scholarly journals Identifying the North American Plum Species Phylogenetic Signal Using Nuclear, Mitochondrial, and Chloroplast DNA Markers

2016 ◽  
Vol 141 (6) ◽  
pp. 623-644 ◽  
Author(s):  
Dario J. Chavez ◽  
Thomas G. Beckman ◽  
José X. Chaparro
Keyword(s):  
Chloroplast Dna ◽  
Prunus Persica ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Its Region ◽  
Single Copy ◽  
Species Level ◽  
Species Relationships ◽  
The North

Prunus phylogeny has been extensively studied using chloroplast DNA (cpDNA) sequences. Chloroplast DNA has a slow rate of evolution, which is beneficial to determine species relationships at a deeper level. The chloroplast-based phylogenies have a limitation due to the transfer of this organelle by interspecific hybridization. This creates difficulties when studying species relationships. Interspecific hybrids in Prunus occur naturally and have been reported, which creates a problem when using cpDNA-based phylogenies to determine species relationships. The main goal of this project was to identify nuclear gene regions that could provide an improved phylogenetic signal at the species level in Prunus. A total of 11 species in Prunus and within section Prunocerasus were used. Two peach (Prunus persica) haploids were used to test the reliability of the molecular markers developed in this project to amplify single-copy genes. A total of 33 major genes associated with vernalization response, 16 with tree architecture, and 3 with isozymes, were tested. Similarly, 41 simple sequence repeat (SSR) markers, seven cpDNA regions, and the internal transcribed spacer (ITS) region, were used. Multiple gene regions were identified and provided the greatest number of characters, greatest variability, and improved phylogenetic signal at the species level in Prunus section Prunocerasus. Out of those, trnH-psbA, PGI, MAX4, AXR1, LFY, PHYE, and VRN1 are recommended for a phylogenetic analysis with a larger number of taxa. The use of potentially informative characters (PICS) as a measure of how informative a region will be for phylogenetic analyses has been previously reported beneficial in cpDNA regions and it clearly was important in this research. This will allow selecting the region(s), which can be used in phylogenetic studies with higher number of taxa.

Discovery of chloroplast capture in Juniperus excelsa complex by multi- locus phylogeny

Phytotaxa ◽  
2019 ◽  
Vol 413 (1) ◽  
pp. 11-26 ◽  
Author(s):  
FATEMEH HOJJATI ◽  
ROBERT P. ADAMS ◽  
RANDALL G. TERRY
Keyword(s):  
Concerted Evolution ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Single Copy ◽  
Species Level ◽  
Lineage Sorting ◽  
Chloroplast Capture ◽  
Juniperus Excelsa ◽  
Cp Genome

Previous studies of nrDNA (nuclear DNA) of Juniperus seravschanica indicated its nuclear DNA (ITS) was from an ancestor of J. polycarpos. However, analysis of cpDNA (chloroplast DNA) suggested the taxon had derived its chloroplast from an ancestor of J. foetidissima. That study has been viewed as putative, because the ITS region is sometimes unreliable for the detection of ancestral hybrids due to concerted evolution and lineage sorting. The recent availability of several single copy nuclear genes (SCNGs) with primers specifically designed for Juniperus presented an opportunity to fully investigate this case of putative chloroplast capture. Three phylogenetic analyses using five SCNGs (LHCA4, maldehy, myb, CnAIP3 and 4CL), ITS region, and four cpDNAs (petN- psbM, trnD-trnT, trnL-trnF and trnS-trnG) were performed on J. seravschanica, as well as other members of the J. excelsa complex: J. excelsa, J. polycarpos, and J. p. var. turcomanica. Analyses revealed incongruence between SCNGs, ITS region and cpDNA showing that J. seravschanica contains an ancestral J. foetidissima/ J. thruifera cp genome. In addition, the phylogenies indicate that the J. excelsa complex is composed of three distinct clades at the species level: J. excelsa, J. polycarpos and J. seravschanica and two varieties of J. polycarpos: J. p. var. polycarpos and J. p. var. turcomanica.

Three new species of Ophryotrocha (Annelida: Dorvilleidae) from a whale-fall in the North-East Atlantic

Zootaxa ◽  
2009 ◽  
Vol 2228 (1) ◽  
pp. 43-56 ◽  
Author(s):  
HELENA WIKLUND ◽  
ADRIAN G. GLOVER ◽  
THOMAS G. DAHLGREN
Keyword(s):  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Close Relative ◽  
North East ◽  
The North ◽  
Organic Carbon Flux ◽  
Naturally Occurring ◽  
Three New Species ◽  
First Time ◽  
Complex Organic

Three new Ophryotrocha species are described from sites with high levels of organic carbon flux including a whale-fall at 125 m depth off the Swedish coast and sediment sampled at 104 m depth beneath a fish farm in a Norwegian fjord. Phylogenetic analyses based on the nuclear gene H3 and the mitochondrial genes COI and 16S using MrBayes and Maximum Likelihood analyses show that Ophryotrocha eutrophila sp. nov. is a close relative to Ophryotrocha puerilis, while Ophryotrocha craigsmithi sp. nov. falls together with Palpiphitime lobifera, and Ophryotrocha scutellus sp. nov. occur within the 'hartmanni' clade. The genus Ophryotrocha is in our study monophyletic only if the genera Iphitime and Palpiphitime are included. Two representatives of Ophryotrocha previously described from anthropogenically-enriched sediments are here reported for the first time in very high abundance from a naturally occurring habitat. We suggest that whale falls are important habitats for the evolution of ecosystem services such as the degradation of complex organic compounds.

scholarly journals Phylogeny of the Genus Chrysanthemum L.: Evidence from Single-Copy Nuclear Gene and Chloroplast DNA Sequences

PLoS ONE ◽  
2012 ◽  
Vol 7 (11) ◽  
pp. e48970 ◽  
Author(s):  
Ping-Li Liu ◽  
Qian Wan ◽  
Yan-Ping Guo ◽  
Ji Yang ◽  
Guang-Yuan Rao
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequences ◽  
Nuclear Gene ◽  
Single Copy ◽  
Single Copy Nuclear Gene ◽  
Chloroplast Dna Sequences

scholarly journals The genus Coprinellus (Basidiomycota; Agaricales) in Pakistan with the description of four new species

MycoKeys ◽  
2018 ◽  
Vol 39 ◽  
pp. 41-61 ◽  
Author(s):  
Shah Hussain ◽  
Muhammad Usman ◽  
Najam-ul-Sehar Afshan ◽  
Habib Ahmad ◽  
Junaid Khan ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Molecular Data ◽  
Species Level ◽  
Rdna Its ◽  
The Family ◽  
Rdna Its Region ◽  
Morphological And Molecular Data ◽  
Species Descriptions

Mushrooms with a thin-fleshed pileus that becomes plicate on opening, deliquescent lamellae and dark brown to blackish basidiospores are commonly called coprinoid mushrooms. The genusCoprinellusis one of the important lineages of coprinoid mushroom in the family Psathyrellaceae. Species-level taxonomy inCoprinellusis based mainly on the presence or absence and the structure of veil and cystidia on the pileus, of cystidia on the lamellae and on basidiospore morphology. In this study, four new species ofCoprinellus(Co.campanulatus,Co.disseminatus-similis,Co.pakistanicusandCo.tenuis) are described from Pakistan. Species descriptions are based on morphological and molecular data. Phylogenetic analyses based on nuc rDNA ITS region show that the new speciesCo.campanulatusandCo.disseminatus-similisare clustered in a clade including members of section Micacei;Co.tenuisfalls in a clade with members of section Domestici; andCo.pakistanicusrecovered in a separate clade adjacent to other recently described clades of genusCoprinellus. Morpho-anatomical descriptions of the new species and comparison with closely allied taxa are provided. With this study, the number of known species ofCoprinellusin Pakistan has reached eight.

Molecular relationships in subtribe Brassicinae (Cruciferae, tribe Brassiceae)

1993 ◽  
Vol 71 (7) ◽  
pp. 906-918 ◽  
Author(s):  
S.I. Warwick ◽  
L.D. Black
Keyword(s):  
Chloroplast Dna ◽  
Restriction Site ◽  
Genetic Relatedness ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Data Sets ◽  
Restriction Site Variation ◽  
Site Variation ◽  
Subtribe Brassicinae ◽  
Molecular Relationships

Restriction-site variation for 17 endonucleases was compared in the large single-copy region of the chloroplast genome in 74 taxa of the genera Brassica, Coincya, Diplotaxis, Eruca, Erucastrwn, Hirschfeldia, Raphanus, Sinapidendron, Sinapis, and Trachystoma (subtribe Brassicinae, tribe Brassiceae, Cruciferae). A total of 422 restriction-site mutations was observed, with 228 (54%) showing variation among taxa. Phylogenetic analyses indicated a clear division of the subtribe into two main lineages designated here as Rapa–Oleracea and Nigra. Polyphyly was evident in five genera (Brassica, Diplotaxis, Erucastrum, Sinapis, and Trachystoma) as indicated by their placement in both lineages and (or) further separation into groups within a lineage. The genera Coincya, Hirschfeldia, and Sinapidendron were monophyletic within the Nigra lineage, as were Eruca and Raphanus in the Rapa–Oleracea lineage. Four major groups were recognized within each lineage. The lowest levels of chloroplast DNA divergence were observed among taxa belonging to the same cytodeme or crossing group and were highest for Brassica rapa and Brassica oleracea versus Brassica nigra at 2.10–3.91% and 2.00–3.78%, respectively. The chloroplast DNA data were incongruent with traditional taxonomic circumscription of 5 of the 10 genera but concordant with other data sets that support the close genetic relatedness of all 10 genera. Key words: Brassica, Coincya, Erucastrum, Sinapidendron, Trachystoma, chloroplast DNA restriction-site variation.

Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences

2009 ◽  
Vol 21 (6) ◽  
pp. 565-570 ◽  
Author(s):  
Kristen L. Kuhn ◽  
Thomas J. Near
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Single Copy ◽  
Morphological Characters ◽  
Mitochondrial Genes ◽  
Phylogenetic Resolution

AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

Molecular phylogeny of Juniperus in Iran with special reference to the J. excelsa complex, focusing on J. seravschanica

Phytotaxa ◽  
2018 ◽  
Vol 375 (2) ◽  
pp. 135 ◽  
Author(s):  
FATEMEH HOJJATI ◽  
SHAHROKH KAZEMPOUR-OSALOO ◽  
ROBERT PETER ADAMS ◽  
MOSTAFA ASSADI
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Single Copy ◽  
Hybrid Origin ◽  
Nrdna Its ◽  
Nw Iran ◽  
Intergenic Spacers ◽  
Single Copy Nuclear Gene ◽  
Sw Iran

A total of over 100 accessions representing 11 species of Juniperus in Iran using multiple DNA regions were included in phylogenetic analyses. Analyses of four plastid intergenic spacers (petN-psbM, trnD-trnT, trnL-trnF, trnS-trnG) and nrDNA ITS sequences retrieved Juniperus in Iran as a monophyletic group with two clades corresponding to sections Juniperus and Sabina. Our data support the recognition of J. communis, J. deltoides, J. foetidissima, J. polycarpos var. polycarpos and var. turcomanica, J. sabina and J. seravschanica in Iran. Based on sequences from nrDNA ITS, plastid petN-psbM and single copy nuclear gene LHCA, specimens from the SE Iran that were previously considered to be a part of the J. excelsa complex were shown to be J. seravschanica. Samples from NE Iran were found to be J. polycarpos var. turcomanica and specimens from NW Iran were shown to be J. polycarpos var. polycarpos. Plants belonging to the J. excelsa complex from SW Iran appear to be of hybrid origin between J. polycarpos from N Iran and J. seravschanica from SE Iran. None of the Juniperus samples from Iran were found to be J. excelsa s str., as compared with typical samples from Greece. The sequence data from nrDNA ITS, plastid petN-psbM, trnD-trnT, trnL-trnF, trnS-trnG and single copy nuclear genes (LHCA4, maldehy, myb, CnAIP3 and 4CL) were utilized in this study to identify Iranian samples R, U, K as J. seravschanica.

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

scholarly journals Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kyung Seok Kim ◽  
Kevin J. Roe
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

Relationships of North American members of Rhodiola (Crassulaceae)

Botany ◽  
2014 ◽  
Vol 92 (12) ◽  
pp. 901-910 ◽  
Author(s):  
Joel P. Olfelt ◽  
William A. Freyman
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Phylogenetic Analyses ◽  
Black Hills ◽  
Trnl Intron ◽  
The North ◽  
Alpine Habitats ◽  
Rare And Endangered ◽  
Chloroplast Dna Sequences ◽  
Rhodiola Integrifolia

Taxa of Rhodiola L. (Crassulaceae) generally grow in arctic or alpine habitats. Some Rhodiola species are used medicinally, one taxon, Rhodiola integrifolia Raf. subsp. leedyi (Rosend. & J.W.Moore) Moran, (Leedy’s roseroot), is rare and endangered, and the group’s biogeography in North America is intriguing because of distributional disjunctions and the possibility that Rhodiola rhodantha (A.Gray) H.Jacobsen (2n = 7II) and Rhodiola rosea L. (2n = 11II) hybridized to form Rhodiola integrifolia Raf. (2n = 18II). Recent studies of the North American Rhodiola suggest that the group’s current taxonomy is misleading. We analyzed nuclear and chloroplast DNA sequences (internal transcribed spacer (ITS), trnL intron, trnL–trnF spacer, trnS–trnG spacer) from the North American Rhodiola taxa. We combined our data with GenBank sequences from Asian Rhodiola species, performed parsimony, maximum likelihood (ML), and Bayesian phylogenetic analyses, and applied a Bayesian clock model to the ITS data. Our analyses reveal two major Rhodiola clades, suggest that hybridization between R. rhodantha and R. rosea lineages was possible, show two distinct clades within R. integrifolia, and demonstrate that a Black Hills, South Dakota, Rhodiola population should be reclassified as Leedy’s roseroot. We recommend that R. integrifolia be revised, and that the Black Hills Leedy’s roseroot population be managed as part of that rare and endangered taxon.

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