scholarly journals TEMPORAL AND MICROGEOGRAPHIC VARIATION IN ALLOZYME FREQUENCIES IN A NATURAL POPULATION OF DROSOPHILA BUZZATII

Genetics ◽  
1986 ◽  
Vol 112 (3) ◽  
pp. 577-611
Author(s):  
J S F Barker ◽  
P D East ◽  
B S Weir
Keyword(s):  
Population Structure ◽  
Environmental Variables ◽  
Allele Frequencies ◽  
Significant Heterogeneity ◽  
Linkage Disequilibria ◽  
Drosophila Buzzatii ◽  
Genotype Frequencies ◽  
Microgeographic Variation ◽  
Significant Linkage ◽  
Over Time

ABSTRACT Temporal variation in allozyme frequencies at six loci was studied by making monthly collections over 4 yr in one population of the cactophilic species Drosophila buzzatii. Ten sites were defined within the study locality, and for all temporal samples, separate collections were made at each of these sites. Population structure over microgeographic space and changes in population structure over time were analyzed using F-statistic estimators, and multivariate analyses of allele and genotype frequencies with environmental variables were carried out.—Allele frequencies showed significant variation over time, although there were no clear cyclical or seasonal patterns. A biplot analysis of allele frequencies over seasons within years and over years showed clear discrimination among years by alleles at four loci. During the 4 yr, three alleles showed directional changes which were associated with directional changes in environmental variables. Significant associations with one or more environmental variables were found for allele frequencies at every locus and for both expected and observed heterozygosities (except those for Est-1 and Est-2). Thus, variation in allele frequencies over time cannot be attributed solely to drift. Significant linkage disequilibria were detected among three loci (Est-2, Hex and Aldox), but there was no evidence for spatial or temporal patterns.—The F-statistic analyses showed significant differentiation among months within years for all loci, but the statistic used (coancestry) was heterogeneous among loci. Estimates of F (inbreeding) for all loci were significantly different from zero, with the loci in four groups, Adh-1 (negative), Pgm (small positive), Est-2 and Hex (intermediate) and Est-1 and Aldox (high positive). The correlation of genes within individuals within populations (f) for each locus in each month by site sample differed among loci, as did the patterns of change in f over time (seasons). Heterogeneity in the F-statistic estimates indicates that natural selection is directly or indirectly affecting allele and genotype frequencies at some loci. However, the F-statistic analyses showed essentially no microgeographic structure (i.e., among sites), although there was significant heterogeneity in allele frequencies among flies emerging from individual rots.—Thus, microspatial heterogeneity probably is most important at the level of individual rots, and coupled with habitat selection, it could be a major factor promoting diversifying selection and the maintenance of polymorphism. Resolution of the nature of this selection and of the apparent inbreeding detected at all loci except Adh-1 will require detailed study of the breeding structure of the population at the microhabitat level (individual rots) and of gene flow within the population.

scholarly journals Polymorphic Inversion and Esterase Loci Complex on Chromosome 2 of Drosophila buzzatii II. Spatial Variation

1988 ◽  
Vol 41 (2) ◽  
pp. 239 ◽  
Author(s):  
WR Knibb ◽  
JSF Barker
Keyword(s):  
Environmental Variables ◽  
Geographic Location ◽  
Allele Frequencies ◽  
Frequency Variation ◽  
Chromosome 2 ◽  
Potential Influence ◽  
Linkage Disequilibria ◽  
Drosophila Buzzatii ◽  
Esterase Loci ◽  
And Inversion

The potential influence of linked inversions on allele frequency variation at the Est-l and Est-210ci among Australian populations of D. buzzatii was determined by statistical analyses of allele and inversion gametic frequencies. Most of the significant spatial and climatic associations found for all Est-l allele frequencies, and for one allele only of Est-2 (Est-2c+), were accounted for by their linkage disequilibria with the inversions, which covaried with environmental variables. Consistent with this result, the spatial and climatic associations for conditional Est-l and Est-2 allele frequencies tended to be different from those for the respective unadjusted allele frequencies. In one important respect, the results for Est-l and Est-2 were not altered by inversions. For both unadjusted and conditional Est-l allele frequencies, few climatic associations remain after correcting for geographic location, whereas for both unadjusted and conditional Est-2 allele frequencies, climatic associations remain after correcting for geographic location. Thus, apparent selection affecting allele frequencies at the Est-2 locus is not accounted for by linked inversions.

scholarly journals Polymorphic Inversion and Esterase Loci Complex on Chromosome 2 of Drosophila buzzatii. I. Linkage Disequilibria

1987 ◽  
Vol 40 (3) ◽  
pp. 257 ◽  
Author(s):  
WR Knibb ◽  
PD East ◽  
JSF Barker
Keyword(s):  
New World ◽  
Genetic Change ◽  
Chromosome 2 ◽  
Population Bottlenecks ◽  
Linkage Disequilibria ◽  
Drosophila Buzzatii ◽  
Conditional Allele ◽  
Esterase Loci ◽  
Almost All ◽  
Significant Linkage

Chromosome 2 inversion, Est-l and Est-2 haplotype frequencies were determined for 19 wild D. buzzatii collections from the known range of this species in Australia. Three different chromosome 2 sequences (ST, j, j z3) were polymorphic across the collections. They occurred at overall frequencies which approximated those in the ancestral New World and colonized Old World populations, which indicated that no radical genetic change was associated with the colonization of Australia by D. buzzatii. Linkage disequilibria of Est-l and Est-2 alleles with the inversions tended to be strong, and consistent in direction, in almost all collections. The distributions of conditional allele frequencies within the different inversions were consistent with stochastic historical explanations for the linkage disequilibria. Significant linkage disequilibria between Est-l and Est-2 were evident after correcting for the inversions, but these disequilibria largely were restricted to southern (higher latitude) populations, and were inconsistent in direction among the collections. Hence, population bottlenecks may underlie these genic disequilibria.

scholarly journals Applications of ancestry estimation in cattle population genetics

2019 ◽  
Author(s):  
◽  
Tamar Crum
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Population Genetic ◽  
Human Population ◽  
Disease Risk ◽  
Allele Frequencies ◽  
Population Substructure ◽  
Association Analyses ◽  
Genotype Frequencies ◽  
Ancestry Estimation

Accounting for ancestry and cryptic population structure is important in population genetic data analysis. The estimation of ancestry can help elucidate the effects of admixture or stratification on allele and genotype frequencies caused by population substructure. Human population genetics has examined these issues in detail and has developed models which incorporate ancestry effects in the estimation of population susceptibilities to disease risk in association analyses, as well as for the interpretation of genotype disease risks in admixed individuals for use in personalized medicine. In livestock, allele frequencies frequently differ between breeds and these breeds frequently also differ for phenotypes of interest. If these population differences are not accounted for in the analysis, the differences in allele frequencies due to population structure can lead to erroneous associations of loci with phenotypes. The effects of domestication and breed formation in shaping the cattle genome along with the rampant use of crossbreeding to form admixed individuals in the modern beef cattle industry provides an opportunity to evaluate the impacts of breed differences on association analyses of economically relevant traits such as the conversion of feed to weight gain and disease susceptibility. Here, we review the methods used for ancestry estimation and the impacts of ancestry prediction in human population genetic analyses and opportunities for use of these techniques in cattle, and more generally in livestock populations. The incorporation of accurate genomic-based predictions of breed composition could fine-tune the resolution of mapping studies targeting the identification of causal loci for livestock species.

Population structure, age and growth rates of conifer species and their relation to environmental variables at Malam Jabba, Swat District, Pakistan

2018 ◽  
Vol 31 (2) ◽  
pp. 429-441
Author(s):  
Arsalan ◽  
Muhammad Faheem Siddiqui ◽  
Moinuddin Ahmed ◽  
Syed Shahid Shaukat ◽  
Alamdar Hussain
Keyword(s):  
Population Structure ◽  
Growth Rates ◽  
Environmental Variables ◽  
Age And Growth ◽  
Conifer Species

Integral projection models

2021 ◽  
pp. 181-196
Author(s):  
Edgar J. González ◽  
Dylan Z. Childs ◽  
Pedro F. Quintana-Ascencio ◽  
Roberto Salguero-Gómez
Keyword(s):  
Population Dynamics ◽  
Environmental Variables ◽  
Linear Models ◽  
Vital Rates ◽  
Matrix Population Models ◽  
Generalised Linear Models ◽  
Integral Projection Models ◽  
Integral Projection ◽  
Over Time

Integral projection models (IPMs) allow projecting the behaviour of a population over time using information on the vital processes of individuals, their state, and that of the environment they inhabit. As with matrix population models (MPMs), time is treated as a discrete variable, but in IPMs, state and environmental variables are continuous and are related to the vital rates via generalised linear models. Vital rates in turn integrate into the population dynamics in a mechanistic way. This chapter provides a brief description of the logic behind IPMs and their construction, and, because they share many of the analyses developed for MPMs, it only emphasises how perturbation analyses can be performed with respect to different model elements. The chapter exemplifies the construction of a simple and a more complex IPM structure with an animal and a plant case study, respectively. Finally, inverse modelling in IPMs is presented, a method that allows population projection when some vital rates are not observed.

Surfacing behaviour and ecology of the marsupial mole (Notoryctes typhlops) at Uluru-Kata Tjuta National Park

2014 ◽  
Vol 36 (2) ◽  
pp. 184 ◽  
Author(s):  
Kerrie Bennison ◽  
Jim Clayton ◽  
Robert Godfree ◽  
Chris Pavey ◽  
Melinda Wilson
Keyword(s):  
Environmental Variables ◽  
National Park ◽  
Survey Methods ◽  
Habitat Preferences ◽  
Rainfall Events ◽  
Significant Relationships ◽  
Cumulative Rainfall ◽  
Sign Surveys ◽  
Distribution And Ecology ◽  
Over Time

Little is known about the distribution and ecology of the cryptic and unique marsupial mole. In this paper we report on the habitat preferences and surfacing behaviour of marsupial moles on the basis of surface sign surveys conducted in Uluru-Kata Tjuta National Park and Ayers Rock Resort over a 12-month period by Uluru-Kata Tjuta National Park staff and traditional owners. A key aim of the study was to assess the potential viability of using surface sign as a rapid, non-intrusive alternative to traditional survey methods. We found that surfacing occurred widely across the study area, but that it was highly variable both across survey sites and over time. Significant relationships existed between surface sign counts and environmental variables, including fire age, timing of significant rainfall events, presence of infrastructure and the cumulative rainfall received in the preceding three months. We concluded that the use of marsupial mole surface sign is likely to be a useful method for monitoring the distribution, abundance and habitat requirements of this cryptic species.

scholarly journals A new set of microsatellite loci for Cattleya walkeriana Gardner, an endangered tropical orchid species and its transferability to Cattleya loddigesii Lindl. and Cattleya nobilior Reichenbach

2017 ◽  
Vol 16 (3) ◽  
pp. 284-287
Author(s):  
Bruno C. Rossini ◽  
Mariá B. Kampa ◽  
Celso L. Marino ◽  
Fernanda Bortolanza Pereira ◽  
Fábio M. Alves ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Null Alleles ◽  
Germplasm Resources ◽  
Significant Linkage Disequilibrium ◽  
Orchid Species ◽  
Expected Heterozygosity ◽  
Tropical Orchid ◽  
Significant Linkage

AbstractIn this study, we isolate and analyse a new set of microsatellite loci for Cattleya walkeriana. Twenty-two primer pairs were screened for C. walkeriana (n = 32) and assessed for their transferability to Cattleya loddigesii (n = 12) and Cattleya nobilior (n = 06). All loci amplified for C. walkeriana; however, for C. loddigesii and C. nobilior, four and five primers, respectively, did not present amplification. The polymorphic loci presented between 2 and 13 alleles per locus for both C. walkeriana and C. loddigesii, with respective averages of 5.1 and 4.2. For C. nobilior, we found between two and five alleles per locus, with an average of 2.6. For C. walkeriana, observed heterozygosity varied from 0.100 to 0.966, whereas expected heterozygosity ranged from 0.097 to 0.900. The observed and expected heterozygosity for C. loddigesii and C. nobilior were also estimated. We found no significant linkage disequilibrium between any pair of loci, and evidence of null alleles at four loci (Cw16, Cw24, Cw30 and Cw31) for C. walkeriana. The combined power to exclude the first parent and combined non-exclusion probability of identity were 0.999 and 2.3 × 10−20, respectively. These new loci can be used in studies of germplasm resources, and assessments of genotypic and genetic diversity and population structure, thus improving the accuracy of such analyses and their applicability in the conservation and protection of these endangered species.

scholarly journals Population Age Structure, Complex Socio-Demographic Systems and Resilience Potential: A Spatio-Temporal, Evenness-Based Approach

2019 ◽  
Vol 11 (7) ◽  
pp. 2050 ◽  
Author(s):  
Massimo Cecchini ◽  
Sirio Cividino ◽  
Rosario Turco ◽  
Luca Salvati
Keyword(s):  
Population Structure ◽  
Age Structure ◽  
Census Data ◽  
Principal Component ◽  
System Thinking ◽  
Italian Population ◽  
Comprehensive Overview ◽  
Population Age Structure ◽  
Evenness Index ◽  
Over Time

The present study illustrates an original approach grounded on entropy theory and complex system thinking with the aim to investigate changes over time and space in population structure by age in Italy, in light of socioeconomic resilience and post-crisis recovery potential. Assuming that population structure may reflect different levels of resilience to exogenous shocks, a Pielou J evenness index was calculated on census data made available every 10 years (1861–2011) with the aim to identify compositional homogeneity (or heterogeneity) in the age structure of the Italian population. Trends over time in the Pielou J evenness index were identified using descriptive statistics, comparison with ancillary demographic indicators and multivariate exploratory techniques including principal component analysis. The empirical results allowed the identification of multiple dimensions of demographic transition in Italy, distinguishing two phases, the former encompassing a relatively long time period between 1861 and 1936, and the latter covering a shorter period between 1936 and 2011. A spatially-explicit analysis of Pielou J evenness indices applied to the population age structure of each Italian municipality at the latest survey (2017) finally provided a comprehensive overview of the demographic characteristics likely influencing the resilience potential of local districts. The empirical evidence outlined the consolidation of a coastal–inland divide as a result of the complex linkage between demographic dynamics and local background contexts.

A Two-Stage Sales Forecasting Procedure Using Discounted Least Squares

1994 ◽  
Vol 31 (1) ◽  
pp. 44-56 ◽  
Author(s):  
Stephen A. Smith ◽  
Shelby H. McIntyre ◽  
Dale D. Achabal
Keyword(s):  
Regression Analysis ◽  
Least Squares ◽  
Environmental Variables ◽  
Market Conditions ◽  
Two Stage ◽  
Sales Data ◽  
Retail Chain ◽  
Stage 1 ◽  
Smoothing Procedure ◽  
Over Time

The authors develop a two-stage forecasting methodology for estimating the sales responses to marketing and environmental variables when it is likely that their impacts will change unpredictably over time. The methodology is based on an integrated least squares procedure that uses regression analysis in Stage 1 to estimate the coefficients of the controllable and environmental variables in combination with a Stage 2 discounted least squares smoothing procedure that updates key parameters in response to changing market conditions. The effectiveness of the methodology is demonstrated by applying it to weekly sales data from a major retail chain.

scholarly journals The Impacts ofSLC22A1rs594709 andSLC47A1rs2289669 Polymorphisms on Metformin Therapeutic Efficacy in Chinese Type 2 Diabetes Patients

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Di Xiao ◽  
Yu Guo ◽  
Xi Li ◽  
Ji-Ye Yin ◽  
Wei Zheng ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Therapeutic Efficacy ◽  
Healthy Subjects ◽  
Allele Frequencies ◽  
Metformin Treatment ◽  
Newly Diagnosed ◽  
Genotype Frequencies ◽  
Metformin Monotherapy ◽  
Significant Difference

Background. We aimed to investigate the distributive characteristics ofSLC22A1rs594709 andSLC47A1rs2289669 polymorphisms and their influence on metformin efficacy in Chinese T2DM patients.Methods. The distributions ofSLC22A1rs594709 andSLC47A1rs2289669 polymorphisms were determined in 267 T2DM patients and 182 healthy subjects. Subsequently, 53 newly diagnosed patients who received metformin monotherapy were recruited to evaluate metformin efficacy.Results. No significant difference was found between T2DM patients and healthy subjects inSLC22A1rs594709 andSLC47A1rs2289669 allele frequencies and genotype frequencies. After metformin treatment,SLC22A1rs594709 GG genotype patients showed a higher increase in FINS (p=0.015) and decrease in HOMA-IS (p=0.001) and QUICKI (p=0.002) than A allele carriers.SLC47A1rs2289669 GG genotype patients had a higher decrease in TChol (p=0.030) and LDL-C (p=0.049) than A allele carriers. AmongSLC22A1rs594709 AA genotype, patients withSLC47A1rs2289669 AA genotype showed a higher decrease in FBG (p=0.015), PINS (p=0.041), and HOMA-IR (p=0.014) than G allele carriers. However, amongSLC22A1rs594709 G allele carriers,SLC47A1rs2289669 AA genotype patients showed a higher decrease in TChol (p=0.013) than G allele carriers.Conclusion. Our data suggest thatSLC22A1rs594709 andSLC47A1rs2289669 polymorphisms may influence metformin efficacy together in Chinese T2DM patients.

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