Performance of Genetic Distance Metrics in Gravity and General Mixed Effects Models

There are many causes for the genetic patterns that arise among populations across a landscape. Effective population size, natal site preference, geographic distance, or barriers to gene flow associated with landscape composition may work in opposition or in concert resulting in varying degrees of population differentiation. Here, we simulate 40 populations under 3 different ecological hypotheses of individual dispersal with random mating for 1500 generations, with scenarios: 1) dispersal and mating is dependent on habitat between populations, 2) dispersal and mating is dependent on individuals finding habitat similar to their natal habitat, and 3) dispersal and mating is dependent on habitat between populations but population size is dependent on surrounding habitat quality. We estimate the efficacy of generalized linear mixed-effect models (GLMMs) and gravity models to identify each of the 3 scenarios. Additionally, we tested the ability of 5 different genetic metrics (Dps, Fst, PCA, Nei’s D, and Cavalli-Sforza Dkf) to identify gene flow across ecological drivers, landscape composition, and time. We predict that more heterogeneous landscapes will influence genetic structure more quickly than more homogeneous landscapes and will be detected sooner by allele frequency approaches. Management of organisms in fragmented habitats, particularly those at risk, requires a knowledge of habitat effect and population genetic structure that can be informed by these types of simulations

Data from: Evolutionary responses to crude oil from the Deepwater Horizon oil spill by the copepod Eurytemora affinis

The BP Deepwater Horizon Oil Disaster was the most catastrophic offshore oil spill in U.S. history, yet we still have a poor understanding of how organisms could evolve in response to the toxic effects of crude oil. This study offers a rare analysis of how fitness-related traits could evolve rapidly in response to crude oil toxicity. We examined evolutionary responses of populations of the common copepod Eurytemora affinis residing in the Gulf of Mexico, by comparing crude oil tolerance of populations collected before versus after the Deepwater Horizon oil spill of 2010. In addition, we imposed laboratory selection for crude oil tolerance for ~8 generations, using an E. affinis population collected from before the oil spill. We found evolutionary increases in crude oil tolerance in the wild population following the oil spill, relative to the population collected before the oil spill. The post-oil spill population showed increased survival and rapid development time in the presence of crude oil. In contrast, evolutionary responses following laboratory selection were less clear; though, development time from metamorphosis to adult in the presence of crude oil did become more rapid after selection. We did find that the wild population, used in both experiments, harbored significant genetic variation in crude oil tolerance, upon which selection could act. Thus, our study indicated that crude oil tolerance could evolve, but perhaps not on the relatively short time scale of the laboratory selection experiment. This study contributes novel insights into evolutionary responses to crude oil, in directly examining fitness-related traits before and after an oil spill, and in observing evolutionary responses following laboratory selection

Data from: Evolutionary responses to crude oil from the Deepwater Horizon oil spill by the copepod Eurytemora affinis

The BP Deepwater Horizon Oil Disaster was the most catastrophic offshore oil spill in U.S. history, yet we still have a poor understanding of how organisms could evolve in response to the toxic effects of crude oil. This study offers a rare analysis of how fitness-related traits could evolve rapidly in response to crude oil toxicity. We examined evolutionary responses of populations of the common copepod Eurytemora affinis residing in the Gulf of Mexico, by comparing crude oil tolerance of populations collected before versus after the Deepwater Horizon oil spill of 2010. In addition, we imposed laboratory selection for crude oil tolerance for ~8 generations, using an E. affinis population collected from before the oil spill. We found evolutionary increases in crude oil tolerance in the wild population following the oil spill, relative to the population collected before the oil spill. The post-oil spill population showed increased survival and rapid development time in the presence of crude oil. In contrast, evolutionary responses following laboratory selection were less clear; though, development time from metamorphosis to adult in the presence of crude oil did become more rapid after selection. We did find that the wild population, used in both experiments, harbored significant genetic variation in crude oil tolerance, upon which selection could act. Thus, our study indicated that crude oil tolerance could evolve, but perhaps not on the relatively short time scale of the laboratory selection experiment. This study contributes novel insights into evolutionary responses to crude oil, in directly examining fitness-related traits before and after an oil spill, and in observing evolutionary responses following laboratory selection

Data from: Do polycultures promote win-wins or tradeoffs in agricultural ecosystem services? A meta-analysis

1. Agriculture comprises the largest global land use, makes it a leading cause of habitat loss. It is therefore critical to identify how to best construct agricultural systems that can simultaneously provide food and other ecosystem services. This challenge requires that we determine how to maximize win-win relationships and minimize trade-offs between services. 2. Through meta-analysis, we tested whether within-field crop diversification (polyculture) can lead to win-win relationships between two ecosystem services: yield of a focal crop species and biocontrol of crop pests. We selected only studies that recorded both services (N = 26 studies; 301 observations), allowing us to better determine the underlying mechanisms of our principal findings. We calculated log-response ratios for both ecosystem services in mono- and polycultures. 3. We found win-win relationships between per-plant yield of the primary crop and biocontrol in polyculture systems that minimized intraspecific competition via substitutive planting. Additionally, we found beneficial effects on biocontrol with no difference in per-unit area yield of the primary crop in polyculture fields at high cropping densities (additive planting) where legumes were used as the secondary crop. These results suggest that there is a strong potential for win-win relationships between biocontrol and per-unit area yield under certain scenarios. Our findings were consistent across geographical regions and by type of primary crop. We did not find evidence that biocontrol had an effect on yield, but rather, both were independently affected by polycultural cropping. 4. Synthesis and applications. We show that well-designed polycultures can produce win-win outcomes between per-plant, and potentially per-unit area, primary crop yield and biocontrol. Biocontrol services are consistently enhanced in polycultures, so polyculture management that focuses on yield optimization is likely to be the best strategy for maximizing both services. In doing so, we suggest that practitioners utilize polycultures that decrease plant–plant competition through a substitution of relatively large quantities of the primary crop for compatibly harvestable secondary crops. Additionally, if planting at high cropping densities, it is important that legumes be the secondary crop

Log response ratios of observations included in meta-analysis

Log response ratios of biocontrol and primary crop yield for every observation included in meta-analysis