AUTHOR BLOG: How do traits change across a scrub-jay hybrid zone?

Devon DeRaad

Linked paper: Phenotypic clines across an unstudied hybrid zone in Woodhouse’s Scrub-Jay (Aphelocoma woodhouseii) by D.A DeRaad, J.M Maley, W.L.E. Tsai, and J.E. McCormack, The Auk: Ornithological Advances.

Devon DeRaad lines up Woodhouse’s Scrub-Jays (left) and Sumichrast’s Scrub-Jays (right) to compare back color between the forms. Photo by John McCormack.

Where should we draw the line between species? Biologists have debated this question for over 100 years. For much of that time, Ernst Mayr’s Biological Species Concept, which defines a species as a group of individuals that is reproductively isolated from other groups, has dominated the conversation. The BSC, as it has come to be abbreviated, led to more conservative species definitions, with many distinctive forms lumped together as single species because of actual or even potential interbreeding. Recently, however, more and more evidence of hybridization between species has accumulated, especially in birds. The question now is often not whether there is gene flow between what we would consider species, but how much is too much for them to still be considered separate? And when gene flow happens, how does it affect the array of traits that we can see in hybridizing forms?

The New World Jay genus Aphelocoma – which includes well-known species such as the California Scrub-Jay (A. californica) and the Mexican Jay (A. wollweberi) – has proven to be a good study system for investigating the role of gene flow in the early stages of speciation. Because Aphelocoma species don’t tend to move around much, many geographically-isolated, locally-adapted forms have evolved, but they have not become so different that they don’t hybridize when they come into contact with each other. Several of these contact zones have been well studied, like the one between the California Scrub-Jay and Woodhouse’s Scrub Jay (A. woodhouseii), which used to be considered a single species called the Western Scrub-Jay. In fact, the species was split based in part on the fact that although gene flow was occurring, it seemed to produce traits that were selected against outside of the small area where the two groups overlap and hybridize.

I was an undergraduate researcher at the Moore Laboratory of Zoology at Occidental College when I learned of another, largely unstudied Aphelocoma hybrid zone, between the northern form of Woodhouse’s Scrub-Jay and a distinct southern lineage called Sumichrast’s Scrub-Jay. The largest collection of Mexican birds in the world, the Moore Lab has an extensive collection of Woodhouse’s Scrub-Jay specimens from throughout Mexico. Using this valuable collection as well as specimens loaned from other natural history museums, we set out to discover whether there really was evidence for gene flow between these two groups and, if so, how much.

I measured the tail, wing, tarsus, bill length, bill width, and bill depth of 133 specimens from throughout Mexico. I also measured the intensity of blue on the back feathers of each specimen with a spectrophotometer, a tool that captures the wavelength of light reflected off of a surface, as back color seemed to be a major difference between the two forms. Our results confirmed that Sumichrast’s Scrub-Jay is significantly larger and has brown back feathers, as opposed to the blue-gray back feathers of Woodhouse’s Scrub-Jays from northern Mexico. A new analytical method for visualizing geographic transitions in traits called HZAR also showed that while body size transitioned gradually, the transition in back color was much more rapid, suggesting potential selection on this trait.

We were excited by our results not only because it was fascinating to see two traits, size and color, behaving differently across a hybrid zone, but also because the confirmation of the hybrid zone presents another opportunity to study speciation in action in Aphelocoma jays. And while we’re proud to publish a study on hybrid zones that does not include genetic data, providing another example of the modern value of museum specimens in their own right, we do hope to collect more specimens from the contact zone in the future and use genetic data to see how the genomes of both forms are responding to hybridization. These future genetic studies, combined with behavioral, vocalization, and ecological data, will provide an integrated portrait of these divergent lineages that have come back into contact and will help us make an informed decision about how best to recognize the taxonomic distinctiveness of these lineages—that is, whether the species once known as the Western Scrub-Jay should be split yet again.

AUTHOR BLOG: Herbicides Don’t Affect Survival of White-Crowned Sparrow Nests & Fledglings

Jim Rivers

Linked paper: No evidence of a demographic response to experimental herbicide treatments by the White-crowned Sparrow, an early successional forest songbird by J.W. Rivers, J. Verschuyl, C.J. Schwarz, A.J. Kroll, and M.G. Betts, The Condor: Ornithological Applications.

A juvenile White-crowned Sparrow. Photo by Jim Rivers.

A number of birds that use forests disturbed by timber harvest have been declining for decades in North America’s Pacific Northwest. In this region, timber management often requires spraying competing vegetation with herbicides so that crop trees can grow, but the consequences of this herbicide treatment on bird nesting are poorly understood. We designed an experiment to find out how herbicide application was affecting nesting in the White-crowned Sparrow, a songbird that’s declining in the Pacific Northwest. We treated study sites with different levels of herbicides, as well as establishing control sites that experienced no herbicide application. Then, we located and monitored sparrow nests at each site to evaluate how herbicide intensity influenced the outcomes of nesting attempts and the survival of fledgling birds immediately after leaving the nest.

Although herbicide treatments had a major effect on the vegetation in our study plots, as we had expected, we found no effect of herbicide treatment on nest survival. That is, nests had similar rates of survival regardless of where they were located across the continuum of herbicide intensity. Similarly, the survival of fledgling sparrows did not differ between control sites that received no herbicide and sites where herbicide was applied in a way that simulated current management of industrial forest plantations. These results were surprising, because we know from previous work that herbicides have a strong influence on the extent of broadleaf vegetation, a key habitat component for foraging and nesting for many declining songbirds including the White-crowned Sparrow.

White-crowned Sparrow nest with eggs. Photo by Jim Rivers.

Although our study demonstrated that herbicides reduced plant cover in the general area around sparrow nests, we did find that the amount of concealment provided by nest site vegetation was similar across treatments. This suggests that despite the reduction in vegetation cover from herbicides, sparrows in even the most intensively-treated stands were still able to find suitable hiding places for their nests. Because most nest failures were due to predators, it’s possible that nest predators were impacted more by vegetation cover right around the nests than by a reduction in vegetation cover at bigger scales. We were unable to measure predators in our study, but hopefully future work in this system can improve our understanding of the ecology of songbird nest predators and how they are—or are not—affected by herbicide treatments.

Many declining bird species in the Pacific Northwest are united by their need for recently-disturbed forests that contain broadleaf vegetation. Our work shows that one declining species, the White-crowned Sparrow, is not influenced by herbicide intensity, but it remains unknown whether these results also apply to other species. Therefore, studies that expand beyond sparrows would be especially useful for understanding the effects of herbicides on other species that have similar habitat requirements yet differ in their foraging behaviors.

Learn more about the work of the Forest Animal Ecology Lab by visiting their website or following them on Twitter.

Mentors, Consider Involving Your Students in Peer Review

The American Ornithological Society is committed to providing professional development opportunities for our members. With that in mind, if you’re a faculty member and are invited to review a paper for The Auk or The Condor, we encourage you to consider involving graduate students you mentor in the peer review process.

If you have an advanced graduate student who has completed or is close to completing at least the first paper of his or her dissertation, have them join you in preparing a review as follows.

  • Read the paper under review with your student, discuss it, and talk about how to write a valuable review, emphasizing the importance of confidentiality throughout the review process.
  • Have your student write a draft review, then go over the strengths and weaknesses of the draft together.
  • From there, your student could write a second draft for further discussion if necessary, or you could complete and submit the review yourself.

We emphasize that the manuscript should be carefully reviewed by the mentor and that the submitted review should reflect the evaluation of both mentor and student. If a mentor and student follow this process, we request that the name, degree being pursued, and year in program of the student be provided in the confidential comments to the editor when the review is submitted. Mentors do not need to check with editors before involving students.

If you’re a graduate student interested in participating in this process to learn the art of peer review, let your mentor know! For more information, contact

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.

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 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.

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