AUTHOR BLOG: Count me in! I am available for detection at 6 AM on May 26th

Péter Sólymos

Linked paper: Evaluating time-removal models for estimating availability of boreal birds during point count surveys: Sample size requirements and model complexity by P.  Sólymos, S.M. Matsuoka, S.G. Cumming, D. Stralberg, P. Fontaine, F.K.A. Schmiegelow, S.J. Song, and E.M. Bayne, The Condor: Ornithological Applications 120:3, August 2018.

Point count survey duration rarely changes within projects but varies greatly among projects. As more and more large-scale studies are compiling and analyzing point count data from disparate sources, standardization becomes critical, because count duration greatly affects observations. The Boreal Avian Modelling (BAM, www.borealbirds.ca) project aims to further continental scale avian conservation through the integration and analysis of point count data collected across northern North America. In order to estimate population density and population size for landbird species, data integration became a real issue for us.

Two of the main sources of variation in the observed counts have nothing to do with ecological variables of interest, such as land cover and climate, but rather are considered nuisance variables. These are point count radius and point count duration. Recognizing that most studies do not follow survey protocol recommendations aimed to facilitate data integration (see e.g. Matsuoka et al. 2014), we opted to use model-based techniques to place our variable data on a common footing.

We first tackled standardizing for varying point count radii through distance sampling (Matsuoka et al. 2012) and eventually combined this with a removal model-based correction for varying point count duration. We named the method QPAD, referring to terms of our statistical notation: probability of detection (q), probability of availability (p), area surveyed (A) and population density (D) (Solymos et al. 2013). In the present paper we assessed different ways of controlling for point count duration. As the title indicates, we performed a cost-benefit analysis to make recommendations about when to use different types of the removal model.

We evaluated a conventional removal model and a finite mixture removal model, with and without covariates, for 152 bird species. We found that the probabilities of predicted availability under conventional and finite mixture models were very similar with respect to the range of probability values and the shape of the response curves to predictor variables. However, finite mixture models were better supported for the large majority of species. We also found overwhelming support for time-varying models irrespective of the parametrization.

So what is a finite mixture model? In our case, it splits the population of birds present at a location into frequent and infrequent singers. In previous parametrizations, researchers assumed that the singing rate of the infrequent group varies with date and time, whereas frequent singers remain frequent singers independent of time of year or time of day. We compared this to an alternate parametrization that assumes that individuals change behaviour over time and switch from frequent to infrequent singing behaviour—so it is the proportion of the two groups that varies. We found that the latter assumption was favoured.

Finite mixture models provide some really nice insight into how singing behaviour changes over time and, due to having more parameters, they provide a better fit and thus minimize bias in population size estimates. But all this improvement comes with a price: Sample size requirements (or more precisely, the number of detections required) are really high. To have all the benefits with reduced variance, one needs about 1000 non-zero observations to fit finite mixture models—20 times more than needed to reliably fit conventional removal models. This is much higher than previously suggested minimum sample sizes.

All of our findings indicate that lengthening the count duration from 3 minutes to 5-10 minutes is an important consideration when designing field surveys to increase the accuracy and precision of population estimates. Well-informed survey design, combined with various forms of removal sampling, is useful in accounting for availability bias in point counts, thereby improving population estimates and allowing for better integration of disparate studies at larger spatial scales. To this end, we provide our removal model estimates as part of the QPAD R package and the R functions required to fit all the above outlined removal models as part of the detect R package. We at the BAM project and our collaborators are already utilizing the removal model estimates to correct for availability bias in our continental and regional projects to inform better management and conservation of bird populations. Read more about these projects in our annual report.

A Better Way to Count Boreal Birds

CONDOR-18-32 C Kolaczan

Common Yellowthroats are among the birds for which new statistical models could provide better population estimates. Photo credit: C. Kolaczan

Knowing approximately how many individuals of a certain species are out there is important for bird conservation efforts, but raw data from bird surveys tends to underestimate bird abundance. The researchers behind a new paper from The Condor: Ornithological Applications tested a new statistical method to adjust for this and confirmed several mathematical tweaks that can produce better population estimates for species of conservation concern.

The University of Alberta’s Péter Sólymos and his colleagues tested a type of mathematical model called a “removal model” using bird count data for 152 species from the Boreal Avian Modelling Project, or BAM, which covers a vast area of Canada, Alaska, and the northeastern U.S. They found that incorporating variation in birds’ singing behavior improved models’ accuracy—how likely birds are to sing changes over the course of the day and the year, affecting how easy they are to detect. Extending the length of individual bird counts from three or five minutes to ten minutes was also beneficial.

“The chances of spotting something—a coin on the pavement, a bear in the mountains, or the apricot jam in the freezer—increases with effort,” explains Sólymos. “The more we walk, travel, look, or listen, the more things we find, but there is also a tradeoff between the number of places one can do a search and the length of the searches. Such decisions drive how long field biologists conduct bird counting at a given place. In our study, we looked at how the duration of counting influenced finding different bird species at different times of the day and the year. We also wanted to find the best way of how to standardize for different count durations and how to use these findings to provide better estimates of bird population sizes.”

This is more than just a math problem, however—accurate estimates of population size can be crucial for effective bird conservation, and many of the boreal bird species this study looked at are experiencing severe declines. This new approach offers a way to combine data from surveys that weren’t standardized in their design. “Population size of different species is one of the key metrics that affects their conservation importance, but estimating population size is a very challenging task that involves numerous assumptions,” says Sólymos. “Besides the ability to hopefully provide more accurate population size estimates, our modeling approach and findings can also help in timing of bird surveys to maximize the number of species detected.”

“While the authors of this study present the results of a rigorous comparison of modeling techniques to achieve better estimates of bird abundance from point counts, they also provide clear and simple recommendations on how and when to apply their findings to any study that expects to use time-interval point counts,” adds Jeff Wells, Science and Policy Director of the Boreal Songbird Initiative, who was not involved in the research. “This is a rich contribution not only to avian research methodology, but in the long run, also to bird conservation.”

Evaluating time-removal models for estimating availability of boreal birds during point count surveys: Sample size requirements and model complexity is available at http://www.bioone.org/doi/full/10.1650/CONDOR-18-32.1.

About the journal: The Condor: Ornithological Applications is a peer-reviewed, international journal of ornithology, published by the American Ornithological Society. For the past two years, The Condor has had the number one impact factor among 27 ornithology journals.

How Does Agriculture Affect Vulnerable Insect-Eating Birds?

CONDOR-18-16 C Michelson

Tree Swallow with prey. Photo credit: C. Michelson

Aerial insectivores—birds that hunt for insect prey on the wing—are declining across North America as agricultural intensification leads to diminishing insect abundance and diversity in many areas. A new study from The Condor: Ornithological Applications looks at how Tree Swallows’ diets are affected by agriculture and finds that while birds living in cropland can still find their preferred prey, they may be working harder to get it.

The University of Saskatchewan’s Chantel Michelson, Robert Clark, and Christy Morrissey monitored Tree Swallow nest boxes at agricultural and grassland sites in 2012 and 2013, collecting blood samples from the birds to determine what they were eating via isotope ratios in their tissues. Tree Swallows usually prefer aquatic insects, which they capture in the air after they emerge from wetlands to complete their life cycles. The researchers suspected that birds living in crop-dominated areas would be forced to shift to eating more terrestrial insects, due to the effects of insecticide use and other agricultural practices on wetland habitat.

Instead, they found that swallows were eating more aquatic than terrestrial insects at all sites, and in 2012 it was actually the grassland birds whose diet contained a higher proportion of terrestrial insects. The results suggest that wetland habitat may provide a buffer against the negative effects of agriculture. However, birds living in cropland weighed less on average than their grassland-dwelling counterparts—a sign that they may be struggling.

“We set up this study to see if insectivorous swallows would be disadvantaged in agricultural croplands by shifting their normally aquatic diet to terrestrial insects to compensate for lower food availability. We were surprised that the birds did not generally do this,” says Morrissey. “Adult swallows in particular were heavily reliant on aquatic prey regardless of land use type. At the grassland dominated site, in fact, they fed their nestlings a wider variety of prey from both aquatic and terrestrial origin. Diet did not seem to influence body condition, but birds in cropland sites were lighter on average which may signal they are working harder in croplands to obtain their preferred aquatic prey. This work shows how important wetlands are for maintaining birds in agricultural landscapes and these are important reservoirs for conserving biodiversity in an otherwise heavily altered landscape.”

“Grasslands are one of the most imperiled ecosystems on the planet because their rich soils are ideal for agriculture. Pesticides and fertilizers are applied in ever-increasing quantities, which has serious implications for organisms that live there,” adds Acadia University’s Dave Shutler, an expert on Tree Swallow ecology who was not involved with the study. “This study compared the diets of Tree Swallows in natural grasslands and croplands, each of which had roughly similar wetland densities. Although diet composition was similar in both areas, it appears that diet quality was better in the natural grasslands, because birds there were heavier and in better condition than those in the cropland.”

Agricultural land cover does not affect diet of Tree Swallows in wetland dominated habitats is available at http://www.bioone.org/doi/full/10.1650/CONDOR-18-16.1.

About the journal: The Condor: Ornithological Applications is a peer-reviewed, international journal of ornithology, published by the American Ornithological Society. For the past two years, The Condor has had the number one impact factor among 27 ornithology journals.

Woodpeckers and Development Coexist in Seattle

CONDOR-17-171 J Tomasevic

Pileated Woodpeckers peek from a tree cavity. Photo credit: J. Tomasevic

The two largest woodpeckers in North America, the Imperial Woodpecker and Ivory-billed Woodpecker, are believed to have gone extinct during the twentieth century. Can their surviving cousin, the Pileated Woodpecker, persist when standing dead trees and other crucial resources are lost to urbanization? A new study published by The Condor: Ornithological Applications tracked birds in suburban Seattle and found that as long as tree cover remains above a certain threshold, Pileated Woodpeckers and housing developments can coexist.

The University of Washington’s Jorge Tomasevic (now at the Universidad Austral de Chile) and John Marzluff trapped and radio-tagged 16 Pileated Woodpeckers at 9 sites with varying degrees of urbanization in suburban Seattle. Tracking each bird for about a year, they found that Pileated Woodpeckers used not only forested areas such as parks, but also lightly and moderately urbanized areas where some trees had been retained, taking advantage of resources such as backyard birdfeeders.

These results show that retaining at least 20% forest cover, including standing dead trees, over large suburban areas may help sustain Pileated Woodpeckers and perhaps even other species tied to them. Despite potential risks from threats such as feral cats and collisions with windows, the researchers believe that cities can play an important role in the conservation of biodiversity.

“You’d think that such large bird would be easy to find, especially when carrying a transmitter, but they did a very good job hiding,” says Tomasevic. “It was also very challenging to work in populated areas. I have so many anecdotes, good and bad, about dealing with people and people dealing with me doing my work. Some people were very friendly, but some were a little nervous with me walking around the neighborhood. I tried to look as official as possible, with University of Washington logos on my jacket, and I created a website for the project and printed some business cards. It was a great opportunity to do outreach, and I’m still friends with some of the neighborhood residents.”

“As suburban sprawl becomes more and more ubiquitous, it’s imperative that we consider which specific yard features can be promoted to share our neighborhoods with wildlife,” according to the University of Delaware’s Desiree Narango, an expert on avian urban ecology. “This paper is a nice example showing that even a mature forest specialist can use and navigate the suburban landscape if we provide the resources they need: large trees and some retained wooded areas.”

Use of suburban landscapes by the Pileated Woodpecker (Dryocopus pileatus) is available at http://www.bioone.org/doi/full/10.1650/CONDOR-17-171.1.

About the journal: The Condor: Ornithological Applications is a peer-reviewed, international journal of ornithology, published by the American Ornithological Society. For the past two years, The Condor has had the number one impact factor among 27 ornithology journals.

Mapping Endangered Red Knots’ Remote Breeding Habitat

CONDOR-17-247_REKN_Mark Peck

A nesting Red Knot. Photo credit: M. Peck

The rufa subspecies of Red Knot travels from its breeding grounds in the Canadian Arctic to its winter habitat in South America and back each year, an incredible 15,000 kilometers each way. Its numbers have fallen precipitously in recent decades, and with such a broad range, determining what’s behind the shorebird’s decline is a huge challenge. A new study from The Condor: Ornithological Applications examines Red Knot nesting habitat preferences across the Arctic and determines that while there is plenty of breeding habitat to support today’s population, climate change could pose a threat in the future.

Rutgers University’s Richard Lathrop, Conserve Wildlife Foundation of New Jersey’s Larry Niles, and their colleagues attached radio tags to 365 knots captured while migrating through Delaware Bay in 1999–2006. To learn where and in what sort of habitat the tagged birds nested, they then conducted surveys via small airplane across the south and central Canadian Arctic, a vast study area spanning from Victoria Island in the west to Baffin Island in the east. They also carried out detailed ground-based surveys on Nunavut’s Southampton Island. Across both scales, knots preferred to nest in sparsely vegetated areas on sedimentary bedrock, near but not directly adjacent to the coast or interior wetlands, to which they commute in order to forage.

The study shows that there are more than 74,000 square kilometers of suitable rufa Red Knot habitat across their Central Arctic breeding range—enough space for at least that many breeding pairs, assuming one square kilometer of territory per nest. Since the entire population currently numbers only around 42,000 individuals, it’s unlikely that a lack of available breeding habitat is contributing to the species’ decline; knots’ problems must lie elsewhere. However, suitable breeding conditions for a number of Arctic shorebirds, including knots, are predicted to shift and decline in coming decades due to climate change. An understanding of species–habitat relationships will be crucial for present and future conservation efforts.

“It took many person-hours over many years of intensive field surveys to find the several dozen occupied Red Knot nests that we located and documented. The area we aerially searched for radio-tagged birds spanned over 1700 km in length, the same distance as from Georgia to Maine,” says Niles.

Lathrop adds, “Using the power of satellite remote sensing, data mining analysis, and geospatial modeling, we were able to extrapolate from the field and radio-telemetry surveys to map potential nesting habitat for these birds across wide expanses of the Canadian Arctic. These same tools and techniques could be applied to advance our knowledge about other Arctic-nesting shorebirds.”

“Implementing effective conservation actions for long-distance migrant birds often involves the systematic elimination of insignificant factors to identify important biotic and abiotic contributors to population dynamics,” according to Brad Andres, National Coordinator for the U.S. Fish and Wildlife Service’s Shorebird Conservation Plan, who was not involved in the study. “For the first time, Lathrop and his colleagues have described environmental conditions conducive for nesting by rufa Red Knots and provide evidence that breeding ground habitats are likely not limiting the recovery of the population. Their work also furnishes a baseline to evaluate the ability of a changing Arctic climate to provide breeding habitat for this shorebird of high conservation concern.”

Mapping and modeling the breeding habitat of the Red Knot, Calidris canutus, at landscape and regional scales is available at http://www.bioone.org/doi/full/10.1650/CONDOR-17-247.1.

About the journal: The Condor: Ornithological Applications is a peer-reviewed, international journal of ornithology, published by the American Ornithological Society. For the past two years, The Condor has had the number one impact factor among 27 ornithology journals.

AUTHOR BLOG: Newly discovered crossbill species numbers few

Craig W. Benkman

Linked paper: Habitat associations and abundance of a range-restricted specialist, the Cassia Crossbill (Loxia sinesciuris) by N.J. Behl and C.W. Benkman, The Condor: Ornithological Applications 120:3, August 2018.

Untitled

A female Cassia Crossbill.

Based on the size and structure of the lodgepole pine cones and the abundance of crossbills in the South Hills and Albion Mountains, Idaho, that I observed on the way to a joint AOU and COS meeting in Boise in 1996, I told several colleagues at the meeting that I might have discovered a new form of crossbill. Although they were skeptical, over the years my students and I have found that this crossbill is engaged in a coevolutionary arms race with the pine, favoring an increase in seed defenses directed at the crossbills. This has caused the crossbill to diverge and speciate into what we now call the Cassia Crossbill (Loxia sinesciuris).

Restricted to the lodgepole pine atop two small ranges on the northeast edge of the Great Basin Desert, this bird was of clear conservation concern, especially given the forecasts of lodgepole pine disappearing from the region late in this century. This became all the more troubling as we watched the Cassia Crossbill population plummet by over 80% between 2003 and 2011. The decline was related to an increase in hot summer days (>32°C or 90°F; 8 days in 2003, 3 in 2005, 4 in 2006, and 4 in 2007) that caused many of the normally closed cones of lodgepole pine to open and shed their seeds, much like they would if there was a stand-replacing fire. Such seeds are lost to Cassia Crossbills, which rely on seeds in the older, closed cones as they weather and gradually become available throughout the year. Fortunately, hot summer days have been few since 2007, allowing the crossbill population to rebound. However, given its restricted range, apparent small population size, and vulnerability to higher temperatures, we needed an estimate of their global population size and habitat preferences to inform and guide us. Nate Behl did just that work for his master’s thesis, and it appears in the article “Habitat associations and abundance of a range-restricted specialist, the Cassia Crossbill (Loxia sinesciuris)” in The Condor: Ornithological Applications.

Cassia Crossbills occupy about 70 km2 of lodgepole pine forest and number only ~5,800 birds. Thus, at the population nadir in 2011 there were probably about 1,500 Cassia Crossbills. That is worrisome, especially given the forecasts for more extreme temperatures later in this century. Nate also found that Cassia Crossbills occur more commonly in larger, mature stands of lodgepole pine on the cooler north-facing slopes where large numbers of seeds can accumulate in closed cones. This makes sense, but the outlook for the continued accumulation of seeds in closed cones in the canopy is bleak. More hot summer days are projected, along with increasing fire frequency, preventing pine from reaching the ages most productive for the Cassia Crossbill.

Agricultural & Urban Habitat Drive Long-Term Bird Population Changes

CONDOR-17-153_CHSP_M. K. Rubey

Chipping Sparrows have expanded their distribution in Illinois by taking advantage of urban habitats. Photo credit: M.K. Rubey

Land use changes are a major driver of species declines, but in addition to the habitat to which they’re best adapted, many bird species use “alternative” habitats such as urban and agricultural land. A new study from The Condor: Ornithological Applications documents a century of land use change in Illinois and shows that species’ long-term fate can depend on the availability and suitability of these alternative habitats.

Between 1906 and 1909, a pair of ornithologists crisscrossed the state of Illinois, creating a unique record of its avian inhabitants across grassland, forest, urban, and agricultural habitats. The University of Illinois Urbana-Champaign’s Michael Ward and his colleagues recreated this survey as closely as possible between 2006 and 2008 and used the data to create mathematical models of bird occupancy, assessing how things had changed over the course of the twentieth century. They found that birds’ use of alternative habitats had changed more than their use of primary habitats: the 40 species in their analysis that expanded their occupancy did so by making more use of urban habitats, while the 26 that decreased did so because they were making less use of agricultural habitats. Urban habitats have become more bird-friendly in the past century as vegetation has matured and bird feeding has become more popular. Agriculture, on the other hand, has seen a shift from small, diversified farms to vast corn and soybean monocultures managed with heavy herbicide and pesticide use.

“We need to understand how species use and respond to changes in not only their primary habitat, but also habitats that they only use occasionally. Species that can take advantage of alternate habitats can expand their populations,” says Ward. “Understanding which species can or can’t take advantage of these alternative habitats will allow us to better predict which species need conservation efforts. Urban habitats are the habitats in which many species have been increasing, and the general public, by providing small bits of habitat in their backyards, have the opportunity to help a range of species.” Species that have been declining, on the other hand, may rebound if agricultural practices change to become more wildlife-friendly.

“When trying to explain changes in population size and distribution, biologists often look first to changes in the habitats that are most closely associated with a species. This study demonstrates that these ‘primary habitats,’ as termed by the authors, do not necessarily drive population changes,” adds the Cornell Lab of Ornithology’s Amanda Rodewald, an expert on birds’ response to land use who was not involved in the study. “Rather, the extent to which a species uses novel or alternative habitats such as urban areas might better explain patterns. One key implication for conservation is that tracking species within alternative habitats may help biologists to understand, anticipate, and potentially mitigate population changes.”

Changes in bird distributions in Illinois, USA, over the 20th century were driven by use of alternative rather than primary habitats is available at http://www.bioone.org/doi/full/10.1650/CONDOR-17-153.1.

About the journal: The Condor: Ornithological Applications is a peer-reviewed, international journal of ornithology, published by the American Ornithological Society. For the past two years, The Condor has had the number one impact factor among 27 ornithology journals.