SSR Based Genetic Diversity Analysis in Diploid Algaroba (Prosopis spp.) Population

Algaroba (Prosopis palida and Prosopis juliflora species) provides important environmental and economic benefits for semi-arid regions of the world. These are resistant to drought, and its fruits are used in the manufacture of flour and algarobina syrup. In the present study, the chromosome number, the ploidy level, and the genetic diversity based on 40 microsatellite loci of Prosopis spp. were determined in samples of a Brazilian algaroba population. The cytogenetic analysis in the metaphase showed only diploid individuals (2n = 28), with multiple cells featuring two CMA3/DAPI- heterochromatic blocks suggesting diploid level. However, polysomatism was found by the presence of some cells with four CMA3/DAPI- blocks, showing the tetraploid level just in some somatic cells. Among all of the primers tested for cross-amplification in algaroba, 22 were selected to characterize the samples. Thirteen loci revealed allele polymorphisms in the population and are recommended for future population studies and genetic improvement. The mean values of the analyzes showed low genetic diversity (two alleles per locus and HE = 0.181), reflecting the history of the introduction of algaroba in this sampled locality, and suggesting the genetic bottleneck and probable events of founders, as well as the characteristics of the species of this genera. However, amplified loci indicated low inbreeding (allelic fixation index of -0.007), although heterozygosis was higher than expected by the Hardy-Weinberg equilibrium. Therefore, this algaroba population is formed by diploid individuals and adjusts to the tendency of low number of alleles per locus SSR commonly observed in different species of Prosopis.

Download Full-text

Intraspecific differentiation of Reed Grass Calamagrostis arundinacea (L.) Roth (Poaceae) populations revealed by peroxidase allozymes

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.2008.038 ◽

2011 ◽

Vol 77 (4) ◽

pp. 299-304

Author(s):

Maria Krzakowa ◽

Zbigniew Celka

Keyword(s):

Genetic Diversity ◽

Genetic Parameters ◽

Electrophoretic Analysis ◽

Fixation Index ◽

Mean Values ◽

Interpopulation Variability ◽

Total Genetic Diversity ◽

Variability Level ◽

Hardy Weinberg Equilibrium ◽

Geographic Regions

The genetic Variation of Reed Grass <em>Calamagrostis arundinacea</em> (L.) Roth was investigated in 25 populations in various geographic regions of Poland. A total of 907 individuals were sampled for electrophoretic analysis of peroxidase loci (11 allozymes). Populations were characterised by genetic parameters e.g. heterozygosity level, Wright's fixation index (F) and polymorphism coefficient (Pg). Mean values of interpopulation variability level (GST=0.0310), total genetic diversity (HT=0.4102) and gene flow between populations (Nm=7.805) were also examined. All the populations were polymorphic and they remain in Hardy Weinberg equilibrium.

Download Full-text

Season of birth interacts with measures of inbreeding in multiplex schizophrenia pedigrees: evidence from genetic isolates in Daghestan

Open Medicine ◽

10.2478/s11536-006-0041-8 ◽

2006 ◽

Vol 1 (4) ◽

pp. 392-398

Author(s):

Kazima Bulayeva ◽

John McGrath

Keyword(s):

Genetic Diversity ◽

Family History ◽

Age Of Onset ◽

Population Genetic Study ◽

Season Of Birth ◽

High Genetic Diversity ◽

Low Genetic Diversity ◽

High Prevalence ◽

History Of ◽

Genetic Isolates

AbstractWhile the season-of-birth effect is one of the most consistent epidemiological features of schizophrenia, there is a lack of consistency with respect to the interaction between season of birth and family history of schizophrenia. Apart from family history, measures related to consanguinity can be used as proxy markers of genomic heterogeneity. Thus, these measures may provide an alternate, indirect index of genetic susceptibility. We had the opportunity to explore the interaction between season of birth and measure of consanguinity in well-described genetic isolates in Daghestan, some of which are known for their relatively high prevalence of schizophrenia. Our previous population-genetic study showed Daghestan has an extremely high genetic diversity between the ethnic populations and a low genetic diversity within them. The isolates selected for this study include some with more than 200 and some with less than 100 generations of demographical history since their founding. Based on pedigrees of multiply-affected families, we found that among individuals with schizophrenia, the measure of consanguinity was significantly higher in the parents of those born in winter/spring compared to those born in summer/autumn. Furthermore, compared to summer/autumn born, winter/spring born individuals with schizophrenia had an earlier age-of-onset, and more prominent auditory hallucinations. Our results suggest that the offspring of consanguineous marriages, and thus those with reduced allelic heterogeneity, may be more susceptible to the environmental factor(s) underpinning the season-of-the effect in schizophrenia.

Download Full-text

No Evidence of Low Genetic Diversity Despite High Levels of Inbreeding and Poor Genetic Connectivity Among Tetrastigma loheri (Vitaceae) Populations in Remaining Forest Areas in Cebu, Philippines

Systematic Botany ◽

10.1600/036364421x16370109698614 ◽

2021 ◽

Vol 46 (4) ◽

pp. 951-961

Author(s):

Jasper John A. Obico ◽

Hemres Alburo ◽

Julie F. Barcelona ◽

Marie Hale ◽

Lisa Paguntalan ◽

...

Keyword(s):

Genetic Diversity ◽

Habitat Fragmentation ◽

Tropical Forests ◽

Forest Cover ◽

Genetic Connectivity ◽

Philippine Island ◽

Low Genetic Diversity ◽

History Of ◽

Gap Data ◽

The Impact

Abstract— Little is known about the effects of habitat fragmentation on the patterns of genetic diversity and genetic connectivity of species in the remaining tropical forests of Southeast Asia. This is particularly evident in Cebu, a Philippine island that has a long history of deforestation and has lost nearly all of its forest cover. To begin filling this gap, data from 13 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common vine species in Philippine forests, were used to study patterns of genetic diversity and genetic connectivity for the four largest of the remaining forest areas in Cebu. Evidence of relatively high levels of inbreeding was found in all four areas, despite no evidence of low genetic diversity. The four areas are genetically differentiated, suggesting low genetic connectivity. The presence of inbreeding and low genetic connectivity in a commonly encountered species such as T. loheri in Cebu suggests that the impact of habitat fragmentation is likely greater on rare plant species with more restricted distributions in Cebu. Conservation recommendations for the remaining forest areas in Cebu include the establishment of steppingstone corridors between nearby areas to improve the movement of pollinators and seed dispersers among them.

Download Full-text

Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

Israel Journal of Ecology and Evolution ◽

10.1163/22244662-20191081 ◽

2020 ◽

Vol 66 (3-4) ◽

pp. 142-150

Author(s):

Jessica Worthington Wilmer ◽

Andrew P. Amey ◽

Carmel McDougall ◽

Melanie Venz ◽

Stephen Peck ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

The West ◽

European Settlement ◽

Low Genetic Diversity ◽

Eastern Australia ◽

Wide Range ◽

History Of ◽

Open Forests ◽

Fossorial Species

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

Download Full-text

Evolution of the U.S. Biological Select AgentRathayibacter toxicus

mBio ◽

10.1128/mbio.01280-18 ◽

2018 ◽

Vol 9 (4) ◽

Cited By ~ 6

Author(s):

Edward W. Davis ◽

Javier F. Tabima ◽

Alexandra J. Weisberg ◽

Lucas Dantas Lopes ◽

Michele S. Wiseman ◽

...

Keyword(s):

Genetic Diversity ◽

Adaptive Immune System ◽

The United States ◽

Genomic Diversity ◽

Data Set ◽

Important Species ◽

Content Type ◽

Low Genetic Diversity ◽

History Of ◽

Short Palindromic Repeat

ABSTRACTRathayibacter toxicusis a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution ofR. toxicusto explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy ofRathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequencedRathayibactergenomes indicated thatRathayibacterforms nine species-level groups.R. toxicusis the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover,R. toxicushas low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates.R. toxicusis the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of theR. toxicusspecies.IMPORTANCERathayibacter toxicusis a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makesR. toxicusa highly regulated species. This work provides novel insights into the evolution ofR. toxicus.R. toxicusis the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of theR. toxicusgenome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.

Download Full-text

New data on the genetic diversity of European bison Bison bonasus (Linnaeus, 1758) in Belarus

Theriologia Ukrainica ◽

10.15407/tu1905 ◽

2020 ◽

Vol 2020 (19) ◽

pp. 45-53

Author(s):

Kanstantsin V. Homel ◽

◽

K. Śliwińska ◽

Arseni A. Valnisty ◽

Mikhail E. Nikiforov ◽

...

Keyword(s):

Genetic Diversity ◽

National Park ◽

Bison Bison ◽

Fixation Index ◽

European Bison ◽

Bison Bonasus ◽

Genetic Structuring ◽

The Past ◽

Low Genetic Diversity ◽

Expected Heterozygosity

The paper presents data on the assessment of the genetic diversity of five subpopulations of the European bison (Bison bonasus) in Belarus — from the National Park “Belovezhskaya Pushcha”, the National Park “Pripyatsky”, the Osipovichi district (Mogilev area), SEI “Berezinsky Biosphere Reserve” and the Grodno region. In general, the work includes 30 samples of muscle tissue from the collection of Gene bank of wild fauna in SSPA “SPC NAS of Belarus on Bioresources” (Minsk, Belarus). Microsatellites were used as markers to assess genetic diversity, structure, and search for signs of a sharp decline in the size of bison subpopulations in the past. A total of 11 microsatellite markers were used, recommended by the Food and Agriculture Organization of the United Nations for cattle research. The analysis of B. bonasus subpopulation from the NP “Pripyatsky” showed signs of passing through the genetic bottleneck. All studied subpopulations are characterized by a similarly low genetic diversity level in all analyzed indicators (mean number of alleles, allelic diversity, observed and expected heterozygosity). The expected heterozygosity (He) for the three subpopulations from the NP “Belovezhskaya Pushcha”, the NP “Pripyatsky” and from the Osipovichi district ranged from 0.37 to 0.39. For the studied subpopulations, the values of the fixation index were negative. The assessment of the presence of genetic structuring between the subpopulations of bison from the NP “Belovezhskaya Pushcha”, the NP “Pripyatsky” and from the Osipovichi district based on the values of such indexes as Fst and DJost which showed no signs of genetic differentiation, which is also confirmed by principal coordinates analysis (PCoA). The European bison conservation in Belarus has required tremendous efforts in the past. So far, even though the impressively large population size reached in Belarus, B. bonasus status still should not be considered as stable, which is closely linked to aspects of its overall low genetic diversity. Our research confirmed the low genetic variability of Belarusian subpopulations. Therefore, the more extensive research concentrated on identifying genetic diversity is necessary to ensure the beneficial control of gene flow and register a potential correlation of unfavorable gene variants with possible inbreeding depression. These attempts are required to lay the groundwork for the management and protection of the European bison in Belarus.

Download Full-text

Low Genetic Diversity in Wide-Spread Eurasian Liver Fluke Opisthorchis felineus Suggests Special Demographic History of This Trematode Species

10.18411/a-2017-114 ◽

2017 ◽

Keyword(s):

Genetic Diversity ◽

Liver Fluke ◽

Demographic History ◽

Trematode Species ◽

Wide Spread ◽

Opisthorchis Felineus ◽

Low Genetic Diversity ◽

History Of

Download Full-text

European Vintage tomatoes galore: a result of farmers combinatorial assorting/swapping of a few diversity rich loci

10.1101/2021.10.26.465840 ◽

2021 ◽

Author(s):

Jose Blanca ◽

Clara Pons ◽

Javier Montero-Pau ◽

David Sanchez-Matarredona ◽

Peio Ziarsolo ◽

...

Keyword(s):

Genetic Diversity ◽

Morphological Traits ◽

Balancing Selection ◽

Genotyping By Sequencing ◽

Polymorphic Loci ◽

Comprehensive Collection ◽

Low Genetic Diversity ◽

Genetic Groups ◽

History Of ◽

Modern Varieties

A comprehensive collection of 1,254 tomato accessions corresponding to European heirlooms and landraces, together with modern varieties, early domesticates and wild relatives, were analyzed by genotyping by sequencing. A continuous genetic gradient between the vintage and modern varieties was observed. European vintage tomatoes displayed very low genetic diversity, with only 298 loci out of 64,943 variants being polymorphic at the 95% threshold. European vintage tomatoes could be classified in several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed a higher genetic diversity than the rest varieties, suggesting that these regions might be independent secondary centers of diversity and with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a GWAS with fruit morphological traits in the European vintage collection, and the corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise diversity-poor genome suggests a history of balancing selection, in which tomato farmers maintained the morphological variation by applying a high selective pressure within different varietal types.

Download Full-text

Assessing Evolutionary Significant Units (ESU) of the Endangered Freshwater Pearl Mussel (Margaritifera margaritifera) in Southeast Norway on the Basis of Genetic Analysis

Genes ◽

10.3390/genes11091061 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1061

Author(s):

Arne N. Linløkken ◽

Silje Garlie ◽

Wenche Johansen ◽

Robert C. Wilson

Keyword(s):

Genetic Diversity ◽

Salmo Trutta ◽

Margaritifera Margaritifera ◽

River Systems ◽

Pearl Mussel ◽

Freshwater Pearl Mussel ◽

Recruitment Failure ◽

Low Genetic Diversity ◽

Brown Trout Salmo Trutta ◽

Hardy Weinberg Equilibrium

A total of 312 specimens of freshwater pearl mussel (Margaritifera margaritifera) were sampled from 11 populations, located in four different river systems in Southeast Norway, and analyzed for 11 simple sequence repeat (SSR) (microsatellite) markers. All study populations have landlocked brown trout (Salmo trutta) as the only possible host. Several populations had experienced recruitment failure, probably due to low pH (about 6.0) and calcium concentration. STRUCTURE clustering analysis revealed two genetic clusters, of which one cluster occurred mainly in the western river systems, and totally dominated in one population (Fallselva (A-FAL)) that had higher genetic diversity than the others. Cluster 2 completely dominated in the populations of the eastern river systems, and all of them had low genetic diversity. Bottleneck events were indicated in all populations and the inbreeding coefficient FIS was significant in all populations, except for the southernmost population (Sørkedalselva (B-SØR)), which was the only population with genotypes in Hardy–Weinberg equilibrium. FIS were especially high in the populations of the eastern river systems, and maximum shell length was negatively correlated to FIS. If artificially breeding and stocking should become necessary for future preservation, it should be based on single populations; alternatively, the eastern populations should be based on cross-breeding of populations within the cluster to increase their genetic diversity.

Download Full-text