THE BALAKRISHNAN LAB

Image Credit: Andy Reago & Chrissy McClarren

Changing English bird names is an idea that has gained significant traction recently, particularly across North America. The issue resurfaced in 2018 when the American Ornithological Society’s (AOS) North American Classification Committee (NACC) published my proposal to change the name “McCown’s Longspur.” Two years later, in the wake of protests and action taken across the world for George Floyd and an expansion of efforts to address systemic racism, the topic of English bird names was discussed heavily on twitter and spread rapidly by #BirdNamesForBirds. At this point the AOS changed McCown’s Longspur to the Thick-billed Longspur. This in turn led the NACC to devise a proposal-based procedure for dealing with the issue of problematic bird names.

Seemingly in response to mounting public pressure, the AOS has now announced a committee to design a new process for renaming English bird names for diversity and inclusion purposes. This decision, combined with the NACC’s announcement to suspend review of all English bird name proposals, has in all likelihood ended the era of a proposal-based system for renaming English bird names. In February, prior to the public announcement of the NACC to suspend review of English name proposals, with the help of Jess McLaughlin’s BirdNamesForBirds biography entry, I wrote a proposal to change the name of Scott’s Oriole to Yucca Oriole, and submitted to the NACC. The NACC responded that they were not currently reviewing English name proposals. In all likelihood then, this proposal won’t make it out to the public, so we’d like to share it here.

Why choose Scott’s Oriole when, according to BirdNamesForBirds resources, there are over 150 honorific bird names in North America? Obviously one issue is the time constraint on writing 150 proposals. So given that I had only so much time, I targeted Scott’s Oriole as the species to write about because it, without a doubt in my mind, is the worst honorific (yes all are bad but this is a special kind of bad). It is named for an individual who clearly, without controversy, directly handed out orders to commit genocidal acts against Indigenous People culminating in personally carrying out the orders for the forced removal of the Cherokee people known as the Trail of Tears. Less important but relevant to the updated 2020 (now expired) NACC English Bird Name guideline policies, Scott had no documented personal of familial connection, monetary relationship, or passing interest with birds, nature, or expeditions. I think publishing the proposal is still worthwhile because it allows ornithologist and birders to understand the name and how we can change it.
 
- Robert Driver

The BALALAB is recruiting a postdoc! The official ad is available here: https://ecu.peopleadmin.com/postings/31524.

Please see the previous blog post for additional details or feel free to contact me directly with questions about the position.

Job Description: The Balakrishnan Lab (www.balalab.com) is seeking a postdoctoral researcher in behavioral and evolutionary genomics. The primary responsibilities of the fellow will be to contribute to ongoing research projects and to assist with lab oversight and student mentoring. The postdoc would be involved in collaborative work on the courtship display behavior and sexual selection in neotropical lekking manakins, brood parasitic behavior, and/or song learning behavior. Most of these projects have (really cool) existing data that could be immediately analyzed for publication. For example, the manakin work extends this study to examine in detail social status-dependent gene expression. The postdoctoral fellow will also be encouraged to develop new research avenues. This position also offers the opportunity for the postdoc to develop their teaching experience by contributing to an established workshop on genomic data analysis taught at ECU.

During the 1-2 years of this fellowship, I will be serving as a rotating program officer at the National Science Foundation. I will be making regular visits to Greenville for mentoring as well as conducting regular meetings via Skype etc.  Because of this somewhat unusual situation, some sort of “remote”-scenario may be possible for applicants to this position, though some weekly time on campus is required.

The postdoctoral researcher will interact with multiple labs and departments where they will gain broad training behavioral and evolutionary genomics.  The evolution/behavior/ecology group at ECU is particularly strong. The Balakrishnan Lab is active in outreach and community engagement through Nerd Nite and projects with Sylvan Heights Birds Park (https://shwpark.com/). Sylvan Heights is a focus of an ECU-wide collaborative initiative and the Fellow would be encouraged to pursue opportunities there. The fellowship could even be structured to more heavily emphasize outreach.

Qualifications: Candidates should hold a Ph.D. in Biology or related disciplines and should have demonstrated experience in the analysis of genome-scale datasets (e.g., RNA-seq, ddRAD-seq, or whole genome resequencing etc.) The successful applicant will be expected to be creative, self-motivated, and able to help mentor and supervise undergraduate and graduate students and work with a diverse team of collaborators. For inquiries contact Chris Balakrishnan.

This year the lab has a bunch of stuff coming out that has been cooking for a good long while. These publications are causing me to reflect a bit on the winding road that occurs between "idea" and "finished product". My favorite stories are those that didn't go at all as planned.  This paper, led by Dr. Allison Lansverk, my first Ph.D. student, is one of those.

Although Allison did the heavy lifting for the published piece, this work has a long origin story beginning when I was a postdoc in Scott Edwards' lab. Scott, in his crystal-balling way, encouraged me to start working on zebra finches, the developing model system that would soon have its genome sequenced. My idea was to take this system back into the wild and to describe genetic variation in the two extant subspecies - one of which, a nifty little bird called the Timor Zebra finch, has been largely ignored (but see this cool series of studies by Nicky Clayton). Back then, Scott and I had the notion to put this important model system, especially for neuroscience, in an evolutionary context. I wrote an F32 postdoc fellowship to look at selection and recombination in the zebra finch  with a focus on both immune and neurobiologically relevant candidate genes (circa 2006, remember). This proposal was not funded, but I did wind up completing a smaller survey of genetic variation and a primary description of the zebra finch MHC. 

The end (part 1)

After my time in Scott's Lab, I joined the lab of David Clayton (then at the University of Illinois). My plan there was to really beef up my genomics chops and to get an intro into neuroscience. Here I was able to convince David to purchase 5 pairs of Timor zebra finches from a domestic breeder. I noticed right away that these birds were much more "wild" than the lab colony of Australian zebra finches (In the figure above, Timor on the left, domestic Australian on the right). So I got to thinking, maybe there is some comparative behavior to be done. The first thing I noticed (well, besides an obvious body size difference) was this song variability pattern, now properly described in this new paper. The Timor finches are also a bit harder to breed, and kind of like to be left alone. In the new paper, the small sample of birds we describe from UIUC were birds I recorded there when I was a postdoc. These data then went into a failed K99 proposal, a failed NSF proposal, and perhaps some other failed attempt at NIH funding. Good times...

The end (part 2)

Enter Allison. Allison joined my lab with a keen interest in speciation. Her plan was to take on a new project looking at the evolution of mimicry in brood parasitic indigobirds in West Africa. We did one field season in Cameroon (the same field site I had used during my own PhD), but fieldwork  in Cameroon had just become untenable. We got all of our computers stolen, got embroiled in a long a complicated dispute with various police, our landlord and our neighbors. Allison soldiered through a tough three months during which she may or may not have had malaria, and returned to Greenville to regroup.

Allison spent some time weighing what to do next, and whether or not to continue with graduate school, but in the end, we came up with this plan to revisit some of these ideas about genetic and behavioral variation in zebra finches.  I'm really thrilled to see this project come to fruition. Many of the key results are described in Allison's dissertation, which you can see here. We continue to refine the genomic results presented in the dissertation with the newly upgraded zebra finch genome.  Look for those results to be published soon! Although a whopping ~14 years have passed since I started dabbling in zebra finches, I think there is a lot to to be gained by enhancing the comparative scope of all of the amazing neurobiology done in zebra finches. Maybe it is time to write another proposal...

​The end (part 3)

The McRae Lab at East Carolina University seeks a Masters student to begin January 2018 http://www.ecu.edu/cs-cas/biology/mastersprograms.cfm to conduct thesis research developing and validating genetic markers to be amplified from environmental DNA (eDNA) for detecting secretive marshbirds, especially Black Rail and King Rail. Lab work will be conducted at ECU using the Biology Department’s Genomics Core Facility. Seasonal fieldwork in coastal wetlands will be based in and around Mackay Island NWR http://www.fws.gov/mackayisland/, where the candidate will lead a team conducting callback surveys to locate breeding rails, find and monitor nests, and catch rails for sampling and banding using a variety of methods. The fieldwork is physically demanding, and entails early morning start times and a non-traditional work week. The field team will spend long hours wading through water, mud and vegetation in the marsh, often in hot, humid conditions. Some night work will also be necessary. The student may also contribute to a larger study of the ecology, behavior and movements of rails.

​Research will be under the direction of Dr. Susan McRae, and the work will be coordinated with USFWS collaborators and the Eastern Black Rail Species Status Assessment working group. Review of applications will begin September 5th and continue until the position is filled. Please write to express your interest in this opportunity by e-mail (mcraesATecuDOTedu) and include academic transcript(s), Curriculum Vita, and the names and contact details of three references. Final acceptance will be contingent on formal application to the ECU Graduate School before October 15th  http://www.ecu.edu/cs-acad/gradschool/Admissions-Information.cfm.

Photo ​© Todd Pusser

Just getting ready to head off to PDX in a few hours! I'm happy to announce that we'll be presenting two talks examining the mechanisms of convergent evolution. First, Jeff McKinnon will present on convergent losses of sexual dimorphism in stickleback. In two populations we've examined, females have convergently evolved (as stickleback seem to like to do) bright red throat coloration as males have. This talk will be in Session: Sexual selection 2, Day: Saturday Time: 3:15 PM - 4:30 PM, Location:C120-122.  I'm going to follow that up by presenting postdoc Matt Louder's work on "Genomic perspectives on the recurrent evolution of brood parasitic behavior",  Session: Behavior / genomics, Day: Sunday,  Time: 4:15 PM - 4:29 PM , Location: B113. I'm excited about both of these talks, so please join in for the fun!

Dr. Kyle Summers is looking for a doctoral student to carry out research associated with a project focused on the genetic underpinnings of color pattern evolution in a mimetic radiation of poison frogs in Peru (see abstract below). The position would begin in the fall of 2017. Desirable qualifications for this position include experience with modern approaches in evolutionary genetics and genomics. Experience working with amphibian breeding programs and fieldwork in Latin America would also be a plus. We encourage applications from minorities and under-represented groups of all kinds. Please send a letter detailing your relevant experience and explaining your interest in the position, as well as a current CV, to Kyle Summers ([email protected]).

​The evolution of color pattern diversity in the context of mimicry has been a focus of theoretical and empirical attention, yet knowledge of the genetic basis of this diversity remains limited. Most work on this topic has focused on a small number of systems (e.g. Heliconius butterflies), limiting the generality of inferences. This proposal combines three research groups with complementary skills and realms of expertise to investigate the genetic basis and population genomic processes underlying color pattern divergence in the context of mimicry in the Peruvian mimic poison frog, Ranitomeya imitator: Dr. Kyle Summers (East Carolina University), Dr. Rasmus Nielsen (UC Berkeley) and Dr. Matthew MacManes (University of New Hampshire). The project focuses on four specific aims: 1. Identify key genetic factors involved in color pattern development in R. imitator by investigating differential gene expression across developmental stages and color pattern morphs. Next generation sequencing will be used to produce developmental stage-specific transcriptomes for each morph, which will be assembled and used to investigate patterns of differential gene expression. 2.Identify the causal gene(s) underlying differences in color pattern between morphs using genome-wide marker arrays (exome capture sequences) to screen transition zone samples and enable admixture mapping. We have identified three admixture zones in the mimetic radiation that will be appropriate for these analyses. 3. Test the association of specific candidate loci with color pattern using pedigree analyses of candidate genes identified from Aims 1 and 2, using a multigenerational pedigree. 4. Test specific hypotheses regarding selection and demographic processes in the transition zones and between mimics and models. These analyses will involve the development of new analytical tools for analyzing selection in admixture zones and targeted sequencing of model species. Together these complementary, mutually reinforcing approaches will begin to reveal the genetic underpinnings and population genomics of color pattern diversity in this mimetic radiation of poison frogs. To summarize, the work proposed here will elucidate the genetic basis of mimetic color pattern diversity in an ecologically relevant context (Mullerian mimicry) that is a central focus of interest in evolutionary biology. By bringing to bear next-generation sequence data, developmental functional genomics, exome capture marker arrays, admixture mapping and population genomic analyses of transition zones, and pedigree analyses, we will investigate the genetic underpinnings of color pattern diversity in this unique mimetic radiation.

Welcome to the new lab site. In lieu of the "under construction" icon, I present this post. Hopefully the site will be complete in a few days, and then can begin its process of slow degeneration.