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Notes from Nature – NYBG: New expeditions to uncover global plant biodiversity!

NYBG - Notes From Nature-2

For over 125 years, the William and Lynda Steere Herbarium at the New York Botanical Garden (NYBG) has served as a crucial resource for researchers around the world seeking to study and conserve plant biodiversity. Through projects dedicated to discovering new species, documenting regional floras, and deciphering complex evolutionary relationships within the plant kingdom, thousands of scientists have helped build our collection of 7.8 million specimens — representing the largest natural history archive of plants in the westen hemisphere. Now, plant lovers everywhere can support future scientific exploration at our institution by helping to document our specimens!

Virtual Herbarium Image

This specimen of Gentiana catesbaei “Elliott’s Gentian” was collected in 2016 by Wayne Longbottom, a former amateur naturalist turned active contributor to the NYBG herbarium.

Each NYBG “virtual expedition” will target a subset of our extraordinary collection to accomplish unique research objectives. Some projects will be dedicated to exploring particular geographic regions or specialized habitat types (such as alpine areas), and documenting plants that have been discovered there. Other projects may follow along on the expeditions of notable plant collectors in order to chronicle significant historical specimens. Lastly, we’ll aim to investigate evolutionary relationships and biogeography by cataloging all the occurrences of specific groups of plants scientists know are closely related. All the extraordinary new digital-datasets that citizen scientists help create will contribute profoundly to our understanding of the living planet and open new avenues for investigating long-term patterns in biodiversity change.

Virtual Herbarium Image

NYBG specimens frequently document occurrences of rare native species, like this carnivorous “pitcher-plant” Saracenia purpurea, collected in 1981 from Adirondack Park in New York State.

Citizen scientists who participate in Notes from Nature – NYBG will learn how to interpret natural history specimens and gather research using a variety of online tools to overcome challenges with deciphering historic collection labels. One of the most important resources for puzzle-solving will be the very database we are working to create, the C. V. Starr Virtual Herbarium, where we openly share all currently available data about our specimens. Your mission will be to help fill the gaps in our knowledge using the collections we have already digitized as a guide!

Virtual Herbarium Image

NYBG’s collections are not limited to land plants! This specimen of marine algae represents a separate branch of the tree-of-life, and demonstrates a more challenging hand-written collection label.

Most NYBG expeditions feature a comprehensive workflow designed to capture every essential detail which scientists routinely use: including precise geographic location, date, and collector information. For newcomers to natural history specimens and participants who are looking for a faster-paced activity, Notes from Nature – NYBG will also host “US State Spotter” expeditions, featuring a simplified workflow intended to efficiently capture basic geographic data about our specimens. Keep a lookout for other project types in the future as we experiment with new approaches for including the public in gathering scientifically relevant information from our renowned botanical collection!

Click to join our virtual expeditions today! 

Then discover The Hand Lens to learn more about the fascinating stories told by NYBG specimens.

–Charles Zimmerman, William and Lynda Steere Herbarium, New York Botanical Garden

 

“Islands in the Sky”: Alpine flowers and Climate Change

Diapensia_Photo 41450788, (c) bigjonel, some rights reserved (CC BY-NC)

Diapensia lapponica is an alpine specialist, growing only above treeline on mountains in the northeastern US. Photo © bigjonel

In the United States, alpine environments located above the trees on mountain peaks provide important habitat for Arctic tundra plants. Unique species grow under extreme conditions within these isolated “islands in the sky” which are rarely found elsewhere south of the Arctic circle. Alpine plants’ reliance on these high-elevation environments also makes them especially vulnerable to climatic change, which can dramatically impact the area and ecological functioning of alpine communities.

To understand how alpine plants are responding and adapting to their changing climate, the New York Botanical Garden (NYBG) and Appalachian Mountain Club (AMC) have teamed up with citizen scientists around the world to track geographic distributions and seasonal changes in these alpine species. Since 2004, AMC has been monitoring the timing of plant seasonal events like flowering and fruiting in conjunction with weather conditions. This is the study of phenology. Long term phenology data is a useful tool to quantify plant responses to climatic change and to identify which species might be most vulnerable to a shifting climate. To understand mountain phenology, researchers need a lot of data from different mountain ranges, elevations, and from many points in time. Fortunately, using herbarium records from the New York Botanical Garden, AMC researchers will be able to continue this investigation using historic records of alpine species collected during the past 200 years.

This is where citizen scientists come in! Our researchers need lots of help to collect data from recently digitized herbarium records of alpine species and other mountain plants. Specifically, we need help documenting when, where, and by whom each historic plant specimen was collected from the wild. Anyone with a computer and access to the internet can participate in this project by joining our virtual expedition on the Notes from Nature crowdsourcing platform. From there, you can view images of preserved plant specimens, interpret and transcribe key details from their collection labels, and report directly to scientists at the AMC and around the world who will use your data to understand and help protect these unique alpine plants.

Join our expedition to uncover historic records of alpine plant biodiversity!

While hiking in alpine areas, you can also provide valuable data for this project by capturing pictures of flowering species along the trail. The AMC is tracking current and future effects of climate change by gathering flowering and fruiting time data with the help of hikers with the Northeast Alpine Flower Watch project on iNaturalist:

–Charles Zimmerman, William and Lynda Steere Herbarium, New York Botanical Garden

Long Beach and LA Herbaria bring us more plants!

California State University herbaria at Long Beach and Los Angeles have teamed up once again to bring us exciting new specimens from California and beyond. Explore the world of dainty sunbonnets, lanky loosestrife, graceful meadowfoam, and fantastic phlox as you help these two small collections capture critical biodiversity data.

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Data from our first California Phenology Network expedition are already served live in our growing data portal. The CAP Network thanks all the dedicated Notes from Nature volunteers for their contributions toward liberating these data for immediate use in research, conservation, and education. Maybe keep track of a favorite specimen or two during this next expedition; in a few months, you may find your hard-earned transcriptions loaded and ready to empower new discoveries.

Katie Pearson

Capturing California’s Flowers

The California Collections Network is excited to introduce a new Notes from Nature expedition for one of our partner institutions, the Fresno State Herbarium at California State University, Fresno!
This expedition contains plant specimens largely from Fresno County, California. Fresno County, just below the geographic center of California, stretches 130 miles across the Central Valley, encompassing portions of the Coast Range to the west and the Sierra Nevada Range to the east. The county has an elevational range of 47 meters on the Valley floor to 4,153 meters in the Sierra Nevada mountain range, and this enormous elevational gradient includes a great diversity of ecosystems, including low-elevation vernal pools and alkali sinks, riparian corridors along the Kings and San Joaquin Rivers, foothill chaparral and grasslands, and high-elevation coniferous forests and meadows. It is also the most agricultural productive county in the United States, and the location of the 5th largest city in California (Fresno), with a total county population of almost a million people and a growth rate of ~0.8% per year. As population pressure increases in the Fresno area, and climate change raises temperatures while decreasing water availability, native habitats all over the county are facing unprecedented threats to their continued existence.
Phlox speciosa

Phlox speciosa is a Sierra Nevada wildflower with a wide elevational range (500-2400 meters), and poorly-understood phenology. Photo: Kate Waselkov. 

 

The Fresno State Herbarium was established in 1925 and contains ~40,000 plant specimens dating from the 1890s to today, with a special concentration on high Sierra Nevada ecosystems by the former Fresno State Biology professor Dr. Charles H. Quibell.  This expedition allows you to contribute to our historical understanding of Fresno County ecosystems, especially those high-elevation habitats particularly threatened by climate change, to establish baseline 20th century data at each elevation for species presence and phenology (when each plant species blooms or sets fruit). Ecologists and evolutionary biologists will be able to use this data to predict the response to climate change in our area by different taxonomic and functional groups of plant species, and develop better plans for conservation and habitat restoration.
Fritillaria pinetorum DSC_4209-27

Fritillaria pinetorum grows at high elevations (1800-3200 meters) on granitic slopes in the Sierra Nevada range. Photo: Chris Winchell.  

To discover plant life from this area and help us document how it changes with time and space, visit our Notes from Nature project, Capturing California’s Flowers and click the “Fresno State Herbarium” expedition. Thank you for your support!
— Katherine Waselkov, California State University, Fresno

Training the Machines Update

Thanks for the great work helping us find fruits, flowers and unfolded leaves on Acer (the maples). That is going gangbusters and we hope you can continue the great pace of effort!

We wanted to pass along some good news about how well you did on the first training the machines expedition which focused on Prunus (cherries and allies). The results below are organized by “trait” and includes the total classifications, correct classifications and percentages. We also provide the true positives and true negatives as well and use that calculate what is called “sensitivity” and “specificity.” Sensitivity is a measure of the correct positive against the total true positives. And specificity is the same idea for true negatives. Accuracy is the overall ratio of correct classifications to total classifications from the gold standard. All of our assessments treat a hand-coded dataset that we created at Notes from Nature as a gold standard for comparison.
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Whenever we do these comparisons, we go back to our hand-coded dataset and check our hand-coded results against what appear to be mistakes. As it turns out, we had a number of mistakes in our “gold standard” that you helped us find. That is, the numbers are even better than what is reported below. You guys helped us find problems in our original “gold standard” scoring! That’s super important when developing supervised machine learning datasets. Overall, these are extremely encouraging results! We will be providing some further details about this work in follow up post but, again, this is very exciting news!
Unfolded leaves:

Overall:
Total classifications: 2998
Correct classifications: 2935
Accuracy: 97.9%

Total true positives: 2806 (0.9359573048699132)
Correct positives: 2750
Sensitivity: 98%
Total true negatives: 192 (0.06404269513008673)
Correct negatives: 185
Specificity: 96.35%

Flowers:

Overall:
Total classifications: 2998
Correct classifications: 2918
Accuracy: 97.33%

Total true positives: 1592 (0.5310206804536357)
Correct positives: 1545
Sensitivity: 97.05%

Total true negatives: 1406 (0.46897931954636424)
Correct negatives: 1373
Specificity: 97.65%

Fruits:

Overall:
Total classifications: 2998
Correct classifications: 2904
Accuracy: 96.86%

Total true positives: 796 (0.26551034022681785)
Correct positives: 739
Sensitivity: 92.84%

Total true negatives: 2202 (0.7344896597731821)
Correct negatives: 2165
Specificity: 98.32%

Training the Machines II

We wanted to thank all the Notes from Nature volunteers who helped with Training the Machines I, which focused on Prunus – the cherries, plums, almonds, peaches and nectarines.  We don’t yet have the accuracy of our NFN volunteers compared to a gold standard dataset we created, but we are hard at work on that. We do have reconciliations done, which provide some information about how consistent everyone was, and here are some of those results:  For flowers, there were 2775 strict matches (all three agreed) and 223 majority matches.  For fruits, there were 2,663 strict matches and 335 majority rule matches.  And for leaves unfolded, there were 2,589 matches and 409 majority rule matches.  These are mostly encouraging results!

We also are going to be looking at other interesting questions with the results from this expedition, including some trends in accuracy over time — does scoring more samples mean people get better at this? Or maybe fatigue sets in? We also want to look at accuracy over different species — some might be more challenging than others (we are looking at you, desert almond!). We also see if strict or majority are more likely to be right or wrong. Anyway, we have some key hypotheses to test and we are working on those results and will report more. And of course all this work will be feeding into approaches to scale up machine learning, which we think is exciting – and which we also will have more to share with you soon.

We also need to ask for your help once more, this time on the plant group Acer, the maples. Acer, like Prunus, is well studied for phenology, and has an impressive historical and current record of observation. But Acer can also be challenging (talking to _you_, box elders!). So please pay close attention the help guides which can really help you out here.

Also, your work is really helping out @naturalista, who will be working on a dissertation chapter and papers comparing these results, so thank you so much for the help, and hopefully you will really enjoy this expedition focused on maples, an iconic shade tree that is especially valued in the heat of the summer.

— Rob Guralnick, University of Florida

Happy Anniversary!

Happy Anniversary to Notes from Nature!

Today — June 16th, 2019 — Notes from Nature is celebrating 6 years!

Why June 16th? For a little history, NfN 1.0 launched on Earth Day (April 22nd) 2013. We upgraded to NfN 2.0 on June 16th, 2016 and NfN 3.0 on May 9th, 2019. Although our history is a bit complicated since we have made major platform changes every 3 years or so, we have made it a tradition to celebrate our anniversary on June 16th.

Please help us celebrate 6 years of Notes from Nature by doing a few transcriptions today! June is a slow time of year and we sure could use some help finishing off those remaining NfN 2.0 expeditions.

With gratitude,

The Notes from Nature Team

p.s. Happy Father’s Day to all of the fathers out there! Thanks for your support!

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