Kristina Dutton

A selection of published writings on science and nature

Scientists sequence coast redwood genome

by Kristina Dutton Point Reyes Light, February 10, 2022,

Following an ambitious multi-year effort, researchers have assembled and annotated the genome of the coast redwood, an iconic species and the world’s tallest tree. Sequencing the genome is fundamental to various efforts, including better understanding the tree’s adaptive potential. 

As new technologies have developed over the last decade, decoding conifer genomes, which are large and difficult to assemble, has come a long way. 

“When we first started, [the coast redwood] was thought to be a genome that might be impossible to sequence with existing technology because of its size and complexity, but we were motivated to take a shot at it,” said Dr. David Neale, a plant sciences professor emeritus at the University of California, Davis and the lead author on the new coast redwood genome research. The results, published in December, were the work of a team from U.C. Davis, Johns Hopkins University and elsewhere.

A genome is all of a living thing’s genetic material—the whole kit and caboodle—and the coast redwood genome is the second largest ever sequenced, at nearly nine times the size of the human genome. The redwood genome has 26.5 billion base pairs of DNA and is hexaploid, meaning it has six sets of chromosomes. Humans have 3 billion base pairs of DNA and are diploid, with two sets of chromosomes.

Though these numbers are impressive, what’s important is the information encoded in the genes, not necessarily the volume of information or how it’s encoded. Sequencing the genome is a step toward understanding the genetic makeup of the trees, including their unique adaptations such as resistance to fungal disease and their relationship to coastal fog. 

“If you live in Point Reyes, you know that redwood grows right along the coastal margins, is adapted to fog, and in fact absorbs moisture not only through the root system but through the needles,” Dr. Neale said. 

Genomes belong to species, but they also belong to individuals, so every redwood has its own genome, and slight genetic variations can provide an edge when faced with environmental pressures. 

In Marin, foresters and conservationists are interested in ecosystem resilience in redwood stands and in harvesting trees, a key component of sustainable forestry. Tom Gaman, a forester from Inverness, says management practices are evolving to include controlled burns, support of old-growth forests, and uneven age management—thinning around the largest and oldest secondary-growth trees.

When trees are planted or thinned, there can be a change to the genetic diversity of that specific redwood population, for better or worse. Using technologies based on the genome sequence can help with monitoring all the way down to an individual tree that might turn out to be particularly resilient when faced with sudden changes in our uncertain climate future. 

Rebound in monarch count leaves questions

by Kristina Dutton Point Reyes Light, January 5th, 2022,

The western monarch butterfly, a migratory population that overwinters on the California coast, has both delighted and befuddled conservationists this year with an apparent surge after last year’s low numbers. According to the Xerces Society for Invertebrate Conservation, more than 200,000 monarchs overwintered in California in 2021. The 2020 Thanksgiving count reached record lows, with a little over 1,900 monarchs found at overwintering sites.

“We’re so grateful the numbers are up,” said Emma Pelton, a senior conservation biologist at the Xerces Society. “While we don’t know if these numbers will sustain, it does give us a reason to hope. Last year the numbers were so low, people were really depressed.”

Yet scientists are struggling to explain the rebound, and some believe the numbers may be misleading.

Chip Taylor, a professor emeritus of ecology and evolutionary biology at the University of Kansas and the director of Monarch Watch, believes monarchs are changing their behavior to adapt to changes in their environment. The low numbers in 2020 may have been the result of a dispersal that led the butterflies to simply not be where scientists and volunteers expected to find them.

Monarchs are found throughout the world, but the two major populations reside in North America. The smaller of these two populations, the western monarch, spends summers from the Rockies to the Pacific Ocean and north as far as southern Canada. They overwinter along the California coast from Mendocino to Baja, sheltering in giant clusters on Monterey cypress and non-native eucalyptus trees.

As recently as the 1980s, the western monarch migration boasted millions of individuals, and West Marin was home to huge, densely populated sites. Even with a significantly higher count this winter, the number of monarchs is a mere fraction of what it once was, with very low numbers in Marin, Sonoma and other Bay Area counties. The majority of this year’s monarchs were found between Santa Cruz and Ventura, though one site near Agate Beach in Bolinas had 105 butterflies.

Although the monarch is a well-studied insect, the population “is now bouncing around in uncharted territory,” Ms. Pelton said. Scientists have attributed the western monarch’s decline in part to pesticide use and habitat loss due to development, but recent studies emphasize the impact of climate change and its domino effects: drought, rising temperatures, fallen trees, fires and habitat reduction.

Dr. Taylor said monarchs took a deep dive starting in 2017, a year that brought unusual heat at critical times of the year. Prolonged periods with temperatures over 90 degrees are unfavorable to butterfly eggs. High heat means the realized fecundity—the number of eggs laid versus the potential total—drops dramatically. Maps of temperature rise across the country are correlated with declining butterfly populations, particularly on the West Coast, where temperatures have been rising 0.7 degrees per decade since 1975.

“Monarchs can be affected by a number of things, and you can track a lot of things in parallel with temperature changes, but monarchs are a species that are going to be greatly affected by temperature changes,” he said.

Dr. Taylor said the 2020 Thanksgiving count was likely not comprehensive enough. Given the mortality that normally occurs in a population, “there’s no way the survivors of [last year’s] count—maybe 400 to 500 females—could account for 200,000 butterflies this fall,” he said.

He suggested that the breeding population on the California coast may have moved inland, leaving them outside the range of the winter count. Larger numbers of butterflies last winter would help explain this winter’s apparent surge.

At the same time the migratory population is collapsing, a small population of resident monarchs has been growing in the Bay Area. Typically, western monarchs, which are dependent on milkweed for reproduction, do not breed in the winter. Native milkweed dies back in winter, and the migrating population goes into reproductive diapause.

Resident monarchs do not migrate, and typically live in parts of the United States where the weather is mild and milkweed plants can grow year-round. But in recent years Bay Area gardeners have been planting more non-native milkweed, such as tropical milkweed, which does not die back, so resident monarch populations are now breeding year-round in urban gardens.

In California, the resident and migratory populations appear to be mingling, though to what extent is unclear. Researchers are looking into “whether that’s helpful or dangerous, or if it impacts the urge to migrate, or if it’s adding to the migratory population,” said Mia Monroe, a ranger for the Golden Gate National Recreation Area who founded the western monarch’s Thanksgiving count.

The resident population, estimated at around 12,000 in the Bay Area, is “not sufficient to make up for the loss of the migratory monarchs,” Ms. Monroe said.

Ms. Pelton sees this year’s count as “a hopeful sign and evidence that the migration is not lost, as some feared after last year.” Yet with only one year of population increase, it’s unclear whether the western monarch is “clawing its way back from the brink, or if this is a blip in the continuation of the migration’s decline,” she said.

For his part, Dr. Taylor is optimistic about monarchs’ abilities to adapt to a changing climate. “The species will still be here, but the migrations will end,” he said. “All of the temperature models indicate that monarch migrations are not sustainable in the long run.”

Many conservation groups are promoting beneficial actions to support the butterfly’s migration, such as making habitat improvements and establishing pockets of wild meadows in agricultural areas. These are efforts they say have made a difference.

At the Environmental Action Committee of West Marin’s offices, a new educational display on western monarchs covers the environmental risks and the life history of the butterfly.

“In Marin County we’re fortunate to host both breeding and overwintering populations of western monarchs, so what you do to help depends on where you live,” said Leslie Adler-Ivanbrook, the nonprofit’s program director. “The monarchs are a window into the whole biodiversity crisis…a piece of the bigger picture.”

The E.A.C. has guidelines for Marin residents both on their website and at the exhibit, and the Salmon Protection and Watershed Network’s website offers a list of native nectar plants, such as coyote mint, that can be found at local nurseries.

Overwintering monarchs fly from their clusters in sheltering trees on sunny days, searching for nectar plants and water. Gardeners on the coast can plant and protect native nectar plants to create a refuge where the butterflies can feed and build fat stores.

By late February, after a flurry of mating, monarchs’ great migration begins, and the females seek milkweed plants to lay their eggs on. Gardeners who live five or more miles from the coast can plant native milkweed to help stabilize and increase the population.

Ms. Monroe also suggests that Marin residents consider common spaces such as libraries, medians and city halls as locations for much-needed habitat for pollinators. Nature is messy, and butterflies will find refuge in unexpected places.

Citizens can also contribute to researchers’ body of data by observing and noting monarchs through the app iNaturalist and at westernmonarchwatch.org. More data will help researchers understand the butterfly’s presence throughout the county: when, where, and what they’re doing throughout the year.

For Dr. Taylor, those interested in helping monarch populations should focus on actions centered around climate change.

Ultimately, monarchs are indicators of a healthy and balanced environment. The sudden change in the population emphasizes the extent to which environmental changes can have unexpected and swift consequences.

“If we want to sustain monarch butterflies and many, many other things, we have to make it personal,” Dr. Taylor said. “We have to connect people with the change that’s going on out there.”

Cordell Bank dives yield deep-sea discoveries

by Kristina DuttonFebruary 16, 2022

Six dives in the Cordell Bank National Marine Sanctuary have shed light on deep-sea diversity off Marin’s shores, including a new sponge species and the first observations of many corals in the sanctuary. 

Between 2017 and 2019, the National Oceanic and Atmospheric Administration and the Ocean Exploration Trust collaborated on the first video surveys of deep-sea canyons and slopes off Cordell Bank. Surveys were taken from the E/V Nautilus, a 210-foot research vessel equipped with the remotely operated vehicle Hercules. 

Hercules allowed the team to record observations in unexplored deep-water coral reef environments like Bodega Canyon, a large seafloor feature more than 12 miles long and over 6,500 feet deep. These were the deepest dives ever made in the sanctuary, half of which has yet to be explored. 

“Before these two cruises, we’d never been to these depths,” said Dani Lipski, a research coordinator at Cordell Bank and the lead scientist for the site. “We’re seeing broad categories of species that have never been recorded in the sanctuary before.” 

Ecosystems in the ocean are structured by depth, and the regions that surround Cordell Bank are suitable habitat for deep-sea corals and sponges. “When you drive out to the Sierra, you see the ecosystems change with elevation. It’s the same thing in the deep sea,” Ms. Lipski said. 

At least 15 sponges were observed for the first time on the Nautilus dives, and one is an entirely new species, dubbed Farrea cordelli. The delicately featured, ruffled white sponge was collected in Box Canyon at a depth of nearly 7,000 feet. 

Sponges can be challenging to identify, and not all specimens collected on the dives have been described. Dr. Henry Reiswig, a sponge expert with the Royal British Columbia Museum, died shortly after describing the Farrea cordelli. “It’s tragic we’ve lost him as a resource because there are not a lot of people practiced at the art of sponge taxonomy,” said Kaitlin Graiff, a research contractor with Cordell Bank. 

One large mushroom-shaped sponge about three feet tall was recorded in Cordell Bank for the first time in 2019 and is thought to range as far north as the Aleutian Islands. “When I saw this sponge, I was so excited I nearly jumped out of my chair, but with the loss of Henry we don’t have anyone to identify it yet,” said Ms. Graiff, who was tasked with combing through hundreds of hours of video from the Nautilus surveys.  

Besides sponges, deep-sea corals collected on the dives are of particular interest to scientists because they are long lived, slow growing and provide habitat for a huge variety of organisms. “They’re almost like a condominium for other animals,” Ms. Graiff said. “We saw eggs and invertebrates like brittle stars and crabs.”

Of the 38 coral species observed, 31 were previously unknown to live in the sanctuary. The corkscrew coral, Radicipes stonei, had previously been found only at two locations in the Aleutian Islands, and Isidella tentaculum and Keratosis sp., long-lived bamboo corals greater than two meters in diameter, were aged up to 400 years old. Bamboo coral, almost like a tree, lays down rings as it grows, and as it ages it keeps a signature of environmental conditions in its rings, much like a tree.

Deep-sea corals and sponges are thought to play an important role in the carbon cycle. They are filter feeders attached to hard seafloor features and catch floating “marine snow” that drifts from surface waters to the seafloor. Corals may also provide refuge for the larvae of commercially important fish species. Like their warm-water cousins, deep-sea corals’ skeletons are made up of colonies of small animals. These corals can live for hundreds to thousands of years in cold, dark waters 200 to 20,000 feet below the surface.

The community of researchers identifying deep-sea animals is small, and much is still unknown about the ecological function of creatures like corals and sponges. Observation data from the Nautilus dives will be shared with taxonomy libraries and databases for a better understanding of deep-sea habitats, Ms. Graiff said. 

Footage of the Nautilus surveys can be found at www.nautiluslive.org.

Ships clutter whale calls year-round, study finds

by Kristina DuttonJanuary 26, 2022

An acoustic study of the underwater soundscape of Cordell Bank National Marine Sanctuary found that sound from shipping lanes in and out of the Bay Area overlaps with whale vocalizations. Data analysis from the recordings also found that whales, previously thought to be seasonal
inhabitants of the sanctuary, are present year-round. Both findings have implications for conservation
efforts. 

“Cordell Bank is a highly connected marine ecosystem with highly mobile species, and what we hear and learn in this sanctuary is relevant over a much greater range,” said John Ryan, a senior research specialist at the Monterey Bay Aquarium Research Institute and one of the study’s co-authors. 

Cordell Bank and the adjacent Greater Farallones National Marine Sanctuary are feeding grounds for blue and humpback whales and are part of a major migration route for gray whales. As human-generated noise has increased on the California coast, the impacts of ocean noise pollution on marine organisms and animals has become an important area of study. Gathering acoustic data is key.

Light doesn’t travel far in water, so in a dark ocean most marine mammals have evolved to use sound as their primary sense. The natural underwater soundscape is complex, and whales rely on sound for communication, foraging, navigation and even predator detection. 

Sound, although dependent on temperature and pressure, can travel thousands of miles underwater, and whales have been known to communicate over great distances. Dr. Samara Haver, a post-doctoral scholar with Oregon State University and the study’s lead author, said the whales in the study—those with low-frequency vocalizations—can hear each other over incredibly long distances.

In 2015, a team of researchers deployed a hydrophone, a microphone that can function as a continuous underwater acoustic monitor, to collect ambient soundscapes for two years in Cordell Bank, a 1,200-square-mile area offshore from Point Reyes. The range of the hydrophone extended to the Greater Farallones, which wraps around Cordell Bank as it hugs the coast from San Francisco north to Point Arena.

Around the country there are 12 such hydrophone recorders, four of which are in marine sanctuaries. The device in Cordell Bank is part of a larger network that the National Oceanic and Atmospheric Administration’s Pacific Marine Environmental Laboratory has created with help from partners, said Danielle Lipinski, the research coordinator for Cordell Bank. 

An analysis of the resulting acoustic data was published in the Journal of the Acoustical Society of America in 2020. It revealed that both large vessels and vocalizing baleen whales—fins, blues and humpbacks—contribute to the low-frequency ambient soundscape of Cordell Bank. In other words, acoustical niches inhabited by whales are cluttered by sound from the shipping lanes. 

“Their communication is being compromised,” said Michael Stocker, executive director of Ocean Conservation Research, a West Marin nonprofit that explores solutions to noise pollution in marine environments. “Shipping noise is the most ubiquitous sound in the ocean. When it’s loud, you raise your voice, up to a point, and when it’s too loud, you just give up,” he said.

Conservative estimates showed the hydrophone was able to pick up sound from its location to the shipping lanes or a ship anywhere in the sanctuary, but more research is needed to understand how the ambient sound levels might be impacting the whales. Shipping noises could be fundamentally altering or overwhelming their communication, or the whales may be adapting—scientists don’t know, Dr. Haver said, but it’s clear that Cordell Bank does not provide refuge from vessel traffic.

The study also found blue and fin whales were present in the fall, winter and spring, and humpback whales were present throughout the year. 

The unique features of Cordell Bank, including its depth, small size and close proximity to ship traffic, increase ambient sound levels. Dr. Haver said the sanctuary is more exposed to the Pacific Ocean than are other research sites, and that magnifies the way sound from fishing vessels is propagated.

Noise from large commercial vessels and other human activities is not specifically regulated in the two sanctuaries, but there are other rules in place. Large vessels are limited to defined shipping routes, and discharging material and disturbing the seafloor is prohibited. 

Currently Cordell Bank and the Greater Farallones request voluntary shipping slowdowns from May 1 to Nov. 15. Sanctuary officials have observed up to 100 whales feeding within shipping lanes; slowing ship speeds not only reduces strikes, but also lowers noise pollution. “We do know that when ships slow down, they’re quieter,” Dr. Haver said. 

The new findings could help sanctuary officials create stronger guidelines for vessel traffic, potentially redefining shipping lanes and adjusting dates for voluntary slowdowns. 

Careful rerouting of shipping lanes and reductions in vessel speeds have helped reduce ship strikes in California, where there were 70 recorded incidents of ship strikes between 2007 and 2020, many related to Bay Area ports. Researchers believe those numbers represent a small fraction of the total, since many incidents go unnoticed and most whales sink after they die. 

According to Cordell Bank’s outreach and education coordinator, Jennifer Stock, the lack of population recovery among blue whales is a prime concern for sanctuary officials. 

Although shipping traffic in the Bay Area is expected to increase, Mr. Stocker says newer ships are being built with greater attention to noise pollution. Low-noise propulsion systems and vibration-isolated mounting systems can tone down the clamor of large ships. 

“Currently the guidelines are only recommendations,” Mr. Stocker said, but “there is a bit of a shift in this direction because it’s more energy-efficient.” He and other researchers say the public can help reduce ocean noise pollution by buying local and reaching out to policymakers. 

Researchers at Cordell Bank—from the National Oceanic and Atmospheric Association, the National Park Service, Point Blue Conservation Science, Oregon State University, Stanford University and the Monterey Bay Aquarium—are now working to better understand whales’ responses to noise levels and where and how often different species are present. Future studies will likely incorporate species that use higher-frequency vocalizations.

Piecing together the puzzle involves both monitoring and research projects that bring together current and long-term visual and acoustic data. 

“We’re integrating what we learn from analysis of sound in the ocean with other forms of observation,” Dr. Ryan said. “This helps us understand how the ecosystem is changing, and how that might affect the marine mammals that rely on it.”