scholarly journals Genetic differentiation and diversity of Callosobruchus chinensis collections from China

2015 ◽  
Vol 106 (1) ◽  
pp. 124-134 ◽  
Author(s):  
C.X. Duan ◽  
W.C. Li ◽  
Z.D. Zhu ◽  
D.D. Li ◽  
S.L. Sun ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Distances ◽  
Fixation Index ◽  
Group Method ◽  
Callosobruchus Chinensis ◽  
Chain Reactions ◽  
Information Index ◽  
Geographic Populations

AbstractCallosobruchus chinensis (Linnaeus) is one of the most destructive pests of leguminous seeds. Genetic differentiation and diversity analysis of 345 C. chinensis individuals from 23 geographic populations using 20 polymorphic simple sequence repeats revealed a total of 149 alleles with an average of 7.45 alleles per locus. The average Shannon's information index was 1.015. The gene flow and genetic differentiation rate values at the 20 loci ranged from 0.201 to 1.841 and 11.0–47.2%, with averages of 0.849 and 24.4%, respectively. In the 23 geographic populations, the effective number of alleles and observed heterozygosity ranged from 1.441 to 2.218 and 0.191–0.410, respectively. Shannon's information index ranged from 0.357 to 0.949, with the highest value in Hohhot and the lowest in Rudong. In all comparisons, the fixation index (FST) values ranged from 0.049 to 0.441 with a total FST value of 0.254 among the 23 C. chinensis populations, indicating a moderate level of genetic differentiation and gene flow among these populations. Analysis of molecular variance revealed that the genetic variation within populations accounted for 76.7% of the total genetic variation. The genetic similarity values between populations varied from 0.617 to 0.969, whereas genetic distances varied from 0.032 to 0.483. Using unweighted pair-group method using arithmetical averages cluster analysis, the 23 geographic collections were classified into four distinct genetic groups but most of them were clustered into a single group. The pattern of the three concentrated groups from polymerase chain reactions analysis showed a somewhat different result with cluster.

scholarly journals Microsatellite Characterization of Malaysian Mahseer (Tor spp.) for Improvement of Broodstock Management and Utilization

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2633
Author(s):  
Poh Chiang Chew ◽  
Annie Christianus ◽  
Jaapar M. Zudaidy ◽  
Md Yasin Ina-Salwany ◽  
Chou Min Chong ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Relatedness ◽  
Genetic Distances ◽  
Group Method ◽  
Genetic Management ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Geographical Regions

In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei’s genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.

scholarly journals Study on the Genetic Differentiation of Geographic Populations of Calliptamus italicus (Orthoptera: Acrididae) in Sino-Kazakh Border Areas Based on Mitochondrial COI and COII Genes

2019 ◽  
Vol 112 (4) ◽  
pp. 1912-1919 ◽  
Author(s):  
Ye Xu ◽  
Ji-wei Mai ◽  
Bing-jie Yu ◽  
Hong-xia Hu ◽  
Liang Yuan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Cytochrome Oxidase ◽  
Fixation Index ◽  
Mitochondrial Cytochrome ◽  
Cytochrome Oxidase Subunit ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Oxidase Subunit ◽  
Geographic Populations ◽  
Mitochondrial Cytochrome Oxidase

Abstract Calliptamus italicus L. is an important pest on the desert and semidesert steppes along the Sino-Kazakh border. To elucidate the molecular mechanism of its continuous outbreaks, we studied 11 different geographic populations of C. italicus to determine: 1) the complete sequences of the entire mitochondrial cytochrome oxidase subunit I (COI) and mitochondrial cytochrome oxidase subunit II (COII) genes, and 2) performed genetic diversity, differentiation, gene flow, and molecular variation analyses. Of the 11 populations, the Yining County (YNX) population had the highest haplotype diversity and Pi values. There are significant differences in Tajima’s D and Fu’s Fs (P < 0.05). The fixation index Fst values of the total C. italicus population were 0.03352, and its gene flow Nm values of the total C. italicus population were 15.32. Taken together, there were five main findings: 1) the current genetic differentiation of C. italicus arose within populations; 2) genetic exchange levels were high between geographical populations; 3) genetic variation level was low; 4) C. italicus populations likely expanded in recently, and 5) there was no significant correlation between genetic distance and geographic distance for any geographic population. Findings from this study indicate that frequent gene exchange between populations may enhance the adaptability of C. italicus along the Sino-Kazakh border, leading to frequent outbreaks.

scholarly journals Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

2019 ◽  
Vol 190 (1) ◽  
pp. 65-78 ◽  
Author(s):  
Kin Onn Chan ◽  
Rafe M Brown
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Variance Partitioning ◽  
Nucleotide Polymorphisms ◽  
Landscape Genomics ◽  
Mountain Ranges ◽  
Historical Factors ◽  
Environmental Attributes

Abstract The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

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

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
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.

Genetic differentiation among various populations of the diamondback moth, Plutella xylostella Lepidoptera Yponomeutidae

2006 ◽  
Vol 96 (2) ◽  
pp. 137-144 ◽  
Author(s):  
A. Pichon ◽  
L. Arvanitakis ◽  
O. Roux ◽  
A.A. Kirk ◽  
C. Alauzet ◽  
...  
Keyword(s):  
South Africa ◽  
New York ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Plutella Xylostella ◽  
Diamondback Moth ◽  
The Philippines ◽  
Fixation Index ◽  
Geographical Distance ◽  
Hardy Weinberg Equilibrium

AbstractGenetic variation among 14 populations of Plutella xylostella (Linnaeus) from USA (Geneva, New York), Brazil (Brasilia), Japan (Okayama), The Philippines (Caragan de Oyo), Uzbekistan (Tashkent), France (Montpellier), Benin (Cotonou), South Africa (Johannesburg), Réunion Island (Montvert), and five localities in Australia (Adelaide, Brisbane, Mareeba, Melbourne, Sydney) were assessed by analysis of allozyme frequencies at seven polymorphic loci. Most of the populations were not in Hardy–Weinberg equilibrium and had a deficit in heterozygotes. The global differentiation among populations was estimated by the fixation index (Fst) at 0.103 for the 14 populations and at 0.047 when populations from Australia and Japan, which differed most and had a strong genetic structure, were excluded from the analysis. By contrast, the populations from Benin (West Africa) and Brazil (South America) were very similar to each other. Genetic differentiation among the populations was not correlated with geographical distance.

Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae)

2008 ◽  
Vol 88 (1) ◽  
pp. 179-186 ◽  
Author(s):  
Chu-Chuan Fan ◽  
Nicola Pecchioni ◽  
Long-Qing Chen
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Population Level ◽  
Conservation Strategy ◽  
Information Index

Calycanthus chinensis Cheng et S.Y. Chang, a tertiary relic species in China, is a shade-loving and deciduous bush withan elegant shape and beautiful flower of high ornamental value. It was widely planted in gardens and miniature scapes in China.The objective of this study was to characterize the genetic variation and structure in the three extant populations of the species, in order to provide useful information for a future conservation strategy. Twenty-two of 120 RAPD primers were selected and a total of 257 stable and clear DNA fragments were scored. Calycanthus chinensis showed a lower level of genetic diversity. At the population level, the percentage of polymorphic loci, Nei's gene diversity and Shannon’s information index were 40.9%, 0.1641 and 0.2386, respectively; while at the species level, the corresponding values were 59.1%, 0.2097 and 0.3123, respectively. The estimates of genetic differentiation based on Shannon’s information index (0.2360), Nei’s gene diversity (0.2175) and AMOVA (24.94%) were very similar, and significantly higher than the average genetic differentiation reported in outcrossed spermatophyte. So it suggested high genetic differentiation emerged among populations of C. chinensis. Genetic relationships among populations were assessed by Nei’s standard genetic distance, which suggested that the Tiantai population was genetically distinct from the other two populations. Moreover, the genetic distance was significantly correlated with geographical distance among populations (r = 0.997, t > t0.05). The gene flow (Nm) was 0.8994, indicating that gene exchange among populations was restricted. A conservation strategy was proposed based on the low gene flow and habitat deterioration, which are contributing to the endangered status of this species. Key words: Genetic diversity, endangered plant, population genetics, RAPD

Genetic and morphological differentiation among populations of the Rivoli’s Hummingbird (Eugenes fulgens) species complex (Aves: Trochilidae)

The Auk ◽  
2020 ◽  
Vol 137 (4) ◽  
Author(s):  
Luz E Zamudio-Beltrán ◽  
Juan Francisco Ornelas ◽  
Andreia Malpica ◽  
Blanca E Hernández-Baños
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Species Complex ◽  
Ecological Niche Modeling ◽  
Demographic History ◽  
Morphological Differentiation ◽  
Last Interglacial ◽  
Haplotype Networks ◽  
Isthmus Of Tehuantepec

Abstract Genetic variation and phylogeographic studies have been crucial for understanding mechanisms of speciation. We analyzed genetic variation and phylogeography to reconstruct the demographic history of the Rivoli’s Hummingbird (Eugenes fulgens) species complex and also evaluated their morphological differentiation. This widely distributed species inhabits the highlands of Mexico and northern Central America, with 2 subspecies separated by the Isthmus of Tehuantepec (west: E. f. fulgens, east: E. f. viridiceps). We surveyed genetic variation in 2 mitochondrial DNA markers (mtDNA, with 129 individuals) and nuclear DNA (6 microsatellites, with 85 individuals). We also inferred the demographic history, estimated divergence times, and analyzed morphological variation using 470 vouchered specimens. We modeled the current potential distribution of the species using ecological niche modeling and projected it into the past to model the effects of the Pleistocene climatic cycles. Haplotype networks, pairwise FST comparisons, AMOVA, and morphological analysis revealed differences between geographically isolated populations separated by the Isthmus of Tehuantepec (IT; corresponding to the 2 recognized subspecies: fulgens and viridiceps), and by the Motagua-Polochic-Jocotán (MPJ) system fault. Demographic scenarios revealed a contraction in distribution during the last interglacial, and expansion during the Last Glacial Maximum (LGM) with little change since the LGM. Divergence between groups separated by the Isthmus of Tehuantepec ~59,600 yr ago occurred in the presence of gene flow, suggesting that the Isthmus of Tehuantepec is a semipermeable barrier to gene flow. STRUCTURE analyses of microsatellite data detected 3 genetically differentiated groups. Several results fit a model of recent lineage divergence, including a significant signal of genetic differentiation, demographic expansion, decreased gene flow from past to present, and northward expansion during the LGM and contraction during the interglacial periods. We conclude that the genetic differentiation of E. fulgens in the Madrean Pine-Oak Woodlands resulted from recent geographical isolation of populations separated by natural barriers (IT and MPJ).

scholarly journals Low genetic divergence and variation in coastal dune populations of the widespread terrestrial orchid Epipactis helleborine

2020 ◽  
Vol 193 (3) ◽  
pp. 419-430 ◽  
Author(s):  
Hans Jacquemyn ◽  
Hanne De Kort ◽  
An Vanden Broeck ◽  
Rein Brys
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Divergence ◽  
Coastal Dune ◽  
Terrestrial Orchid ◽  
Colonization Event ◽  
History Of ◽  
Epipactis Helleborine ◽  
Seed Introduction

Abstract Reconstructing the early history of species divergence and quantifying the level of standing genetic variation in diverging populations are central to our understanding of ecotype formation and ultimately speciation. In this study, we used single nucleotide polymorphisms to reconstruct the evolutionary history of species divergence in coastal dune populations of the widespread terrestrial orchid Epipactis helleborine and to investigate the level of standing genetic variation in 29 coastal dune populations in a fragmented dune landscape along the Belgian and French coast. Additionally, we used seed introduction experiments to assess the potential for gene flow into existing populations after long-distance seed dispersal and the ability to colonize vacant sites. Our results showed that coastal dune populations diverged only recently from inland populations, went through a significant bottleneck and were most probably the result of a single colonization event. Current levels of population genetic diversity are low and not related to population size or spatial isolation. The sampled dune populations also showed little genetic differentiation, and no apparent spatial genetic structure was observed. Seed introduction experiments showed that seeds of coastal dune populations germinated easily in both occupied and unoccupied sites in dune habitat, indicating that the availability of suitable mycorrhizal fungi is not limiting the distribution of coastal dune populations and that gene flow through seeds has probably contributed to the observed low levels of genetic differentiation. Overall, these results are consistent with a process of genetic divergence after a single, recent colonization event, followed by extensive gene flow among populations.

scholarly journals Assessment of genetic variation in Bapedi sheep using microsatellite markers

2020 ◽  
Vol 50 (2) ◽  
pp. 318-324
Author(s):  
A. Maqhashu ◽  
N.O. Mapholi ◽  
H.A. O’Neill ◽  
K.A. Nephawe ◽  
F.V. Ramukhithi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Microsatellite Markers ◽  
South African ◽  
Agricultural Research ◽  
Germplasm Conservation ◽  
Genetic Distances ◽  
Fixation Index ◽  
Indigenous Sheep ◽  
Agricultural Research Council

This study was conducted to assess genetic variation in Bapedi sheep using 14 microsatellite markers. Blood samples were collected from 174 unrelated Bapedi sheep on six farms in various districts of Limpopo and from the Agricultural Research Council Animal Production Institute (ARC-API) in Gauteng. Genotypes from other South African indigenous sheep, namely Zulu (N = 14), Damara (N = 11), Dorper (N = 8), and Namaqua (N = 11), were included to represent reference populations. The effective number of alleles averaged 5.6 for across the Bapedi flocks and was 4.9 for the reference breeds. Among the Bapedi flocks, the observed heterozygosity (Ho) ranged from 0.56 ± 0.05 to 0.69 ± 0.03 and expected heterozygosity (He) values were between 0.75 ± 0.04 and 0.88 ± 0.01. Thus, there is considerable genetic diversity within the Bapedi sheep populations. However, the fixation index was high, indicating the possibility of inbreeding becoming a problem for these flocks. A neighbour-joining tree was constructed from the estimates of Nei’s genetic distances among flocks. The presence of Bapedi sheep flocks on all of the main branches of the tree along with one of the reference breeds suggests the present-day Bapedi is not an entirely distinct breed and that there are genetic differences between flocks of these South African indigenous sheep. Sustainable breeding and conservation programmes are needed to control inbreeding and to foreclose possible genetic dilution of Bapedi sheep. Keywords: genetic diversity, germplasm conservation, inbreeding, indigenous sheep

scholarly journals Genetic differentiation of common reed (Phragmites australis) populations from selected lakes of Pomerania (NW Poland), revealed by electrophoretically detected peroxidase variability

2010 ◽  
Vol 17 (1) ◽  
pp. 19-22 ◽  
Author(s):  
Maria Krzakowa ◽  
Marcin Michalak
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Phragmites Australis ◽  
Common Reed ◽  
Genetic Distances ◽  
Edaphic Conditions ◽  
The Town ◽  
North Western ◽  
Nw Poland

Genetic differentiation of common reed (Phragmites australis) populations from selected lakes of Pomerania (NW Poland), revealed by electrophoretically detected peroxidase variabilityThree populations of common reed (Phragmites australis(Cav) Trin. ex Steud.), growing under differing edaphic conditions in lakes near the town of Koszalin (the Pomerania region in north-western Poland), were studied in respect to frequencies of electrophoretically detected allozymes in two peroxidase loci: a monomeric locus with three alleles and a dimeric locus with two alleles. On the basis of genetic distances, similarity between these populations and levels of variation were assessed both within populations (GST = 0.0376) and between populations (DST = 0.0194). Gene flow between populations was low (Nm= 6.399).

Sign in / Sign up

Export Citation Format

Share Document