Tag: RAD-seq
Tracing the introduction of the invasive common myna using population genomics
Acclimatisation (6 January 1877) Southland Times. Page 2. paperspast.natlib.govt.nz/newspapers/ST18770105.2.7. Accessed 21 January 2022 Adamack AT, Gruber B (2014) PopGenReport: simplifying basic population genetic analyses in R. Methods Ecol Evol 5:384–387. doi.org/10.1111/2041-210x.12158 Article Google Scholar Andrews S (2010) FastQC. A quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc/ Andrews KR,…
Virtual RAD-seq Analysis Workshop!
News:Virtual RAD-seq Analysis Workshop! 0 The Computational Biology Core at the University of Connecticut’s Institute for Systems Genomics is offering a virtual RAD-seq analysis workshop April 17-20 2023. The workshop will cover an introduction to linux and high performance computing before going through a complete analysis starting with raw reads…
Investigating the genetic basis of vertebrate dispersal combining RNA-seq, RAD-seq and quantitative genetics
Although animal dispersal is known to play key roles in ecological and evolutionary processes such as colonization, population extinction and local adaptation, little is known about its genetic basis, particularly in vertebrates. Untapping the genetic basis of dispersal should deepen our understanding of how dispersal behaviour evolves, the molecular mechanisms…
Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes
Luo, M. C. et al. Synteny analysis in rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials. BMC Genom. 16, 707 (2015). Article Google Scholar Martinez-Garcia, P. J. et al. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of…
Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe
Charlesworth, B. & Charlesworth, D. Population genetics from 1966 to 2016. Heredity 118, 2–9 (2017). CAS Google Scholar Orsini, L., Vanoverbeke, J., Swillen, I., Mergeay, J. & Meester, L. Drivers of population genetic differentiation in the wild: Isolation by dispersal limitation, isolation by adaptation and isolation by colonization. Mol. Ecol….
Best BLAST hit alone cannot be used as evidence of fraud
Blanco-Fernandez, C. et al. Fraud in highly appreciated fish detected from DNA in Europe may undermine the development goal of sustainable fishing in Africa. Sci. Rep. 11, 11423. doi.org/10.1038/s41598-021-91020-w (2021). Article ADS CAS Google Scholar Lewis, S. G. & Boyle, M. The expanding role of traceability in seafood: Tools and…
Tiny crustacean reveals deepest parts of oceans like isolated islands
A tiny crustacean measuring just three centimetres in length is helping scientists unlock one of the most perplexing questions of the oceans’ hadal zone–how isolated are the animals that live in our deepest ocean trenches? A new paper Barriers to gene flow in the deepest ocean ecosystem: Evidence from global population…
Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq
The cultivated peanut (Arachis hypogaea L.) is an important oil crop but has a narrow genetic diversity. Molecular markers can be used to probe the genetic diversity of various germplasm. In this study, the restriction site associated DNA (RAD) approach was utilized to sequence 31 accessions of Taiwanese peanut germplasm,…
Genetic diversity of loquat (Eriobotrya japonica) revealed using RAD-Seq SNP markers & More Science News
Our research analyzed the genetic diversity of 95 cultivars and strains of loquat collected from everywhere in the world. On the premise of the evaluation of the inhabitants construction of 19 Chinese loquat cultivars and strains by RAD-Seq, Hubei Province in China has been recommended as the middle of origin…
Read counts an order of magnitude higher on one chromosome
Read counts an order of magnitude higher on one chromosome 3 Hi, I am having an issue with a sequencing run that when demultiplexed, aligned, and filtered each individual has 1-2 million reads, but these reads are predominantly on one chromosome. For background these are oncorhynchus mykiss and o. clarki…
Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data
Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…
Detection of candidate gene LsACOS5 and development of InDel marker for male sterility by ddRAD-seq and resequencing analysis in lettuce
Ryder, E. J. Lettuce, Endive and Chicory (CABI Publishing, 1999). Google Scholar Seki, K. et al. A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.). Hortic. Res. 7, 1–14 (2020). Article Google Scholar Odland,…
Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs
1. Thompson, J. N. & Pellmyr, O. Evolution of oviposition behavior and host preference in Lepidoptera. Annu. Rev. Entomol. 36, 65–89 (1991). Article Google Scholar 2. Bowers, M. D. Iridoid glycosides and host-plant specificity in larvae of the buckeye butterfly, Junonia coenia (Nymphalidae). J. Chem. Ecol. 10, 1567–1577 (1984). CAS …
