scholarly journals Characterizing Cell-Decomposable Metrics

10.37236/882 ◽  
2008 ◽  
Vol 15 (1) ◽  
Author(s):  
Katharina T. Huber ◽  
Jacobus Koolen ◽  
Vincent Moulton ◽  
Andreas Spillner
Keyword(s):  
Phylogenetic Analysis ◽  
Convex Hull ◽  
Metric Space ◽  
Molecular Data ◽  
Multicommodity Flow ◽  
Flow Problems ◽  
Canonical Metric ◽  
Tight Span ◽  
Finite Metric Space ◽  
A Cell

To a finite metric space $(X,d)$ one can associate the so called tight-span $T(d)$ of $d$, that is, a canonical metric space $(T(d),d_\infty)$ into which $(X,d)$ isometrically embeds and which may be thought of as the abstract convex hull of $(X,d)$. Amongst other applications, the tight-span of a finite metric space has been used to decompose and classify finite metrics, to solve instances of the server and multicommodity flow problems, and to perform evolutionary analyses of molecular data. To better understand the structure of $(T(d),d_\infty)$ the concept of a cell-decomposable metric was recently introduced, a metric whose associated tight-span can be decomposed into simpler tight-spans. Here we show that cell-decomposable metrics and totally split-decomposable metrics — a class of metrics commonly applied within phylogenetic analysis — are one and the same thing, and also provide some additional characterizations of such metrics.

A new species of Cynomops (Chiroptera: Molossidae) from the northwestern slope of the Andes

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Daniela Arenas-Viveros ◽  
Pamela Sánchez-Vendizú ◽  
Alan Giraldo ◽  
Jorge Salazar-Bravo
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Data ◽  
Mtdna Sequences ◽  
The Andes ◽  
Western Side ◽  
Morphological And Molecular Data ◽  
A New Species ◽  
Lines Of Evidence

Abstract The systematics and taxonomy of the broadly distributed bats of the genus Cynomops has changed considerably in the last few years. Among the major changes, Cynomops abrasus was split into two species of large-bodied forms (Cynomops mastivus and C. abrasus) distributed east of the Andes. However, large Colombian specimens identified as C. abrasus from the western side of the Andes had yet to be included in any revisionary work. Phylogenetic analysis performed in this study, using mtDNA sequences (Cytochrome-b), revealed that these Colombian individuals are more closely related to Cynomops greenhalli. Morphological and molecular data allowed us to recognize populations from western Colombia, western Ecuador and northwestern Peru, as members of a new species of Cynomops. Characters that allow for its differentiation from C. greenhalli include a larger forearm, paler but more uniform ventral pelage, more globular braincase, and well-developed zygomatic processes of the maxilla (almost reaching the postorbital constriction). This study serves as another example of the importance of including multiple lines of evidence in the recognition of a new species. Given its rarity and the advanced transformation of its habitat, this new species is particularly important from a conservation perspective.

Description of a new species of Auriculostoma (Digenea: Allocreadiidae) from Characidium heirmostigmata (Characiformes: Crenuchidae) from Argentina, using morphological and molecular data

2021 ◽  
Vol 95 ◽  
Author(s):  
M.M. Montes ◽  
J. Barneche ◽  
Y. Croci ◽  
D. Balcazar ◽  
A. Almirón ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
National Park ◽  
Molecular Data ◽  
Rrna Gene ◽  
28S Rrna ◽  
The Family ◽  
Parasitological Survey ◽  
Morphological And Molecular Data ◽  
A New Species

Abstract During a parasitological survey of fishes at Iguazu National Park, Argentina, specimens belonging to the allocreadiid genus Auriculostoma were collected from the intestine of Characidium heirmostigmata. The erection of the new species is based on a unique combination of morphological traits as well as on phylogenetic analysis. Auriculostoma guacurarii n. sp. resembles four congeneric species – Auriculostoma diagonale, Auriculostoma platense, Auriculostoma tica and Auriculostoma totonacapanensis – in having smooth and oblique testes, but can be distinguished by a combination of several morphological features, hosts association and geographic distribution. Morphologically, the new species can be distinguished from both A. diagonale and A. platense by the egg size (bigger in the first and smaller in the last); from A. tica by a shorter body length, the genital pore position and the extension of the caeca; and from A. totonacapanensis by the size of the oral and ventral sucker and the post-testicular space. Additionally, one specimen of Auriculostoma cf. stenopteri from the characid Charax stenopterus (Characiformes) from La Plata River, Argentina, was sampled and the partial 28S rRNA gene was sequenced. The phylogenetic analysis revealed that A. guacurarii n. sp. clustered with A. tica and these two as sister taxa to A. cf. stenopteri. The new species described herein is the tenth species in the genus and the first one parasitizing a member of the family Crenuchidae.

Two new freshwater planarian species (Platyhelminthes: Tricladida: Dugesiidae) partially sympatric in Argentinean Patagonia

2021 ◽  
pp. 269-278
Author(s):  
M. Lenguas Francavilla ◽  
L. Negrete ◽  
A. Martínez-Aquino ◽  
C. Damborenea ◽  
F. Brusa
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Data ◽  
Neotropical Region ◽  
Free Living ◽  
Mitochondrial Coi ◽  
Argentinean Patagonia ◽  
The Family ◽  
Taxonomic Approach ◽  
Morphological And Molecular Data ◽  
Endemic Flora

Girardia Ball, 1974 is the most diverse and widely distributed genus of the family Dugesiidae (Platyhelminthes: Continenticola) in the Neotropical region. Seven out of the 52 species of the genus are known for Argentina. The Somuncurá Plateau is a region in northern Patagonia with several endemic flora and fauna, but little is known about the free-living Platyhelminthes. We describe two new species of Girardia partially inhabiting in sympatry in the Somuncurá Plateau: Girardia somuncura sp. nov. and Girardia tomasi sp. nov. The identification criteria that we followed was an integrative taxonomic approach based on morphological and molecular data. Thus, we used anatomical features focused on the reproductive system, together with a phylogenetic analysis, using a mitochondrial (COI barcode region) genetic marker. This study is the first phylogenetic analysis of the genus Girardia in which we include the southernmost representatives of America here described, thus making it possible to incorporate them in global phylogenies.

Molecular and Ultrastructural Analysis of a Porocephalus sp. (Arthropoda: Pentastomida) Removed from a Rattlesnake

2021 ◽  
Vol Vol 66 (1) (January (1)) ◽  
pp. 1-5
Author(s):  
Jerome Goddard ◽  
Gerald Baker ◽  
Petra Jericke ◽  
Lawrence Birchman ◽  
Ethan Woodward ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Adult Female ◽  
Sequence Data ◽  
Molecular Data ◽  
Ultrastructural Analysis ◽  
Oxidase Subunit ◽  
Data Support ◽  
Partial 18S

Ultrastructural and molecular data are provided from a single adult female pentastomid opportunistically collected from a road-killed rattlesnake in Russell, KS. Ultrastructural data consisted of light and SEM microscopy of the pentastomid and its eggs, while molecular data consisted of partial 18S and 28S ribosomal sequences and a partial cytochrome c oxidase subunit 1 sequence from the same specimen used for SEM. Ultrastructural and molecular data support generic identification of the pentastomid as Porocephalus sp. These molecular data were also used with previously published pentastomid sequence data for a concatenated phylogenetic analysis, which support the current, morphology-based taxonomic placement of the genus.

Entomophilic nematodes, Diploscapter coronatus and Oscheius tipulae from Afghanistan

Zootaxa ◽  
2021 ◽  
Vol 4926 (3) ◽  
pp. 401-416
Author(s):  
MOHAMMAD HUSSAIN FALAHZADAH ◽  
EBRAHIM SHOKOOHI ◽  
GHOLAM HOSSEIN MORAVEJ ◽  
PHATU WILLIAM MASHELA ◽  
ABDUL KHALID MADADI ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Galleria Mellonella ◽  
Morphological Characters ◽  
Molecular Data ◽  
Soil Samples ◽  
The Body ◽  
Morphometric Data ◽  
Molecular Approaches ◽  
The Relationship

Several soil samples from different habitats in Badakhshan province of Afghanistan were collected to isolate and characterize bacteria feeding nematodes. The Galleria mellonella-baiting method was used for the isolation of the Afghan insect-associated nematodes. The nematodes were studied using morphological and morphometric data. The Oscheius specimen was characterized by a longer body (630–820 µm) and shorter pharynx (125–145 µm), whereas other morphological characters were not unusual. The Diploscapter specimen had an annulated cuticle, with lip region width 1.5 times shorter than the stoma, and had separated pharyngeal corpus from the isthmus and vulva located in the middle of the body. The molecular data were derived using three loci; 18S, 28S (D2/D3 segment), and ITS rRNA region, which were utilized to measure the genetic distance. The phylogenetic analysis was conducted to reconstruct the relationship tree. Both morphological and molecular approaches confirmed the identity of nematode isolates as Oscheius tipulae and Diploscapter coronatus. This is the first report of insect-associated nematodes from the soil of Afghanistan. Both species were capable of infecting and killing G. mellonella larvae in less than 96 h. 

Species delimitation of colour polymorphic Cladophorus (Coleoptera: Lycidae) from New Guinea

Zootaxa ◽  
2017 ◽  
Vol 4320 (3) ◽  
pp. 505 ◽  
Author(s):  
ROMANA KALOUSOVA ◽  
LADISLAV BOCAK
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Related Species ◽  
Species Delimitation ◽  
Morphological Differentiation ◽  
Morphological Characters ◽  
Molecular Data ◽  
Closely Related Species ◽  
Dna Fragment ◽  
Colour Patterns

Cladophorus Guérin-Méneville, 1830 are endemic Papuan net-winged beetles which take part in highly diverse Müllerian mimicry rings. Available specimens were sequenced for cox1–tRNA-Leu–cox2 mitochondrial DNA fragment and the species delimitations were based on the genetic distance, phylogenetic analysis, and morphology. Three earlier described species were identified in the recently collected material and further 10 species are described: C. pallescens sp. nov., C. bicolor sp. nov., C. craterensis sp. nov., C. motykai sp. nov., C. mindikensis sp. nov., C. kailakiensis sp. nov., C. manokwarensis sp. nov., C. haiaensis sp. nov., C. humeralis sp. nov., and C. boceki sp. nov. DNA-based identifications provided some ambiguous results and closely related species could not be robustly delimited using solely molecular data. Additionally, the species limits were based on clearly defined morphological characters and the morphological differentiation was found unlinked from the genetic divergence. Colour patterns cannot be used for identification because all species available in more specimens were polymorphic and followed various local co-mimics. The Papuan fauna of Cladophorus is very diverse and the closely related species regularly occur in limited regions. Differentiation within restricted ranges is therefore considered as the main speciation mode. 

scholarly journals Single-Tube Flow Cytometry Assay for the Detection of Mature Lymphoid Neoplasms in Paucicellular Samples

2016 ◽  
Vol 60 (4) ◽  
pp. 385-394
Author(s):  
Alessandra Stacchini ◽  
Anna Demurtas ◽  
Sabrina Aliberti ◽  
Antonella Barreca ◽  
Domenico Novero ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Hodgkin Lymphoma ◽  
Final Diagnosis ◽  
Molecular Data ◽  
Malignant Lymphomas ◽  
Flow Cytometry Assay ◽  
Single Tube ◽  
Fine Needle Aspirates ◽  
Non Hodgkin Lymphoma ◽  
A Cell

Objectives: Flow cytometry (FC) has become a useful support for cytomorphologic evaluation (CM) of fine-needle aspirates (FNA) and serous cavity effusions (SCE) in cases of suspected non-Hodgkin lymphoma (NHL). FC results may be hampered by the scarce viability and low cellularity of the specimens. Study Design: We developed a single-tube FC assay (STA) that included 10 antibodies cocktailed in 8-color labeling, a cell viability dye, and a logical gating strategy to detect NHL in hypocellular samples. The results were correlated with CM and confirmed by histologic or molecular data when available. Results: Using the STA, we detected B-type NHL in 31 out of 103 hypocellular samples (81 FNA and 22 SCE). Of these, 8 were not confirmed by CM and 2 were considered to be only suspicious. The FC-negative samples had a final diagnosis of benign/reactive process (42/72), carcinoma (27/72), or Hodgkin lymphoma (3/72). Conclusions: The STA approach allowed obtainment of maximum immunophenotyping data in specimens containing a low number of cells and a large amount of debris. The information obtained by STA can help cytomorphologists not only to recognize but also to exclude malignant lymphomas.

Molecular phylogeny of Pemphiginae (Hemiptera: Aphididae) inferred from nuclear gene EF-1α sequences

2008 ◽  
Vol 98 (5) ◽  
pp. 499-507 ◽  
Author(s):  
H.C. Zhang ◽  
G.X. Qiao
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Host Specificity ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Molecular Phylogenetic Analysis ◽  
Phylogenetic Study ◽  
Primary Host ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic

AbstractThree traditional tribes of Fordini, Pemphigini and Eriosomatini comprise Pemphiginae, and there are two subtribes in Fordini and Pemphigini, respectively. Most of the species in this subfamily live heteroecious holocyclic lives with distinct primary host specificity. The three tribes of Pemphigini (except Prociphilina), Eriosomatini and Fordini use three families of plants, Salicaceae (Populus), Ulmaceae (Ulums) and Anacardiaceae (Pistacia and Rhus), as primary hosts, respectively, and form galls on them. Therefore, the Pemphigids are well known as gall makers, and their galls can be divided into true galls and pseudo-galls in type. We performed the first molecular phylogenetic study of Pemphiginae based on molecular data (EF-1α sequences). Results show that Pemphiginae is probably not a monophylum, but the monophyly of Fordini is supported robustly. The monophyly of Pemphigini is not supported, and two subtribes in it, Pemphigina and Prociphilina, are suggested to be raised to tribal level, equal with Fordini and Eriosomatini. The molecular phylogenetic analysis does not show definite relationships among the four tribes of Pemphiginae, as in the previous phylogenetic study based on morphology. It seems that the four tribes radiated at nearly the same time and then evolved independently. Based on this, we can speculate that galls originated independently four times in the four tribes, and there is no evidence to support that true galls are preceded by pseudo-galls, as in the case of thrips and willow sawflies.

scholarly journals A project for analyzing the ecology and phylogeny of western Pacific echinoids

Zoosymposia ◽  
2019 ◽  
Vol 15 (1) ◽  
pp. 83-87
Author(s):  
K. KANAZAWA ◽  
M. SAITOH ◽  
N. WAKAYAMA ◽  
M. OBUCHI ◽  
S. NAKACHI ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sea Urchins ◽  
Molecular Data ◽  
Western Pacific ◽  
The West ◽  
The World ◽  
The Western Pacific ◽  
Gathering Data ◽  
Northern Japan

In 2017 we started a project to analyze the ecology and phylogeny of western Pacific echinoids. As the first step, we are establishing methods to infer their phylogenetic relationships using molecular data; we developed effective methods to obtain complete mitochondrial DNA sequences, and determined their effectiveness in phylogenetic analysis. We have also been gathering data concerning the ecology and systematics of Japanese extant echinoids, which arguably has among the highest genus-level diversities in the West Pacific or perhaps even in the world. We have collected 58 species from middle and southern Japan representing 48 genera. In the next year, we will collect sea urchins from northern Japan, and within 2 years we will finish collecting data on ecology and systematics of Japanese echinoids, and provide a set of standardized data that will be useful for many researchers studying western Pacific echinoids. At that time, we will start comparative analyses of echinoid faunas distributed in the western Pacific.

Rhodocybe formosa (Agaricales, Entolomataceae): new collections, molecular data and synonymy, and Rhodocybe griseonigrella comb. nov.

Phytotaxa ◽  
2016 ◽  
Vol 255 (1) ◽  
pp. 34 ◽  
Author(s):  
ALFREDO VIZZINI ◽  
BERNARDO PICILLO ◽  
ENRICO ERCOLE ◽  
JORDI VILA ◽  
MARCO CONTU
Keyword(s):  
Phylogenetic Analysis ◽  
Distinct Species ◽  
Molecular Data ◽  
Its Sequences ◽  
European Species ◽  
Molecular Comparison

Rhodocybe formosa (sect. Rhodocybe), a species so far known only from Spain, is here reported from Italy. A detailed description, including also macrophotographs, microphotographs and drawings together with a phylogenetic analysis of the ITS sequences, are provided.                According to the molecular comparison of the type collections, R. minutispora, a species recently described on the basis of collections from Spain, is a synonym of R. formosa. Clitopilus griseonigrellus is recognized as a distinct species and recombined in Rhodocybe. A key to the European species of Rhodocybe sect. Rhodocybe is provided.

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