Population structure and species delimitation of rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae), in China

2019 ◽  
Vol 69 (1) ◽  
pp. 159-167 ◽  
Author(s):  
X. Xu ◽  
X. Qing ◽  
J. L. Xie ◽  
F. Yang ◽  
Y. L. Peng ◽  
...  
Keyword(s):  
Population Structure ◽  
Species Delimitation ◽  
Aphelenchoides Besseyi ◽  
Rice White Tip Nematode

Species delimitation and population structure in three Onosma (Boraginaceae) species

Biologia ◽  
2015 ◽  
Vol 70 (10) ◽  
Author(s):  
Masoud Sheidai ◽  
Samira Sadeghi ◽  
Mahnaz-Arab Ameri ◽  
Ahmad-Reza Mehrabeian
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Species Delimitation ◽  
Genetic Difference ◽  
Morphological Variability ◽  
Morphological Diversity ◽  
Mantel Test ◽  
Geographical Distance ◽  
Nj Tree ◽  
Issr Molecular Markers

AbstractThe present study aimed to reveal genetic diversity and population structure in three Onosma species i.e., Onosma bulbotrichum DC., O. elwendicum Wettst. and O. sericeum Willd. (Boraginaceae) growing in Iran. This study was performed to check if the ISSR molecular markers could be used in the Onosma species delimitation. We also investigated the infra-specific morphological variability and if we can identify infra-species taxonomic forms. The present study revealed within species genetic and morphological diversity. ISSR data could delimit the studied species as they were separated from each other in NJ tree, maximum parsimony and STRUCTURE analysis. AMOVA and Hickory tests produced significant genetic difference among the studied species. The Mantel test showed no correlation between genetic distance and geographical distance of the populations for all three species. Reticulation analysis and Nm estimation showed gene flow among these populations. We could identify a few ISSR loci that are adaptive. Data obtained can be used in conservation of these medicinal plants in Iran.

scholarly journals Studies on the efficiency of different inoculation methods of rice white-tip nematode, Aphelenchoides besseyi

Nematology ◽  
2019 ◽  
Vol 21 (7) ◽  
pp. 673-678
Author(s):  
Jialian Xie ◽  
Fang Yang ◽  
Yanping Wang ◽  
Yunliang Peng ◽  
Hongli Ji
Keyword(s):  
Oryza Sativa ◽  
Success Rate ◽  
Success Rates ◽  
Flowering Stage ◽  
Recovery Rates ◽  
Inoculation Methods ◽  
Seed Soaking ◽  
Aphelenchoides Besseyi ◽  
Flotation Method ◽  
Rice White Tip Nematode

Summary To fulfil different research purposes, five methods to inoculate Aphelenchoides besseyi onto seedlings and panicles of rice, Oryza sativa, were evaluated in this study and the efficiency of the inoculation methods assessed by success rates and recovery rates. Among the three methods leading to the infection of young seedlings without obvious mechanical wounds, i.e., water flotation, seed soaking and leaf spraying, the inoculation of 125 nematodes plant−1 by the water flotation method gave rise to the highest success rate and recovery rate, 95.6 and 8.3%, respectively, in growth chamber experiments. When conducted in the plastic house, seed soaking and leaf spraying of 125 nematodes plant−1 resulted in 75.6 and 66.7% success rate, respectively, and 155.7 and 178.1% recovery rates, respectively. The injection or spraying of 2000 nematodes panicle−1 at the booting or flowering stage gave 100% infection.

scholarly journals New approaches to species delimitation and population structure of corals: two case studies using ultraconserved elements and exons

2020 ◽  
Author(s):  
Katie L. Erickson ◽  
Alicia Pentico ◽  
Andrea M. Quattrini ◽  
Catherine S. McFadden
Keyword(s):  
Population Structure ◽  
Case Studies ◽  
Species Delimitation ◽  
Conservation Status ◽  
Target Enrichment ◽  
Clustering Methods ◽  
Ecological Data ◽  
Ultraconserved Elements ◽  
New Approaches ◽  
Wide Range

AbstractAs coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,363 baits) to target-capture 3,040 UCE and exon loci, recovering a mean of 1,910 ± 168 SD per sample with a mean length of 1,055 ± 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 ± 227 SD) and Alcyonium (1,863 ± 177 SD). Species-level phylogenies were highly supported for both genera. Clustering methods based on filtered SNPs delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using Restriction Site Associated DNA Sequencing. Both case studies demonstrate the utility of target-enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow time scales in corals.

scholarly journals Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e91591 ◽  
Author(s):  
Feng Wang ◽  
Danlei Li ◽  
Zhiying Wang ◽  
Airong Dong ◽  
Lihong Liu ◽  
...  
Keyword(s):  
Transcriptomic Analysis ◽  
Aphelenchoides Besseyi ◽  
Rice White Tip Nematode

scholarly journals Characterization and Functional Importance of Two Glycoside Hydrolase Family 16 Genes from the Rice White Tip Nematode Aphelenchoides besseyi

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 374
Author(s):  
Hui Feng ◽  
Dongmei Zhou ◽  
Paul Daly ◽  
Xiaoyu Wang ◽  
Lihui Wei
Keyword(s):  
Glycoside Hydrolase ◽  
Amino Acid Sequences ◽  
Parasitic Nematodes ◽  
Glycoside Hydrolase Family ◽  
Plant Parasitic Nematodes ◽  
Aphelenchoides Besseyi ◽  
Rice White Tip Nematode ◽  
Hydrolase Family ◽  
Plant Parasitic

The glycoside hydrolase family 16 (GH16) is widely found in prokaryotes and eukaryotes, and hydrolyzes the β-1,3(4)-linkages in polysaccharides. Notably, the rice white tip nematode Aphelenchoides besseyi harbors a higher number of GH16s compared with other plant-parasitic nematodes. In this work, two GH16 genes, namely AbGH16-1 and AbGH16-2, were isolated and characterized from A. besseyi. The deduced amino acid sequences of AbGH16-1 and AbGH16-2 contained an N-terminal signal peptide and a fungal Lam16A glucanase domain. Phylogenetic analysis revealed that AbGH16-1 and AbGH16-2 clustered with ascomycete GH16s, suggesting AbGH16-1 and AbGH16-2 were acquired by horizontal gene transfer from fungi. In situ hybridization showed that both AbGH16-1 and AbGH16-2 were specifically expressed in the nematode gonads, correlating with qPCR analysis that showed the high transcript levels of the two genes in the female nematodes. AbGH16-1 and AbGH16-2 were also significantly induced in nematodes feeding on Botrytis cinerea. Characterization of the recombinant protein showed AbGH16-1 and AbGH16-2 displayed pronounced inhibition of both conidial germination and germ tube elongation of B. cinerea. In addition, silencing of AbGH16-1 and AbGH16-2 by RNA interference significantly decreased the reproduction ability of A. besseyi and had a profound impact on the development process of offspring in this nematode. These findings have firstly proved that GH16s may play important roles in A.besseyi feeding and reproduction on fungi, which thus provides novel insights into the function of GH16s in plant-parasitic nematodes.

scholarly journals Phylogeography, Population Structure, and Species Delimitation in Rockhopper Penguins (Eudyptes chrysocome and Eudyptes moseleyi)

2019 ◽  
Author(s):  
Herman L Mays ◽  
David A Oehler ◽  
Kyle W Morrison ◽  
Ariadna E Morales ◽  
Alyssa Lycans ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Species Delimitation ◽  
Diversity Index ◽  
Divergence Time ◽  
Distinct Species ◽  
Effective Population ◽  
Heuristic Approaches

Abstract Rockhopper penguins are delimited as 2 species, the northern rockhopper (Eudyptes moseleyi) and the southern rockhopper (Eudyptes chrysocome), with the latter comprising 2 subspecies, the western rockhopper (Eudyptes chrysocome chrysocome) and the eastern rockhopper (Eudyptes chrysocome filholi). We conducted a phylogeographic study using multilocus data from 114 individuals sampled across 12 colonies from the entire range of the northern/southern rockhopper complex to assess potential population structure, gene flow, and species limits. Bayesian and likelihood methods with nuclear and mitochondrial DNA, including model testing and heuristic approaches, support E. moseleyi and E. chrysocome as distinct species lineages with a divergence time of 0.97 Ma. However, these analyses also indicated the presence of gene flow between these species. Among southern rockhopper subspecies, we found evidence of significant gene flow and heuristic approaches to species delimitation based on the genealogical diversity index failed to delimit them as species. The best-supported population models for the southern rockhoppers were those where E. c. chrysocome and E. c. filholi were combined into a single lineage or 2 lineages with bidirectional gene flow. Additionally, we found that E. c. filholi has the highest effective population size while E. c. chrysocome showed similar effective population size to that of the endangered E. moseleyi. We suggest that the current taxonomic definitions within rockhopper penguins be upheld and that E. chrysocome populations, all found south of the subtropical front, should be treated as a single taxon with distinct management units for E. c. chrysocome and E. c. filholi.

scholarly journals Phylogeography, species delimitation and population structure of a Western Australian short-range endemic mite harvestman (Arachnida: Opiliones: Pettalidae: Karripurcellia)

2018 ◽  
Vol 2 (1) ◽  
pp. 81-87
Author(s):  
Martin Schwentner ◽  
Gonzalo Giribet
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Species Delimitation ◽  
National Park ◽  
Short Range ◽  
Cryptic Speciation ◽  
Mtdna Sequences ◽  
Single Population ◽  
Eucalypt Forests ◽  
Western Australian

The mite harvestmen of the genusKarripurcelliaGiribet, 2003 are endemic to the tall, wet eucalypt forests of south-western Western Australia, a region known as a hotspot for biodiversity. Currently, there are two accepted species,K.peckorumGiribet, 2003 andK.sierwaldaeGiribet, 2003, both with type localities within the Warren National Park. We obtained 65COImtDNA sequences from across the entire distributional range of the genus. These sequences, falling into two to three geographically separate groups, probably correspond to two species. Morphologically, all of the studied specimens correspond toK.peckorum, suggesting cryptic speciation within that species. A few common haplotypes occur in more than one population, but most haplotypes are confined to a single population. As a result, populations are genetically differentiated and gene flow after initial colonization appears to be very limited or completely lacking. Our study provides another example of short-range endemism in an invertebrate from the south-western mesic biome.

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