scholarly journals A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

2015 ◽  
Author(s):  
Adam Kuester ◽  
Ariana Wilson ◽  
Shu-mei Chang ◽  
Regina S. Baucom
Keyword(s):  
Genetic Diversity ◽  
Ecological Impact ◽  
Allelic Diversity ◽  
Agricultural Fields ◽  
Evolutionary Mechanisms ◽  
Heterozygosity Excess ◽  
Neutral Genetic Diversity ◽  
Agricultural Weed ◽  
Noxious Weed ◽  
Greenhouse Assay

AbstractDespite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection ecology approach and compare the genetic and phenotypic divergence of temporally sampled seed progenies of Ipomoeapurpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs 2012), suggesting that populations of this species sampled from agricultural fields have experienced genetic bottleneck events that have led to lower neutral genetic diversity. Heterozygosity excess tests indicate that this bottleneck may have occurred prior to 2003. Further, a greenhouse assay of individuals sampled from the field as seed found that populations of this species, on average, exhibited modest increases in herbicide resistance over time. Our results show that populations of this noxious weed, capable of adapting to strong selection imparted by herbicide application, may lose genetic variation as a result of this or other environmental factors. We likely uncovered only modest increases in resistance between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that non-resistant migrants germinate from the seed bank.

Is neutral genetic diversity related to quantitative variation in semen traits in bulls?

2021 ◽  
Author(s):  
Eddington Gororo ◽  
Fungayi Primrose Chatiza ◽  
Farisai Chidzwondo ◽  
Stanley Marshall Makuza
Keyword(s):  
Genetic Diversity ◽  
Quantitative Variation ◽  
Neutral Genetic Diversity

scholarly journals Allelic diversity in populations of Solanum lycocarpum A. St.-Hil (Solanaceae) in a protected area and a disturbed environment

2011 ◽  
Vol 25 (4) ◽  
pp. 937-940 ◽  
Author(s):  
Tânia Maria de Moura ◽  
Alexandre Magno Sebbenn ◽  
Karina Martins ◽  
Maria Andreia Moreno ◽  
Giancarlo Conde Xavier Oliveira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Protected Areas ◽  
Allelic Diversity ◽  
Rare Allele ◽  
Conservation Unit ◽  
Long Distance ◽  
Disturbed Area ◽  
Disturbed Areas ◽  
Pasture Area ◽  
Two Populations

This study aimed to compare the genetic diversity of populations of Solanum lycocarpum A.St.-Hil between natural and human disturbed environments, with the assumption that protected areas have greater genetic diversity than disturbed areas. For this study, two populations were sampled in Goiás State, Brazil. One was located in a conservation unit, Serra de Caldas Novas State Park, in the Caldas Novas municipality. The other was located in a pasture area in the municipality of Morrinhos. The two populations are 41 km apart. We sampled 60 individuals from each population, which were genotyped with five microsatellite loci (SSR). The highest number of alleles was recorded in the population of the conservation unit, where we found 11 exclusive and five rare alleles. In the disturbed area, we recorded only three exclusive alleles and one rare allele. Although we did not observe significant inbreeding in these populations, genetic divergence between them was high (G ST (Hedrick)=0.147 =0.147) for a species with long distance seed dispersal. The results corroborate the hypothesis that the population in the less disturbed area harbors greater allelic diversity. They also confirm the effectiveness of using protected areas to preserve the genetic diversity of the species.

scholarly journals High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Amali Malshani Samaraweera ◽  
Ranga Liyanage ◽  
Mohamed Nawaz Ibrahim ◽  
Ally Mwai Okeyo ◽  
Jianlin Han ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sri Lanka ◽  
Microsatellite Markers ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Population Substructure ◽  
High Genetic Diversity ◽  
Naked Neck ◽  
Local Chicken ◽  
Local Chickens

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

scholarly journals Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems

2020 ◽  
Author(s):  
Danny Ionescu ◽  
Luca Zoccarato ◽  
Artur Zaduryan ◽  
Sina Schorn ◽  
Mina Bizic ◽  
...  
Keyword(s):  
Species Concept ◽  
Single Cells ◽  
Bacterial Species ◽  
Expression Patterns ◽  
Allelic Diversity ◽  
Evolutionary Mechanisms ◽  
Genomic Features ◽  
Bacterial Speciation ◽  
Depth Ranges ◽  
Functional Versatility

Abstract Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

Intact genetic structure and high levels of genetic diversity in bottlenecked sockeye salmon (Oncorhynchus nerka) populations of the Fraser River, British Columbia, Canada

2000 ◽  
Vol 57 (10) ◽  
pp. 1985-1998 ◽  
Author(s):  
Ruth E Withler ◽  
Khai D Le ◽  
R John Nelson ◽  
Kristina M Miller ◽  
Terry D Beacham
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Allelic Diversity ◽  
Lower Proportion ◽  
Fraser River ◽  
Rare Alleles ◽  
Genetic Bottlenecks

Analysis of six microsatellite loci in 5800 sockeye salmon (Oncorhynchus nerka) from 29 Fraser River populations provided little evidence of genetic bottlenecks or mass straying in upper Fraser sockeye salmon resulting from reduced abundances following 1913-1914 rockslides in the Fraser canyon and successive decades of high exploitation. Upper Fraser populations were not characterized by a paucity of rare alleles, a sensitive indicator of populations in which effective size has been recently reduced. Heterozygosity and allelic diversity did not differ consistently between lower and upper Fraser populations. Throughout the watershed, early-migrating populations had lower allelic diversity and a lower proportion of rare alleles than did late-migrating ones. Genetic differentiation between upper and lower Fraser populations and heterogeneity among lower Fraser populations supported the suggestion that Fraser sockeye salmon are descendants of at least two postglacial "races." Variation among lakes within regions was the strongest component of genetic structure, accounting for five times the variation among populations within lakes and more than two times the variation among regions. Extensive historical transplants of eggs and juveniles apparently resulted in lit tle gene flow among regions, but three populations were reestablished or rebuilt as the result of more recent transplants.

Spatial and temporal genetic diversity of the Texas kangaroo rat, Dipodomys elator (Rodentia: Heteromyidae)

2019 ◽  
Vol 100 (4) ◽  
pp. 1169-1181 ◽  
Author(s):  
Russell S Pfau ◽  
Jim R Goetze ◽  
Robert E Martin ◽  
Kenneth G Matocha ◽  
Allan D Nelson
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
Allelic Diversity ◽  
Effective Population ◽  
Kangaroo Rat ◽  
Time Periods ◽  
Mtdna Diversity ◽  
Using Data

Abstract The Texas kangaroo rat (Dipodomys elator) is listed as a threatened species in Texas because of its scarcity and small geographic range. We assessed patterns of genetic diversity in D. elator that could affect extinction risk or influence management decisions. Specific objectives included: 1) document levels of genetic diversity, 2) document the degree and patterns of genetic divergence among localities, and 3) compare levels of genetic diversity between different time periods at the same locality. Portions of the mitochondrial genome (mtDNA; control region, cytochrome c oxidase subunit I, and cytochrome b) were sequenced and nuclear microsatellites were examined. Low mtDNA diversity was observed, which could be explained by an historical, species-wide genetic bottleneck. In contrast, microsatellites exhibited ample variation, and analyses were conducted using data from 11 loci and four populations (designated Quanah, Iowa Park, Vernon, and Harrold). Allelic diversity and heterozygosity were similar between populations and temporal samples. Estimates of effective population size (Ne) ranged from 5 to 856, depending on method and population, with Iowa Park showing consistently lower values than Quanah. All methods addressing population structure indicated that the Iowa Park population was divergent from the others, with Vernon and Harrold showing a somewhat intermediate relationship but with a closer affiliation with Quanah than Iowa Park, despite their closer proximity to Iowa Park. This pattern did not conform to isolation by distance, thus genetic drift appears to have played a greater role than gene flow in establishing genetic structure. There was much less difference between temporal samples compared to geographic samples, indicating that genetic drift has had only minimal impacts in shifting allelic frequencies over the time periods examined (17–36 years).

scholarly journals Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

2012 ◽  
Vol 37 (3) ◽  
pp. 389-398 ◽  
Author(s):  
S Islam ◽  
MS Haque ◽  
RM Emon ◽  
MM Islam ◽  
SN Begum
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Triticum Aestivum L ◽  
Allele Number ◽  
Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

scholarly journals A unified approach to characterize and conserve adaptive and neutral genetic diversity in subdivided populations

2014 ◽  
Vol 96 ◽  
Author(s):  
ROBIN WELLMANN ◽  
JÖRN BENNEWITZ ◽  
THEO H. E. MEUWISSEN
Keyword(s):  
Genetic Diversity ◽  
Large Range ◽  
Simulated Data ◽  
Time Span ◽  
Unified Approach ◽  
Neutral Genetic Diversity ◽  
Adaptive Diversity ◽  
Subdivided Populations ◽  
Conservation Values ◽  
Conservation Decisions

SummaryAs extinction of local domestic breeds and of isolated subpopulations of wild species continues, and the resources available for conservation programs are limited, prioritizing subpopulations for conservation is of high importance to halt the erosion of genetic diversity observed in endangered species. Current approaches usually only take neutral genetic diversity into account. However, adaptation of subpopulations to different environments also contributes to the diversity found in the species. This paper introduces two notions of adaptive variation. The adaptive diversity in a trait is the excess of variance found in genotypic values relative to the variance that would have been expected in the absence of selection. The adaptivity coverage of a set of subpopulations quantifies how well the subpopulations could adapt to a large range of environments within a limited time span. Additionally, genome-based notions of neutral diversities were obtained that correspond to well known pedigree-based definitions. The values of subpopulations for conservation of adaptivity coverage were compared with their conservation values for adaptive diversity and neutral diversities using simulated data. Conservation values for adaptive diversity and neutral diversities were only slightly correlated, but the values for conservation of adaptivity coverage showed a reasonable correlation with both kinds if the time span was chosen appropriately. Hence, maintaining adaptivity coverage is a promising approach to prioritize subpopulations for conservation decisions.

Landscape prerequisites for the survival of a modelled metapopulation and its neutral genetic diversity are affected by climate change

2011 ◽  
Vol 27 (2) ◽  
pp. 227-237 ◽  
Author(s):  
Marleen M. P. Cobben ◽  
Jana Verboom ◽  
Paul F. M. Opdam ◽  
Rolf F. Hoekstra ◽  
René Jochem ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Neutral Genetic Diversity
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