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Darwin’s Pigeon “Enigma”

Darwin’s short-beak enigma solved


Charles Darwin was obsessed with domestic pigeons. He thought they held the secrets of selection in their beaks. Free from the bonds of natural selection, the 350-plus breeds of domestic pigeons have beaks of all shapes and sizes within a single species (Columba livia). The most striking are beaks so short that they sometimes prevent parents from feeding their own young. Centuries of interbreeding taught early pigeon fanciers that beak length was likely regulated by just a few heritable factors. Yet modern geneticists have failed to solve Darwin’s mystery by pinpointing the molecular machinery controlling short beaks—until now.

In a new study, biologists from the University of Utah discovered that a mutation in the ROR2 gene is linked to beak size reduction in numerous breeds of domestic pigeons. Surprisingly, mutations in ROR2 also underlie a human disorder called Robinow syndrome.

“Some of the most striking characteristics of Robinow syndrome are the facial features, which include a broad, prominent forehead and a short, wide nose and mouth, and are reminiscent of the short-beak phenotype in pigeons,” said Elena Boer, lead author of the paper who completed the research as a postdoctoral fellow at the U and is now a clinical variant scientist at ARUP Laboratories. “It makes sense from a developmental standpoint, because we know that the ROR2 signaling pathway plays an important role in vertebrate craniofacial development.”

The paper published in the journal Current Biology on Sept. 21, 2021.

Mapping genes and skulls

Two domestic pigeon breeds photos facing each other, the left one has a very short beak, big black eye, white feathers on the head with a crest sticking up. The right pigeon has gray brown feathers on the head with a red eye ball, and a beak that's about twice as long as the other birds.

PHOTO CREDIT: Sydney Stringham

Old German Owl (left) and Racing Homer (right) domestic pigeon breeds.

The researchers bred two pigeons with short and medium beaks—the medium-beaked male was a Racing Homer, a bird bred for speed with a beak length similar to the ancestral rock pigeon. The small-beaked female was an Old German Owl, a fancy pigeon breed that has a little, squat beak.

“Breeders selected this beak purely for aesthetics to the point that it’s detrimental—it would never appear in nature. So, domestic pigeons are a huge advantage for finding genes responsible for size differences,” said Michael Shapiro, the James E. Talmage Presidential Endowed Chair in Biology at the U and senior author of the paper. “One of Darwin’s big arguments was that natural selection and artificial selection are variations of the same process. Pigeon beak sizes were instrumental in figuring out how that works.”

The short- and medium-beaked parents produced an initial F1 brood of children with intermediate-length beaks. When the biologists mated the F1 birds to one another, the resulting F2 grandchildren had beaks ranging from big to little, and all sizes in between. To quantify the variation, Boer measured beak size and shape in the 145 F2 individuals using micro-CT scans generated at the University of Utah Preclinical Imaging Core Facility. 

“The cool thing about this method is that it allows us to look at size and shape of the entire skull, and it turns out that it’s not just beak length that differs—the braincase changes shape at the same time,” Boer said. “These analyses demonstrated that beak variation within the F2 population was due to actual differences in beak length and not variation in overall skull or body size.”

An animation of the skulls of birds showing the variety of beak lengths from short to long.

PHOTO CREDIT: Elena Boer

High-resolution scans of the grandchildren of the Racing Homer and German Owl cross. The animation shows the variety of beak lengths from shortest to longest.

Next, the researchers compared the pigeons’ genomes. First, using a technique called quantitative trait loci (QTL) mapping, they identified DNA sequence variants scattered throughout the genome, and then looked to see if those mutations appeared in the F2 grandkids’ chromosomes.

“The grandkids with small beaks had the same piece of chromosome as their grandparent with the small beak, which told us that piece of chromosome has something to do with small beaks,” said Shapiro. “And it was on the sex chromosome, which classical genetic experiments had suggested, so we got excited.”

The team then compared the entire genome sequences of many different pigeon breeds; 56 pigeons from 31 short-beaked breeds and 121 pigeons from 58 medium- or long-beaked breeds. The analysis showed that all individuals with small beaks had the same DNA sequence in an area of the genome that contains the ROR2 gene.

“The fact that we got the same strong signal from two independent approaches was really exciting and provided an additional level of evidence that the ROR2 locus is involved,” said Boer.

The authors speculate that the short-beak mutation causes the ROR2 protein to fold in a new way, but the team plans to do functional experiments to figure out how the mutation impacts craniofacial development.

Headshots of domestic pigeon breeds. The left four have short beaks, the right four have medium or long beaks.

PHOTO CREDIT: Thomas Hellmann, adapted from Boer et al. (2021) Current Biology

Representative images of individuals representing short beak (left four birds) and medium or long beak (right four birds) pigeon breeds (image credit: Thomas Hellmann). Short beak pigeons, from left to right: English Short Face Tumbler, African Owl, Oriental Frill, Budapest Tumbler. (B) Medium/long beak pigeons, from left to right: West of England, Cauchois, Scandaroon, Show King. The short-beak birds all had the same ROR2 mutation.

Pigeon enthusiasts

The lure of the domestic pigeon that mesmerized Darwin is still captivating the curious to this day. Many of the blood samples that the research team used for genome sequencing were donated from members of the Utah Pigeon Club and National Pigeon Association, groups of pigeon enthusiasts who continue to breed pigeons and participate in competitions to show off the striking variation among breeds.

“Every paper our lab has published in the last 10 years has relied on their samples in some way,” said Shapiro. “We couldn’t have done this without the pigeon breeding community."

 

by Lisa Potter - originally published in @theU

Healthy, Safe & Well

Healthy, Safe & Well

September Updates


HEalthy:  College of Science Flu Shot Clinic


On September 29th, the College of Science will host a Flu Shot Clinic for faculty, staff, students, and family members on the University insurance or any providers listed here.  Community Nursing Services (CNS) will be onsite in Crocker Science Center, room 206, from 8am-12pm. Please sign up for your flu shot.

For details on COVID vaccination clinics hosted on campus, please visit this site: https://alert.utah.edu/covid/vaccine/.

SAfe:  Campus Safety month


University Safety will be messaging about Campus Safety Month throughout September in @theU. In the meantime, check out their Safety Tips and FAQs page to learn more about staying safe on campus.

Well:  National yoga Month


In 2008, the Department of Health & Human Services designated September as National Yoga Month to promote the health and wellness benefits of doing yoga. Physical benefits can include increased strength, flexibility, and mobility in addition to mental benefits such as decreased stress and increased happiness and self-awareness.

In celebration of National Yoga Month, on September 22, from 12-1pm, the College of Science will host a virtual yoga session provided by Campus Recreation Services. RSVP for a calendar invite to this session.

Addressing Covid-19 Impacts in Faculty Review Materials

Addressing COVID-19 Impacts in Faculty Review Materials


The COVID-19 pandemic has likely impacted your professional life in many ways.  As you come up for informal or formal review, it may be important to contextualize your productivity and performance in research, teaching, and/or service for your colleagues and any external evaluators.  Impacts may include changes to your workload distribution, specific changes to duties, difficulties or delays due to COVID-19-related safety protocols, or the effects of increased care-giving obligations on your ability to complete professional obligations or projects.  

Alerting reviewers and colleagues about particular pandemic-related issues and how they have affected you is optional.  Should you choose to do so, here are two possibilities:

  • COVID-19 Impact Statement.  This is a brief statement enumerating specific consequences of the COVID-19 pandemic for your research, teaching, and/or service.
  • Addressing impacts within existing written materials.  Examples include mentioning delays in data collection within your research statement or discussing the shift to online instruction in your teaching statement.

It is recommended that discussions of COVID impacts be brief and specific.  Consider what you would like a reviewer to know that is relevant for evaluating your progress and productivity.  The consequences of the pandemic will be felt for many years, so consider documenting relevant impacts now if you haven’t already.  If you are uncertain about what to include in your review materials, you are encouraged to consult with mentors, your chair/director, or the Associate Dean for Faculty Affairs.

For reference, below is a non-exhaustive list of possible ways that one might document the impacts of COVID-19 on the work of a faculty member (from M. Subramaniam, 2020).

Research and Creative Work: 

  • Access to lab; access to equipment/orders for consumables; limiting work because of space and required rotation/coordination of lab personnel (such as students, postdocs, technicians); repairs or the need to fix systems. 
  • Writing time (plausibly because of care work – self and others; lack of access to books etc. from libraries). 
  • Access to studios and spaces for creative work. 
  • Loss in time due to increased teaching or service responsibilities. 
  • Note canceled fellowships, conference, or speaking engagements. 
  • Challenges in networking virtually versus being physically present at conferences and annual meetings (important especially for assistant and associate professors). 
  • Note canceled sabbatical time, paid/unpaid leave. 
  • Effects on research time due to care work, filing additional paperwork for changing/maintaining immigrant status. 
  • Research group/lab virtual meetings involving challenges such as students not having access to high speed broadband. 
  • Limited home connectivity for many reasons, including leaving WiFi during the day for school-age children. 
  • Disruptions in field-based work because of funding and travel and visa restrictions or overall research restrictions. 
  • Access to animals, cell cultures, inability to gather data/access to human subjects. 
  • Note inability of collaborators to visit and engage; including the disruptions in collaborators locations (domestic and international). 
  • Additional work and time to become familiar with protocol and ensuring research groups/lab groups are aware of and adhere to them. 
  • Access to internal/external funds for research perhaps due to funding being redirected to COVID-19 topics. 
  • Restrictions in use of funds such as discretionary funds and/or additional approvals needed to use funds for regular research activities. 
  • Access to office equipment and workspace environments (reliable internet, ergonomic furniture, professional workspace) for self and/or mentoring students. 
  • Disruptions in access to funds for open access publishing. 
  • Note cancellation of in-person workshops and disruptions in fulfilling grant outcomes. 
  • On a weekly basis, document how much virtual to on-site work is being done (virtual versus on-site spaces have their own challenges; remote work can be isolating, anxiety-producing, and stressful. On-site work can increase fears of bringing the virus home to loved ones and seeing former physical spaces now “look like a ghost town” can cause anxiety). 
  • Limits to collaborative research because of restrictions to travel, access to labs, and so impacts on interdisciplinary/multidisciplinary work. 

Teaching:

  • Time spent to retool and/or redesign curriculum to be used in a virtual format. Document revisions to courses: moving courses online, building skills to handle new technology and new online platform (can note how a typical # of work hours for teaching a particular course changed for that course). 
  • Note trainings attended to retool for teaching in revised modes. 
  • Note lack of resources for faculty and students (internet and broadband access; closure of campus computer labs or limited seats available at campus computer labs). 
  • Identify any additional teaching responsibilities (including new course preps such as due to retirement of a colleague); issues with teaching assistants; assisting others. 
  • Additional workload because of administering high flex, hybrid, and online courses such as, handling emails from students who may be quarantined; suspended; or absent from class including figuring out procedures and who to contact with questions. 
  • Note concerns and disruptions from students’ disregard of instructions in courses (particularly for women and women of color). 
  • Mentoring (faculty and students): 
    • note especially additional work needed to support those experiencing health, economic, and social consequences of COVID-19. 
    • note additional advising time because of physical or mental health concerns. 
    • note disruptions because of concerns of status of international students or newly admitted international students being unable to travel. 
    • concerns due to uncertainty and lag times in communication between when a student raises a concern and when a university response is received. 
  • Note concerns about intellectual property rights questions and posting all materials online. 
  • Note concerns about creating safe spaces for classroom dialogue offline and online. 

Service: 

  • List attending or leading meetings (additional ones) that may typically not have been required. 
  • Challenges of attending meetings virtually and how some inequalities may be further amplified in virtual settings. 
  • Note disruptions in community-based engagement and activities. 
  • Note if committee work is equitable. 
  • List limitations in advising student organizations, if any; and disruptions in those activities. 
  • Note additional workload to support communities and collaborations within which you work particularly during COVID-19. 
  • Note additional hurdles in disseminating or finishing products or services for the scholarship of engagement, especially if the target community does not have regular access to internet. 
  • Note how communities/partners have been disrupted in accessing university labs or services. 

SRI Leaders

Inspire the Next Generation


The Science Research Initiative (SRI) creates opportunities for first-year and transfer students to join a research lab in the College of Science, to begin to learn and master the skills they will need for a successful career in a STEM field.

Faculty can lead a stream of SRI students (3-10 students) in their lab on a project of their choosing, that relates to overall research productivity. By participating, faculty can help students gain research skills and mentorship that lead to academic retention, a more positive undergraduate experience and paths to graduate school.

The SRI process:

  1. First-year students, upon accepted to the University of Utah, can apply to the SRI if they intend to declare a major in the College of Science.
  2. Upon admittance to the SRI, students are placed into research streams - a group of fellow students working together in the same lab.
  3. Once in a lab, the stream is taught the necessary lab skills they will need, as well as begin creating community with their fellow students, faculty, and research lab members.
  4. Students work with their stream for an academic year. They will then have the choice to continue with the SRI for a second year, becoming mentors for the next cohort of students, or leaving the lab for new opportunities.

We want you to be involved! Email the SRI Director today.


>> SRI HOME <<

 

 

Prospective Faculty

Why Utah?


 


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Faculty Stories


Darwin’s Pigeon “Enigma”

Darwin's short-beak enigma solved

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Physics Innovation

Yue Zhao Receives Physics Innovation Award.

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William D. Ohlsen

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Be the Light

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Mysteries of the Universe

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Let’s Get Kraken

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Camille-Dreyfus Award

Luisa Whittaker-Brooks receives Teacher-Scholar award.

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NAS Membership

Mary Beckerle receives the significant recognition of NAS membership.

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AAAS Membership

Valeria Molinero joins the prestigious ranks of the American Academy.

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Patterns in Sound

Exciting new math research by Fernando Guevara Vasquez.

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Amanda Cangelosi

Mathematics faculty receives U's Early Career Teaching Award.

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Allergy Season

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Sloan Research Fellow

Luisa Whittaker-Brooks awarded prestigious 2021 Sloan Research Fellowship.

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Cottrell Scholar

Gail Zasowski named a Cottrell Scholar.

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Ken Golden brings the principles of mathematics to the Earth’s most remote environments.

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Carsten Rott

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Mixing chemistry and martial arts for CBS television.

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Priyam Patel

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COVID Connections

Creating opportunity during COVID-19

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Karl Schwede

The latest faculty to be named a Fellow of the American Mathematical Society.

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Giant Poisonous Rats

The secret social lives of giant poisonous rats.

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A Catalyst for Safety

Chemistry labs lead the way in university safety.

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Productivity Resources

Resources for faculty to help during the Covid-19 pandemic.

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Next-Gen Astronomy

The Sloan Digital Sky Survey is providing groundbreaking insight.

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$602 Million in Funding

Research funding passes $602 million for 2020.

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Debate 2020

STEM students least likely of any subject group to vote in U.S. elections.

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Equity, Diversity & Inclusion Committee

Working together for a better tomorrow.

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Presidential Scholar

Pearl Sandick has been named a University of Utah Presidential Scholar.

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11 Billion Years

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HIV Microscopy

Ipsita Saha is using electron microscopy to reveal the dynamic structure in HIV.

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Forest Futures

William Anderegg explains the risks of investing in forests.

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Karl Gordon Lark

Honoring Karl Gordon Lark, 1930-2020.

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Courtship Condos

Why is Dean Castillo managing the sexual relations of fruit flies?

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Tino Nyawelo

I see myself in those kids who are brought here as refugees.

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Running with Scissors

In gene-targeting, CRISPR makes a really good pair of "scissors".

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Electrochemistry

Henry S. White - A positive force in Electrochemistry.

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Commutative Algebra

Can commutative algebra help us solve real-world problems?

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Engaging STEM Students

How can we make STEM education more inclusive and effective?

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TreeTop Barbie

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AMS Fellow

Davar Khoshnevisan, named Fellow of American Mathematical Society.

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Going with the Flow

John Sperry studies how plant hydraulics and xylem tissue influence regional weather.

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Royal Fellow

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Teaching Excellence

Kelly MacArthur is recognized for her extraordinary dedication to her students.

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Teaching Excellence

Recognizing extraordinary skill in university teaching.

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Distinguished Research

Professor Molinero’s work is a hallmark of what research and scholarship should be about.

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Distinguished Teaching

Gernot Laicher, Professor/Lecturer in the Department of Physics & Astronomy.

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2019 Hatch Prize

Professor Joel Harris has been awarded the 2019 Hatch Prize for outstanding teaching!

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Diane Pataki is now Associate Vice President for Research at the University of Utah.

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AMS Fellow

Tommaso de Fernex, Ph.D. Associate Department Chair of Mathematics.

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AMS Fellow

“I was delighted to learn the news from the AMS,” said Peter Trapa.

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Plant Genomics

QUESTION: How does RNA decay contribute to gene expression?

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Breakthrough Prize

Christopher Hacon, has been interested in math for as long as he can remember.

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Under Pressure

Unravelling the mystery of a fundamental property of lithium.

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Strategic Plan

Strategic Plan


As of July 2020, the College of Science has finalized its Strategic Plan. You can view it here:

 

 

Many thanks to all students, faculty, and staff who participated in the process described below to help shape the future of the College of Science.

 

May 7-15, 2020 - Survey

Input from students, faculty, and staff is solicited.

1
May 22, 2020 - Summary

2
May 29, 2020 - Draft

Draft Strategic Plan available to stakeholders (UNID required)

3
May 29-June 5, 2020 - Comments

Comment phase for Draft Strategic Plan

4
June 2020 - Update

  • Summary of comments available to stakeholders
  • Preliminary Strategic Plan available to stakeholders

5
July, 2020 - Finalize

  • Presentation to College Executive Committee for approval
  • Strategic Plan finalized

6