scholarly journals What is a dingo – origins, hybridisation and identity

2021 ◽  
Author(s):  
Kylie M Cairns
Keyword(s):  
Native Species ◽  
Evolutionary Relationship ◽  
Domestic Dog ◽  
Ongoing Debate ◽  
Dna Test ◽  
Southeastern Australia ◽  
Snp Data ◽  
Genome Wide ◽  
Future Work ◽  
The Impact

ABSTRACT Controversy about the nomenclature and taxonomy of dingoes has sparked interest in their complex identity. At the root of taxonomy debates are differences in the species concepts employed, differing opinions about the domestication status of dingoes (and their ancestors) and a simplistic handling of the complex evolutionary relationship between wolves, dingoes and domestic dogs. I explore the relationship of dingoes to village dogs, modern breed dogs and wolves using genome-wide SNP data and discuss the implications of these findings to the ongoing debate about dingo identity and nomenclature. Importantly, despite controversy about what to call dingoes and whether they are a full species, these animals represent an important, distinct and unique evolutionary unit worthy of high conservation priority, as a native species. There is growing concern about the spread of domestic dog genes into dingo populations, particularly in southeastern Australia, and the impact this has on conservation goals. However, the discovery of biogeographic subdivision within dingoes raises questions about the accuracy of the current methods used for estimating dog vs dingo ancestry. I caution scientists and wildlife managers to carefully consider the limitations of current ancestry estimate methods when assessing DNA test results. Future work using genome-wide DNA technology to improve dingo ancestry estimates will be fundamental to ongoing debate about what dingoes are, how to identify dingoes and how to conserve them.

scholarly journals The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly

2019 ◽  
Vol 286 (1911) ◽  
pp. 20191311 ◽  
Author(s):  
Vlad Dincă ◽  
Kyung Min Lee ◽  
Roger Vila ◽  
Marko Mutanen
Keyword(s):  
Species Delimitation ◽  
Dna Analysis ◽  
Restriction Site ◽  
Significant Proportion ◽  
Ongoing Debate ◽  
Snp Data ◽  
Genome Wide ◽  
A Genome ◽  
Mtdna Lineages ◽  
Eastern Kazakhstan

The Palaearctic butterfly Melitaea didyma stands out as one of the most striking cases of intraspecific genetic differentiation detected in Lepidoptera: 11 partially sympatric mitochondrial lineages have been reported, displaying levels of divergence of up to 7.4%. To better understand the evolutionary processes underlying the diversity observed in mtDNA, we compared mtDNA and genome-wide SNP data using double-digest restriction site-associated DNA sequencing (ddRADseq) results from 93 specimens of M. didyma ranging from Morocco to eastern Kazakhstan. We found that, between ddRADseq and mtDNA results, there is a match only in populations that probably remained allopatric for long periods of time. Other mtDNA lineages may have resulted from introgression events and were probably affected by Wolbachia infection. The five main ddRADseq clades supported by STRUCTURE were parapatric or allopatric and showed high pairwise F ST values, but some were also estimated to display various levels of gene flow. Melitaea didyma represents one of the first cases of deep mtDNA splits among European butterflies assessed by a genome-wide DNA analysis and reveals that the interpretation of patterns remains challenging even when a high amount of genomic data is available. These findings actualize the ongoing debate of species delimitation in allopatry, an issue probably of relevance to a significant proportion of global biodiversity.

Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome‐wide SNP data from seven native species

2020 ◽  
Vol 29 (7) ◽  
pp. 1235-1249 ◽  
Author(s):  
Nathan K. Lujan ◽  
Jason T. Weir ◽  
Brice P. Noonan ◽  
Nathan R. Lovejoy ◽  
Nicholas E. Mandrak
Keyword(s):  
Gene Flow ◽  
Native Species ◽  
Niagara Falls ◽  
Snp Data ◽  
Genome Wide

scholarly journals Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

2020 ◽  
Author(s):  
Nicholas P. Howard ◽  
Michela Troggio ◽  
Charles-Eric Durel ◽  
Hélène Muranty ◽  
Caroline Denancé ◽  
...  
Keyword(s):  
Data Integration ◽  
New Technology ◽  
Snp Array ◽  
Probe Design ◽  
Array Data ◽  
Snp Data ◽  
Array Technology ◽  
Depth Analysis ◽  
Future Work ◽  
The Impact

AbstractBackgroundSingle nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20K and Affymetrix Axiom® 480K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n=3,141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls.ResultsConcordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8,412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3’ end of the probe.ConclusionsThe Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development.

scholarly journals Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations

2020 ◽  
Author(s):  
Aaron J. Sams ◽  
Brett Ford ◽  
Adam Gardner ◽  
Adam R. Boyko
Keyword(s):  
Genetic Diversity ◽  
Random Mating ◽  
Companion Animals ◽  
Genetic Erosion ◽  
Population Level ◽  
Domestic Dog ◽  
Animal Populations ◽  
Genome Wide ◽  
Long Term Impact ◽  
The Impact

ABSTRACTIn many ways dogs are an ideal model for the study of genetic erosion and population recovery, problems of major concern in the field of conservation genetics. Genetic diversity in many dog breeds has been declining systematically since the beginning of the 1800’s, when modern breeding practices came into fashion. As such, inbreeding in domestic dog breeds is substantial and widespread and has led to an increase in recessive deleterious mutations of high effect as well as general inbreeding depression. Pedigrees can in theory be used to guide breeding decisions, though are often incomplete and do not reflect the full history of inbreeding. Small microsatellite panels are also used in some cases to choose mating pairs to produce litters with low levels of inbreeding. However, the long-term impact of such practices have not been thoroughly evaluated. Here, we use forward simulation on a model of the dog genome to examine the impact of using limited markers panels to guide pairwise mating decisions on genome-wide population level genetic diversity. Our results suggest that in unsupervised mating schemes, where breeding decisions are made at the pairwise-rather than population-level, such panels can lead to accelerated loss of genetic diversity compared to random mating at regions of the genome unlinked to panel markers and demonstrate the importance of genome-wide genetic panels for managing and conserving genetic diversity in dogs and other companion animals.

scholarly journals Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Nicholas P. Howard ◽  
Michela Troggio ◽  
Charles-Eric Durel ◽  
Hélène Muranty ◽  
Caroline Denancé ◽  
...  
Keyword(s):  
Data Integration ◽  
New Technology ◽  
Snp Array ◽  
Probe Design ◽  
Array Data ◽  
Snp Data ◽  
Array Technology ◽  
Depth Analysis ◽  
Future Work ◽  
The Impact

Abstract Background Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20 K and Affymetrix Axiom® 480 K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n = 3141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls. Results Concordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3′ end of the probe. Conclusions The Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in the literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development.

The Impact of BRICS in Reconstructing the International Order

2020 ◽  
pp. 87
Author(s):  
Tareq Mohammed Dhannoon AL Taie
Keyword(s):  
International System ◽  
Political Influence ◽  
Active Role ◽  
International Order ◽  
First Century ◽  
International Affairs ◽  
Strategic Action ◽  
Brics Countries ◽  
Future Work ◽  
The Impact

The BRICS countries have a historical aspiration for global leadership, especially Russia and China, and other countries trying to have a position in the pyramid of international powers in the twenty-first century, especially Brazil, India and South Africa, they worked to unify their efforts, in order to achieve integration in the strategic action, activate its role in International affairs, ending American domination , and restructuring an international system that have an active role in its interactions.       The research hypothesis is based on the idea that the BRICS group, despite the nature of its economic composition and its long-term goals, but its political influence as a bloc, is greater than the proportion of its economic influence in restructuring the new international order. The BRICS group has the capabilities to reshape the international order, but disputes among some of its members represent a challenge to its future work. Its goals will not be achieved without teamwork. Third world countries, especially those that reject unipolarism, have regarded one of the pillars supporting multi-polarity, aiming of giving them freedom of movement in international relations. The ultimate goal of the BRICS is a political nature, as economic mechanisms are used to achieve political goals.

Relay Selection-aware Non-orthogonal Multiple Access Networks: Direct and Relaying Mode

2020 ◽  
Vol 13 (3) ◽  
pp. 348-354
Author(s):  
Dinh-Thuan Do ◽  
Minh-Sang V. Nguyen
Keyword(s):  
Relay Selection ◽  
Multiple Access ◽  
Decode And Forward ◽  
Selection Scheme ◽  
Fixed Power ◽  
Transmission Quality ◽  
Improved Performance ◽  
Outage Probabilities ◽  
Future Work ◽  
The Impact

Objective: In this paper, Decode-and-Forward (DF) mode is deployed in the Relay Selection (RS) scheme to provide better performance in cooperative downlink Non-orthogonal Multiple Access (NOMA) networks. In particular, evaluation regarding the impact of the number of multiple relays on outage performance is presented. Methods: As main parameter affecting cooperative NOMA performance, we consider the scenario of the fixed power allocations and the varying number of relays. In addition, the expressions of outage probabilities are the main metric to examine separated NOMA users. By matching related results between simulation and analytical methods, the exactness of derived formula can be verified. Results: The intuitive main results show that in such cooperative NOMA networks, the higher the number of relays equipped, the better the system performance can be achieved. Conclusion: DF mode is confirmed as a reasonable selection scheme to improve the transmission quality in NOMA. In future work, we will introduce new relay selections to achieve improved performance.

scholarly journals Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kyung Seok Kim ◽  
Kevin J. Roe
Keyword(s):  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Conservation Strategies ◽  
Nucleotide Polymorphisms ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Snp Data ◽  
Genome Wide ◽  
Significant Difference

AbstractDetailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.

scholarly journals Genome-wide SNP data unravel the ancestry and signatures of divergent selection in Ghurrah pigs of India

2021 ◽  
pp. 104587
Author(s):  
Arnav Mehrotra ◽  
Bharat Bhushan ◽  
Karthikeyan A ◽  
Akansha Singh ◽  
Snehasmita Panda ◽  
...  
Keyword(s):  
Divergent Selection ◽  
Snp Data ◽  
Genome Wide
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