When evolution is the solution to pollution : key principles, and lessons from rapid repeated adaptation of killifish (Fundulus heteroclitus) populations

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Evolutionary Applications 10 (2017): 762–783, doi:10.1111/eva.12470.For most species, evolutionary adaptation is not expected to be sufficiently rapid to buffer the effects of human-mediated environmental changes, including environmental pollution. Here we review how key features of populations, the characteristics of environmental pollution, and the genetic architecture underlying adaptive traits, may interact to shape the likelihood of evolutionary rescue from pollution. Large populations of Atlantic killifish (Fundulus heteroclitus) persist in some of the most contaminated estuaries of the United States, and killifish studies have provided some of the first insights into the types of genomic changes that enable rapid evolutionary rescue from complexly degraded environments. We describe how selection by industrial pollutants and other stressors has acted on multiple populations of killifish and posit that extreme nucleotide diversity uniquely positions this species for successful evolutionary adaptation. Mechanistic studies have identified some of the genetic underpinnings of adaptation to a well-studied class of toxic pollutants; however, multiple genetic regions under selection in wild populations seem to reflect more complex responses to diverse native stressors and/or compensatory responses to primary adaptation. The discovery of these pollution-adapted killifish populations suggests that the evolutionary influence of anthropogenic stressors as selective agents occurs widely. Yet adaptation to chemical pollution in terrestrial and aquatic vertebrate wildlife may rarely be a successful “solution to pollution” because potentially adaptive phenotypes may be complex and incur fitness costs, and therefore be unlikely to evolve quickly enough, especially in species with small population sizes.National Science Foundation Grant Numbers: DEB-1265282, OCE-1314567, DEB-1120263; National Institutes of Environmental Health Sciences Grant Numbers: R01ES021934-01, P42ES007381; Postdoctoral Research Program at the US Environmental Protection (US EPA); Office of Research and Development; Oak Ridge Institute for Science and Education (ORISE) Grant Number: DW92429801; US Department of Energ

Role of Eddies in the Carbon Pump of Eastern Boundary Upwelling Systems, REEBUS, Cruise No. M156, 03.07. – 01.08.2019 Mindelo (Cap Verde) – Mindelo

Summary The major goal of the RV METEOR cruise M156 to Cape Verdian waters and the Mauritanian upwelling area off West Africa was to contribute to a better quantitative understanding of the effects of mesoscale eddies on CO2 source/sink mechanisms and the biological carbon pump in eastern boundary upwelling areas as well as their effects to the oligotrophic periphery including the deep-sea floor. The cruise M156 (MOSES Eddy Study I) was conducted within the framework of the BMBF funded REEBUS project (Role of Eddies in the Carbon Pump of Eastern Boundary Upwelling Systems) by a consortium of physical, biological (benthic microbiology, bacterial plankton, protists) and biogeochemical oceanographers. Specific aims were i. the quantification of solute and particle fluxes within and at the periphery of eddies; ii. to determine the turnover of carbon species, air-sea gas exchange of CO2, iii. the determination of the protistan and bacterial plankton community structures in the surface layers of an eddy, and iv. to quantify the magnitude and variability of material fluxes to the seabed and turnover in the sediment underneath the eddy passage. To achieve these aims, the cruise had two major observing strategies: i. an intense benthic/pelagic program along the zonal eddy passage at 18°N. Along this corridor ranging from 24°20’ to 16°30’W, five benthic/pelagic stations (E1 to E5) in different water depths and distances from the Mauritanian coast were performed. The motivation for this survey has been to resolve zonal gradients in pelagic element cycling as well as of organic matter degradation and burial in the seabed, which in turn could potentially be linked with changes in eddy induced primary- and export production. ii. the detailed investigation of an individual eddy to investigate physical, biogeochemical and biological processes on meso- to submeso-scales (100km to 10m). Satellite data analysis was performed before and during the cruise to identify a suitable eddy from a combination of sea-level anomaly, ocean color as Chl-a proxy, and sea-surface temperature supplemented with shipboard current velocity measurements. A total of 171 stations were sampled. The water column program consists of 59 CTD casts, 29 MSS and 20 Marine Snow Catcher deployments. For biogeochemical measurements at the sea surface two deployments of a Lagrangian Surface Drifter and one Waveglider deployment were conducted. At the seafloor, we conducted 10 BIGO deployments. Ten seafloor imaging surveys were performed using the towed camera system OFOS, supplemented with 7 Multibeam and 1 Sidescan surveys. In deviation from the cruise proposal, the planned long-term deployment of a Lander, which was planned to record a time series of oxygen fluxes during the passage of an eddy, was not deployed due to a major delay in its design and manufacturing. The planned AUV (Girona 500) deployments at the shallow E5 station close to the Mauritanian coast station did also not take place. Despite moderate weather conditions, all deployments were successful, hence all the data and sample material aimed for has been achieved. It is to expect that as planned all scientific questions can be addressed. Especially in the synthesis of all REEBUS cruises and the consideration of data from earlier cruises (MSM17/4, M107) into this region a high scientific potential can be expected

Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans

High-throughput sequence analysis of variants of human cytomegalovirus strains Towne and AD169

The genomes of commonly used variants of human cytomegalovirus (HCMV) strains Towne and AD169 each contain a substantial mutation in which a region (UL/b′) at the right end of the long unique region has been replaced by an inverted duplication of a region from the left end of the genome. Using high-throughput technology, we have sequenced HCMV strain Towne (ATCC VR-977) and confirmed the presence of two variants, one exhibiting the replacement in UL/b′ and the other intact in this region. Both variants are mutated in genes RL13, UL1, UL40, UL130, US1 and US9. We have also sequenced a novel AD169 variant (varUC) that is intact in UL/b′ except for a small deletion that affects genes UL144, UL142, UL141 and UL140. Like other AD169 variants, varUC is mutated in genes RL5A, RL13, UL36 and UL131A. A subpopulation of varUC contains an additional deletion affecting genes IRS1, US1 and US2

Climate-Biogeochemistry Interactions in the Tropical Ocean: Data collection and legacy

From 2008 through 2019, a comprehensive research project, SFB 754, Climate - Biogeochemistry Interactions in the Tropical Ocean, was funded by the German Research Foundation to investigate the climate-biogeochemistry interactions in the tropical ocean with a particular emphasis on the processes determining the oxygen distribution. During three 4-year long funding phases, a consortium of more than 150 scientists conducted or participated in 34 major research cruises and collected a wealth of physical, biological, chemical, and meteorological data. A common data policy agreed upon at the initiation of the project provided the basis for the open publication of all data. Here we provide an inventory of this unique data set and briefly summarize the various data acquisition and processing methods used

Convergent evolution of the genomes of marine mammals

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and are therefore a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and de novo assembled the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome, and that a subset were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that while convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare

Inherent limits of light-level geolocation may lead to over-interpretation

In their 2015 Current Biology paper, Streby et al. [1] reported that Golden-winged Warblers (Vermivora chrysoptera), which had just migrated to their breeding location in eastern Tennessee, performed a facultative and up to “>1,500 km roundtrip” to the Gulf of Mexico to avoid a severe tornadic storm. From light-level geolocator data, wherein geographical locations are estimated via the timing of sunrise and sunset, Streby et al. [1] concluded that the warblers had evacuated their breeding area approximately 24 hours before the storm and returned about five days later. The authors presented this finding as evidence that migratory birds avoid severe storms by temporarily moving long-distances. However, the tracking method employed by Streby et al. [1] is prone to considerable error and uncertainty. Here, we argue that this interpretation of the data oversteps the limits of the used tracking technique. By calculating the expected geographical error range for the tracked birds, we demonstrate that the hypothesized movements fell well within the geolocators’ inherent error range for this species and that such deviations in latitude occur frequently even if individuals remain stationary