Genetic differentiation of Southeast Asian Paragonimus Braun, 1899 (Digenea: Paragonimidae) and genetic variation in the Paragonimus heterotremus complex examined by nuclear DNA sequences

2021 ◽  
Vol 90 ◽  
pp. 104761
Author(s):  
Chairat Tantrawatpan ◽  
Sumonta Tapdara ◽  
Takeshi Agatsuma ◽  
Oranuch Sanpool ◽  
Pewpan M. Intapan ◽  
...  
2019 ◽  
Vol 113 (3) ◽  
pp. 149-159
Author(s):  
Atsalek Rattanawannee ◽  
Kanyanat Wongsa ◽  
Orawan Duangphakdee

Abstract Aphis craccivora Koch (Hemiptera: Aphididae) or cowpea aphid is a polyphagous insect pest that feeds on a variety of leguminous plants. We determined the contribution of host-associated genetic differentiation on population structure using the sequence data generated from analysis of mitochondrial cytochrome b oxidase (Cytb) and nuclear elongation factor-1 alpha (EF1-alpha) of A. craccivora collected from cultivated yardlong bean [Vigna unguiculata (L.) Walp. ssp. sesquipedalis (L.) H. Ohashi.] (Fabales: Fabaceae) and winged bean [Psophocarpus tetragonolobus (L.) D.C.] (Fabales: Fabaceae). Phylogenetic and haplotype network analyses revealed no evidence of strong host plant or geographical clustering in both the mitochondrial and nuclear gene dataset. A moderate, low-magnitude genetic distance (FST) between host plants and geographical localities was found in this study. An analysis of molecular variance (AMOVA) revealed that host plant and geography do not influence the structure of genetic variation in A. craccivora populations. Genetic variation between host plants at a location and host plants among locations demonstrated no consistent result for population subdivision of A. craccivora. These results suggest that geographical location and host plants do not significantly influence the genetic structure of A. craccivora, and this might be due to their high reproductive (parthenogenesis) ability and high migration (airborne) between host plants and regions of the country.


2021 ◽  
Author(s):  
Evandro Pires Lopes ◽  
Rui Freitas ◽  
Raquel Xavier ◽  
João Deus Soares ◽  
António M Santos

Abstract The snowflake coral Carijoa riisei is one of the most invasive and successfully adapting species in the coastal marine environment. This species can disperse through ballast waters or fouling on the hull of ships, which allows it to expand very quickly to areas where it is not native. Recently C. riisei was identified in the Porto Grande Bay in São Vicente island in Cabo Verde Islands. We analysed mitochondrial and nuclear DNA sequences from specimens collected at this locality to determine the potential origin of this invasion. Lack of genetic variation in both mitochondrial and nuclear genes suggest a very recent invasion (bottleneck effect) but did not permit to establish its origin with total confidence.


2018 ◽  
Vol 52 (6) ◽  
pp. 596-602
Author(s):  
Pimnapat Parimittr ◽  
Theeraphap Chareonviriyaphap ◽  
Michael J. Bangs ◽  
Uraiwan Arunyawat

2015 ◽  
Vol 6 (2) ◽  
pp. 338-349 ◽  
Author(s):  
Jess W. Jones ◽  
Nathan Johnson ◽  
Paul Grobler ◽  
Daniel Schilling ◽  
Richard J Neves ◽  
...  

Abstract We conducted a genetic characterization of two extant populations of an endangered freshwater mussel, the rough pigtoe Pleurobema plenum, in the Clinch River, Tennessee of the Tennessee River basin, and the Green River, Kentucky, of the Ohio River basin for purposes of conservation recovery planning. First, phylogenetic status of this species within the Pleurobema cordatum species complex (P. cordatum, plenum, rubrum, sintoxia) was assessed using mitochondrial ND1 deoxyribonucleic acid (DNA) sequences, which showed that all investigated species of Pleurobema are genetically distinct. Our results indicated that P. cordatum, P. plenum, P. rubrum, and P. sintoxia each represent monophyletic clades; however, the latter two species were closely related, separated by only one to three nucleotide differences. Further, DNA sequence haplotypes from both populations of P. plenum grouped together into one monophyletic clade and did not support characterizing the populations as separate species. Thus, our phylogenetic analysis confirms that populations of P. plenum in the Clinch and Green rivers are the same species. Second, we assessed genetic differentiation between P. plenum populations in each river by analyzing variation at eight nuclear DNA microsatellite loci, where FST (=0.023) and Jost’s D (=0.175) indicated genetically differentiated populations. Because these populations are geographically and demographically independent, and differentiated at nuclear microsatellite loci, recognition as management units is recommended. Additional studies are needed to determine whether there are differences at adaptive or life-history traits, such as fish host usage, shell morphology, and soft anatomy between populations, and to further investigate the phylogenetic relationship of P. rubrum and P. sintoxia.


2008 ◽  
Vol 29 (1) ◽  
pp. 25-34 ◽  
Author(s):  
David James Harris ◽  
Catarina Rato

Abstract Phylogenetic relationships of the three morphological forms within the gecko genus Saurodactylus were estimated using mtDNA (12S rRNA and ND4) sequences. High between morphological forms variation (up to 25% with ND4), confirms that all three deserve specific status. Saurodactylus mauritanicus and Saurodactylus brosseti are strongly supported as sister taxa. Our results again highlight the extremely high mtDNA variability almost universally reported from within gecko species. The position of Saurodactylus within the Gekkonoidea was also investigated. Although considered as a member of the sphaerodactyl geckos, its taxonomic position is still highly uncertain. Evaluation of C-mos nuclear DNA sequences supports many of the recent taxonomic rearrangements within the Gekkonoidea. Using this marker, Saurodactylus is paraphyletic, with S. mauritanicus and S. brosseti sister taxa to Teratoscincus przewalskii rather than Saurodactylus fasciatus. This is supported by a further nuclear marker, RAG1, although for this gene region sampling is more limited. Based on this paraphyly, supported by two independent nuclear markers, we suggest it likely that Saurodactylus will need to be partitioned into two genera, pending further investigations.


Author(s):  
Francisco J. Ayala ◽  
Camilo J. Cela-Conde

This chapter deals with the similarities and differences between Homo neanderthalensis and Homo sapiens, by considering genetic, brain, and cognitive evidence. The genetic differentiation emerges from fossil genetic evidence obtained first from mtDNA and later from nuclear DNA. With high throughput whole genome sequencing, sequences have been obtained from the Denisova Cave (Siberia) fossils. Nuclear DNA of a third species (“Denisovans”) has been obtained from the same cave and used to define the phylogenetic relationships among the three species during the Upper Palaeolithic. Archaeological comparisons make it possible to advance a four-mode model of the evolution of symbolism. Neanderthals and modern humans would share a “modern mind” as defined up to Symbolic Mode 3. Whether the Neanderthals reached symbolic Mode 4 remains unsettled.


Author(s):  
Rui Zang ◽  
Ying Zhao ◽  
Kangdi Guo ◽  
Kunqi Hong ◽  
Huijun Xi ◽  
...  

AbstractBitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.


Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 751
Author(s):  
Francesco Dovana ◽  
Paolo Gonthier ◽  
Matteo Garbelotto

Phlebiopsis gigantea (Fr.) Jülich is a well-known generalist conifer wood saprobe and a biocontrol fungus used in several world countries to prevent stump infection by tree pathogenic Heterobasidion fungal species. Previous studies have reported the presence of regional and continental genetic differentiation in host-specific fungi, but the presence of such differentiation for generalist wood saprobes such as P. gigantea has not been often studied or demonstrated. Additionally, little information exists on the distribution of this fungus in western North America. The main purposes of this study were: (I) to assess the presence of P. gigantea in California, (II) to explore the genetic variability of P. gigantea at the intra and inter-continental levels and (III) to analyze the phylogeographic relationships between American and European populations. Seven loci (nrITS, ML5–ML6, ATP6, RPB1, RPB2, GPD and TEF1-α) from 26 isolates of P. gigantea from coniferous forests in diverse geographic distribution and from different hosts were analyzed in this study together with 45 GenBank sequences. One hundred seventy-four new sequences were generated using either universal or specific primers designed in this study. The mitochondrial ML5–ML6 DNA and ATP6 regions were highly conserved and did not show differences between any of the isolates. Conversely, DNA sequences from the ITS, RPB1, RPB2, GPD and TEF1-α loci were variable among samples. Maximum likelihood analysis of GPD and TEF1-α strongly supported the presences of two different subgroups within the species but without congruence or geographic partition, suggesting the presence of retained ancestral polymorphisms. RPB1 and RPB2 sequences separated European isolates from American ones, while the GPD locus separated western North American samples from eastern North American ones. This study reports the presence of P. gigantea in California for the first time using DNA-based confirmation and identifies two older genetically distinct subspecific groups, as well as three genetically differentiated lineages within the species: one from Europe, one from eastern North America and one from California, with the latter presumably including individuals from the rest of western North America. The genetic differentiation identified here among P. gigantea individuals from coniferous forests from different world regions indicates that European isolates of this fungus should not be used in North America (or vice versa), and, likewise, commercially available eastern North American P. gigantea isolates should not be used in western North America forests. The reported lack of host specificity of P. gigantea was documented by the field survey and further reinforces the need to only use local isolates of this biocontrol fungus, given that genetically distinct exotic genotypes of a broad generalist microbe may easily spread and permanently alter the microbial biodiversity of native forest ecosystems.


Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 2011-2014 ◽  
Author(s):  
Richard R Hudson

Abstract A new statistic for detecting genetic differentiation of subpopulations is described. The statistic can be calculated when genetic data are collected on individuals sampled from two or more localities. It is assumed that haplotypic data are obtained, either in the form of DNA sequences or data on many tightly linked markers. Using a symmetric island model, and assuming an infinite-sites model of mutation, it is found that the new statistic is as powerful or more powerful than previously proposed statistics for a wide range of parameter values.


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