ConGen Course Publications
This course/workshop should lead to a publication (meeting review) describing the course's main topics, course outcomes, genome assembly (quality testing), and recent advances in population genetics and phylogenetics worldwide.
Course Publications
References cited
Allendorf, F.W., W.C. Funk, S.N. Aitken, M. Byrne, G. Luikart. 2022. Conservation and the Genomics of Populations. [3rd Edition]. Oxford University Press. Pp. 784
Bailey, R. I. (2024). Bayesian hybrid index and genomic cline estimation with the R package gghybrid. Molecular Ecology Resources, 24(2), e13910.
Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. doi: 10.1093/bioinformatics/btr521
Hemstrom, W., & Jones, M. (2023). snpR: User friendly population genomics for SNP data sets with categorical metadata. Molecular Ecology Resources, 23(4), 962-973.
Hoban, S., Paz-Vinas, I., Shaw, R. E., Castillo-Reina, L., Silva, J. M., DeWoody, J. A., ... & Grueber, C. E. (2024). DNA-based studies and genetic diversity indicator assessments are complementary approaches to conserving evolutionary potential. Conservation Genetics, 1-7.
Jenkins, T. L. (2024). mapmixture: An R package and web app for spatial visualisation of admixture and population structure. Molecular Ecology Resources, 24(4), e13943.
Kamvar, Z. N., López-Uribe, M. M., Coughlan, S., Grünwald, N. J., Lapp, H., & Manel, S. (2016). Developing educational resources for population genetics in R: An open and collaborative approach. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.12558
Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front. Genet. 6:208. doi: 10.3389/fgene.2015.00208
Kardos, M., and G. Luikart. 2021. The genomic architecture of fitness drives population viability in
changing environments. American Naturalist, 197:511–525. doi.org/10.1086/713469
Kardos M, Armstrong EE, Fitzpatrick SW, Hauser S, Hedrick PW, Miller JM, Tallmon DA, Funk WC. The crucial role of genome-wide genetic variation in conservation. (2021) Proc Natl Acad Sci USA. 118(48):e2104642118. doi: 10.1073/pnas.2104642118.
Mastretta‐Yanes, A., Da Silva, J. M., Grueber, C. E., Castillo‐Reina, L., Köppä, V., Forester, B. R., ... & Hoban, S. (2024). Multinational evaluation of genetic diversity indicators for the Kunming‐Montreal Global Biodiversity Framework. Ecology Letters, 27(7), e14461.
Paradis, E. (2020). Population genomics with R. Chapman and Hall/CRC.
Zhang, R., Jia, G., & Diao, X. (2023). geneHapR: an R package for gene haplotypic statistics and visualization. BMC bioinformatics, 24(1), 199.
Yang, C., Mai, J., Cao, X., Burberry, A., Cominelli, F., & Zhang, L. (2023). ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization. Bioinformatics, 39(8), btad470.