Conservation genetics and geographic patterns of genetic variation of the endangered officinal herbFritillaria pallidiflora

2015 ◽  
Vol 33 (4) ◽  
pp. 506-512 ◽  
Author(s):  
Zhihao Su ◽  
Borong Pan ◽  
Stewart C. Sanderson ◽  
Xiaolong Jiang ◽  
Mingli Zhang
Keyword(s):  
Genetic Variation ◽  
Conservation Genetics ◽  
Geographic Patterns

scholarly journals Geographic patterns of human allele frequency variation: a variant-centric perspective

2020 ◽  
Author(s):  
Arjun Biddanda ◽  
Daniel P. Rice ◽  
John Novembre
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Allele Frequency ◽  
Human Genetics ◽  
Geographic Region ◽  
Frequency Variation ◽  
Human Genetic Variation ◽  
Alternative Representation ◽  
Geographic Patterns

AbstractA key challenge in human genetics is to describe and understand the distribution of human genetic variation. Often genetic variation is described by showing relationships among populations or individuals, in each case drawing inferences over a large number of variants. Here, we present an alternative representation of human genetic variation that reveals the relative abundance of different allele frequency patterns across populations. This approach allows viewers to easily see several features of human genetic structure: (1) most variants are rare and geographically localized, (2) variants that are common in a single geographic region are more likely to be shared across the globe than to be private to that region, and (3) where two individuals differ, it is most often due to variants that are common globally, regardless of whether the individuals are from the same region or different regions. To guide interpretation of the results, we also apply the visualization to contrasting theoretical scenarios with varying levels of divergence and gene flow. Our variant-centric visualization clarifies the major geographic patterns of human variation and can be used to help correct potential misconceptions about the extent and nature of genetic differentiation among populations.

scholarly journals Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2504 ◽  
Author(s):  
Katarzyna Bilska ◽  
Monika Szczecińska
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Conservation Genetics ◽  
Ssr Markers ◽  
Full Range ◽  
Mantel Test ◽  
Evolutionary Potential ◽  
Functional Variation ◽  
Genetics Research ◽  
Outlier Loci

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

scholarly journals The distinctive geographic patterns of common pigmentation variants at the OCA2 gene

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Kenneth K. Kidd ◽  
Andrew J. Pakstis ◽  
Michael P. Donnelly ◽  
Ozlem Bulbul ◽  
Lotfi Cherni ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Oculocutaneous Albinism ◽  
Selection Effects ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Eye Color ◽  
Geographic Patterns ◽  
Population Genetic Variation ◽  
Oca2 Gene

Abstract Oculocutaneous Albinism type 2 (OCA2) is a gene of great interest because of genetic variation affecting normal pigmentation variation in humans. The diverse geographic patterns for variant frequencies at OCA2 have been evident but have not been systematically investigated, especially outside of Europe. Here we examine population genetic variation in and near the OCA2 gene from a worldwide perspective. The very different patterns of genetic variation found across world regions suggest strong selection effects may have been at work over time. For example, analyses involving the variants that affect pigmentation of the iris argue that the derived allele of the rs1800407 single nucleotide polymorphism, which produces a hypomorphic protein, may have contributed to the previously demonstrated positive selection in Europe for the enhancer variant responsible for light eye color. More study is needed on the relationships of the genetic variation at OCA2 to variation in pigmentation in areas beyond Europe.

Geographic Patterns of Genetic Variation and Conservation Consequences in Three South American Rodents

2007 ◽  
Vol 45 (11-12) ◽  
pp. 839-856 ◽  
Author(s):  
Gustavo B. Miranda ◽  
Jaqueline Andrades-Miranda ◽  
Luiz F. B. Oliveira ◽  
Alfredo Langguth ◽  
Margarete S. Mattevi
Keyword(s):  
Genetic Variation ◽  
South American ◽  
Geographic Patterns

scholarly journals Widespread inbreeding and unexpected geographic patterns of genetic variation in eastern hemlock (Tsuga canadensis), an imperiled North American conifer

2011 ◽  
Vol 13 (2) ◽  
pp. 475-498 ◽  
Author(s):  
Kevin M. Potter ◽  
Robert M. Jetton ◽  
William S. Dvorak ◽  
Valerie D. Hipkins ◽  
Rusty Rhea ◽  
...  
Keyword(s):  
Genetic Variation ◽  
North American ◽  
Tsuga Canadensis ◽  
Eastern Hemlock ◽  
Geographic Patterns

Conservation genetics and ecology of the endangered rainforest shrub, Triunia robusta, from the Sunshine Coast, Australia

2002 ◽  
Vol 50 (1) ◽  
pp. 93 ◽  
Author(s):  
Alison Shapcott
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
Conservation Genetics ◽  
Population Size ◽  
Genetic Similarity ◽  
Small Region ◽  
Geographic Proximity ◽  
Close Proximity ◽  
The Mean

Triunia robusta, which until recently was thought to be extinct, is now classified nationally as endangered. It is an understorey species restricted to the subcoastal rainforests in a small region of the Sunshine Coast, Queensland. The project involved sampling the genetic variation and measuring the population size and size distribution of T. robusta and its geographically closest congener T. youngiana, which occurs further south and has a wider geographic distribution. A total of 877 T. robusta plants were recorded across the 11 populations, approximately half (56.8%) of these were juveniles less than 1 m tall, whereas in T. youngiana only about 36.4% of a population was composed of juveniles. Genetic diversity was similar but significantly higher for T. robusta than T. youngiana if the very small T. robusta populations (2 or 3 plants) were excluded from analysis (P < 0.05). The mean percentage of polymorphic loci among populations was high for both species. Triunia robusta is not, on average, more inbred than the more common T. youngiana. There was more differentiation between the T. robusta populations, which were in close proximity, than between the more geographically separated T. youngiana populations. Thus, there is evidence of more gene flow between populations of T. youngiana than between those of T. robusta. However, there was no geographic relationship between genetic similarity and geographic proximity in T. robusta

scholarly journals Geographic patterns in morphometric and genetic variation for coyote populations with emphasis on southeastern coyotes

2019 ◽  
Vol 9 (6) ◽  
pp. 3389-3404 ◽  
Author(s):  
Joseph W. Hinton ◽  
Elizabeth Heppenheimer ◽  
Kyla M. West ◽  
Danny Caudill ◽  
Melissa L. Karlin ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Geographic Patterns

Geographic patterns of genetic variation in native pecans

2011 ◽  
Vol 7 (5) ◽  
pp. 917-932 ◽  
Author(s):  
L. J. Grauke ◽  
Maria Azucena Mendoza-Herrera ◽  
Allison J. Miller ◽  
Bruce. W. Wood
Keyword(s):  
Genetic Variation ◽  
Geographic Patterns

Geographic Patterns of Genetic Variation in Pinus monticola

1984 ◽  
Vol 145 (2) ◽  
pp. 229-239 ◽  
Author(s):  
G. E. Rehfeldt ◽  
R. J. Hoff ◽  
R. J. Steinhoff
Keyword(s):  
Genetic Variation ◽  
Pinus Monticola ◽  
Geographic Patterns
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