Uses of statistical parsimony in HIV analyses

Abstract Among Antarctic amphipods of the genus Eusirus, a highly distinctive clade of giant species is characterized by a dorsal, blade-shaped tooth on pereionites 5–7 and pleonites 1–3. This lineage, herein named ‘crested Eusirus’, includes two potential species complexes, the Eusirus perdentatus and Eusirus giganteus complexes, in addition to the more distinctive Eusirus propeperdentatus. Molecular phylogenies and statistical parsimony networks (COI, CytB and ITS2) of crested Eusirus are herein reconstructed. This study aims to formally revise species diversity within crested Eusirus by applying several species delimitation methods (Bayesian implementation of the Poisson tree processes model, general mixed Yule coalescent, multi-rate Poisson tree processes and automatic barcode gap discovery) on the resulting phylogenies. In addition, results from the DNA-based methods are benchmarked against a detailed morphological analysis of all available specimens of the E. perdentatus complex. Our results indicate that species diversity of crested Eusirus is underestimated. Overall, DNA-based methods suggest that the E. perdentatus complex is composed of three putative species and that the E. giganteus complex includes four or five putative species. The morphological analysis of available specimens from the E. perdentatus complex corroborates molecular results by identifying two differentiable species, the genuine E. perdentatus and a new species, herein described as Eusirus pontomedon sp. nov.

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Species delimitation of the northeastern Anatolian Symphytum (Boraginaceae) taxa

Phytotaxa ◽

10.11646/phytotaxa.516.3.3 ◽

2021 ◽

Vol 516 (3) ◽

Author(s):

KURTULUŞ ÖZGİŞİ ◽

BURCU TARIKAHYA-HACIOĞLU

Keyword(s):

Species Delimitation ◽

Sequence Data ◽

Molecular Data ◽

Morphological Data ◽

Infrageneric Classification ◽

Number Of Species ◽

Morphological Studies ◽

Statistical Parsimony ◽

Taxonomical Status ◽

Parsimony Network Analysis

Symphytum is regarded one of the most complicated genera in terms of the classification of its members among the Boraginaceae. In addition to different infrageneric classification methods, several species complex or aggregates have been proposed to deal with the taxonomical problem of genus members. Symphytum asperum aggregate was first introduced by Kurtto, who proposed six taxa within this aggregate. However, according to further studies by different researchers based on morphological data, total number of species of the complex was variable. The number of species was reduced to three, comprising S. asperum, S. savvalense, and S. sylvaticum, after the phylogenetic and morphological studies of Tarıkahya-Hacıoğlu and Erik. However, the taxonomical status of some of these species (i.e., S. savvalense and S. sylvaticum, and S. sepulcrale), which was assigned as a member of this complex by Kurtto, has been regarded as unresolved. To solve this uncertainty, different species delimitation methods were used, including statistical parsimony network analysis (TCS), generalized mixed Yule coalescent (GMYC), and Bayesian Phylogenetics and Phylogeography (BPP) of the ITS, trnL-F and trnS-G sequence data. In addition to members of this complex, S. ibericum, which is phylogenetically nested within the S. asperum aggregate, was also used. The TCS and GMYC analyses demonstrated more complicated clusters, whereas high posterior probabilities of BPP clusters were more compatible with the morphological data. In accordance with the morphological approach of Tarıkahya-Hacıoğlu and Erik, the species delimitation analyses based on molecular data support the recognition of S. asperum, S. ibericum, S. savvalense, and S. sylvaticum as different species.

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Genetic diversity and relationships among Prunus cerasifera (cherry plum) clones

Botany ◽

10.1139/b08-097 ◽

2008 ◽

Vol 86 (11) ◽

pp. 1311-1318 ◽

Cited By ~ 12

Author(s):

Aniko Horvath ◽

Hélène Christmann ◽

Frédéric Laigret

Keyword(s):

Ssr Markers ◽

Genetic Relationships ◽

Molecular Data ◽

Mean Value ◽

Factorial Correspondence Analysis ◽

Prunus Cerasifera ◽

Statistical Parsimony ◽

Natural Forms ◽

Cpdna Markers ◽

Morphological And Molecular Data

Prunus cerasifera (Ehrh.) (cherry or Myrobalan plum) is a diverse species with several recognized subspecies and natural forms. It is used as rootstock or as an ornamental tree, and is considered to be one progenitor of the garden plum ( Prunus domestica L.). This study considers the genetic relationships among different P. cerasifera clones, including horticultural cultivars. Twenty nine P. cerasifera accessions of the Prunus Genetic Resources Collection of INRA were analysed using morphological traits, maternally inherited chloroplastic DNA (cpDNA) markers, and biparentally inherited microsatellite (SSR) markers. Ploidy information was obtained by flow cytometry. Multiple factorial correspondence analysis of morphological descriptors shows important differences between some clones, but most of the samples are grouped. Fifteen haplotypes of cpDNA were identified and clustered into three groups after statistical parsimony analysis. SSR markers revealed a total of 74 alleles, with a mean value of 10.6 alleles per locus. After analysis of ploidy level, P. cerasifera subsp. caspica was shown to have a hexaploid genome. Morphological and molecular data suggest that the taxonomic classification of some subspecies and of P. cerasifera subsp. caspica may need to be revised after analysis of additional individuals.

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Origin and evolution of the Italian subterranean termite Reticulitermes lucifugus (Blattodea, Termitoidae, Rhinotermitidae)

Bulletin of Entomological Research ◽

10.1017/s0007485313000400 ◽

2013 ◽

Vol 103 (6) ◽

pp. 734-741 ◽

Cited By ~ 6

Author(s):

A. Luchetti ◽

V. Scicchitano ◽

B. Mantovani

Keyword(s):

Gene Marker ◽

Data Set ◽

Origin And Evolution ◽

Anticlockwise Rotation ◽

Parsimony Network ◽

Statistical Parsimony ◽

Coii Gene ◽

Cytochrome Oxidase Ii ◽

Diversity Estimates ◽

Mitochondrial Cytochrome Oxidase

AbstractThe Holarctic genus Reticulitermes shows seven species within the Mediterranean Basin. While phylogeny and systematics at continental level has been deeply investigated, a few studies concentrated on local ranges. To gain a clearer picture of the diversity and evolution of the Italian species Reticulitermes lucifugus, we analyzed the mitochondrial cytochrome oxidase II (COII) gene marker in newly collected colonies across the Peninsula. Data were gathered with all R. lucifugus sequences available from previous studies; COII sequences of the closely related Iberian taxa were also added to the data set. Maximum-likelihood, median-joining and statistical parsimony network elaborations on the resulting 119 colonies all agreed in indicating that: (i) the Sardo-Corsican subspecies R. lucifugus corsicus, strictly related to Southern Italian populations (including the Sicilian ones), is phylogenetically closer to the Iberian Reticulitermes grassei; and (ii) R. lucifugus lucifugus peninsular populations are structured into three clusters. The phylogenetic relationships and the biogeography of extant taxa suggest a scenario in which R. lucifugus ancestors colonized the Italian region through the Sardo-Corsican microplate during its Oligocene-Miocene anticlockwise rotation. Moreover, well after the colonization took place, northward range expansion might have produced the presently observed genetic diversity, as inferred from haplotype and nucleotide diversity estimates. On the whole, this study highlights the evolution of Italian Reticulitermes taxa and supports the importance of a wide taxon sampling especially when dealing with organisms easily dispersed by human activities.

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Things fall apart: biological species form unconnected parsimony networks

Biology Letters ◽

10.1098/rsbl.2007.0307 ◽

2007 ◽

Vol 3 (5) ◽

pp. 509-512 ◽

Cited By ~ 192

Author(s):

Michael W Hart ◽

Jennifer Sunday

Keyword(s):

Dna Sequences ◽

Objective Measure ◽

Single Species ◽

Haplotype Network ◽

Biological Species ◽

Phylogenetic Species ◽

Population Genetic Analysis ◽

Phylogenetic Species Concept ◽

Statistical Parsimony ◽

Species Definitions

The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.

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Genetic variation in relation to substratum preferences of Hypogymnia physodes

The Lichenologist ◽

10.1017/s0024282909990247 ◽

2009 ◽

Vol 41 (5) ◽

pp. 547-555 ◽

Cited By ~ 6

Author(s):

Jan-Eric MATTSSON ◽

Anne-Charlotte HANSSON ◽

Louise LINDBLOM

Keyword(s):

Dna Sequences ◽

Sequence Variation ◽

Its Region ◽

Small Subunit ◽

Hypogymnia Physodes ◽

Gene Fragment ◽

Statistical Parsimony ◽

Total Dna ◽

Study Sites ◽

Group 1

AbstractGenetic variability and its relationship to substratum preferences within and among populations of the sorediate foliose lichen Hypogymnia physodes was investigated using sequence variation in the complete nrDNA internal transcribed spacer (ITS) region. A few samples of the putatively closely related, sorediate, H. tubulosa were also included. Samples were collected from each tree species in study sites in Estonia, Finland, and Sweden. In total, DNA sequences from 104 individuals of H. physodes and 16 of H. tubulosa were obtained. A group 1 intron situated at the end of the small subunit (SSU) of the nrDNA was detected in both species. Within-species variability was observed in both species: fifteen haplotypes were found for H. physodes and seven for H. tubulosa for the combined alignment of the intron and the ITS. Possible recombination within the total gene fragment was detected and hence the different regions (intron, ITS1, 5.8S, ITS2) were analysed separately. They show a different degree of variability both between each other and between the species. The number of haplotypes of H. physodes in the four regions are 5, 5, 1, and 5 and for H. tubulosa 5, 2, 1 and 2, respectively. A statistical parsimony estimation resulted in two unconnected networks; one containing all the samples of H. physodes and one containing all H. tubulosa samples. It was not possible to show different potentials of the different haplotypes for establishment on different substrata as the network of H. physodes indicates recombination within the ITS region which may be frequent enough to make this primarily clonally reproducing species to behave like a sexual species.

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Are the Great Plains wildrye (Elymus canadensis) and the Siberian wildrye (Elymus sibiricus) conspecific? A study based on the nuclear 5S rDNA sequences

Botany ◽

10.1139/b2012-013 ◽

2012 ◽

Vol 90 (6) ◽

pp. 407-421 ◽

Cited By ~ 5

Author(s):

Bernard R. Baum ◽

Tara Edwards ◽

Ekaterina Ponomareva ◽

Douglas A. Johnson

Keyword(s):

North America ◽

Great Plains ◽

Dna Sequences ◽

5S Rdna ◽

Sequence Polymorphism ◽

Analysis Of Molecular Variance ◽

Elymus Sibiricus ◽

Rdna Sequences ◽

Statistical Parsimony ◽

Elymus Canadensis

Elymus canadensis L. and Elymus sibiricus L. are difficult to separate by morphology. The latter is found mainly in Asia and extends into northern North America; the former is confined to North America. We obtained the DNA sequences of 135 5S rDNA units collected from 19 localities throughout their respective ranges. The results of statistical parsimony, analysis of molecular variance, and sequence polymorphism analyses show that the two taxa are not conspecific.

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Molecular epidemiology ofSchistosoma mansoniin Uganda: DNA barcoding reveals substantial genetic diversity within Lake Albert and Lake Victoria populations

Parasitology ◽

10.1017/s003118200999031x ◽

2009 ◽

Vol 136 (13) ◽

pp. 1813-1824 ◽

Cited By ~ 38

Author(s):

J. R. STOTHARD ◽

B. L. WEBSTER ◽

T. WEBER ◽

S. NYAKAANA ◽

J. P. WEBSTER ◽

...

Keyword(s):

Dna Barcoding ◽

Nucleotide Diversity ◽

Lake Victoria ◽

Population Diversity ◽

Cytochrome Oxidase Subunit ◽

Mitochondrial Cytochrome Oxidase Subunit ◽

Statistical Parsimony ◽

Mitochondrial Cytochrome Oxidase ◽

Representative Samples

SUMMARYRepresentative samples of UgandanSchistosoma mansonifrom Lake Albert and Lake Victoria were examined using DNA barcoding, sequence analysis of two partially overlapping regions – ASMIT (396 bp) & MORGAN (617 bp) – of the mitochondrial cytochrome oxidase subunit I (cox1). The Victorian sample exhibited greater nucleotide diversity, 1·4%vs. 1·0%, and a significant population partition appeared as barcodes did not cross-over between lakes. With one exception, Lake Albert populations were more mixed by sampled location, while those from Lake Victoria appeared more secluded. Using statistical parsimony, barcode ASMIT 1 was putatively ancestral to all others and analysis of MORGAN cox1 confirmed population diversity. All samples fell into two of five well-resolved lineages; sub-lineages therein broadly partitioning by lake. It seems that barcode ASMIT 1 (and close variants) was likely widely dispersed throughout the Nilotic environment but later diversifiedin situ, and in parallel, within Lake Albert and Lake Victoria. The genetic uniformity of UgandanS. mansonican no longer be assumed, which might better explain known epidemiological heterogeneities. While it appears plausible that locally evolved heritable traits could spread through most of the Lake Albert populations, it seems unlikely they could quickly homogenise into Lake Victoria or amongst populations therein.

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Molecular identification, phylogeny and phylogeography of the entomopathogenic nematodes of the genus Heterorhabditis Poinar, 1976: a multigene approach

Nematology ◽

10.1163/15685411-bja10052 ◽

2020 ◽

pp. 1-17

Author(s):

Manoj Dhakal ◽

Khuong B. Nguyen ◽

David J. Hunt ◽

Ralf-Udo Ehlers ◽

Sergei E. Spiridonov ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Sequence Analysis ◽

Thin Filament ◽

Entomopathogenic Nematodes ◽

Entomopathogenic Nematode ◽

Nematode Species ◽

28S Rrna ◽

Genes Encoding ◽

Statistical Parsimony ◽

Its Rrna

Summary Presently, the genus Heterorhabditis contains 16 valid entomopathogenic nematode species. In this study we used samples from 11 species: H. amazonensis, H. bacteriophora, H. baujardi, H. beicherriana, H. downesi, H. floridensis, H. georgiana, H. indica, H. megidis, H. noenieputensis, and H. zealandica to amplify and sequence five gene fragments: the D2-D3 expansion segments of 28S rRNA, ITS rRNA, COI mtDNA genes and unc-87 and cmd-1 genes encoding thin filament (F-actin)-associated protein and calmodulin, respectively. Fifty new sequences for 11 species were generated. More than 980 sequences of five genes were analysed. Phylogenetic and sequence analysis of these genes using Bayesian inference, maximum likelihood and statistical parsimony confirmed a division of the genus into three clades (groups): ‘Indica’, ‘Bacteriophora’ and ‘Megidis’. The analysis of gene sequences downloaded from GenBank and identified as Heterorhabditis revealed many cases of species misidentifications and presence of reading mistakes in some sequences. Synonymisation of H. somsookae with H. baujardi, H. gerrardi, H. pakistanensis with H. indica, and H. sonorensis with H. taysearae, are confirmed by sequence and phylogenetic analysis. The ITS rRNA and COI genes could be considered as informative markers for species identification, barcoding and phylogeographical studies of Heterorhabditis.

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Overcoming paralogy and incomplete lineage sorting to detect a phylogeographic signal: a GapC study of Armeria pungens

Botany ◽

10.1139/b08-133 ◽

2009 ◽

Vol 87 (2) ◽

pp. 164-177 ◽

Cited By ~ 4

Author(s):

Rosalía Piñeiro ◽

Andrea Costa ◽

Javier Fuertes Aguilar ◽

Gonzalo Nieto Feliner

Keyword(s):

Allelic Variation ◽

Incomplete Lineage Sorting ◽

Direct Sequencing ◽

Nuclear Gene ◽

Amino Acid Sequences ◽

Population History ◽

Lineage Sorting ◽

Genetic Lineages ◽

Statistical Parsimony ◽

Promising Source

Low-copy nuclear genes have been suggested as a promising source of independent phylogeographic markers in plants. However, the available studies at the intraspecific level have revealed that extracting information from them is frequently hampered by paralogy and lack of coalescence of alleles. It is thus relevant to test their utility with plants for which solid data from other markers are available. The aims of this study are to retrieve phylogeographic useful information in a low-copy nuclear gene by examining the congruence of the genetic variation with the geography, as well as with previous nuclear ribosomal, plastid, and amplified fragment length polymorphism (AFLP) markers. Seven combinations of primers have been assayed to characterize the structure of GapC (cytosolic glyceraldehyde 3-phosphate dehydrogenase) in Armeria pungens (Link) Hoffmanns. & Link, a linearly distributed Atlantic–Mediterranean disjunct sand-dune species. A matrix of 101 direct sequences from 71 individuals was analysed with statistical parsimony. To check the reliability of direct sequencing, 216 cloned sequences were also generated. Tests of recombination have also been attempted. By comparing nucleotide and amino acid sequences, three different paralogs (1, 2, 3) were identified of which paralog 2 was sampled for phylogeographic inference. Within this paralog, 13 alleles belonging in three different sequence types (I, II, III) were detected. These types are shown to correspond with lineages from the same locus whose splitting predates the origin of A. pungens, although type III could be a recent paralog. Allelic variation within types I and II followed a clear geographic trend supporting the two main genetic lineages detected in A. pungens with previous markers. This study suggests that information on the population history of a species can be retrieved, even if some uncertainty remains on the source of variation of low-copy nuclear gene sequences, either alleles from the same locus or paralogs.

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