Genetic relationships and variation in the Stylosanthes guianensis species complex assessed by random amplified polymorphic DNA

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 43-49 ◽  
Author(s):  
Kemal Kazan ◽  
John M. Manners ◽  
Don F. Cameron
Keyword(s):  
Species Complex ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Random Sequence ◽  
Distinct Species ◽  
Similar Species ◽  
Protein Patterns ◽  
Stylosanthes Guianensis ◽  
Taxonomic Groups

Genetic variation in the five taxonomic groups of the Stylosanthes guianensis (Aubl.) Sw. complex was investigated using random amplified polymorphic DNA markers (RAPDs). DNA samples from four plants of each of 45 accessions within the S. guianensis species complex were analyzed using 20 oligonucleotides of random sequence. Little variation was found within each of the 18 accessions (1–7% of total RAPD bands in pairwise comparisons) and none within each of the other 27 accessions. However, higher levels of polymorphisms were observed both within (index of genetic distance = 1 − F = 0.16–0.248) and between (1 − F = 0.254–0.408) the five taxa. This level of differentiation at the DNA level supported an earlier classification of the taxa as distinct species. A phenogram based on band sharing was constructed to show genetic relationships among the taxa studied. This phenogram corroborated the description of relationships based on morphological–agronomic characteristics, seed protein patterns, rhizobial affinities, crossability, and pollen stainability of the hybrids. In this phenogram, the most similar species were S. grandiflora and S. hippocampoides (1 − F = 0.264), with S. acuminata also showing closest similarity to these two species (1 − F = 0.277 and 0.283, respectively). Stylosanthes gracilis accessions showed the closest similarity (1 − F = 0.296) to S. guianensis ssp. guianensis accessions. Lowest similarity values (1 − F = 0.335–0.411) were found between these two species and S. grandiflora, S. acuminata, and S. hippocampoides.Key words: polymerase chain reaction, random amplified polymorphic DNA, Stylosanthes guianensis species complex.

An Assessment of Genetic Relationships between Members of the Phytophthora megasperma Complex and Phytophthora vignae using Molecular Markers

1993 ◽  
Vol 6 (4) ◽  
pp. 295 ◽  
Author(s):  
SC Whisson ◽  
BJ Howlett ◽  
ECY Liew ◽  
DJ Maclean ◽  
JM Manners ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Protein Patterns ◽  
Separate Species ◽  
Phytophthora Megasperma ◽  
Polymerase Chain ◽  
Mitochondrial Rflps

Genetic relationships between Phytophora megasperma f. sp. glycinea (Pmg) and morphologically similar taxa, P. megasperma f. sp. medicaginis (Pmm), P. megasperma f. sp. trifolii (Pmt), P. megasperma from Douglas Fir (PmDF) and asparagus (PmAS) and Phytophthora vignae, were explored by restriction fragment length polymorphism (RFLP) analysis of nuclear DNA using random genomic multi-copy, cDNA, and ribosomal DNA probes as well as random amplified polymorphic DNA (RAPDs) and RFLP analysis of ribosomal intergenic spacer regions amplified by the polymerase chain reaction (PCR). Each method detected large differences between these taxa and P. megasperma f. sp. glycinea. P. vignae was more closely related to P. megasperma f. sp. glycinea than the other taxa on the basis of the cDNA RFLPs and RFLPs of PCR amplified rDNA intergenic spacer regions. We conclude that each of the taxa examined represent separate species. This supports the most recent reclassification based on mitochondrial RFLPs and electrophoretic protein patterns of the host-specific taxa to P. sojae (Pmg), P. trifolii (Pmt) and P. medicaginis (Pmm).

Identification of sibling species in the genus Eucyclops from water-bodies of Ukraine and Russia using crossbreeding studies

2014 ◽  
Vol 25 (1-2) ◽  
pp. 61-68 ◽  
Author(s):  
V. I. Monchenko ◽  
L. P. Gaponova ◽  
V. R. Alekseev
Keyword(s):  
Cryptic Species ◽  
River Basin ◽  
Black Sea ◽  
Species Complex ◽  
River Basins ◽  
Water Bodies ◽  
Similar Species ◽  
Basin Water ◽  
Different Populations ◽  
Baltic Sea Basin

Crossbreeding experiments were used to estimate cryptic species in water bodies of Ukraine and Russia because the most useful criterion in species independence is reproductive isolation. The problem of cryptic species in the genus Eucyclops was examined using interpopulation crosses of populations collected from Baltic Sea basin (pond of Strelka river basin) and Black Sea basin (water-reservoires of Dnieper, Dniester and Danube rivers basins). The results of reciprocal crosses in Eucyclops serrulatus-group are shown that E. serrulatus from different populations but from water bodies belonging to the same river basin crossed each others successfully. The interpopulation crosses of E. serrulatus populations collected from different river basins (Dnipro, Danube and Dniester river basins) were sterile. In this group of experiments we assigned evidence of sterility to four categories: 1) incomplete copulation or absence of copulation; 2) nonviable eggs; 3) absence of egg membranes or egg sacs 4) empty egg membranes. These crossbreeding studies suggest the presence of cryptic species in the E. serrulatus inhabiting ecologically different populations in many parts of its range. The same crossbreeding experiments were carries out between Eucyclops serrulatus and morphological similar species – Eucyclops macruroides from Baltic and Black Sea basins. The reciprocal crossings between these two species were sterile. Thus taxonomic heterogeneity among species of genus Eucyclops lower in E. macruroides than in E. serrulatus. The interpopulation crosses of E. macruroides populations collected from distant part of range were fertile. These crossbreeding studies suggest that E. macruroides species complex was evaluated as more stable than E. serrulatus species complex.

Paepalanthus fabianeae (Eriocaulaceae): A New Microendemic Species from a Morphologically Coherent Clade

2020 ◽  
Vol 45 (4) ◽  
pp. 794-801
Author(s):  
Caroline Oliveira Andrino ◽  
Marcelo Fragomeni Simon ◽  
Jair Eustáquio Quintino Faria ◽  
André Luiz da Costa Moreira ◽  
Paulo Takeo Sano
Keyword(s):  
New Species ◽  
Iucn Red List ◽  
Phylogenetic Position ◽  
Similar Species ◽  
Infrageneric Classification ◽  
Espinhaço Range ◽  
Nuclear Its ◽  
Two Populations

Abstract—We describe and illustrate Paepalanthus fabianeae, a new species of Eriocaulaceae from the central portion of the Espinhaço Range in Minas Gerais, Brazil. Previous phylogenetic evidence based on analyses of nuclear (ITS and ETS) and plastid (trnL-trnF and psba-trnH) sequences revealed P. fabianeae as belonging to a strongly supported and morphologically coherent clade containing five other species, all of them microendemic, restricted to the Espinhaço range. Due to the infrageneric classification of Paepalanthus being highly artificial, we preferred not assigning P. fabianeae to any infrageneric group. Paepalanthus fabianeae is known from two populations growing in campos rupestres (highland rocky fields) in the meridional Espinhaço Range. The species is characterized by pseudodichotomously branched stems, small, linear, recurved, and reflexed leaves, urceolate capitula, and bifid stigmas. Illustrations, photos, the phylogenetic position, and a detailed description, as well as comments on habitat, morphology, and affinities with similar species are provided. The restricted area of occurrence allied with threats to the quality of the habitat, mainly due to quartzite mining, justifies the preliminary classification of the new species in the Critically Endangered (CR) category using the guidelines and criteria of the IUCN Red List.

Discovery of New Genera Challenges the Subtribal Classification of Tok-Tok Beetles (Coleoptera: Tenebrionidae: Sepidiini)

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Olivia M Gearner ◽  
Marcin J Kamiński ◽  
Kojun Kanda ◽  
Kali Swichtenberg ◽  
Aaron D Smith
Keyword(s):  
Dna Sequences ◽  
Species Group ◽  
Phylogenetic Placement ◽  
Darkling Beetles ◽  
Species Groups ◽  
Taxonomic Groups ◽  
Inference Methods ◽  
A New Species ◽  
Coleoptera Tenebrionidae

Abstract Sepidiini is a speciose tribe of desert-inhabiting darkling beetles, which contains a number of poorly defined taxonomic groups and is in need of revision at all taxonomic levels. In this study, two previously unrecognized lineages were discovered, based on morphological traits, among the extremely speciose genera Psammodes Kirby, 1819 (164 species and subspecies) and Ocnodes Fåhraeus, 1870 (144 species and subspecies), namely the Psammodes spinosus species-group and Ocnodes humeralis species-group. In order to test their phylogenetic placement, a phylogeny of the tribe was reconstructed based on analyses of DNA sequences from six nonoverlapping genetic loci (CAD, wg, COI JP, COI BC, COII, and 28S) using Bayesian and maximum likelihood inference methods. The aforementioned, morphologically defined, species-groups were recovered as distinct and well-supported lineages within Molurina + Phanerotomeina and are interpreted as independent genera, respectively, Tibiocnodes Gearner & Kamiński gen. nov. and Tuberocnodes Gearner & Kamiński gen. nov. A new species, Tuberocnodes synhimboides Gearner & Kamiński sp. nov., is also described. Furthermore, as the recovered phylogenetic placement of Tibiocnodes and Tuberocnodes undermines the monophyly of Molurina and Phanerotomeina, an analysis of the available diagnostic characters for those subtribes is also performed. As a consequence, Phanerotomeina is considered as a synonym of the newly redefined Molurina sens. nov. Finally, spectrograms of vibrations produced by substrate tapping of two Molurina species, Toktokkus vialis (Burchell, 1822) and T. synhimboides, are presented.

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

Phylogenetic relationships of five morphological groups of hexaploid wheat (Triticum aestivum L. em Thell.) based on RAPD analysis

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 724-727 ◽  
Author(s):  
Wenguang Cao ◽  
G Scoles ◽  
P Hucl ◽  
R N Chibbar
Keyword(s):  
Hexaploid Wheat ◽  
Phylogenetic Relationships ◽  
Genetic Similarity ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Triticum Aestivum L ◽  
Similarity Coefficients ◽  
Morphological Classification ◽  
Wild Wheat

The genetic relationships among the five groups of hexaploid wheat: common, spelta, macha, vavilovii, and semi-wild wheat (SWW) are not clear. Random amplified polymorphic DNA (RAPD) analysis was used to assess phylogenetic relationships among these five morphological groups of hexaploid wheat. RAPD data were analyzed using the NTSYS-PC computer program to generate Jaccard genetic similarity coefficients. A dendrogram based on RAPD analysis grouped 15 accessions into five distinct clusters. These results are in agreement with those based on morphological classification, suggesting that common wheat is most closely related to SWW, followed by spelta, vavilovii, and macha.Key words: RAPD, macha, spelta, vavilovii, semi-wild wheat, phylogenetic relationships.

Two new species in the Ficinia indica complex (Cyperaceae, tribe Cypereae) from South Africa

Phytotaxa ◽  
2017 ◽  
Vol 295 (1) ◽  
pp. 49
Author(s):  
ALUWANI A. TSHIILA ◽  
SAMSON B.M. CHIMPHANGO ◽  
JAN-ADRIAAN VILJOEN ◽  
A. MUTHAMA MUASYA
Keyword(s):  
New Species ◽  
Region Growing ◽  
Distinct Species ◽  
Cape Floristic Region ◽  
Morphological Data ◽  
Similar Species ◽  
Ecological Features ◽  
Dichotomous Key ◽  
As Species ◽  
Two New Species

Unclear boundaries between species hinder identification in the field and in herbaria, especially in species groups that can only be distinguished on the basis of subtle morphological and ecological features. One such taxon is Ficinia indica, widespread in the Greater Cape Floristic Region, growing on deep sandy soils between sea level and 1000 m elevation. Within its range, several phylogenetically related and morphologically similar species co-occur or occupy distinct habitats. Studies in herbaria show species in the Ficinia indica complex to be largely misidentified based on the use of qualitative information. Here, we investigate whether the six taxa recognized, based on one or a few characters, are supported as distinct species based on multivariate analysis of macro-morphological data. Two of the taxa were mostly separated whereas the other four taxa overlapped in multivariate space, but all the taxa could be distinguished using a single or a combination of morphological and ecological characters. We uphold the four previously recognized taxa (Ficinia argyropus, F. elatior, F. indica, F. laevis) as species, describe two new species (F. arnoldii and F. montana), and provide a dichotomous key for their identification.

scholarly journals Multigene phylogeny and morphology reveal Phaeobotryon rhois sp. nov. (Botryosphaeriales, Ascomycota)

Phytotaxa ◽  
2015 ◽  
Vol 205 (2) ◽  
pp. 90 ◽  
Author(s):  
XIN-LEI FAN ◽  
KEVIN D. HYDE ◽  
JIAN-KUI LIU ◽  
YING-MEI LIANG ◽  
CHENG-MING TIAN
Keyword(s):  
New Species ◽  
Distinct Species ◽  
Similar Species ◽  
Multigene Phylogeny ◽  
Fruiting Bodies ◽  
Canker Disease ◽  
Multigene Analysis ◽  
The Family ◽  
Rhus Typhina ◽  
A New Species

The family Botryosphaeriaceae encompasses important plant-associated pathogens, endophytes and saprobes with a wide geographical and host distribution. Two dark-spored botryosphaeriaceous taxa associated with Rhus typhina dieback and canker disease were collected from Ningxia Province, in northwestern China. Morphology and multigene analysis (ITS, LSU and EF-1α) clearly distinguished this clade as a distinct species in the genus. Phaeobotryon rhois is introduced and illustrated as a new species in this paper. The species is characterized by its globose, unilocular fruiting bodies and small, brown, 1-septate conidia. It can be distinguished from the similar species P. cercidis, P. cupressi, P. mamane and P. quercicola based on host association and conidial size and colour.

scholarly journals Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

2021 ◽  
Author(s):  
Viola Kurm ◽  
Ilse Houwers ◽  
Claudia E. Coipan ◽  
Peter Bonants ◽  
Cees Waalwijk ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
In Silico ◽  
Species Complex ◽  
Sequence Data ◽  
In Silico Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

Phenotypic and Genotypic Associations Between Migraine and Lipoprotein Subtractions

Neurology ◽  
2021 ◽  
pp. 10.1212/WNL.0000000000012919
Author(s):  
Yanjun Guo ◽  
Iyas Daghlas ◽  
Padhraig Gormley ◽  
Franco Giulianini ◽  
Paul M Ridker ◽  
...  
Keyword(s):  
Genetic Correlation ◽  
Genetic Relationships ◽  
Meta Analysis ◽  
European Ancestry ◽  
Health Study ◽  
Lipoprotein Subfractions ◽  
Genetic Components ◽  
The Uk ◽  
Summary Data

Background and Objective:To evaluate phenotypic and genetic relationships between migraine and lipoprotein subfractions.Methods:We evaluated phenotypic associations between migraine and 19 lipoprotein subfractions measures in the Women’s Genome Health Study (WGHS, N=22,788). We then investigated genetic relationships between these traits using summary statistics from the International Headache Genetics Consortium (IHGC) for migraine (Ncase=54,552, Ncontrol=297,970) and combined summary data for lipoprotein subfractions (N up to 47,713).Results:There was a significant phenotypic association (odds ratio=1.27 [95% confidence interval:1.12-1.44]) and a significant genetic correlation at 0.18 (P=0.001) between migraine and triglyceride-rich lipoproteins (TRLP) concentration but not for LDL or HDL subfractions. Mendelian randomization (MR) estimates were largely null implying that pleiotropy rather than causality underlies the genetic correlation between migraine and lipoprotein subfractions. Pleiotropy was further supported in cross-trait meta-analysis revealing significant shared signals at four loci (chr2p21 harboring THADA, chr5q13.3 harboring HMGCR, chr6q22.31 harboring HEY2, and chr7q11.23 harboring MLXIPL) between migraine and lipoprotein subfractions. Three of these loci were replicated for migraine (P<0.05) in a smaller sample from the UK Biobank. The shared signal at chr5q13.3 colocalized with expression of HMGCR, ANKDD1B, and COL4A3BP in multiple tissues.Conclusions:The current study supports the association between certain lipoprotein subfractions, especially for TRLP, and migraine in populations of European ancestry. The corresponding shared genetic components may be help identify potential targets for future migraine therapeutics.Classification of Evidence:This study provides Class I evidence that migraine is significantly associated with some lipoprotein subfractions.

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