Evolutionary history underlies plant physiological responses to global change since the last glacial maximum

New uses for ancient middens: bridging ecological and evolutionary perspectives

Rodent middens provide a fine-scale spatiotemporal record of plant and animal communities over the late Quaternary. In the Americas, middens have offered insight into biotic responses to past environmental changes and historical factors influencing the distribution and diversity of species. However, few studies have used middens to investigate genetic or ecosystem level responses. Integrating midden studies with neoecology and experimental evolution can help address these gaps and test mechanisms underlying eco-evolutionary patterns across biological and spatiotemporal scales. Fully realizing the potential of middens to answer cross-cutting ecological and evolutionary questions and inform conservation goals in the Anthropocene will require a collaborative research community to exploit existing midden archives and mount new campaigns to leverage midden records globally.

Evidence, causes, and consequences of declining nitrogen availability in terrestrial ecosystems

The productivity of ecosystems and their capacity to support life depends on access to reactive nitrogen (N). Over the past century, humans have more than doubled the global supply of reactive N through industrial and agricultural activities. However, long-term records demonstrate that N availability is declining in many regions of the world. Reactive N inputs are not evenly distributed, and global changes-including elevated atmospheric carbon dioxide (CO₂) levels and rising temperatures-are affecting ecosystem N supply relative to demand. Declining N availability is constraining primary productivity, contributing to lower leaf N concentrations, and reducing the quality of herbivore diets in many ecosystems. We outline the current state of knowledge about declining N availability and propose actions aimed at characterizing and responding to this emerging challenge.

Natural variation in stress response induced by low CO2 in Arabidopsis thaliana

Variation in atmospheric carbon dioxide (CO₂) concentration can dictate plant growth and development and shape plant evolution. For paired populations of 31 Arabidopsis accessions, respectively, grown under 100 or 380 ppm CO₂, we compared phenotypic traits related to vegetative growth and flowering time. Four accessions showed the least variation in measured growth traits between 100 ppm CO₂ and 380 ppm CO₂ conditions, though all accessions exhibited a dwarf stature with reduced biomass under low CO₂. Our comparison of accessions also incorporated the altitude (indicated in meters) above sea level at which they were originally collected. Notably, An-1 (50 m), Est (50 m), Ws-0 (150 m), and Ler-0 (600 m) showed the least differences (lower decrease or increase) between treatments in flowering time, rosette leaf number, specific leaf weight, stomatal density, and less negative δ¹³C values. When variations for all traits and seedset were considered together, Ws-0 exhibited the least change between treatments. Our results showed that physiological and phenotypic responses to low CO₂ varied among these accessions and did not correlate linearly with altitude, thus suggesting that slower growth or smaller stature under ambient CO₂ may potentially belie a fitness advantage for sustainable growth under low CO₂ availability.

North American temperate conifer (Tsuga canadensis) reveals a complex physiological response to climatic and anthropogenic stressors

Rising atmospheric CO₂ (c_a) is expected to promote tree growth and lower water loss via changes in leaf gas exchange. However, uncertainties remain if gas-exchange regulation strategies are homeostatic or dynamical in response to increasing c_a, as well as evolving climate and pollution inputs. Using a suite of tree ring-based δ¹³C-derived physiological parameters (Δ¹³C, c_i, iWUE) and tree growth from a mesic, low elevation stand of canopy-dominant Tsuga canadensis in north-eastern USA, we investigated the influence of rising c_a, climate and pollution on, and characterised the dynamical regulation strategy of, leaf gas exchange at multidecadal scales. Isotopic and growth time series revealed an evolving physiological response in which the species shifted its leaf gas-exchange strategy dynamically (constant c_i; constant c_i/c_a; constant c_a - c_i) in response to rising c_a, moisture availability and site conditions over 111 yr. Tree iWUE plateaued after 1975, driven by greater moisture availability and a changing soil biogeochemistry that may have impaired a stomatal response. Results suggested that trees may exhibit more complex physiological responses to the changing environmental conditions over multidecadal periods, and complicating the parameterisation of Earth system models and the estimation of future carbon sink capacity and water balance in midlatitude forests and elsewhere.

Lineage-based functional types: characterising functional diversity to enhance the representation of ecological behaviour in Land Surface Models

Process-based vegetation models attempt to represent the wide range of trait variation in biomes by grouping ecologically similar species into plant functional types (PFTs). This approach has been successful in representing many aspects of plant physiology and biophysics but struggles to capture biogeographic history and ecological dynamics that determine biome boundaries and plant distributions. Grass-dominated ecosystems are broadly distributed across all vegetated continents and harbour large functional diversity, yet most Land Surface Models (LSMs) summarise grasses into two generic PFTs based primarily on differences between temperate C₃ grasses and (sub)tropical C₄ grasses. Incorporation of species-level trait variation is an active area of research to enhance the ecological realism of PFTs, which form the basis for vegetation processes and dynamics in LSMs. Using reported measurements, we developed grass functional trait values (physiological, structural, biochemical, anatomical, phenological, and disturbance-related) of dominant lineages to improve LSM representations. Our method is fundamentally different from previous efforts, as it uses phylogenetic relatedness to create lineage-based functional types (LFTs), situated between species-level trait data and PFT-level abstractions, thus providing a realistic representation of functional diversity and opening the door to the development of new vegetation models.

Post-Wildfire Regeneration in a Sky-Island Mixed- Conifer Ecosystem of the North American Great Basin

Information on wildfire impacts and ecosystem responses is relatively sparse in the Great Basin of North America, where subalpine ecosystems are generally dominated by five-needle pines. We analyzed existing vegetation, with an emphasis on regeneration following the year 2000 Phillips Ranch Fire, at a sky-island site in the Snake Range of eastern Nevada. Our main objective was to compare bristlecone pine (Pinus longaeva; PILO) post-fire establishment and survival to that of the co-occurring dominant conifers limber pine (Pinus flexilis; PIFL) and Engelmann spruce (Picea engelmannii; PIEN) in connection with site characteristics. Field data were collected in 40 circular 0.1 ha plots (17.8 m radius) randomly located using GIS so that half of them were inside (“burned”) and half were outside (“unburned”) the 2000 fire boundary. While evidence of previous burns was also found, we focused on impacts from the Phillips Ranch Fire. Mean total basal area, including live and dead stems, was not significantly different between plots inside the burn and plots outside the fire perimeter, but the live basal area was significantly less in the former than in the latter. Wildfire impacts did not limit regeneration, and indeed bristlecone seedlings and saplings were more abundant in plots inside the 2000 fire perimeter than in those outside of it. PILO regeneration, especially saplings, was more abundant than PIFL and PCEN combined, indicating that PILO can competitively regenerate under modern climatic conditions. Surviving PILO regeneration in burned plots was also taller than that of PIFL. By contrast, PCEN was nearly absent in the plots that had been impacted by fire. Additional research should explicitly address how climatic changes and disturbance processes may interact in shaping future vegetation dynamics.

Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA

Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C14 years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI "nt" database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well-preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.

Fire deficits have increased drought sensitivity in dry conifer forests: Fire frequency and tree-ring carbon isotope evidence from Central Oregon

A century of fire suppression across the Western United States has led to more crowded forests and increased competition for resources. Studies of forest thinning or stand conditions after mortality events have provided indirect evidence for how competition can promote drought stress and predispose forests to severe fire and/or bark beetle outbreaks. Here, we demonstrate linkages between fire deficits and increasing drought stress through analyses of annually resolved tree-ring growth, fire scars, and carbon isotope discrimination (Δ¹³ C) across a dry mixed-conifer forest landscape. Fire deficits across the study area have increased the sensitivity of leaf gas exchange to drought stress over the past >100 years. Since 1910, stand basal area in these forests has more than doubled and fire-return intervals have increased from 25 to 140 years. Meanwhile, the portion of interannual variation in tree-ring Δ¹³ C explained by the Palmer Drought Severity Index has more than doubled in ca. 300-500-year-old Pinus ponderosa as well as in fire-intolerant, ca. 90-190-year-old Abies grandis. Drought stress has increased in stands with a basal area of ≥25 m² /ha in 1910, as indicated by negative temporal Δ¹³ C trends, whereas stands with basal area ≤25 m² /ha in 1910, due to frequent or intense wildfire activity in decades beforehand, were initially buffered from increased drought stress and have benefited more from rising ambient carbon dioxide concentrations, [CO₂ ], as demonstrated by positive temporal Δ¹³ C trends. Furthermore, the average Δ¹³ C response across all P. ponderosa since 1830 indicates that photosynthetic assimilation rates and stomatal conductance have been reduced by ~10% and ~20%, respectively, compared to expected trends due to increasing [CO₂ ]. Although disturbance legacies contribute to local-scale intensity of drought stress, fire deficits have reduced drought resistance of mixed-conifer forests and made them more susceptible to challenges by pests and pathogens and other disturbances.

Photosynthesis and carbon allocation are both important predictors of genotype productivity responses to elevated CO2 in Eucalyptus camaldulensis

Intraspecific variation in biomass production responses to elevated atmospheric carbon dioxide (eCO2) could influence tree species' ecological and evolutionary responses to climate change. However, the physiological mechanisms underlying genotypic variation in responsiveness to eCO2 remain poorly understood. In this study, we grew 17 Eucalyptus camaldulensis Dehnh. subsp. camaldulensis genotypes (representing provenances from four different climates) under ambient atmospheric CO2 and eCO2. We tested whether genotype leaf-scale photosynthetic and whole-tree carbon (C) allocation responses to eCO2 were predictive of genotype biomass production responses to eCO2. Averaged across genotypes, growth at eCO2 increased in situ leaf net photosynthesis (Anet) (29%) and leaf starch concentrations (37%). Growth at eCO2 reduced the maximum carboxylation capacity of Rubisco (-4%) and leaf nitrogen per unit area (Narea, -6%), but Narea calculated on a total non-structural carbohydrate-free basis was similar between treatments. Growth at eCO2 also increased biomass production and altered C allocation by reducing leaf area ratio (-11%) and stem mass fraction (SMF, -9%), and increasing leaf mass area (18%) and leaf mass fraction (5%). Overall, we found few significant CO2 × provenance or CO2 × genotype (within provenance) interactions. However, genotypes that showed the largest increases in total dry mass at eCO2 had larger increases in root mass fraction (with larger decreases in SMF) and photosynthetic nitrogen-use efficiency (PNUE) with CO2 enrichment. These results indicate that genetic differences in PNUE and carbon sink utilization (in roots) are both important predictors of tree productivity responsiveness to eCO2.

Continental scale variability of foliar nitrogen and carbon isotopes in Populus balsamifera and their relationships with climate

Variation across climate gradients in the isotopic composition of nitrogen (N) and carbon (C) in foliar tissues has the potential to reveal ecological processes related to N and water availability. However, it has been a challenge to separate spatial patterns related to direct effects of climate from effects that manifest indirectly through species turnover across climate gradients. Here we compare variation along environmental gradients in foliar N isotope (δ15N) and C isotopic discrimination (Δ13C) measured in 755 specimens of a single widely distributed tree species, Populus balsamifera, with variation represented in global databases of foliar isotopes. After accounting for mycorrhizal association, sample size, and climatic range, foliar δ15N in P. balsamifera was more weakly related to mean annual precipitation and foliar N concentration than when measured across species, yet exhibited a stronger negative effect of mean annual temperature. Similarly, the effect of precipitation and elevation on Δ13C were stronger in a global data base of foliar Δ13C samples than observed in P. balsamifera. These results suggest that processes influencing foliar δ15N and Δ13C in P. balsamifera are partially normalized across its climatic range by the habitat it occupies or by the physiology of the species itself.

Changes in biomass allocation buffer low CO2 effects on tree growth during the last glaciation

Isotopic measurements on junipers growing in southern California during the last glacial, when the ambient atmospheric [CO2] (ca) was ~180 ppm, show the leaf-internal [CO2] (ci) was approaching the modern CO2 compensation point for C3 plants. Despite this, stem growth rates were similar to today. Using a coupled light-use efficiency and tree growth model, we show that it is possible to maintain a stable ci/ca ratio because both vapour pressure deficit and temperature were decreased under glacial conditions at La Brea, and these have compensating effects on the ci/ca ratio. Reduced photorespiration at lower temperatures would partly mitigate the effect of low ci on gross primary production, but maintenance of present-day radial growth also requires a ~27% reduction in the ratio of fine root mass to leaf area. Such a shift was possible due to reduced drought stress under glacial conditions at La Brea. The necessity for changes in allocation in response to changes in [CO2] is consistent with increased below-ground allocation, and the apparent homoeostasis of radial growth, as ca increases today.

Host Plant Physiology and Mycorrhizal Functioning Shift across a Glacial through Future [CO2] Gradient

Rising atmospheric carbon dioxide concentration ([CO2]) may modulate the functioning of mycorrhizal associations by altering the relative degree of nutrient and carbohydrate limitations in plants. To test this, we grew Taraxacum ceratophorum and Taraxacum officinale (native and exotic dandelions) with and without mycorrhizal fungi across a broad [CO2] gradient (180-1,000 µL L-1). Differential plant growth rates and vegetative plasticity were hypothesized to drive species-specific responses to [CO2] and arbuscular mycorrhizal fungi. To evaluate [CO2] effects on mycorrhizal functioning, we calculated response ratios based on the relative biomass of mycorrhizal (MBio) and nonmycorrhizal (NMBio) plants (RBio = [MBio - NMBio]/NMBio). We then assessed linkages between RBio and host physiology, fungal growth, and biomass allocation using structural equation modeling. For T. officinale, RBio increased with rising [CO2], shifting from negative to positive values at 700 µL L-1 [CO2] and mycorrhizal effects on photosynthesis and leaf growth rates drove shifts in RBio in this species. For T. ceratophorum, RBio increased from 180 to 390 µL L-1 and further increases in [CO2] caused RBio to shift from positive to negative values. [CO2] and fungal effects on plant growth and carbon sink strength were correlated with shifts in RBio in this species. Overall, we show that rising [CO2] significantly altered the functioning of mycorrhizal associations. These symbioses became more beneficial with rising [CO2], but nonlinear effects may limit plant responses to mycorrhizal fungi under future [CO2]. The magnitude and mechanisms driving mycorrhizal-CO2 responses reflected species-specific differences in growth rate and vegetative plasticity, indicating that these traits may provide a framework for predicting mycorrhizal responses to global change.

Examining Plant Physiological Responses to Climate Change through an Evolutionary Lens

Integrating knowledge from physiological ecology, evolutionary biology, phylogenetics, and paleobiology provides novel insights into factors driving plant physiological responses to both past and future climate change.

Earlier springs are causing reduced nitrogen availability in North American eastern deciduous forests

There is wide agreement that anthropogenic climate warming has influenced the phenology of forests during the late twentieth and early twenty-first centuries(1,2). Longer growing seasons can lead to increased photosynthesis and productivity(3), which would represent a negative feedback to rising CO2 and consequently warming(4,5). Alternatively, increased demand for soil resources because of a longer photosynthetically active period in conjunction with other global change factors might exacerbate resource limitation(6,7), restricting forest productivity response to a longer growing season(8,9). In this case, increased springtime productivity has the potential to increase plant nitrogen limitation by increasing plant demand for nitrogen more than nitrogen supplies, or increasing early-season ecosystem nitrogen losses(10,11). Here we show that for 222 trees representing three species in eastern North America earlier spring phenology during the past 30 years has caused declines in nitrogen availability to trees by increasing demand for nitrogen relative to supply. The observed decline in nitrogen availability is not associated with reduced wood production, suggesting that other environmental changes such as increased atmospheric CO2 and water availability are likely to have overwhelmed reduced nitrogen availability. Given current trajectories of environmental changes, nitrogen limitation is likely to continue to increase for these forests, possibly further limiting carbon sequestration potential.

Environmental drivers of cambial phenology in Great Basin bristlecone pine

The timing of wood formation is crucial to determine how environmental factors affect tree growth. The long-lived bristlecone pine (Pinus longaeva D. K. Bailey) is a foundation treeline species in the Great Basin of North America reaching stem ages of about 5000 years. We investigated stem cambial phenology and radial size variability to quantify the relative influence of environmental variables on bristlecone pine growth. Repeated cellular measurements and half-hourly dendrometer records were obtained during 2013 and 2014 for two high-elevation stands included in the Nevada Climate-ecohydrological Assessment Network. Daily time series of stem radial variations showed rehydration and expansion starting in late April-early May, prior to the onset of wood formation at breast height. Formation of new xylem started in June and lasted until mid-September. There were no differences in phenological timing between the two stands, or in the air and soil temperature thresholds for the onset of xylogenesis. A multiple logistic regression model highlighted a separate effect of air and soil temperature on xylogenesis, the relevance of which was modulated by the interaction with vapor pressure and soil water content. While air temperature plays a key role in cambial resumption after winter dormancy, soil thermal conditions coupled with snowpack dynamics also influence the onset of wood formation by regulating plant-soil water exchanges. Our results help build a physiological understanding of climate-growth relationships in P. longaeva, the importance of which for dendroclimatic reconstructions can hardly be overstated. In addition, environmental drivers of xylogenesis at the treeline ecotone, by controlling the growth of dominant species, ultimately determine ecosystem responses to climatic change.

A dynamic leaf gas-exchange strategy is conserved in woody plants under changing ambient CO2 : evidence from carbon isotope discrimination in paleo and CO2 enrichment studies

Rising atmospheric [CO2 ], ca , is expected to affect stomatal regulation of leaf gas-exchange of woody plants, thus influencing energy fluxes as well as carbon (C), water, and nutrient cycling of forests. Researchers have proposed various strategies for stomatal regulation of leaf gas-exchange that include maintaining a constant leaf internal [CO2 ], ci , a constant drawdown in CO2 (ca  - ci ), and a constant ci /ca . These strategies can result in drastically different consequences for leaf gas-exchange. The accuracy of Earth systems models depends in part on assumptions about generalizable patterns in leaf gas-exchange responses to varying ca . The concept of optimal stomatal behavior, exemplified by woody plants shifting along a continuum of these strategies, provides a unifying framework for understanding leaf gas-exchange responses to ca . To assess leaf gas-exchange regulation strategies, we analyzed patterns in ci inferred from studies reporting C stable isotope ratios (δ(13) C) or photosynthetic discrimination (∆) in woody angiosperms and gymnosperms that grew across a range of ca spanning at least 100 ppm. Our results suggest that much of the ca -induced changes in ci /ca occurred across ca spanning 200 to 400 ppm. These patterns imply that ca  - ci will eventually approach a constant level at high ca because assimilation rates will reach a maximum and stomatal conductance of each species should be constrained to some minimum level. These analyses are not consistent with canalization toward any single strategy, particularly maintaining a constant ci . Rather, the results are consistent with the existence of a broadly conserved pattern of stomatal optimization in woody angiosperms and gymnosperms. This results in trees being profligate water users at low ca , when additional water loss is small for each unit of C gain, and increasingly water-conservative at high ca , when photosystems are saturated and water loss is large for each unit C gain.

Winners always win: growth of a wide range of plant species from low to future high CO2

Evolutionary adaptation to variation in resource supply has resulted in plant strategies that are based on trade-offs in functional traits. Here, we investigate, for the first time across multiple species, whether such trade-offs are also apparent in growth and morphology responses to past low, current ambient, and future high CO 2 concentrations. We grew freshly germinated seedlings of up to 28 C3 species (16 forbs, 6 woody, and 6 grasses) in climate chambers at 160 ppm, 450 ppm, and 750 ppm CO 2. We determined biomass, allocation, SLA (specific leaf area), LAR (leaf area ratio), and RGR (relative growth rate), thereby doubling the available data on these plant responses to low CO 2. High CO 2 increased RGR by 8%; low CO 2 decreased RGR by 23%. Fast growers at ambient CO 2 had the greatest reduction in RGR at low CO 2 as they lost the benefits of a fast-growth morphology (decoupling of RGR and LAR [leaf area ratio]). Despite these shifts species ranking on biomass and RGR was unaffected by CO 2, winners continued to win, regardless of CO 2. Unlike for other plant resources we found no trade-offs in morphological and growth responses to CO 2 variation, changes in morphological traits were unrelated to changes in growth at low or high CO 2. Thus, changes in physiology may be more important than morphological changes in response to CO 2 variation.