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Liberating Data, Empowering Research: Episode 1

7/28/2021

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You can do a lot of science with 3 million herbarium specimen records.
By making our digitized specimen data available not only through the CCH2 portal, but also through global aggregators GBIF and iDigBio, researchers across the world can view and use this valuable resource for studies in their fields. Research topics vary from species endemism and distributions, to invasive species, to human health and fire ecology. In this and upcoming blog posts, we will highlight recently-published papers from research communities outside of California that nevertheless use data from California herbarium specimens to explore and explain our natural world in new and exciting ways.

Patterns of diversity of American alpine species

Figueroa, H.F., Marx, H.E., de Souza Cortez, M.B. et al. Contrasting patterns of phylogenetic diversity and alpine specialization across the alpine flora of the American mountain range system. Alp Botany (2021). https://doi.org/10.1007/s00035-021-00261-y
One of the great questions facing biologists is "how do biological communities assemble?", in other words: "how did all these species come to live in this same place?" This research published in Alpine Botany by PhD student Hector Figueroa of University of Michigan, and colleagues, focuses on this very question for the unique plant communities of alpine regions.
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Skypilot (Polemonium eximium), a high-alpine species endemic to the Sierra Nevada
Alpine ecosystems are characterized by inhospitable abiotic conditions; bitter cold, high UV exposure, harsh winds, and rocky, eroding soil are just a few factors that plant species in these areas have faced over evolutionary time. Despite this, thousands of species (2,937 of which are included in this paper) have evolved to live in these environments, and Figueroa et al. wanted to understand how they came to be. Figueroa et al. used species distribution models to compare patterns of diversity due to phylogenetic (i.e., evolutionary relatedness) and abiotic factors. They found that different alpine communities across the Americas—for example, Patagonian versus Rocky Mountain communities--showed different patterns of diversity, suggesting that each region assembled due to unique factors. In other words, harsh climatic conditions alone don't necessarily determine which species can exist in an area, yet assembly does not depend solely on species being at the right place at the right time (the history-filtering hypothesis). They also found that species richness did not follow a simple latitudinal gradient (species in other environments and taxonomic groups have been shown to display a latitudinal gradient in species richness, with highest diversity around the equator).
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Fig. 2 from Figueroa et al. 2021 (reproduced with permission of Hector Figueroa). This figure shows a heat map that demonstrates how alpine species richness across the Americas did not follow a simple latitudinal gradient.
​This work represents an important use of millions of herbarium specimen records to answer a foundational question in evolutionary biology; and many hundreds of thousands (over 600,000, to be more precise) of these specimens originated from our very own California herbaria! The dataset included specimens from the San Diego Natural History Museum Herbarium, UC Riverside Herbarium, CSU Chico Herbarium, Robert F. Hoover Herbarium at Cal Poly State University, and several others. California herbaria play an important role in shaping our understanding of global evolutionary patterns.
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Specimen of the alpine plant Penstemon davidsonii likely included in the dataset used by Figueroa et al. to create species distribution models. Prior to the CAP project, the originating herbarium, Cal State LA, was 0% digitized. The project has liberated this unique collection to contribute to such broad-scale analyses.
​Glossary
  • Aggregator ​- organization that gathers data from multiple sources and makes them accessible from a single site. The Global Biodiversity Information Facility (GBIF) and iDigBio are two major aggregators of natural history specimen data.
  • Assembly - the process of species moving/evolving over evolutionary time, resulting in the communities of species we see co-occurring today
  • History-filtering hypothesis - the scientific hypothesis that phylogenetic and biogeographic factors primarily influence the assembly of communities
  • Species richness - the number of species found in a particular region
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Do Plants Care when Rain is Rare?

7/13/2021

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Drought: it's a reality for the warm, Mediterranean climatic region of California, especially as human land use changes the landscape and greenhouse grasses trap heat.
Drought can affect plants in many ways. On a physiological level, lack of water produces stress, which can inhibit plant growth and reproduction. Some plants change in appearance or stature under drought stress, often remaining small in size or limiting fruit set, like what might have happened to the Gilia on the left below. Some plants' foliage may wilt, shrivel, and/or die back, like the discoloring manzanita on the right.
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In the face of annual "droughts" during the summer months, many species in California have evolved to be "drought deciduous", meaning they die back in the summer and resume growth and reproduction after winter and spring rains. The iconic species black sage (Salvia mellifera) and California sagebrush (Artemisia californica), for example, are drought deciduous and will often turn brown and lose their leaves in the hot summer months. Still, these plants can be negatively affected by long-term droughts. Too many drought years in a row can kill individuals of even these hardy, well-adapted species.
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Green Salvia mellifera inflorescences in March
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Dried Salvia mellifera inflorescences in September
Drought can also alter plant communities, for example, by allowing drought-tolerant, often "weedy" species to take advantage of the open real estate and weakened competition. The specimens below serve as striking examples; as Laguna Lake in San Luis Obispo shrunk into a cracked, dry bed during the 2012-2016 California drought, three different species of opportunistic goosefoot (Chenopodium) sprung up abundantly in its absence.
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Other species can temporarily (or permanently) disappear in the face of ongoing drought, as one astute collector noted in some of her collections. She discovered populations of the native annual "clustered tarweed" (Hemizonia/Deinandra fasciculata) the year after the severe drought of 2002, even though the species was "not seen at all in 2002 during severe drought year" (check out the specimen here!).
​Sometimes even aggressive, non-native species succumb to the lack of water, as captured on the label of this specimen. Here, Dr. Andy Sanders of the UC Riverside Herbarium (a California Phenology Network collaborator!) discovered that populations of the widespread non-native, redstem stork's bill (Erodium cicutarium) "seem[ed] to have crashed locally in the drought of recent years." Drought can shift the dominance of certain species, alter species abundances as individuals of some species die off from stress, and even drive extirpation of species when the climate becomes too unfavorable. While many plant species have adapted to long periods without water (think cacti, succulents, and deep-rooted oaks), many others have not been able to evolve quickly enough to face the oncoming tide of climate change.
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​Herbarium specimens document botanical changes and can help us understand the changing distributions of plants as environmental factors shift, as demonstrated by the examples above. We're so lucky to have such a dedicated community of collectors and botanists who are creating and caring for this resource.
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This project made possible by National Science Foundation Award 1802312.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.


Poppy images courtesy of Matt Ritter

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