skip to main content

Title: Landscape Genomics Provides Evidence of Ecotypic Adaptation and a Barrier to Gene Flow at Treeline for the Arctic Foundation Species Eriophorum vaginatum
Global climate change has resulted in geographic range shifts of flora and fauna at a global scale. Extreme environments, like the Arctic, are seeing some of the most pronounced changes. This region covers 14% of the Earth’s land area, and while many arctic species are widespread, understanding ecotypic variation at the genomic level will be important for elucidating how range shifts will affect ecological processes. Tussock cottongrass ( Eriophorum vaginatum L.) is a foundation species of the moist acidic tundra, whose potential decline due to competition from shrubs may affect ecosystem stability in the Arctic. We used double-digest Restriction Site-Associated DNA sequencing to identify genomic variation in 273 individuals of E. vaginatum from 17 sites along a latitudinal gradient in north central Alaska. These sites have been part of 30 + years of ecological research and are inclusive of a region that was part of the Beringian refugium. The data analyses included genomic population structure, demographic models, and genotype by environment association. Genome-wide SNP investigation revealed environmentally associated variation and population structure across the sampled range of E. vaginatum , including a genetic break between populations north and south of treeline. This structure is likely the result of subrefugial isolation, more » contemporary isolation by resistance, and adaptation. Forty-five candidate loci were identified with genotype-environment association (GEA) analyses, with most identified genes related to abiotic stress. Our results support a hypothesis of limited gene flow based on spatial and environmental factors for E. vaginatum , which in combination with life history traits could limit range expansion of southern ecotypes northward as the tundra warms. This has implications for lower competitive attributes of northern plants of this foundation species likely resulting in changes in ecosystem productivity. « less
Authors:
; ; ; ; ;
Award ID(s):
2220863
Publication Date:
NSF-PAR ID:
10400870
Journal Name:
Frontiers in Plant Science
Volume:
13
ISSN:
1664-462X
Sponsoring Org:
National Science Foundation
More Like this
  1. Reproductive isolation is necessary for population divergence to lead to the formation of separate species. This can occur due to physical isolation of populations, which drives allopatric speciation, or other methods of isolation, such as sympatric speciation where the diverging species are physically in the same range, but structural genomic changes or mutations cause the population to diverge into two different species. Parapatric speciation occurs when populations that are geographically adjacent to each other diverge, which can be driven by adaptations to environmental differences, even with ongoing gene flow. Two desert- adapted brittlebush species, Encelia farinosa and Encelia californica, diverged less than 1 million years ago (Singhal et al., 2020) and have a parapatric distribution, residing in different environments in the Mojave and Sonoran deserts. Encelia farinosa (Brittlebush) has unique silvery leaves that are covered in tiny hairs (leaf pubescence) to better control leaf temperature in the hot and arid conditions of the Sonoran Desert. Encelia californica (California Brittlebush) does not display leaf pubescence and is found in a smaller region of the Mediterranean-like environment of the west coast of North America. Encelia californica is exposed to more precipitation than most other Encelia species. Even with their different morphologies, thesemore »two species are still able to hybridize and create fertile offspring (Clark, 1998). Using PacBio sequencing and Hi-C scaffolding, we assembled and annotated reference genomes for both species to investigate the genomic basis of reproductive isolation in these two species. The scaffold N50/L50 are 10 scaffolds and 76.3 Mbp, and 12 scaffolds and 64.5 Mbp for E. farinosa and E. californica, respectively. Using comparative genomic analyses such as tests for differential adaptation and chromosomal translocations will help reveal whether the drivers of speciation in the Encelia radiation were external (e.g., geologic/climatic) or internal (e.g., genomic rearrangement). These analyses will also help answer how accumulated genomic differences can cause speciation in populations that are not geographically isolated. Analyses such as these are new, exciting sources of information for testing geogenomic and other Earth- life hypotheses.« less
  2. Abstract

    Foundation species have disproportionately large impacts on ecosystem structure and function. As a result, future changes to their distribution may be important determinants of ecosystem carbon (C) cycling in a warmer world. We assessed the role of a foundation tussock sedge (Eriophorum vaginatum) as a climatically vulnerable C stock using field data, a machine learning ecological niche model, and an ensemble of terrestrial biosphere models (TBMs). Field data indicated that tussock density has decreased by ∼0.97 tussocks per m2over the past ∼38 years on Alaska’s North Slope from ∼1981 to 2019. This declining trend is concerning because tussocks are a large Arctic C stock, which enhances soil organic layer C stocks by 6.9% on average and represents 745 Tg C across our study area. By 2100, we project that changes in tussock density may decrease the tussock C stock by 41% in regions where tussocks are currently abundant (e.g. −0.8 tussocks per m2and −85 Tg C on the North Slope) and may increase the tussock C stock by 46% in regions where tussocks are currently scarce (e.g. +0.9 tussocks per m2and +81 Tg C on Victoria Island). These climate-induced changes to the tussock C stock were comparable to, butmore »sometimes opposite in sign, to vegetation C stock changes predicted by an ensemble of TBMs. Our results illustrate the important role of tussocks as a foundation species in determining future Arctic C stocks and highlight the need for better representation of this species in TBMs.

    « less
  3. The phenology of Arctic plants is an important determinant of the pattern of carbon uptake and may be highly sensitive to continued rapid climate change. Eriophorum vaginatum L. (Cyperaceae) has a disproportionate influence over ecosystem processes in moist acidic tundra, but it is unclear whether its growth and phenology will remain competitive in the future. We investigated whether northern tundra ecotypes of E. vaginatum could extend their growing season in response to direct warming and transplanting into southern ecosystems. At the same time, we examined whether southern ecotypes could adjust their growth patterns in order to thrive further north, should they disperse quickly enough. Detailed phenology measurements across three reciprocal transplant gardens over a 2-year period showed that some northern ecotypes were capable of growing for longer when conditions were favourable, but their biomass and growing season length was still shorter than those of the southern ecotype. Southern ecotypes retained large leaf length when transplanted north and mirrored the growing season length better than the others, mainly owing to immediate green-up after snowmelt. All ecotypes retained the same senescence timing, regardless of environment, indicating a strong genetic control. Eriophorum vaginatum may remain competitive in a warming world if southern ecotypesmore »can migrate north.« less
  4. Increasing deoxygenation (loss of oxygen) of the ocean, including expansion of oxygen minimum zones (OMZs), is a potentially important consequence of global warming. We examined present-day variability of vertical distributions of 23 calanoid copepod species in the Eastern Tropical North Pacific (ETNP) living in locations with different water column oxygen profiles and OMZ intensity (lowest oxygen concentration and its vertical extent in a profile). Copepods and hydrographic data were collected in vertically stratified day and night MOCNESS (Multiple Opening/Closing Net and Environmental Sensing System) tows (0–1000 m) during four cruises over a decade (2007– 2017) that sampled four ETNP locations: Costa Rica Dome, Tehuantepec Bowl, and two oceanic sites further north (21– 22 N) off Mexico. The sites had different vertical oxygen profiles: some with a shallow mixed layer, abrupt thermocline, and extensive very low oxygen OMZ core; and others with a more gradual vertical development of the OMZ (broad mixed layer and upper oxycline zone) and a less extensive OMZ core where oxygen was not as low. Calanoid copepod species (including examples from the genera Eucalanus, Pleuromamma, and Lucicutia) demonstrated different distributional strategies (implying different physiological characteristics) associated with this variability. We identified sets of species that (1) changedmore »their vertical distributions and depth of maximum abundance associated with the depth and intensity of the OMZ and its oxycline inflection points; (2) shifted their depth of diapause; (3) adjusted their diel vertical migration, especially the nighttime upper depth; or (4) expanded or contracted their depth range within the mixed layer and upper part of the thermocline in association with the thickness of the aerobic epipelagic zone (habitat compression concept). These distribution depths changed by tens to hundreds of meters depending on the species, oxygen profile, and phenomenon. For example, at the lower oxycline, the depth of maximum abundance for Lucicutia hulsemannae shifted from  600 to  800 m, and the depth of diapause for Eucalanus inermis shifted from  500 to  775 m, in an expanded OMZ compared to a thinner OMZ, but remained at similar low oxygen levels in both situations. These species or life stages are examples of “hypoxiphilic” taxa. For the migrating copepod Pleuromamma abdominalis, its nighttime depth was shallow ( 20 m) when the aerobic mixed layer was thin and the low-oxygen OMZ broad, but it was much deeper ( 100 m) when the mixed layer and higher oxygen extended deeper; daytime depth in both situations was  300 m. Because temperature decreased with depth, these distributional depth shifts had metabolic implications. The upper ocean to mesopelagic depth range encompasses a complex interwoven ecosystem characterized by intricate relationships among its inhabitants and their environment. It is a critically important zone for oceanic biogeochemical and export processes and hosts key food web components for commercial fisheries. Among the zooplankton, there will likely be winners and losers with increasing ocean deoxygenation as species cope with environmental change. Changes in individual copepod species abundances, vertical distributions, and life history strategies may create potential perturbations to these intricate food webs and processes. Present-day variability provides a window into future scenarios and potential effects of deoxygenation.« less
  5. Identifying the evolutionary and ecological mechanisms that drive lineage diversification in the species-rich tropics is of broad interest to evolutionary biologists. Here, we use phylogeographic and demographic analyses of genomic scale RADseq data to assess the impact of a large geographic feature, the Amazon River, on lineage formation in a venomous pitviper, Bothrops atrox. We compared genetic differentiation in samples from four sites near Santarem, Brazil that spanned the Amazon and represented major habitat types. A species delimitation analysis identified each population as a distinct evolutionary lineage while a species tree analysis with populations as taxa revealed a phylogenetic tree consistent with dispersal across the Amazon from north to south. Phylogenetic analyses of mtDNA variation confirmed this pattern and suggest that all lineages originated during the mid- to late-Pleistocene. Historical demographic analyses support a population model of lineage formation through isolation between lineages with low ongoing migration between large populations and reject a model of differentiation through isolation by distance alone. Our results provide a rare example of a phylogeographic pattern demonstrating dispersal over evolutionary time scales across a large tropical river and suggest a role for the Amazon River as a driver of in-situ divergence by both impeding (butmore »not preventing) gene flow and through parapatric differentiation along an ecological gradient.« less