scholarly journals Genome-wide SNPs of vegetable leafminer, Liriomyza sativae: insights into the recent Australian invasion

2022 ◽  
Author(s):  
Xuefen Xu ◽  
Tom L. Schmidt ◽  
Jiaxin Liang ◽  
Peter M. Ridland ◽  
Jessica Chung ◽  
...  
Keyword(s):  
Isolation By Distance ◽  
Principal Component ◽  
Global Scale ◽  
Invasion History ◽  
Nucleotide Polymorphisms ◽  
Multiple Sources ◽  
Liriomyza Sativae ◽  
Local Spread ◽  
Genome Wide ◽  
Torres Strait

Liriomyza sativae, the vegetable leafminer, is a serious agricultural pest originally from the Americas which has now colonized all continents except Antarctica. In 2015, L. sativae arrived on the Australian mainland and established on the Cape York Peninsula in the northeast of the country. Here, we assessed genetic variation in L. sativae based on genome-wide single nucleotide polymorphisms (SNPs) generated by double-digest restriction-site associated DNA sequencing (ddRAD-seq) to uncover the potential origin(s) of this pest in Australia and contribute to reconstructing its global invasion history. Our principal component analyses (PCA) results suggested that Australian mainland populations were genetically close to populations from the Torres Strait and had connections to Bali and Papua New Guinea (PNG), whereas populations from Asia and Africa were more distantly related. Hawaii was genetically distinct from populations from Asia, Africa and Australia. Co-ancestry analyses pointed to signals of gene flow from the Torres Strait into the Australian mainland, while Indonesia/PNG were the likely sources of the initial invasion into the Torres Strait. Admixture analyses further revealed that L. sativae from the Torres Strait had genetic diversity originating from multiple sources, which has now spread to the Australian mainland. The L. sativae lineages from Asia/Africa appear closely related and may share co-ancestry. Isolation by distance (IBD) was found at a broad global scale, but not within small regions, suggesting human-mediated factors contribute to the local spread of this pest. Overall, our findings highlight the challenges in quarantine measures aimed at restricting the distribution of this global pest.

scholarly journals Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 832
Author(s):  
Nina Moravčíková ◽  
Radovan Kasarda ◽  
Radoslav Židek ◽  
Luboš Vostrý ◽  
Hana Vostrá-Vydrová ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Structure ◽  
Principal Component ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
German Shepherd ◽  
German Shepherd Dog ◽  
Genome Wide ◽  
Scale Population ◽  
History Effect

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

scholarly journals Genomic response to natural selection within alpine cattle breeds

2018 ◽  
Vol 63 (No. 4) ◽  
pp. 136-143
Author(s):  
N. Moravčíková ◽  
M. Simčič ◽  
G. Mészáros ◽  
J. Sölkner ◽  
V. Kukučková ◽  
...  
Keyword(s):  
Natural Selection ◽  
Principal Component ◽  
Selection Response ◽  
Population Based ◽  
Nucleotide Polymorphisms ◽  
Data Quality Control ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Genomic Regions ◽  
Genomic Response

The aim of this study was to analyse the genomic regions that have been target of natural selection with respect to identifying the loci responsible mainly for fitness traits across six alpine cattle breeds. The genome-wide scan for selection signatures was performed using genotyping data from totally 465 animals. After applying data quality control, overall 35 873 single nucleotide polymorphisms were useable for the subsequent analysis. The detection of genomic regions affected by natural selection was carried out using the approach of principal component analysis. The analysis was based on the assumption that markers extremely related to the population structure are also candidates for local adaptation potential of the population. Based on the expected false discovery rate equal to 10% up to 1138 loci were identified as outliers. The strongest signals of selection were found in genomic regions on BTA 1, 2, 3, 6, 9, 11, 13, and 22. Most genes located in the identified regions have been previously associated with immunity system as well as body growth and muscle formation that mainly reflect the pressure of both natural and artificial selection in respect to adaptation of analysed breeds to the local environmental conditions. The results also signalized that those regions represent a correlated selection response in way to maintain the fitness of analysed breeds.

scholarly journals Inference of Population Genetic Structure and High Linkage Disequilibrium Among Alternaria spp. Collected from Tomato and Potato Using Genotyping by Sequencing

2019 ◽  
Author(s):  
Tika B. Adhikari ◽  
Brian J. Knaus ◽  
Niklaus J. Grünwald ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Plant Pathogens ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Allelic Association ◽  
Nucleotide Polymorphisms ◽  
Entire Genome ◽  
Genome Wide ◽  
A Genome

ABSTRACTGenotyping by sequencing (GBS) is considered a powerful tool to discover single nucleotide polymorphisms (SNPs), which are useful to characterize closely related genomes of plant species and plant pathogens. We applied GBS to determine genome-wide variations in a panel of 187 isolates of three closely related Alternaria spp. that cause diseases on tomato and potato in North Carolina (NC) and Wisconsin (WI). To compare genetic variations, reads were mapped to both A. alternata and A. solani draft reference genomes and detected dramatic differences in SNPs among them. Comparison of A. linariae and A. solani populations by principal component analysis revealed the first (83.8% of variation) and second (8.0% of variation) components contained A. linariae from tomato in NC and A. solani from potato in WI, respectively, providing evidence of population structure. Genetic differentiation (Hedrick’s G’ST) in A. linariae populations from Haywood, Macon, and Madison counties in NC were little or no differentiated (G’ST 0.0 - 0.2). However, A. linariae population from Swain county appeared to be highly differentiated (G’ST > 0.8). To measure the strength of the linkage disequilibrium (LD), we also calculated the allelic association between pairs of loci. Lewontin’s D (measures the fraction of allelic variations) and physical distances provided evidence of linkage throughout the entire genome, consistent with the hypothesis of non-random association of alleles among loci. Our findings provide new insights into the understanding of clonal populations on a genome-wide scale and microevolutionary factors that might play an important role in population structure. Although we found limited genetic diversity, the three Alternaria spp. studied here are genetically distinct and each species is preferentially associated with one host.

scholarly journals Population Differentiation at the HLA Genes

2017 ◽  
Author(s):  
Débora Y. C. Brandt ◽  
Jônatas César ◽  
Jérôme Goudet ◽  
Diogo Meyer
Keyword(s):  
Population Differentiation ◽  
Balancing Selection ◽  
Global Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Hla Genes ◽  
Genome Wide ◽  
Different Populations ◽  
Genomic Regions

ABSTRACTBalancing selection is defined as a class of selective regimes that maintain polymorphism above what is expected under neutrality. Theory predicts that balancing selection reduces population differentiation, as measured by FST. However, balancing selection regimes in which different sets of alleles are maintained in different populations could increase population differentiation. To tackle this issue, we investigated population differentiation at the HLA genes, which constitute the most striking example of balancing selection in humans. We found that population differentiation of single nucleotide polymorphisms (SNPs) at the HLA genes is on average lower than that of SNPs in other genomic regions. However, this result depends on accounting for the differences in allele frequency between selected and putatively neutral sites. Our finding of reduced differentiation at SNPs within HLA genes suggests a predominant role of shared selective pressures among populations at a global scale. However, in pairs of closely related populations, where genome-wide differentiation is low, differentiation at HLA is higher than in other genomic regions. This pattern was reproduced in simulations of overdominant selection. We conclude that population differentiation at the HLA genes is generally lower than genome-wide, but it may be higher for recently diverged population pairs, and that this pattern can be explained by a simple overdominance regime.

scholarly journals Population Genomic Analysis of Two Endemic Schizothoracins Reveals Their Genetic Differences and Underlying Selection Associated with Altitude and Temperature

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 447
Author(s):  
Tianyan Yang ◽  
Wei Meng ◽  
Baocheng Guo
Keyword(s):  
Mixed Model ◽  
Isolation By Distance ◽  
Genomic Analysis ◽  
Principal Component ◽  
Mantel Test ◽  
Tibet Plateau ◽  
Tarim River ◽  
Genome Wide ◽  
Isolation By Environment ◽  
Kaidu River

Schizothoracins are a group of cyprinid fishes distributed throughout the Qinghai–Tibet Plateau, which can be classified in three grades: primitive, specialised and highly specialised according to adaptation ability to plateau environments. As the only specialised schizothoracins in Xinjiang, China, Diptychus maculates and Gymnodiptychus dybowskii are ideal materials for adaptive evolution research. Based on single-nucleotide polymorphism (SNP) loci detected by specific-locus amplified fragment (SLAF) technology, the genome-wide genetic diversities of these two species from nine sites in Xinjiang were evaluated. D.maculates in the Muzat River (BM) and G. dybowskii in the Kaidu River (LKG) presented the lowest genetic diversity levels, whereas D. maculates in the Kumarik River (BK) and G.dybowskii in the Kashi River (LK) were just the opposite. Cluster and principal component analysis demonstrated a distant genetic affinity between D. maculates in the Tashkurgan River (BT) and other populations. Outlier SNP loci were discovered both in D. maculates and G. dybowskii. The coalescent Bayenv and latent factor mixed model (LFMM) methods showed that a total of thirteen and eighteen SNPs in D. maculates were associated with altitude and temperature gradient, respectively. No intersection was revealed in G. dybowskii. The results indicated that D. maculates was subject to much greater divergent selection pressure. A strong signal of isolation-by-distance (IBD) was detected across D. maculates (Mantel test, rs = 0.65; p = 0.05), indicating an evident geographical isolation in the Tarim River. Isolation-by-environment (IBE) analysis implied that temperature and altitude selections were more intensive in D. maculates, with greater environmental variation resulting in weak gene flow.

scholarly journals Genome-wide identification of breed-informative single-nucleotide polymorphisms in three South African indigenous cattle breeds

1970 ◽  
Vol 46 (3) ◽  
pp. 302-312
Author(s):  
A.A. Zwane ◽  
A. Maiwashe ◽  
M.L. Makgahlela ◽  
A. Choudhury ◽  
J.F. Taylor ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Single Nucleotide Polymorphisms ◽  
South African ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Indigenous Cattle ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
Polymorphic Snps ◽  
Genome Wide

Access to genotyping assays enables the identification of informative markers that discriminate between cattle breeds. Identification of these markers can assist in breed assignment, improvement and conservation. The objective of this study was to identify breed informative markers to discriminate between three South African indigenous cattle breeds. Data from BovineSNP50 and GeneSeek Genomic Profiler (GGP-80K) assays were generated for Afrikaner, Drakensberger and Nguni, and were analysed for their genetic differentiation. Hereford and Angus were included as outgroups. Breeds were differentiated using principal component analysis (PCA). Single-nucleotide polymorphisms (SNPs) within the breeds were determined when minor allele frequency (MAF) was ≥ 0.05. Breed-specific SNPs were identified using Reynolds Fst and extended Lewontin and Krakauer's (FLK) statistics. These SNPs were validated using three African breeds, namely N’Dama, Kuri and Zebu from Madagascar. PCA discriminated among the breeds. A larger number of polymorphic SNPs was detected in Drakensberger (73%) than in Afrikaner (56%) and Nguni (65%). No substantial numbers of informative SNPs (Fst ≥ 0.6) were identified among indigenous breeds. Eleven SNPs were validated as discriminating the indigenous breeds from other African breeds. This is because the SNPs on BovineSNP50 and GGP-80K assays were ascertained as being common in European taurine breeds. Lower MAF and SNP informativeness observed in this study limits the application of these assays in breed assignment, and could have other implications for genome-wide studies in South African indigenous breeds. Sequencing should therefore be considered to discover new SNPs that are common among indigenous South African breeds and also SNPs that discriminate among these indigenous breeds.

scholarly journals Genome-Wide SNP Discovery and Population Genetic Analysis of Mesocentrotus nudus in China Seas

2021 ◽  
Vol 12 ◽  
Author(s):  
Quanchao Wang ◽  
Ying Liu ◽  
Lang Yan ◽  
Linlin Chen ◽  
Baoquan Li
Keyword(s):  
Diversity Index ◽  
Principal Component ◽  
Genetic Connectivity ◽  
Nucleotide Polymorphisms ◽  
China Seas ◽  
Natural Habitats ◽  
Population Genetic Analysis ◽  
Genome Wide ◽  
Geographical Populations ◽  
Mesocentrotus Nudus

Mesocentrotus nudus is an important commercially aquatic species because of its high edible and medicinal values. However, wild stocks have dramatically decreased in recent decades. Understanding the population structure and genetic diversity can provide vital information for genetic conservation and improvement. In the present study, the genotyping-by-sequencing (GBS) approach was adopted to identify the genome-wide single-nucleotide polymorphisms (SNPs) from a collection of 80 individuals consisting of five geographical populations (16 individuals from each population), covering the natural habitats of M. nudus in China seas. An average of 0.96-Gb clean reads per sample were sequenced, and a total of 51,738 biallelic SNPs were identified. Based on these SNPs, diversity index analysis showed that all populations have a similar pattern with positive Fis (0.136) and low Ne (724.3). Low genetic differentiation and high genetic connectivity among five geographical populations were detected by pairwise Fst, principal component analysis (PCA), admixture, and phylogenetic analysis. Besides, two YWL individuals originating from an isolated ancestor may imply that there is a genetically differentiated population in the adjacent sea. Overall, the results showed that GBS is an effective method to detect genome-wide SNPs for M. nudus and suggested that the protective measures and the investigation with larger spatial scale and sample size for M. nudus should be carried out in the future.

scholarly journals Genetic Diversity of South African Indigenous Goat Population from Four Provinces Using Genome-Wide SNP Data

2020 ◽  
Vol 12 (24) ◽  
pp. 10361
Author(s):  
Tlou Caswell Chokoe ◽  
Khanyisile Mdladla-Hadebe ◽  
Farai Muchadeyi ◽  
Edgar Dzomba ◽  
Tlou Matelele ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
South African ◽  
Principal Component ◽  
Chromosome 8 ◽  
Nucleotide Polymorphisms ◽  
North West ◽  
Genome Wide ◽  
Goat Population ◽  
Indigenous Goat

Genome-wide assessments of the genetic landscape of Farm Animal Genetic Resources (FAnGR) are key to developing sustainable breed improvements. Understanding the FAnGR adaptation to different environments and supporting their conservation programs from community initiative to national policymakers is very important. The objective of the study was to investigate the genetic diversity and population structure of communal indigenous goat populations from four provinces of South Africa. Communal indigenous goat populations from the Free State (FS) (n = 24), Gauteng (GP) (n = 28), Limpopo (LP) (n = 30), and North West (NW) (n = 35) provinces were genotyped using the Illumina Goats SNP50 BeadChip. An Illumina Goats SNP50 BeadChip data from commercial meat-type breeds: Boer (n = 33), Kalahari Red (n = 40), and Savanna (n = 31) was used in this study as reference populations. The Ho revealed that the genetic diversity of a population ranged between 0.39 ± 0.11 Ho in LP to 0.42 ± 0.09 Ho in NW. Analysis of molecular variance revealed variations of 3.39% (p < 0.0001) and 90.64% among and within populations, respectively. The first two Principal Component Analyses (PCAs) revealed a unique Limpopo population separated from GP, FS, and NW communal indigenous goat populations with high levels of admixture with commercial goat populations. There were unique populations of Kalahari and Savanna that were observed and admixed individuals. Marker FST (Limpopo versus commercial goat populations) revealed 442 outlier single nucleotide polymorphisms (SNPs) across all chromosomes, and the SNP with the highest FST value (FST = 0.72; chromosome 8) was located on the UHRF2 gene. Population differentiation tests (PCAdapt) revealed PC2 as optimal and five outlier SNPs were detected on chromosomes 10, 15, 20, and 21. The study revealed that the SNPs identified by the first two principal components show high FST values in LP communal goat populations and allowed us to identify candidate genes which can be used in the development of breed selection programs to improve this unique LP population and other communal goat population of FS, GP, and NW, and find genetic factors contributing to the adaptation to harsh environments. Effective management and utilization of South African communal indigenous goat populations is important, and effort should be made to maintain unique genetic resources for conservation.

scholarly journals A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito

2019 ◽  
Author(s):  
Moshe Jasper ◽  
Thomas L. Schmidt ◽  
Nazni W. Ahmad ◽  
Steven P. Sinkins ◽  
Ary A Hoffmann
Keyword(s):  
Yellow Fever ◽  
Isolation By Distance ◽  
Dispersal Distance ◽  
Pest Species ◽  
Nucleotide Polymorphisms ◽  
Yellow Fever Mosquito ◽  
Genome Wide ◽  
Genomic Approach ◽  
Geographical Distances ◽  
Dispersal Events

AbstractUnderstanding past dispersal and breeding events can provide insight into ecology and evolution, and can help inform strategies for conservation and the control of pest species. However, parent-offspring dispersal can be difficult to investigate in rare species and in small pest species such as mosquitoes. Here we develop a methodology for estimating parent-offspring dispersal from the spatial distribution of close kin, using pairwise kinship estimates derived from genome-wide single nucleotide polymorphisms (SNPs). SNPs were scored in 162 Aedes aegypti (yellow fever mosquito) collected from eight close-set, high-rise apartment buildings in an area of Malaysia with high dengue incidence. We used the SNPs to reconstruct kinship groups across three orders of kinship. We transformed the geographical distances between all kin pairs within each kinship category into axial standard deviations of these distances, then decomposed these into components representing past dispersal events. From these components, we isolated the axial standard deviation of parent-offspring dispersal, and estimated neighbourhood area (129 m), median parent-offspring dispersal distance (75 m), and oviposition dispersal radius within a gonotrophic cycle (36 m). We also analysed genetic structure using distance-based redundancy analysis and linear regression, finding isolation by distance both within and between buildings and estimating neighbourhood size at 268 individuals. These findings indicate the scale required to suppress local outbreaks of arboviral disease and to target releases of modified mosquitoes for mosquito and disease control. Our methodology is readily implementable for studies of other species, including pests and species of conservation significance.

Sign in / Sign up

Export Citation Format

Share Document