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. For example, see pubs below:
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.