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!

Searching for Salamanders – April 2021

It’s a very special season in Rochester! With the first few warm, rainy nights of the year comes an assortment of amphibians! Last week, several groups from the department went out to the nearby Mendon Ponds Park in search for salamanders and other pond pals. We specifically looked for vernal pools, bodies of water that form in the early spring due to snowmelt and evaporate away as the year goes on. These temporary ponds are perfect nurseries for many organisms, including frogs and salamanders, because predatory fish cannot access them.

Heading out around 9-11PM, each of the groups found a wide range of species! Including …

Spring Peepers (Pseudacris crucifer): These small frogs produce a lot of noise as their chorus of raspy chirps can be heard throughout the night.

Northern Green Frog (Lithobates clamitans melanota): A common frog in ponds, if you think you hear someone plucking a banjo, it might just be a green frog!

American Toad (Anaxyrus americanus): These toads are big and will further deter predators by secreting a bufotoxin, a poisonous substance that makes the toad unpalatable.

Eastern Newt (Notophthalmus viridescens): These can be found in a juvenile stage called an eft (shown here). Due to their color during this stage, they are often called “red efts”.

Jefferson Salamander (Ambystoma jeffersonianum): A medium sized mole salamander, these animals spend most of their time in burrows. They emerge this time of year to feed on worms in the rain and reproduce.

Red-backed Salamander (Plethodon cinereus): These small salamanders have a color polymorphism: some have red stripe (“red-backed”) while others have grey backs (“lead-backed”). The red striped individuals are also less likely to run away from predators, possibly relying on camouflage or aposematic coloration.

Yellow-Spotted Salamander (Ambystoma maculatum): The main goal of our trips, this large mole salamander is extremely hard to find outside of March-May. On only a few nights during this period, large masses of salamanders will move into vernal pools to breed all at once. Here’s hoping a later outing will catch this!

Fairy Shrimp (Eubranchipus vernalis): These are freshwater shrimp that only appear in vernal pools. They reproduce while the pool is full and their eggs remain dormant for the rest of the year until the pools form again in the spring.

Overall, these trips were a great way to familiarize ourselves with local wildlife and appreciate the biodiversity of vernal pools!

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!

Journal Club Sept 15, 2020

After a certainly unique summer featuring many adjustments but also many great online conferences, classes are back in session at UR. To bring back something familiar, here are the papers that will be discussed during this week’s Journal Club on Tuesday the 15th at 11:05 (see department emails for access to the zoom link).

The focus is on the Bateson-Dobzhansky-Muller Model and will include a classic 1936 paper by Theodosius Dobzhansky, “Studies of hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids” and a 1995 by our own Allen Orr, “The population genetics of speciation: the evolution of hybrid



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!

Journal Club Dec 10, 2019

Please join us this Tuesday at 11:05 – 12:15 in Hutch 316. Lindsey and Songeun will be presenting these papers:

“Disruptive selection and the genetic basis of bill size polymorphism in the African finch Pyrenestes” by Smith (1993)

“Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus” by vonHoldt et al (2018)

“Divergence and Functional Degradation of a Sex Chromosome-like Supergene” by Tuttle et al (2016)

Journal Club Nov 26, 2019

Please join us this Tuesday at 11:05 – 12:15 in Hutch 316. Rose and I will be presenting these papers:

“Barson et al. 2015. “Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon”

Ruzicka et al. 2019. “Genome-wide sexually antagonistic variants reveal long-standing constraints on sexual dimorphism in fruit flies”.