ◽  
Key Characters

A key to the six known species of Calliphora Robineau-Desvoidy (Diptera: Calliphoridae) from the Neotropical Regionis given. Species distributions and key characters are discussed. Calliphora irazuana Townsend, 1908 is resurrected as avalid name for a species found in Central America and Mexico, stat. nov. Calliphora triseta sp. nov. is described fromnumerous specimens from Costa Rica, El Salvador and Mexico. Nominal species Calliphora nigra Mello, 1974 and Cal-liphora antojuanae Mariluis, 1982 are synonymized with Calliphora nigribasis Macquart, 1851, n. syn. An Appendix isprovided that clarifies the status of the names Calliphora peruviana Robineau-Desvoidy, 1830, Lucilia peruviana Robineau-Desvoidy, 1830, and Calliphora peruviana Macquart, 1851.

The Microsynodontis (Teleostei: Siluriformes: Mochokidae) of the lower Guinea region, west central Africa, with the description of eight new species

Zootaxa ◽  
2004 ◽  
Vol 531 (1) ◽  
pp. 1 ◽  
Author(s):  
HEOK H. Ng
Keyword(s):  
New Species ◽  
Sexual Dimorphism ◽  
Central Africa ◽  
Valid Species ◽  
Nominal Species ◽  
Cross River ◽  
West Central ◽  
The Status ◽  
First Time ◽  
River Drainages

Species of the mochokid catfish genus Microsynodontis Boulenger 1903 from the lower Guinea region in west central Africa (from the Cross River southwards to the Chiloango River drainages) are reviewed. Nine species (of which eight are described as new) are recognized. The status of other nominal species is also reviewed in this study; Microsynodontis christyi Boulenger, 1920 (previously considered a junior synonym of M. batesii) is shown to be a valid species. Characters useful for diagnosing Microsynodontis species are discussed and sexual dimorphism in the genus is also recorded for the first time.

Two new species of Hirschmanniella Luc and Goodey, 1963 (Nematoda: Pratylenchidae) with a key to the nominal species

1982 ◽  
Vol 60 (4) ◽  
pp. 530-535 ◽  
Author(s):  
B. A. Ebsary ◽  
R. V. Anderson
Keyword(s):  
Hong Kong ◽  
New Species ◽  
Species Range ◽  
Nominal Species ◽  
Lateral Field ◽  
Two New Species ◽  
Stylet Length

Hirschmanniella anchoryzae n. sp. from Canada and Hirschmanniella areolata n. sp. from Hong Kong are described and illustrated. The former is characterized by a flattened head, stylet length of 16–17 μm, an elongate–conoid tail with 60–88 annules, ending in an axial mucro, and location of the phasmids 37–57 μm from the tail terminus. Hirschmanniella areolata n. sp. has a hemispherical head, stylet length of 24–27 μm, complete areolation of the lateral field, a tail with 48–61 annules, ending in a ventral mucro, and phasmids 22–29 μm from the tail terminus. Spicule lengths from both species range from 28 to 31 μm. A key is presented to 24 nominal species of the genus.

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