scholarly journals Epigenetic and genetic variation among three separate introductions of the house sparrow ( Passer domesticus ) into Australia

2018 ◽  
Vol 5 (4) ◽  
pp. 172185 ◽  
Author(s):  
E. L. Sheldon ◽  
A. Schrey ◽  
S. C. Andrew ◽  
A. Ragsdale ◽  
S. C. Griffith
Keyword(s):  
Genetic Diversity ◽  
Invasive Species ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
House Sparrow ◽  
Passer Domesticus ◽  
Epigenetic Variation ◽  
Population Bottlenecks ◽  
Introduction History ◽  
Founder Events

Invasive populations are often associated with low levels of genetic diversity owing to population bottlenecks at the initial stages of invasion. Despite this, the ability of invasive species to adapt rapidly in response to novel environments is well documented. Epigenetic mechanisms have recently been proposed to facilitate the success of invasive species by compensating for reduced levels of genetic variation. Here, we use methylation sensitive-amplification fragment length polymorphism and microsatellite analyses to compare levels of epigenetic and genetic diversity and differentiation across 15 sites in the introduced Australian house sparrow population. We find patterns of epigenetic and genetic differentiation that are consistent with historical descriptions of three distinct, introductions events. However unlike genetic differentiation, epigenetic differentiation was higher among sample sites than among invasion clusters, suggesting that patterns of epigenetic variation are more strongly influenced by local environmental stimuli or sequential founder events than the initial diversity in the introduction population. Interestingly, we fail to detect correlations between pairwise site comparisons of epigenetic and genetic differentiation, suggesting that some of the observed epigenetic variation has arisen independently of genetic variation. We also fail to detect the potentially compensatory relationship between epigenetic and genetic diversity that has been detected in a more recent house sparrow invasion in Africa. We discuss the potential for this relationship to be obscured by recovered genetic diversity in more established populations, and highlight the importance of incorporating introduction history into population-wide epigenetic analyses.

scholarly journals Epigenetic Variation May Compensate for Decreased Genetic Variation with Introductions: A Case Study Using House Sparrows (Passer domesticus) on Two Continents

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Aaron W. Schrey ◽  
Courtney A. C. Coon ◽  
Michael T. Grispo ◽  
Mohammed Awad ◽  
Titus Imboma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Phenotypic Variation ◽  
Passer Domesticus ◽  
Phenotypic Traits ◽  
Epigenetic Variation ◽  
House Sparrows ◽  
Introduction History ◽  
Outlier Loci

Epigenetic mechanisms impact several phenotypic traits and may be important for ecology and evolution. The introduced house sparrow (Passer domesticus) exhibits extensive phenotypic variation among and within populations. We screened methylation in populations from Kenya and Florida to determine if methylation varied among populations, varied with introduction history (Kenyan invasion <50 years old, Florida invasion ~150 years old), and could potentially compensate for decrease genetic variation with introductions. While recent literature has speculated on the importance of epigenetic effects for biological invasions, this is the first such study among wild vertebrates. Methylation was more frequent in Nairobi, and outlier loci suggest that populations may be differentiated. Methylation diversity was similar between populations, in spite of known lower genetic diversity in Nairobi, which suggests that epigenetic variation may compensate for decreased genetic diversity as a source of phenotypic variation during introduction. Our results suggest that methylation differences may be common among house sparrows, but research is needed to discern whether methylation impacts phenotypic variation.

scholarly journals Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 291
Author(s):  
Biao Ni ◽  
Jian You ◽  
Jiangnan Li ◽  
Yingda Du ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Soil Properties ◽  
Changbai Mountains ◽  
Epigenetic Variation ◽  
Geographical Distance ◽  
Mantel Tests ◽  
Epigenetic Diversity ◽  
Different Populations

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Stone Pine ◽  
Arithmetic Means ◽  
Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred

2004 ◽  
Vol 52 (3) ◽  
pp. 259-265
Author(s):  
Daniela Šátková-Jakabová ◽  
J. Trandžík ◽  
Ľudmila Hudecová-Kvasňáková ◽  
Erika Hegedüšová-Zetochová ◽  
A. Bugarský ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
International Society ◽  
Microsatellite Loci ◽  
Genetic Relationships ◽  
Allele Frequencies ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the observed and expected heterozygosities were calculated. POPGENE v. 1.31 (Yeh et al., 1997) was used to test for deviations from the Hardy-Weinberg (H-W) equilibrium and to assign FIS estimates (Weir, 1990). The utility of microsatellites for evaluating genetic diversity of horses is discussed.

Limited Genetic Diversity and High Differentiation in Angelica Dahurica Resulted by Domestication: Insights to Breeding and Conservation

2021 ◽  
Author(s):  
Rong Huang ◽  
Yinrong Liu ◽  
Jianling Chen ◽  
Zuyu Lu ◽  
Jiajia Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Clustering Analysis ◽  
Large Scale ◽  
Angelica Dahurica ◽  
Significant Genetic Differentiation ◽  
Large Scale Analysis ◽  
Domestication Process ◽  
Resources Conservation

Abstract Background： Angelica dahurica, belonging to the Apiaceae family, whose dry root is a famous traditional Chinese medicine named as “Bai zhi”. There are two cultivars (A. dahurica cv. ‘Hangbaizhi’ and A. dahurica cv. ‘Qibaizhi’), which have been domesticated for thousands of years. Long term artificial selection has led to great changes in root phenotypes of the two cultivars, and also decreased their adaptability to environment. We proposed hypothesis that the cultivars may lose some genetic diversity and highly differentiate from wild A. dahurica during the domestication process. However, few studies have been carried out on how domestication affects the genetic variation of this species. Here, we accessed the levels of genetic variation and differentiation within and between wild A. dahurica and its cultivars using 12 SSR markers. Results: The results revealed that the genetic diversity of the cultivars was much lower than that of wild A. dahurica, and A. dahurica cv. ‘Qibaizhi’ had lower genetic diversity compared to A. dahurica cv. ‘Hangbaizhi’. AMOVA analysis showed significant genetic differentiation between the wild and cultivated A. dahurica, and between A. dahurica cv. ‘Hangbaizhi’ and A. dahurica cv. ‘Qibaizhi’. The results of Bayesian, UPGMA, NJ and PcoA clustering analysis indicated that all 15 populations were assigned to two genetic clusters corresponding to the wild and cultivated resources. Bayesian clustering analysis further divided the cultivated resources into two sub-clusters corresponding to the two cultivars. Conclusions：Our study suggests that domestication process is likely the major factor resulting in the loss of genetic diversity in cultivated A. dahurica and significant genetic differentiation from the wild resources due to founder effect and/or artificially directional selections. This large-scale analysis of population genetics could provide valuable information for genetic resources conservation and breeding programs of Angelica dahurica.

scholarly journals Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
Zulfahmi Zulfahmi ◽  
Parjanto Parjanto ◽  
Edi Purwanto ◽  
Ahmad Yunus
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Genetic Material ◽  
Ex Situ ◽  
Breeding Programs ◽  
The Mean

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

Conservation genetics of Hill’s thistle (Cirsium hillii)

Botany ◽  
2010 ◽  
Vol 88 (12) ◽  
pp. 1073-1080 ◽  
Author(s):  
Joanna R. Freeland ◽  
Joy Gillespie ◽  
Claudia Ciotir ◽  
Marcel E. Dorken
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Habitat Loss ◽  
Perennial Herb ◽  
Great Lakes Region ◽  
Species At Risk ◽  
Foreseeable Future ◽  
Species Combination ◽  
Private Alleles

Populations at the edges of their geographical ranges are often characterized by reduced genetic diversity and increased genetic differentiation. These patterns may be exacerbated by specialized associations between plants and uncommon habitats. Together, reduced diversity and increased subdivision may increase the risk of population extirpation, an issue that is particularly important for plants classified as rare or threatened. Hill’s thistle (Cirsium hillii (Canby) Fernald), is a perennial herb endemic to the Great Lakes region and is considered threatened in Canada where its northernmost distribution occurs. We used microsatellite markers to genotype plants from 11 populations of Hill’s thistle that span the range of the species distribution within Canada. These data were used to investigate levels of genetic diversity within populations and genetic differentiation between populations, and to evaluate associations between patterns of genetic variation and those expected under ongoing habitat loss. Genetic differentiation among populations was low, although significant pairwise FST values, along with the presence of private alleles in most populations, was consistent with moderate to low gene flow. Nevertheless, in comparison with a congeneric rare species (Cirsium pitcheri) that occurs in the same geographical region in Canada, genetic diversity within most populations was high, and we suggest that this is at least partially attributable to this species’ combination of sexual and clonal reproduction. Despite high levels of genetic diversity, Hill’s thistle should probably remain a designated species at risk because of ongoing habitat loss; however, our data suggest that Hill’s thistle is unlikely to suffer from reduced genetic diversity in the foreseeable future.

scholarly journals High Genetic Diversity and Insignificant Interspecific Differentiation inOpisthopappusShih, an Endangered Cliff Genus Endemic to the Taihang Mountains of China

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Rongmin Guo ◽  
Lihua Zhou ◽  
Hongbo Zhao ◽  
Fadi Chen
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Species Level ◽  
Endangered Plants ◽  
High Genetic Diversity ◽  
Fragmented Distribution ◽  
Polymorphic Bands ◽  
Genetic Structures ◽  
Different Levels

OpisthopappusShih is endemic to the Taihang Mountains, China. It grows in the crevice of cliffs and is in fragmented distribution. This genus consists of two species, namely,O. taihangensis(Ling) Shih andO. longilobusShih, which are both endangered plants in China. This study adopted intersimple sequence repeat markers (ISSR) to analyze the genetic diversity and genetic structure from different levels (genus, species, and population) in this genus. A total of 253 loci were obtained from 27 primers, 230 of which were polymorphic loci with a proportion of polymorphic bands (PPB) of up to 90.91% at genus level. At species level, bothO. taihangensis(PPB=90.12%,H=0.1842, andI=0.289) andO. longilobus(PPB=95.21%,H=0.2226, andI=0.3542) have high genetic diversity. Their respective genetic variation mostly existed within the population. And genetic variation inO. longilobus(84.95%) was higher than that inO. taihangensis(80.45%). A certain genetic differentiation among populations inO. taihangensiswas found (Gst=0.2740,Φst=0.196) and genetic differentiation inO. longilobuswas very small (Gst=0.1034,Φst=0.151). Gene flow in different degrees (Nm=1.325and 4.336, resp.) and mating system can form the existing genetic structures of these two species. Furthermore, genetic differentiation coefficient (Gst=0.0453) between species and the clustering result based on the genetic distance showed that interspecific differentiation betweenO. taihangensisandO. longilobuswas not significant and could occur lately.

Prominent genetic structure across native and introduced ranges of Pluchea indica, a mangrove associate, as revealed by microsatellite markers

2020 ◽  
Vol 13 (3) ◽  
pp. 341-353
Author(s):  
Yuting Lin ◽  
Achyut Kumar Banerjee ◽  
Haidan Wu ◽  
Fengxiao Tan ◽  
Hui Feng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Spatial Scales ◽  
Large Spatial Scale ◽  
Introduced Range ◽  
Native And Introduced Ranges ◽  
Mangrove Associate

Abstract Aims Pluchea indica is a mangrove-associate species, known for its medicinal properties in its native range and being invasive in part of its introduced range. This study aimed to assess geographic distribution of genetic variation of this species across its distribution range, identify the factors influencing its genetic structure and use this information to suggest conservation and management strategies in its native and introduced ranges, respectively. Methods We assessed the genetic diversity and population structure of 348 individuals from 31 populations across its native (Asia) and introduced (USA) ranges for 15 nuclear microsatellite loci. The spatial pattern of genetic variation was investigated at both large and regional spatial scales with the hypothesis that geographic distance and natural geographic barriers would influence the population structure with varying levels of differentiation across spatial scales. Important Findings We found relatively high genetic diversity at the population level and pronounced genetic differentiation in P. indica, as compared with the genetic diversity parameters of mangroves and mangrove associates in this region. Most of the populations showed heterozygote deficiency, primarily due to inbreeding and impediment of gene flow. Analysis of population structures at large spatial scale revealed the presence of two major clusters across the species’ natural range separating populations in China from those in Indonesia, Malaysia, Singapore, Thailand, Cambodia and Philippines, and that the USA population might have been introduced from the population cluster in China. Genetic differentiation between populations was also observed at the regional scale. A large number of populations showed evidence of genetic bottleneck, thereby emphasizing the risk of local extinction. Based on these findings, our study recommends in situ conservation strategies, such as to prioritize populations for conservation actions and to maintain genetic diversity.

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