How are rare species maintained?: Reproductive barriers between Layia jonesii, a rare serpentine endemic, and L. platyglossa

Reproductive barriers are vital to generating new species as well as maintaining distinct species. Investigating reproductive barriers between closely related plant taxa helps us to understand how these barriers are maintained, particularly between rare and widespread relatives. Layia jonesii, a rare San Luis Obispo County serpentine endemic, and L. platyglossa, a common coastal species, co-occur on serpentine derived hillsides and are interfertile. At these locations, L. jonesii is isolated to dry soils near serpentine rock outcrops and L. platyglossa is located on slightly deeper grassland soils surrounding the rock outcrops. On hillsides where they co-occur, I observe two morphologically distinct species, therefore the two species must be maintaining reproductive barriers, yet mechanisms that maintain this isolation are unknown. I studied this system to investigate possible mechanisms contributing to the maintenance of reproductive barriers. I hypothesize prezygotic reproductive isolation in this system is due to (1) habitat isolation due to local adaptation to differential edaphic environments on the hillside, (2) flowering time differences, and (3) reduced seed set resulting from hybrid crosses. To investigate the local adaptation of L. jonesii and L. platyglossa, I reciprocally transplanted both species into the center of each species’ distribution. I also conducted a competition experiment to determine if L. jonesii is sensitive to resource competition beyond its natural distribution. To investigate flowering time differences, I tracked flowering time of both wild and reciprocally transplanted populations. I also performed controlled crosses to determine if heterospecific, or hybrid crosses, result in lowered seed set than conspecific crosses. The reciprocal transplants showed L. platyglossa is locally adapted to the grassland habitat. Local adaptation likely prevents L. playtyglossa from dispersing into the rock outcrop habitat. Results of the competition experiment revealed L. jonesii is sensitive to competition and this may contribute to its constrained distribution to shallow soils. Local adaptation and competition likely contribute to habitat isolation between the two species. I also documented stark differences in flowering time between the species which contributes to reproductive isolation by reducing pollen flow. Hybrid crosses also resulted in lowered seed set than conspecific crosses. These results suggest prezygotic barriers to reproduction likely maintain the majority of isolation between the two species. These results provide insight into mechanisms that maintain reproductive barriers between closely related taxa existing in similar habitats. The results also contribute to our understanding of how rare plants preserve genetic integrity near common and interfertile relatives

Old Plants, New Tricks:Phenological Research Using Herbarium Specimens

The timing of phenological events, such as leaf-out and flowering, strongly influence plant success and their study is vital to understanding how plants will respond to climate change. Phenological research, however, is often limited by the temporal, geographic, or phylogenetic scope of available data. Hundreds of millions of plant specimens in herbaria worldwide offer a potential solution to this problem, especially as digitization efforts drastically improve access to collections. Herbarium specimens represent snapshots of phenological events and have been reliably used to characterize phenological responses to climate. We review the current state of herbarium-based phenological research, identify potential biases and limitations in the collection, digitization, and interpretation of specimen data, and discuss future opportunities for phenological investigations using herbarium specimens

Data from: Phenological responsiveness to climate differs among four species of Quercus in North America

1.The timing of the seasonal activity of organisms is a tractable indicator of climate change. Many studies in North America have investigated the role of temperature on the onset date of phenological transitions in temperate deciduous trees and found that the onset of leafing and flowering in numerous species has occurred earlier in recent years, apparently in response to higher temperatures in winter and spring. 2.Few studies have examined the climatic and biogeographic drivers of phenological responses in water-limited ecosystems or explored inter-specific variation in responses of phenological metrics other than the timing of onset, such as the periodicity or duration of phenological activity. 3.This study used phenological observations of four species of Quercus contributed to the USA National Phenology Network database from 2009-2014 to investigate how responses to climate (temperature and precipitation) and geographic location (latitude, longitude and elevation) varied among two western North American species (Q. agrifolia and Q. lobata) and two eastern and central North American species (Q. alba and Q. rubra). 4.Within years, in species in the western, water-limited ecosystems, the phenological phases observed here (bud break, flowers or flower buds) tend to occur intermittently throughout the growing season, and each event is of longer duration than the same phenophases of the temperate-zone species, rendering a single onset date an incomplete metric with which to track responsiveness or to compare species. By contrast, the eastern/central U.S. species were phenologically more responsive than the western species to spatial and temporal variation in winter, spring, and fall precipitation and maximum temperature. 5.Synthesis: Within and between regions these congeners exhibited a diversity of responses to seasonal temperature and precipitation. This indicates that for predictive model development it is critical to understand how each underlying driver influences species that are adapted to different climatic regimes. These results underscore the value of studying a range of phenological metrics and species from a variety of ecosystems to better predict phenological responses to short-term variation and to long-term change in climate

A new phenological metric for use in pheno-climatic models: A case study using herbarium specimens of Streptanthus tortuosus.

PremiseHerbarium specimens have been used to detect climate-induced shifts in flowering time by using the day of year of collection (DOY) as a proxy for first or peak flowering date. Variation among herbarium sheets in their phenological status, however, undermines the assumption that DOY accurately represents any particular phenophase. Ignoring this variation can reduce the explanatory power of pheno-climatic models (PCMs) designed to predict the effects of climate on flowering date.MethodsHere we present a protocol for the phenological scoring of imaged herbarium specimens using an ImageJ plugin, and we introduce a quantitative metric of a specimen's phenological status, the phenological index (PI), which we use in PCMs to control for phenological variation among specimens of Streptanthus tortuosus (Brassicaceeae) when testing for the effects of climate on DOY. We demonstrate that including PI as an independent variable improves model fit.ResultsIncluding PI in PCMs increased the model R 2 relative to PCMs that excluded PI; regression coefficients for climatic parameters, however, remained constant.DiscussionOur protocol provides a simple, quantitative phenological metric for any observed plant. Including PI in PCMs increases R 2 and enables predictions of the DOY of any phenophase under any specified climatic conditions

Quercus phenology data

These data were obtained from the USA National Phenology Network (USA-NPN) database, accessible at www.usanpn.org/results/data. Data were collected by citizen and professional scientists through the Nature's Notebook monitoring program (www.naturesnotebook.org). This dataset was selected from the "Individual Phenometrics" data type available from the USA-NPN Phenology Observation Portal which delivers derived estimates of phenophase onset and end for individual plants. This dataset was customized by selecting all available data for four species of Quercus: Q. alba, Q. agrifolia, Q. lobata, and Q. rubra from 2009-2014 on two phenophases, "breaking leaf buds" and "flowers and flower buds". The dataset was filtered to only include onset dates that were detected within 7 days of a negative observation record. This data files includes one tab with estimated onset and end dates for phenophase activity and one tab with data field descriptions. For additional information on USA-NPN protocols and phenophase definitions visit www.usanpn.org/data

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

PremiseHerbarium 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.MethodsWe 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.ResultsThe 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.DiscussionThis 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

Old Plants, New Tricks: Phenological Research Using Herbarium Specimens.

The timing of phenological events, such as leaf-out and flowering, strongly influence plant success and their study is vital to understanding how plants will respond to climate change. Phenological research, however, is often limited by the temporal, geographic, or phylogenetic scope of available data. Hundreds of millions of plant specimens in herbaria worldwide offer a potential solution to this problem, especially as digitization efforts drastically improve access to collections. Herbarium specimens represent snapshots of phenological events and have been reliably used to characterize phenological responses to climate. We review the current state of herbarium-based phenological research, identify potential biases and limitations in the collection, digitization, and interpretation of specimen data, and discuss future opportunities for phenological investigations using herbarium specimens

Digitization protocol for scoring reproductive phenology from herbarium specimens of seed plants

Premise of the Study Herbarium specimens provide a robust record of historical plant phenology (the timing of seasonal events such as flowering or fruiting). However, the difficulty of aggregating phenological data from specimens arises from a lack of standardized scoring methods and definitions for phenological states across the collections community. Methods and Results: To address this problem, we report on a consensus reached by an iDigBio working group of curators, researchers, and data standards experts regarding an efficient scoring protocol and a data‐sharing protocol for reproductive traits available from herbarium specimens of seed plants. The phenological data sets generated can be shared via Darwin Core Archives using the Extended MeasurementOrFact extension. Conclusions: Our hope is that curators and others interested in collecting phenological trait data from specimens will use the recommendations presented here in current and future scoring efforts. New tools for scoring specimens are reviewed