The easy road to genome‐wide medium density <scp>SNP</scp> screening in a non‐model species: development and application of a 10 K <scp>SNP</scp>‐chip for the house sparrow (<i><scp>P</scp>asser domesticus</i>)

Hagen, Ingerid Julie; Billing, Anna Maria; Rønning, Bernt; Pedersen, Sindre Andre; Pärn, Henrik; Slate, Jon; Jensen, Henrik

doi:10.1111/1755-0998.12088

Cited by 42 publications

(59 citation statements)

References 66 publications

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“…( 55 ). Detailed information on the reference individual has been deposited in the National Center for Biotechnology Information (NCBI) BioSample database under accession number SAMN02929199.…”

Section: Methodsmentioning

confidence: 99%

The genomic mosaicism of hybrid speciation

et al. 2017

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Section: Methodsmentioning

confidence: 99%

The genomic mosaicism of hybrid speciation

et al. 2017

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“…A way to avoid this issue is to select a discovery panel representative of the range of the species (or at least across the desired range of the populations), and by selecting loci with different levels of heterozygosity (Morin et al, 2004). Next-generation sequencing approaches have greatly facilitated the use of SNPs in studies of natural populations (Hagen et al, 2013). Thousands of SNPs can be identified for population genomic studies, similar to AFLPs.…”

Section: Molecular Tools For Population Geneticsmentioning

confidence: 99%

Thirty years of tick population genetics: A comprehensive review

Araya-Anchetta

Busch

Scoles

et al. 2015

Infection, Genetics and Evolution

118

109

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Population genetic studies provide insights into the basic biology of arthropod disease vectors by estimating dispersal patterns and their potential to spread pathogens. In wingless vectors, such as ticks, gene flow will be defined in large part by the mobility of their hosts. However, tick behaviors and life cycle strategies can limit their dispersal even on highly mobile hosts and lead to an increase in genetic structure. In this review we synthesize the published literature from three decades of tick population genetic studies. Based on studies from 22 tick species (including representatives from Amblyomma, Bothriocroton, Dermacentor, Ixodes, Ornithodoros, and Rhipicephalus), observed levels of population genetic structure in ticks varied from no structure to very high levels. In about half of the species (including representatives from Amblyomma, Bothriocroton, Dermacentor, and Ornithodoros), tick genetic structure appeared to be determined primarily by the movement capacity of hosts, with low gene flow observed in ticks that use smaller bodied less mobile hosts and high gene flow in ticks using highly mobile hosts. In a number of other species (primarily from Ixodes, Ornithodoros, and Rhipicephalus), behavioral limitations to gene flow appeared to result in greater genetic structure than expected based upon host movement capability alone. We also discuss the strengths and limitations of genetic markers and their applicability to ticks and suggest possible analyses when planning population genetic studies for ticks.

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“…SNPs are abundant in the genome and can be found especially in non-coding but also in coding regions, and are hence valuable markers for many types of research questions or to see whether genetic variants are associated with a certain trait or disease. SNPs have been discovered using transcriptomics in many avian species (Balakrishnan et al 2013;Ekblom and Wang 2017;Ekblom et al 2014;Hagen et al 2013;Kaiser et al 2017;Lundberg et al 2013;Ramstad et al 2016;Santure et al 2011;Srivastava 2011;Srivastava et al 2012;Vijayakumar et al 2014;Zhang et al 2014b) (Box 3). Whole body transcriptomics was used to find candidate loci explaining the divergence between two subspecies of songbirds with several phenotypically different characteristics inhabiting either the mainland or islands of Alaska (Srivastava 2011).…”

Section: Genetic Marker Discoverymentioning

confidence: 99%

Avian transcriptomics: opportunities and challenges

Jax

Kraus

2018

J Ornithol

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Recent developments in next-generation sequencing technologies have greatly facilitated the study of whole transcriptomes in model and non-model species. Studying the transcriptome and how it changes across a variety of biological conditions has had major implications for our understanding of how the genome is regulated in different contexts, and how to interpret adaptations and the phenotype of an organism. The aim of this review is to highlight the potential of these new technologies for the study of avian transcriptomics, and to summarise how transcriptomics has been applied in ornithology. A total of 81 peer-reviewed scientific articles that used transcriptomics to answer questions within a broad range of study areas in birds are used as examples throughout the review. We further provide a quick guide to highlight the most important points which need to be take into account when planning a transcriptomic study in birds, and discuss how researchers with little background in molecular biology can avoid potential pitfalls. Suggestions for further reading are supplied throughout. We also discuss possible future developments in the technology platforms used for ribonucleic acid sequencing. By summarising how these novel technologies can be used to answer questions that have long been asked by ornithologists, we hope to bridge the gap between traditional ornithology and genomics, and to stimulate more interdisciplinary research.

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The easy road to genome‐wide medium density SNP screening in a non‐model species: development and application of a 10 K SNP‐chip for the house sparrow (Passer domesticus)

Abstract: 25With the advent of next generation sequencing, new avenues have opened to study genomics 26 in wild populations of non-model species. Here, we describe a successful approach to a

Cited by 42 publications

References 66 publications

The genomic mosaicism of hybrid speciation

The genomic mosaicism of hybrid speciation

Thirty years of tick population genetics: A comprehensive review

Avian transcriptomics: opportunities and challenges

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