scholarly journals First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes (Canis latrans)

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 66 ◽  
Author(s):  
Javier Monzón
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Markers ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Canis Latrans ◽  
Regional Analysis ◽  
Model Organism ◽  
Nucleotide Polymorphisms ◽  
Genomic Markers

Previous genetic studies of eastern coyotes (Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

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 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 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 Single Nucleotide Polymorphisms and Indel Markers from the Transcriptome of Garlic

2016 ◽  
Vol 141 (1) ◽  
pp. 62-65 ◽  
Author(s):  
Michael J. Havey ◽  
Yul-Kyun Ahn
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Characteristics ◽  
Single Nucleotide ◽  
Germplasm Collections ◽  
Indel Markers ◽  
Production Environments ◽  
Culinary Uses

Garlic (Allium sativum) is cultivated worldwide and appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great morphological variation and adaptability to diverse production environments. Molecular markers and phenotypic characteristics have been used to assess the genetic diversity among garlics. In this study, we undertook transcriptome sequencing from a single garlic plant to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid (DH) of onion (Allium cepa). Single nucleotide polymorphisms (SNPs) and insertion–deletion (indel) events were identified in 4355 independent garlic assemblies. A sample of the indels was verified using the original complementary DNA (cDNA) library and genomics DNAs from diverse garlics, and segregations confirmed by sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for estimates of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.

scholarly journals Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1190 ◽  
Author(s):  
Eunju Seo ◽  
Kipoong Kim ◽  
Tae-Hwan Jun ◽  
Jinsil Choi ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Principal Component ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Useful Knowledge ◽  
Population Structure Analysis ◽  
Group 3 ◽  
Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

scholarly journals Population Genomics of Bettongia lesueur: Admixing Increases Genetic Diversity with no Evidence of Outbreeding Depression

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 851 ◽  
Author(s):  
Kate Rick ◽  
Kym Ottewell ◽  
Cheryl Lohr ◽  
Rujiporn Thavornkanlapachai ◽  
Margaret Byrne ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Threatened Species ◽  
Population Genomics ◽  
Fold Increase ◽  
Recruitment Rate ◽  
Outbreeding Depression ◽  
Nucleotide Polymorphisms ◽  
Isolated Populations ◽  
Genomic Markers ◽  
Founder Populations

Small and isolated populations are subject to the loss of genetic variation as a consequence of inbreeding and genetic drift, which in turn, can affect the fitness and long-term viability of populations. Translocations can be used as an effective conservation tool to combat this loss of genetic diversity through establishing new populations of threatened species, and to increase total population size. Releasing animals from multiple genetically diverged sources is one method to optimize genetic diversity in translocated populations. However, admixture as a conservation tool is rarely utilized due to the risks of outbreeding depression. Using high-resolution genomic markers through double-digest restriction site-associated sequencing (ddRAD-seq) and life history data collected over nine years of monitoring, this study investigates the genetic and fitness consequences of admixing two genetically-distinct subspecies of Bettongia lesueur in a conservation translocation. Using single nucleotide polymorphisms (SNPs) identified from 215 individuals from multiple generations, we found an almost 2-fold increase in genetic diversity in the admixed translocation population compared to the founder populations, and this was maintained over time. Furthermore, hybrid class did not significantly impact on survivorship or the recruitment rate and therefore we found no indication of outbreeding depression. This study demonstrates the beneficial application of mixing multiple source populations in the conservation of threatened species for minimizing inbreeding and enhancing adaptive potential and overall fitness.

scholarly journals Genetic diversity in portuguese native Vitis vinifera L. ssp. vinifera and ssp. sylvestris

2010 ◽  
Vol 46 (Special Issue) ◽  
pp. S54-S56 ◽  
Author(s):  
J. Cunha ◽  
M. Teixeira Santos ◽  
J. Brazăo ◽  
L.C. Carneiro ◽  
M. Veloso ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Structure ◽  
Vitis Vinifera ◽  
Gene Pool ◽  
Western Europe ◽  
Eastern European ◽  
Starting Point ◽  
Probable Origin ◽  
Different Origins

To assess the different origins of Portuguese grapevine varieties, we used six nuclear and four chloroplastidal microsatellites as molecular markers, in order to compare the genetic structure of native wild-vines with native grapevine varieties. Both native subspecies have a great diversity, and a high interrelationship across the six nuclear microsatellites. Although identical numbers of alleles were found in each population, their distribution was different in the <I>vinifera </I>and <I>sylvestris </I>subspecies. Portuguese wild-vines have only chlorotypes A and B; A being the most frequent. The fifty-seven analysed Portuguese varieties have chlorotypes A, B, C, and D. The most frequent was the chlorotype A (75%), followed by D (21%). The results obtained reinforced the idea of Western Europe as having been one of the domestication centres for the grapevine, with contributions from the Eastern European gene pool. The observed genetic structure is a starting point from which to clarify the high number of native cultivars found in Portugal, and reinforces their probable origin in the Iberian Peninsula.

Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers

Parasitology ◽  
2002 ◽  
Vol 125 (7) ◽  
pp. S51-S59 ◽  
Author(s):  
J. CURTIS ◽  
R. E. SORENSEN ◽  
D. J. MINCHELLA
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Microsatellite Markers ◽  
Natural Populations ◽  
Mitochondrial Marker ◽  
Tropical Regions ◽  
Blood Flukes

Blood flukes in the genus Schistosoma are important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found in Schistosoma mansoni and some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers for S. mansoni provided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.

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