scholarly journals Population Genetics Revealed a New Locus That Underwent Positive Selection in Barley

2019 ◽  
Vol 20 (1) ◽  
pp. 202 ◽  
Author(s):  
Stephan Reinert ◽  
Alina Osthoff ◽  
Jens Léon ◽  
Ali Ahmad Naz
Keyword(s):  
Population Genetics ◽  
Positive Selection ◽  
Wild Barley ◽  
Diversity Index ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Outlier Locus ◽  
Evolutionary Forces ◽  
Outlier Loci ◽  
Significant Difference

Trait variation among natural populations and their cultivated relatives occurs due to evolutionary forces, including selection and drift. In the present study, we analyzed these forces at the locus level in a global barley diversity set using population genetics analysis. Genome-wide outlier loci detection found a locus on chromosome 2H at which a common single nucleotide polymorphism (SNP) marker SCRI_RS_170235 accounted for the highest diversity index (Fst) values between cultivars and landraces and between cultivars and wild accessions. For a population wide genetic analysis, we developed a Polymerase Chain Reaction (PCR)-based cleaved amplified polymorphic marker at the identified locus. Marker genotyping of 115 genotypes identified a characteristic distribution of polymorphisms among the cultivated, landraces, and wild barley accessions. Using this marker, we screened a library of wild barley introgression lines (IL) and selected IL S42IL-109 that carried the wild introgression of the outlier locus in cultivar ‘Scarlett’ background. A plethora of phenotypic evaluation was performed between the S42IL109 and ‘Scarlett’ to dissect the putative effect of the identified outlier locus. Comparison of S42IL109 and ‘Scarlett’ revealed significant difference in the development of phyllochron two (Phyl-2), phyllochron three (Phyl-3), and phyllochron four (Phyl-4). Across the three phyllochrons, it was consistently observed that S42IL109 developed successive leaves in a shorter time span, by one to two days, compared to ‘Scarlett’. These data suggest that outlier locus may influence phyllochron variation which underwent positive selection in barley.

Assemblage Patterns of Hymenoptera at Different Elevations of Gunung Datuk, Rembau

2017 ◽  
Vol 14 (2) ◽  
pp. 1 ◽  
Author(s):  
Noor Nasuha Abd Aziz ◽  
Siti Khairiyah Mohd Hatta ◽  
Idris Abd Ghani ◽  
Saiyid Jalaluddin Saiyid Shaifuddin
Keyword(s):  
Species Richness ◽  
Diversity Index ◽  
High Elevation ◽  
Significant Difference ◽  
Index Site ◽  
Evenness Index ◽  
Abundance And Diversity ◽  
Richness Index ◽  
Paired T Test ◽  
Malaise Traps

A study on abundance and diversity of Hymenoptera was conducted in Gunung Datuk, Rembau. Samplings were conducted from November 2014 to February 2015 using six Malaise traps. Three traps were placed at Site 1 at 700m height for high elevation and the remaining traps were placed at Site 2 at 200m height for low elevation. A total number of 221 Hymenopteran were collected which consist of nine families namely Ichneumonidae, Formicidae, Braconidae, Bethylidae, Evaniidae, Tiphiidae, Vespidae, Pompilidae and Apidae. In this study, 93 individuals were obtained from Site 1, comprising nine families and 43 morphospecies while 127 individuals were obtained from Site 2 with nine families and 45 morphospecies. Formicidae was the most dominant family collected from both sites with a total of 104 individuals while the least family recorded was Apidae with only one individual. Shannon’s Weiner Diversity Index (H’) showed Site 1 had the higher diversity value with H’ = 3.17 compared to Site 2 with value H’ = 3.12. For Evenness Index, Site 1 had higher value compared to Site 2 with E’ = 0.84 and E’ = 0.82 respectively. Moreover, for Margalef Richness Index, Site 1 recorded R’ = 9.24 while site two recorded R’ = 9.08 which concluded that Site 1 had higher species richness compared to Site 2. Paired t-test showed that both sites had no significant difference with p>0.05. Overall study showed that the diversity and abundance of Hymenoptera in Gunung Datuk were low since the value of H’ is less than 3.50.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

scholarly journals Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 667-677
Author(s):  
Hitoshi Araki ◽  
Nobuyuki Inomata ◽  
Tsuneyuki Yamazaki
Keyword(s):  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Natural Populations ◽  
Sliding Window ◽  
Selective Constraint ◽  
Proximal Region ◽  
Coding Regions ◽  
Asian Populations ◽  
Flanking Region

Abstract In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.

scholarly journals Effects of Ecological Restoration Using Non-Native Mangrove Kandelia obovata to Replace Invasive Spartina alterniflora on Intertidal Macrobenthos Community in Maoyan Island (Zhejiang, China)

2021 ◽  
Vol 9 (8) ◽  
pp. 788
Author(s):  
Qiuxuan Wang ◽  
Carlos Duarte ◽  
Li Song ◽  
George Christakos ◽  
Susana Agusti ◽  
...  
Keyword(s):  
Community Structure ◽  
Ecological Restoration ◽  
Spartina Alterniflora ◽  
Diversity Index ◽  
Invasion History ◽  
Kandelia Obovata ◽  
Wiener Diversity Index ◽  
Significant Difference ◽  
Spatial Differences ◽  
Average Biomass

Spartina alterniflora has extensively invaded the coastline of China, including in Maoyan Island of Zhejiang Province. Ecological restoration has been conducted using non-native mangrove Kandelia obovata to replace S. alterniflora in an attempt to restore the impacted intertidal zones. To illustrate the ecological effectiveness of the restoration projects, macrobenthos communities were studied among different habitats within the restored areas, including one non-restored S. alterniflora marsh (SA) and three differently-aged restored K. obovata stands planted in 2003, 2009, and 2011 respectively (KF14, KF8, and KF6). Besides, one unvegetated mudflat (MF) adjacent to the non-restored S. alterniflora marsh and one K. obovata forest transplanted in 2006 (RKF) at a previously barren mudflat without invasion history of S. alterniflora were set as reference sites. A total of 69 species of macrobenthos were collected from Maoyan Island, and the species richness was dominated by gastropoda (23 species), polychaeta (18 species), and malacostraca (16 species). There was no significant difference between the six sites in terms of the abundance of macrobenthos, with the average values of abundance peaking in KF6 (734.7 ind m−2) and being lowest in RKF (341.3 ind m−2). The six sites had significant differences in terms of the biomass of macrobenthos. The KF8 site contained the highest average biomass (168.3 g m−2), whereas the MF site had the lowest (54.3 g m−2). The Shannon-Wiener diversity index and Pielou’s evenness index of the macrobenthos did not exhibit significant differences among the six sites. However, the results of permutational multivariate analysis of variance (PERMANOVA) revealed significant spatial differences in the macrobenthos community structure between the sites. Since KF14 shared a similar macrobenthos community structure with RKF, while representing a strikingly different structure from SA, we infer that ecological restoration using K. obovata can restore the macrobenthos community to resemble to a normally planted K. obovata forest about 15 years after restoration.

scholarly journals piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions

2020 ◽  
Vol 12 (5) ◽  
pp. 736-749 ◽  
Author(s):  
Robert Kofler
Keyword(s):  
Population Genetics ◽  
Transposable Element ◽  
Minimum Size ◽  
Total Size ◽  
Evolutionary Forces ◽  
A Genome ◽  
In Trans ◽  
Single Insertion

Abstract piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. Moreover, larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high, and TE insertions are recessive. If piRNA clusters are too small, the load of deleterious TE insertions that accumulate during a TE invasion may drive populations extinct before an effective piRNA-based defense against the TE can be established. Our findings are solely based on three well-supported assumptions: 1) TEs multiply within genomes, 2) TEs are mostly deleterious, and 3) piRNA clusters act as transposon traps, where a single insertion in a cluster silences all TE copies in trans. Interestingly, the piRNA clusters of some species meet our observed minimum size requirements, whereas the clusters of other species do not. Species with small piRNA clusters, such as humans and mice, may experience severe fitness reductions during invasions of novel TEs, which is possibly even threatening the persistence of some populations. This work also raises the important question of how piRNA clusters evolve. We propose that the size of piRNA clusters may be at an equilibrium between evolutionary forces that act to expand and contract piRNA clusters.

scholarly journals The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens

2015 ◽  
Vol 25 (1) ◽  
pp. 42-66 ◽  
Author(s):  
Benjamin A. Wilson ◽  
Nandita R. Garud ◽  
Alison F. Feder ◽  
Zoe J. Assaf ◽  
Pleuni S. Pennings
Keyword(s):  
Drug Resistance ◽  
Population Genetics ◽  
Natural Populations ◽  
Resistance Evolution

scholarly journals Effects of grazing on plant species diversity and above ground biomass in a Trans- Himalayan Rangeland

1970 ◽  
Vol 17 (1) ◽  
pp. 25-31 ◽  
Author(s):  
Anita Pokharel ◽  
Madhu Chhetri ◽  
Chiranjibi P Upadhyaya
Keyword(s):  
Species Diversity ◽  
Species Composition ◽  
Plant Species ◽  
Diversity Index ◽  
Livestock Grazing ◽  
Above Ground Biomass ◽  
Ground Biomass ◽  
Grazing Effect ◽  
Significant Difference ◽  
Palatable Species

Limited information is available on the species composition, above ground biomass and its relations to grazing in a trans-Himalayan rangeland. Its assessment is essential for long term conservation and management. In the present study, we compared species composition, phenology, diversity index and biomass between controlled (without grazing) and open (free grazing) plots to assess the effects of grazing in the selected experimental sites of Upper Mustang during July and November 2005. Species encountered were classified as high, medium, low and non palatable and in three life form categories-grasses, shrubs and forbs. The experimental sites are dominated by forbs (80%) followed by grasses (15%) and shrubs (5%). Disturbance caused by grazing affects the phenological characteristics of the plant community. Result also reveals that species diversity, maximum possible diversity, evenness and species richness was higher in the grazed plots during July and November. A comparison of the aboveground biomass in July showed that mean percentage biomass of high, medium and low palatable species is higher in ungrazed plots. In November, the percentage biomass of only medium palatable species was higher in ungrazed plots and rest of the category is higher in grazed plots. Significant difference in July, a peak growing seasons for most of the plant species in the region reveals that the pasture has impact of livestock grazing. Keywords: Biomass, diversity, grazing effect, rangeland, species Banko Janakari: A journal of forestry information for Nepal Vol.17(1) 2007 pp.25-31

scholarly journals Using neutral and outlier loci to uncover the genetic structure of 'Mytilus galloprovincialis' populations from the eastern Adriatic coast using population genetic and seascape genetic approaches

2021 ◽  
Author(s):  
◽  
Joanna Szondy Hamilton
Keyword(s):  
Genetic Structure ◽  
Mytilus Galloprovincialis ◽  
Blue Mussel ◽  
Strong Association ◽  
Outlier Locus ◽  
Outlier Loci ◽  
Adriatic Coast ◽  
Low Levels ◽  
Polymorphic Microsatellite ◽  
Highly Correlated

<p>The genetic variation of the Mediterranean blue mussel, Mytilus galloprovincialis from the eastern coastline of the Adriatic Sea was investigated using polymorphic microsatellite markers. In total, 843 individuals were sampled from 18 populations representing a variety of coastal environments in Croatia, Bosnia-Herzegovina, Montenegro and Albania. Neutral loci revealed low levels of genetic structure in this continuously distributed species, while one outlier locus, MGE7, which may be under selection, provided strong evidence of genetic structure. The distribution of one of the alleles of this locus, MGE7²⁴³, was significantly correlated with latitude. A genetic seascape analysis using 9 environmental and 3 geospatial variables revealed a strong association between MGE7²⁴³ and three highly correlated environmental variables, maximum sea surface temperature, minimum salinity and maximum chlorophyll-a. This association was maintained for homozygous genotypes for the MGE7²⁴³ allele, but not for heterozygotes, providing further evidence that the locus MGE7 may be under selection or closely linked to a gene under selection. These findings highlight how previously unrecognised genetic structure can be identified through the use of genetic seascape approaches.</p>

scholarly journals Intraspecific variation in symbiont density in an insect-microbe symbiosis

2020 ◽  
Author(s):  
Benjamin J. Parker ◽  
Jan Hrček ◽  
Ailsa H.C. McLean ◽  
Jennifer A. Brisson ◽  
H. Charles J. Godfray
Keyword(s):  
Intraspecific Variation ◽  
Fungal Pathogens ◽  
Acyrthosiphon Pisum ◽  
Natural Populations ◽  
Pea Aphid ◽  
Optimal Density ◽  
Evolutionary Forces ◽  
Standing Variation ◽  
Dramatic Decline

AbstractMany insects host vertically-transmitted microbes, which can confer benefits to their hosts but are costly to maintain and regulate. A key feature of these symbioses is variation: for example, symbiont density can vary among host and symbiont genotypes. However, the evolutionary forces maintaining this variation remain unclear. We studied variation in symbiont density using the pea aphid (Acyrthosiphon pisum) and the bacterium Regiella insecticola, a symbiont that can protect its host against fungal pathogens. We found that relative symbiont density varies both between two Regiella phylogenetic clades and among aphid ‘biotypes’. Higher-density symbiont infections are correlated with stronger survival costs, but variation in density has little effect on the protection Regiella provides against fungus. Instead, we found that in some aphid genotypes, a dramatic decline in symbiont density precedes the loss of a symbiont infection. Together, our data suggest that the optimal density of a symbiont infection is likely different from the perspective of aphid and microbial fitness. Regiella might prevent loss by maintaining high within-host densities, but hosts do not appear to benefit from higher symbiont numbers and may be advantaged by losing costly symbionts in certain environments. The standing variation in symbiont density observed in natural populations could therefore be maintained by antagonistic coevolutionary interactions between hosts and their symbiotic microbes.

scholarly journals Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm

2019 ◽  
Author(s):  
Kiwoong NAM ◽  
Sandra Nhim ◽  
Stéphanie Robin ◽  
Anthony Bretaudeau ◽  
Nicolas Nègre ◽  
...  
Keyword(s):  
Positive Selection ◽  
Driving Force ◽  
Migration Rate ◽  
Early Stage ◽  
Fall Armyworm ◽  
Whole Genome ◽  
Low Level ◽  
Evolutionary Forces ◽  
Genome Differentiation ◽  
Genetic Linkages

Abstract Background: The process of speciation inherently involves the transition from genetic to genomic differentiation. In the absence of a geographic barrier, the whole genome differentiation may occur only when the homogenizing effect of recombination is overcome across the whole genome. The fall armyworm is observed as two sympatric strains with different host-plant preferences across the entire habitat. These two strains exhibit a very low level of genetic differentiation across the whole genome, suggesting that whole genome differentiation occurred at an early stage of speciation. In this study, we aim at identifying critical evolutionary forces responsible for the whole genome differentiation in the fall armyworm. Results: We found that these two strains exhibit a low level of genomic differentiation (Fst = 0.0176), while 91.3% of 10kb windows have genetically differentiated sequences (Fst > 0). We observed that a genomic reduction in migration rate due to combined effects of mild positive selection and genetic linkages to selectively targeted loci are responsible for the whole genome differentiation. Phylogenetic analysis shows that positive selection generates the whole genome differentiation by sub-setting of variants in one strain from the other. Conclusions: From these results, we concluded that positive selection alone is sufficient for whole genome differentiation during the process of speciation. This study demonstrates that the propensity of adaptation alone determines the speciation events, suggesting that adaptive evolution is a single critical driving force for species diversity.

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