Unravelling allopolyploid origins in the Alyssum montanum–A. repens species complex (Brassicaceae): low-copy nuclear gene data complement plastid DNA sequences and AFLPs

2017 ◽  
Vol 184 (4) ◽  
pp. 485-502 ◽  
Author(s):  
Andrea Melichárková ◽  
Stanislav Španiel ◽  
Daniela Brišková ◽  
Karol Marhold ◽  
Judita Zozomová-Lihová
Keyword(s):  
Dna Sequences ◽  
Species Complex ◽  
Nuclear Gene ◽  
Plastid Dna ◽  
Gene Data

A comparative analysis of genetic differentiation of the E. affinis species complex and some other Eurytemora species, using the CO1, nITS and 18SrRNA genes (Copepoda, Calanoida)

Crustaceana ◽  
2020 ◽  
Vol 93 (8) ◽  
pp. 931-955
Author(s):  
Natalia Sukhikh ◽  
Ekaterina Abramova ◽  
Anne-Catherine Holl ◽  
Sami Souissi ◽  
Victor Alekseev
Keyword(s):  
Comparative Analysis ◽  
Genetic Differentiation ◽  
Cryptic Species ◽  
Dna Sequences ◽  
Species Complex ◽  
Nuclear Gene ◽  
Nuclear Genes ◽  
Group Species

Abstract Eurytemora represents a challenging group of species due to their taxonomy, in particular the former group of cryptic species known as E. affinis sensu lato. In this paper, we analyse DNA sequences that are all available in GenBank, along with our own data on the genus Eurytemora. For this study, a set of mitochondrial and nuclear genes (CO1, nITS and 18SrRNA) was used. In total 543 sequences were analysed (437 CO1; 54 nITS; 52 18SrRNA). However, this work is mainly meta-analytical, and only 67 sequences from unstudied earlier populations or species were obtained specifically for this work to analyse the genetic differentiation of the morphologically described species. We found that relatively young species of the E. affinis complex are different from each other in the CO1 and nITS genes, but not in the conservative 18SrRNA nuclear gene. Nucleotide differences among affinis-group species in the CO1 gene are 9.4-11.8%; in the nITS genes, 1.1-5.0%. At the same time, all other studied Eurytemora species have significant differences from each other in the CO1 and nITS genes, as well as in 18SrRNA. The level of differences among the species is 13.2-19.2% for the CO1 gene, 18.0-27.6.2% for nITS genes, and 0.4-1.8% for the 18SrRNA gene.

scholarly journals Coupling of Bacterial Endosymbiont and Host Mitochondrial Genomes in the Hydrothermal Vent Clam Calyptogena magnifica

2003 ◽  
Vol 69 (4) ◽  
pp. 2058-2064 ◽  
Author(s):  
Luis A. Hurtado ◽  
Mariana Mateos ◽  
Richard A. Lutz ◽  
Robert C. Vrijenhoek
Keyword(s):  
Dna Sequences ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Nuclear Gene ◽  
Sexual Population ◽  
Origin And Evolution ◽  
Bacterial Endosymbionts ◽  
Sulfur Oxidizing ◽  
Tight Association ◽  
Clam Population

ABSTRACT The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Vesicomyidae) depends for its nutrition on sulfur-oxidizing symbiotic bacteria housed in its gill tissues. This symbiont is transmitted vertically between generations via the clam's eggs; however, it remains uncertain whether occasionally symbionts are horizontally transmitted or acquired from the environment. If symbionts are transmitted strictly vertically through the egg cytoplasm, inheritance of symbiont lineages should behave as if coupled to the host's maternally inherited mitochondrial DNA. This coupling would be obscured, however, with low rates of horizontal or environmental transfers, the equivalent of recombination between host lineages. Population genetic analyses of C. magnifica clams and associated symbionts from eastern Pacific hydrothermal vents clearly supported the hypothesis of strictly maternal cotransmission. Host mitochondrial and symbiont DNA sequences were coupled in a clam population that was polymorphic for both genetic markers. These markers were not similarly coupled with sequence variation at a nuclear gene locus, as expected for a randomly mating sexual population. Phylogenetic analysis of the two cytoplasmic genes also revealed no evidence for recombination. The tight association between vesicomyid clams and their vertically transmitted bacterial endosymbionts is phylogenetically very young (<50 million years) and may serve as a model for the origin and evolution of eukaryotic organelles.

scholarly journals Molecular phylogeny ofSolms-laubachia(Brassicaceae) s.l., based on multiple nuclear and plastid DNA sequences, and its biogeographic implications

2009 ◽  
Vol 47 (5) ◽  
pp. 402-415 ◽  
Author(s):  
Ji-Pei YUE ◽  
Hang SUN ◽  
David A. BAUM ◽  
Jian-Hua LI ◽  
Ihsan A. AL-SHEHBAZ ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Plastid Dna

Generating single-copy nuclear gene data for a recent adaptive radiation

2006 ◽  
Vol 39 (1) ◽  
pp. 124-134 ◽  
Author(s):  
Justen B. Whittall ◽  
Andrew Medina-Marino ◽  
Elizabeth A. Zimmer ◽  
Scott A. Hodges
Keyword(s):  
Adaptive Radiation ◽  
Nuclear Gene ◽  
Single Copy ◽  
Single Copy Nuclear Gene ◽  
Gene Data

Mitosis and Interphase of the Highly Polyploid Palm Voanioalagerardii (2n = 606 ± 3)

2015 ◽  
Vol 147 (1) ◽  
pp. 70-79 ◽  
Author(s):  
Martin Röser
Keyword(s):  
Nuclear Gene ◽  
Point Of View ◽  
Fluorochrome Banding ◽  
Dna Amount ◽  
Metaphase Chromosomes ◽  
Banding Patterns ◽  
High Polyploid ◽  
Molecular Phylogenetic ◽  
Gene Data ◽  
First Time

The endemic, highly polyploid, monotypic Madagascan palm genus Voanioala (2n ≈ 606) was studied with regard to mitotic stages and interphase. Features of the cell cycle, morphology and sizes of metaphase chromosomes, fluorochrome banding patterns, and silver staining of NORs of such an extremely high polyploid organism are reported for the first time. On a whole, karyokinesis appears to be stable and efficient. A comparison with closely related palm taxa reveals that V. gerardii is 38-ploid, and comparison with the closely related genera Butia, Cocos (coconut) and Jubaea shows that Voanioala has lost ∼35% of its DNA amount subsequent to polyploidization and has suppressed between 74 and 88% of the original nucleolar organizers. About 10 active NORs are present in the nuclei. An auto- or allopolyploid origin of Voanioala is discussed with respect to currently available nuclear gene data. The biogeographic relations to Jubaeopsis, a closely related, monotypic, apparently likewise relict palm genus from eastern mainland South Africa are discussed. From a cytogenetic point of view, a common polyploid ancestor of both genera is most likely, but the available molecular phylogenetic data are not univocal.

scholarly journals Phylogenetic Position and Generic Placement of The Socorro Wren (Thryomanes Sissonii)

The Auk ◽  
2005 ◽  
Vol 122 (1) ◽  
pp. 50-56 ◽  
Author(s):  
Juan E. Martínez Gómez ◽  
Brian R. Barber ◽  
A. Townsend Peterson
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Species Complex ◽  
Taxonomic Classification ◽  
Phylogenetic Position ◽  
Base Pairs ◽  
House Wren ◽  
Taxonomic History ◽  
Socorro Island ◽  
Nd2 Gene

Abstract Since early in its taxonomic history, placement of the Socorro Wren (Thryomanes sissonii) has been an object of contention. Of particular interest is its current placement in the genus Thryomanes, which makes that genus ditypic and leads to an odd biogeographic scenario for the Socorro Wren's colonization of Socorro Island. We assessed its phylogenetic position by analyzing 516 base pairs of mitochondrial DNA sequences from the ND2 gene of this species and 14 additional wren taxa. Contrary to its present placement, the Socorro Wren is nested phylogenetically within the House Wren species complex, being placed as sister to the clade Troglodytes aedon + T. musculus. The current hypothesis (i.e. sister to Thryomanes bewickii) is strongly invalidated by our analysis. Our analyses indicate that the most appropriate taxonomic classification for the Socorro Wren is Troglodytes sissonii. Posición Filogenética y Ubicación Genérica de Thryomanes sissonii

A molecular phylogeny of the “Madascincus polleni species complex”, with description of a new species of scincid lizard from the coastal dune area of northern Madagascar

Zootaxa ◽  
2011 ◽  
Vol 2876 (1) ◽  
pp. 1 ◽  
Author(s):  
AURÉLIEN MIRALLES ◽  
JÖRN KÖHLER ◽  
FRANK GLAW ◽  
MIGUEL VENCES
Keyword(s):  
Dna Sequences ◽  
Species Complex ◽  
Nuclear Dna ◽  
Taxonomic Status ◽  
Nominal Species ◽  
Morphological Examination ◽  
Closely Related Species ◽  
A New Species ◽  
Evolutionary Lineages ◽  
Dune Area

The present paper constitutes a study on a taxonomically confusing group of closely related species belonging to the Malagasy skink genus Madascincus, currently encompassing the nominal species M. polleni, M. intermedius and M. stumpffi. Based on combined analyses of mitochondrial and nuclear DNA sequences (ND1 and RAG2 genes, respectively), and morphological examination, we provide evidence for the existence of at least four distinct evolutionary lineages within this complex: Madascincus stumpffi; Madascincus arenicola sp. nov. from northern Madagascar; and two cryptic species morphologically similar to the name-bearing types of M. polleni and M. intermedius. The two latter species, although genetically distinct, appear to be morphologically indistinguishable and their taxonomic status cannot be resolved until a better sampling will be available.

Phylogenetic relationships based on nuclear and plastid DNA sequences reveal recent diversification and discordant patterns of morphological evolution of the Chilean genera of Gilliesieae (Amaryllidaceae: Allioideae)

2020 ◽  
Vol 194 (1) ◽  
pp. 84-99
Author(s):  
Inelia Escobar ◽  
Eduardo Ruiz-Ponce ◽  
Paula J Rudall ◽  
Michael F Fay ◽  
Oscar Toro-Núñez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Incomplete Lineage Sorting ◽  
Morphological Evolution ◽  
Strong Support ◽  
Plastid Dna ◽  
Lineage Sorting ◽  
Generic Level ◽  
Molecular Analyses ◽  
Floral Diversity

Abstract Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.

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