Pitfalls in phylogenetic analysis of large molecular data sets

1998 ◽  
pp. 253-274
Author(s):  
Paul Z. Goldstein ◽  
Chelsea D. Specht
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Data ◽  
Data Sets

scholarly journals Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4349 ◽  
Author(s):  
Aristóteles Góes-Neto ◽  
Marcelo V.C. Diniz ◽  
Daniel S. Carvalho ◽  
Gilberto C. Bomfim ◽  
Angelo A. Duarte ◽  
...  
Keyword(s):  
Biological Sciences ◽  
Phylogenetic Analysis ◽  
Complex Networks ◽  
Complex Network ◽  
Bootstrap Method ◽  
Molecular Data ◽  
Data Sets ◽  
Fungal Cell ◽  
Taxonomic Groups ◽  
Inference Methods

Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.

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. 

Partitioning of Multiple Data, Sets Phylogenetic Analysis

2002 ◽  
pp. 102-119 ◽  
Author(s):  
Patrick M. O’Grady ◽  
James Remsen ◽  
John E. Gatesy
Keyword(s):  
Phylogenetic Analysis ◽  
Data Sets ◽  
Multiple Data ◽  
Multiple Data Sets
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