#GlobalAOS: Luiz Dos Anjos

This July and August, we’re running a special series of blog posts profiling AOS members around the world, in honor of the recent change to AOS’s bylaws eliminated any reference specifying the Western Hemisphere as the Society’s geographic sphere of influence. This week, meet Luiz Dos Anjos, a professor at a university in Brazil.

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Dr. Dos Anjos (second from right) taking a group of students birdwatching in Londrina.

What’s your current affiliation and title?

I am an Associate Professor at the State University of Londrina in Brazil. I received my doctoral degree from the Federal University of Paraná in 1992, and also spent one year of sabbatical at the University of Florida in 2009, where I worked with Robert Douglas Holt.

What are you working on right now?

I am doing research and teach at the State University of Londrina. I teach a class on animal ecology for undergraduates and classes on ornithology and the biological dynamics of forest fragments for graduate students. At the moment I am involved in five research projects. The largest one is on monitoring forest bird communities at ten sites in two large nature reserves. I have worked on this for ten years, and my intention is to complete fifteen years of monitoring.    

On a typical day, I advise master’s and doctoral degree students, prepare and teach classes, and work on analyzing and writing up my field data. My field work is now concentrated in spring (September to December in the southern hemisphere), when I stay for four non-consecutive weeks on the field. 

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Dr. Dos Anjos in the field.

When did you join AOS, and why did you decide to join?

I joined AOS [then the AOU] in 1996. To me, the AOU represented the opportunity to learn more about ornithology, in particular about how to develop research projects on birds. I have attended several meetings of the AOU, in Veracruz, Portland, Jacksonville, and Washington. At all these meetings, I have learned a great deal about birds, and I feel it was important for my career. Another point is the journals, The Auk and The Condor. Although I haven’t been published in an AOS journal, I have learned a lot from the suggestions and recommendations of reviewers on submitted manuscripts.  

What do you see as the best benefit of being an AOS member?

I have maintained contact with colleagues from North America and other countries for years, and it has been important to me. This opportunity to share experiences has been the key point. And I enjoy the friendly meetings, where I can have an easy talk with people that share the same passion for birds.

Guest Post: Taking the Next Steps in R

Contributed by Auriel FournierFirst in a series of blog posts developed from workshops presented at AOS’s 2019 annual meeting in Anchorage, Alaska.

I have co-taught a workshop on R at every AOS meeting since Oklahoma in 2015. The exact content has changed based on participant feedback, but the goal has remained the same: to help those who have some R experience already gain new skills that we feel are valuable to most ecologists who are working with data in R as apart of their scientific work. Our goal is to introduce several skills and concepts and to leave participants better able to help themselves learn whatever R task they need to do next.

If you haven’t been able to attend one these workshops, however, you can work through the lessons yourself online! The lessons are designed for someone who has some R experience and don’t include an orientation to the R interface or instructions about how to use the console. If you’ve never used R before, the R lessons provided by Data Carpentry are a good starting point.

We start by covering two R packages, tidyr and dplyr, which provide functions for the manipulation of data into different forms and the generation of summary information. There are multiple ways to get to most end goals in R, and these packages are just one of those ways. Based on our experience teaching R to folks who do not have a background in programming, the language used by these package functions is more intuitive then the bracket notation often used in other ways in R. We cover subsetting, summarization, and joins in these lessons. View these lessons on GitHub.

Next we dive into graphing, which we teach through the ggplot2 package. There are three main ways to graph in R: through R’s base graphics, through the lattice package, and through ggplot2. Which is best is largely a matter of personal opinion. We teach ggplot2 because it is our preference, and we have found it to be flexible for creating graphics that meet the criteria of a variety of publications and other uses.

In these lessons we work with some eBird data to generate different kinds of graphs, from scatterplots to box plots, and explore some of the important “grammar” of how ggplot works and some of the unexpected results you will get if you don’t follow those rules. We work through a fun exercise where a really visually assaulting graph is created, and we use the theme() function to make it into something closer to publication quality bit by bit. This really shows the level of detailed control you have in ggplot of each small element of a graph. We also take about how to bring in custom color schemes to your graphs and the importance of using color schemes which are red/green colorblind friendly. Lastly we talk about how to bring together multiple graphs into the same panel through the cowplot package. View these lessons on GitHub.

In our final set of lessons, we get into how to use R to automate tasks (to avoid copy/paste or other tedious hand-based analysis tasks). This can be in done several ways. Two that we discuss are for loops and building custom functions, and we work through some basic examples pulled from our own experiences using these to analyze ecological datasets.

We also cover functions such as the paste functions, which can be useful when building workflows where you’ll be reading in or writing out large series of files. Our goal here is not to make participants experts in these topics, but to show them examples that may be relevant to their work and show them the utility of these tools so that they can adapt them to their own projects. View these lessons on GitHub.

Our hope is that these lessons give folks a good start in exploring the wide range of tasks for which R can be used to help make our scientific workflows more efficient, less prone to human error, and more reproducible. If you have any questions about these R lessons, feel free to get in touch with me, and good luck!

#GlobalAOS: Alice Cibois

This July and August, we’re running a special series of blog posts profiling AOS members around the world, in honor of the recent change to AOS’s bylaws eliminated any reference specifying the Western Hemisphere as the Society’s geographic sphere of influence. This week, meet Alice Cibois, a researcher at a museum in Switzerland.

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Alice at work with specimens from the museum’s collection.

What’s your current job title and affiliation?

I work at the Natural History Museum of Geneva, in Switzerland. I’m a research officer and I work on birds. So I curate the museum’s the bird collection, and I also work on public exhibits related to birds, and I also do research, which is mostly focused on the phylogeny, biogeography, and systematics of different groups of birds. It’s supposed to be a third of your time for each part of the mission.

What are you working on right now?

Some days, like today, I spend almost all my day working on papers. I also work in the lab a bit, because I do molecular phylogenies, but other days I’m up near the lake to show waterfowl to children or working with the public team to plan the new exhibits. I have to be very flexible — a few years ago we had a whole exhibit on birds, so for that year I didn’t have so much time for research! I do very little teaching compared to colleagues that are at universities, but on the other hand I’m doing much more public outreach.

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Birdwatching along the Rhone River.

When did you join AOS, and why did you decide to join?

I became a member while I was doing a postdoc at the American Museum of Natural History in New York. That was in 2000, and I’ve been a member since then, even after I returned to Europe, because I wanted to keep coming to the meetings.

I don’t come every year, at this point I come to an AOS meeting every five or six years, but I really enjoy keeping in contact with colleagues. I also enjoy being able to have The Auk and The Condor, and I was also very interested for a while in having the Birds of North America subscription that’s included in the membership. And I think it’s fun to keep up with news about the society, like a few years ago when the two societies merged, I was glad to keep in touch with what was happening in America.

What’s the best benefit that you’ve gained from being a member of AOS?

Coming to the meetings. The meetings are really great. I really enjoy going, because there are always a lot of interesting talks and I get to catch up with colleagues. The meetings and the journals are the main interest for me, being far away from the rest of the activities of AOS.

Revisiting the Classics: What factors influence the start of the dawn chorus of House Wrens?

Sharon Gill, Erin Grabarczyk, and Maarten Vonhof

Linked paper: Social factors, not anthropogenic noise or artificial light, influence onset of dawn singing in a common songbird by C.J. Stuart, E.E. Grabarczyk, M.J. Vonhof, and S.A. Gill, The Auk: Ornithological Advances.

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A House Wren sings at its nest box. Photo by Erin Grabarczyk.

One of the daily joys of summer is waking to the sounds of bird song. Those early morning bursts of singing herald the start of our days, for birds and people alike. If we listen carefully, though, the dawn chorus also reveals something about the state of nature. We might channel Rachel Carson and, based on when birds start to sing each morning, consider what they are telling us about their environment.

What might birds tell us? Historically, they might have told us that cool temperatures on cloudy nights delayed the start of dawn singing. Or that female breeding partners were fertile and males were guarding them closely, either by singing more and earlier or singing less and later depending on the particular species. Today, birds might tell us about how they react to changes in their environment: do they sing earlier when the night sky is brighter, or later if it’s noisier at night, at dawn, or throughout the day?

It was the latter question that initially motivated us and led undergraduate Carley Stuart to do her honors thesis research on whether artificial light and human-caused noise affect the daily onset of the dawn chorus. But given the classic research that shows social context also modifies onset of singing, we considered the role of social factors such as the number of competitors or the mate’s fertility on the start of singing as well. We studied a common songbird, the House Wren, which breeds in nature preserves as well as urban environments. Our ongoing research on this species has found that males alter the structure of their songs and their responses to intruders under noisy conditions, but also that social context matters too. By considering anthropogenic influences and social context together, we hoped to get a broad perspective on the onset of the dawn chorus.

With these questions in mind, we headed to our field sites, positioning autonomous sound recorders at nest boxes to record the onset of singing by male House Wrens and ambient noise levels and using light meters to record sky brightness. We also color-banded and monitored the breeding activities of males, documenting their complex social lives.

We were glad we took this broader perspective. House Wrens began singing around civil twilight, when the sun was just starting to brighten the night sky. We found that it was social factors, not anthropogenic influences, that affected when males began to sing. More neighbours? Sing earlier. Nest building or fertile mate? Sing earlier. More noise and artificial light? Don’t change the timing of the dawn chorus. In regards to when males start their day, our research told us that House Wrens don’t appear to be bothered by artificial light and noise.

We were surprised by this result, as other species that begin dawn singing at similar times of day as House Wrens do sing earlier with brighter skies and more noise. Also, our previous studies have shown that noise affects male House Wrens in other ways, changing how they sing and how they interact with intruders. This makes our job of listening more complicated, as it means that just because one aspect of a bird’s life isn’t affected by human-generated environmental change doesn’t mean birds aren’t affected in other ways. That is a humbling prospect at this time of rapid environmental change and threats to our natural world. It means we need more information and broad assessments to fully understand the responses of animals to changing environments. We need to listen even more carefully.

https://birdsoundscapes.wixsite.com/gilllabwmu

#GlobalAOS: Prashant Ghimire

This July and August, we’re running a special series of blog posts profiling AOS members around the world, in honor of the recent change to AOS’s bylaws eliminated any reference specifying the Western Hemisphere as the Society’s geographic sphere of influence. This week, meet Prashant Ghimire, a student in Nepal.

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Prashant observing Asian Woollynecks in the field.

What’s your current job title and affiliation?

I just graduated with a Bachelor in Forestry from the Tribhuvan University Institute of Forestry in Pokhara, Nepal.

What are you working on right now?

I study the Asian Woollyneck, which is a kind of stork found only in Asia that is threatened but has not been well-studied. I initiated a research project on the woollyneck in 2016. Our first project was studying its population status in the western lowlands of Nepal, and then we moved to the hills of Nepal to study its nesting behavior and ecology with support from the Rufford Foundation in the UK. Woollynecks nest in tall trees, so finding a good vantage point to study a nest can be difficult, and sometimes we have to climb a nearby hill! We have also conducted educational programs in schools and communities, providing bird identification training and bird guide training and teaching them about our research.

In 2018, I received a Student Research Award from AOS to fund research on the foraging activities of Asian Woollyneck in the western lowlands of Nepal. We studied their foraging ecology by recording and analyzing video of their behaviors in the field, and I just completed my report on this project.

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Prashant conducting an outreach program in rural Nepal.

When did you join AOS, and why did you decide to join?

I have been a member since 2018, and I joined because the American Ornithological Society is a global platform. To conserve birds, we must work together, whether in Nepal or in the U.S. or in any other country, because birds are global citizens. But in a developing country like Nepal, we lack some technological advances, so I joined the American Ornithological Society to collaborate with global researchers and scientists.

What do you see as the best benefit of being an AOS member?

The student research award that I received was probably the best thing, but I’m also able to explore different opportunities through the American Ornithological Society. Currently I am searching for opportunities for further studies around the world, so through my membership in the American Ornithological Society I explore different job, research, and scholarship opportunities. I think it is helping researchers like me around the world.

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An Asian Woollyneck maintaining its nests and eggs.