RAPD Analysis of Genetic Variation Within and Among Four Natural Populations of Betula maximowicziana

SummaryBetula maximowicziana is a long-lived pioneer tree species in cool temperate forests that plays an important role in the forest ecosystem and has high economic value. Random amplified polymorphic DNA (RAPD) markers were used to evaluate the genetic variation of four natural populations of B. maximowicziana (three in central Honshu and the other in Hokkaido) to obtain fundamental information on this natural resource. Sixty-one reproductive amplified bands were obtained with 23 primers. Of these 61 bands, 22 were monomorphic and 39 were polymorphic. The level of genetic variation within each population may be very similar, because the population rankings according to number of polymorphic loci, Shannon’s indices and intra-population genetic variance revealed no definite patterns. Global analysis of AMOVA (analysis of molecular variance) showed that genetic variation among populations accounted for 15.6% of the total variation, with the remainder (84.4%) occurring within population. These results demonstrate that genetic differentiation among the four populations is moderate. Hierarchical AMOVA analysis showed that variation among regions (Hokkaido and central Honshu) accounted for 10.4% of the total genetic variation, suggesting that regional genetic differentiation is relatively high. Significant correlations between pairwise ΦPTvalues and geographic distance were detected, and results of both a neighbor-joining dendrogram based on pairwise ΦPTvalues, and principal coordinate analysis (PCO) based on a Euclidean metric revealed that the Furano population in Hokkaido was genetically different from the three populations in central Honshu. The data obtained in this study should have important implications for the conservation and management of regional genetic variation of B. maximowicziana.

Download Full-text

Genetic Variation Among Natural Populations of Tilletia controversa and T. bromi

Phytopathology ◽

10.1094/phyto.2000.90.4.376 ◽

2000 ◽

Vol 90 (4) ◽

pp. 376-383 ◽

Cited By ~ 16

Author(s):

Guillermo Pimentel ◽

Tobin L. Peever ◽

Lori M. Carris

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Gene Diversity ◽

Random Amplified Polymorphic Dna ◽

Natural Populations ◽

Host Population ◽

Natural Hybridization ◽

Character State ◽

Phenotypic Analysis ◽

Tilletia Controversa

Isolates of Tilletia controversa and T. bromi were sampled from wheat and two Bromus species hosts, respectively, in the Pacific Northwest, and genetic variation within and among populations was determined. Fifty-one random amplified polymorphic DNA markers from eleven primers were treated as phenotypic 1 and 0 character state data to estimate similarities and analyze molecular variance (AMOVA) among populations and as putative genetic loci to carry out analyses of gene diversity. Phenotypic analysis of T. controversa and T. bromi isolates revealed two distinct clusters that were 37% similar. The T. bromi cluster was subdivided further into two groups, corresponding to host, with 40% similarity. Cluster analysis based on allele frequencies produced similar results and also supported two T. bromi groups based on host. No evidence of natural hybridization and introgression was detected between the T. controversa and T. bromi populations. Both AMOVA and gene diversity analyses detected moderate levels of differentiation among T. controversa populations, whereas T. bromi populations were highly differentiated. The level of genetic differentiation observed between the T. bromi populations on different Bromus species hosts supports the hypothesis that a high degree of host specificity exists in the wild grass-infecting smuts. We speculate that the higher level of genetic differentiation among the T. bromi populations compared with the T. controversa populations on wheat may be due to selection by a more genetically diverse host population.

Download Full-text

Spatial Structure and Genetic Variation of a Mangrove Species (Avicennia marina (Forssk.) Vierh) in the Farasan Archipelago

Forests ◽

10.3390/f11121287 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1287

Author(s):

Rahmah N. Al-Qthanin ◽

Samah A. Alharbi

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Species Conservation ◽

Natural Populations ◽

Avicennia Marina ◽

Conservation Strategies ◽

Isolated Populations ◽

Mangrove Species ◽

Population Genetic Differentiation ◽

Sea Currents

Avicennia marina (Forssk.) Vierh is distributed in patches along the Farasan archipelago coast and is the most common mangrove species in the Red Sea. However, to date, no studies have been directed towards understanding its genetic variation in the Farasan archipelago. In this investigation, genetic variations within and among natural populations of Avicennia marina in the Farasan archipelago were studied using 15 microsatellite markers. The study found 142 alleles on 15 loci in nine populations. The observed (Ho) and expected (He) heterozygosity values were 0.351 and 0.391, respectively, which are much lower than those of earlier studies on A. marina in the Arabian Gulf. An inbreeding effect from self-pollination might explain its heterozygote deficiency. Population genetic differentiation (FST = 0.301) was similar to other mangrove species. Our findings suggest that the sea current direction and coastal geomorphology might affect genetic dispersal of A. marina. The more isolated populations with fewer connections by sea currents exhibited lower genetic variation and differentiation between populations. The genetic clustering of populations fell into three main groups—Group 1 (populations of Farasan Alkabir Island), Group 2 (populations of Sajid Island), and Group 3 (mix of one population of Farasan Alkabir Island and a population of Zifaf Island). More genetic variation and less genetic differentiation occurred when the population was not isolated and had a direct connection with sea currents. Both of these factors contributed to limited propagule dispersal and produced significant structures among the population. It is expected that the results of this research will be useful in determining policy and species-conservation strategies and in the rehabilitation of A. marina mangrove stands on the Farasan islands in an effort to save this significant natural resource.

Download Full-text

Does advertisement call variation coincide with genetic variation in the genetically diverse frog taxon currently known as Leptodactylus fuscus (Amphibia: Leptodactylidae)?

Anais da Academia Brasileira de Ciências ◽

10.1590/s0001-37652003000100006 ◽

2003 ◽

Vol 75 (1) ◽

pp. 39-54 ◽

Cited By ~ 25

Author(s):

W. RONALD HEYER ◽

YANA R. REID

Keyword(s):

Genetic Variation ◽

South America ◽

Genetic Differentiation ◽

Related Species ◽

Geographic Distance ◽

Single Species ◽

Advertisement Call ◽

Closely Related Species ◽

Multiple Species ◽

Disturbed Habitats

The frog Leptodactylus fuscus is found throughout much of South America in open and disturbed habitats. Previous study of genetic differentiation in L. fuscus demonstrated that there was lack of genetic exchange among population units consistent with multiple species, rather than a single species. We examine advertisement vocalizations of L. fuscus to determine whether call variation coincides with genetic differentiation. Calls were analyzed for 32 individual frogs from 25 localities throughout the distributional range of L. fuscus. Although there is variation in calls among geographic samples, call variation is not concordant with genetic variation or geographic distance and the call variation observed is less than that typically found among other closely related species of Leptodactylus. This study is an example of the rare pattern of strong genetic differentiation unaccompanied by salient differences in advertisement calls. The relative infrequency of this pattern as currently understood may only reflect the lack of detailed analyses of genetic and acoustic differentiation within population systems currently understood as single species with substantial geographic distributions.

Download Full-text

Genetic variation and dispersal patterns in three varieties of Pinus caribaea (Pinaceae) in the Caribbean Basin

Plant Ecology and Evolution ◽

10.5091/plecevo.2018.1343 ◽

2018 ◽

Vol 151 (1) ◽

pp. 61-76

Author(s):

Virginia Rebolledo Camacho ◽

Lev Jardón Barbolla ◽

Ivón Ramírez Morillo ◽

Alejandra Vázquez-Lobo ◽

Daniel Piñero ◽

...

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Central America ◽

Migration Rate ◽

Geographic Distance ◽

Caribbean Basin ◽

Pinus Caribaea ◽

The Bahamas ◽

Geological Processes ◽

The Caribbean

Background – Pinus caribaea Morelet comprises three varieties of tropical pines distributed in the Caribbean Basin: P. caribaea var. hondurensis, var. caribaea, and var. bahamensis. The insular and continental distribution of these varieties, as well as the geological processes in the region, have been important factors for analysing evolutionary processes implicated in the diversification of these lineages. In this study, we evaluate the genetic and geographic structure within and between these three varieties in order to infer the possible origin and dispersal routes of these taxa.Methods – We used six polymorphic nuclear microsatellites (nSSR) in fifteen representative populations of the three pine varieties, sampled throughout their natural range in Central America, Cuba and the Bahamas islands.Results – The varieties contain similar levels of genetic variation (mean He = 0.571), with several populations out of Hardy-Weinberg equilibrium, and significant levels of inbreeding (0.097–0.184, P ≤ 0.05). A slight but significant genetic differentiation was found between the varieties (RST = 0.088) and populations (RST= 0.082), and genetic differentiation increased with geographic distance (r2 = 0.263). Distance and Bayesian BAPS analyses generated seven groups; two represented by the two island varieties and the remainder by the Central American populations of var. hondurensis. Migration rate estimates between pairs of groups ranged from M = 0.47 to M = 20.16. Estimates were generally higher from the continent to islands, with the highest migration rate estimated from a continental genetic group to the Cuba island group of var. hondurensis (M = 20.16).Conclusions – This study supports the hypothesis of a recent origin of these pine taxa through the migration of an ancestor from Central America, where the historical demography is associated with events of colonization, expansion and contraction of populations. The genetic variation and differentiation suggest that the three varieties are divergent lineages that currently share allelic variants, indicating that their speciation has not yet completed.

Download Full-text

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

Canadian Journal of Forest Research ◽

10.1139/x26-162 ◽

1996 ◽

Vol 26 (8) ◽

pp. 1454-1462 ◽

Cited By ~ 31

Author(s):

Naoki Tani ◽

Nobuhiro Tomaru ◽

Masayuki Araki ◽

Kihachiro Ohba

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Differentiation ◽

Phylogenetic Trees ◽

Genetic Relationships ◽

Natural Populations ◽

Group Method ◽

Stone Pine ◽

Arithmetic Means ◽

Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

Download Full-text

Analisis Keragaman Genetik Acremonium yang Berasosiasi dengan Tanaman Gaharu Menggunakan Teknik Random Amplified Polymorphic DNA (RAPD)

Jurnal AgroBiogen ◽

10.21082/jbio.v5n2.2009.p65-70 ◽

2016 ◽

Vol 5 (2) ◽

pp. 65

Author(s):

Dewi Rahmawati ◽

Nurita Toruan-Mathius

Keyword(s):

Cluster Analysis ◽

Genetic Variation ◽

Genetic Similarity ◽

Random Amplified Polymorphic Dna ◽

Economic Value ◽

Similarity Index ◽

Similarity Coefficients ◽

West Sumatra ◽

High Degree ◽

Geographical Locations

Agarwood or gaharu is a plant that has a high economic value in Asia, due to its use for production of incense and traditional medicines. The agarwood formation occurs in the trunk and roots of trees that have been infected by a fungus, such as Acremonium spp. Various fungi were associated with the agarwood formation. Acremonium is generally considered as highly polyphyletic, contains distantly related fungi. A study was done to identify genetic diversities in 10 isolates of Acremonium spp. from four different areas in Indonesia that are associated with Aquilaria and Gyrinops verstigii using the Random Amplified Polymorphic DNA (RAPD) technique. Eight RAPD primers, i.e., OPA 02, OPB 04, OPB 07, OPB 17, OPC 11, OPD 03, OPD 05, and OPE 07 were used in the analyses. The results indicated that similarity index values of the genetic variation ranged from 0.21 to 0.97. Based on the Nei and Li’s similarity coefficients, these values indicating the presence of high degree of genetic variability. The lowest degree of genetic similarity were found between isolates F (Acremonium spp., which is associated with G. verstigii from Mataram, Nusa Tenggara Barat), and LM2 from south coastal area of West Sumatra. The highest genetic similarity value (0.97) was found between isolates Sr2 and Sr4 from Sorong, Papua. Results from the cluster analysis indicated that the isolates could be grouped into two major clusters that were associated with their geographical locations.

Download Full-text

Genetic Differentiation in Natural Populations of Grevillea robusta

Australian Journal of Botany ◽

10.1071/bt96073 ◽

1997 ◽

Vol 45 (4) ◽

pp. 669 ◽

Cited By ~ 11

Author(s):

C. E. Harwood ◽

G. F. Moran ◽

J. C. Bell

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Natural Populations ◽

Grevillea Robusta ◽

Distance Analysis ◽

Riverine Habitat ◽

Natural Range ◽

Isozyme Loci ◽

The Difference ◽

Genetic Distance Analysis

Genetic variation in 23 natural populations of Grevillea robusta A.Cunn. from across the natural range of the species was examined using 20 isozyme loci assayed in young seedlings. Mean expected heterozygosity per population, He , varied from 0.080 to 0.131 with an average of 0.105. The genetic diversity of individual populations did not appear to be related to their ecological characteristics (araucarian vine forest or riverine habitat types) or their geographic locations. A genetic distance analysis indicated a significant separation of the populations into two regional groups, eight from the northern part of the natural range and the remaining 15 from central and southern areas. Between-population differences accounted for 17.9% of the total genetic variation, one-third of which was attributable to the difference between the two regional groups. Most alleles at the 20 loci occurred across most or all of the geographic range. This, and the low level of genetic differentiation between populations, suggest that genetic exchange between populations has been maintained, despite the pattern of natural distribution of the species in small, separated populations.

Download Full-text

Genetic Differentiation Studies among Natural Populations of Tilapia zillii

Notulae Scientia Biologicae ◽

10.15835/nsb749649 ◽

2015 ◽

Vol 7 (4) ◽

pp. 423-429

Author(s):

Tofunmi E. OLADIMEJI ◽

Michael O. AWODIRAN ◽

Olaniyi O. KOMOLAFE

Keyword(s):

Genetic Differentiation ◽

Random Amplified Polymorphic Dna ◽

Natural Populations ◽

Principal Component ◽

Genetic Distances ◽

Morphological Studies ◽

Tilapia Zillii ◽

Meristic Counts ◽

Ctab Method ◽

Group Relationships

The population structure of Tilapia zillii (Gervais 1848) from three reservoirs in Nigeria, Osun State (Opa, Osu and Igun) was determined by employing morphological and molecular (Random Amplified Polymorphic DNA) methods. For morphological studies, 25 morphometric measurements and six meristic counts were recorded on 40 individuals within each population. Principal Component Analysis (PCA) was performed on the morphometric and meristic data using the PAST software. For RAPD studies, genomic DNA was extracted from caudal fin tissue using CTAB method and five primers were used to initiate PCR amplifications. All the clusters produced by the Principal components analysis (PCA) of the morphometric and meristic parameters overlapped indicating a low level of genetic differentiation between the three populations of T. zillii studied. The UPGMA cluster diagram from RAPD analysis identified two major genotypic groups with inter and intra group relationships. All individuals in the first cluster were from the Osu reservoir, while individuals from Opa and Igun reservoirs constituted the second cluster. Nei’s unbiased measure of genetic distances was 0.8532, 0.7321 and 0.7111 for Osu, Igun and Opa populations respectively. This revealed that Opa and Igun populations were genetically closer, while Osu populations is distant from them. The results suggest that the RAPD technique could be used to differentiate populations of T. zillii. However, additional methods such as microsatellite and sequence analysis can be used to maximize the efficiency of genetic differentiation studies.

Download Full-text

Identifying environmental factors associated with the genetic structure of the New Zealand scallop: linking seascape genetics and ecophysiological tolerance

ICES Journal of Marine Science ◽

10.1093/icesjms/fsv240 ◽

2015 ◽

Vol 73 (7) ◽

pp. 1925-1934 ◽

Cited By ~ 6

Author(s):

Catarina N. S. Silva ◽

Jonathan P. A. Gardner

Keyword(s):

Genetic Variation ◽

New Zealand ◽

Genetic Structure ◽

Environmental Factors ◽

Genetic Differentiation ◽

Environmental Variables ◽

Evolutionary Dynamics ◽

Geographic Distance ◽

Suspended Particulate Matter Concentration ◽

Seascape Genetics

Abstract Understanding the processes responsible for shaping the spatial genetic patterns of species is critical for predicting evolutionary dynamics and defining significant evolutionary and/or management units. Here, we investigated the potential role of environmental factors in shaping the genetic structure of the endemic New Zealand scallop Pecten novaezelandiae using a seascape genetics approach. For this, we assayed genetic variation at 12 microsatellite markers in 952 individuals collected from 14 sites throughout New Zealand, and used data for 9 site-specific environmental variables (3 geospatial and 6 environmental variables). Our results indicate that a combination of environmental factors may be contributing to the observed patterns of genetic differentiation, but in particular, freshwater discharge and suspended particulate matter concentration were identified as being important. Environmental variation in these parameters may be acting as a barrier to gene flow. In terms of their ecophysiology, scallops are not particularly tolerant of high concentrations of either freshwater input or suspended sediment, making the identification of an association between these environmental variables and genetic variation particularly relevant across the full distributional range of this species. Although geographic distance between populations was also an important variable explaining the genetic variation among populations, it appears that levels of genetic differentiation are not a simple function of interpopulation distance. This study has identified previously unknown environmental factors that may be acting on the genetic structure of the New Zealand scallop and highlights the utility of seascape genetic studies to better understand the processes shaping the genetic structure of organisms.

Download Full-text

GENETIC VARIATION IN NATURAL POPULATIONS OF FIVE DROSOPHILA SPECIES AND THE HYPOTHESIS OF THE SELECTIVE NEUTRALITY OF PROTEIN POLYMORPHISMS

Genetics ◽

10.1093/genetics/77.2.343 ◽

1974 ◽

Vol 77 (2) ◽

pp. 343-384

Author(s):

Francisco J Ayala ◽

Martin L Tracey ◽

Lorraine G Barr ◽

John F McDonald ◽

Santiago Pérez-Salas

Keyword(s):

Genetic Variation ◽

Genetic Differentiation ◽

Natural Populations ◽

Evolutionary Divergence ◽

Average Value ◽

Local Populations ◽

Selective Neutrality ◽

Average Proportion ◽

Substantial Degree ◽

Protein Polymorphisms

ABSTRACT We have studied genetic variation at 30-32 loci coding for enzymes in natural populations of five species of Drosophila. The average proportion of heterozygous loci per individual is 17.7 ± 0.4%. The average proportion of polymorphic loci per population is 69.2 ± 2.6% or 49.8 ± 2.2%, depending on what criterion of polymorphism is used. The following generalizations are advanced: (1) The amount of genetic polymorphism varies considerably from locus to locus. (2) At a given locus, populations of the same species are very similar in the amount and pattern of genetic variation. (3) However, at some loci large differences sometimes occur between local populations of the same species. (4) The amount of variation at a given locus is approximately the same in all five species. (5) When different species are compared, the pattern of the variation is either essentially identical or totally different at a majority of loci. We have tested the hypothesis that protein polymorphisms are selectively neutral by examining four predictions derived from the hypothesis. Our results are at variance with every one of the predictions. We have measured the amount of genetic differentiation, D, between taxa of various degrees of evolutionary divergence. The average value of D is 0.033 for local populations, 0.228 for subspecies, 0.226 for semispecies, 0.538 for sibling species, and 1.214 for morphologically distinguishable species. Our results indicate that a substantial degree of genetic differentiation (22.8 allelic substitutions for every 100 loci) occurs between allopatric populations that have diverged to the point where they might become different species if they were to become sympatric. However, very little additional genetic change is required for the development of complete reproductive isolation. After the speciation process is completed, species continue to diverge genetically from each other.

Download Full-text