Ken's Pond in Late Summer /  by Michael Johns

A brief visit from our good friend Laura prompted a much needed cabin retreat, this time a return trip to Ken's Pond. This public use cabin offers sweeping views of the snow-capped Alaska Range towering over a small beaver pond. Accessible by "highway vehicle" in the summer, we traversed the 5 mile rutted dirt road in my Tacoma to a pullout at the top of a ridge line, where we walked the remaining 800 yards down to the cabin. Highway vehicle is a bit generous for this road, as 4 wheel drive and a high clearance was necessary for navigating the deep mud puddles and trenches.   

As is typical for Ken's Pond, the wind was fierce. The high altitude wind shear, however, created some awesome lenticular clouds; stationary UFO-shaped features formed when a steady stream of moist air encounters an obstacle, in this case a mountain range.  

Highlights from our quick overnighter included circumnavigating the pond, a rousing game of scattergories categories, admiring Noosa, pond-chilled beer, finding coal, wind, and sightings of a beaver (Ken), caribou, and a bull moose. Another memorable visit to Ken's Pond.

Listers /  by Michael Johns

The Farallon Islands are uniquely situated for people interested in the hobby of finding and identifying birds, otherwise known as "birding". The cluster of jagged rocks are located just far enough offshore to provide a stable platform for spotting rare pelagic species like the Cook's petrel, and close enough to the mainland to catch vagrant song birds and other terrestrial species lost in the fog at sea. Over the course of 50 years of research out on the Farallones, some biologists and staff have been keeping a detailed list of all of the different bird species they've encountered while out on the island, a record known as "The Faralist". This figure is a graphical interpretation of that list, modified from R code for a similar graphic depicting the number of days spent on island by various people over the years. Collectively, a total of 429 different species have been seen from the Farallones; not bad for a small collection of guano-covered rocks with only 3 trees.

Download a high resolution file of this figure HERE.  

Final Chicks of the Season /  by Michael Johns

Ashy storm-petrels are endemic to the California Current System, which means their entire population occurs in the offshore waters of the California coast. Half of the world's estimated 10,000 individuals breed on Southeast Farallon Island, their chattery calls a regular sound after the sun goes down in the summer. They are amazing swallow-sized seabirds that spend much of their lives exposed to harsh winds and rough seas, thriving on small planktonic items they pluck from the productive surface waters of the Pacific. These enigmatic relatives of the albatrosses have a more prolonged occupation on the Farallones compared to the other breeding seabird species, extending chick provisioning efforts well into early October. They are generally the last chicks to hatch on the island, small grey puff balls that can be viewed on occasion in shallow crevices if you look hard enough. 

Rabbit Cave /  by Michael Johns

We monitor the breeding population of Rhinoceros auklets on the Farallones by checking artificial wooden nest boxes distributed across the island. These boxes are visited on a regular basis to note which ones contain an active breeding pair, whether those pairs are successful at hatching an egg, and ultimately how many pairs end up fledging a chick; giving us an estimate of the annual breeding success for this species. In addition to the nest boxes, we also monitor breeding activity in Rabbit Cave, a large vestige of the islands geologic past that acts as a kind of massive burrow for Rhinoceros auklets. The entrance to Rabbit Cave starts out as a narrow crawl space that opens up into a cavernous amphitheatre at the back. 

Landscape of a Year /  by Michael Johns

Animals tend to be fairly predictable in their reproductive timing and migration patterns. The figure above depicts a series of density curves, with peaks and troughs corresponding to the average timing of key biological events for a select number of marine species that are monitored on or from Southeast Farallon Island.

Pinnipeds, a taxonomic group that includes seals and sea lions, are found hauled out on the island year round, with peak pupping events occurring in the summer. Northern fur seals, which have made an astounding recovery on the Farallones following the days of the Russian Fur Trade, remain at sea for several months of the year and are only seen in force from summer to late fall. Whales are also visible from the island year round. Gray whale numbers peak in January as they migrate south to their breeding grounds off Baja California Mexico, and again in March during a northward migration back to their feeding grounds in Alaska. Humpback and blue whales are most abundant in the productive summer months, where they are seen gorging themselves on krill and schooling fish. For seabirds, breeding occurs only in the summer months, with the exception of the ashy storm-petrel which extends chick rearing well into October. Three distinct peaks represent the timing of egg laying, hatching, and chick fledging. 

The study of seasonal life-history patterns is called phenology, and it can tell us a lot about the stability of a system. As I mentioned, animals tend to be fairly predictable in their phenology. Individuals cue in on environment and biological signals, so shifts in the timing of reproduction or migration can indicate changes in environmental condition, food availability, or the health of a population. For species found on the Farallones, the major cause for concern in the face of a warming ocean is the availability of key prey items, namely krill, which sustain the rich biodiversity in this region. A mismatch between the timing of krill and the timing of reproduction for seabirds can lead to major declines in breeding success, and subsequent declines in population numbers. 

Data courtesy of a partnership between Point Blue Conservation Science and the USFWS. The plot was created in R with the ggplot2 and ggridges packages. 

Sei Whales Off The Farallones /  by Michael Johns

In addition to daily opportunistic sightings, we conduct standard 1-hour whale watches from atop Lighthouse Hill to document the timing and abundance of Cetaceans around the Farallon Islands. These data are useful in particular for showing where whales are in relation to shipping lanes leading into San Francisco Bay, to better inform mitigation measures aimed at reducing the number of ship strikes.

On one particular whale watch, during an exceptionally calm day, I came across a feeding flock of 6 black-footed albatross and several dozen pink-footed shearwaters. I considered the possibility that this flock was associated with killer whales, since albatross have been known to scavenge on orca kills, and killer whales had been reported in recent days just south of us in Monterey Bay. Sure enough, after watching for a few minutes a tall black dorsal fin came into view, followed by two smaller fins. A pod of transient killer whales that were feeding on some unknown pinniped at the surface. After radioing the sighting to the rest of the crew, everyone made it up to the lighthouse for a look before they eventually departed to the west. 

After the killer whales had left we decided to keep looking around for other sightings. Within minutes a blue whale surfaced right next to the East Landing mooring ball, in water probably half as deep as the length of the animal itself. As if that wasn't good enough, someone pointed out a small pod of whales swimming toward the island. They were all dark baleen whales with a visible blow, six of them traveling in tight formation towards an islet we call Sugar Loaf. Initially, I assumed perhaps it was a group of minke whales, clumping together in response to a pod of their natural predators nearby. The shape of their rostrums, size, behavior, and blow were all wrong though, and as they got closer we couldn't see an signs of white patches indicative of minkes on their pec fins. They were too small to be fin or blue whales, too big to be minkes, and definitely not a toothed whale. The only other obvious possibility for this part of the world is the sei whale, a species of rorqual found in temperate waters worldwide, but generally seen much further offshore and rarely sighted off California. 

To put this sighting into context, only 17 sei whales have ever been seen on the Farallones since 1987, and generally the sightings consisted of a solitary individual. Not only did this group contain a Farallon record breaking 6 animals, but they swam close enough to the island for us to get excellent looks for a prolonged period of time, and even photos of the event (of which my favorite is of a western gull pondering whether it can eat one of the whales). Truly a rare and amazing sight. 

Photos taken through Point Blue Conservation Science | USFWS

Relative Size /  by Michael Johns

Probably the most important question in the conservation work that we do, and the most popular question people have about the Farallones, is the population size of the various seabird species on the island. The answer, such as roughly 250,000 murres, 20,000 auklets, and 500 puffins, may not be fully appreciated when taken at face value. The figure above is an attempt to put these numbers into context by representing each population as a collection of boxes, where the area of each box is scaled in proportion to the other boxes. With this visualization, you can see just how abundant Common Murres are in relation to Pigeon Guillemots or Tufted Puffins. With continued monitoring and management, hopefully all of these boxes will continue to grow in size.

Data courtesy of a partnership between Point Blue Conservation Science and the USFWS. The plot is called a "Treemap", created in R with the ggplot2 and treemapify packages. 

Spring Snowfall /  by Michael Johns

During my brief break from the island, it snowed, in May. Winter is reluctant to release its icy grip on Fairbanks, which doesn't seem to bother our dog Noosa all that much. I won't be back up north until August, just before another long winter settles in. 

Cassin's Known-age /  by Michael Johns

One of the more exciting projects we conduct on the Farallones is the Cassin's auklet known-age study, which was first initiated in 1983. The birds are known-age because they are banded as checks, and once those chicks recruit into an unoccupied nest box we can gather valuable information on mate selection and retention, changes in breeding performance with experience and age, and signals of individual quality; all of which help managers better understand how individual contributions lead to population level changes. The work involves checking the contents of over 400 nest boxes distributed across the island, and taking various measurements of adult birds like bill depth, wing chord, and weight, which are used to determine body condition and sex. 

Photo taken through Point Blue Conservation Science | USFWS

April Showers /  by Michael Johns

This spring has been dominated by unsettled weather. We've been receiving a steady stream of moisture from the south, with descent downpours occurring every week. The weather makes for some dramatic early morning scenes, and has also been keeping the yellow flowers of the Farallon weed around for a little bit longer. 

Photo: Point Blue Conservation Science and USFWS

50 Years of Bands /  by Michael Johns

It's been 50 years since scientists from Point Blue Conservation Science (then Point Reyes Birds Observatory) began a continuous monitoring effort on SE Farallon Island. Some of this work includes banding certain species of seabirds to learn more about their movement patterns, survival and mortality rates, population status, and individual breeding behavior and success; all important information guiding management decisions and tracking the potential effects of climate change. Point Blue has amassed an impressive sample of banded birds since work first started in 1967, totaling nearly 125,000 individuals as of 2016. The graphic below illustrates the total bands put out by year and cumulatively since 1967 for 8 target species. 

Navigating With The Sun /  by Michael Johns

One of the easiest ways to study basic life-history and behavior of seabirds is to outfit them with devices the passively record data for you. The tricky part is getting those devices back in order to download and analyze those data. So far this season, we have recovered 19 geolocator tags that were secured to the legs of Cassin's auklets breeding in artificial nest boxes last year. These tags are designed to be very small and light, and have zero affect on the breeding performance and survival of birds that carry them. Geolocators record ambient light levels experienced by the bird as it flies around it's environment. These light level recordings are later used to estimate roughly where the bird was twice a day throughout the deployment period, using the timing of sunrise and sunset (which varies depending on longitude) and the duration of day-length (which varies by latitude). The photo above shows a row of tags calibrating in the sun on SE Farallon Island. 

Noting The Weather /  by Michael Johns

For roughly 50 years now, researchers on the Farallones have recorded daily island weather observations that include the wind intensity and direction, air temperature, and sea conditions. And for roughly 50 years the instruments used to collect these data haven't changed much. This long time series of direct weather observations provides information on meteorological and oceanographic patterns that impact the productivity and success of species that breed on the island, from short-term phenomena such as El Nino, to long-term trends associated with climate change. Recently, strong gusts from the Northwest have been tipping the anemometer needle beyond the 30 knot mark, a good spring wind to drive the upwelling.

Watching The Sea /  by Michael Johns

Well, I'm back on the Farallones for another seabird season, and so begins another series of stories from the field. I've decided this year to briefly describe all of the different projects we do out here during the summer. From simple tasks such as taking the weather, to complex tasks like keeping track of 400+ Cassin's auklet nest boxes. To kick off this series, I choose one of my favorite morning rituals, "sea watch". Every morning, the designated sea watch person (Katie in the case of the photo above) sets up a 50x spotting scope on the front porch of the PRBO House where we live, orients it southwest over the marine terrace, and watches the sea for a standard 5-minute period. The idea is to count any pelagic species other than the ones that breed on the island that pass through the fixed field of view, to get a sense of long-term changes in the timing and abundance of seabirds that use the waters around the Farallones. 

Visualizing Effort on SEFI /  by Michael Johns

As the name would suggest, long-term datasets take a long time to develop. Not only does it take a continuous supply of resources to support the work, someone has to physically go out every year and collect the data. To visualize the time investment and sheer number of people required to collect 50 years of seabird and marine mammal data, I designed this circular bar plot, illustrating the extreme commitment by some and small contributions by many over the years. It depicts the total number of days spent on Southeast Farallon Island (SEFI) by current and former staff and interns of PRBO (now Point Blue Conservation Science). Each concentric circle radiating from the map of SEFI in the center represents an additional 500 days of service, with Pete Warzybok in the lead at over 2,000 days! To keep the plot from getting too cramped, I narrowed the number of names displayed to just partial or full PRBO associates with more than two months spent on island, so this plot excludes many more island residents affiliated with various agencies, contracts, and universities, as well as people with brief stints – sorry if that applies to you. The graphic was created entirely with the ggplot2 package in R, aside from the border and line below the title that were added later in Photoshop. A high resolution 16 x 20 .png file of the graphic can be downloaded here: DOWNLOAD FILE 

La Paz /  by Michael Johns

The Pacific Seabird Group puts on an annual conference to bring together scientists and students studying seabirds around the Pacific. Last year the conference was held in rainy Tacoma Washington. This year it was held in sunny La Paz, on the southern end of Baja California Mexico (see map below). I used the timing and location of this year's conference to give a talk on my double brooding work with Cassin's auklets, and take a much needed vacation from Fairbanks with Casey before I head out to the Farallones for another summer field season. Once the conference ended, we spent much of our time wading through the thigh-deep turquoise water of Balandra Beach, lounging in the sand, hiking among cacti, birding the Malecon, and drinking margaritas. 

The highlight of our trip was the chance to swim with the world's largest fish, the whale shark. These massive filter feeders can reach lengths of up to 40 feet, and are found in warm tropical waters throughout the world. According to a paper by Ramírez-Macías and colleagues published in 2012, La Paz is one of several sites in the Sea of Cortez where predominately juvenile whale sharks congregate to feed in shallow plankton-rich waters. The site is a short panga ride from La Paz, on the north side of a long sand spit called El Mogote. We spent roughly 40 minutes watching a small (20 foot?) male slowly strain tiny plankton from the surface waters, which during this time of year felt less tropical and more temperate. The photo below was taken in Bahia de los Angeles, another important juvenile staging area further north, during my first encounter with whale sharks in 2006. 

The images above, in order of appearance are: marbled godwits, magnificent frigatebird, tricolored heron, reddish egret, yellow-footed gull (eating a puffer fish), unknown mangrove crab, parade of brown nudibranchs found at low tide in the mangroves (presumably breeding). 

Map of Baja California created with ggplot2 in R. Colored regions indicate topography of land, grays indicate bathymetry of the sea, for those not familiar with the region. La Paz is tucked away on a shallow bay at the southern tip on the Sea of Cortez side. The color pallette for this plot was inspired by the local geology.

Data Into Art /  by Michael Johns

R is an open source statistical computing and graphics platform, where tasks are implemented through a coding language entered by the user. The flexibility of R is limited only by the collective ability of its community of users to dream up new functions and functionality; which means its potential is basically limitless. It has become the environment for researchers to carry out statistical analyses and produce publication-ready figures. 

Inspired by some cool new plots floating around the internet that mimic Joy Division's "Unknown Pleasures" 1979 album cover, I created the above image of Southeast Farallon Island using a new R package developed to better visualize changes in distributions over time. The image depicting the the change in elevation across a range on longitude for each line of latitude was produced with the packages ggplot2 and ggridges, using a dataset containing elevation information of the island at equally spaced points of lat and long. An example of using R for more than just stats and figures, creating something that could even pass for art. 

Download this .asc file and use this code to recreate the above image in R. 

Here's another way of looking at the same dataset using geom_polygon in ggplot2, where each polygon is colored by latitude. This shows the vertical relief of the island from the perspective of the waterline, looking north. The tallest peak at just over 100 meters is the top of Lighthouse Hill. The second largest at just below 75 meters is Maintop, which is separated from the main island by a very narrow channel.