Genetic homogeneity of weathervane scallops (Patinopecten caurinus) in the northeastern Pacific

2010 ◽  
Vol 67 (11) ◽  
pp. 1827-1839 ◽  
Author(s):  
Patrick M. Gaffney ◽  
Carita M. Pascal ◽  
Jeffery Barnhart ◽  
W. Stewart Grant ◽  
James E. Seeb
Keyword(s):  
Genetic Differentiation ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Gulf Of Alaska ◽  
Nucleotide Sequencing ◽  
Mt Dna ◽  
Northeastern Pacific ◽  
Nuclear Loci ◽  
Allozyme Loci

We assessed genetic differentiation among populations of weathervane scallop ( Patinopecten caurinus ) in the northeastern Pacific, extending over 2500 km in the Gulf of Alaska and southeastern Bering Sea. Variability was surveyed at nuclear loci with allozyme, microsatellite, and single nucleotide polymorphism (SNP) methods, and at mitochondrial (mt)DNA loci with SNPs and nucleotide sequencing. High levels of gene diversity were detected for allozymes (H = 0.080), microsatellites (H = 0.734), and mtDNA (h = 0.781). Genotypes at nuclear loci generally fit Hardy–Weinberg proportions, except for some microsatellite loci, for which null-allele frequencies of 0.02 to 0.34 were estimated. No allele-frequency differences were detected among samples, except for the allozyme loci Gpi and Pep-4. Overall levels of differentiation ranged from FST = 0.0004 for allozymes, FST = 0.0008 for mtDNA to FST = 0.0004 for microsatellites. No isolation by distance was found for any of the markers. A unimodal mtDNA mismatch distribution and significant excesses of low-frequency variants for allozymes, microsatellites, and mtDNA may reflect a post-glacial population expansion. The lack of genetic differentiation measured by neutral markers does not preclude the existence of locally adapted, self-sustaining populations that are important in the harvest management of this species.

scholarly journals Genetic differentiation of the neotropical tree species Protium spruceanum (Benth.) Engler (Burseraceae) between fragments and vegetation corridors in Brazilian Atlantic forest

2009 ◽  
Vol 23 (4) ◽  
pp. 1180-1185 ◽  
Author(s):  
Fábio de Almeida Vieira ◽  
Dulcinéia de Carvalho
Keyword(s):  
Genetic Differentiation ◽  
Secondary Forest ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Neotropical Tree ◽  
Second Growth ◽  
Human Habitat ◽  
Protium Spruceanum ◽  
Allozyme Loci ◽  
Vegetation Corridors

We studied patterns of genetic differentiation in a connected landscape with an interesting history of human habitat conversion that began two centuries ago, during the Brazilian colonization period. In the fragments of Brazilian Atlantic seasonal forest and corridors of secondary forest, Protium spruceanum is an abundant native, mass-flowering/insect-pollinated and bird-dispersed tree. Genetic diversity was analyzed from 230 individuals in five fragments (1 to 11.8 ha) and four corridors (460 to 1000 m length) using allozyme loci. We did not find evidence of inbreeding within fragments or corridors, but the proportion of heterozygotes (<IMG SRC="/img/revistas/abb/v23n4/a28simb1.gif" WIDTH=287 HEIGHT=96>) were significantly higher in fragments than in the secondary vegetation corridors, based on Goudet's G-test (P = 0.036). Genetic differentiation was low and no pattern of isolation by distance was detected. All fragments generally present low historical genetic differentiation with corridors that they are connected, indicating possible gene flow via seeds and pollen. Due to the consistently low differentiation observed among them and the absence of a significant reduction in gene diversity in second-growth forests, we conclude that corridors of second-growth forests would be an important alternative in the genetic connection of isolated forest fragments.

Allozyme variation, differentiation, and inbreeding in populations of Pinus mugo in Bulgaria

2004 ◽  
Vol 34 (12) ◽  
pp. 2611-2617 ◽  
Author(s):  
Gancho T Slavov ◽  
Peter Zhelev
Keyword(s):  
Genetic Variation ◽  
Growth Form ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Conservation Status ◽  
Allozyme Variation ◽  
Near Neighbor ◽  
Pinus Mugo ◽  
Mean Values ◽  
Allozyme Loci

Genetic variation of 17 populations of Pinus mugo Turra was studied using 10 polymorphic allozyme loci. Polymorphism and gene diversity in these populations were comparable to mean values for gymnosperm species, but slightly lower than in pines with large and continuous ranges. We did not find significant interpopulation differentiation (FST = 0.041) or isolation by distance, suggesting that gene flow might be extensive or that the time elapsed since the species range became fragmented has been too short for genetic differentiation to arise via genetic drift. We detected moderate and statistically significant levels of inbreeding (mean FIS = 0.252) for all loci in all populations. Although there are many possible explanations for this nonequilibrium population structure, we propose that the main reasons for its ubiquity are the peculiar growth form and reproductive biology of P. mugo, which promote excessive near-neighbor pollinations. Populations in Vitosha Mountain and western Stara Planina had the highest levels of inbreeding and the lowest observed heterozygosities. All populations in these mountains are small and isolated, but none of them is under a special regime of protection. Thus, the conservation status of P. mugo populations in Vitosha Mountain and western Stara Planina may deserve reevaluation. Future gene conservation efforts should focus on obtaining information on the genetic variation of adaptive traits in P. mugo.

scholarly journals Genetic Structure of Cronartium ribicola Populations in Eastern Canada

1999 ◽  
Vol 89 (10) ◽  
pp. 915-919 ◽  
Author(s):  
K. Et-touil ◽  
L. Bernier ◽  
J. Beaulieu ◽  
J. A. Bérubé ◽  
A. Hopkin ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Distribution Systems ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Random Amplified Polymorphic Dna ◽  
Cronartium Ribicola ◽  
Eastern Canada ◽  
Long Distance ◽  
Evolutionary Forces

The genetic structure of populations of Cronartium ribicola was studied by sampling nine populations from five provinces in eastern Canada and generating DNA profiles using nine random amplified polymorphic DNA markers. Most of the total gene diversity (Ht = 0.386) was present within populations (Hw = 0.370), resulting in a low level of genetic differentiation among populations in northeastern North America (Fst = 0.062). A hierarchical analysis of genetic structure using an analysis of molecular variance (AMOVA) revealed no statistically significant genetic differentiation among provinces or among regions. Yet, genetic differentiation among populations within regions or provinces was small (AMOVA φst = 0.078) but statistically significant (P < 0.001) and was several orders of magnitude larger than differentiation among provinces. This is consistent with a scenario of subpopulations within a metapopulation, in which random drift following migration and new colonization are major evolutionary forces. A phenetic analysis using genetic distances revealed no apparent correlation between genetic distance and the province of origin of the populations. The hypothesis of isolation-by-distance in the eastern populations of C. ribicola was rejected by computing Mantel correlation coefficients between genetic and geographic distance matrices (P > 0.05). These results show that eastern Canadian provinces are part of the same white pine blister rust epidemiological unit. Nursery distribution systems are controlled provincially, with virtually no seedling movement among provinces; therefore, infected nursery material may not play an important role in the dissemination of this disease. Long-distance spore dispersal across provincial boundaries appears to be an epidemiologically important factor for this pathogen.

Genetic variation and phylogeography of Psammosilene tunicoides (Caryophyllaceae), a narrowly distributed and endemic species in south-western China

2011 ◽  
Vol 59 (5) ◽  
pp. 450 ◽  
Author(s):  
Qing-Ying Zhang ◽  
Yu-Juan Zhao ◽  
Xun Gong
Keyword(s):  
Genetic Differentiation ◽  
Endemic Species ◽  
Nuclear Dna ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Population History ◽  
Western China ◽  
Phylogeographic Structure ◽  
Population Subdivision ◽  
Chloroplast Haplotypes

Psammosilene tunicoides is a narrowly distributed and endemic species in south-western China. An investigation of sequence variation at two chloroplast DNA (cpDNA) regions (rpL16, trnQ-5′rps16) and one nuclear DNA (nDNA) locus (GPA1) were carried out to survey the population structure and population history of the species. Among the 22 populations across its geographical range, nine chloroplast haplotypes and 17 nuclear alleles were identified. Both cpDNA and nDNA consistently revealed high levels of population differentiation (GST = 0.604 and 0.540, respectively), suggesting a distinct phylogeographic structure (NST > GST, P < 0.01). This high genetic differentiation might be a combined effect of breeding system, limited pollen and seed dispersal and geographic isolation of populations. The level of haplotype diversities (cpDNA, hT = 0.575; nDNA, hT = 0.724) were high, but the nucleotide diversities (cpDNA, π = 0.00099; nDNA, π = 0.00105) were low. These results together with the star-like phylogenetic pattern and neutrality tests indicate that P. tunicoides has experienced a population expansion event in its evolution. Limited genetic exchange after population expansion was supported by the pronounced genetic differentiation among populations as well as evidence for ‘isolation-by-distance’ revealed by cpDNA. Due to high population subdivision and complex landscape, as many populations as possible should be considered for genetic conservation.

Genetic differentiation of Culex pipiens (Diptera: Culicidae) in China

2007 ◽  
Vol 97 (3) ◽  
pp. 291-297 ◽  
Author(s):  
F. Cui ◽  
C.-L. Qiao ◽  
B.-C. Shen ◽  
M. Marquine ◽  
M. Weill ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Culex Pipiens ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Mosquito Species ◽  
Regional Scale ◽  
Geographic Location ◽  
Geographical Pattern ◽  
Allozyme Loci ◽  
Genetic Structures

AbstractThe population genetic structures of Culex pipiens Linnaeus were evaluated in China over a 2000 km transect that encompasses the two subspecies, C. p. pallens and C. p. quinquefasciatus. Four polymorphic allozyme loci were investigated in 1376 mosquitoes sampled from 20 populations across four provinces. These loci were not statistically dependent with no apparent heterozygote deficit or excess. On a regional scale (intra-province), a low (Fst=0.007–0.016) and significant genetic differentiation was found, with no clear geographical pattern. On a wider scale (inter-province), the genetic differentiation was higher (Fst=0.059), and an isolation by distance emerged. The results are compared with previous population genetic surveys of this mosquito species in different geographic areas over the world. The overall pattern suggests that Culex pipiens requires considerable distance (500–1000 km) to show isolation by distance, irrespective of the subspecies (C. p. pipiens, C. p. quinquefasciatus and C. p. pallens) or the geographic location.

scholarly journals Genetic Differentiation Within and Between Two Habitats

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 397-407 ◽  
Author(s):  
François Rousset
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Population Differentiation ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Host Races ◽  
Wide Range ◽  
Parameter Values ◽  
Ecological Types ◽  
F Statistics

Abstract We investigate the usefulness of analyses of population differentiation between different ecological types, such as host races of parasites or sources and sink habitats. To that aim, we formulate a model of population structure involving two classes of subpopulations found in sympatry. Extensions of previous results for Wright's F-statistics in island and isolation-by-distance models of dispersal are given. It is then shown that source and sinks cannot in general be distinguished by F-statistics nor by their gene diversities. The excess differentiation between two partially isolated classes with respect to differentiation within classes is shown to decrease with distance, and for a wide range of parameter values it should be difficult to detect. In the same circumstances little differentiation will be observed in “hierarchical analyses between pools of samples from each habitat, and differences between levels of differentiation within each habitat will only reflect differences between levels of gene diversity within each habitat. Exceptions will indicate strong isolation between the different classes or habitat-related divergent selection.

Broad-ranging low genetic diversity among populations of the yellow finger marsh crab Sesarma rectum Randall, 1840 (Sesarmidae) revealed by DNA barcode

Crustaceana ◽  
2017 ◽  
Vol 90 (7-10) ◽  
pp. 845-864
Author(s):  
Raquel C. Buranelli ◽  
Fernando L. Mantelatto
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Dna Barcode ◽  
Population Expansion ◽  
Haplotype Network ◽  
Sudden Expansion ◽  
Restricted Gene Flow ◽  
Western Atlantic

Population genetic studies on marine taxa, specifically in the field of phylogeography, have revealed distinct levels of genetic differentiation in widely distributed species, even though they present long planktonic larval development. A set of factors have been identified as acting on gene flow between marine populations, including physical or physiological barriers, isolation by distance, larval behaviour, and geological and demographic events. In this way, the aim of this study was to analyse the genetic variability among populations of the crab speciesSesarma rectumRandall, 1840 along the western Atlantic in order to check the levels of genetic diversity and differentiation among populations. To achieve this purpose, mtDNA cytochrome-coxidase subunit I (COI) (DNA-barcode marker) data were used to compute a haplotype network and a Bayesian analysis for genetic differentiation, to calculate an Analysis of Molecular Variance (AMOVA), and haplotype and nucleotide diversities. Neutrality tests (Tajima’sDand Fu’s ) were accessed, as well as pairwise mismatch distribution under the sudden expansion model. We found sharing of haplotypes among populations ofS. rectumalong its range of distribution and no significant indication for restricted gene flow between populations separately over 6000 km, supporting the hypothesis of a high dispersive capacity, and/or the absence of strong selective gradients along the distribution. Nevertheless, some results indicated population structure suggesting the presence of two genetic sources (i.e., groups or lineages), probably interpreted as a result of a very recent bottleneck effect due to habitat losses, followed by the beginning of a population expansion.

scholarly journals Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Maysa Tiemi Motoki ◽  
Dina Madera Fonseca ◽  
Elliott Frederic Miot ◽  
Bruna Demari-Silva ◽  
Phoutmany Thammavong ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Aedes Albopictus ◽  
Isolation By Distance ◽  
Genetic Locus ◽  
Lao Pdr ◽  
Phylogenetic Network ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
The Usa

Abstract Background The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. Methods We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. Results We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. Conclusions Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.

scholarly journals Population genetic variation analysis of bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae in China using inter simple sequence repeats (ISSR) molecular markers

2021 ◽  
Author(s):  
Rui Zang ◽  
Ying Zhao ◽  
Kangdi Guo ◽  
Kunqi Hong ◽  
Huijun Xi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Fusarium Oxysporum ◽  
Diversity Index ◽  
Gene Diversity ◽  
Pcr Amplification ◽  
Bitter Gourd ◽  
Diseased Plant ◽  
Variation Analysis ◽  
Group I

AbstractBitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.

scholarly journals Genetic differentiation in Scottish populations of the pine beauty moth, Panolis flammea (Lepidoptera: Noctuidae)

2005 ◽  
Vol 95 (6) ◽  
pp. 517-526 ◽  
Author(s):  
A.J. Lowe ◽  
B.J. Hicks ◽  
K. Worley ◽  
R.A. Ennos ◽  
J.D. Morman ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Scots Pine ◽  
Rapd Analysis ◽  
Isolation By Distance ◽  
Long Distance ◽  
Panolis Flammea ◽  
Colonization Dynamics ◽  
Low Levels ◽  
Lepidoptera Noctuidae ◽  
Limited Exchange

AbstractPine beauty moth, Panolis flammea (Denis & Schiffermüller), is a recent but persistent pest of lodgepole pine plantations in Scotland, but exists naturally at low levels within remnants and plantations of Scots pine. To test whether separate host races occur in lodgepole and Scots pine stands and to examine colonization dynamics, allozyme, randomly amplified polymorphic DNA (RAPD) and mitochondrial variation were screened within a range of Scottish samples. RAPD analysis indicated limited long distance dispersal (FST = 0.099), and significant isolation by distance (P < 0.05); but that colonization between more proximate populations was often variable, from extensive to limited exchange. When compared with material from Germany, Scottish samples were found to be more diverse and significantly differentiated for all markers. For mtDNA, two highly divergent groups of haplotypes were evident, one group contained both German and Scottish samples and the other was predominantly Scottish. No genetic differentiation was evident between P. flammea populations sampled from different hosts, and no diversity bottleneck was observed in the lodgepole group. Indeed, lodgepole stands appear to have been colonized on multiple occasions from Scots pine sources and neighbouring populations on different hosts are close to panmixia.

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