South of a Sunburnt Country by Michael Johns

Using a gridded sea surface temperature dataset from NOAA, and a handy orthographic projection of Earth centered on the South Pole, you can see Tasmania hovering just above a cold ring of water wrapping around the frozen continent of Antarctica. Although a part of the sunburnt country of Australia, Tasmania’s southern position and proximity to this cooler band of ocean temperatures gives the island a more temperate climate. February in the Southern Hemisphere means shorter days and cooler nights, marking the beginning of a transition to fall. Cooler temps and rain couldn’t come soon enough, as the whole of Australia has been hit with the one of the most extreme heat waves on record, with bush fires sparked by lightning strikes raging across much of Tasmania. These heat waves may become the new norm for this and many other parts of the world, as global average temperatures begin to creep up from a long-term baseline. While not as pronounced as places like the Arctic, records indicate sea and air temperatures are slowly on the rise for this unique southern island of Australia.

Graphics created in R with packages ggplot2 and touched up in Photoshop. SST data are interpolated high resolution average daily values for January 30th, 2019. I tested out a cool new package put out by the BBC graphics team on the temperature anomaly plot, which allows you to apply the graphing styles they use for publications. Check out the link HERE.

Where Are the People? by Michael Johns

Aside from a major city and a handful of townships, Tasmania is mostly an island of rugged landscapes and remote wilderness. There are roughly 522,000 people currently living on this island state of Australia, nearly half of whom reside in the greater Hobart region; Tasmania’s only city center. The heat maps above depict the spatial distribution and densities of people across the island. Each circle represents a 0.05 x 0.05 degree pixel within a larger spatial grid, colored by the total number and density of people within each pixel. Rather than using a raster or contours to display the population data, I went with a simple grid of points using the package ggplot2 in R, which I think gives it a retro “Lite-brite” look. If you never had one as a kid then you missed out. Hobart glows red hot, followed by the town Launceston (called “Launy” by the Aussies) and the northern coastline. We will be flying into Hobart and exploring the city for a few days, before heading out in a camper van rental to check out some of the darker corners of these maps.

Population data used to create the maps above can be found at the following link:

Rather messy but mostly functional R code used to make maps can be downloaded HERE.

Waiting for Australia by Michael Johns

Casey and I still have 5 weeks to go before our belated honeymoon to Tasmania, and already I’m dreaming up cool ways to display data from our trip. So far I have plans for comparing our heart rates in response to different situations using data collected from our Fitbits, tracking the routes we take during our 3-week road trip around the island, and summarizing the different species of plants and animals encountered along the way. To kick things off, I’ve put together a map showing the 8 different flights required to complete a roundtrip ticket from Fairbanks Alaska to Hobart Tasmania. Aside from some text, airplane vector art, and a custom legend (designed to look like a passport stamp) which I added in Photoshop, all of the features of the plot were assembled in R using the ggplot2 package. The coord_map( ) function in ggplot created a spherical projection of the earth, and the white stipples you see on the continents depicts light pollution data, highlighting the city centers. Not counting layover times, it will take us nearly 46 hours to complete the journey.

Seabird Sizes by Michael Johns

This figure depicts the relative sizes of seabirds that breed on the Farallon Islands. Larger circles mean more massive birds, smaller circles less massive. Species in the order Pelecaniformes, colored in shades of blue, are among the largest birds that breed on the island. The Ashy Storm-petrel in yellow, although a part of the order Procellariiformes which includes some of the largest seabirds like albatrosses, is small enough to fit inside the palm of your hand. The diverse order Charadriiformes in shades of red includes all of the gulls and auks, the latter of which contains all of the wing-propelled pursuit divers like puffins, murres, guillemots, and auklets. Mass information was gathered from the Sibley guide to birds. This plot was made almost entirely in R, with a few minor tweaks made in Photoshop. A full size image can be downloaded HERE.

Make It An Animation by Michael Johns


Sometimes, an animated figure tells the story better than a static one. We have been tracking the non-breeding movement patterns of Cassin’s auklets from Southeast Farallon Island since 2015, in an effort to understand the environmental drivers of their winter dispersal. Part of the work I’m doing for my PhD is linking the movements of auklets to remotely sensed conditions relevant to their foraging ecology, in the case of this animation chlorophyll-a concentration (left) and sea surface temperature (right) from November 2017 through January 2018. Chlorophyll, the photosynthetically active molecule that gives plants, algae, and certain types of bacteria their green pigment, is used as a measure of the concentration of phytoplankton. Krill, which comprises much of the Cassin's auklet diet, graze on phytoplankton, so it’s reasonable to assume productive areas with high concentrations of chlorophyll-a likely contain greater densities of krill than areas of low chlorophyll-a. Similarly, lower sea surface temperatures are generally associated with nutrient rich cold water from depth, which help spark blooms of phytoplankton. One hypothesis, visualized with this animation, is that Cassin’s auklets are searching for colder regions of higher productivity during the winter months. The next step is to test this hypothesis with a series of competing models, to see which best explains the patterns observed in the data.

Denali Road Lottery by Michael Johns

More than a century ago, the United States congress was persuaded to create Denali National Park, a now 6 million acre wildlife preserve named after the tallest mountain in North America. By design, the human footprint within the park remains minimal, with few facilities, no real hiking trails, and a single 92 mile-long dirt road. Private vehicles are restricted beyond the Savage River Campground, at mile 15 on the park road. From there, a fleet of buses services the remainder of the road, allowing visitors to hop on and off wherever they like. This enables the public to access the spectacular wildlife and scenery the park has to offer, without the headache and chaos of thousands of vehicles clogging up the road every time a brown bear crosses.

At the end of the summer tourist season in mid September, the buses are parked for the winter and the full length of the Denali park road opens to select group of lottery winners. Every year people can enter what is called the Denali Road Lottery, where up to 1600 private vehicles (400 per day over a 4-day period) are selected at random and allowed to drive the 92 mile stretch of wilderness road all the way to its terminus at Wonder Lake. Winners of this lottery have the freedom to drive at their leisure, stopping whenever and wherever scenic vistas and wild animals are encountered.

According to the National Parks Service website, roughly 11,400 applications were received in 2017, equating to a 1 and 7 odds of getting drawn. Casey was lucky enough to be drawn, which aligned perfectly with a visit from our good friend Amy. So on the final day of the road lottery, we got to experience the fall colors, sweeping views, and iconic Alaskan wildlife of Denali. Except the actual mountain itself, which was cloaked in low clouds and fog…

One of the big draws to visiting Denali National Park is the chance to get close looks at wildlife that is otherwise more elusive outside the park’s boundaries. Just minutes into the drive, we spotted a large flock of willow ptarmigan waddling along the gravel shoulder. Birds don’t stop up traffic in quite the same way as the large mammals like bears, moose, and caribou do. It was easy to tell when a grizzly had been sighted, where sometimes 20 or more cars would pull over with long expensive lenses sticking out of passenger windows, aiding newcomers by pointing out which direction to look for the bear. The following is our sightings list for the day:

Horned Grebe - 2
Greater Scaup - 12
American Widgeon - 8
Spruce Grouse - 1
Willow Ptarmigan - 27
Grey Jay - 5
Black-billed Magpie - 10

Brown Bear - 3
Moose - 3
Caribou - 8
Dall Sheep - 49
Red Fox - 1
Porcupine - 1
Arctic Ground Squirrel - 1

We were lucky to win the road lottery, but not so lucky with the weather. A very wet and rainy fall this year in interior Alaska meant that most of the towering mountains, including the biggest of them all, were obscured from view. Still, what we could see at ground level was more than enough to make the trip worth while. Perhaps next year we will win another day in the park and try our luck again.

Visualizing Long-term Data by Michael Johns

Point Blue Conservation Science has amassed an impressive long-term dataset on the breeding histories of known-age Cassin's auklets on Southeast Farallon Island. These data are visualized in the figure above. The dedication to maintaining and checking 400+ artificial nest boxes every 5-days for the past 34 years has allowed researchers to reveal some unique patterns in the life history of this small seabird. For example, Cassin's auklets are the only member of the taxonomic Alcid family to attempt two complete broods in a single breeding season, known as double brooding. In a recent study published in the journal Proceedings of the Royal Society B, my colleagues and I used these data to examine how double brooding impacts future reproductive potential and survival for birds that attempt such a behavior multiple times over the course of their lives. It turns out that so called "repeat double brooders" represent a subset of high quality individuals that can offset the short-term costs of increased reproductive effort, living well into old age and producing more offspring than birds that never double brood. Visit the publisher’s website by clicking HERE

Orange is the New Fairbanks by Michael Johns

For a brief moment in time, vegetative colors in the far north shift from the middle of the visible spectrum (green, where photosynthesis occurs), to the " far right" shades of amber and red. September in interior Alaska offers a narrow window for fall foliage, with reduced day-lengths and colder nightly temperatures signaling to the trees and shrubs a change in the season. The tundra is particularly breathtaking this time of year, as the grasses become fiery orange and the ground cover of blue and bear berries develops a rich red hue. Contrasting this warm color palette are patches of mint green lichen, wind swept grey granite, and the occasional stunted dark green spruce. The golden hour of sunset, still prolonged given the sun's path at such a high latitude, only serves to enhance the overwhelming golden look of the landscape. 

To take advantage of this narrow window of fall colors, we packed up the truck for a quick overnight camping trip with our friend Kyle, at his "secret" berry picking spot just over an hour's drive outside of town. Clear skies offered sweeping views of Minto Flats, a 500,000 acre wetland and state game refuge. As darkness fell, a complete absence of the moon allowed the Milky Way an it's billions of other worlds to shine. Later in the night, material flowing from our own star triggered a decent display of northern lights over our tents, with subtle pinks and purples not visible to the naked eye revealed with a long-exposure of the camera. Waking up to a frosty morning tundra and sundogs were a sobering reminder that winter is just around the corner. 

Winter Movements by Michael Johns

After several years of geolocator tagging work (see image below), we finally have enough information to begin to paint a better picture of the non-breeding winter distribution of Cassin's auklets from Southeast Farallon Island. At the start of any research project, the most important first step in the analysis process is to visualize the data. The idea behind this visualization was to depict three key environmental characteristics of the auklet's winter habitat in a single plot; sea surface temperature (SST), depth, and distance from island. SST will be used as a proxy for productivity, as colder water in this region is generally associated with nutrient rich upwelling processes, depth to characterize the preferred ocean zone (shallow shelf, steep slope, or deep abyssal plain), and distance from island to explore the possible limits of their dispersal. 

Glancing at this plot, you can see by October birds are fairly spread out between 45°N (dark purple colors - Northern California area) and roughly 33°N (orange colors - Southern California). They are also exposed to quite a range of SST, from 14°C up to nearly 22°C. By late January, all of the birds are relatively close to the island (small bubble size) and experiencing roughly the same SST, before spreading out again in late February, with most birds staying at around 35°N. The 2015-16 season was a particularly warm year for SST, which my explain why only birds in the northern reaches were finding water colder than 14°C. The next step in this exploratory process is to look at auklet movements during the 2016-17 and 2017-18 seasons, which were moderate to average years for SST in the eastern north Pacific. Ultimately, these and possibly additional environmental covariates will be used to model the winter habitat use of Cassin's auklets off the California Coast. 

Note the geolocator tag on the left leg of this Cassin's auklet. Geolocators are devices which record ambient light levels that are later used to estimate latitude and longitude. 

Tagging data courtesy of a partnership between Point Blue Conservation Science and the USFWS. Remotely sensed environmental data were downloaded from the NOAA repository This plot was created in R with the ggplot2 package. 

New Aurora Season by Michael Johns

The Kp index, a measure of the strength of geomagnetic storms from the sun, spiked last night; jumping from a mild 3 to a strong 7. It turns out the Earth had passed through the wake of a coronal mass ejection, where the sun essentially burps out a giant plasma cloud that travels outward from the source as solar wind. This wake weakened the magnetosphere of our planet, allowing solar wind to spill into the upper atmosphere and take on the form of bright green aurora. Space weather forecasters were not predicting this event, a surprise display of northern lights that kicked off the 2018-19 aurora season. 

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.