Allozyme variation in Piceamariana from Newfoundland: genetic diversity, population structure, and analysis of differentiation

1986 ◽  
Vol 16 (4) ◽  
pp. 713-720 ◽  
Author(s):  
Francis C. Yeh ◽  
M. A. K. Khalil ◽  
Yousry A. El-Kassaby ◽  
Diane C. Trust
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Complex Structure ◽  
Allozyme Variation ◽  
Allele Frequencies ◽  
Discriminant Functions ◽  
Migration Patterns ◽  
Forest Regions ◽  
F Statistics

Seeds from 21 populations of Piceamariana (Mill.) B.S.P. from five forest sections of the boreal forest regions in Newfoundland were analyzed for electrophoretically detectable variation in 15 proteins coded by 23 genetic loci. On the average, 38% of the loci per population were polymorphic, the number of alleles per locus was 1.44, and the expected and observed heterozygosities were 0.107 and 0.120, respectively. Contingency χ2 analysis for homogeneity of allele frequencies indicated differentiation (P < 0.05) among the 21 populations and among populations within regions. The spatial pattern of allele frequencies was correlated with geographic variables at six loci. Analysis of F-statistics showed a 6.9% excess of heterozygotes relative to Hardy–Weinberg expectations. Only 5.9% of the observed genetic variation appeared to be interpopulational, the remainder was due to differences among individuals within populations. Estimates of genetic distance among regions were only slightly larger on average (0.014) than among populations within regions (0.012). Two significant (P < 0.05) canonical discriminant functions accounted for 55% of the total variance in the 13 polymorphic loci. A complex structure of genetic variation associated with regional and altitudinal differentiation was evident, possibly the expression of underlying genetic processes such as natural selection and past migration patterns.

Allozyme variation and population structure of Carex humilis var. nana (Cyperaceae) in Korea

2001 ◽  
Vol 79 (4) ◽  
pp. 457-463 ◽  
Author(s):  
Man Kyu Huh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
North American ◽  
Population Level ◽  
Allozyme Variation ◽  
Population Divergence ◽  
Geographic Ranges ◽  
The Mean ◽  
Allozyme Loci

Genetic diversity and population structure of 22 Carex humilis var. nana Ohwi (Cyperaceae) populations in Korea were determined using genetic variation at 23 allozyme loci. This is a long-lived herbaceous species with a widespread distribution in eastern Asia. The 12 enzymes revealed 23 putative loci, of which 11 were polymorphic (47.8%). Genetic diversity at the varietal level and at the population level was 0.131 and 0.118, respectively. Total genetic diversity (HT = 0.274) and within population genetic diversity (HS = 0.256) were high, whereas the extent of the population divergence was relatively low (GST = 0.068). An indirect estimate of the number of migrants per generation (Nm = 3.42) indicated that gene flow was high among Korean populations. Wide geographic ranges, perennial herbaceous nature, and the persistence of multiple generations are associated with the high level of genetic variation. A distinct difference between Asian and North American Carex is shown in the proportion of genetic variation (GST) (p < 0.001). The mean GST of Asian Carex was estimated as 0.056; thus, only 5.6% of genetic variability was distributed among populations, whereas the mean GST of North American Carex was estimated as 19.5% (3.5 times higher). It is probable that the geographical distance between population pairs and presence or absence of glacial history may play roles in the substantial difference between both groups.Key words: Carex humilis var. nana, genetic diversity, population structure.

Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

1995 ◽  
Vol 85 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Philippe Borsa ◽  
D. Pierre Gingerich
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Allozyme Variation ◽  
Inbreeding Coefficient ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Biological Features ◽  
High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

scholarly journals The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10274 ◽  
Author(s):  
Mirella Pupo Santos ◽  
João V.S. Rabelo Araujo ◽  
Arthur V. Sant’anna Lopes ◽  
Julio Cesar Fiorio Vettorazzi ◽  
Marcela Santana Bastos Boechat ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Geographical Location ◽  
Inter Simple Sequence Repeat ◽  
Shannon Index ◽  
Conservation Strategies ◽  
Amazon Forest ◽  
Mass Extinctions ◽  
Effective Conservation

Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.

Genetic diversity and population structure of Hemibagrus guttatus (Bagridae, Siluriformes) in the larger subtropical Pearl River based on COI and Cyt b genes analysis

2021 ◽  
Vol 57 ◽  
pp. 7
Author(s):  
Tianxu Kuang ◽  
Fangmin Shuai ◽  
Xinhui Li ◽  
Weitao Chen ◽  
Sovan Lek
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sustainable Use ◽  
Haplotype Diversity ◽  
Pearl River ◽  
Germplasm Resources ◽  
Geographical Populations ◽  
Commercially Important ◽  
The Pearl River ◽  
F Statistics

Understanding the genetic diversity and population structure of fish species is crucial for the sustainable use and protection of fish germplasm resources. Hemibagrus guttatus (Bagridae, Siluriformes) is widely distributed in the large subtropical Pearl River (China) and is commercially important. It's population have been declining. The genetic diversity of wild H. guttatus is not clear, despite its important ecological significance. In this paper, genes mitochondrial cytochrome c oxidase subunit I (COI) and cytochrome b (Cyt b) were used to analyze the genetic structure of H. guttatus population collected from six geographical populations in the main streams of the Pearl River. The results showed that the nucleotide diversity (π) and haplotype diversity (Hd) of wild H. guttatus was low (π < 0.005; Hd < 0.5). In addition, H. guttatus haplotypes did not cluster into clades according to geographical distribution, as revealed by neighbor-joining tree analysis. Analysis of molecular variance analysis (AMOVA) and F-statistics (Fst) values showed high homogeneity among wild H. guttatus populations. Our results suggest that there is degradation in germplasm resources of H. guttatus that could destabilize the sustainable use of this species and there was an urgent need for conservation of this species in South China.

Genetic diversity and population structure of the rice false smut pathogen Ustilaginoidea virens in Sichuan-Chongqing region

Plant Disease ◽  
2021 ◽  
Author(s):  
Anfei Fang ◽  
Zhuangyuan Fu ◽  
Zexiong Wang ◽  
Yuhang Fu ◽  
Yubao Qin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Recombination ◽  
Resistance Breeding ◽  
Ustilaginoidea Virens ◽  
Breeding Lines ◽  
Rice False Smut ◽  
Geographical Populations ◽  
False Smut

Rice false smut caused by Ustilaginoidea virens is currently one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from SNP-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in Sichuan-Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. The groups Ⅰ and Ⅵ were the largest including 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. AMOVA showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup. The UPGMA dendrogram and population structure revealed that the genetic composition of isolates collected from ST (Santai), NC (Nanchong), YC (Yongchuan), and WS (Wansheng) dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

scholarly journals Genetic variation analysis of superior cotton varieties of Gossypium hirsutum through microsatellite markers

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Dede Nuraida ◽  
Yusuf Abdurrajak ◽  
Moh Amin ◽  
Utami S. Hastutik
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gossypium Hirsutum ◽  
Microsatellite Markers ◽  
Size Range ◽  
Allele Frequencies ◽  
Variation Analysis ◽  
Ctab Method

This study was conducted in order to obtain information on genetic variation in populations rated as superior cotton (<em>Gossypium</em> <em>hirsutum</em> L.) varieties in Balittas Malang, Indonesia. The samples used 10 varieties of cotton Kanesia series and 2 other superior varieties that are LRA 5166 and ISA 205A. Indicators of genetic diversity are the number of alleles per <em>locus</em>, allele frequencies, and heterozygosity values. DNA was isolated from the leaves of 3- week-old seedlings using the CTAB method. Amplification was performed using 5 SSRs primer pairs of the JESPR series. The results showed five microsatellite <em>loci</em>, yielding 12 alleles with a size range of 80–500 bp, with an average number of alleles per <em>locus</em> of 4.60. The average values of heterozygosity of the five loci was high, at 0.71. Based on the number of alleles, allele frequencies and heterozygosity values, the genetic variation sampled in the superior cotton varieties studied here is quite high.

Patterns of allozyme variation within and among Douglas-fir breeding zones in southwest Oregon

1987 ◽  
Vol 17 (5) ◽  
pp. 402-407 ◽  
Author(s):  
S. A. Merkle ◽  
W. T. Adams
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Frequency ◽  
Quantitative Traits ◽  
Allozyme Variation ◽  
Douglas Fir ◽  
Expected Heterozygosity ◽  
Breeding Zone ◽  
Southwest Oregon ◽  
Environmental Distance

Gametophytes from wind-pollinated seeds of Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco var. menziesii) parent trees (mean 56) in each of 22 breeding zones in southwest Oregon were analyzed electrophoretically for gene frequency patterns at 27 loci. Allozyme variability levels were high, as shown by breeding-zone averages for the percentage of polymorphic loci (71.7%, 0.99 criterion), mean number of alleles per locus (2.46), and expected heterozygosity (0.178). Differences among zones in allele frequency were significant (p < 0.05) for only 2 of the 27 loci surveyed, and analysis of hierarchical population structure showed that less than 1% of genetic diversity was attributable to differences among breeding zones. Genetic distance between zones was small [Formula: see text] and, in general, bore no relation to geographical or environmental distance. The limited allozyme differentiation among zones contrasts strikingly with the environment-related variation in seedling quantitative traits previously reported for southwest Oregon Douglas-fir. Allozymes do not appear to be useful for mapping patterns of adaptive variation or for certifying Douglas-fir seed in this region.

scholarly journals How diverse can rare species be on the margins of genera distribution?

AoB Plants ◽  
2019 ◽  
Vol 11 (4) ◽  
Author(s):  
Alice Backes ◽  
Geraldo Mäder ◽  
Caroline Turchetto ◽  
Ana Lúcia Segatto ◽  
Jeferson N Fregonezi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Habitat Loss ◽  
Evolutionary History ◽  
Founder Effects ◽  
Geographical Isolation ◽  
Genetic Diversity And Structure ◽  
Genetic Patterns

Abstract Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.

Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers

Parasitology ◽  
2002 ◽  
Vol 125 (7) ◽  
pp. S51-S59 ◽  
Author(s):  
J. CURTIS ◽  
R. E. SORENSEN ◽  
D. J. MINCHELLA
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Microsatellite Markers ◽  
Natural Populations ◽  
Mitochondrial Marker ◽  
Tropical Regions ◽  
Blood Flukes

Blood flukes in the genus Schistosoma are important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found in Schistosoma mansoni and some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers for S. mansoni provided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.

scholarly journals High-Level Genetic Diversity but No Population Structure Inferred from Nuclear and Mitochondrial Markers of the Peritrichous Ciliate Carchesium polypinum in the Grand River Basin (North America)

2009 ◽  
Vol 75 (10) ◽  
pp. 3187-3195 ◽  
Author(s):  
E. Gentekaki ◽  
D. H. Lynn
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
River Basin ◽  
Large Subunit ◽  
Population Level ◽  
Nuclear Markers ◽  
Mitochondrial Markers ◽  
Intraspecific Genetic Variation ◽  
Grand River

ABSTRACT Studies that assess intraspecific genetic variation in ciliates are few and quite recent. Consequently, knowledge of the subject and understanding of the processes that underlie it are limited. We sought to assess the degree of intraspecific genetic variation in Carchesium polypinum (Ciliophora: Peritrichia), a cosmopolitan, freshwater ciliate. We isolated colonies of C. polypinum from locations in the Grand River basin in Southwestern Ontario, Canada. We then used the nuclear markers—ITS1, ITS2, and the hypervariable regions of the large subunit rRNA—and an 819-bp fragment of the mitochondrial cytochrome c oxidase I gene (cox-1) to investigate the intraspecific genetic variation of C. polypinum and the degree of resolution of the above-mentioned markers at the population level. We also sought to determine whether the organism demonstrated any population structure that mapped onto the geography of the region. Our study shows that there is a high degree of genetic diversity at the isolate level, revealed by the mitochondrial markers but not the nuclear markers. Furthermore, our results indicate that C. polypinum is likely not a single morphospecies as previously thought.

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