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Inference of genetic clusters is a key aim of population genetics, sparking development of numerous analytical methods. Within these, there is a conceptual divide between finding de novo structure versus assessment of a priori groups. Recently developed, Discriminant Analysis of Principal Components (DAPC), combines discriminant analysis (DA) with principal component (PC) analysis. When applying DAPC, the groups used in the DA (specified a priori or described de novo) need to be carefully assessed. While DAPC has rapidly become a core technique, the sensitivity of the method to misspecification of groups and how it is being empirically applied, are unknown. To address this, we conducted a simulation study examining the influence of a priori versus de novo group designations, and a literature review of how DAPC is being applied. We found that with a priori groupings, distance between genetic clusters reflected underlying F ST . However, when migration rates were high and groups were described de novo there was considerable inaccuracy, both in terms of the number of genetic clusters suggested and placement of individuals into those clusters. Nearly all (90.1%) of 224 studies surveyed used DAPC to find de novo clusters, and for the majority (62.5%) the stated goal matched the results. However, most studies (52.3%) omit key run parameters, preventing repeatability and transparency. Therefore, we present recommendations for standard reporting of parameters used in DAPC analyses. The influence of groupings in genetic clustering is not unique to DAPC, and researchers need to consider their goal and which methods will be most appropriate.

Tripartite motif (TRIM) proteins are involved in development, innate immunity, and viral restriction. TRIM gene repertoires vary between species, likely due to diversification caused by selective pressures from pathogens; however, this has not been explored in birds. We mined a de novo assembled transcriptome for the TRIM gene repertoire of the domestic mallard duck ( Anas platyrhynchos ), a reservoir host of influenza A viruses. We found 57 TRIM genes in the duck, which represent all 12 subfamilies based on their C-terminal domains. Members of the C-IV subfamily with C-terminal PRY-SPRY domains are known to augment immune responses in mammals. We compared C-IV TRIM proteins between reptiles, birds, and mammals and show that many C-IV subfamily members have arisen independently in these lineages. A comparison of the MHC-linked C-IV TRIM genes reveals expansions in birds and reptiles. The TRIM25 locus with related innate receptor modifiers is adjacent to the MHC in reptile and marsupial genomes, suggesting the ancestral organization. Within the avian lineage, both the MHC and TRIM25 loci have undergone significant TRIM gene reorganizations and divergence, both hallmarks of pathogen-driven selection. To assess the expression of TRIM genes, we aligned RNA-seq reads from duck tissues. C-IV TRIMs had high relative expression in immune relevant sites such as the lung, spleen, kidney, and intestine, and low expression in immune privileged sites such as in the brain or gonads. Gene loss and gain in the evolution of the TRIM repertoire in birds suggests candidate immune genes and potential targets of viral subversion.

Identifying genetic variants responsible for phenotypic variation under selective pressure has the potential to enable productive gains in natural resource conservation and management. Despite this potential, identifying adaptive candidate loci is not trivial, and linking genotype to phenotype is a major challenge in contemporary genetics. Many of the population genetic approaches commonly used to identify adaptive candidates will simultaneously detect false positives, particularly in nonmodel species, where experimental evidence is seldom provided for putative roles of the adaptive candidates identified by outlier approaches. In this study, we use outcomes from population genetics, phenotype association, and gene expression analyses as multiple lines of evidence to validate candidate genes. Using lodgepole and jack pine as our nonmodel study species, we analyzed 17 adaptive candidate loci together with 78 putatively neutral loci at 58 locations across Canada (N > 800) to determine whether relationships could be established between these candidate loci and phenotype related to mountain pine beetle susceptibility. We identified two candidate loci that were significant across all population genetic tests, and demonstrated significant changes in transcript abundance in trees subjected to wounding or inoculation with the mountain pine beetle fungal associate Grosmannia clavigera. Both candidates are involved in central physiological processes that are likely to be invoked in a trees response to stress. One of these two candidate loci showed a significant association with mountain pine beetle attack status in lodgepole pine. The spatial distribution of the attack‐associated allele further coincides with other indicators of susceptibility in lodgepole pine. These analyses, in which population genetics was combined with laboratory and field experimental validation approaches, represent first steps toward linking genetic variation to the phenotype of mountain pine beetle susceptibility in lodgepole and jack pine, and provide a roadmap for more comprehensive analyses.

Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.

Millions of lodgepole pine seedlings are planted each year to replace losses due to harvest or large-scale natural disturbances such as fires and forest pests. In Canada, replacement seeds and seedlings used for reforestation are often regulated by explicit policies. For example, in the province of Alberta, seedlings must be grown from seeds collected within a strictly defined zone that includes the harvested area where the seedlings will be planted. Thus, traceability along the entire reforestation chain of custody, from seed collection to seedling outplanting, is vital to ensure policy compliance. Here, we report a case study in which we used genomic tools to determine if seedlings were sown from a contaminated seed source. The 165,000 seedlings under scrutiny were scheduled for deployment the same year in which the seeds were sown, necessitating fast processing to make decisions on deployment. The scenario was made more complex by the fact that most of the potentially contaminated seed sources represented wild-collected genetic material in close geographic proximity to each other, rather than pedigree genetic material. With genotyping data obtained from a high-density single nucleotide polymorphism array analyzed with clustering analyses, kinship estimations, and genetic assignment tests, we were able to determine the probable seed source of this suspect group of seedlings and make data-guided recommendations on whether these seedlings could be confidently deployed onto the landscape without violating policy guidelines. This case study demonstrates the unique utility of molecular markers to confidently assign seedlings to a non-pedigree parent seed source originating within a limited geographic range, thereby ensuring traceability within a reforestation pipeline.

Angiosperms are the largest and most successful clade of land plants with >250,000 species distributed in nearly every terrestrial habitat. Many phylogenetic studies have been based on DNA sequences of one to several genes, but, despite decades of intensive efforts, relationships among early diverging lineages and several of the major clades remain either incompletely resolved or weakly supported. We performed phylogenetic analyses of 81 plastid genes in 64 sequenced genomes, including 13 new genomes, to estimate relationships among the major angiosperm clades, and the resulting trees are used to examine the evolution of gene and intron content. Phylogenetic trees from multiple methods, including model-based approaches, provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales. The plastid genome trees also provide strong support for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids. Resolution of relationships among the major clades of angiosperms provides the necessary framework for addressing numerous evolutionary questions regarding the rapid diversification of angiosperms. Gene and intron content are highly conserved among the early diverging angiosperms and basal eudicots, but 62 independent gene and intron losses are limited to the more derived monocot and eudicot clades. Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements.

Expertise in the broader impacts of scientific research is an increasingly important aspect of professional development, particularly because federal grant proposals are commonly reviewed using both the Intellectual Merit and the Broader Impacts Criteria. Unfortunately, training in broader impacts, such as science communication and outreach, is not typically part of undergraduate or graduate curricula. We initiated one of the first graduate-level biology courses on broader impacts, focusing on giving graduate students firsthand, authentic experiences with grant writing, science communication, and educational outreach. Students in this interdisciplinary course learned from experts, wrote for a broad audience about their own research, and proposed and implemented outreach in collaboration with local organizations. We outline our approach, discuss outcomes from each activity, assess our impact, and finally consider how future programs might expand on this model.

Wild parsnip is an invasive species with a global distribution in temperate climates. Parsnips are native to Eurasia and have been cultivated for more than five centuries. It is unclear whether the global invasion of this species is a consequence of escape from cultivation or the accidental introduction of a Eurasian wild subspecies. In this study, we used nuclear ribosomal DNA internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) markers to evaluate the genetic structure of wild parsnip in its native range (Europe) and in three distinct geographic regions where it is considered invasive: eastern North America, western North America, and New Zealand. We also compared wild and cultivated parsnips to determine whether they are genetically distinct. From 112 individuals, we recovered 14 ITS and 27 cpDNA haplotypes. One ITS haplotype was widespread; few haplotypes were rare singletons. In contrast, at least two lineages of cpDNA haplotypes were recovered, with several novel haplotypes restricted to Europe. Cultivated parsnips were not genetically distinct from wild parsnips, and numerous wild parsnip populations shared haplotypes with cultivars. High genetic diversity was recovered in all three regions, suggesting multiple introductions. Nomenclature: Wild parsnip, Pastinaca sativa L. PASA2. Management Implications: The availability of molecular data and advances in population genetic analysis have made it possible to estimate the patterns of species migrations with considerable precision. Findings from historical colonization and dispersal studies can shed light on human-mediated transport of biological materials and provide a broad understanding of how humans may have contributed to the introduction and spread of an invasive species. Evidence obtained in this study indicates that escape from cultivation led to the globalization of wild parsnips and introduced populations have high genetic diversity. Increased levels of diversity in invasive populations can act as a primer for rapid adaptive evolution of this noxious invasive species. Future studies with increased sampling and additional loci have the potential to elucidate specific patterns of colonization and admixture in this agriculturally entwined invasive plant and may serve as a model for investigating the natural and agricultural history of plant species that exist in wild, cultivated, and feral forms.