Spring- and fall-flowering species show diverging phenological responses to climate in the Southeast USA

Dynamic transcriptome analysis provides molecular insights into underground floral differentiation in Adonis Amurensis Regel & Radde

Understanding flower developmental processes is a prerequisite for improving flowering 'plants' production. Adonis amurensis is a fascinating spring ephemeral plant that develops its flower organs underground. Nevertheless, knowledge of the molecular mechanisms driving this particular process is scarce. Herein, we examined transcriptional changes during underground flower differentiation in A. amurensis and unveiled key differently regulated genes and pathways. High-throughput RNA sequencing of meristems at different flower developmental stages, including flower primordium (FP), sepal stage (SE), perianth primordium (PE), stamen stage (ST), and pistil stage (PI), identified 303,234 unigenes that showed 44.79% similarity with sequences in Aquilegia coerulea. Correlations, principal component, and differentially expressed genes (DEGs) analyses revealed that few molecular changes occurred during the transition from PE to ST. Many DEGs exhibited stage-specific regulations. Transcription factor (TF) and phytohormone family genes are critical regulators of the floral differentiation process in A. amurensis. The most differentially regulated TFs were MADS, FAR1, MYBs, AP2/ERF, B3, C2H2, and LOBs. We filtered out 186 candidate genes for future functional studies, including 18 flowering/circadian-related, 32 phytohormone-related, and TF family genes. Our findings deepen our understanding of the underground flower differentiation process and offer critical resources to dissect its regulatory network in A. amurensis. These findings establish a foundational platform for researchers dedicated to exploring the unique phenotypic characteristics of this specific flowering modality and delving into the intricate molecular mechanisms underpinning its regulation and expression.

Complex climate-mediated effects of urbanization on plant reproductive phenology and frost risk

Urbanization can affect the timing of plant reproduction (i.e. flowering and fruiting) and associated ecosystem processes. However, our knowledge of how plant phenology responds to urbanization and its associated environmental changes is limited. Herbaria represent an important, but underutilized source of data for investigating this question. We harnessed phenological data from herbarium specimens representing 200 plant species collected across 120 yr from the eastern US to investigate the spatiotemporal effects of urbanization on flowering and fruiting phenology and frost risk (i.e. time between the last frost date and flowering). Effects of urbanization on plant reproductive phenology varied significantly in direction and magnitude across species ranges. Increased urbanization led to earlier flowering in colder and wetter regions and delayed fruiting in regions with wetter spring conditions. Frost risk was elevated with increased urbanization in regions with colder and wetter spring conditions. Our study demonstrates that predictions of phenological change and its associated impacts must account for both climatic and human effects, which are context dependent and do not necessarily coincide. We must move beyond phenological models that only incorporate temperature variables and consider multiple environmental factors and their interactions when estimating plant phenology, especially at larger spatial and taxonomic scales.

Shifts in flowering phenology in response to spring temperatures in eastern Tennessee

PREMISE

Plant phenological shifts are among the clearest indicators of the effects of climate change. In North America, numerous studies in the northeastern United States have demonstrated earlier spring flowering compared to historical records. However, few studies have examined phenological shifts in the southeastern United States, a highly biodiverse region of North America characterized by dramatic variations in abiotic conditions over small geographic areas.

METHODS

We examined 1000+ digitized herbarium records along with location-specific temperature data to analyze phenological shifts of 14 spring-flowering species in two adjacent ecoregions in eastern Tennessee.

RESULTS

Spring-flowering plant communities in the Blue Ridge and the Ridge and Valley ecoregions differed in their sensitivity to temperature; plants in the Ridge and Valley flower 0.73 days earlier/°C on average compared to 1.09 days/°C for plants in the Blue Ridge. Additionally, for the majority of species in both ecoregions, flowering is sensitive to spring temperature; i.e., in warmer years, most species flowered earlier. Despite this sensitivity, we did not find support for community-level shifts in flowering within eastern Tennessee in recent decades, likely because increases in annual temperature in the southeast are driven primarily by warming summer (rather than spring) temperatures.

CONCLUSIONS

These results highlight the importance of including ecoregion as a predictor in phenological models for capturing variation in sensitivity among populations and suggest that even small shifts in temperature can have dramatic effects on phenology in response to climate in the southeastern United States.

The influence of climate warming on flowering phenology in relation to historical annual and seasonal temperatures and plant functional traits

Climate warming has the potential to influence plant flowering phenology which in turn can have broader ecological consequences. Herbarium collections offer a source of historical plant data that makes possible the ability to document and better understand how warming climate can influence long-term shifts in flowering phenology. We examined the influence of annual, winter, and spring temperatures on the flowering phenology of herbarium specimens for 36 species collected from 1884-2015. We then compared the response to warming between native and non-native, woody and herbaceous, dry and fleshy fruit, and spring vs summer blooming species. Across all species, plants flowered 2.26 days earlier per 1 °C increase in annual average temperatures and 2.93 days earlier per 1 °C increase in spring onset average temperatures. Winter temperatures did not significantly influence flowering phenology. The relationship of temperature and flowering phenology was not significantly different between native and non-native species. Woody species flowered earlier than herbaceous species only in response to increasing annual temperatures. There was no difference in the phenological response between species with dry fruits and those fleshy fruits for any of the temperature periods. Spring blooming species exhibited a significantly greater phenological response to warming yearly average temperatures than summer blooming species. Although herbarium specimens can reveal climate change impacts on phenology, it is also evident that the phenological responses to warming vary greatly among species due to differences in functional traits such as those considered here, as well as other factors.

Modeling past and future spatiotemporal distributions of airborne allergenic pollen across the contiguous United States

Exposures to airborne allergenic pollen have been increasing under the influence of changing climate. A modeling system incorporating pollen emissions and atmospheric transport and fate processes has been developed and applied to simulate spatiotemporal distributions of two major aeroallergens, oak and ragweed pollens, across the contiguous United States (CONUS) for both historical (year 2004) and future (year 2047) conditions. The transport and fate of pollen presented here is simulated using our adapted version of the Community Multiscale Air Quality (CMAQ) model. Model performance was evaluated using observed pollen counts at monitor stations across the CONUS for 2004. Our analysis shows that there is encouraging consistency between observed seasonal mean concentrations and corresponding simulated seasonal mean concentrations (oak: Pearson = 0.35, ragweed: Pearson = 0.40), and that the model was able to capture the statistical patterns of observed pollen concentration distributions in 2004 for most of the pollen monitoring stations. Simulation of pollen levels for a future year (2047) considered conditions corresponding to the RCP8.5 scenario. Modeling results show substantial regional variability both in the magnitude and directionality of changes in pollen metrics. Ragweed pollen season is estimated to start earlier and last longer for all nine climate regions of the CONUS, with increasing average pollen concentrations in most regions. The timing and magnitude of oak pollen season vary across the nine climate regions, with the largest increases in pollen concentrations expected in the Northeast region.

Flowering time advances since the 1970s in a sagebrush steppe community: Implications for management and restoration

Climate change is widely known to affect plant phenology, but little is known about how these impacts manifest in the widespread sagebrush ecosystem of the Western United States, which supports a number of wildlife species of concern. Shifts in plant phenology can trigger consequences for the plants themselves as well as the communities of consumers that depend upon them. We assembled historical observations of first-flowering dates for 51 species collected in the 1970s and 1980s in a montane sagebrush community in the Greater Yellowstone Ecosystem and compared these to contemporary phenological observations targeting the same species and locations (2016-2019). We also assembled regional climate data (average spring temperature, day of spring snowmelt, and growing degree days) and tested the relationship between first-flowering time and these variables for each species. We observed the largest change in phenology in early-spring flowers, which, as a group, bloomed on average 17 days earlier, and as much as 36 days earlier, in the contemporary data set. Mid-summer flowers bloomed on average 10 days earlier, nonnative species 15 days earlier, and berry-producing shrubs 5 days earlier, while late summer flowering plants did not shift. The greatest correlates of early-spring and mid-summer flowering were average spring temperature and day of snowmelt, which was 21 days earlier, on average, in 2016-2019 relative to the 1973-1978 observations. The shifts in flowering phenology that we observed could indicate developing asynchronies or novel synchronies of these plant resources and wildlife species of conservation concern, including Greater Sage-grouse, whose nesting success is tied to availability of spring forbs; grizzly bears, which rely heavily on berries for their fall diet; and pollinators. This underscores the importance of maintaining a diverse portfolio of native plants in terms of species composition, genetics, phenological responsiveness to climatic cues, and ecological importance to key wildlife and pollinator species. Redundancy within ecological niches may also be important considering that species roles in the community may shift as climate change affects them differently. These considerations are particularly relevant to restoration and habitat-enhancement projects in sagebrush communities across western North America.

Seasonal Climate Trends across the Wild Blueberry Barrens of Maine, USA

Wild blueberries in Maine, USA are facing threats from our changing climate. While summer climate variations have been affecting this important commercial crop directly, significant climate variations in other seasons also can be potentially detrimental to blueberry production. Therefore, we analyzed annual and seasonal climate trends (temperature, rainfall, snow cover) over the past 41 years (1980–2020) for seven Maine counties (Piscataquis, Washington, Hancock, Knox, Lincoln, Kennebec, York) with large wild blueberry areas. We found that, across all blueberry production fields (or “barrens”), historical temperatures increased significantly (p < 0.05) in the fall and winter followed by summer, but not in the spring. Additionally, precipitation increased slightly (0.5–1.2 mm/year) in the winter and fall, whereas no changes were found in the spring and summer. Furthermore, we found that historical temperatures were lower in Piscataquis (north-central) and Washington (north-east) counties, whereas in south-western counties (Hancock to York) experienced a relatively warmer climate. The rate of increasing temperature was comparatively slower in the warmer barrens located towards the south-west (Hancock to York). Moreover, the growing season lengthened towards the fall season consistently in all locations, whereas lengthening towards the spring was inconsistent. These findings inform the wild blueberry growers in different locations of Maine about the seasonal shifts occurring for their crop. This knowledge may assist with land management planning in order for the growers to prepare for future impacts.

Phenological advance in the South African Namaqualand Daisy First and Peak Bloom: 1935-2018

The annual Namaqualand daisy flowering spectacle is a world-renowned environmental event. Using documentary sources, including newspaper archives from The Rand Daily Mail, Volksblad and Die Burger and social media records from Flickr and iNaturalist, the first long-term phenological dataset spanning 1935-2018 was compiled for the Namaqualand region. The dataset contains first flowering, full bloom and end of bloom dates for the Namaqualand daisies. This study explores shifts in the timing of Namaqualand daisy bloom, and the role of climate in driving these phenological shifts. First flowering and full bloom phenology of the Namaqualand daisies are advancing at statistically significant rates of 2.6 days decade^-1 and 2.1 days decade^-1 respectively. Climatic data from seven Namaqualand weather stations, collectively spanning 1959-2018, were interrogated. For the periods spanned by both climate and phenology data, the relationships between the two were explored. Increasing temperatures are driving the calculated advances of the daisy flowering dates at statistically significant rates of change ranging from 0.01 to 0.11 days °C^-1. The main climate drivers of Namaqualand daisy flowering phenology are winter and spring temperatures, the onset of the winter rainy season during April and May, and total winter precipitation. The rates of advance and climate drivers are broadly consistent with global phenological meta-analyses and records for the Southern Hemisphere. The advances in the timing of Namaqualand daisy flowering will have a significant impact on the tourism sector in the region, as flower viewing tours need to be prearranged months in advance.

Spatiotemporal Variation of Osmanthus fragrans Phenology in China in Response to Climate Change From 1973 to 1996

Climate change greatly affects spring and autumn plant phenology around the world consequently, and significantly impacts ecosystem function and the social economy. However, autumn plant phenology, especially autumn flowering phenology, has not been studied so far. In this study, we examined the spatiotemporal pattern of Osmanthus fragrans phenology, including both leaf phenology (the date of bud-bust, BBD; first leaf unfolding, FLD; and 50% of leaf unfolding, 50 LD) and flowering phenology (the date of first flowering, FFD; peak of flowering, PFD; and end of flowering, EFD). Stepwise multiple linear regressions were employed to analyze the relationships between phenophases and climatic factors in the long term phenological data collected by the Chinese Phenological Observation Network from 1973 to 1996. The results showed that spring leaf phenophases and autumn flowering phenophases were strongly affected by latitude. BBD, FLD, and 50LD of O. fragrans were delayed by 3.98, 3.93, and 4.40 days as per degree of latitude increased, while FFD, PFD and EFD in O. fragrans advanced 3.11, 3.26, and 2.99 days, respectively. During the entire study period, BBD was significantly delayed across the region, whereas no significant trends were observed either in FLD or 50LD. Notably, all flowering phenophases of O. fragrans were delayed. Both leaf and flowering phenophases negatively correlated with growing degree-days (GDD) and cold degree-days (CDD), respectively. BBD and FLD were negatively correlated with total annual precipitation. In addition to the effects of climate on autumn flowering phenology, we found that earlier spring leaf phenophases led to delayed autumn flowering phenophases. Our results suggest that future climate change and global warming might delay the phenological sequence of O. fragrans. Our findings also advanced the flowering mechanism study of autumn flowering plants, and facilitated the accurate prediction of future phenology and climate change.

Extirpated prairie species demonstrate more variable phenological responses to warming than extant congeners

PREMISE

Shifting phenology in response to climate is one mechanism that can promote population persistence and geographic spread; therefore, species with limited ability to phenologically track changing environmental conditions may be more susceptible to population declines. Alternatively, apparently nonresponding species may demonstrate divergent responses to multiple environmental conditions experienced across seasons.

METHODS

Capitalizing on herbarium records from across the midwestern United States and on detailed botanical surveys documenting local extinctions over the past century, we investigated whether extirpated and extant taxa differ in their phenological responses to temperature and precipitation during winter and spring (during flowering and the growing season before flowering) or in the magnitude of their flowering time shift over the past century.

RESULTS

Although warmer temperatures across seasons advanced flowering, extirpated and extant species differed in the magnitude of their phenological responses to winter and spring warming. Extirpated species demonstrated inconsistent phenological responses to warmer spring temperatures, whereas extant species consistently advanced flowering in response to warmer spring temperatures. In contrast, extirpated species advanced flowering more than extant species in response to warmer winter temperatures. Greater spring precipitation tended to delay flowering for both extirpated and extant taxa. Finally, both extirpated and extant taxa delayed flowering over time.

CONCLUSIONS

This study highlights the importance of understanding phenological responses to seasonal warming and indicates that extirpated species may demonstrate more variable phenological responses to temperature than extant congeners, a finding consistent with the hypothesis that appropriate phenological responses may reduce species' likelihood of extinction.

Tracking biological footprints of climate change using flowering phenology of the geophytes: Pancratium tenuifolium and Scadoxus multiflorus

Drought-adapted geophytes are responding to the effects of climate change in arid and semi-arid environments. In this study, herbarium and historical rainfall data were used to examine the impact of rainfall changes on flowering trends of Pancratium tenuifolium Hochst. ex A.Rich and Scadoxus multiflorus (Martyn) Raf. subsp. multiflorus. Flowering was delayed by approximately 7 days per decade for P. tenuifolium during the period 1930 to 2018 and by approximately 14 days per decade for S. multiflorus subsp. multiflorus during the period 1924 to 2008. Scadoxus multiflorus subsp. multiflorus delayed the day of flowering by approximately 0.3 days per millimetre increase of rainfall, with Pancratium tenuifolium showing a non-significant response to summer rainfall during the same period. Overall, a linear mixed-effects model revealed that the day of flowering was delayed by approximately 8 days per degree rise in latitude and advanced by approximately 9 days per degree rise in longitude. Additionally, summer rainfall had significant effects on the day of flowering with a 1-mm increase in summer rainfall delaying the day of flowering by approximately 0.16 days. These changes in flowering times may ultimately alter the distribution of geophytes in Namibia.

Review: Plant eco-evolutionary responses to climate change: Emerging directions

Contemporary climate change is exposing plant populations to novel combinations of temperatures, drought stress, [CO₂] and other abiotic and biotic conditions. These changes are rapidly disrupting the evolutionary dynamics of plants. Despite the multifactorial nature of climate change, most studies typically manipulate only one climatic factor. In this opinion piece, we explore how climate change factors interact with each other and with biotic pressures to alter evolutionary processes. We evaluate the ramifications of climate change across life history stages,and examine how mating system variation influences population persistence under rapid environmental change. Furthermore, we discuss how spatial and temporal mismatches between plants and their mutualists and antagonists could affect adaptive responses to climate change. For example, plant-virus interactions vary from highly pathogenic to mildly facilitative, and are partly mediated by temperature, moisture availability and [CO₂]. Will host plants exposed to novel, stressful abiotic conditions be more susceptible to viral pathogens? Finally, we propose novel experimental approaches that could illuminate how plants will cope with unprecedented global change, such as resurrection studies combined with experimental evolution, genomics or epigenetics.

Small herbaria contribute unique biogeographic records to county, locality, and temporal scales

PREMISE

With digitization and data sharing initiatives underway over the last 15 years, an important need has been prioritizing specimens to digitize. Because duplicate specimens are shared among herbaria in exchange and gift programs, we investigated the extent to which unique biogeographic data are held in small herbaria vs. these data being redundant with those held by larger institutions. We evaluated the unique specimen contributions that small herbaria make to biogeographic understanding at county, locality, and temporal scales.

METHODS

We sampled herbarium specimens of 40 plant taxa from each of eight states of the United States of America in four broad status categories: extremely rare, very rare, common native, and introduced. We gathered geographic information from specimens held by large (≥100,000 specimens) and small (<100,000 specimens) herbaria. We built generalized linear mixed models to assess which features of the collections may best predict unique contributions of herbaria and used an Akaike information criterion-based information-theoretic approach for our model selection to choose the best model for each scale.

RESULTS

Small herbaria contributed unique specimens at all scales in proportion with their contribution of specimens to our data set. The best models for all scales were the full models that included the factors of species status and herbarium size when accounting for state as a random variable.

CONCLUSIONS

We demonstrated that small herbaria contribute unique information for research. It is clear that unique contributions cannot be predicted based on herbarium size alone. We must prioritize digitization and data sharing from herbaria of all sizes.

Willow phenological modelling at different altitudes in central Italy

In order to estimate the impact of climate change on the phenological parameters and to compare them with the historical record, a decision support system (DSS) has been applied employing a Phenological Modelling Platform. Biological observations of two willow species (Salix acutifolia and smithiana Willd) in 3 gardens at different altitudes located in Central Italy were utilized to identify suitable phenological models related to four main vegetative phase timings (BBCH11, BBCH91, BBCH 94, BBCH95), and male full flowering (BBCH 65) clearly identifiable in these species. The present investigation identifies the best phenological models for the main phenophases allowing their practical application as real-time monitoring and plant development prediction tools. Sigmoid model revealed high performances in simulating spring vegetative phases, BBCH11 (First leaves unfolded), and BBCH91 (Shoot and foliage growth completed). Salix acutifolia Willd. development appeared to be more related to temperature amount interpreted by phenological models in comparison to Salix smithiana Willd. above all during spring (BBCH11 and 91), probably due to a different grade of phenotypic plasticity between the 2 considered species.

Climate change effects on biodiversity, ecosystems, ecosystem services, and natural resource management in the United States

Climate change is a pervasive and growing global threat to biodiversity and ecosystems. Here, we present the most up-to-date assessment of climate change impacts on biodiversity, ecosystems, and ecosystem services in the U.S. and implications for natural resource management. We draw from the 4th National Climate Assessment to summarize observed and projected changes to ecosystems and biodiversity, explore linkages to important ecosystem services, and discuss associated challenges and opportunities for natural resource management. We find that species are responding to climate change through changes in morphology and behavior, phenology, and geographic range shifts, and these changes are mediated by plastic and evolutionary responses. Responses by species and populations, combined with direct effects of climate change on ecosystems (including more extreme events), are resulting in widespread changes in productivity, species interactions, vulnerability to biological invasions, and other emergent properties. Collectively, these impacts alter the benefits and services that natural ecosystems can provide to society. Although not all impacts are negative, even positive changes can require costly societal adjustments. Natural resource managers need proactive, flexible adaptation strategies that consider historical and future outlooks to minimize costs over the long term. Many organizations are beginning to explore these approaches, but implementation is not yet prevalent or systematic across the nation.

A new fine-grained method for automated visual analysis of herbarium specimens: A case study for phenological data extraction

PREMISE

Herbarium specimens represent an outstanding source of material with which to study plant phenological changes in response to climate change. The fine-scale phenological annotation of such specimens is nevertheless highly time consuming and requires substantial human investment and expertise, which are difficult to rapidly mobilize.

METHODS

We trained and evaluated new deep learning models to automate the detection, segmentation, and classification of four reproductive structures of Streptanthus tortuosus (flower buds, flowers, immature fruits, and mature fruits). We used a training data set of 21 digitized herbarium sheets for which the position and outlines of 1036 reproductive structures were annotated manually. We adjusted the hyperparameters of a mask R-CNN (regional convolutional neural network) to this specific task and evaluated the resulting trained models for their ability to count reproductive structures and estimate their size.

RESULTS

The main outcome of our study is that the performance of detection and segmentation can vary significantly with: (i) the type of annotations used for training, (ii) the type of reproductive structures, and (iii) the size of the reproductive structures. In the case of Streptanthus tortuosus, the method can provide quite accurate estimates (77.9% of cases) of the number of reproductive structures, which is better estimated for flowers than for immature fruits and buds. The size estimation results are also encouraging, showing a difference of only a few millimeters between the predicted and actual sizes of buds and flowers.

DISCUSSION

This method has great potential for automating the analysis of reproductive structures in high-resolution images of herbarium sheets. Deeper investigations regarding the taxonomic scalability of this approach and its potential improvement will be conducted in future work.

Toward a large-scale and deep phenological stage annotation of herbarium specimens: Case studies from temperate, tropical, and equatorial floras

PREMISE OF THE STUDY

Phenological annotation models computed on large-scale herbarium data sets were developed and tested in this study.

METHODS

Herbarium specimens represent a significant resource with which to study plant phenology. Nevertheless, phenological annotation of herbarium specimens is time-consuming, requires substantial human investment, and is difficult to mobilize at large taxonomic scales. We created and evaluated new methods based on deep learning techniques to automate annotation of phenological stages and tested these methods on four herbarium data sets representing temperate, tropical, and equatorial American floras.

RESULTS

Deep learning allowed correct detection of fertile material with an accuracy of 96.3%. Accuracy was slightly decreased for finer-scale information (84.3% for flower and 80.5% for fruit detection).

DISCUSSION

The method described has the potential to allow fine-grained phenological annotation of herbarium specimens at large ecological scales. Deeper investigation regarding the taxonomic scalability of this approach is needed.

A new method and insights for estimating phenological events from herbarium specimens

PREMISE OF THE STUDY

A novel method of estimating phenology of herbarium specimens was developed to facilitate more precise determination of plant phenological responses to explanatory variables (e.g., climate).

METHODS AND RESULTS

Simulated specimen data sets were used to compare the precision of phenological models using the new method and two common, alternative methods (flower presence/absence and ≥50% flowers present). The new "estimated phenophase" method was more precise and extracted a greater number of significant species-level relationships; however, this method only slightly outperformed the simple "binary" (e.g., flowers present/absent) method.

CONCLUSIONS

The new method enables estimation of phenological trends with greater precision. However, when time and resources are limited, a presence/absence method may offer comparable results at lower cost. Using a more restrictive approach, such as only including specimens in a certain phenophase, is not advised given the detrimental effect of decreased sample size on resulting models.