Phylogenetic relationships of the ciliate class Heterotrichea (Protista, Ciliophora, Postciliodesmatophora) inferred from multiple molecular markers and multifaceted analysis strategy

Verbascum is one of the main genera of Scrophulariaceae, but delimitation and phylogenetic relationships of this genus are unclear and have not yet been studied using DNA sequences. Here, using four selected molecular markers (nrDNA ITS and the plastid spacers trnS/G, psbA-trnH and trnY/T), we present a phylogeny of Verbascum and test previous infrageneric taxonomic hypotheses as well as its monophyly with respect to Scrophularia. We additionally discuss morphological variation and the utility of morphological characters as predictors of phylogenetic relationships. Our results show that while molecular data unambiguously support the circumscription of Verbascum inferred from morphology, they prove to be of limited utility in resolving infrageneric relationships, suggesting that Verbascum ‘s high species diversity is due to rapid and recent radiation. Our work provides phylogenetic estimation of the genus Verbascum using molecular data and can serve as a starting point for future investigations of Verbascum and relatives.

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Phylogeny and classification of the New World suboscines (Aves, Passeriformes)

Zootaxa ◽

10.11646/zootaxa.3613.1.1 ◽

2013 ◽

Vol 3613 (1) ◽

pp. 1-35 ◽

Cited By ~ 46

Author(s):

JAN I. OHLSON ◽

MARTIN IRESTEDT ◽

PER G. P. ERICSON ◽

JON FJELDSÅ

Keyword(s):

Molecular Markers ◽

Phylogenetic Relationships ◽

New World ◽

Remarkable Difference ◽

Phylogenetic Hypothesis ◽

New Family ◽

Climatic Optimum

Here we present a phylogenetic hypothesis for the New World suboscine radiation, based on a dataset comprising of 219 terminal taxa and five nuclear molecular markers (ca. 6300 bp). We also estimate ages of the main clades in this radiation. This study corroborates many of the recent insights into the phylogenetic relationships of New World suboscines. It further clarifies a number of cases for which previous studies have been inconclusive, such as the relationships of Conopophagidae, Melanopareiidae and Tityridae. We find a remarkable difference in age of the initial divergence events in Furnariida and Tyrannida. The deepest branches in Furnariida are of Eocene age, whereas the extant lineages of Tyrannida have their origin in the Oligocene. Approximately half of the New World suboscine species are harboured in 5 large clades that started to diversify around the Mid Miocene Climatic Optimum (16–12 Mya). Based on our phylogenetic results we propose a revised classification of the New World suboscines. We also erect new family or subfamily level taxa for four small and isolated clades: Berlepschiinae, Pipritidae, Tachurididae and Muscigrallinae.

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Phylogeny of Dorippoidea (Crustacea : Decapoda : Brachyura) inferred from three mitochondrial genes

Invertebrate Systematics ◽

10.1071/is09020 ◽

2009 ◽

Vol 23 (3) ◽

pp. 223 ◽

Cited By ~ 4

Author(s):

Y. W. Sin ◽

Joelle C. Y. Lai ◽

Peter K. L. Ng ◽

K. H. Chu

Keyword(s):

Molecular Markers ◽

Cytochrome C ◽

16S Rrna ◽

Cytochrome C Oxidase ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Mitochondrial Genes ◽

12S Rrna ◽

Generic Relationships ◽

I Gene

The phylogenetic relationships between 10 of 13 genera of crabs from the superfamily Dorippoidea were investigated using mitochondrial 16S rRNA, 12S rRNA and cytochrome c oxidase subunit I gene sequences. The resultant phylogenetic trees based on the three molecular markers support the division of Dorippidae and Ethusidae as monophyletic families within the Dorippoidea. The inferred inter-generic relationships within Dorippidae concur with groupings based on the overall morphology of the carapace and structures of the male first pleopods.

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The use of RAPD markers in Hordeum phylogeny

Genome ◽

10.1139/g96-082 ◽

1996 ◽

Vol 39 (4) ◽

pp. 646-654 ◽

Cited By ~ 29

Author(s):

Elizabeth F. Marillia ◽

Graham J. Scoles

Keyword(s):

Molecular Markers ◽

Key Words ◽

Phylogenetic Relationships ◽

Rapd Markers ◽

Rapd Analysis ◽

Tree Topology ◽

Binary Matrix ◽

Phylogenetic Studies ◽

Cultivated Barley ◽

Hordeum Species

The phylogenetic relationships among 39 wild Hordeum species, subspecies, and cultivated barley were investigated using RAPD markers as discriminating characters. Seventy-six RAPD fragments were generated using 12 single decameric primers of arbitrary nucleotide sequences. Amplification reactions resulted in fragments ranging in length between 200 and 2000 bp. Clearly resolved bands were scored for their presence or absence in a binary matrix. Amplified products were treated as independent characters to generate a phenogram using the NTSYS-PC package. Tree topology was generally found to be consistent with those based on morphological treatments. However, a few species like H. erectifolium, H. jubatum and, to a lesser extent, H. bulbosum occupied a position different from previous classifications. The results demonstrated that RAPD technology represents a useful and reliable tool for detecting polymorphism for phylogenetic studies. Key words : RAPD analysis, molecular markers, phylogenetic studies, Hordeum species, barley.

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Phylogenetic analyses using molecular markers reveal ecological lineages in Medetera (Diptera: Dolichopodidae)

The Canadian Entomologist ◽

10.4039/n11-031 ◽

2011 ◽

Vol 143 (6) ◽

pp. 662-673 ◽

Cited By ~ 3

Author(s):

Marc Pollet ◽

Christoph Germann ◽

Marco Valerio Bernasconi

Keyword(s):

Molecular Markers ◽

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Sister Group ◽

Species Group ◽

Global Distribution ◽

Sister Group Relationship ◽

Mitochondrial Coi ◽

Terrestrial Habitats

AbstractMedetera Fischer von Waldheim is the most speciose genus in the Medeterinae, with a nearly ubiquitous global distribution. Phylogenetic relationships within Medetera and between Medetera and four other medeterine genera were investigated using mitochondrial (COI, 16S) and nuclear (18S) markers to test morphological hypotheses. Our results confirm most of Bickel's hypotheses. Thrypticus Gerstäcker shows a sister-group relationship with Medetera + Dolichophorus Lichtwardt. The Medetera species included here split into two clades. One clade corresponds to the M. diadema L. – veles Loew species group sensu Bickel. The second clade is largely composed of the M. apicalis (Zetterstedt) species group sensu Bickel and the M. aberrans Wheeler species group sensu Bickel + Dolichophorus. Although most Medeterinae are associated with plants (mainly trees), species in at least two separate lineages demonstrate a secondary return to terrestrial habitats. The implication of this evolutionary phenomenon is briefly discussed.

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The influence of molecular markers and methods on inferring the phylogenetic relationships between the representatives of the Arini (parrots, Psittaciformes), determined on the basis of their complete mitochondrial genomes

BMC Evolutionary Biology ◽

10.1186/s12862-017-1012-1 ◽

2017 ◽

Vol 17 (1) ◽

Cited By ~ 10

Author(s):

Adam Dawid Urantowka ◽

Aleksandra Kroczak ◽

Paweł Mackiewicz

Keyword(s):

Molecular Markers ◽

Phylogenetic Relationships ◽

Mitochondrial Genomes ◽

Complete Mitochondrial Genomes

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Effectiveness of SSR molecular markers in evaluating the phylogenetic relationships among eight Actinidia species

Scientia Horticulturae ◽

10.1016/j.scienta.2008.01.011 ◽

2008 ◽

Vol 116 (3) ◽

pp. 305-310 ◽

Cited By ~ 15

Author(s):

A.E. Korkovelos ◽

A.G. Mavromatis ◽

W.G. Huang ◽

M. Hagidimitriou ◽

A. Giakoundis ◽

...

Keyword(s):

Molecular Markers ◽

Phylogenetic Relationships

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Low-Copy Nuclear Genes Reveal New Evidence of Incongruence in Relationships Within Malvaceae s. l.

Systematic Botany ◽

10.1600/036364421x16370109698551 ◽

2021 ◽

Vol 46 (4) ◽

pp. 1042-1052

Author(s):

Rebeca Hernández-Gutiérrez ◽

Carolina Granados Mendoza ◽

Susana Magallón

Keyword(s):

Molecular Markers ◽

Phylogenetic Relationships ◽

Its Region ◽

Nuclear Genes ◽

Phylogenetic Informativeness ◽

The Family ◽

Nuclear Regions ◽

The One ◽

Genome Information ◽

New Evidence

Abstract— The family Malvaceae s. l. is a clade that comprises nine subfamilies. Phylogenetic relationships among them are not completely resolved and are inconsistent among studies, probably due to low phylogenetic informativeness of conventional molecular markers. In the present study, we provide new phylogenetic information for Malvaceae s. l. derived from newly-designed group-specific nuclear markers. By mining transcriptome data from the One Thousand Plants Project (1KP) and publicly available genome information from cotton, cacao, and Arabidopsis, we designed a set of molecular markers of potentially single- or low-copy nuclear genes for Malvaceae s. l. Phylogenetic potential of these new loci was compared to previously applied conventional markers (i.e. plastid trnK-matK region and rbcL gene and the nrDNA ITS region) using the phylogenetic informativeness method. The results show that, when the mined nuclear regions are used in combination, it is possible to resolve relationships at different taxonomic levels within the phylogeny. However, incongruence among nuclear loci is frequent in the group, explaining the prevalence of unresolved phylogenetic relationships.

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Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales)

Genes ◽

10.3390/genes11070830 ◽

2020 ◽

Vol 11 (7) ◽

pp. 830

Author(s):

Delil A. Chincoya ◽

Alejandro Sanchez-Flores ◽

Karel Estrada ◽

Clara E. Díaz-Velásquez ◽

Antonio González-Rodríguez ◽

...

Keyword(s):

Population Genetics ◽

Molecular Markers ◽

Dna Sequences ◽

Phylogenetic Relationships ◽

Molecular Variation ◽

Short Sequence ◽

Dna Variation ◽

Chloroplast Genomes ◽

Evolutionary Studies ◽

Phylogenetic Resolution

In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500–1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of Mammillaria. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was M. solisioides (256), whereas M. pectinifera contained the highest amount of SSRs (84). In contrast, M. zephyranthoides contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.

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