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)
A primary goal of the Manakin Genomics Research Coordination Network (RCN) is to facilitate new interdisciplinary research collaborations that will advance our understanding of the genomic underpinnings of evolutionary processes important in shaping the ecology, physiology, behavior and diversification of organisms.
The Manakin Genomics RCN is pleased to announce the release of five new genome assemblies that promises to meet a critical first step in accomplishing our consortium's objectives.
We have publicly released the genomes in order to facilitate research on these species. As with other consortia, we request users abide by the following data use policy (which is drawn from that of the B10K and VGP projects). Two of the genome assemblies have been formally shared with the B10K and are bound by their policies as well.
The Manakin Genomics RCN has released the raw reads, assembled genomes, transcriptome sequence data, and annotations (forthcoming) as a service to the research community. We encourage others to use these data, but hope that they will respect our right to first presentation (including journal publications, pre-prints such as in bioRxiv, public conference talks, and press releases) of a genome-wide analysis of the data we generate, including the use of genome-wide data for phylogenetic and evolutionary analysis, on behalf of ourselves as data producers, the sample providers and collaborators. Therefore, please respect the embargo on the presentation of analyses using pre-publication data that we release via the relevant archives. Exceptions to the policy are for analyses of either a single locus, or a single gene family in a species, or for use as a reference for mapping reads from independent studies.
For any queries about using the data, referencing/publishing analyses based on pre-publication data from this project please contact Chris Balakrishnan. For the full list of team members please see the RCN member bios page.
Manacus vitellinus: Golden-collared Manakin (upgraded assembly)
Lepidothrix coronata: Blue-crowned Manakin
Pipra filicauda: Wire-tailed Manakin
Corapipo altera: White-ruffed Manakin
Neopelma chrysocephalum: Saffron-crested tyrant manakin
Check out our manakin resources to learn more about these species.
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@example.com).
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.