Friday, January 5, 2018

Nantucket faces a rising sea

Posted by Richard B. Primack

“The sea-shore is a sort of neutral ground, a most advantageous point from which to contemplate this world.” 
-Thoreau, in Cape Cod

Over the past half-century the mid-Atlantic coast, including Massachusetts, has experienced a sea level rise that is 3-4 times higher than the global average, according to a report by Sallenger and colleagues in Nature Climate Change. The effects of sea level rise are increasingly felt on Nantucket Island where powerful storm surges dramatically alter beaches and destroy houses.


A storm surge recently eroded the Nantucket coastline in Madaket, leaving this house isolated and vulnerable to being destroyed by the next storm

Homeowners are moving their houses further inland where possible, or building massive sea walls. Such efforts are understandable, but perhaps just delay the inevitable effects of climate change.


Near the town of Nantucket, homeowners build massive walls in front of their houses to keep back the rising sea

Because of its mild oceanic climate, Nantucket gardeners can grow cold-sensitive plants, such as camellias and crepe myrtles that cannot survive Boston winters. As the global climate warms, we will likely be able to grow these beautiful plants in Boston in coming decades.


Camellias are still flowering in early November in protected gardens

The efforts of Nantucket’s people to balance economic development and environmental protection faces new urgency because of rising sea levels and climate change. Some of these same issues have been described in the recent book A Meeting of Land and Sea: Nature and the Future of Martha’s Vineyard by the eminent Harvard Forest ecologist David Foster, that I reviewed for the journal Ecology.

Wednesday, December 27, 2017

Nesting success is linked to breeding phenology for California's birds

Posted by Amanda Gallinat

Many birds around the world have responded to warming temperatures by advancing their breeding phenology, initiating and fledging nests earlier in warmer years. These shifts are primarily considered a means to maintain synchrony with insect availability in the spring. Meanwhile, poleward range shifts are thought to be the main mechanism by which birds track their optimal environmental conditions for survival and reproduction.


White-crowned Sparrow (Zonotrichia leucophrys) nestlings in California. Photo by Sam Roberts.

However, a study of bird communities in California that was recently published in PNAS suggests that phenology shifts can also serve to maintain environmental niches in the spring. The research team, led by Jacob Socolar, found that birds have advanced their breeding phenology between 5-12 days over the past century, essentially negating a 1 degree C temperature increase over the same time period. In other words, the birds have used phenological shifts to maintain a particular temperature niche, which may reduce the need for range shifts. Socolar's group also found that nesting success changes with temperature anomalies; in the warmer parts of a species' range, hot years are associated with low nesting success.


Socolar's team combined observations by Joseph Grinnell (pictured above, preparing specimens in the field) and other observers in the early 1900's with more recent observations, to examine phenology shifts over the past century. Photo from the Bancroft Library/University of California.

This study is an important step forward in understanding the mechanisms behind shifting phenology: birds that nest earlier encounter cooler temperatures and increase their nesting success. As Richard Primack pointed out in an Audubon article highlighting this study, the next important step is to identify the specific links between temperature and nesting success, which may include heat or drought stress, or even insect availability.

Tuesday, December 19, 2017

New Insights from Old Herbarium Specimens

Posted by Richard B. Primack (Boston University; primack@bu.edu) and Charles G. Willis (Harvard University; charleswillis@fas.harvard.edu)

“Live in each season as it passes - breathe the air, drink the drink, taste the fruit & resign yourself to the influence of each.” -Thoreau, in his Journal, 1835

Millions of herbarium specimens are being digitized every year and made available online. In the USA, this effort is being led by the iDigBio program, and involves hundreds of institutions in the USA, Europe, China, Australia, and elsewhere. These massive digital datasets allow scientists to carry out ecological, evolutionary, and climate change research far more quickly and easily than ever before. In three recent papers many scientists, including ourselves, have shown some of the opportunities and limitations of research using herbarium specimens.

Willis, C.G., E.R. Ellwood, R.B. Primack, C.C. Davis, K.D. Pearson, A.S. Gallinat, J.M. Yost, G. Nelson, S.J. Mazer, N.L. Rossington, T.H. Sparks, P.S. Soltis. 2017. Old plants, new tricks: Phenological research using herbarium specimens. Trends in Ecology and Evolution 32: 531-546.

Botanists have always known that herbarium specimens can be a valuable source of information on when plants flower and mature their fruits. In their review article, Willis et al. (2017) summarize the range of climate change projects that have used herbarium specimens to study phenology and climate change in contrast with long-term field studies. In two case studies, they demonstrate that herbarium specimens typically cover a broader geographic area and sample from a wider variety of climatic situations than field studies, and that herbarium specimens can be used to detect the effects of climate change on a wider range of phenological events, like the leafing out times of trees. The review also underscores the promise of integrating herbarium specimen data of flowering dates with other historical datasets of flowering times, such as field observations and dated photographs, to best characterize the impacts of climate change on plant phenology.


Figure 1. Phenology studies using herbarium specimens (blue-gray dots) are increasing in number and their geographical distribution, and this process is being facilitated in regions of the world with a high density of digitized herbarium specimens (yellow-to-red dots). (From Willis et al. 2017; Figure 1) 

Pearse, W.D., C.C. Davis, D. Inouye, R.B. Primack, T.J. Davies. 2017. Measuring the limits of phenology: estimating synchrony and variation in contemporary, historic, and citizen-science datasets. Nature Ecology and Evolution 1, 1876–1882.


Until recently, climate change researchers did not have a good method for combining first observations of flowering time in the field with dates of peak flowering obtained from herbarium specimens. To deal with this problem, Pearse et al. (2017) demonstrate a new, robust statistical method to estimate historical first flowering dates from herbarium specimens collected from around Massachusetts and then compare these dates to observations of first flowering from Concord, MA made by the famous environmental philosopher Henry David Thoreau in Concord in the 19th century. Pearse and colleagues also demonstrate that their approach can be applied to large citizen science datasets like those gathered by the National Phenology Network and the extensive flowering time records collected over decades at the Rocky Mountain Biological Lab. This new statistical method opens the way for an expanded role for herbarium specimens in climate change research that combines diverse types of phenological data.


Figure 2. For each of seven orchid species in Massachusetts, the estimated date of first flowering (red dot) was calculated using the dates of herbarium specimens collected in full flower (black tick marks) and compared to the earliest first flowering date observed in the field by Thoreau and Hosmer (blue dot). (From Pearse et al. 2017; Figure 3, Credit: images of plant species Pogonia ophioglossoides, Platanthera lacera, Cypripedium acaule, Corallorhiza maculata and Arethusa bulbosa, Steven J. Baxter; Platanthera psycodes, Rob Routledge/Sault College; Platanthera grandifolia, Arnold T. Drooz/USDA Forest Service). 

Daru, B.H., D.S. Park, R.B. Primack, C.G. Willis, D.S. Barrington, T.J.S. Whitfeld, T.G. Seidler, P.W. Sweeney, D.R. Foster, A.M. Ellison, C.C. Davis. 2017. Widespread sampling biases in herbaria revealed from large-scale digitization. New Phytologist, doi: 10.1111/nph.14855

If ecologists, climate change biologists, and other researchers do not appreciate the biases of herbarium collections and other museum collections, this could lead to mistaken conclusions. In this study, Daru and his colleagues examined over 5 million digitized herbarium specimens from South Africa, Australia, and New England and determined that specimens were more frequently collected closer to roads and herbaria than other places, threatened species were collected less than other species, and collection efforts were disproportionately focused in some closely related groups. Also, a high percentage of specimens were collected by a small number of very active collectors, likely biasing collections toward the groups of plants these collectors preferred. Future studies using herbarium specimens for novel research projects, especially focused on diversity, distribution, and comparative evolution, will need to take these biases into account in order to avoid erroneous conclusions.


Figure 3. There is a strong geographical bias in collecting in Australia, South Africa and New England, with a greater density of collections nearer to herbaria, roads, and urban centers, with smaller, redder triangles expressing greater sampling effort and larger, blue triangles representing less sampling effort. (From Daru et al. 2017; Figure 1a, b, c.)

As these three papers demonstrate, there are many exciting new opportunities for ecological, evolutionary, and climate change studies using herbarium specimens, and the potential of these studies will greatly expand in coming years as millions more digitized herbarium specimens become available online.

Tuesday, December 12, 2017

Imagination and Reality: Thoreau’s journal and objects

Posted by Richard B. Primack


“I have as much property as I can command and use.” -Thoreau in his Journal

The Concord Museum has a new special exhibit that combines Henry David Thoreau’s journals and objects, highlighting many facets of his life, such as being an observer, a writer, a naturalist, a surveyor, and a writer. The exhibit reunites journals from the Morgan Library in New York with objects from the Concord Museum and elsewhere that are normally housed separately. The exhibit will continue until January 21, 2018.



Thoreau’s flute and one of his journals

A box of pencils from the Thoreau family business along with a journal

A yearly table made by Thoreau showing important weather events

A herbarium specimen of blue irises made by Thoreau; note that the specimen does not have a date or label, which limits its value for phenological research

Saturday, November 25, 2017

Congratulations Dr. Amanda Gallinat!

Posted by Richard B. Primack

“If one advances confidently in the direction of [her] dreams, and endeavors to live the life in which [she] has imagined, [she] will meet with success unimagined in more common hours.”  -Thoreau, in Walden. 

Amanda during her final thesis seminar


Congratulations to Amanda Gallinat for the successful defense of her doctoral dissertation “Effects of climate change and species invasions on autumn phenology and bird-fruit interactions in Massachusetts, USA.” Amanda’s thesis was notable for the strong connections between successive chapters, and her large number of collaborators and co-authors both at BU and elsewhere in the USA and internationally. Also, the first chapter of the thesis, “Autumn, the neglected season in climate change research” has already been published in the high-impact journal Trends in Ecology and Evolution. And the second chapter on using herbarium specimens to monitor fruiting phenology was accepted for publication in the American Journal of Botany two hours before the defense; great timing!

Amanda with her committee members after her successful defense!

Monday, November 13, 2017

An International Network of Trees, published in Silva

Posted by Amanda Gallinat

"Nothing makes the earth seem so spacious as to have friends at a distance; they make the latitudes and longitudes" -Thoreau in a letter, May 22, 1832

For the last five years, the Primack Lab has been part of a collaborative effort to monitor leaf-out, leaf senescence, and fruiting times at a network of seven international botanical gardens. We recently published an overview of this collaborative work in the Arnold Arboretum's magazine, Silva

Richard Primack carefully monitors leaf senescence at the Arnold Arboretum

In the article, we describe how the living collections of botanical gardens have allowed us to monitor the phenology of an enormous range of species; with our colleagues, we have monitored >1600 species for leaf-out, 1360 species for leaf senescence, and several hundred species for fruiting. Our lab conducts our observations right here in Boston, MA, at the Arnold Arboretum.

Young leaves of Acer japonicum observed on April 24th at the Arnold Arboretum

The group's observations across botanical gardens and years have demonstrated that species leaf-out and fruit in a consistent order from year to year and place to place (and related species have similar timing), while the order in which species change color and drop their leaves is not consistent across space and time.

I record fruiting times for plants in the vast Viburnum collection at the Arnold Arboretum

Uncovering these and other patterns in the spring and autumn phenology of many species has given us new insight into the rich natural history present at the Arnold Arboretum (our home site) and other botanical gardens, and helps us understand how plant schedules will respond to climate change.

Wednesday, November 8, 2017

Humidity does not appear to trigger leaf out in woody plants

Posted by Lucy Zipf

Leaf-out phenology in woody trees and shrubs is considered to be strongly controlled by a combination of spring warming, winter chilling requirement, and photoperiod. In 2014 researchers suggested that humidity, rather than temperature itself, might be also be a main trigger of the spring leaf-out of woody plants – with plants leafing out earlier in higher humidity environments. We tested this hypothesis in our recent paper titled “Humidity does not appear to trigger leaf-out in woody plants.”


Gathering dormant twigs from the Hammond Woods in Newton, MA 

We gathered dormant twigs from 15 species of woody plants and exposed twigs from each species to four humidities ranging from 20% to 94% relative humidity. We then monitored the twigs daily for a month to see if twigs in higher humidity treatments leafed out before those exposed to lower humidities.


Twigs of the 15 study species in the highest humidity treatment halfway through the experiment 

The title of the paper gives away our main result: We did not find any consistent, measurable effect of high humidity advancing leaf-out. We also did not see patterns of progressively earlier leaf-out in successively higher humidities. Given our results, humidity does not appear to be a determinant of spring leaf-out in these New England plants.