Influence of historical events and contemporary estuarine circulation on the genetic structure of the banded killifish (Fundulus diaphanus) in the  St. Lawrence River (Quebec, Canada)

2007 ◽  
Vol 85 (8) ◽  
pp. 891-901 ◽  
Author(s):  
O. Rey ◽  
J. Turgeon
Keyword(s):  
Isolation By Distance ◽  
Secondary Contact ◽  
Clinal Variation ◽  
Allele Size ◽  
Frequency Distributions ◽  
Factors Influencing ◽  
River Stretch ◽  
St Lawrence River ◽  
Differentiation Indices ◽  
Fundulus Diaphanus

Eight microsatellite markers were used to examine the historical and contemporary factors influencing the distribution of genetic variation within and among populations of Fundulus diaphanus (Lesueur, 1817) in the St. Lawrence River. Our results show that the contemporary hydrodynamics of the river affect levels of diversity and differentiation in this species. Genetic diversity increased towards downstream sites and levelled off at the upstream end of the tidal section, in the vicinity of Lake St-Pierre outlet. Likewise, differentiation and isolation-by-distance were most pronounced in the upstream, strictly fluvial section of the river. Surprisingly, however, we did not detect any significant intershore differentiation in this riparian fish species. Historical influence was also clearly detected and transcended the contemporary pattern, as revealed by an extremely strong isolation-by-distance pattern along the entire river stretch. This pattern likely results from the historical, postglacial secondary contact between two glacial races, as indicated by the clinal variation of constrasting allele size frequency distributions along the river and the significantly greater values of differentiation indices considering mutational information.

The Future of the Nigerian Agricultural Industries: A Case Study of Oil Palm Production in Edo State

2013 ◽  
Vol 824 ◽  
pp. 561-567 ◽  
Author(s):  
U.J. Udosen ◽  
A.P. Ugboya
Keyword(s):  
Growth Rate ◽  
Oil Palm ◽  
Frequency Distributions ◽  
Factors Influencing ◽  
The Future ◽  
Edo State ◽  
Agricultural Industries ◽  
Fresh Fruit Bunches ◽  
Planting Materials

This study analyzes oil palm production from 2001 - 2008 in Edo State, with a view of establishing the future of Nigerian Agricultural oil palm industries. The specific objectives were to identify and quantify the factors influencing the production of oil palm, reveal the constraints to the production of oil palm; analyze the viability of oil palm production as an investment and predict the future of oil palm enterprise in Edo State. Three Local Government Areas of high oil palm concentration in Edo State were covered. Ninety selected oil palm producers from nine villages in the study area were selected. Frequency distributions and multiple regression analysis were used to analyze the results. The results showed that for the period under review (2001 - 2008) on a per hectare basis, seedlings cost, and labour cost were significant inputs, positively influencing the production of oil palm in the Edo State. A growth rate of 6.2% and 23.5% were projected for oil palm with reference to palm oil and fresh fruit bunches (FFB), respectively, up to the year 2020, an indication that oil palm production in the State is viable and the future is bright. The study revealed that inadequate storage facilities, poor planting materials and lack of government assistance, among others, are major bottlenecks in oil palm production in Edo State. However, since oil palm production in Edo State is viable, it is an indication that the future of Nigerian Agricultural Industries is bright.

scholarly journals VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach.

Genetics ◽  
1993 ◽  
Vol 134 (3) ◽  
pp. 983-993 ◽  
Author(s):  
M D Shriver ◽  
L Jin ◽  
R Chakraborty ◽  
E Boerwinkle
Keyword(s):  
Tandem Repeats ◽  
Repeat Unit ◽  
Allele Size ◽  
Frequency Distributions ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
One Step ◽  
Simulation Results ◽  
Summary Measures ◽  
The One

Abstract Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). We estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. We then compared our simulation expectations with actual data reported in the literature. We used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, we hypothesize that these three classes of loci are subject to different mutational forces.

scholarly journals Factors Influencing the Use by Radiation Therapists of Cancer Symptom Guides: A Mixed-Methods Study

2019 ◽  
Vol 26 (1) ◽  
pp. 56-64
Author(s):  
C. Ludwig ◽  
J. Renaud ◽  
L. Barbera ◽  
M. Carley ◽  
C. Henry ◽  
...  
Keyword(s):  
Content Analysis ◽  
Mixed Methods ◽  
Organizational Support ◽  
Symptom Management ◽  
Background Radiation ◽  
Radiation Treatment ◽  
Scope Of Practice ◽  
Moral Norms ◽  
Frequency Distributions ◽  
Factors Influencing

Background: Radiation therapists play an important role in helping patients to safely manage and triage potentially life-threatening symptoms. The purpose of the present study was to assess factors influencing the use by radiation therapists of evidence-informed symptom practice guides for patients experiencing cancer treatment–related symptoms. Methods: In a mixed-methods descriptive study guided by the Knowledge-to-Action framework, interviews and a barriers survey were conducted. Two independent reviewers conducted a content analysis of interview transcripts. Barriers survey data were analyzed using frequency distributions and univariate descriptive statistics. Open-ended data from the surveys underwent content analysis and were triangulated with interview findings. Results: Of 90 radiation therapists approached, 58 completed the survey (64%), and 14 were interviewed. Of the 98% who reported providing symptom management to patients undergoing radiation treatment, 53% used evidence-informed practice guidelines. Radiation therapists had moderate moral norms (4.6 of 7) and beliefs about the consequences of using costars (pan-Canadian Oncology Symptom Triage and Remote Support) practice guides (4.8), but neutral intention (3.4) and beliefs about their own capabilities (3.9). Environmental barriers included lack of time (2.0), lack of access (2.5), and neutral organizational support (3.0). Radiation therapists identified a need for training (5.5). Common unique barriers to practice guide use were lack of time during radiation treatments, unclear fit with scope of practice, disparate focus on site-specific symptoms, and lack of medication knowledge. Conclusions: The symptom practice guides were perceived by the radiation therapists to benefit patients, enhance their own knowledge of symptom management, and promote consistent practice. Additional work is required to identify the scope of practice of radiation therapists within the interprofessional team.

Historical allopatry and secondary contact or primary intergradation in the Puerto Rican crested anole, Anolis cristatellus, on Vieques Island in the Caribbean

2019 ◽  
Author(s):  
Quynh N Quach ◽  
R Graham Reynolds ◽  
Liam J Revell
Keyword(s):  
Isolation By Distance ◽  
Mitochondrial Gene ◽  
Gene Tree ◽  
Genotyping By Sequencing ◽  
Secondary Contact ◽  
Single Nucleotide Polymorphic ◽  
Caribbean Island ◽  
Single Nucleotide ◽  
The Caribbean ◽  
Historical Range

Abstract Recent work has revealed surprisingly deep mitochondrial genetic divergence in the lizard Anolis cristatellus among samples obtained from the small Caribbean island of Vieques. Here we sought to determine whether this had resulted from natural or anthropogenic causes, and (if the former) whether divergence occurred in a biogeographical context of allopatry followed by secondary contact, or via isolation-by-distance across the species’ historical range. We first estimated a mitochondrial gene tree for 379 samples and then genotyped 3407 single nucleotide polymorphic sites from 48 individuals using a modified genotyping-by-sequencing approach. We found that A. cristatellus samples from Vieques belong to two highly divergent mitochondrial subclades, but the geographical distribution of these haplogroups indicates that this pattern is probably natural in origin. Analysis of our single nucleotide polymorphic dataset revealed differentiation that is consistent with isolation-by-distance between the western and eastern ends of Vieques, suggesting that the overall pattern of divergence probably reflects primary intergradation with a mitochondrial break on the historical Puerto Rico Bank palaeo-island that happened to coincide with the present-day location of Vieques. Our findings help to underline the growing consensus that results from a single genetic marker can prove highly misleading in studies of historical population genetic structure.

scholarly journals Resprouters Versus Reseeders: Are Wild Rooibos Ecotypes Genetically Distinct?

2021 ◽  
Vol 12 ◽  
Author(s):  
J. Brooks ◽  
N. P. Makunga ◽  
K. L. Hull ◽  
M. Brink-Hull ◽  
R. Malgas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Isolation By Distance ◽  
Haplotype Diversity ◽  
Cape Floristic Region ◽  
Conservation Strategies ◽  
Clinal Variation ◽  
Survival Strategy ◽  
Western Cape ◽  
Northern Cape

Aspalathus linearis (Burm. F.) R. Dahlgren (Fabaceae) or rooibos, is a strict endemic species, limited to areas of the Cederberg (Western Cape) and the southern Bokkeveld plateau (Northern Cape) in the greater Cape Floristic Region (CFR) of South Africa. Wild rooibos, unlike the cultivated type, is variable in morphology, biochemistry, ecology and genetics, and these ecotypes are broadly distinguished into two main groups, namely, reseeders and resprouters, based on their fire-survival strategy. No previous assessment of genetic diversity or population structure using microsatellite markers has been conducted in A. linearis. This study aimed to test the hypothesis that wild rooibos ecotypes are distinct in genetic variability and that the ecotypes found in the Northern Cape are differentiated from those in the Cederberg that may be linked to a fire-survival strategy as well as distinct morphological and phytochemical differences. A phylogeographical and population genetic analyses of both chloroplast (trnLF intergenic region) and newly developed species-specific nuclear markers (microsatellites) was performed on six geographically representative wild rooibos populations. From the diversity indices, it was evident that the wild rooibos populations have low-to-moderate genetic diversity (He: 0.618–0.723; Ho: 0.528–0.704). The Jamaka population (Cederberg, Western Cape) had the lowest haplotype diversity (H = 0.286), and the lowest nucleotide diversity (π = 0.006) even though the data revealed large variations in haplotype diversity (h = 0.286–0.900) and nucleotide diversity (π = 0.006–0.025) between populations and amongst regions where wild rooibos populations are found. Our data suggests that populations of rooibos become less diverse from the Melkkraal population (Suid Bokkeveld, Northern Cape) down towards the Cederberg (Western Cape) populations, possibly indicative of clinal variation. The largest genetic differentiation was between Heuningvlei (Cederberg, Western Cape) and Jamaka (FST = 0.101) localities within the Cederberg mountainous region, and, Blomfontein (Northern Cape) and Jamaka (Cederberg) (FST = 0.101). There was also a significant isolation by distance (R2 = 0.296, p = 0.044). The presence of three main clusters is also clearly reflected in the discriminant analysis of principal components (DAPC) based on the microsatellite marker analyses. The correct and appropriate management of wild genetic resources of the species is urgently needed, considering that the wild Cederberg populations are genetically distinct from the wild Northern Cape plants and are delineated in accordance with ecological functional traits of reseeding or resprouting, respectively. The haplotype divergence of the ecotypes has also provided insights into the genetic history of these populations and highlighted the need for the establishment of appropriate conservation strategies for the protection of wild ecotypes.

Genetic structure in Cumbria

1981 ◽  
Vol 13 (3) ◽  
pp. 317-336 ◽  
Author(s):  
D. F. Roberts ◽  
L. B. Jorde ◽  
R. J. Mitchell
Keyword(s):  
Genetic Structure ◽  
Genetic Distance ◽  
Isolation By Distance ◽  
Geographical Location ◽  
Great Length ◽  
Lake District ◽  
Frequency Distributions ◽  
Highly Correlated ◽  
Inbreeding Level ◽  
Migration Analysis

SummaryGenetic structure of the Cumbrian population is examined from data on gene and genotype frequency distributions, on geographical location, and on population movement in two generations.The population is genetically heterogeneous; the central Lake District particularly, and also Carlisle and the southern periphery, stand out as distinct from the remainder and from each other. Regional subdivision of the population is sufficient to lead to some increased overall homozygosity, but its effect on inbreeding is considerably lower than the inbreeding level within regions, the latter being highest in the Lake District and the southern periphery. Examination of isolation by distance shows distance to be an important determinant of genetic differentiation in Cumbria; local and regional kinship levels are similar to those in alpine Swiss areas. Migration analysis suggests the distinctness of the west coast and southern periphery, and a slight increase in kinship between regions in the last generation.The measures of genetic distance are closely correlated with each other. The measures of kinship derived from migration frequencies between regions are highly correlated with each other, and with geographical distance, but not with genetic distance. Present migration patterns are insufficient to account for the affinities within and between regions indicated by the genetic variation. It is possible that retention of Norwegian influence over a great length of time in the central Lake District is a major contributory element in present-day genetic heterogeneity in Cumbria.

scholarly journals Morphological variation in two genetically distinct groups of the golden-striped salamander, Chioglossa lusitanica (Amphibia: Urodela)

2005 ◽  
Vol 74 (3-4) ◽  
pp. 213-222 ◽  
Author(s):  
J. Alexandrino ◽  
N. Ferrand ◽  
J.W. Arntzen ◽  
João Alexandrino
Keyword(s):  
Contact Zone ◽  
Environmental Gradient ◽  
Early Pleistocene ◽  
Colour Pattern ◽  
Secondary Contact ◽  
Clinal Variation ◽  
The North ◽  
Secondary Contact Zone ◽  
Pattern Variability ◽  
Chioglossa Lusitanica

Morphometric and colour pattern variation in the endemic Iberian salamander Chioglossa lusitanica is concordant with the genetic differentiation of two groups of populations separated by the Mondego river in Portugal. Salamanders from the south have shorter digits than those from the north. Clinal variation with a south to north increase in limb, toe and finger length was found superimposed on this dichotomy, resulting in stepped clines for characters describing appendage size. Genetic variability was paralleled by colour pattern variability in the contact zone and in northern populations. To explain the observed parallels we invoke the neutral processes of vicariant isolation, admixture in a secondary contact zone, genetic drift in addition to selection acting along an environmental gradient. Morphological constraints imposed by a highly specialized ecological niche may explain why the genetic subdivision of C. lusitanica since the early Pleistocene has remained fairly cryptic.

Delineating genetic groupings in continuously distributed species across largely homogeneous landscapes: a study of American black bears (Ursus americanus) in Ontario, Canada

2012 ◽  
Vol 90 (8) ◽  
pp. 999-1014 ◽  
Author(s):  
A. Pelletier ◽  
M.E. Obbard ◽  
K. Mills ◽  
E.J. Howe ◽  
F.G. Burrows ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Large Scale ◽  
Ursus Americanus ◽  
Isolation By Distance ◽  
Black Bears ◽  
Clinal Variation ◽  
Isolated Populations ◽  
Anthropogenic Pressures ◽  
American Black ◽  
American Black Bears

There is a crucial need to understand the genetic consequences of landscape modifications on continuous populations that could become fragmented, and to evaluate the degree of differentiation of isolated populations that were historically part of the core. Using 15 microsatellite loci, we evaluated the genetic structure of American black bears ( Ursus americanus Pallas, 1780) across a vast, contiguous Ontario landscape (>1 × 106 km2) that largely represents their pre-European settlement distribution. Because geographic barriers are absent, we predicted that isolation by distance would drive genetic structure. We identified three genetic clusters (Northwest, Southeast, and Bruce Peninsula) that were less differentiated than when assessed with mtDNA, suggesting the influence of male-biased dispersal on large-scale genetic differentiation. Isolation by distance (r = 0.552, P = 0.001) was supported by a weak, clinal variation between Northwest and Southeast, illustrating the challenges to delineate populations in wide-ranging taxa. The Bruce Peninsula cluster, confined to a small area under strong anthropogenic pressures, was more differentiated from neighbouring clusters (FST > 0.13, P < 0.0001), with a genetic diversity corresponding to disjunct populations of black bears. Our results could be used in landscape genetics models to project the evolution of population differentiation based on upcoming landscape modifications in northern regions of North America.

Peromyscus populations and their Cuterebra parasites display congruent phylogeographical structure

Parasitology ◽  
2005 ◽  
Vol 131 (2) ◽  
pp. 237-245 ◽  
Author(s):  
S. NOËL ◽  
B. ANGERS ◽  
F.-J. LAPOINTE
Keyword(s):  
Parasite Species ◽  
Isolation By Distance ◽  
Deer Mouse ◽  
Genetic Distances ◽  
Limited Sample ◽  
The North ◽  
Mitochondrial Sequences ◽  
North And South ◽  
White Footed Mouse ◽  
St Lawrence River

The relationships between populations of the Deer Mouse (Peromyscus maniculatus) and the White-footed Mouse (P. leucopus) and their respective Cuterebra parasites were examined. Population genetic structure of hosts and parasites was inferred using cytochrome oxidase mitochondrial sequences of specimens from 7 populations. Genetic analyses revealed that isolation-by-distance applies for P. maniculatus and its associated parasite (C. grisea). A significant correlation was also observed between the genetic distances of these host and parasite species. Furthermore, populations of P. maniculatus and C. grisea from the North and South shores of the St Lawrence River were found to be significantly different. This structure may be explained by the St Lawrence River being a dispersal barrier for both species. A robust analysis of the other species pair (P. leucopus and C. fontinella) could not be performed because of limited sample sizes.

scholarly journals Complex population structure of the Atlantic puffin revealed by whole genome analyses

2020 ◽  
Author(s):  
Oliver Kersten ◽  
Bastiaan Star ◽  
Deborah M. Leigh ◽  
Tycho Anker-Nilssen ◽  
Hallvard Strøm ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Secondary Contact ◽  
Whole Genome ◽  
Genome Data ◽  
Complex Population ◽  
Genome Analyses ◽  
Atlantic Puffin

AbstractThe factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.

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