scholarly journals Population genetics and host specificity of Varroa destructor mites infesting eastern and western honeybees

2021 ◽  
Author(s):  
Zheguang Lin ◽  
Shuai Wang ◽  
Peter Neumann ◽  
Gongwen Chen ◽  
Paul Page ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Population Genetics ◽  
Population Structure ◽  
Genetic Structure ◽  
Host Specificity ◽  
Varroa Destructor ◽  
Reproductive Potential ◽  
Original Host ◽  
Globalized World ◽  
Mite Genus

AbstractIn a globalized world, parasites are often brought in contact with new potential hosts. When parasites successfully shift host, severe diseases can emerge at a large cost to society. However, the evolutionary processes leading to successful shifts are rarely understood, hindering risk assessment, prevention, or mitigation of their effects. Here, we screened populations of Varroa destructor, an ectoparasitic mite of the honeybee genus Apis, to investigate their genetic structure and reproductive potential on new and original hosts. From the patterns identified, we deduce the factors that influenced the macro- and microevolutionary processes that led to the structure observed. Among the mite variants identified, we found two genetically similar populations that differed in their reproductive abilities and thus in their host specificity. These lineages could interbreed, which represents a threat due to the possible increased virulence of the parasite on its original host. However, interbreeding was unidirectional from the host-shifted to the nonshifted native mites and could thus lead to speciation of the former. The results improve our understanding of the processes affecting the population structure and evolution of this economically important mite genus and suggest that introgression between shifted and nonshifted lineages may endanger the original host.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals Adaptive population structure shifts in invasive parasitic mites, Varroa destructor

2021 ◽  
Author(s):  
Arrigo Moro ◽  
Tjeerd Blacquière ◽  
Bjørn Dahle ◽  
Vincent Dietemann ◽  
Yves Le Conte ◽  
...  
Keyword(s):  
Population Structure ◽  
Varroa Destructor ◽  
Parasitic Mites

scholarly journals CHANGING POPULATION STRUCTURE THROUGH THE USE OF COMPOUND CHROMOSOMES

Genetics ◽  
1972 ◽  
Vol 72 (1) ◽  
pp. 183-186
Author(s):  
D Childress
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Theoretical Calculations ◽  
Population Cage ◽  
Insect Populations

ABSTRACT Theoretical calculations and population cage data are presented to illustrate the use of compound chromosomes to change the genetic structure of insect populations.

scholarly journals Whole-genome SNP analysis elucidates the genetic population structure and diversity of Acrocomia species

2020 ◽  
Author(s):  
Brenda G. Díaz ◽  
Maria I. Zucchi ◽  
Alessandro. Alves-Pereira ◽  
Caléo P. de Almeida ◽  
Aline C. L. Moraes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Structure ◽  
Genetic Relationships ◽  
Geographical Area ◽  
Taxonomic Classification ◽  
Genomic Diversity ◽  
Productive Capacity ◽  
Snp Analysis ◽  
Genetic Population

AbstractAcrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of seven species of Acrocomia including 117 samples of A. aculeata covering a wide geographical area of occurrence, using single nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS). The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

scholarly journals A differential expression of pyrethroid resistance genes in the malaria vector Anopheles funestus across Uganda is associated with patterns of gene flow

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0240743
Author(s):  
Maurice Marcel Sandeu ◽  
Charles Mulamba ◽  
Gareth D. Weedall ◽  
Charles S. Wondji
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Insecticide Resistance ◽  
Pyrethroid Resistance ◽  
Anopheles Funestus ◽  
Metabolic Resistance ◽  
Transcription Analysis ◽  
Genome Wide

Background Insecticide resistance is challenging the effectiveness of insecticide-based control interventions to reduce malaria burden in Africa. Understanding the molecular basis of insecticides resistance and patterns of gene flow in major malaria vectors such as Anopheles funestus are important steps for designing effective resistance management strategies. Here, we investigated the association between patterns of genetic structure and expression profiles of genes involved in the pyrethroid resistance in An. funestus across Uganda and neighboring Kenya. Methods Blood-fed mosquitoes An. funestus were collected across the four localities in Uganda and neighboring Kenya. A Microarray-based genome-wide transcription analysis was performed to identify the set of genes associated with permethrin resistance. 17 microsatellites markers were genotyped and used to establish patterns of genetic differentiation. Results Microarray-based genome-wide transcription profiling of pyrethroid resistance in four locations across Uganda (Arua, Bulambuli, Lira, and Tororo) and Kenya (Kisumu) revealed that resistance was mainly driven by metabolic resistance. The most commonly up-regulated genes in pyrethroid resistance mosquitoes include cytochrome P450s (CYP9K1, CYP6M7, CYP4H18, CYP4H17, CYP4C36). However, expression levels of key genes vary geographically such as the P450 CYP6M7 [Fold-change (FC) = 115.8 (Arua) vs 24.05 (Tororo) and 16.9 (Kisumu)]. In addition, several genes from other families were also over-expressed including Glutathione S-transferases (GSTs), carboxylesterases, trypsin, glycogenin, and nucleotide binding protein which probably contribute to insecticide resistance across Uganda and Kenya. Genotyping of 17 microsatellite loci in the five locations provided evidence that a geographical shift in the resistance mechanisms could be associated with patterns of population structure throughout East Africa. Genetic and population structure analyses indicated significant genetic differentiation between Arua and other localities (FST>0.03) and revealed a barrier to gene flow between Arua and other areas, possibly associated with Rift Valley. Conclusion The correlation between patterns of genetic structure and variation in gene expression could be used to inform future interventions especially as new insecticides are gradually introduced.

Reply to the comment by Morales et al. on “Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species”

2021 ◽  
pp. 423-432
Author(s):  
C.L. Lausen ◽  
Michael F. Proctor ◽  
David Paetkau ◽  
David W. Nagorsen ◽  
Purnima Govindarajulu ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Single Species ◽  
Distinct Species ◽  
Background Information ◽  
Distribution Data ◽  
Supporting Evidence ◽  
Post Mortem ◽  
The Impact ◽  
New Evidence

A.E. Morales et al. (2021. Can. J. Zool. 99(5): 415–422) provided no new evidence to alter the conclusions of C.L. Lausen et al. (2019. Can. J. Zool. 97(3): 267–279). We present background information, relevant comparisons, and clarification of analyses to further strengthen our conclusions. The genesis of the original “evotis–keenii” study in British Columbia (Canada) was to differentiate Myotis keenii (Merriam, 1895) (Keen’s myotis), with one of the smallest North American bat distributions, from sympatric Myotis evotis (H. Allen, 1864) (long-eared myotis), using something other than the suggested post-mortem skull size comparison, but no differentiating trait could be found, leading to the molecular genetics examination of C.L. Lausen et al. (2019). We present cumulative data that rejects the 1979 hypothesis of M. keenii as a distinct species. A.E. Morales et al. (2021) inaccurately portray C.L. Lausen et al.’s (2019) question and results; present inaccurate morphological and outdated distribution data; overstate the impact of homoplasy without supporting evidence; and misinterpret evidence of population structure.

Population Structure

2001 ◽  
Author(s):  
Leonard Nunney
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Empirical Studies ◽  
Good Reason ◽  
Genetic Correlations ◽  
Evolutionary Change ◽  
Dispersal Ability ◽  
The Face ◽  
Family Associations ◽  
Proximity Structure

Population structure is a ubiquitous feature of natural populations that has an important influence on evolutionary change. In the real world, populations are not homogenous units; instead, they develop an internal structure, created by the physical properties of the environment and the biological characteristics of the species (such as dispersal ability). However, our basic ecological and population genetic models generally ignore population structure and focus on randomly mating (panmictic) populations. Such structure can profoundly change the evolution of a population. In fact, the myriad of influences that population structure exerts can only be hinted at in a single chapter. Since an exhaustive review is not possible, I will focus on presenting the conceptual issues linking mathematical models of population structure to empirical studies. To do this, it is useful to recognize two different kinds of population structure that both reflect and influence evolutionary change. The first is genetic structure. This is defined as the nonrandom distribution of genotypes in space and time. Thus, genetic structure reflects the genetic differences that develop among the different components of one or more populations. The second is what I will call proximity structure, defined by the size and composition of the group of neighbors that influence an individual’s fitness. Fitness is commonly influenced by local intraspecific interactions. Perhaps the most obvious example is competition. When individuals compete for some resource, they don’t usually compete equally with every other member of the population; in general, they compete only with a few of the most proximate individuals. These two forms of population structure, genetic structure and proximity structure, provide a foundation for understanding why we have shifted away from viewing populations as homogenous units. For good reason, this is a theme that is explored in many of the other chapters in this book. Genetic structure can develop within a population over a single generation, generally either as a result of local family associations or as a result of spatial variation in selection. For example, limited seed dispersal results in genetic correlations among neighbors even in the face of long-distance pollen movement, due to the clustering of maternal half sibs.

scholarly journals Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Forests ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 681 ◽  
Author(s):  
Huiquan Zheng ◽  
Dehuo Hu ◽  
Ruping Wei ◽  
Shu Yan ◽  
Runhui Wang
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Breeding Population ◽  
Population Diversity ◽  
Chinese Fir ◽  
High Density ◽  
Population Structure Analysis ◽  
Snp Panel

Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low FST (0.0285–0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies.

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