Journal Club 4/12/23 – Similar ranges, similar history, similar genomes?

Trying out something new, here is a summary of the discussion members of the department had this past Wednesday during our weekly journal club. We discussed the paper “Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age” by Moreira, Klicka, and Smith, published in Molecular Ecology in 2023.

The main idea of the paper was to compare the genomic diversity found in populations across North America of two diverged woodpeckers that share extremely similar ranges, the Hairy and Downy woodpeckers. These species are also expected to share their historic ranges that were shaped by glacial patterns that affected many North American species during the Pleistocene, possibly resulting in similar demographic histories. The authors compare reconstructed historic demographies, genetic structure across populations, and relationships between genetic diversity and various genomic features including GC content and recombination rate to determine how this shared range history resulted in similar or different patterns in each species.

We were impressed by how well the different approaches agreed with each other, supporting the idea that both species experienced similar bottleneck events in response to glaciation. However, we did discuss some challenges the authors faced with measuring differences in genetic load. The metric used to measure load will heavily affect your results, and Justin recommended a review by Simons and Sella ( that explores the impact of these metrics on results.

We also had a fun discussion on why these two woodpeckers are so similar despite being diverged by several millions of years. Maria shared some hypotheses in the literature on how social mimicry or defensive mimicry could have driven convergent evolution in plumage between these birds (see and for more details).

Spring 2023 Review

2023 isn’t even half over yet, but already there are a lot of things to celebrate in the E2G2 department!

First, there have been a lot of grant and award recipients in our department:

  • Cheyenne and Faye both received the NSF GRFP based on their proposed research!
  • Shailee and Kevin both received the NSF PRFB!
  • María received the ABS Student Research Grant with recognition for contributions to justice, equity diversity and inclusion to fund her upcoming behavioral experiments in Colombia!
  • Jeremy received the SSE Rosemary Grant Award to fund sequencing Florida Scrub-Jay genomes! He also received the the Edward Peck Curtis Award from the U of R for excellence in teaching!
  • Emiliano was selected to present at the upcoming Genetics Day!
  • Matt received an award for his poster at the Annual Drosophila Research Conference!

We have also been able to attend or hold some great events:

  • Matt, Emiliano, and Cecile all presented at the Annual Drosophila Research Conference!
  • We celebrated Xiaolu’s thesis defense with our traditional tricycle race “Tour de Franzia” (pictured below)
  • After several years worth of attempts, on the warm, wet night of April 5th we got to witness the yellow-spotted salamander spawning! Our previous amphibian searches were usually too early or too late, but this time we witnessed tens of salamanders writhing together in a vernal pool!

Summer 2022 Review

A lot happened this summer, and as the fall semester starts now is a good time to celebrate!

  • Congratulations to Matthew, Xiaomi, and María on passing your qualifying exams!
  • Several department members presented at Evolution, ABS, and GSA’s Yeast Genetics Meeting and GLAM-EvoGen. Special shout out to Shailee for winning the Allee Award at ABS for her presentation!
  • Nilima did an internship at Amyris in California.
  • Jeremy submitted his first paper on species distribution models.
  • The Fay lab did some intense sample collecting across vineyards and wineries in the finger lakes region to isolate yeasts. Bob Minckley also joined to collect bees.
  • The Chen lab traveled together to Archbold Biological station in Florida to meet their collaborators and the Florida Scrub-Jays.
  • We had a great time with the summer kickball league, and even won some games!

Chen lab members and alumnus at the Rock and Roll Hall of Fame as part of Evolution 2022

UR Biology kickball team glowing with pride!

Bikes and Biology: Multispecies coalescence

Bikes and Biology are back! Join us after Friday seminars (4-5pm) to discuss papers with wine and cheese. Weather permitting, we bike out to a fun park to enjoy the weather. Here’s what Rochester summers look like:

We discussed this Heliconius paper:

Yuttapong Thawornwattana, Fernando A Seixas, Ziheng Yang, James Mallet, Full-Likelihood Genomic Analysis Clarifies a Complex History of Species Divergence and Introgression: The Example of the erato-sara Group of Heliconius Butterflies, Systematic Biology, 2022;, syac009,

Join us next time!

This week we undertook our first attempts at learning to prepare museum mounts of dead birds (found around campus by big windows) under the tutelage of recent Uy lab graduate Dr. Diego Ocampo himself!

Find a dead bird? Keep it and join us next time!

2020 Review

Last year introduced us all to a new set of challenges that have brought hardship and tragedy to many. However, despite these difficulties, good news did exist during 2020, and here I will present some of the reasons for celebration that occurred for the E2G2 graduate students!

  • Three new graduate students started their PhDs with us! Maria Castaño, Matthew Lindsay, and Xiaomi Liu!
  • Rose Driscoll, a PhD student in the Brisson Lab, received the GRFP, recognizing her great skills as a researcher and promising contributions to science!
  • Emery Logan received the Edward Peak Curtis Award for excellence in teaching as a graduate student!
  • The University of Rochester hosted the second Great Lakes Annual Meeting of  Evolutionary Genomics! Despite needing to shift to an online platform, the meeting has a huge success with many fascinating presenters!
  • Four PhD students passed their qualifying exams: Rose Driscoll, Lauren Gregory, Jeremy Summers, and Nilima Walunjkar!

2021 will be sure to offer its own set of challenges, but we hope that the members of our community will continue to do great things!

Science Now!

Last Thursday the Chen and Meyer labs set up booths at Wayne Central Middle School for the Science Now Expo. The night was a chance for students of the middle school and their parents to talk to members of the local STEM community and see some of the demonstrations. The booths included a guessing game of genetic inheritance, 3D printing, and a box of live bumblebees!

The Uy lab relocates to E2G2

We’re happy to announce the recruitment of Drs. Al Uy and Floria Mora Kepfer Uy to Rochester’s E2G2 program!  Al and Floria will move their Tropical Biology Lab from the University of Miami to our own Biology Department in January 2020.  Al brings his research program on the ecology and genomics of speciation in birds, and Floria hers on the evolution and neural basis of cooperative behavior in social wasps.

Wasp Venom Research makes the Cover of Current Biology

Nasonia parasitoids wasps, minute insects that inject venom and lay their eggs on fly pupae, are pictured in the Goergen Hall lab of Nathaniel & Helen Wisch Professor of Biology John (Jack) H. Werren May 26, 2017. Were, along with postdoctoral fellow Ellen Martinson uses the rapidly evolving venom repertoires of these parasitoid wasps (including the ectoparasitoid model Nasonia vitripennis, pictured) to investigate the question of how new genes are recruited for venom function. In contrast to expected model of gene duplication, they find that many venom genes evolve by the co-option of single copy non-venom genes. These findings could have broad implications for how new gene functions evolve, as co-option of single copy genes may be a common but relatively understudying mechanism for the evolution of new gene functions, particularly in tissues subject to rapid evolutionary change. // photo by J. Adam Fenster / University of Rochester

Ellen Martinson, Mrinalini, Yogeshwar Kelkar, Ching-Ho Chang, and Jack Werren’s recent paper in Current Biology was featured in the Rochester Newscenter. Their research uses wasp venom to propose a new idea about how genes can gain new functional roles. The UR write-up has great photos and a video explaining their study, check it out.