Population-Based Cytogenetic Banding Analysis and Phylogenetic Relationships of the Neotropical Fungus-Farming Ant Trachymyrmex holmgreni Wheeler, 1925

2019 ◽  
Vol 159 (3) ◽  
pp. 151-161 ◽  
Author(s):  
Ricardo Micolino ◽  
Maykon P. Cristiano ◽  
Danon C. Cardoso
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Reconstruction ◽  
Population Based ◽  
Population Variation ◽  
Incipient Speciation ◽  
Telomeric Sequences ◽  
New Information ◽  
Banding Analysis ◽  
Pattern Characteristic ◽  
Northern Brazil

Trachymyrmex is one of the most species-rich genera within fungus-farming ants and presents intraspecific cytogenetic polymorphisms as well as possible cryptic species. This ant genus is currently paraphyletic. Therefore, to unravel systematic and taxonomic misunderstandings, it is necessary to incorporate new information. We aimed to cytogenetically and genetically examine Trachymyrmex holmgreni populations from southern and northern Brazil to identify intraspecific chromosomal variations that support incipient speciation and reveal the species' position in a molecular phylogeny. Our cytogenetic approach did not show population variation in the mapping of both 18S rDNA and the TTAGG(6) motif, presenting instead a pattern characteristic of correlated species. However, the clustered pattern of the microsatellite GA(15) showed significant differences among populations: a well-defined block in each homologue, distinctly irregular signs between homologues, and blocks in 2 pairs of homologues. Our phylogenetic reconstruction yielded unexpected results, grouping representatives of 3 former morphological groups into 1 clade, namely T. urichii, T. papulatus, and T. holmgreni. Previously, it was suggested that northern and southern populations of T. holmgreni may be undergoing incipient speciation, but we can only indicate that the southernmost population differs prominently from the others in its distribution pattern of the microsatellite GA(15). Our study also supports the uniformity of karyotypes and repetitive DNA from both telomeric sequences and ribosomal DNA in Trachymyrmex studied here. In addition, we clarify some phylogenetic uncertainties within the genus and suggest further relevant systematic changes. Finally, additional studies utilizing other probes and additional populations may allow the detection of hidden genetic variation.

Abstract P237: Common Genetic Variation in Caspase Enzymes and Survival of Sudden Cardiac Arrest

Circulation ◽  
2012 ◽  
Vol 125 (suppl_10) ◽  
Author(s):  
Catherine O Johnson ◽  
Rozenn N Lemaitre ◽  
Nona Sotoodehnia ◽  
Barbara McKnight ◽  
Kenneth M Rice ◽  
...  
Keyword(s):  
Cardiac Arrest ◽  
Genetic Variation ◽  
Hospital Admission ◽  
Hospital Discharge ◽  
A Priori ◽  
Sudden Cardiac Arrest ◽  
Population Based ◽  
Minor Allele ◽  
P Value ◽  
Brain Resuscitation

Background: Reperfusion following ischemia due to sudden cardiac arrest (SCA) is necessary for survival, but results in additional injury to affected tissues. Regulation of apoptosis has been shown to be important in determining the extent of reperfusion injury. Caspases (CASP) are essential enzymes in the apoptotic cascade and we therefore hypothesized that genetic variation in these enzymes might influence cardiac and brain resuscitation after SCA. To test this, we examined three genes (CASP2, CASP3, CASP9) in a population-based study of SCA survival. Methods: Subjects (mean age 67, 80% male, of European descent) were out-of-hospital SCA patients found in ventricular fibrillation (VF) and attended by paramedics in King County, WA (n=1614). To investigate cardiac resuscitation, we compared subjects who survived to hospital admission (n=827) with those who did not (n=787); for brain resuscitation, we compared subjects who survived to hospital discharge (n=448) with those who did not (n=1166). Associations of 19 SNPs were examined using logistic regression comparing each additional copy of the minor allele. Based on a priori hypotheses, models were adjusted for: age; gender; time from 911 call to arrival of emergency medical services; whether the event was witnessed; occurred in public; and whether bystander CPR was administered. We used within-gene permutation tests to adjust p-values for multiple comparisons. Results: Two SNPs in CASP3 were associated with SCA survival. The A allele of rs4647688 (minor allele frequency (MAF) 0.20) was associated with lower rates of survival to hospital admission (OR (95% CI), adjusted p-value: 0.78 (0.65, 0.93), p =0.043). The T allele of rs2705897 (MAF 0.26) was associated with a higher rate of survival to hospital admission (1.27 (1.07, 1.51), p =0.049). These two SNPs are in almost complete linkage equilibrium (r 2 =0.091). No SNPs in CASP3 were significantly associated with survival to hospital discharge, and no SNPs in CASP2 or CASP9 were significantly associated with either outcome. Conclusions: CASP3 variants are associated with SCA survival in this population. Further work is needed to explore the effect of these variants on regulation of apoptosis during reperfusion following VF arrest, and to replicate these findings in other populations.

scholarly journals Aggregation of population‐based genetic variation over protein domain homologues and its potential use in genetic diagnostics

2017 ◽  
Vol 38 (11) ◽  
pp. 1454-1463 ◽  
Author(s):  
Laurens Wiel ◽  
Hanka Venselaar ◽  
Joris A. Veltman ◽  
Gert Vriend ◽  
Christian Gilissen
Keyword(s):  
Genetic Variation ◽  
Population Based ◽  
Protein Domain ◽  
Genetic Diagnostics ◽  
Potential Use

scholarly journals Evaluating the genetic variability of rubber hybrid progenies of the two crosses PB260 x RO44/71 and PB260 x RO62/54 by RAPD technique

2019 ◽  
Vol 2 (3) ◽  
pp. 36-43
Author(s):  
Thien Minh Nguyen ◽  
Tien Thi My Pham
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Similarity ◽  
Field Experiments ◽  
Agronomic Traits ◽  
Genetic Relationships ◽  
Genetic Material ◽  
Population Based ◽  
Shannon Index ◽  
Polymorphic Bands

The agronomic values of this population have been evaluated in the field experiments based on their phenotypic performance of agronomic traits, but the genetic variability of this population needs to be evaluated via techniques based on genetic material - DNA. In this study, the genetic variability in the investigated population of 71 hybrids and their parents was evaluated by RAPD technique, using eight selected arbitrarily primers; Genetic parameters and dendrogram expressing the genetic relationships among the investigated population were analyzed by GenALEx 6.1, Popgene 1.31 and NTSYSpc 2.1 softwares. Eight primers were used to generate the amplify products on each individual in the investigated population. From 74 genotypes, a total of 109 fragments were generated, among which, there were 89 polymorphic bands representing 81.65% with an average of 11 polymorphic bands/primer. Genetic similarity coefficient among the investigated population, based on DICE coefficient, ranged from 0.560 (LH05/0822 and PB260) to 0.991 (LH05/0781 and LH05/0841) with an average of 0,796, meaning that the genetic distance among ranged from 0.009 to 0.440 with an average of 0.231. The Shannon index and mean heterozygosity values were 0.328 and 0,176, respectively. This indicated that the progenies of the two investigated crosses possessed a relatively high range of genetic variability. The analysis of molecular variance (AMOVA) showed that genetic variation within population represented 62%, while genetic variation among two different crosses contributes 38% to the total genetic variability. Dendrogram based on DICE’s genetic similarity using UPGMA method showed that the hybrids divide into two major genetic groups (0.75), but the crosses were scattered independently of the hybrid.

scholarly journals Characterization of Mycobacterium tuberculosis Isolates from Patients in Houston, Texas, by Spoligotyping

2000 ◽  
Vol 38 (2) ◽  
pp. 669-676 ◽  
Author(s):  
Hanna Soini ◽  
Xi Pan ◽  
Amol Amin ◽  
Edward A. Graviss ◽  
Anees Siddiqui ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Population Based ◽  
Nucleotide Polymorphisms ◽  
Genetic Groups ◽  
Tuberculosis Epidemiology ◽  
New Information ◽  
Catalase Peroxidase ◽  
A Subunit ◽  
Group 2 ◽  
Group 1

Mycobacterium tuberculosis isolates (n= 1,429) from 1,283 patients collected as part of an ongoing population-based tuberculosis epidemiology study in Houston, Texas, were analyzed by spoligotyping and IS6110 profiling. The isolates were also assigned to one of three major genetic groups on the basis of nucleotide polymorphisms located at codons 463 and 95 in the genes (katG and gyrA) encoding catalase-peroxidase and the A subunit of DNA gyrase, respectively. A total of 225 spoligotypes were identified in the 1,429 isolates. There were 54 spoligotypes identified among 713 isolates (n= 623 patients) assigned to 73 IS6110 clusters. In addition, among 716 isolates (n = 660 patients) with unique IS6110 profiles, 200 spoligotypes were identified. No changes were observed either in the IS6110 profile or in the spoligotype for the 281 isolates collected sequentially from 133 patients. Five instances in which isolates with slightly different spoligotypes had the same IS6110 profile were identified, suggesting that in rare cases isolates with different spoligotypes can be clonally related. Spoligotypes correlated extremely well with major genetic group designations. Only three very similar spoligotypes were shared by isolates from genetic groups 2 and 3, and none was shared by group 1 and group 2 organisms or by group 1 and group 3 organisms. All organisms belonging to genetic groups 2 and 3 failed to hybridize with spacer probes 33 to 36. Taken together, the results support the existence of three distinct genetic groups of M. tuberculosis organisms and provide new information about the relationship between IS6110 profiles, spoligotypes, and major genetic groups of M. tuberculosis.

scholarly journals Effects of common germline genetic variation in cell cycle control genes on breast cancer survival: results from a population-based cohort

2008 ◽  
Vol 10 (3) ◽  
Author(s):  
Elizabeth M Azzato ◽  
Kristy E Driver ◽  
Fabienne Lesueur ◽  
Mitul Shah ◽  
David Greenberg ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Cycle ◽  
Genetic Variation ◽  
Cancer Survival ◽  
Cell Cycle Control ◽  
Population Based ◽  
Breast Cancer Survival

Genetic diversity and differentiation in populations of invasive Eurasian (Myriophyllum spicatum) and hybrid (Myriophyllum spicatum × Myriophyllum sibiricum) watermilfoil

2020 ◽  
Vol 13 (2) ◽  
pp. 59-67
Author(s):  
Ryan A. Thum ◽  
Gregory M. Chorak ◽  
Raymond M. Newman ◽  
Jasmine A. Eltawely ◽  
Jo Latimore ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Population Genetic ◽  
Myriophyllum Spicatum ◽  
Population Variation ◽  
Efficacy Evaluation ◽  
Submerged Aquatic Plant ◽  
Myriophyllum Sibiricum ◽  
Control Response ◽  
Herbicide Response

AbstractPopulation genetic studies of within- and among-population genetic variability are still lacking for managed submerged aquatic plant species, and such studies could provide important information for managers. For example, the extent of within-population genetic variation may influence the potential for managed populations to locally adapt to environmental conditions and control tactics. Similarly, among-population variation may influence whether specific control tactics work equally effectively in different locations. In the case of invasive Eurasian watermilfoil (Myriophyllum spicatum L.), including interspecific hybrids with native northern watermilfoil (Myriophyllum sibiricum Kom.), managers recognize that there is genetic variation for growth and herbicide response. However, it is unclear how much overall genetic variation there is, and how it is structured within and among populations. Here, we studied patterns of within- and among-lake genetic variation in 41 lakes in Michigan and 62 lakes in Minnesota using microsatellite markers. We found that within-lake genetic diversity was generally low, and among-lake genetic diversity was relatively high. However, some lakes were genetically diverse, and some genotypes were shared across multiple lakes. For genetically diverse lakes, managers should explicitly recognize the potential for genotypes to differ in control response and should account for this in monitoring and efficacy evaluation and using pretreatment herbicide screens to predict efficacy. Similarly, managers should consider differences in genetic composition among lakes as a source of variation in the growth and herbicide response of lakes with similar control tactics. Finally, laboratory or field information on control efficacy from one lake may be applied to other lakes where genotypes are shared among lakes.

scholarly journals Inter- and intra-population variation of local maize (Zea mays L.) populations from Slovakia and Czech Republic

2008 ◽  
Vol 43 (No. 1) ◽  
pp. 7-15 ◽  
Author(s):  
P. Múdry ◽  
J. Kraic
Keyword(s):  
Zea Mays ◽  
Genetic Variation ◽  
Czech Republic ◽  
Population Variation ◽  
Polymorphic Loci ◽  
Maize Populations ◽  
Expected Heterozygosity ◽  
Isoenzyme Polymorphism ◽  
New Alleles

Evaluation of genetic variation was performed within 62 local maize populations originating from Slovakia and Czech Republic. In total 48 alleles at 22 analyzed isoenzyme loci with an average of 2.2 alleles per locus were revealed. The percentage of polymorphic loci ranged from 14% to 59% and the frequencies of detected alleles varied from null to four per locus. No polymorphism was detected at the loci <i>Dia2</i>, <i>Got3</i>, <i>Mdh4</i>, <i>Mmm</i>, and <i>Pgm1</i>. The highest number of alleles (four) was detected at loci <i>Acp1</i>, <i>Cat3</i>, <i>Pgm2</i>. No new alleles were identified, nevertheless the frequency of seven alleles was only about 1%. The expected heterozygosity ranged from null to 0.492 with an average of 0.197. The revealed isoenzyme polymorphism confirmed that all analyzed populations were heterogeneous and as many as 17 of them were completely heterogeneous. None of the analyzed populations was identical in the frequency of alleles at all 22 analyzed loci.

Mapping genes for growth rate and fatness in a Large White x Meishan F2 pig population

1998 ◽  
Vol 1998 ◽  
pp. 7-7 ◽  
Author(s):  
G.A. Walling ◽  
A.L Archibald ◽  
P.M. Visscher ◽  
C.S. Haley
Keyword(s):  
Growth Rate ◽  
Genetic Variation ◽  
Experimental Design ◽  
Statistical Methods ◽  
Population Based ◽  
Genetic Maps ◽  
Large White ◽  
Backcross Population ◽  
Livestock Species ◽  
Reproduction Traits

DNA-based markers and genetic maps of major livestock species have been developed in the last few years. These, together with experimental populations and appropriate statistical methods, provide the tools to dissect causes of economically important genetic variation in livestock. A cross between genetically diverse lines is a powerful experimental design for such a study. In an F2 or backcross population from such a cross, markers are likely to be highly informative and the genes that control the differences between the lines will be segregating. We have been developing such a resource population based on a cross between the British Large White and Chinese Meishan pigs. These breeds differ for many traits, with the Meishan being inferior for growth rate and fatness, but superior for reproduction traits. Here we report the mapping of major genetic effects on growth rate and fatness in our cross.

Distribution of genetic diversity in wild European populations of prickly lettuce (Lactuca serriola): implications for plant genetic resources management

2010 ◽  
Vol 8 (2) ◽  
pp. 171-181 ◽  
Author(s):  
C. C. M. van de Wiel ◽  
T. Sretenović Rajičić ◽  
R. van Treuren ◽  
K. J. Dehmer ◽  
C. G. van der Linden ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Crop Wild Relatives ◽  
Population Variation ◽  
Lactuca Serriola ◽  
Genetic Resources Management ◽  
Nbs Profiling ◽  
The Uk

Genetic variation in Lactuca serriola, the closest wild relative of cultivated lettuce, was studied across Europe from the Czech Republic to the United Kingdom, using three molecular marker systems, simple sequence repeat (SSR, microsatellites), AFLP and nucleotide-binding site (NBS) profiling. The ‘functional’ marker system NBS profiling, targeting disease resistance genes of the NBS/LRR family, did not show marked differences in genetic diversity parameters to the other systems. The autogamy of the species resulted in low observed heterozygosity and high population differentiation. Intra-population variation ranged from complete homogeneity to nearly complete heterogeneity. The highest genetic diversity was found in central Europe. The SSR results were compared to SSR variation screened earlier in the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN). In the UK, practically only a single SSR genotype was found. This genotype together with a few other common SSR genotypes comprised a large part of the plants sampled on the continent. Among the ten most frequent SSR genotypes observed, eight were already present in the CGN collection. Overall, the CGN collection appears to already have a fair representation of genetic variation from NW Europe. The results are discussed in relation to sampling strategies for improving genebank collections of crop wild relatives.

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