An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time.

Native Americans domesticated maize (Zea mays ssp. mays) from lowland teosinte parviglumis (Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 (HPC1), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.

Ecological Restoration Practices within a Semi-arid Natural Gas Field Improve Insect Abundance and Diversity during Early and Late Growing Season.

Insects are critical components of terrestrial ecosystems and are often considered ecosystem engineers. Due to the vast amount of ecosystem services they provide, because statistically valid samples can be captured in short durations, and because they respond rapidly to environmental change, insects have been used as indicators of restoration success and ecosystem functionality. In Wyoming (USA), ecological restoration required on thousands of acres of land surface have been disturbed to extract natural gas. In this study, we compared early seral reclamation sites to reference areas at two points within a growing season. We compared insect abundance and family richness on 6 natural gas well pads with early season perennial forbs and 6 well pads with the late season to insect communities on adjacent reference areas. A total of 237 individual insects were found on early season reclaimed sites compared to 84 on reference sites, while 858 insects were found on late season reclaimed sites compared to 38 on reference sites. Insect abundance was significantly higher on reclaimed well pads compared to reference areas at both points in the growing season, while reclaimed sites had significantly higher Shannon Diversity Index in early season and significantly higher family richness in late season compared to their paired reference sites. We also found interesting differences in abundance at family levels.

Implications of genetic heterogeneity for plant translocation during ecological restoration.

Ecological restoration often requires translocating plant material from distant sites. Importing suitable plant material is important for successful establishment and persistence. Yet, published guidelines for seed transfer are available for very few species. Accurately predicting how transferred plants will perform requires multiyear and multi-environment field trials and comprehensive follow-up work, and is therefore infeasible given the number of species used in restoration programs. Alternative methods to predict the outcomes of seed transfer are valuable for species without published guidelines. In this study, we analyzed the genetic structure of an important shrub used in ecological restoration in the Southern Rocky Mountains called alder-leaf mountain mahogany (Cercocarpus montanus). We sequenced DNA from 1,440 plants in 48 populations across a broad geographic range. We found that genetic heterogeneity among populations reflected the complex climate and topography across which the species is distributed. We identified temperature and precipitation variables that were useful predictors of genetic differentiation and can be used to generate seed transfer recommendations. These results will be valuable for defining management and restoration practices for mountain mahogany.

Asymmetrical selection maintains heritable phenotypic variation between two subspecies of Monardella villosa.

PREMISE: Monardella villosa is an evolutionarily young species complex distributed across a large geographic range. Our goal was to determine whether the phenotypic difference between two subspecies of M. villosa was heritable and whether the alternative phenotypes were adaptive to their respective local habitats. METHODS: We collected seeds from 25 populations of M. villosa, 14 from subspecies franciscana, which grows closer to the coast, and 11 from subspecies villosa, which has a larger and more inland geographic distribution. We reciprocally transplanted the two subspecies into their respective habitats and compared plant germination, post-emergence survival, and growth. We used linear mixed models to quantify the effects of genotype and environment to determine whether subspecies were locally adapted and whether leaf traits that distinguish these subspecies were genetically based. RESULTS: Plants of both subspecies grown at the coastal site had significantly lower survival and biomass than the inland site. The subspecies were not locally adapted; however, the coastal subspecies franciscana did have a home site advantage. We also found that distinctive leaf morphological traits were genetically based, with high broad-sense heritability of traits. CONCLUSIONS: The two subspecies of Monardella villosa were not locally adapted to their respective habitat, but rather we found that selection for local genotypes may be stronger at the coastal site. Despite the lack of evidence for local adaptation in the strict sense, the subspecies had heritable variation in several leaf phenotypes, indicating that heterogeneous selection imposes an adaptive trade-off for leaf trichome production within this species.

Combining Genotype, Phenotype, and Environment to Infer Potential Candidate Genes.

Population genomic analysis can be an important tool in understanding local adaptation. Identification of potential adaptive loci in such analyses is usually based on the survey of a large genomic dataset in combination with environmental variables. Phenotypic data are less commonly incorporated into such studies, although combining a genome scan analysis with a phenotypic trait analysis can greatly improve the insights obtained from each analysis individually. Here, we aimed to identify loci potentially involved in adaptation to climate in 283 Loblolly pine (Pinus taeda) samples from throughout the species' range in the southeastern United States. We analyzed associations between phenotypic, molecular, and environmental variables from datasets of 3082 single nucleotide polymorphism (SNP) loci and 3 categories of phenotypic traits (gene expression, metabolites, and whole-plant traits). We found only 6 SNP loci that displayed potential signals of local adaptation. Five of the 6 identified SNPs are linked to gene expression traits for lignin development, and 1 is linked with whole-plant traits. We subsequently compared the 6 candidate genes with environmental variables and found a high correlation in only 3 of them (R2 > 0.2). Our study highlights the need for a combination of genotypes, phenotypes, and environmental variables, and for an appropriate sampling scheme and study design, to improve confidence in the identification of potential candidate genes.