The spatial genetic pattern of Castanopsis chinensis in a large forest plot with complex topography

2014 ◽  
Vol 318 ◽  
pp. 318-325 ◽  
Author(s):  
Zheng-Feng Wang ◽  
Ju-Yu Lian ◽  
Wan-Hui Ye ◽  
Hong-Lin Cao ◽  
Zhang-Ming Wang
Keyword(s):  
Forest Plot ◽  
Complex Topography ◽  
Genetic Pattern ◽  
Spatial Genetic Pattern

Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern

2011 ◽  
Vol 12 (2) ◽  
pp. 276-284 ◽  
Author(s):  
ERIN L. LANDGUTH ◽  
BRADLEY C. FEDY ◽  
SARA J. OYLER‐McCANCE ◽  
ANDREW L. GAREY ◽  
SARAH L. EMEL ◽  
...  
Keyword(s):  
Sample Size ◽  
Allelic Richness ◽  
Size Number ◽  
Genetic Pattern ◽  
Spatial Genetic Pattern

scholarly journals Grain trade between China and the United States shapes the spatial genetic pattern of common ragweed populations in East China cities

2021 ◽  
Author(s):  
Siran lu ◽  
Xiangyu Luo ◽  
Hongfang Wang ◽  
Rodolfo Gentili ◽  
Sandra Citterio ◽  
...  
Keyword(s):  
United States ◽  
The United States ◽  
East China ◽  
Effective Control ◽  
Common Ragweed ◽  
Control Programs ◽  
Grain Trade ◽  
Genetic Pattern ◽  
Spatial Genetic Pattern ◽  
Occurrence Records

Abstract Common ragweed (Ambrosia artemisiifolia L.) is an invasive alien species (IAS) that can cause severe allergies among urban residents. Understanding its invasion pathways is critical for designing effective control programs. However, studies on the invasion of common ragweed normally skip urban areas. Results from a few studies based on analyzing occurrence records contain high uncertainties. We attempted to address this knowledge gap through a case study in East China cities by combining the population genetic method with the occurrence records. We first collected leaf samples of 37 common ragweed populations from 15 cities. We then quantified the spatial genetic pattern of common ragweed populations by analyzing genomic and chloroplast DNA extracted from the leaf samples. Combined with the analysis of occurrence data and trade data, we discovered that multiple introductions have impacted the spatial genetic pattern of common ragweed populations in East China Cities. We inferred that the modern-day grain trade between the United States and China could be the primary invasion source while the bridgehead introduction passage through Japan played a minor role. Among the studied cities, Nanjing and Shenyang dispersed more gene flows than other cities. The two cities' central roles in transportation and grain importation might explain the observed pattern. Based on our findings, we suggest that invasive species control programs should consider the potential role of cities as landing points and dispersal hubs of common ragweed in invaded countries.

scholarly journals Spatial genetic pattern in the land mollusc Helix aspersa inferred from a ‘centre-based clustering’ procedure

2006 ◽  
Vol 88 (1) ◽  
pp. 27-44 ◽  
Author(s):  
ANNIE GUILLER ◽  
ALAIN BELLIDO ◽  
ALAIN COUTELLE ◽  
LUC MADEC
Keyword(s):  
Spatial Arrangement ◽  
Land Snail ◽  
Helix Aspersa ◽  
Western Mediterranean ◽  
Spatial Constraint ◽  
New Approach ◽  
Homogeneous Groups ◽  
Genetic Pattern ◽  
Microarray Datasets ◽  
Spatial Genetic Pattern

The present work provides the first broad-scale screening of allozymes in the land snail Helix aspersa. By using overall information available on the distribution of genetic variation between 102 populations previously investigated, we expect to strengthen our knowledge on the spread of the invasive aspersa subspecies in the Western Mediterranean. We propose a new approach based on a centre-based clustering procedure to cluster populations into groups following rules of geographical proximity and genetic similarity. Assuming a stepping-stone model of diffusion, we apply a partitioning algorithm which clusters only populations that are geographically contiguous. The algorithm used, which is actually part of leading methods developed for analysing large microarray datasets, is that of the k-means. Its goal is to minimize the within-group variance. The spatial constraint is provided by a list of connections between localities deduced from a Delaunay network. After testing each optimal group for the presence of spatial arrangement in the genetic data, the inferred genetic structure was compared with partitions obtained from other methods published for defining homogeneous groups (i.e. the Monmonier and SAMOVA algorithms). Competing biogeographical scenarios inferred from the k-means procedure were then compared and discussed to shed more light on colonization routes taken by the species.

The Orchard Plot: Cultivating a Forest Plot for Use in Ecology, Evolution and Beyond

2019 ◽  
Author(s):  
Shinichi Nakagawa ◽  
Malgorzata Lagisz ◽  
Rose E O'Dea ◽  
Joanna Rutkowska ◽  
Yefeng Yang ◽  
...  
Keyword(s):  
Meta Analysis ◽  
R Package ◽  
Effect Sizes ◽  
Forest Plot ◽  
Point Estimates ◽  
Aggregate Effect ◽  
The Individual ◽  
Meta Analyses ◽  
Heterogeneous Effect ◽  
Intuitive Interpretation

‘Classic’ forest plots show the effect sizes from individual studies and the aggregate effect from a meta-analysis. However, in ecology and evolution meta-analyses routinely contain over 100 effect sizes, making the classic forest plot of limited use. We surveyed 102 meta-analyses in ecology and evolution, finding that only 11% use the classic forest plot. Instead, most used a ‘forest-like plot’, showing point estimates (with 95% confidence intervals; CIs) from a series of subgroups or categories in a meta-regression. We propose a modification of the forest-like plot, which we name the ‘orchard plot’. Orchard plots, in addition to showing overall mean effects and CIs from meta-analyses/regressions, also includes 95% prediction intervals (PIs), and the individual effect sizes scaled by their precision. The PI allows the user and reader to see the range in which an effect size from a future study may be expected to fall. The PI, therefore, provides an intuitive interpretation of any heterogeneity in the data. Supplementing the PI, the inclusion of underlying effect sizes also allows the user to see any influential or outlying effect sizes. We showcase the orchard plot with example datasets from ecology and evolution, using the R package, orchard, including several functions for visualizing meta-analytic data using forest-plot derivatives. We consider the orchard plot as a variant on the classic forest plot, cultivated to the needs of meta-analysts in ecology and evolution. Hopefully, the orchard plot will prove fruitful for visualizing large collections of heterogeneous effect sizes regardless of the field of study.

Questions to the Article of the Infection Rate of the Coronavirus Disease 2019 (COVID-19) in Wuhan, China: a Combined Analysis of Population Samples (Preprint)

2020 ◽  
Author(s):  
CHIEN WEI
Keyword(s):  
Confidence Intervals ◽  
Infection Rate ◽  
Standard Error ◽  
Recent Article ◽  
Forest Plot ◽  
Combined Analysis ◽  
Infected People ◽  
Heterogeneity Test

UNSTRUCTURED The recent article published on July 22 in 2020 remains several questionable issues that are required to clarifications further, particularly for readers who hope to replicate Figure 1 from the data in Table 1. Although I reproduced a similar forest plot based on the effect ratios and their 95% confidence intervals(Cis) similar to Figure 1 in that article, no detailed information about the source of standard error(SE) for each country was seen and addressed. Others like the positive 95% Cis reflecting the negative Z values in the forest plot and the Q statistics used for examining the heterogeneity test are requied to interpretations and classifications. Most importantly, authors did not explain how to estimate the number of infected people in Wuhan, China, to be 143,000 ,significantly higher than the number of confirmed cases(=75,815 in Wuhan, China) that is required to provide the equations or methodologies in an article.

scholarly journals AB0576 BONE EROSION IN PSORIATIC ARTHRITIS ASSOCIATED WITH PSORIASIS DURATION, SKIN, NAIL AND JOINT DISEASE SEVERITY

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1325.2-1326
Author(s):  
M. Chamurlieva ◽  
E. Loginova ◽  
T. Korotaeva ◽  
Y. Korsakova ◽  
E. Gubar ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Psoriatic Arthritis ◽  
Disease Severity ◽  
Bone Erosion ◽  
Joint Disease ◽  
Practice Research ◽  
Forest Plot ◽  
Clinical Practice Research Datalink ◽  
Increased Risk ◽  
Nail Disease

Background:Psoriatic arthritis (PsA) is heterogeneous in its clinical presentation and disease course, but many patients (pts) develop a destructive form of arthritis. Psoriasis (PsO) precedes arthritis by an average of 7 years. [1]. Theory of transition from PsO to PsA has been proposed recently [2]. But association between skin disease severity and joint disease are still unclear.Objectives:to evaluate association between bone erosion, PsO duration, skin and nail disease severity in PsA pts based on data from clinical practice (RU-PsART cohort).Methods:737 (M/F=350/387) PsA pts fulfilling the CASPAR criteria were included. Mean age 47.4±12.7 years (yrs), PsA duration 55[17;120] mos., PsO duration 165[74.5;292] mos., mean DAPSA 23.3[14;36.9] mos., HAQ-DI - 0.98 [0.5;1.38], CRP - 7.4 [2.1;18] mg/l. All pts underwent standard clinical examination (tender joins count (TJC)/68, swelling joints count (SJC)/66, CRP (mg/l), DAPSA, dactylitis, enthesitis by LEI + Plantar Facia (PF), HAQ-DI. Mild disease was defined as body surface area (BSA)≤10%, moderate to severe as BSA>10%. The presence/absent of nail PsO was evaluated. X-ray of feet and hand were done in 622 out of 737 pts. The one-factor model of logistic regression was used to identify a group of features that are associated with achievement MDA. M±SD, Me [Q25; Q75], Min-Max, %, t-test, Pierson-χ2, Manna-Whitney tests, ORs with 95% CI were performed. All p<0.05 were considered to indicate statistical significance.Results:PsO precedes of PsA by an average of 9.2 years. BSA≤10% was found in 615 out of 672 pts (91.5%), BSA>10% - in 57 out of 672 pts (8.5%). Nail PsO were seen in 230 out of 737 (31.2%). Bone erosion was found in 237 out of 622 of pts (38.1%). Among these pts nail PsO were seen in 67 out of 237 pts (28.3%). Enthesitis found in 236 out of 737 pts (42.1%), dactylitis – in 197 out 731 pts (27%), axial PsA – in 315 out of 731 pts (43.1%). Bone erosion significantly associated with PsO duration more than 5 yrs., skin and nail PsO severity, high PsA activity by DAPSA, axial manifestation and duration of PsA > 36 mos. (Figure 1).Figure 1Forest plot of factors associated with bone erosion in PsA pts.Conclusion:In our cohort the majority of PsA pts had mild PsO preceded PsA on average of 9.2 yrs. Bone erosion was found in 30% of PsA pts which associated with PsO duration, skin and nail disease severity as well as with PsA activity. Early diagnosis and therapeutic intervention within a “window of opportunity” are very important for improving outcomes and prevent structural damage in PsA.References:[1]Tillett W, et al. Interval between onset of psoriasis and psoriatic arthritis comparing the UK Clinical Practice Research Datalink with a hospital-based cohort. Rheumatol. 2017; 56, 2109–2113[2]Scher JU, et al. Preventing psoriatic arthritis: focusing on patients with psoriasis at increased risk of transition. Nat Rev Rheumatol. 2019;15(3):153-166. doi: 10.1038/s41584-019-0175-0. PMID: 30742092.Disclosure of Interests:None declared.

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