Contrasting the population genetic structure of two velvet worm taxa (Onychophora : Peripatopsidae : Peripatopsis) in forest fragments along the south-eastern Cape, South Africa

2017 ◽  
Vol 31 (6) ◽  
pp. 781 ◽  
Author(s):  
Savel R. Daniels ◽  
Megan Dreyer ◽  
Prashant P. Sharma
Keyword(s):  
South Africa ◽  
Population Genetic ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Forest Fragments ◽  
Eastern Cape ◽  
Dna Sequence Data ◽  
Mtdna Coi ◽  
Haplotype Networks ◽  
Velvet Worm

During the present study, we examined the phylogeography and systematics of two species of velvet worm (Peripatopsis Pocock, 1894) in the forested region of the southern Cape of South Africa. A total of 89 P. moseleyi (Wood-Mason, 1879) and 65 P. sedgwicki (Purcell, 1899) specimens were collected and sequenced for the cytochrome c oxidase subunit I mtDNA (COI). In addition, a single P. sedgwicki specimen per sample locality was sequenced for the 18S rRNA locus. Furthermore, morphological variation among P. sedgwicki sample localities were explored using traditional alpha taxonomic characters. DNA sequence data were subjected to phylogenetic analyses using Bayesian inference and population genetic analyses using haplotype networks and analyses of molecular variance (AMOVAs). Phylogenetic results revealed the presence of four and three clades within P. moseleyi and P. sedgwicki respectively. Haplotype networks were characterised by the absence of shared haplotypes between clades, suggesting genetic isolation, a result corroborated by the AMOVA and highly significant FST values. Specimens from Fort Fordyce Nature Reserve were both genetically and morphologically distinct from the two remaining P. sedgwicki clades. The latter result suggests the presence of a novel lineage nested within P. sedgwicki and suggests that species boundaries within this taxon require re-examination.

scholarly journals Biological and Phylogenetic Analyses Suggest that Two Cryphonectria spp. Cause Cankers of Eucalyptus in Africa

Plant Disease ◽  
2003 ◽  
Vol 87 (11) ◽  
pp. 1329-1332 ◽  
Author(s):  
J. Roux ◽  
H. Myburg ◽  
B. D. Wingfield ◽  
M. J. Wingfield
Keyword(s):  
South Africa ◽  
South America ◽  
South African ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Eucalyptus Grandis ◽  
Its Region ◽  
South African Isolate ◽  
Dna Sequence Data ◽  
The Republic

Cryphonectria cubensis is an economically important pathogen of commercial Eucalyptus spp. Differences have been reported for disease symptoms associated with Cryphonectria canker in South Africa and other parts of the world, and recent DNA-based comparisons have confirmed that the fungus in South Africa is different from that in South America and Australasia. During a disease survey in the Republic of Congo, Cryphonectria canker was identified as an important disease on Eucalyptus grandis and E. urophylla. In this study, we compared Congolese and South African isolates of C. cubensis using DNA sequence data and pathogenicity under greenhouse conditions. The β-tubulin and internal transcribed spacer (ITS) region sequences show that C. cubensis in Congo is different from the fungus in South Africa and that Congolese isolates group most closely with South American isolates. Furthermore, pathogenicity tests showed that a South African isolate was more aggressive than two Congolese isolates. We conclude that two distinct Cryphonectria spp. occur in Africa and hypothesize that the fungus in the Congo probably was introduced into Africa from South America. Both fungi are important pathogens causing disease and death of economically important plantation trees. However, they apparently have different origins and must be treated separately in terms of disease management and quarantine considerations.

scholarly journals New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa

MycoKeys ◽  
2018 ◽  
Vol 43 ◽  
pp. 1-21 ◽  
Author(s):  
Malte Ebinghaus ◽  
Wolfgang Maier ◽  
Michael J. Wingfield ◽  
Dominik Begerow
Keyword(s):  
South Africa ◽  
Sequence Data ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Principal Component ◽  
Morphological Characters ◽  
Rust Fungi ◽  
New Host ◽  
Dna Sequence Data ◽  
Molecular Phylogenetic

Trees in the genusVachellia(previouslyAcacia) are commonly infected by the gall-inducing rustsRaveneliamacowanianaandR.evansii. Rust galls bearing aecial infections and relating uredinial and telial infections on the leaves of nineVachelliaspecies not previously recorded to be infected byRaveneliaspp. have recently been collected in South Africa. The rust fungi causing these infections were characterised using molecular phylogenetic analyses of DNA sequence data of the LSU and ITS rDNA regions as well as morphological examinations. The host range ofR.macowanianaandR.evansiiwas thus re-assessed and extended from four to nine species and from one to three species, respectively. Application of Principal Component Analyses (PCA) of telial morphological characters provided evidence of an effect of the host species on the teliospore morphology inR.evansii, but only minor effects inR.macowaniana. A novel gall-inducingRaveneliasp. closely related toR.macowaniana, was found onVachelliaxanthophloeaand it is described here asR.xanthophloeae.

Morphological assessment supports the recognition of four novel species in the widely distributed velvet worm Peripatopsis moseleyi sensu lato (Onychophora : Peripatopsidae)

2013 ◽  
Vol 27 (2) ◽  
pp. 131 ◽  
Author(s):  
Hilke Ruhberg ◽  
Savel R. Daniels
Keyword(s):  
South African ◽  
Sequence Data ◽  
Novel Species ◽  
Morphological Characteristics ◽  
Morphological Characters ◽  
Phylogenetic Study ◽  
Eastern Cape ◽  
Dna Sequence Data ◽  
Kwazulu Natal ◽  
Velvet Worm

A recent phylogenetic study based on DNA sequence data (COI + 18S rDNA) together with basic morphological characteristics demonstrated the presence of four novel lineages within the widely distributed South African velvet worm species Peripatopsis moseleyi sensu lato (Onychophora, Peripatopsidae). In the present study, the morphological variation within P. moseleyi (Wood-Mason, 1879) is quantified and the novel species delineated and described. A total of 31 new specimens were collected from the Amathole Mountains in the Eastern Cape while a further 12 specimens were collected from Mount Currie Nature Reserve, KwaZulu-Natal, South Africa. These samples together with selected specimens from the DNA study material were subjected to scanning electron microscopy (SEM) to investigate the presence of diagnostic morphological characters that could potentially be utilised in the delineation of the four novel lineages. The species diagnosis of P. moseleyi (Wood-Mason, 1879) is elucidated and amended since the original type description is inadequate and could apply to several Peripatopsis taxa. A neotype for P. moseleyi is designated because the syntypes appear lost. Four new species of Peripatopsis Pocock, 1894 are described; viz. Peripatopsis birgeri, sp. nov., P. hamerae, sp. nov., P. janni, sp. nov. and P. storchi, sp. nov.

scholarly journals New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa

MycoKeys ◽  
2018 ◽  
Vol 42 ◽  
pp. 125-145
Author(s):  
Malte Ebinghaus ◽  
Wolfgang Maier ◽  
Michael J. Wingfield ◽  
Dominik Begerow
Keyword(s):  
South Africa ◽  
Sequence Data ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Principal Component ◽  
Morphological Characters ◽  
Rust Fungi ◽  
New Host ◽  
Dna Sequence Data ◽  
Molecular Phylogenetic

Trees in the genusVachellia(previouslyAcacia) are commonly infected by the gall-inducing rustsRaveneliamacowanianaandR.evansii. Rust galls bearing aecial infections and relating uredinial and telial infections on the leaves of nineVachelliaspecies not previously recorded to be infected byRaveneliaspp. have recently been collected in South Africa. The rust fungi causing these infections were characterised using molecular phylogenetic analyses of DNA sequence data of the LSU and ITS rDNA regions as well as morphological examinations. The host range ofR.macowanianaandR.evansiiwas thus re-assessed and extended from four to nine species and from one to three species, respectively. Application of Principal Component Analyses (PCA) of telial morphological characters provided evidence of an effect of the host species on the teliospore morphology inR.evansii, but only minor effects inR.macowaniana. A novel gall-inducingRaveneliasp. closely related toR.macowaniana, was found onVachelliaxanthophloeaand it is described here asR.xanthophloeae.

scholarly journals Fusarium species isolated from Pennisetum clandestinum collected during outbreaks of kikuyu poisoning in cattle in South Africa

2014 ◽  
Vol 81 (1) ◽  
Author(s):  
Christo J. Botha ◽  
Mariëtte Truter ◽  
Adriaana Jacobs
Keyword(s):  
South Africa ◽  
Species Complex ◽  
Sequence Data ◽  
Fusarium Species ◽  
Phylogenetic Analyses ◽  
Fusarium Culmorum ◽  
Elongation Factor ◽  
Eastern Cape ◽  
Pennisetum Clandestinum ◽  
Fusarium Redolens

Kikuyu poisoning occurs sporadically in South Africa. It is of major economic importance, as valuable dairy cows are often poisoned by it, and once affected, the mortality rate is high. Pennisetum clandestinum samples were collected during eight outbreaks of kikuyu poisoning in cattle in the Eastern Cape Province of South Africa from 2008 to 2010. The kikuyu grass samples were submitted specifically for the isolation and molecular identification of Fusarium species, as it was recently suggested that mycotoxins synthesised by Fusarium torulosum could be the cause of this intoxication. Ninety-four Fusarium isolates were retrieved from the grass samples, of which 72 were members of the Fusarium incarnatum/Fusarium equiseti species complex based on morphology and phylogenetic analyses of the translation elongation factor 1α sequence data. The South African isolates from kikuyu identified as members of the F. incarnatum/F. equiseti species complex grouped together in six separate clades. The other isolates were Fusarium culmorum (n = 3), Fusarium redolens (n = 4) and Fusarium oxysporum (n = 15). Although F. torulosum could not be isolated from P. clandestinum collected during kikuyu poisoning outbreaks in South Africa, the mycotoxicosis theory is still highly plausible.

scholarly journals Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

2021 ◽  
Vol 9 (3) ◽  
pp. 666
Author(s):  
Niccolò Forin ◽  
Alfredo Vizzini ◽  
Federico Fainelli ◽  
Enrico Ercole ◽  
Barbara Baldan
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Illumina Miseq ◽  
Botanical Garden ◽  
Molecular Study ◽  
Its2 Sequence ◽  
Type Specimens ◽  
Its1 Sequence ◽  
Dna Sequence Data ◽  
Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

scholarly journals Disentangling selection on genetically correlated polygenic traits using whole-genome genealogies

2020 ◽  
Author(s):  
Aaron J. Stern ◽  
Leo Speidel ◽  
Noah A. Zaitlen ◽  
Rasmus Nielsen
Keyword(s):  
Dna Sequence ◽  
Population Genetic ◽  
Sequence Data ◽  
Directional Selection ◽  
Likelihood Method ◽  
Correlated Response ◽  
Correlated Traits ◽  
Dna Sequence Data ◽  
Polygenic Traits ◽  
Polygenic Trait

AbstractWe present a full-likelihood method to estimate and quantify polygenic adaptation from contemporary DNA sequence data. The method combines population genetic DNA sequence data and GWAS summary statistics from up to thousands of nucleotide sites in a joint likelihood function to estimate the strength of transient directional selection acting on a polygenic trait. Through population genetic simulations of polygenic trait architectures and GWAS, we show that the method substantially improves power over current methods. We examine the robustness of the method under uncorrected GWAS stratification, uncertainty and ascertainment bias in the GWAS estimates of SNP effects, uncertainty in the identification of causal SNPs, allelic heterogeneity, negative selection, and low GWAS sample size. The method can quantify selection acting on correlated traits, fully controlling for pleiotropy even among traits with strong genetic correlation (|rg| = 80%; c.f. schizophrenia and bipolar disorder) while retaining high power to attribute selection to the causal trait. We apply the method to study 56 human polygenic traits for signs of recent adaptation. We find signals of directional selection on pigmentation (tanning, sunburn, hair, P=5.5e-15, 1.1e-11, 2.2e-6, respectively), life history traits (age at first birth, EduYears, P=2.5e-4, 2.6e-4, respectively), glycated hemoglobin (HbA1c, P=1.2e-3), bone mineral density (P=1.1e-3), and neuroticism (P=5.5e-3). We also conduct joint testing of 137 pairs of genetically correlated traits. We find evidence of widespread correlated response acting on these traits (2.6-fold enrichment over the null expectation, P=1.5e-7). We find that for several traits previously reported as adaptive, such as educational attainment and hair color, a significant proportion of the signal of selection on these traits can be attributed to correlated response, vs direct selection (P=2.9e-6, 1.7e-4, respectively). Lastly, our joint test uncovers antagonistic selection that has acted to increase type 2 diabetes (T2D) risk and decrease HbA1c (P=1.5e-5).

Comparative host–parasite population genetic structures: obligate fly ectoparasites on Galapagos seabirds

Parasitology ◽  
2013 ◽  
Vol 140 (9) ◽  
pp. 1061-1069 ◽  
Author(s):  
IRIS I. LEVIN ◽  
PATRICIA G. PARKER
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Sequence Data ◽  
Population Genetic Study ◽  
Haemosporidian Parasite ◽  
Dna Sequence Data ◽  
Sula Granti ◽  
Breeding Attempt ◽  
Genetic Structures

SUMMARYParasites often have shorter generation times and, in some cases, faster mutation rates than their hosts, which can lead to greater population differentiation in the parasite relative to the host. Here we present a population genetic study of two ectoparasitic flies, Olfersia spinifera and Olfersia aenescens compared with their respective bird hosts, great frigatebirds (Fregata minor) and Nazca boobies (Sula granti). Olfersia spinifera is the vector of a haemosporidian parasite, Haemoproteus iwa, which infects frigatebirds throughout their range. Interestingly, there is no genetic differentiation in the haemosporidian parasite across this range despite strong genetic differentiation between Galapagos frigatebirds and their non-Galapagos conspecifics. It is possible that the broad distribution of this one H. iwa lineage could be facilitated by movement of infected O. spinifera. Therefore, we predicted more gene flow in both fly species compared with the bird hosts. Mitochondrial DNA sequence data from three genes per species indicated that despite marked differences in the genetic structure of the bird hosts, gene flow was very high in both fly species. A likely explanation involves non-breeding movements of hosts, including movement of juveniles, and movement by adult birds whose breeding attempt has failed, although we cannot rule out the possibility that closely related host species may be involved.

Species delimitation of Hymenasplenium obliquissimum group (Aspleniaceae) in southwestern China

Phytotaxa ◽  
2021 ◽  
Vol 480 (1) ◽  
pp. 29-44
Author(s):  
GUO-CHENG ZHANG ◽  
HUA-FENG HONG ◽  
GE-HONG CHEN ◽  
SHU-GANG LU ◽  
YAN-FEN CHANG
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Reticulate Evolution ◽  
Southwestern China ◽  
Natural Classification ◽  
Ploidy Levels ◽  
Dna Sequence Data ◽  
Taxonomic Implications ◽  
Taxonomic Approach ◽  
Locus Classicus

The Hymenasplenium obliquissimum group contains the widespread H. obliquissimum and several geographically restricted species, including H. retusulum, H. wuliangshanense, H. latidens, H. changputungense, H. quercicola, H. szechuanense, H. furfuraceum, H. adiantifrons, and H. filipes. However, the taxonomy of this group is still unclear and needs to be revised because some entities were treated infraspecifically or as synonyms and the validation of some species still needs to be assessed. To formulate a natural classification and investigate the relationships in this group, we collected and studied specimens of species related to the H. obliquissimum group and obtained specimens of species described by Ching at their locus classicus in southwestern China. An integrative taxonomic approach was taken to delimit species in the group using cytological, morphological, and DNA sequence data. Specifically, in the phylogenetic analyses, the H. obliquissimum group was recovered as a monophyletic group, comprising five principal chloroplast lineages. Based on our inferences, we provided taxonomic implications of chloroplast lineages discovered in this study and suggested possible reticulate evolution in the H. obliquissimum group which was interpreted by the incongruence of chloroplast and nuclear phylogenies. Further studies to strengthen the taxonomic of taxa especially those with the co-existence of different ploidy levels are still warranted.

scholarly journals Introducing Chaetothyriothecium, a new genus of Microthyriales

Phytotaxa ◽  
2014 ◽  
Vol 161 (2) ◽  
pp. 157 ◽  
Author(s):  
Sinang Hongsanan ◽  
Putarak Chomnunti ◽  
Pedro W. Crous ◽  
Ekachai Chukeatirote ◽  
Kevin D. Hyde
Keyword(s):  
New Genus ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Plant Host ◽  
Dna Sequence Data ◽  
Limited Sampling ◽  
Black Spots ◽  
Gene Data ◽  
Central Thailand

The order Microthyriales comprises foliar biotrophs, epiphytes, pathogens or saprobes that occur on plant leaves and stems. The order is relatively poorly known due to limited sampling and few in-depth studies. There is also a lack of phylogenetic data for these fungi, which form small black spots on plant host surfaces, but rarely cause any damage to the host. A "Microthyriaceae"-like fungus collected in central Thailand is described as a new genus, Chaetothyriothecium (type species Chaetothyriothecium elegans sp. nov.). Phylogenetic analyses of LSU gene data showed this species to cluster with other members of Microthyriales, where it is related to Microthyrium microscopicum the type of the order. The description of the new species is supplemented by DNA sequence data, which resolves its placement in the order. Little molecular data is available for this order, stressing the need for further collections and molecular data.

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