Collin W. Ahrens

The search for loci under selection: trends, biases and progress

Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAAs) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field‐based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends and biases across biological systems, sequencing methods, approaches, parameters, environmental variables and their influence on detecting signatures of selection. We found striking variability in both the use and reporting of environmental data and statistical parameters. For example, linkage disequilibrium among SNPs and numbers of unique SNP associations identified with EAA were rarely reported. The proportion of putatively adaptive SNPs detected varied widely among studies, and decreased with the number of SNPs analysed. We found that genomic sampling effort had a greater impact than biological sampling effort on the proportion of identified SNPs under selection. OA identified a higher proportion of outliers when more individuals were sampled, but this was not the case for EAA. To facilitate repeatability, interpretation and synthesis of studies detecting selection, we recommend that future studies consistently report geographical coordinates, environmental data, model parameters, linkage disequilibrium, and measures of genetic structure. Identifying standards for how OA and EAA studies are designed and reported will aid future transparency and comparability of SNP‐based selection studies and help to progress landscape and evolutionary genomics.

Bentgrass Distribution Surveys and Habitat Suitability Maps Support Ecological Risk Assessment in Cultural Landscapes

The bentgrasses comprise an adaptable group of grasses that include introduced species, cultivated turfgrasses, and native plants in North America. Their distribution in cultural landscapes has not been documented, and this gap in knowledge has limited the development of predictive ecological risk assessments for creeping bentgrass engineered for herbicide resistance. In this study, bentgrass distribution and abundance were surveyed in 289 plots in an 8.5 km2 site surrounding a golf course in the northeastern United States. Four introduced species and two native bentgrasses were identified in seminatural and managed plant communities. Across the study site, 77% of the plots containing creeping bentgrass also had invasive plants. Bentgrasses co-occurred with critical habitat for threatened or endangered animals. Multivariate logistic regression analysis showed that bentgrasses were positively correlated with herbaceous plant cover and mowing, but negatively correlated with tree canopy cover, shrub cover, poorly drained soils, and leaf litter. The most influential ecological factors were tree canopy cover and soil moisture. Geospatial information about these two ecological factors was combined with mathematical models to generate two habitat suitability maps. The favorable environments map (FEM) showed that highly suitable bentgrass habitat covered 36% of the study site and included common features such as home lawns and railroad right-of-ways. Our results suggest that release of herbicide-resistant creeping bentgrass in this cultural landscape could potentially result in pollen-mediated gene flow, interspecific hybridization, environmental hazards, and herbicide selection pressure in some areas. Habitat suitability maps could be critical tools for predictive ecological risk assessments, monitoring projects, and management of herbicide-resistant bentgrasses. Nomenclature: Creeping bentgrass, Agrostis stolonifera L.; AGSST

Distribution models for Panicum virgatum (Poaceae) reveal an expanded range in present and future climate regimes in the northeastern United States

PREMISE OF THE STUDY Expanded area cultivated with the bioenergy crop Panicum virgatum (switchgrass) could alter the genetics of native populations through gene flow, so understanding current and future species distribution is a first step toward estimating ecological impacts. We surveyed switchgrass distribution in the northeastern United States and generated statistical models to address hypotheses about current distribution relative to historical records and responses to climate change. METHODS Surveys were conducted on 1600 km of road verges along environmental gradients. Switchgrass abundance became the training data for two multivariate generalized linear models that generated maps representing the probability of switchgrass in road verges. Models were evaluated and the superior model was used with variables from three climate change scenarios for 2050 and 2099. KEY RESULTS Switchgrass populations were found in 41% of roadside plots and up to 188 km from the coast. The environmental variables temperature, urban areas, and sandy soils were positively correlated with switchgrass presence, while elevation, soil pH, and distance to the coast were negatively correlated. The model without spatial autocorrelation performed better. Models and maps incorporating climate change predictions showed a sharp northward shift in suitable habitat. CONCLUSIONS Switchgrass populations in the northeastern United States occur on inland road verges, supporting the idea that species distribution has expanded relative to historical descriptions of a restricted coastal habitat. The optimal model showed that mean temperature, elevation, and urban development were important in switchgrass distribution today, and climate change will increase suitable habitat for future bioenergy production and wild populations.

Adaptation and acclimation both influence photosynthetic and respiratory temperature responses in Corymbia calophylla

Short-term acclimation and long-term adaptation represent two ways in which forest trees can respond to changes in temperature. Yet, the relative contribution of thermal acclimation and adaptation to tree physiological responses to temperature remains poorly understood. Here, we grew two cool-origin and two warm-origin populations of a widespread broad-leaved evergreen tree species (Corymbia calophylla (Lindl.) K.D.Hill & L.A.S.Johnson) from a Mediterranean climate in southwestern Australia under two growth temperatures representative of the cool- and warm-edge of the species distribution. The populations selected from each thermal environment represented both high and low precipitation sites. We measured the short-term temperature response of leaf photosynthesis (A) and dark respiration (R), and attributed observed variation to acclimation, adaptation or the combination of both. We observed limited variation in the temperature optimum (Topt) of A between temperature treatments or among populations, suggesting little plasticity or genetic differentiation in the Topt of A. Yet, other aspects of the temperature response of A and R were dependent upon population and growth temperature. Under cooler growth temperatures, the population from the coolest, wettest environment had the lowest A (at 25 °C) among all four populations, but exhibited the highest A (at 25 °C) under warmer growth temperatures. Populations varied in R (at 20 °C) and the temperature sensitivity of R (i.e., Q10 or activation energy) under cool, but not warm growth temperatures. However, populations showed similar yet lower R (at 20 °C) and no differences in the temperature sensitivity of R under warmer growth temperatures. We conclude that C. calophylla populations from contrasting climates vary in physiological acclimation to temperature, which might influence how this ecologically important tree species and the forests of southwestern Australia respond to climate change.

Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain

Background and Aims Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage‐specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south‐eastern Australia. Methods Four putative species were sampled from a total of 16 populations in the Victorian Volcanic Plain (VVP) bioregion and one population of a sub‐alpine outgroup in south‐eastern Australia. Morphological measurements were taken in situ along with leaf material for genotyping by sequencing (GBS) and microsatellite analyses. Key Results Species could not be differentiated using morphological measurements. Microsatellite and GBS markers confirmed the outgroup as distinct, but only GBS markers provided resolution of population genetic structure. The nationally endangered Diuris basaltica was indistinguishable from two related species (D. chryseopsis and D. behrii), while the state‐protected D. gregaria showed genomic differentiation. Conclusions Genomic diversity identified among the four Diuris species suggests that conservation of this taxonomically complex group will be best served by considering them as one ESU rather than separately aligned with species as currently recognized. This approach will maximize evolutionary potential among all species during increased isolation and environmental change. The methods used here can be applied generally to conserve evolutionary processes for groups where taxonomic uncertainty hinders the use of species as conservation units.

Regional Genetic Structure and Environmental Variables Influence our Conservation Approach for Feather Heads (Ptilotus macrocephalus)

Continued alterations to the Australian environment compromise the long-term viability of many plant species. We investigate the population genetics of Ptilotus macrocephalus, a perennial herb that occurs in 2 nationally endangered communities on the Victorian Volcanic Plain Bioregion (VVP), Australia, to answer key questions regarding regional differentiation and to guide conservation strategies. We evaluate genetic structure and diversity within and among 17 P. macrocephalus populations from 3 regions of southeastern Australia using 17 microsatellite markers developed de novo. Genetic structure was present in P. macrocephalus between the 3 regions but not at the population level. Environmental factors, namely temperature and precipitation, significantly explained differentiation between the North region and the other 2 regions indicating isolation by environment. Within regions, genetic structure currently shows a high level of gene flow and genetic variation. Our results suggest that within-region gene flow does not reflect current habitat fragmentation in southeastern Australia whereas temperature and precipitation are likely to be responsible for the differentiation detected among regions. Climate change may severely impact P. macrocephalus on the VVP and test its evolutionary resilience. We suggest taking a proactive conservation approach to improve long-term viability by sourcing material for restoration to assist gene flow to the VVP region to promote an increased adaptive capacity.

Characterization of Microsatellite Markers for the Vulnerable Grassland Forb Senecio macrocarpus (Asteraceae)

Premise of the study: Development of microsatellite markers for the vulnerable forb Senecio macrocarpus was performed to begin an assessment of its population structure and breeding method to aid in the conservation of the species in Victoria, Australia. Methods and Results: Fifteen microsatellite markers were developed for S. macrocarpus from 454 pyrosequencing. The markers were tested on 104 individuals from four populations. The markers produced between two and seven alleles per locus while the expected heterozygosity ranged from 0.20 to 0.67 and the observed heterozygosity ranged from 0.00 to 1.00. The observed heterozygosity is suggestive that the populations may be apomictic. Conclusions: The microsatellite markers developed for S. macrocarpus are intended to be used on future studies that aim to assess the population genetics and local breeding dynamics of the species with an emphasis on conservation.

Characterization of 13 Microsatellite Markers for Diuris basaltica (Orchidaceae) and Related Species

Premise of the study: Diuris basaltica (Orchidaceae) is an endangered forb on the Victorian grasslands and has many close relatives. Microsatellite markers have been developed to facilitate assessment of population structure within D. basaltica and among related taxa within the species complex. Methods and Results: Twenty-five microsatellite markers (13 polymorphic and 12 monomorphic) were developed from D. basaltica using 454 pyrosequencing, and all primer pairs were amplified in D. gregaria and D. chryseopsis. For the set of polymorphic markers, the number of alleles per locus ranged from one to 10, two to nine, and two to 18 for D. basaltica, D. gregaria, and D. chryseopsis, respectively. The expected and observed heterozygosities ranged from 0.18 to 0.95 and 0.14 to 0.86, respectively. Conclusions: The microsatellite markers developed in this study can be used to analyze the population genetic structure of D. basaltica and other Diuris species.

Genetic Relationship between Cultivated and Feral Creeping Bentgrass (Agrostis stolonifera) in a Cultural Landscape

Abstract Gene flow is an important consideration in the adoption of crops with novel traits or transgenes when sexually compatible relatives occur in the landscape. Unfortunately, gene flow and its long-term environmental impacts are very difficult to predict without releasing and studying the novel genotype. This project uses a retrospective population genetics approach to characterize the relationship between cultivated creeping bentgrass (CB) on a golf course and the same species in five feral populations nearby. CB plants were collected from an 8-yr-old golf course, five weedy populations up to 1,020 m from the golf course, and four modern CB cultivars. Using microsatellite markers and Bayesian inference, two major genetic clusters were distinguished: (1) CB cultivars and individuals from the golf course (cultivar genotype), and (2) the majority of individuals (62%) from the five feral populations (feral genotype). Two feral CB individuals (3.3% of all feral plants) were partially assigned to the cultivar genotype. Principal coordinates analysis agreed with this assignment, suggesting that an intraspecific hybridization event may have occurred. Plants in four feral populations showed a high degree of genetic similarity, but one feral population (Reservoir) was heterogeneous indicating that genetically complex CB populations can develop in cultural landscapes. While recognizing the limitations inherent in a single study of CB population genetics, these results add to the relevant knowledge for predictive ecological risk assessment. Nomenclature: Creeping bentgrass, Agrostis stolonifera L.

Annual Glyphosate Treatments Alter Growth of Unaffected Bentgrass (Agrostis) Weeds and Plant Community Composition

Herbicide resistance is becoming more common in weed ecotypes and crop species including turfgrasses, but current gaps in knowledge limit predictive ecological risk assessments and risk management plans. This project examined the effect of annual glyphosate applications on the vegetative growth and reproductive potential of two weedy bentgrasses, creeping bentgrass (CB) and redtop (RT), where the glyphosate resistance (GR) trait was mimicked by covering the bentgrass plants during glyphosate application. Five field plots were studied in habitats commonly inhabited by weedy bentgrasses including an agricultural hayfield, natural meadow, and wasteland. Results showed that annual glyphosate treatment improved bentgrass survivorship, vegetative growth, and reproductive potential compared with bentgrass in unsprayed subplots. In the second year of growth, RT plants had an 86-fold increase in flower number in glyphosate-treated subplots versus controls, while CB plants had a 20-fold increase. At the end of the three year study, plant community composition had changed in glyphosate-treated subplots in hayfield and meadow plots compared to controls. Soils in subplots receiving glyphosate had higher nitrate concentrations than controls. This is the first study to mimic the GR trait in bentgrass plants with the goal of quantifying bentgrass response to glyphosate selection pressure and understanding the impacts on surrounding plant communities.