Characterization of AFLP markers in damselflies: prevalence of codominant markers and implications for population genetic applications

Amplified fragment length polymorphism (AFLP) analysis is becoming increasingly popular as a method for generating molecular markers for population genetic applications. For practical considerations, it is generally assumed in population studies that AFLPs segregate as dominant markers, i.e., that present and absent are the only possible states of a given locus. We tested the assumption of dominance in natural populations of the damselfly Nehalennia irene (Hagen) (Odonata: Coenagrionidae). Electro-blotted AFLP products from 21 samples were probed with individual markers. Eleven markers were analyzed, of which two were monomorphic and nine were polymorphic. Only two of the polymorphic markers behaved in a strictly dominant manner. The remaining seven polymorphic markers displayed various degrees of codominance, with 210 visible alleles in the sample. Of the three markers displaying the highest degree of variability, two contained microsatellite repeat tracts. Our results suggest that the assumption of dominance is unfounded. As a result, AFLP analysis may be unsuitable for estimating several important population genetic parameters, including genetic diversity.Key words: AFLP, population genetics, dominant markers, microsatellite, insect, damselfly.

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The Limits to Estimating Population-Genetic Parameters with Temporal Data

Genome Biology and Evolution ◽

10.1093/gbe/evaa056 ◽

2020 ◽

Vol 12 (4) ◽

pp. 443-455

Author(s):

Michael Lynch ◽

Wei-Chin Ho

Keyword(s):

Population Genetic ◽

Genetic Parameters ◽

Natural Populations ◽

Estimation Methods ◽

Frequency Change ◽

Sampling Variance ◽

Effective Population ◽

Closed Population ◽

Temporal Variance ◽

Population Genetic Parameters

Abstract The ability to obtain genome-wide sequences of very large numbers of individuals from natural populations raises questions about optimal sampling designs and the limits to extracting information on key population-genetic parameters from temporal-survey data. Methods are introduced for evaluating whether observed temporal fluctuations in allele frequencies are consistent with the hypothesis of random genetic drift, and expressions for the expected sampling variances for the relevant statistics are given in terms of sample sizes and numbers. Estimation methods and aspects of statistical reliability are also presented for the mean and temporal variance of selection coefficients. For nucleotide sites that pass the test of neutrality, the current effective population size can be estimated by a method of moments, and expressions for its sampling variance provide insight into the degree to which such methodology can yield meaningful results under alternative sampling schemes. Finally, some caveats are raised regarding the use of the temporal covariance of allele-frequency change to infer selection. Taken together, these results provide a statistical view of the limits to population-genetic inference in even the simplest case of a closed population.

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Characterization of Verticillium albo-atrum Field Isolates Using Pathogenicity Data and AFLP Analysis

Plant Disease ◽

10.1094/pdis.2003.87.6.633 ◽

2003 ◽

Vol 87 (6) ◽

pp. 633-638 ◽

Cited By ~ 35

Author(s):

Sebastjan Radišek ◽

Jernej Jakše ◽

Andrej Simončič ◽

Branka Javornik

Keyword(s):

Fragment Length Polymorphism ◽

Economic Losses ◽

Aflp Analysis ◽

Mild Form ◽

Aflp Data ◽

Green Pepper ◽

Clear Separation ◽

Pathogenicity Tests ◽

Verticillium Albo Atrum

Since 1997, hop wilt induced by a virulent pathotype of Verticillium albo-atrum has caused considerable economic losses in hop fields in Slovenia. In all, 20 isolates of V. albo-atrum, including 12 from plants affected with the lethal form (PG2) of hop wilt, 6 from plants with the mild form (PG1), 1 from cucumber, and 1 from petunia, as well as 1 isolate of V. dahliae each from hop and green pepper, were analyzed by amplified fragment length polymorphism (AFLP). Differences in the virulence of hop isolates were confirmed by pathogenicity tests on hop cultivars. The AFLP method was optimized for analysis of these fungi and 7 of 39 primer combinations tested were used for the analysis of polymorphism among isolates. Cluster analysis of AFLP data divided the isolates into two, well-separated V. albo-atrum and V. dahliae clusters, confirming that the two species are genetically distinct. Within the V. albo-atrum cluster, isolates were further separated into two distinct groups: the A1 group contained PG1 hop pathotype and cucumber and petunia isolates, and the A2 group all hop isolates of the PG2 pathotype. Minor genetic variation was detected within pathotype-associated AFLP groups, but the clear separation of V. albo-atrum hop isolates according to their level of virulence shows genetic differentiation among hop V. albo-atrum pathotypes.

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Development and characterization of fungal specific microsatellite markers in the lichenLobarina scrobiculata(Lobariaceae, Ascomycota)

The Lichenologist ◽

10.1017/s0024282915000109 ◽

2015 ◽

Vol 47 (3) ◽

pp. 183-186 ◽

Cited By ~ 6

Author(s):

Maria Prieto ◽

Lidia Romera ◽

Sonia Merinero ◽

Gregorio Aragón ◽

Isabel Martínez

Keyword(s):

Microsatellite Markers ◽

Iberian Peninsula ◽

Population Studies ◽

Gene Diversity ◽

Conservation Status ◽

Natural Populations ◽

Conservation Strategies ◽

Unbiased Gene ◽

Effective Conservation

AbstractLobarina scrobiculata(better known asLobaria scrobiculata) is a widespread lichen, threatened and Red-Listed in various European countries. Microsatellite markers for the mycobiont ofL. scrobiculatawere developed in order to investigate its genetic diversity in the Iberian Peninsula and Europe and to design effective conservation strategies. A total of 7 polymorphic markers were isolated and characterized. These microsatellites were tested in natural populations found in the Iberian Peninsula. The number of observed alleles ranged from 3 to 8, and the Nei's unbiased gene diversity from 0·26 to 0·59. These microsatellite markers are the first to be developed forL. scrobiculataand they will be useful for population studies and for the assessment of the conservation status of this species.

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The genetic structure of natural populations of Drosophila melanogaster. XXIV. Effects of hybrid dysgenesis on the components of genetic variance of variability.

Genetics ◽

10.1093/genetics/127.3.545 ◽

1991 ◽

Vol 127 (3) ◽

pp. 545-552

Author(s):

D S Suh ◽

T Mukai

Keyword(s):

Drosophila Melanogaster ◽

Population Genetic ◽

Genetic Parameters ◽

Genetic Variance ◽

Additive Genetic Variance ◽

Natural Populations ◽

Deleterious Mutations ◽

Degree Of Dominance ◽

Population Genetic Parameters ◽

P Type

Abstract Eight hundred second chromosomes were extracted from the Ishigakijima population, one of the southernmost populations of Drosophila melanogaster in Japan. Half of them were extracted in Native cytoplasm (P-type), and half in Foreign cytoplasm (M-type). Various population-genetic parameters, including the frequency of lethal-carrying second chromosomes (Q = 0.235 for the Native; 0.218 for the Foreign), the allelism rate of lethal second chromosome (Ic = 0.0217 for the Native; 0.0134 for the Foreign), the homozygous detrimental and lethal loads (D = 0.179 for the Native; 0.270 for the Foreign; L = 0.262 for the Native; 0.240 for the Foreign), the average degree of dominance of mildly deleterious mutations (ĥE = 0.244 for the Native; 0.208 for the Foreign), and the components of genetic variance for viability [additive (sigma A2) and dominance (sigma D2)](ŝigma A2 = 0.0187 for the Native; 0.0172 for the Foreign; ŝigma D2 = 0.0005 for the Native; 0.0009 for the Foreign) were estimated. The data indicate that D was significantly larger and hE was significantly smaller in the Foreign cytoplasm. However, the estimates of additive and dominance variances were not significantly different between the two cytoplasms. The additive genetic variance for viability in the Ishigakijima population was greater than expected on the basis of mutation-selection balance confirming previous studies on papers of D. melanogaster in warm climates.

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Isolation and Characterization of Polymorphic Microsatellite Markers for Two Subterranean Termites

Sociobiology ◽

10.13102/sociobiology.v64i3.1692 ◽

2017 ◽

Vol 64 (3) ◽

pp. 352 ◽

Cited By ~ 1

Author(s):

Yu-Lei Dang ◽

Hong-Gui Zhang ◽

Yu-Feng Meng ◽

Min Zhang ◽

Sha Zhao ◽

...

Keyword(s):

Microsatellite Markers ◽

Microsatellite Loci ◽

Population Genetic ◽

Subterranean Termites ◽

Polymorphic Markers ◽

Isolation And Characterization ◽

Expected Heterozygosity ◽

Hardy Weinberg Equilibrium ◽

Polymorphic Microsatellite

We isolated 15 and 18 highly polymorphic genomic microsatellite markers from two subterranean termites, Reticulitermes aculabialis and R. labralis, respectively. A total of 53 alleles were detected in 15 microsatellite loci of R. aculabialis, and the alleles were 3.533±1.302 (mean±SD), while the corresponding data of R. labralis were 115 detected alleles in 18 microsatellite loci with 6.389±1.754 alleles. The observed and expected heterozygosity was 0.496±0.236 and 0.564±0.125 in R. aculabialis, and 0.368±0.263 and 0.702±0.115 in R. labralis, respectively. Seven loci were highly polymorphic (PIC>0.5) in R. aculabialis, and 15 loci were highly polymorphic (PIC>0.5) in R. labralis. All loci showed Hardy–Weinberg equilibrium. These polymorphic markers provide useful tools for population genetic and breeding system studies of subterranean termites.

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Bayesian inference of species hybrids using multilocus dominant genetic markers

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2008.0043 ◽

2008 ◽

Vol 363 (1505) ◽

pp. 2841-2850 ◽

Cited By ~ 49

Author(s):

Eric C Anderson

Keyword(s):

Bayesian Inference ◽

Genetic Markers ◽

Length Polymorphism ◽

Fragment Length Polymorphism ◽

Natural Populations ◽

Short Description ◽

Aflp Data ◽

Dominant Markers ◽

The One ◽

Species Hybrids

Neutral genetic markers are useful for identifying species hybrids in natural populations, especially when used in conjunction with statistical methods like the one implemented in the software NewHybrids . Here, a short description of the extension of NewHybrids to dominant markers is given. Subsequently, an extensive series of simulations of amplified fragment length polymorphism (AFLP) data is performed to evaluate the prospects for hybrid identification with (possibly non-diagnostic) dominant markers. Distinguishing between F 1 's and F 2 's is shown to be difficult, possibly requiring upwards of 100 AFLP markers to be done accurately. Discriminating between pure-bred and non-pure (hybrid) individuals, however, is shown to be much easier, requiring perhaps as few as 10 dominant markers, even from relatively weakly diverged species.

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Identification and characterization of the contact zone between short-tailed shrews (Blarina) in Iowa and Missouri

Canadian Journal of Zoology ◽

10.1139/z11-001 ◽

2011 ◽

Vol 89 (4) ◽

pp. 278-288 ◽

Cited By ~ 6

Author(s):

C.W. Thompson ◽

R.S. Pfau ◽

J.R. Choate ◽

H.H. Genoways ◽

E.J. Finck

Keyword(s):

Fragment Length Polymorphism ◽

Putative Hybrid ◽

Aflp Analysis ◽

Contact Zones ◽

Blarina Brevicauda ◽

Field Identification ◽

The One ◽

Blarina Hylophaga ◽

Identification And Characterization

Short-tailed shrews (genus Blarina Gray, 1838) are characterized by divergent karyotypes and are genetically distinct. Blarina species are similar morphologically but, in most cases, can be distinguished morphometrically. Blarina distributions tend to be parapatric along well-defined contact zones; however, it has been suggested that the northern short-tailed shrew ( Blarina brevicauda (Say, 1823)) and Elliot’s short-tailed shrew ( Blarina hylophaga Elliot, 1899) occur sympatrically in Iowa and Missouri. To evaluate this possibility, 179 specimens were collected in southwestern Iowa and northwestern Missouri. Karyotypes and total length were used for field identification, and amplified fragment length polymorphism (AFLP) analysis was used to verify field identifications and to investigate the extent of hybridization. One hundred seventy-eight of 179 specimens were identified to species. The one exception had a karyotype of B. brevicauda (2n = 50, FN = 48); however, AFLP analysis indicated that this individual was likely an F1 hybrid. No backcrosses were detected, so it appears that introgression is minimal. The putative hybrid was trapped at a locality with B. brevicauda just north of a locality having only B. hylophaga. No locality contained both species. Therefore, these species are not broadly sympatric as has been suggested, but rather exhibit a distribution similar to the pattern of parapatry seen in most of the contact zones of Blarina.

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Fourier Transform Infrared and Raman Spectroscopy for Characterization of Listeria monocytogenes Strains

Applied and Environmental Microbiology ◽

10.1128/aem.72.1.228-232.2006 ◽

2006 ◽

Vol 72 (1) ◽

pp. 228-232 ◽

Cited By ~ 59

Author(s):

Astrid Oust ◽

Trond Møretrø ◽

Kristine Naterstad ◽

Ganesh D. Sockalingum ◽

Isabelle Adt ◽

...

Keyword(s):

Fatty Acids ◽

Raman Spectroscopy ◽

Fourier Transform ◽

Listeria Monocytogenes ◽

Fragment Length Polymorphism ◽

Fourier Transform Infrared ◽

Aflp Analysis ◽

Aflp Data ◽

Infrared And Raman Spectroscopy

ABSTRACT The purpose of this study was to characterize the variation in biochemical composition of 89 strains of Listeria monocytogenes with different susceptibilities towards sakacin P, using Fourier transform infrared (FTIR) spectroscopy and Raman spectroscopy. The strains were also analyzed using amplified fragment length polymorphism (AFLP) analysis. Based on their susceptibilities to sakacin P, the 89 strains have previously been divided into two groups. Using the FTIR spectra and AFLP data, the strains were basically differentiated into the same two groups. Analyses of the FTIR and Raman spectra revealed that the strains in the two groups contained differences in the compositions of carbohydrates and fatty acids. The relevance of the variation in the composition of carbohydrates with respect to the variation in the susceptibility towards sakacin P for the L. monocytogenes strains is discussed.

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Amplified-Fragment Length Polymorphism Fingerprinting of Mycoplasma Species

Journal of Clinical Microbiology ◽

10.1128/jcm.37.10.3300-3307.1999 ◽

1999 ◽

Vol 37 (10) ◽

pp. 3300-3307 ◽

Cited By ~ 54

Author(s):

Branko Kokotovic ◽

Niels F. Friis ◽

Jørgen S. Jensen ◽

Peter Ahrens

Keyword(s):

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Mycoplasma Hominis ◽

Amplified Fragment Length Polymorphism ◽

Animal Origin ◽

Mycoplasma Species ◽

Aflp Analysis ◽

Pattern Similarity

Amplified-fragment length polymorphism (AFLP) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. The potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including Mycoplasma genitalium(n = 11), Mycoplasma pneumoniae(n = 5), Mycoplasma hominis(n = 5), Mycoplasma hyopneumoniae(n = 9), Myco plasma flocculare(n = 5), Mycoplasma hyosynoviae(n = 10), and Mycoplasma dispar(n = 5). AFLP templates were prepared by the digestion of mycoplasmal DNA with BglII and MfeI restriction endonucleases and subsequent ligation of corresponding site-specific adapters. The amplification of AFLP templates with a single set of nonselective primers resulted in reproducible fingerprints of approximately 60 to 80 fragments in the size range of 50 to 500 bp. The method was able to discriminate the analyzed strains at species and intraspecies levels as well. Each of the testedMycoplasma species developed a banding pattern entirely different from those obtained from other species under analysis. Subtle intraspecies genomic differences were detected among strains of all of the Mycoplasma species analyzed. The extent of polymorphism varied markedly between the analyzed mycoplasmas, comprising pattern similarity levels from 61.7% detected among M. disparstrains to 95.9% detected among M. genitalium strains. The results of the present study provide evidence of the high discriminatory power of AFLP analysis, suggesting the possible applicability of this method to the molecular characterization of mycoplasmas.

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