scholarly journals Genetic diversity and population structure of two subspecies of western honey bees (Apis mellifera L.) in the Republic of South Africa as revealed by microsatellite genotyping

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8280
Author(s):  
Amin Eimanifar ◽  
Johanna T. Pieplow ◽  
Alireza Asem ◽  
James D. Ellis
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Population Structure ◽  
Apis Mellifera ◽  
Honey Bees ◽  
Molecular Ecology ◽  
Apis Mellifera Capensis ◽  
Nucleotide Polymorphisms ◽  
Invasive Pests ◽  
The Republic

Apis mellifera scutellata and Apis mellifera capensis, two native subspecies of western honey bees in the Republic of South Africa (RSA), are important to beekeepers in their native region because beekeepers use these bees for honey production and pollination purposes. Additionally, both bees are important invasive pests outside of their native ranges. Recently, whole mitogenome sequencing and single nucleotide polymorphisms were used to study their genetic diversity. To add to our knowledge of the molecular ecology of both bees, we tested the ability of microsatellites to be used as a tool to discriminate between A.m. capensis and A.m. scutellata. We analyzed the genetic variability and overall population structure of both bee subspecies and hybrids of the two by genotyping individuals collected from RSA (N = 813 bees from 75 apiaries) at 19 microsatellite DNA loci. Overall, populations averaged between 9.2 and 11.3 alleles per locus, with unbiased heterozygosity values ranging from 0.81 to 0.86 per population. Bayesian clustering analyses revealed two distinct evolutionary units, though the results did not match those of earlier morphometric and molecular analyses. This suggests that the microsatellites we tested were not sufficient for subspecies identification purposes, especially for Cape and hybrid bees. Nevertheless, the microsatellite data highlight the considerable genetic diversity within both populations and a larger-than-expected hybridization zone between the natural distributions of A.m. capensis and A.m. scutellata.

scholarly journals Population genomics and morphometric assignment of western honey bees (Apis mellifera L.) in the Republic of South Africa

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Amin Eimanifar ◽  
Samantha A. Brooks ◽  
Tomas Bustamante ◽  
James D. Ellis
Keyword(s):  
South Africa ◽  
Apis Mellifera ◽  
Honey Bees ◽  
Population Genomics ◽  
The Republic

scholarly journals Mitochondrial DNA Variation of Feral Honey Bees (Apis mellifera L.) from Utah (USA)

2018 ◽  
Vol 62 (2) ◽  
pp. 223-232
Author(s):  
Dylan Cleary ◽  
Allen L. Szalanski ◽  
Clinton Trammel ◽  
Mary-Kate Williams ◽  
Amber Tripodi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Western Europe ◽  
Dna Variation ◽  
Bee Colony ◽  
The Us ◽  
Coii Gene

Abstract A study was conducted on the mitochondrial DNA genetic diversity of feral colonies and swarms of Apis mellifera from ten counties in Utah by sequencing the intergenic region of the cytochrome oxidase (COI-COII) gene region. A total of 20 haplotypes were found from 174 honey bee colony samples collected from 2008 to 2017. Samples belonged to the A (African) (48%); C (Eastern Europe) (43%); M (Western Europe) (4%); and O (Oriental) lineages (5%). Ten African A lineage haplotypes were observed with two unique to Utah among A lineage haplotypes recorded in the US. Haplotypes belonging to the A lineage were observed from six Utah counties located in the southern portion of the State, from elevations as high as 1357 m. All five C lineage haplotypes that were found have been observed from queen breeders in the US. Three haplotypes of the M lineage (n=7) and two of the O lineage (n=9) were also observed. This study provides evidence that honey bees of African descent are both common and diverse in wild populations of honey bees in southern Utah. The high levels of genetic diversity of A lineage honey bee colonies in Utah provide evidence that the lineage may have been established in Utah before the introduction of A lineage honey bees from Brazil to Texas in 1990.

scholarly journals Insight into the Current Genetic Diversity and Population Structure of Domestic Reindeer (Rangifer tarandus) in Russia

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1309
Author(s):  
Veronika Kharzinova ◽  
Arsen Dotsev ◽  
Anastasiya Solovieva ◽  
Olga Sergeeva ◽  
Georgiy Bryzgalov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Rangifer Tarandus ◽  
Allelic Richness ◽  
Environmental Changes ◽  
Principal Component ◽  
Genetic Structuring ◽  
Habitat Location ◽  
The Republic ◽  
Insight Into

To examine the genetic diversity and population structure of domestic reindeer, using the BovineHD BeadChip, we genotyped reindeer individuals belonging to the Nenets breed of the five main breeding regions, the Even breed of the Republic of Sakha, the Evenk breed of the Krasnoyarsk and Yakutia regions, and the Chukotka breed of the Chukotka region and its within-breed ecotype, namely, the Chukotka–Khargin, which is bred in Yakutia. The Chukotka reindeer was shown to have the lowest genetic diversity in terms of the allelic richness and heterozygosity indicators. The principal component analysis (PCA) results are consistent with the neighbor-net tree topology, dividing the reindeer into groups according to their habitat location and origin of the breed. Admixture analysis indicated a genetic structuring of two groups of Chukotka origin, the Even breed and most of the geographical groups of the Nenets breed, with the exception of the Murmansk reindeer, the gene pool of which was comprised of the Nenets and apparently the native Sami reindeer. The presence of a genetic component of the Nenets breed in some reindeer inhabiting the Krasnoyarsk region was detected. Our results provide a deeper insight into the current intra-breeding reindeer genetic diversity, which is an important requirement for future reindeer herding strategies and for animal adaptation to environmental changes.

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 Characterisation of the UK honey bee (Apis mellifera) metagenome

2018 ◽  
Author(s):  
Tim Regan ◽  
Mark W. Barnett ◽  
Dominik R. Laetsch ◽  
Stephen J. Bush ◽  
David Wragg ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Molecular Ecology ◽  
Emerging Pathogens ◽  
Complex Product ◽  
Bee Health ◽  
Honey Bee Health ◽  
The Uk ◽  
Bee Colonies

AbstractThe European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a complex product of environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of bee genetics and their molecular ecology can help manage modern challenges to bee health and production. Sampling bee and cobiont genomes, we characterised the metagenome of 19 honey bee colonies across Britain. Low heterozygosity was observed in bees from many Scottish colonies, sharing high similarity to the native dark bee, A. mellifera mellifera. Apiaries exhibited high diversity in the composition and relative abundance of individual microbiome taxa. Most non-bee sequences derived from known honey bee commensal bacteria or known pathogens, e.g. Lotmaria passim (Trypanosomatidae), and Nosema spp. (Microsporidia). However, DNA was also detected from numerous additional bacterial, plant (food source), protozoan and metazoan organisms. To classify sequences from cobionts lacking genomic information, we developed a novel network analysis approach clustering orphan contigs, allowing the identification of a pathogenic gregarine. Our analyses demonstrate the power of high-throughput, directed metagenomics in agroecosystems identifying potential threats to honey bees present in their microbiota.

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.

scholarly journals GENETIC DIVERSITY OF HONEY BEE POPULATIONS IN TURKEY BASED ON MICROSATELLITE MARKERS: A COMPARISON BETWEEN MIGRATORY VERSUS STATIONARY APIARIES AND ISOLATED REGIONS VERSUS REGIONS OPEN TO MIGRATORY BEEKEEPING

2019 ◽  
Author(s):  
Mert Kükrer
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Honey Bee ◽  
Honey Bees ◽  
Phylogenetic Trees ◽  
The Status ◽  
Genetic Impact ◽  
Geographic Populations ◽  
Ecological Importance

The honey bee (Apis mellifera L.) is a globally significant species of apparent economic and ecological importance. Recent reports from Spain, Italy and Greece point to an intense admixture of honey bee populations signified by a loss of population structure. This is mostly attributed to migratory beekeeping practices and replacement of queens or colonies with commercial ones that are usually from non-native races or hybrids of different subspecies. These two practices are also heavily carried out in parts of Turkey where almost three-quarters of the 6 million colonies are transferred seasonally from one region to other.Past research using microsatellite and RAPD markers, mtDNA, allozymes and geometric morphometry revealed the presence of five different subspecies of honey bees (meda, syriaca,caucasica, anatoliaca and an ecotype from Carniolan subspecies group) inTurkey. Here, we carried out an analysis of population structure of Turkish honeybees sampled from six different regions (n = 250) during the period 2010-2012. A total of 29 microsatellite markers were used in four multiplex reactions. The results show that population structure is preserved in general although there are signs of gene flow between the clusters.Overall FST between stationary colonies was calculated as 0,067. For migratory colonies the value was 0,015 and for all the 250 samples the value was 0,047. Four different clusters corresponding to geographical distributions of four subspecies were revealed in structure analysis. The differentiation between the clusters was also apparent in PCA and FCA as well as phylogenetic trees constructed based on genetic distances.The genetic impact of migratory beekeeping was demonstrated for the first time based on a comparison of assignment probabilities of individuals from migratory and stationary colonies to their geographic populations. Another comparison between regions that are either open to migratory beekeeping or closed let us to evaluate the status of isolated regions and showed the importance of establishing such regions. The effects of queen and colony trade were revealed by the presence of introgression from the highly commercial Caucasian bees. Our findings confirm the previously observed high levels geographically structured genetic diversity in honey bees of Turkey and emphasize the need to develop policies to maintain this diversity.

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