Molecular Evolution of the Internal Transcribed Spacers (ITS1 and ITS2) and Phylogenetic Relationships among Species of the Family Cucurbitaceae

1998 ◽  
Vol 9 (2) ◽  
pp. 204-219 ◽  
Author(s):  
Jürgen Jobst ◽  
Klaus King ◽  
Vera Hemleben
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacers ◽  
The Family ◽  
Its1 And Its2

scholarly journals In Silico Study Suggesting the Bias of Primers Choice in the Molecular Identification of Fungal Aerosols

2021 ◽  
Vol 7 (2) ◽  
pp. 99
Author(s):  
Hamza Mbareche ◽  
Marc Veillette ◽  
Guillaume J. Bilodeau
Keyword(s):  
In Silico ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
In Silico Analysis ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Sequence Length ◽  
Universal Method ◽  
Continuous Work ◽  
Its1 And Its2

This paper presents an in silico analysis to assess the current state of the fungal UNITE database in terms of the two eukaryote nuclear ribosomal regions, Internal Transcribed Spacers 1 and 2 (ITS1 and ITS2), used in describing fungal diversity. Microbial diversity is often evaluated with amplicon-based high-throughput sequencing approaches, which is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of the primers used for amplification. The goal of this study is to validate if the mismatches of the primers on the binding sites of the targeted taxa could explain the differences observed when using either ITS1 or ITS2 in describing airborne fungal diversity. Hence, the choice of the pairs of primers for each barcode concur with a study comparing the performance of ITS1 and ITS2 in three occupational environments. The sequence length varied between the amplicons retrieved from the UNITE database using the pair of primers targeting ITS1 and ITS2. However, the database contains an equal number of unidentified taxa from ITS1 and ITS2 regions in the six taxonomic levels employed (phylum, class, order, family, genus, species). The chosen ITS primers showed differences in their ability to amplify fungal sequences from the UNITE database. Eleven taxa consisting of Trichocomaceae, Dothioraceae, Botryosphaeriaceae, Mucorales, Saccharomycetes, Pucciniomycetes, Ophiocordyceps, Microsporidia, Archaeorhizomycetes, Mycenaceae, and Tulasnellaceae showed large variations between the two regions. Note that members of the latter taxa are not all typical fungi found in the air. As no universal method is currently available to cover all the fungal kingdom, continuous work in designing primers, and particularly combining multiple primers targeting the ITS region is the best way to compensate for the biases of each one to get a larger view of the fungal diversity.

scholarly journals Tracing phylogenetic relationships in the family Gryllotalpidae

2002 ◽  
Vol 11 (2) ◽  
pp. 169-174 ◽  
Author(s):  
Peggy S. M. Hill ◽  
Cara Hoffart ◽  
Mark Buchheim
Keyword(s):  
Phylogenetic Relationships ◽  
The Family

Phylogenetic analysis of the subfamily Hylodinae (Anura, Leptodactylidae) based on morphological characters

2005 ◽  
Vol 26 (2) ◽  
pp. 139-147 ◽  
Author(s):  
Francisca do Val ◽  
Paulo Nuin
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
The Other ◽  
The Family

AbstractThe systematics and phylogenetic relationships of the family Leptodactylidae are controversial as is the intrafamilial phylogeny of the leptodactylids. Here we analyze the relationships of the leptodactylid subfamily Hylodinae. This subfamily has been considered to be monophyletic and composed of three genera, Hylodes, Crossodactylus and Megaelosia. In the present study 49 characters were used, based on different studies on Leptodactylidae phylogeny. Maximum parsimony methods with unweighted and successively weighted characters were used to estimate the phylogeny of the Hylodinae. Upon analysis, the data provided further evidence of the monophyletic status of the three genera, with Megaelosia being the basal genus and the other two genera being sister taxa. The analysis with successive weighting results in a more resolved topology of the species subgroups of the genus Hylodes and separates this genus from Crossodactylus and confirms that the hylodines are monophyletic.

The first zoeal stage of the yellow land crab Johngarthia lagostoma (Milne Edwards, 1837) (Decapoda: Brachyura: Gecarcinidae)

Zootaxa ◽  
2021 ◽  
Vol 4990 (1) ◽  
pp. 192-200
Author(s):  
SIMONE MARIA DE ALBUQUERQUE LIRA ◽  
CYNTHIA DAYANNE MELLO DE LIMA ◽  
IGOR DE ÁVILA TEIXEIRA ◽  
RALF SCHWAMBORN
Keyword(s):  
Phylogenetic Relationships ◽  
Zoeal Stage ◽  
Dorsal Seta ◽  
Tropical Atlantic ◽  
Larval Morphology ◽  
Land Crab ◽  
The Family ◽  
Fernando De Noronha ◽  
Morphological Differences

The objective of this paper is to describe and illustrate the first zoeal stage of the largest land crab of the Tropical Atlantic, Johngarthia lagostoma (Milne Edwards, 1837) (Brachyura: Gecarcinidae). A larval description of J. lagostoma was previously not available. Larvae were obtained from ovigerous females on Rocas Atoll and Fernando de Noronha Archipelago, Brazil. Twenty larvae were randomly chosen to be dissected and described in detail, while 40 others (20 larvae from each island) were measured only. The published description of the congener J. planatus (Stimpson, 1860) larvae was used for a comparison of larval morphology. Some morphological differences between the first zoeal stage of these two species were: The absence or presence of a simple shorter seta on antennule, number of the minute terminal spines on the antenna, setation of the coxal endite of the maxilla, exopod unsegmented of the first and second maxilliped, and a single mid-dorsal seta on first pleonite. These results and differences observed between these species can assist in studies on phylogenetic relationships within the Family Gecarcinidae MacLeay, 1838, as well as in the identification of the larvae of J. Lagostoma in plankton samples from the tropical Atlantic.  

Phylogenetic relationships of Mediterranean black corals (Cnidaria : Anthozoa : Hexacorallia) and implications for classification within the order Antipatharia

2018 ◽  
Vol 32 (5) ◽  
pp. 1102 ◽  
Author(s):  
M. Bo ◽  
M. Barucca ◽  
M. A. Biscotti ◽  
M. R. Brugler ◽  
A. Canapa ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Data ◽  
Coral Fauna ◽  
Black Coral ◽  
Phylogenetic Studies ◽  
Black Corals ◽  
The Family ◽  
The Mediterranean ◽  
Its1 And Its2 Rdna ◽  
Its1 And Its2

The Mediterranean black coral fauna includes type species of four antipatharian genera belonging to four different families, therefore phylogenetic studies hold great potential for enhancing systematics within the order. The analysis of six Mediterranean antipatharian species by means of nuclear sequence data of internal transcribed spacer (ITS1 and ITS2) rDNA confirms the separation into different families, as was previously noted on a morphological basis, with a clear distinction of the family Leiopathidae, whose position is supported by a unique number of mesenteries and lack of spines on thicker ramifications. The position of a newly recorded black coral species for the Mediterranean basin belonging to the genus Phanopathes is discussed. Antipathes dichotoma, the type species of the genus Antipathes, on which the order Antipatharia was based, does not group with other members of the family Antipathidae. Supporting a recent finding based on mitochondrial markers, this suggests a critical need for revision of the families that will be impacted by reassignment of this nomenclaturally important taxon.

scholarly journals Review of the family Rivulidae (Cyprinodontiformes, Aplocheiloidei) and a molecular and morphological phylogeny of the annual fish genus Austrolebias Costa 1998

2018 ◽  
Vol 16 (3) ◽  
Author(s):  
Marcelo Loureiro ◽  
Rafael de Sá ◽  
Sebastián W. Serra ◽  
Felipe Alonso ◽  
Luis Esteban Krause Lanés ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
The Self ◽  
Phylogenetic Hypothesis ◽  
Annual Life Cycle ◽  
Internal Fertilization ◽  
Annual Fish ◽  
Diapausing Eggs ◽  
Neotropical Fishes ◽  
Seasonal Ponds ◽  
The Family

ABSTRACT The family Rivulidae is the fourth most diverse clade of Neotropical fishes. Together with some genera of the related African family Nothobranchiidae, many rivulids exhibit a characteristic annual life cycle, with diapausing eggs and delayed embryonic development, which allows them to survive in the challenging seasonal ponds that they inhabit. Rivulidae also includes two species known as the only the self-fertilizing vertebrates and some species with internal fertilization. The first goal of this article is to review the systematics of the family considering phylogenetic relationships and synapomorphies of subfamilial clades, thus unifying information that is dispersed throughout the literature. From this revision, it is clear that phylogenetic relationships within Rivulidae are poorly resolved, especially in one of the large clades that compose it, the subfamily Rivulinae, where conflicting hypotheses of relationships of non-annual and annual genera are evident. The second goal of this work is to present an updated phylogenetic hypothesis (based on mitochondrial, nuclear, and morphological information) for one of the most speciose genus of Rivulidae, Austrolebias. Our results confirm the monophyly of the genus and of some subgeneric clades already diagnosed, but propose new relationships among them and their species composition, particularly in the subgenus Acrolebias.

scholarly journals Revisiting Orthotospovirus Phylogeny Using Whole Genomic Data and a Hypothesis for their Geographic Origin and Diversification

2020 ◽  
Author(s):  
Anamarija Butković ◽  
Rubén González ◽  
Santiago F. Elena
Keyword(s):  
Phylogenetic Relationships ◽  
Geographic Origin ◽  
Genome Shuffling ◽  
Genomic Data ◽  
Genomic Sequences ◽  
Genome Database ◽  
Evolutionary Forces ◽  
The Family ◽  
Plant Families ◽  
Negative Sense

ABSTRACTThe family Tospoviridae, a member of the Bunyavirales order, is constituted of tri-segmented negative-sense single-stranded RNA viruses that infect plants and are also able of replicating in their insect vectors in a persistent manner. The family is composed of a single genus, the Orthotospovirus, whose type species is Tomato spotted wilt virus (TSWV). Previous studies assessing the phylogenetic relationships within this genus were based upon partial genomic sequences, thus resulting in unresolved clades and a poor assessment of the roles of recombination and genome shuffling during mixed infections. Complete genomic data for most Orthotospovirus species are now available at NCBI genome database. In this study we have used 62 complete genomes from 20 species. Our study confirms the existence of four phylogroups (A to D), grouped in two major clades (A-B and C-D), within the genus. We have estimated the split between the two major clades ∼3,100 years ago shortly followed by the split between the A and B phylogroups ∼2,860 years ago. The split between the C and D phylogroups happened more recently, ∼1,465 years ago. Segment reassortment has been shown to be important in the generation of novel viruses. Likewise, within-segment recombination events have been involved in the origin of new viral species. Finally, phylogeographic analyses of representative viruses suggests the Australasian ecozone as the possible origin of the genus, followed by complex patterns of migration, with rapid global spread and numerous reintroduction events.IMPORTANCEMembers of the Orthotospovirus genus infect a large number of plant families, including food crops and ornamentals, resulting in multimillionaire economical losses. Despite this importance, phylogenetic relationships within the genus were established years ago based in partial genomic sequences. A peculiarity of orthotospoviruses is their tri-segmented negative sense genomes, which makes segment reassortment and within-segment recombination, two forms of viral sex, potential evolutionary forces. Using full genomes from all described orthotospovirus species, we revisited their phylogeny and confirmed the existence of four major phylogroups with uneven geographic distribution. We have also shown a pervasive role of sex in the origin of new viral species. Finally, using Bayesian phylogeographic methods, we assessed the possible geographic origin and historical dispersal of representative viruses from the different phylogroups.

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