John Kelly, who retired last month, pioneered bird research on Tomales Bay.   David Briggs

John Kelly says that when he arrived in Marshall, in 1988, virtually no one was studying birds on Tomales Bay. Mr. Kelly, who has a master’s in wildlife from Humboldt State and a doctorate in ecology from the University of California, Davis, had just landed a job at Audubon Canyon Ranch’s newly acquired property: an old hunting lodge where herons, egrets and numerous other birds still live, eat and gather on shores just outside the offices. 

With experience working at avian-centric organizations like Point Reyes Bird Observatory (now Point Blue) and the National Audubon Society, Mr. Kelly hit the ground running at the Cypress Grove Research Center, spearheading long-term monitoring programs of birds that use Tomales Bay. He also leads the organization’s conservation science program, helping A.C.R. cultivate deep expertise in heron and egret science. Mr. Kelly, who retired last week, talked to the Light in June about why monitoring is his religion, what exactly conservation science means and more.


John Kelly: When I came [to Marshall], there was virtually no bird research on Tomales Bay, other than a few flyover flights. It was an opportunity I couldn’t resist: I got to pioneer bird research on Tomales Bay. What else is there in life except for birds? 

I started long-term monitoring programs here—that’s one of the things I’m really proud of. I always tell people that monitoring is my religion. We [monitor] wintering water birds [and] year-round shorebird use of Tomales Bay. Helen Pratt, a scientist at A.C.R. who started in 1967, monitored every nest attempt by herons and egrets at the colony [around the Bolinas Lagoon] that was active in those days. She worked for A.C.R. for 30 years, and I worked with her. Then I took what she started and expanded it to the Bay Area, [documenting] every known nest and colony of herons and egrets in the northern half of the Bay Area. The nesting colonies south of the Bay Bridge are monitored by the San Francisco Bay Bird Observatory, using protocols we developed. So they are partners. 

One of the things I’m most proud of here is that A.C.R., aside from the other science we do, is now the go-to organization for anything to do with heron and egret ecology. It’s given A.C.R. prominent standing in the world. 


Samantha: You said before this research, there wasn’t really any bird research on Tomales Bay. Why?


John: There were a lot of places with no bird research. It was just one of those things, you know? Ornithology ecology has been expanding by leaps and bounds ever since it began. The golden era for ecology was really in the ‘60s, and it’s been exploding ever since. One of the first things I tried to do here was establish the value of this place to birds. There are 50,000 birds here. We published papers on that and added it into the body of knowledge—that this was an important place. Those data were used ultimately to qualify Tomales Bay as a wetland of international importance in the RAMSAR convention.


Samantha: What have been your major findings about water birds here?


John: That’s a hard question. I’ve been here for 30 years and we’ve done a lot of different things. I’ll tell you what might be interesting: I had three papers published this year. One was on the Giacomini Wetlands. It showed that the wetland [restoration] increased the number of shorebirds along the shoreline. Another one, just published in Marine Ecology, shows that the number of water birds in Tomales Bay strongly depends on the health of the Pacific herring population that spawns here. That’s a pretty important paper. People have known that water birds eat herring and herring roe; that’s old knowledge. The back story is that there was a state policy established in 2012 by the state Fish and Game Commission that the forage fisheries in California should be managed to protect the ecosystems they depend on. That’s a very advanced concept for California; that’s cutting-edge conservation ecology. But that’s a policy, not a management action. The policy depends on demonstrating dependence. 

Forage fishes are on a worldwide decline right now. That is one of the biggest threats to the ocean, period. The problem is that even though there’s a ton of literature on water bird relationships with Pacific herring, there’s no evidence of dependence, which is a technical thing. With management, you have to have the data, so we provided the data. I’m very hopeful that it can have an effect on California forage fisheries. It’s a first. 

The third one is another paper that’s in press now on the importance of managing heron and egret numbers within each local wetland. Typically, the unit of conservation used in most management and conservation policy is a population or a species or subspecies—that big-level stuff.  The smallest unit is usually a population, which has a genetic definition. The problem is, we don’t know what populations are for most species, what the geographic extent is. It’s hard to do local work on a species. This paper argues the importance of managing heron and egret numbers within each wetland, like Tomales Bay, Suisun Marsh, Central San Francisco Bay—each spot.


Samantha: What does that mean, practically speaking?


John: For example, in the Bay Area herons and egrets have dynamic but stable numbers, so they’re not in trouble. But they are in certain spots. I talked to you [a few years ago] about the colony going down [at our preserve in Stinson Beach]. The outcome of that is that we lost the top predators in that system. So Bolinas Lagoon suffers, even though the San Francisco Bay population is not suffering. So it’s just an argument for local action and management.


Samantha: What happened with the nests in Stinson?


John: The numbers are coming back up. They’re nesting right now in Bolinas—we call it Smiley’s preserve—right near downtown, hanging over the Bolinas channel. They need a place to nest and to feed, and as long as the wetland is healthy, the numbers should come back up.


Samantha: Did you ultimately decide that a predator bird caused the nesting failures?


John: Bald eagles. They got hammered in their new spot, too, by bald eagles. But you can’t hide from bald eagles. What can you do? They colonized Marin in 2008. Since then, they’re in all counties in the Bay Area, and their numbers are gradually going up. They’re fun to watch. They’re part of the system. But everything shifts when you get a change like that.


Samantha: You said monitoring is a religion. What did you mean by that?


John: As a science person, I really love to do formal science. Anytime you can control the structure of the investigation, you get better science. But in conservation, often it’s the descriptive work that people listen to. Just counting birds sometimes has a stronger outcome in conservation action on a broad scale than the fancy science. We try to do both. But that’s why monitoring is valuable: you learn stuff over a long period of time. You wouldn’t see a lot of the patterns unless you did it for a long time.

With our long-term projects, the first part was to do the descriptive work. Then, when you have enough information, you can do all kinds of stuff. What we’re doing now is population dynamics: we can measure how populations fluctuate over time. We started that 10 years ago because the databases were getting big enough. So we could measure the dynamics and what causes populations to go up and down. We’ve paired that with a new project to work on individual egrets that have transmitters. That’s a completely different thing, because we’re looking at individual behavior. Those things go together perfectly. 

Twenty years is about the minimum to get a good sense of population change. We’re passing 30 now. Populations change at many time scales, but at that scale, you can see things like climate change. There are processes in nature that happen gradually over long periods of time. Populations grow and decline because of birth and death rates, birds leaving and coming. You can’t track that until you’ve tracked it for a long time. 


Samantha: With 30 years of data, has some particular story about egrets emerged?


John: I’m very concerned about blue-crowned night herons in the central San Francisco Bay. They’ve been declining 5 percent per year for 10 years. We don’t know why. I have a lot of guesses. I think they’ve been disturbed by nest predators, like eagles and river otters and stuff like that. But I don’t have the evidence to nail it down. But there’s lots of smaller stories that arise. On Tomales, we’ve learned exactly which species prefer which part of the bay, when and where over time. That’s not answering a particular conservation issue or problem, but it could in the future. Monitoring is like that: you don’t know what the questions are yet, but you’ll have the data if a question comes up. For our heron and egret work, we’ve written papers on climate change and the effects of rainfall, but we didn’t plan it beforehand. We got interested later and had the data and were able to answer some questions.


Samantha: What short-term studies have stood out?


John: We worked on ravens for five years; that was kind of fun. In the late ‘90s, everyone, including the park service, was worried about raven predation on sensitive species, and raven numbers seemed to be going up dramatically. We tracked their changes around the Bay Area and tagged them and followed them, found their home ranges and found out a lot of basic stuff. Their number just plateaued. People don’t worry about it much anymore. 


Samantha: From the beginning of your career in conservation science to now, what major shifts have there been in the field?


John: I’ll tell you one that I really like. When I was studying to be me, most ecologists really had one ambition: to publish papers and work in a university and be scientists. But now, if you talk to graduate students, a lot of them want to work for nonprofits. Back when I was a youngster, conservation didn’t drive science. Science drove science. Now conservation drives science. Conservation biology has been defined and redefined a million times. But the best definition, the one I would choose, is that a conservation scientist doesn’t just do science. They do full spectrum conservation science. If you do the science, you have a responsibility to hand-carry it to the decision makers and make sure they understand it. And you also take the responsibility to reach out and make sure the public understands it. That’s A.C.R. We do science-based advocacy when we have something special to say. We do science, we do education and we apply it to the preserves. We get involved when it’s appropriate. If it affects our property, or there’s a conservation issue we have special expertise on, we definitely speak up. A.C.R. is becoming more and more engaged in public policy as we go along, but we’re cautious.


Samantha: Has A.C.R. been involved in an advocacy issue that didn’t go the way it hoped?


John: A lot of smaller things get lost. We’ll provide information to protect heronries, for example, in the Bay Area. A lot get mowed down anyway, they get developed. Planning departments make their own decisions. We’re not the decision makers. 

Here’s another part of the concept of conservation science: if someone asks me for my opinion on an issue, I’m not bound by how it affects traffic or human health or any of those things. My job is to give the straight, objective story on how it affects birds, or the ecosystem. The agencies and decision makers have to put all that together; we don’t. 


Samantha: Is part of A.C.R.’s goal to acquire more land?


John: That’s a good question. We’re too small now; it’s too expensive. We own properties all around here, but most either we got a long time ago or they were given to us. If someone walks up to us and says, “I want to give you 100 acres,” we won’t take it unless they give us money to manage it, in most cases, unless it’s a sensitive spot that needs protection. We’re not a nature conservancy. We’re just as happy if we can help someone get a conservation easement or protect some land without owning it. We’re not just focused on our property, but on the northern Bay Area. 


Samantha: Do you see that geographical focus remaining the same? Do you see it going bigger?


John: We’re very local in the sense that we’re Marin and Sonoma, because of our history. Our science is global. The birds we’re watching go to the Central Valley. One of our tagged birds spent this last winter in the Tulare Basin near Bakersfield, another in the Sierra foothills. The science operates on a global basis, but we set up our work in the region. Work locally but be globally relevant. Our conservation science program is growing leaps and bounds. We’re tracking mountain lions and that project is growing. We’re building a fire science program. 


Samantha: Why is that an interest?


John: We had a fire science Ph.D. on staff who’s not with us anymore, but we’re going to build that program anyway. I don’t know where that’s going to go, to be honest. It’s a climate change response; trying to stay relevant. We’re going to see more fires. But A.C.R. is excited about growing its conservation science program. 


Samantha: What does that mean practically?


John: It’s hard to predict. We want to do more and have more influence. Sometimes that doesn’t mean broadening the subject areas you work on. Sometimes it means gaining more expertise and prestige or being more involved in certain things. You don’t have to study everything to make big changes. The nice thing about herons and egrets is that they aren’t endangered. They’re actually doing pretty good. But they are charismatic, and they’re important ecologically because they are top predators in wetlands. The wetlands ecosystem depends on them. But because they are charismatic, and everybody knows them, it’s a handle for conservation. 

We have an atlas of all the known colonies in the Bay Area. We took the GIS from that to all county planning departments in the Bay Area. When  proposals come up, if there’s a heron colony within 200 feet, they’ll know. It’s not because they’re endangered, it’s because people care about them. And if you care about one thing in a system, you want to protect the system.


Samantha: It’s like pandas. Pandas are a focus of conservation because of the way they look, in part. They are very cute.


John: And they’re endangered. You get both. You want to hug it.