Paternity Exclusion using Multiple Hypervariable Microsatellite Loci Amplified from Nuclear DNA of Hair Cells

2015 ◽  
pp. 63-81
Author(s):  
A. Morin Phillip ◽  
S. Woodruff David
Keyword(s):  
Hair Cells ◽  
Microsatellite Loci ◽  
Nuclear Dna ◽  
Paternity Exclusion

Microsatellite polymorphism in Dioscorea tokoro, a wild yam species

Genome ◽  
1994 ◽  
Vol 37 (5) ◽  
pp. 794-801 ◽  
Author(s):  
Ryohei Terauchi ◽  
Akihiro Konuma
Keyword(s):  
Microsatellite Loci ◽  
Simple Sequence Repeat ◽  
Population Genetic ◽  
Natural Populations ◽  
Allozyme Analysis ◽  
Sequence Repeat ◽  
Expected Heterozygosity ◽  
Simple Sequence ◽  
Paternity Exclusion ◽  
Wild Yam

Six microsatellite loci were characterized in Dioscorea tokoro, a wild yam species in East Asia. All six loci were polymorphic in a sample of 23 individuals from natural populations in Japan. The microsatellite loci displayed many alleles (6.2 alleles per locus on average), and the observed heterozygosity (Ho = 0.54) as well as expected heterozygosity (He = 0.68) were high. The heterozygosities were far more than that previously detected by allozyme analysis of D. tokoro (Ho = 0.23, He = 0.28). Five microsatellite loci were sufficient to provide a paternity exclusion rate (Q) of Q = 0.98, which enables monitoring of the pollen-mediated gene flow between plants in a population. Microsatellite loci are abundant and highly polymorphic in D. tokoro and other plants and are therefore ideal markers for plant population genetic studies.Key words: microsatellite, simple sequence repeat, population genetics, Dioscorea tokoro.

scholarly journals Microsatellite Polymorphism and Genetic Structure of Florida Mottled Duck Populations

The Condor ◽  
2002 ◽  
Vol 104 (2) ◽  
pp. 424-431 ◽  
Author(s):  
Christen L. Williams ◽  
Richard C. Brust ◽  
Olin E. Rhodes Jr
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Habitat Loss ◽  
Microsatellite Loci ◽  
Nuclear Dna ◽  
Gene Frequencies ◽  
Limited Distribution ◽  
Mottled Duck ◽  
Anas Fulvigula ◽  
High Level

Abstract Little is understood concerning the effects regional isolation and habitat loss have had upon the genetic structure of Mottled Ducks (Anas fulvigula), a nonmigratory waterfowl species with a limited distribution. Our objective was to identify nuclear DNA-based markers for Mottled Ducks and determine levels of subdivision among populations in Florida. We screened 13 microsatellite primer pairs and identified six microsatellite loci that were variable in Mottled Ducks. These markers revealed a low level of genetic differentiation and a high level of genetic exchange among four Mottled Duck subpopulations within Florida. Over all populations, single-locus expected heterozygosities over the six loci surveyed ranged from 0.13–0.85. There were no significant differences in gene frequencies among the populations examined, and the Fst over 5 biparental loci was not different from zero. Our analysis of the Florida Mottled Duck population indicated high levels of heterozygosity and no evidence of genetic subdivision among breeding units. Polimorfismo en Microsatélites y Estructura Genética en Poblaciones de Anas fulvigula Resumen. Se tiene escaso conocimiento acerca de los efectos del aislamiento regional y de la pérdida de hábitat sobre la estructura genética de poblaciones de Anas fulvigula, un ave acuática no migratoria de distribución restringida. Nuestro objetivo fue identificar marcadores genéticos de ADN para A. fulvigula y determinar los niveles de subdivisión entre poblaciones en Florida. Examinamos 13 pares de iniciadores (i.e., primers) para microsatélites e identificamos seis loci que fueron variables en A. fulvigula. Estos marcadores revelaron un bajo nivel de diferenciación genética y un alto grado de intercambio genético entre cuatro subpoblaciones de A. fulvigula en Florida. Para todas las poblaciones, la heterocigocidad esperada en un locus varió entre 0.13–0.85 para los seis loci examinados. No hubo diferencias significativas en las frecuencias génicas entre las subpoblaciones examinadas, y el valor de Fst para los 5 loci biparentales no fue diferente de cero. Nuestros análisis de las poblaciones de A. fulvigula de Florida indicaron altos niveles de heterocigocidad y no mostraron evidencia de subdivisión genética entre las unidades reproductivas.

scholarly journals Electric eels galore: microsatellite markers for population studies

2020 ◽  
Vol 18 (4) ◽  
Author(s):  
Lenice Souza-Shibatta ◽  
Dhiego G. Ferreira ◽  
Kátia F. Santos ◽  
Bruno A. Galindo ◽  
Oscar A. Shibatta ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Population Studies ◽  
Genetic Identity ◽  
Amazon Rainforest ◽  
Cross Amplification ◽  
Electric Eel ◽  
Electric Fishes ◽  
Paternity Exclusion

Abstract Fourteen novel microsatellite loci are described and characterized in two species of electric eels, Electrophorus variiand E. voltaifrom floodplains and rivers of the Amazon rainforest. These loci are polymorphic, highly informative, and have the capacity to detect reliable levels of genetic diversity. Likewise, the high combined probability of paternity exclusion value and low combined probability of genetic identity value obtained demonstrate that the new set of loci displays suitability for paternity studies on electric eels. In addition, the cross-amplification of electric eel species implies that it may also be useful in the study of the closely related E. electricus, and to other Neotropical electric fishes (Gymnotiformes) species as tested herein.

Multiple paternity in the Black Caiman (Melanosuchus niger) population in the Anavilhanas National Park, Brazilian Amazonia

2011 ◽  
Vol 32 (3) ◽  
pp. 428-434 ◽  
Author(s):  
Ronis Da Silveira ◽  
Izeni P. Farias ◽  
William E. Magnusson ◽  
Fabio L. Muniz ◽  
Tomas Hrbek ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Microsatellite Loci ◽  
Multiple Paternity ◽  
Likelihood Estimation ◽  
Genetic Identity ◽  
Alligator Mississippiensis ◽  
Dominant Male ◽  
Effective Population ◽  
Negro River ◽  
Paternity Exclusion

AbstractThe formation of dominance hierarchies in which the female mates with a large dominant male is common among crocodilians. However, there is the possibility of polyandry, in which females mate with multiple partners during a single breeding season and generate offspring with multiple paternity. In the present study, eight pairs of heterologous primers developed for Alligator mississippiensis and Caiman latirostris were used to determine whether multiple paternity exists in the Black Caiman, Melanosuchus niger. For such, we analyzed 34 Black Caiman offspring from the Anavilhanas Archipelago in the Negro River (state of Amazonas, Brazil). The specimens came from six groups, each containing five or six hatchlings. Paternity exclusion and genetic identity indices were calculated to test the robustness of the microsatellite loci. Simple allele counts and maximum likelihood estimation of family clusters were used to determine the likelihood of occurrence of multiple paternity. Among the eight loci tested, five were effective at determining paternity, with paternity exclusion values close to 1.0 (QC = 0.92) and genetic identity values close to zero (IC < 0.01). Using the simple allele count, six cases of multiple paternity were detected and confirmed in three hatchling groups by four different microsatellite loci. However, maximum likelihood analysis indicated multiple paternity in all the groups analyzed, with five family clusters identified in one hatchling group alone. Considering that this species is listed according to IUCN as Lower Risk/Conservation Dependent, our results have direct conservation implications. Multiple paternity increases effective population size by maintaining genetic variation, and thus could be an important mechanism to maintain genetic diversity in isolated local populations.

scholarly journals Endangered Rough Pigtoe Pearlymussel: Assessment of Phylogenetic Status and Genetic Differentiation of Two Disjunct Populations

2015 ◽  
Vol 6 (2) ◽  
pp. 338-349 ◽  
Author(s):  
Jess W. Jones ◽  
Nathan Johnson ◽  
Paul Grobler ◽  
Daniel Schilling ◽  
Richard J Neves ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
River Basin ◽  
Dna Sequences ◽  
Microsatellite Loci ◽  
Nuclear Dna ◽  
Fish Host ◽  
Shell Morphology ◽  
Ohio River ◽  
Separate Species ◽  
Phylogenetic Status

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.

scholarly journals Detection of Heterozygosity and Allelic Frequency of Indian and Southeast Asian Types of Oecophylla smaragdina (Fabricius) (Hymenoptera, Formicidae) in Bangladesh using Microsatellite Markers

2021 ◽  
Author(s):  
Md Mamunur Rahman ◽  
Shingo Hosoishi ◽  
Kazuo Ogata
Keyword(s):  
Gene Flow ◽  
Microsatellite Loci ◽  
Nuclear Dna ◽  
Allelic Frequency ◽  
Microsatellite Analysis ◽  
Cytb Gene ◽  
Oecophylla Smaragdina ◽  
Interspecific Gene Flow ◽  
Mitochondrial Coi ◽  
Weaver Ant

Background: The two types of Asian weaver ant species, Oecophylla smaragdina, Indian types and Southeast (SE) Asian types can co-occur in the same habitat. Previous study on mtDNA based phylogenesis of O. smaragdina in Bangladesh has revealed the presence of the mixture of both Indian and SE Asian type of O. smaragdina. However, the nuclear DNA based study showed some inconsistency leading the chance of hybridization as colonies encountered from two localities contained O. smaragdina workers from more than one type as identified via longwave length rhodopsin (LWRh) and mitochondrial COI and Cytb gene analysis. The purpose of present study was to detect hybridization status and to find out the identical allele for Indian and SE Asian type of O. smaragdina from different colonies. Method: A total of seven O. smaragdina colonies had been collected from Bangladesh during 2013 to December 2016. Microsatellite analysis were performed for Gene mapping and heterozygosity study with 11 microsatellite loci through electropherogrum study generated by peak scanner software.Result: Among 11 microsatellite loci, two loci, MS 8.24 and MS 6.45 provided the identical allele position for Indian and SE Asian types while no allelic position were identified with nine microsatellite loci. The results inferred that weaver ant of both Indian and SE Asian type engage in bidirectional interspecific gene flow. The strong possibility of hybridization between these two types is inferred, which indicates that barriers to hybridization do not exist or can be completely overcome. This is unexpected, given that they are non-sister species and broadly sympatric in nature. These findings also indicate the possible occurrence of hybrid-hybrid crosses in some localities of weaver ant, a phenomenon rarely observed in ants. 

Global Population Genetic Structure and Male-Mediated Gene Flow in the Green Sea Turtle (Chelonia mydas): Analysis of Microsatellite Loci

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1857-1870
Author(s):  
Mark A Roberts ◽  
Tonia S Schwartz ◽  
Stephen A Karl
Keyword(s):  
Gene Flow ◽  
Microsatellite Loci ◽  
Genetic Divergence ◽  
Nuclear Dna ◽  
Chelonia Mydas ◽  
Single Copy ◽  
Sea Turtle ◽  
Population Connectivity ◽  
Population Subdivision ◽  
Cryptic Variation

Abstract We assessed the degree of population subdivision among global populations of green sea turtles, Chelonia mydas, using four microsatellite loci. Previously, a single-copy nuclear DNA study indicated significant male-mediated gene flow among populations alternately fixed for different mitochondrial DNA haplotypes and that genetic divergence between populations in the Atlantic and Pacific Oceans was more common than subdivisions among populations within ocean basins. Even so, overall levels of variation at single-copy loci were low and inferences were limited. Here, the markedly more variable microsatellite loci confirm the presence of male-mediated gene flow among populations within ocean basins. This analysis generally confirms the genetic divergence between the Atlantic and Pacific. As with the previous study, phylogenetic analyses of genetic distances based on the microsatellite loci indicate a close genetic relationship among eastern Atlantic and Indian Ocean populations. Unlike the single-copy study, however, the results here cannot be attributed to an artifact of general low variability and likely represent recent or ongoing migration between ocean basins. Sequence analyses of regions flanking the microsatellite repeat reveal considerable amounts of cryptic variation and homoplasy and significantly aid in our understanding of population connectivity. Assessment of the allele frequency distributions indicates that at least some of the loci may not be evolving by the stepwise mutation model.

scholarly journals Development and characterization of microsatellite loci of Microglanis cottoides (Siluriformes: Pseudopimelodidae) and cross-species amplification

2013 ◽  
Vol 11 (3) ◽  
pp. 581-585 ◽  
Author(s):  
Lenice Souza-Shibatta ◽  
Dhiego Gomes Ferreira ◽  
Claudio Oliveira ◽  
Fernanda Simões de Almeida ◽  
Oscar Akio Shibatta ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Wild Population ◽  
Genetic Identity ◽  
Microsatellite Primers ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Low Probability ◽  
Paternity Exclusion

Thirteen microsatellite loci were isolated and characterized in Microglanis cottoides. Of these, two were monomorphic and 11 were polymorphic. These polymorphic loci tested on 24 individuals from a wild population produced a total of 108 different alleles, with levels of variability high, ranging from 2 to 20, with an average of 8.3 alleles per locus. The observed and expected heterozygosity ranged from 0.125 to 0.958 and from 0.119 to 0.931, respectively. A high combined probability of paternity exclusion value and a low probability combined genetic identity value obtained show that the set of loci described herein displays good suitability for paternity studies and differentiation of M. cottoides. Additionally, all thirteen microsatellite primers developed for M. cottoides were tested in four other Pseudopimelodidae species and successful cross-species amplification was achieved for the majority of loci.

Fluorocitrate Neural Dystrophy of the Guinea Pig Cochlea

1975 ◽  
Vol 33 ◽  
pp. 368-369
Author(s):  
G.J. Spector ◽  
C.D. Carr ◽  
I. Kaufman Arenberg ◽  
R.H. Maisel
Keyword(s):  
Hearing Loss ◽  
Hair Cells ◽  
Sodium Phosphate ◽  
Sensory Cells ◽  
Barium Salt ◽  
Perfusion Medium ◽  
Cochlear Hair Cells ◽  
Neural Degeneration ◽  
Sodium Phosphate Buffer ◽  
Cochlear Neurons

All studies on primary neural degeneration in the cochlea have evaluated the end stages of degeneration or the indiscriminate destruction of both sensory cells and cochlear neurons. We have developed a model which selectively simulates the dystrophic changes denoting cochlear neural degeneration while sparing the cochlear hair cells. Such a model can be used to define more precisely the mechanism of presbycusis or the hearing loss in aging man.Twenty-two pigmented guinea pigs (200-250 gm) were perfused by the perilymphatic route as live preparations using fluorocitrate in various concentrations (15-250 ug/cc) and at different incubation times (5-150 minutes). The barium salt of DL fluorocitrate, (C6H4O7F)2Ba3, was reacted with 1.0N sulfuric acid to precipitate the barium as a sulfate. The perfusion medium was prepared, just prior to use, as follows: sodium phosphate buffer 0.2M, pH 7.4 = 9cc; fluorocitrate = 15-200 mg/cc; and sucrose = 0.2M.

Ultrastructure of superficial neuromasts in the mottled sculpin, Cottus bairdi

1989 ◽  
Vol 47 ◽  
pp. 958-959
Author(s):  
W.R. Jones ◽  
S. Coombs ◽  
J. Janssen
Keyword(s):  
Hair Cells ◽  
Lateral Line System ◽  
Electron Microscopic ◽  
Line System ◽  
Dense Cores ◽  
Sensory Hair Cells ◽  
Cytoplasmic Vesicles ◽  
Cottus Bairdi ◽  
Mottled Sculpin ◽  
Upper Third

The lateral line system of the mottled sculpin, like that of most bony fish, has both canal (CNM) and superficial (SNM) sensory end organs, neuromasts, which are distributed on the head and trunk in discrete, readily identifiable groupings (Fig. 1). CNM and SNM differ grossly in location and in overall size and shape. The former are located in subdermal canals and are larger and asymmetric in shape, The latter are located directly on the surface of the skin and are much smaller and more symmetrical It has been suggested that the two may differ at a more fundamental level in such functionally related parameters as extent of myelination of innervating fibers and the absence of efferent innervation in SNM. The present study addresses the validity of these last two features as distinguishing criteria by examining the structure of those SNM populations indicated in Fig. 1 at both the light and electron microscopic levels.All of the populations of SNM examined conform in general to previously published descriptions, consisting of a neuroepithelium composed of sensory hair cells, support cells and mantle cells, Several significant differences from these accounts have, however, emerged. Firstly, the structural composition of the innervating fibers is heterogeneous with respect to the extent of myelination. All SNM groups, with the possible exception of the TRrs and CFLs, possess both myelinated and unmyelinated fibers within the neuroepithelium proper (Fig. 2), just as do CNM. The extent of myelina- tion is quite variable, with some fibers sheath terminating just before crossing the neuroepithelial basal lamina, some just after and a few retaining their myelination all the way to the base of the hair cells in the upper third of the neuroepithelium. Secondly, all SNMs possess fibers that may, on the basis of ultrastructural criteria, be identified as efferent. Such fibers contained numerous cytoplasmic vesicles, both clear and with dense cores. In regions where such fibers closely apposed hair cells, subsynaptic cisternae were observed in the hair cell (Fig. 3).

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