AUTHOR BLOG: Resighting errors are easy to make and hard to measure

Anna Tucker

Linked paper: Effects of individual misidentification on estimates of survival in long-term mark–resight studies by A.M .Tucker, C.P. McGowan, R.A. Robinson, J.A. Clark, J.E. Lyons, A. DeRose-Wilson, R. Du Feu, G.E. Austin, P.W. Atkinson, and N.A. Clark, The Condor: Ornithological Applications 121:1, February 2019.

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A Delaware Shorebird Project volunteer scans a flock of foraging shorebirds looking for leg flags. Photo by Jean Hall.

Color bands, leg flags, and other field-readable marks are a core component of the ornithologist’s toolkit. Mark-resight studies have led to invaluable insights into the demographics, movements, territoriality, and migration patterns of birds. But clear, confident IDs can be hard to obtain in the field. Colors are difficult to distinguish in low light or when worn, alphanumeric codes are easily mis-remembered or mis-recorded, and was it blue on the left, red on the right, or the other way around? The potential for misidentification is high, and that could have serious consequences for analysis and inference.

Mark-recapture models allow us to estimate demographic rates, but they assume that tags are not lost or misidentified, which is not always the case. Consider a bird that is captured in 2005 and marked with a leg flag with code A4T. This bird is resighted each year and dies in 2010. Now fast forward to 2015, when another bird, this one with flag 4AT, is seen but mistakenly recorded as A4T. Not only do we miss 4AT, but we have also mistakenly increased the apparent survival rate of A4T, and this could become a big problem if misread rates are high. In our recent paper published in The Condor, “Effects of individual misidentification on estimates of survival in long-term mark-resight studies,” we try to work out how frequently this happens and its effect on our ability to accurately estimate survival rate.

Delaware Bay is a globally important spring stopover site for Arctic-breeding shorebirds, a group of high conservation concern. Over the last 13 years, the Delaware Shorebird Project [http://www.dnrec.delaware.gov/fw/Shorebirds/Pages/default.aspx] has marked Red Knots, Ruddy Turnstones, and Sanderlings passing through the area with individually identifiable leg flags. This work relies on volunteers who count, trap, and band birds and resight individuals each year. These volunteers have widely varying backgrounds and experience and spend differing lengths of time with the project, resulting in a lot of variation among observers’ level of training and experience with resighting birds.

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A red knot marked with a plastic leg flag in Delaware Bay. Photo by Jean Hall.

The leg flags we use in Delaware Bay are commonly deployed on shorebirds around the world. For many years, my coauthor Dr. Nigel Clark has been concerned about the potential for misidentification and its consequences, but misread error rates are hard to quantify. So, in 2008 he randomly withheld 20% of the flags manufactured for that field season. This provided us with real possible codes that were never deployed and a way to directly estimate the minimum error rate in our dataset if erroneous resightings of those codes appeared in the data.

We also estimated a maximum possible error rate to get a sense of the range of possible error rates in our dataset. In Delaware Bay, individuals are often seen several times a year and by multiple different observers. Considering this, we identified records where a bird was only recorded once in a year as possible misreads, which we used to estimate maximum possible misread rate, since it seemed unlikely that the same misread error would occur more than once in a year.

Based on resighting data from 2009-2018, we estimated that the minimum misread error rate in our data was 0.31% and the maximum was 6.6%. We found that both average error rate and the variation among observers decreased with experience (the total number of flags an observer had resighted). Our study showed that failing to account for misreads can lead to an apparent negative trend in survival probability over time when none exists. In our paper, we also explore some ways to help mitigate the effects of misreads through data filtering.

Volunteer-based citizen science programs provide rich datasets that can help us understand the drivers of population dynamics and declines. However, when individual misidentification is possible, it’s important to understand error rates and filter potentially suspicious records to avoid biased inferences. Failing to do so could have serious implications not only for our understanding of population declines, but also for the conservation decisions we made based on those analyses.

AUTHOR BLOG: Old-growth specialist Helmeted Woodpeckers roost exclusively in decay-formed tree cavities

Martjan Lammertink, Juan Manuel Fernández, and Kristina Cockle

Linked paper: Helmeted Woodpeckers roost in decay-formed cavities in large living trees: A clue to an old-growth forest association by M. Lammertink, J.M. Fernández, and K.L. Cockle, Jr, The Condor: Ornithological Applications 121:1, February 2019.

Woodpeckers make holes in trees. Don’t they?

Many species of woodpeckers depend on mature forest. Usually, it’s because they need large decaying or dead trees for foraging and excavating nest holes. Since they roost overnight in their old nest cavities, we usually don’t think about roost cavities as a separate consideration for conservation management.

The Helmeted Woodpecker (Celeus galeatus) is different. We know this globally vulnerable species is associated with well-preserved, native Atlantic Forest, but why? We radio-tracked Helmeted Woodpeckers in Argentina’s Misiones province to learn more about their foraging, nesting, and ranging ecology, as well as their coexistence with other woodpecker species. We expected their roosting behavior to follow the pattern of other woodpeckers, with roost sites predominantly in excavated cavities.

Not so. We found 21 roost cavities used by at least 15 individual Helmeted Woodpeckers. Incredibly, none of them were excavated. All of the roosts were in cavities formed by natural decay in large, usually living trees. This makes the Helmeted Woodpecker unique.

Helmeted Woodpeckers, it turns out, have a lot of unusual roosting habits. Although other woodpeckers descend into their cavity to roost, Helmeted Woodpeckers go up inside the cavity and cling to the wall above the entrance. After nesting, each parent takes a fledgling to its separate decay-formed roost cavity, where they roost together for up to 67 days. So they don’t just need decay-formed roost cavities, they need decay-formed roost cavities with sufficient interior space above the entrance for two individuals.

Helmeted Woodpeckers can excavate cavities – they do it for nesting. They often forage on small dead branches and bamboo stalks, which are common in disturbed forest patches. But these birds are found primarily in old forests, and the fact that they roost in decay-formed cavities, which occur mainly in large, old trees, may go a long way toward explaining this association.

The cavities that Helmeted Woodpeckers use as roosts are in high demand by other forest animals, too. We found eight other bird species and at least two species of social insects using these cavities. Helmeted Woodpeckers fought to defend their roost cavities and sometimes lost them to White-eyed Parakeets (Psittacara leucophthalmus) and White-throated Woodcreepers (Xiphocolaptes albicollis). We think these roost cavities are a high-quality, limited resource, critical not just for Helmeted Woodpeckers but for a broad suite of forest species.

Helmeted Woodpeckers have already lost over 90% of their former range to deforestation, and nearly all remaining forests in their range have a history of selective logging. Unfortunately, logging operations target the same species and sizes of trees that typically hold Helmeted Woodpeckers roost cavities. To stop the ongoing decline of Helmeted Woodpeckers, the largest living trees should be retained in logging concessions, and more forested areas should be spared permanently from timber production so that they can return to old-growth conditions.


Sharing of a roost site in a decay-formed cavity by an adult male and juvenile Helmeted Woodpecker. This is a still from a video archived in Macaulay Library. Photo credit: Martjan Lammertink

AUTHOR BLOG: How Google Images can help us understand Martial Eagles’ diet and decline

Vincent Naude

Linked paper: Using web-sourced photography to explore the diet of a declining African raptor, the Martial Eagle (Polemaetus bellicosus) by V.N. Naude, L.K. Smyth, E.A. Weideman, B.A. Krochuk, and A. Amar, The Condor: Ornithological Applications 121:1, February 2019.

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A Martial Eagle prepares to eat a monitor lizard. Photo by Riaan Marais.

The Martial Eagle is one of the largest and most powerful of the booted eagles. These menacing giants dominate the skies over sub-Saharan Africa, ranging from Senegal to Somalia and down to South Africa. Their name is derived from the Latin word Martialis, meaning “from Mars,” referring to the Roman god of war—quite fitting, as these raptors are expert hunters, whether swooping in on their quarry from breathtaking heights or sitting secretly perched in the dense foliage of a tree ready to ambush. Unfortunately, a recent, rapid decline across much of their range has led to their uplisting from “Near Threatened” to “Vulnerable” on the IUCN Red List of Threatened Species. While it is still unclear what factors are driving this decline, evidence suggests that it may be related to their diet, specifically a reduction or shift in the availability of prey species. So, what do Martial Eagles eat, how do we measure that, and what can we do with this information?

Very little data is available on the diet of Martial Eagles. Regrettably, only three published studies exist to date, and these were conducted in South Africa in the 1980s. Traditionally, raptor diet is measured by examining prey remains or pellets at nest sites, as well as through hide watches, camera traps, and even stable isotopes. However, large eagle nests are surprisingly hard to find, and these approaches only measure diet in the breeding season. Eagles have enormous home ranges (>100km2) and nest at low densities (1 pair per 140km2), which makes studying them costly and logistically challenging.

To overcome some of these challenges, we turned to a form of citizen science: using Google Images to determine Martial Eagle diet across their range from uploaded photographs. Using a specialized, open-access software platform called MORPHIC to scan Google Image results for a series of twelve unique search terms, we found 4872 photographs, 254 of which turned out to be of Martial Eagles and their prey after checking for duplication and filtering by relevance. They were taken in eight African countries between 1998 and 2016. From these photographs, we determined relative eagle age based on plumage, recorded the eagle’s feeding position, identified the prey items, and estimated prey weight.

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Martial Eagle diets in different areas of Africa.

We were pleasantly surprised to find that not only did our data agree with the only existing studies in South Africa, but it also agrees with a recently completed master’s thesis on Martial Eagle diet and behavior in the Maasai Mara of Kenya. We were able to expand on the data produced for South Africa and even reliably determine diet for four new countries.

Overall, Martial Eagles everywhere feed on the same combination of bird, mammal, and reptile prey, but the proportions of these prey types differ drastically between eastern and southern Africa. While eagles in both regions consume equal proportions of bird prey, eagles in eastern Africa rely more heavily on mammals, and those in southern Africa eat more reptiles. Martial Eagles in largely arid areas like Namibia, Botswana, and western South Africa consume mostly bird prey, whereas in wetter areas like Tanzania and Kenya, they feed more on mammals. This is obviously dependent on the relative abundance of these prey species, but the overall trends can tell us something about how dietary declines or shifts in prey numbers might be affecting these eagles. Adult eagles also consumed more bird prey than non-adults overall, which makes sense as adults are more experienced and birds are harder to catch.

Bird prey consisted mostly of guineafowl and spurfowl species, with some surprising rarities such as Spur-winged Geese, flamingos, and Kori Bustards. Antelope and small mammal species were the most frequently taken mammals, but eagles were also observed eating lion cubs, caracal, and even chacma baboons. Reptile prey included monitor lizards, a rock python, and even small Nile crocodiles.

While our study doesn’t have the fine-scale power of the nest-site surveys, we have been able accurately replicate these existing studies and provide landscape-level diet data on Martial Eagles at a fraction of the effort and cost. We hope that these new, citizen science-based and open access data approaches find a place in a conservation, as they provide new perspectives to old problems and can sometimes unveil landscape-level trends which had previously been nearly impossible to assess.

AUTHOR BLOG: How do Gunnison Sage-Grouse fare after translocation?

Shawna Zimmerman

Linked paper: Evaluation of genetic change from translocation among Gunnison Sage-Grouse (Centrocercus minimus) populations by S.J. Zimmerman, C.L. Aldridge, A.D. Apa, and S.J. Oyler-McCance, The Condor: Ornithological Applications 121:1, February 2019.

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Researchers collected Gunnison Sage-Grouse feathers for genetic analysis. Photo by Shawna Zimmerman.

Humans moving animals around for conservation?! This may not immediately sound like an action we should advocate for, but the purposeful movement of individuals from one place to another is often an effective way to give small, declining populations a boost in size or increase their genetic diversity. As human alteration of landscapes continues to fragment wildlife habitat and species distribution, this type of action is becoming increasingly common.

Despite their common use, the long-term effects of these purposeful movements, called “translocation,” are difficult to measure. One way to evaluate their impact is through genetic sampling—collecting genetic samples before individuals are moved between locations, and then comparing those data to genetic samples collected after individuals have been released in their new location and given some time to acclimate.

The Gunnison Sage-Grouse (Centrocercus mimimus) is a federally threatened bird species that persists as seven geographically separated populations, which are far enough apart that birds don’t frequently move between them. One population, located in the Gunnison Basin of Colorado, includes approximately 86% of the remaining individuals in the species, maintains a relatively stable population size from year to year, and is the most genetically diverse of all the populations. The six much smaller satellite populations have seen dramatic fluctuations in their population sizes and also have much lower genetic diversity.

Colorado Parks and Wildlife (CPW) were concerned about the viability of the satellite populations because of their small size and low genetic diversity, so in 2005 they began moving birds from the Gunnison Basin to four of the satellite populations. These efforts continued through 2014.  While CPW was able to use radio collars to track some of the translocated individuals for a year, longer-term information on the fate of these individuals was lacking. Specifically, they were uncertain if these birds survived for more than a single year, or if they were integrating into the population and reproducing with the local birds. My co-authors and I set out to answer these two specific unknowns.

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Researcher Shawna Zimmerman walks to a sage-grouse lek site to collect feathers. Photo by Keith Williams.

Genetic sampling can provide insight into both of these questions. Fortunately, we still had samples collected from all of the populations as part of a previous study done prior to translocation efforts, and we used these samples as our reference for change. In another stroke of luck, Gunnison Sage-Grouse have a lek mating system. This means birds gather in approximately the same location each spring to display and choose mates, leaving feathers behind. By visiting the mating sites to pick up these feathers, we could collect genetic samples without needing to disturb the birds. We collected feathers from leks predominantly between 2012 and 2014, and we used these samples to determine the current genetic state of the species.

To find out whether translocated birds were surviving, we first looked at the genetic diversity of each population and how different the individual populations are from each other, detecting some degree of change in all populations that received Gunnison Basin transplants. Looking at changes in genetic diversity at the individual level, we also found that individuals in populations that received Gunnison Basin transplants had increased genetic diversity which originated from Gunnison Basin, suggesting that translocated birds were reproducing.

Our results also showed that levels of genetic change varied among populations, indicating that the impacts of translocation differed from place to place. The two populations with the largest detected increase in genetic diversity also had a corresponding increase in population size, which indicates that translocation efforts may have had a particularly positive impact on these populations.

Our approach to evaluating translocation efforts in Gunnison Sage-Grouse was effective at detecting change that could be attributed to a conservation action, and the non-invasive sampling methods we used could be continued in the future if additional translocation efforts occur. The ability to evaluate the effects of conservation efforts non-invasively is particularly important for a species with federal protection, which makes other sampling approaches less feasible. The positive impact of translocation efforts increases hope for the persistence of the small satellite populations. However, if translocation efforts do not continue or natural dispersal among populations is not increased, observed gains in genetic diversity will ultimately be lost.

AUTHOR BLOG: How vulnerable are California’s Great Gray Owls to wildfire?

Rodney Siegel

Linked paper: Short-term resilience of Great Gray Owls to a megafire in California, USA by R.B. Siegel, S.A. Eyes, M.W. Tingley, J.X. Wu, S.L. Stock, J.R. Medley, R.S. Kalinowski, A. Casas, M. Lima-Baumbach, and A.C. Rich, The Condor: Ornithological Applications 121:1, February 2019.

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A Great Gray Owl nest within an area recently burned by the 2013 Rim Fire in Yosemite National Park. Photo credit: Dustin Garrison

Throughout western North America, the combination of longer, hotter dry seasons and dense forests is yielding more frequent, larger, and more severe wildfires, including immense “megafires.” Habitat loss from increased fire activity could put wildlife species that depend on mature forest at risk. Concern over this threat is an increasingly important driver of forest management efforts in California’s Sierra Nevada, but recent efforts to assess the consequences of megafires on one bird species associated with the region’s mature forest, the California Spotted Owl (Strix occidentalis), have yielded conflicting results. Some research suggests that California Spotted Owls may be vulnerable to habitat loss and local extirpation due to forest fire, while other studies indicate that the owls may be fairly resilient, at least to low- and mixed-severity fire.

Like Spotted Owls, the Great Gray Owl (Strix nebulosa) is imperiled in California (where it is listed by the state as endangered) and is associated with mature forest. California’s Great Gray Owls typically nest in large, dead trees in shady forests adjacent to mountain meadows. In 2013 the Rim Fire, the largest fire on record in the Sierra Nevada, burned 104,000 hectares in Yosemite National Park and Stanislaus National Forest – the heart of Great Gray Owl’s range in California. Within the burned area were 23 meadows known to be occupied by Great Gray Owls during the decade prior to the fire, nearly a quarter of all known or suspected territories in California at the time.

We analyzed 13 years (2004–2016) of Great Gray Owl survey data from 144 meadows in the central Sierra Nevada, including meadows inside and outside the Rim Fire perimeter in Yosemite National Park and Stanislaus National Forest, to assess the effect of the fire on Great Gray Owls’ persistence during the early post-fire years. Would Great Gray Owls continue to use historically occupied meadows within the burned area, or would the fire cause those sites to go vacant?

During three years of surveys after the fire, we detected Great Gray Owls at nearly all (21 of 22) surveyed meadows within the burned area that were occupied during the decade prior to the fire, and anecdotal evidence indicated that the owls were not only present but actually nested at many of these sites during the post-fire years. Analyzing the full dataset, including surveys conducted before and after the fire as well as inside and outside the burned area, revealed that rather than decreasing after the fire, owls’ persistence actually increased at meadows across the study area. This increase suggests that the owls remained resilient during the three years after the Rim Fire and that other factors such as weather were likely favorable to Great Gray Owls during those post-fire years.

Our results indicate that wildfires, including unusually large megafires, may not pose a great threat to Great Gray Owls in the short term. However, processes not apparent during our study’s short timeframe, including the eventual decay and loss of the large snags that the fire created, could affect the owls’ longer-term persistence after fire. Further study is needed to determine whether Great Gray Owls continue to be resilient to fire over longer timeframes.

More information about The Institute for Bird Populations’ Great Gray Owl research and conservation efforts is available at http://birdpop.org/pages/greatGrayOwlResearch.php.