Teeth- integrating developmental genomics, biomechanics, ecology & illuminating our history

In January of 2020, at SICB’s annual conference, Darrin Hulsey and Gareth Fraser (@garethjfraser) organized a symposia:

S3 – Biology at the Cusp: Teeth as a Model Phenotype for Integrating Developmental Genomics, Biomechanics, and Ecology

https://sicb.burkclients.com/meetings/2020/symposia/teeth.php

“Teeth have long been a subject of integrative inquiry, but the breadth of studies on teeth is increasing at an exceptional rate. Our understanding of the genomic basis of tooth differentiation is rapidly increasing as non-traditional vertebrate model systems become tractable to genetic dissection…

In light of her interest in this subject as well, we asked Professor Tanya Smith if she’d talk with us about her book The Tales Teeth Tell.

Here’s what she had to say about her work and its importance followed by our book chat.

The Tales Teeth Tell was inspired, in part, by an undergraduate course I taught for several years at Harvard University on teeth and human evolutionary biology. My aim in the book was to engage and excite people who may not have a background in this subject – nor a love of teeth – but who are curious about human development, evolution, and ancient behavior. 

Given how politicized science can be, and how insular academic writing often is, I believe that it’s part of my professional responsibility to explain why science is interesting and important.

Tanya Smith

Many of us have to work to be accessible writers in order to help readers understand how we evaluate information and draw logical conclusions. This helps people think critically, which is of particular relevance now as we see how misinformation can corrode social trust in science. 

For example, my partner is a nutritionist, and dietary recommendations seem to constantly shift – giving me ample opportunities to playfully critique “food science.” But this changing landscape is often due to advances in our understanding of human biology, more rigorous study designs, and new analytical tools. If we can bring a spirit of transparency to the scientific process, and possibly even cast researchers as “advanced students” rather than “static experts,” things might be safer in the world. 

Unfortunately, I don’t perceive institutional incentives for American academics to engage in extensive science communication, particularly for women in the middle of their careers who work in competitive fields. There is a lot of pressure on early career academics to publish in big name “high-impact” journals, build large lab groups, and bring in large research grants. 

In Australian universities, we are encouraged to contribute to public discourse and media outlets like The Conversation, which publishes a daily digest of short public interest articles written by academics. I’ve contributed three pieces that have been read over 33,000 times; thus the reach is much greater than through traditional publishing mechanisms or even in a classroom. 

What in particular led you to anthropology and biology? Was there a defining moment that lead you in this direction?

I was initially lit up by an introductory biological anthropology course I took during my first semester at SUNY Geneseo. The field encompasses so many of my personal interests in natural history, skeletal biology, and human uniqueness. While majoring in biology, I took every biological anthropology course offered and participated in two field seasons in the Great Divide Basin of Wyoming — where we recovered Eocene mammalian fossils, including tiny primate teeth. 

During my senior year at Geneseo I began to read about how scholars were using biological rhythms in teeth to explore ancient human development, and using electron microscopy, I started my own search for these lines in the fossil teeth we found in Wyoming. I write more about a transformative “Ah-Ha moment” in The Tales Teeth Tell that eventually led me to experimentally document the timing of growth lines during my PhD research at Stony Brook University. 

                                                                                                      Photo by Jeffrey Camden

You state that teeth are examples of how as omnivores we’ve hedged our bets evolutionarily. In your opinion, with the plant based diet aficionados growing in numbers, do you feel our teeth and their history thereof, provide evidence we were meant to be vegetarians? 

We are primates, a broad radiation of mammals found throughout much of the world, and primates eat many things—including plants, insects, mammals, and even other primates occasionally. Our closest living relatives, the great apes, are mostly vegetarian, but it’s clear that ancient hominins were scavengers, and ultimately, hunters. 

Some anthropologists suggest that consuming highly dense protein sources, such as meat or seafood, has been integral in our brain evolution. We first find evidence for stone tool use associated with butchery ~3 millions of years ago, which became commonplace about the time our teeth started to reduce in size ~2 million years ago. 

In The Tales Teeth Tell I refer to the “oral Swiss army knife” in our mouths, reflecting omnivorous hominin diets as well as our deeper history as primates. We have broad front teeth that allow for incision, as exemplified by those of frugivorous primates, and thick-enameled teeth that are good for breaking up hard objects rather like specialized seed-eaters. Our back teeth — premolars and molars — are moderately crested, but not as extremely crested as primates that only shear leaves or crunch insects.  

So, we’ve “hedged our bets” evolutionarily as omnivores that ate what we needed to survive in different seasons and disparate environments. Of course, all this changed once humans began to cultivate the land, domesticate animals, and settle down — a good topic for a future blog! 

Tell us a bit about this quote: “Teeth illuminate our human history like no other part of our anatomy”  

It is amazing to me that several months before we even begin to breathe or chew, cellular blueprints are assembled to construct the hardest substance in the body. Each day of our early lives is then recorded by faithful 24-hour cellular clocks ticking away in utero and immortalizing their rhythmic microscopic secretions of enamel and dentine. Because teeth start mineralizing early, we have a permanent developmental record of when you’re born, a birth certificate in your mouth.

(https://thereader.mitpress.mit.edu/birth-certificate-neonatal-lines/)

This is an even more precise permanent record than what our bones record since our teeth do not remodel in response to adulthood wear and tear like bone. Many of my colleagues like to compare tiny lines in teeth to the rings in tree trunks, although teeth are even more sensitive and durable.

On an even broader level, teeth hold meaningful clues to nearly everything you can think of: growth rates, age, disease, evolutionary relationships, life history, diet, migration, climate, nursing behaviour, and social status — humans have even used teeth as a form of artistic expression for thousands of years. And they are great sources of ancient proteins and ancient DNA! 

Tanya Smith

You wrote about how engineers are using studies of limpets(snails) teeth in order to make better artificial materials. Are there other areas(fields) where you feel the study of teeth is contributing to other types of research?

Teeth have helped inform how we understand the evolution of human development. Since tooth crowns are made up of more than 95% mineral when they finish forming, these durable “rocks” are the most common body part to be recovered from ancient mammals. The human fossil record contains numerous teeth from over 30 hominin species extending back 7 million years; allowing access to our ancestors’ early lives in astounding detail. This includes hominins such as the australopithecines that ultimately gave rise to humans over millions of years of evolutionary twists and turns. 

The permanent microscopic records of tooth growth that are laid down every day allow us to determine the precise age of children in the human fossil record. From this starting point we can probe the developmental mechanics of human evolution such as when did brain development begin to slow down, (https://theconversation.com/baby-steps-this-ancient-skull-is-helping-us-trace-the-path-that-led-to-modern-childhood-130535) or which fossils show the elongated period of childhood that distinguishes us from the great apes. Evolutionary anthropologists have been debating these questions for a century, but this analytical approach has been carefully refined and validated over the past few decades. 

It turns out that modern humans are quite unusual: our species downshifted its growth, forming teeth more slowly over a longer childhood than our ancestors and evolutionary cousins, including Neanderthals. This may have given us more time to grow our brains or learn complex behaviors before having our own kids. Teeth can also help us to understand the end of the lifecycle. Some scholars have concluded that “old age” only became common very late in our evolutionary history, as there are more fossil human adults with heavily worn teeth than Neanderthal or australopithecine adults.

          Since writing your book, have you happened upon anything you wish you could’ve included ? 

Yes – we published a recent study in Science Advances showing how teeth record climate variation that can be read on a weekly scale. (https://theconversation.com/what-teeth-can-tell-about-the-lives-and-environments-of-ancient-humans-and-neanderthals-104923?utm_source=twitter&utm_medium=twitterbutton)

We can now explore which season prehistoric individuals were born in, when illnesses were most common, and even when mothers stopped nursing their children. And all of this can be learned from a single fossilized tooth! 




First molar tooth from a 250,000-year-old Neanderthal child. Yellow dotted lines indicate the beginning and end of nursing, a red dotted line corresponds to an illness, and blue dotted lines indicate lead exposures. Tanya Smith and Daniel Green.

First molar tooth from a 250,000-year-old Neanderthal child. Yellow dotted lines indicate the beginning and end of nursing, a red dotted line corresponds to an illness, and blue dotted lines indicate lead exposures. Tanya Smith and Daniel Green.

Amazingly we also found lead in the teeth of 250,000 year old Neanderthal children. This may have been due to their groups moving into caves with natural lead deposits, drinking contaminated water, or burning combustible materials tainted with lead. 

Being able to paint an intimate and detailed portrait of the first few years of a young Neanderthals’ life is an exciting example of the phenomenal secrets one can coax from their precious teeth. 

Twitter

@DrTanyaSmith

Further articles

@sciam  

Why We Have So Many Problems with Our Teeth

https://www.scientificamerican.com/article/why-we-have-so-many-problems-with-our-teeth/

A few of s3’s ARTICLES FOR ICB

The dental lamina: An essential structure for perpetual tooth regeneration in sharks

https://doi.org/10.1093/icb/icaa102

Phenotypic Plasticity in Vertebrate Dentitions

https://doi.org/10.1093/icb/icaa077

Grand Challenges in Comparative Tooth Biology

https://doi.org/10.1093/icb/icaa038

s4 Reproduction: the Female Perspective from an Integrative and Comparative Framework – Sarah Lipshutz – an authors science “playlist”

Sara on a hike in Hawaii

In January of 2020, Dr. Sara Lipshutz participated in a symposia headed by Dr. Virginia Hayssen and Dr. Teri Orr on reproduction.

(Also see : https://integrativeandcomparativebiology.wordpress.com/2019/12/12/s4-sicb-austin-why-reproduction-shouldnt-take-a-backseat/)

Sara’s focus of study has been behavioral and genomic processes of reproductive isolation (endocrine and neuro-genomic underpinnings of female competition)

Her recent work that she collaborated on, It takes two to tango: including a female perspective in reproductive biology can be read via ICB https://doi.org/10.1093/icb/icaa084

Below are some of Sara’s recommendations :

science podcasts: 

Ologies, This Podcast Will Kill You,

Big Biology (from SICB colleague Marty Martin),

and The Memory Palace (especially the Sixty Starlings episode).

Most of my podcasts are not science-related though (my brain needs a break!). I listen to Call Your Girlfriend, On the Media, Code Switch, Snap Judgment, Dolly Parton’s America and recently, Nice White Parents).


*science publication : (book, article, magazine) 

Why Zebras Don’t Get Ulcers by Robert Sapolsky. Currently reading Superior by Angela Saini.

Recent Sapolsky talk – Heartland Future Talks 2019: Robert Sapolsky & Lone Frank https://youtu.be/PV6XKnVWNsk via @YouTube

*Workshop or conference I don’t miss(though online now)

I really enjoyed the virtual Animal Behavior Society conference and the virtual Early Career Research edition of Evolution. Although virtual is less expensive and more carbon neutral, conferences are one of the main ways I keep in touch with my colleagues from other institutions, and I really miss that aspect.


*Scientific documentary film– The Sounds of the Sounds of Science – Jean Painleve’s underwater documentary shorts, accompanied by Yo La Tengo


*my scientist social media faves- @itatiVCS, @ambikamath, @DNLEE, @GinaGoesOutside, @BeccaCalisi, @christineliuart


connect with Sara on Twitter

@jacanamama

S3 – Biology at the Cusp: Teeth as a Model Phenotype for Integrating Developmental Genomics, Biomechanics, and Ecology

During SICB2020 in Austin this symposium covered shark tooth development and regeneration coupled with gene expression, dentition patterning in all sorts of mammals, as well as plasticity and bio mechanics.

Taking a bite out of this topic was a bit more complex than just looking at how teeth grew and comparing genes. During SICB2020 in Austin this symposium covered shark tooth development and regeneration coupled with gene expression, dentition patterning in all sorts of mammals, as well as plasticity and bio mechanics.

The evolutionary novelty of teeth have significantly aided vertebrates. Dental variation is often referred to as a defining characteristic attributed to isometric scaling with body size, however, trophic specializations (i.e. crushing hard-shelled prey or piercing) provide a clear functional basis for predicting components of dental diversification. Among the many articles we can’t wait to sink our teeth into for issue 3 this year is Dr. Crofts (@S_B_Crofts) and colleagues, Beyond description: the many facets of dental biomechanics, which provides an overview of dental biomechanics in mammalian and non-mammalian teeth. The review aims to synthesize the field of dental biomechanics by developing an integrative framework for classifying and evaluating dental functional morphology (Fig. 1).

Fig. 1. Future work in dental biomechanics (From Crofts et al. 2020)

Their framework reviews advances in technology and brings together food processing and materials, energy transfer, and mechanical considerations that may have shaped tooth morphology.

What what processes result in such dental diversity?

In order to explain the potential evolutionary influences shaping the modular organization of gene regulatory networks Dr. Sadier (@aigverte) and colleagues explain how these diverse forms emerge through modular organization of gene regulatory networks (GRNs) early on in development. In this issue, their study The role of core and variable Gene Regulatory Network modules in tooth development and evolution, sets the stage for a theoretical landscape where a cascade of regulatory mechanisms may be responsible for dental morphological variation (Fig. 2).

Fig 2. Theoretical Gene Regulatory Network (From Sadier et al. 2020)

In this issue Sadier et al. (2020) propose that vertebrate teeth be used as a model for testing GRN in dental developmental determination. In vertebrates both conservation of developmental mechanisms and extraordinary diversity of teeth may be linked to a dental diversity with relaxed sub-modules being activated in dental specialists. However, we cannot ignore the potential phenotypic plasticity may have as well. Nidal Karagic (@NidalKaragic) and co-authors in their paper titled Phenotypic Plasticity in Vertebrate Dentitions provide a thorough literature review concerning phenotypic plasticity in vertebrate teeth (Fig. 3).

Fig 3. Phenotypic plasticity in teeth (from Karagin et al. 2020)

Even phenotypic plasticity in teeth remains largely overlooked, understanding the physiological, developmental, and genetic mechanisms that generate phenotypic plasticity in teeth can clarify its potential role in the evolution of dental phenotypes seen across all the tree of life.

Seems like there may be multiple ways to make a mouth full of teeth?

Absolutely, and there may be no more famous teeth in the animal tree of life than Sharks (Chondrichthyes), but where did their teeth come from? In this issue Dr. Zerina Johanson and colleagues investigated Jaws cousins, the Holocephalans, also known as chimeras, in a study titled Evolution of the Dentition in Holocephalans (Chondrichthyes) Through Tissue Disparity. The contrast between extant Sharks and Rays (Elasmobranchii) the Holocephalans have a very different pattern of dentition (Fig. 4).

Fig. 4. Comparison of a (A) shark, (B) ray, and (C) chimera (modified from Johanson et al. 2020)

The Holocephali provided a sharp contrast to their sister Elasmobranchii as they lack individual tooth renewal, but instead use dental plates made of self-renewing dentine. The fossil record of the holocephalans provide a sharp contrast to their current dental pattern. Evolutionary processes have resulted in hypermineralized dentine in holocephalans losing defined teeth but retaining dentine production from the inherited developmental package.

How Our Thoughts Matter When It Comes To Wildlife Conservation


Guest post by Melissa Cristina Márquez

Our thoughts are powerful- they shape how we view the world and, ultimately, our decisions. Meaning our thoughts can also determine the fate of an animal – life or death.

“Which animal is worth conserving?”

We live in a world of accelerated biodiversity loss but limited resources for the conservation and management of these animals. That means we need to prioritize what animals we will funnel our resources to.

It seems straight forward: identify the animals that are at risk of going extinct and implement management to conserve them. But that isn’t how real-life works. It’s messier than that, especially for animals with a bad reputation who need help.

People and wildlife have coexisted for a long time and occasionally we have run-ins with them. There are quite a few different ‘dangerous’ animals out there, such as lions, wolves, bears, coyotes, and spiders. But few elicit the fear and terror people feel when they hear ‘shark.’

We need sharks. They are vital to our oceans (e.g. balance food webs, keep prey populations in check, and keep vital habitats healthy)! But they face numerous environmental threats that are increasingly putting them in peril such as climate change, habitat degradation, shark finning, and overfishing. In reality, they have more to fear from us than we do of them.

It may shock you to know that humans were not always scared of sharks. The portrayal of sharks has evolved over the years from heroes and tricksters to villains in literature, film, and folklore. Tales range from shark gods who usually protected people to symbols of vengeance and show the complex relationships that indigenous communities had with sharks and how they co-existed. While folklore has little influence in today’s conservation initiatives, the stories we tell about sharks shouldn’t be discounted because portrayal matters. Why? Well, basically, if there’s not broad public support for shark conservation policies, it’s not really going to happen. 

Arguments for shark conservation based on their critical ecological roles have been overshadowed by shark attack headlines calling them “monsters” and “man-eaters.”

Couple that with the fact that our thoughts are influenced by the physical and behavioural characteristics of the animal and sharks… well, they’re in trouble. We’ve seen how the media can destroy an animal’s reputation… but it can also help build it back up. Just look at how much joy IKEA shark, Katy Perry’s “Left Shark,” and “Baby Shark” brings to people!

We can—and must—envision better ways of living with other animals. The way we talk about these animals’ matters. Public support or condemnation for an animal informs the kinds of conservation policies that we create. If we want to conserve sharks and other similar predators, we need to change our relationship with nature… starting with you, reader. I’m asking you to think carefully about how you talk about wildlife, question the headlines you read, and think about conservation in a way that includes humans and animals co-existing. 

It’s up to our generation to make sure ‘monsters’ like sharks don’t become just stories we all tell in the future.

https://www.melissacristinamarquez.com/

and connect with Melissa on Twitter via @mcmsharksxx

Podcast spotlight- Herstory – amplifying voices of women

Jewell plummer herstory   women of herstoryreyes herstory

 

                           “Well behaved women rarely make history”

                                                            -Laurel Thatcher Ulrich

 

COVID-19 has been a trying time for everyone, and it can be difficult to find motivation, and inspiration when you are not even sure what day it is, what time that virtual meeting is supposed to be, and whoops the cat just destroyed the makeshift home office that you created at your kitchen table. Good news! There is a show with more than enough inspiration and laughter, sometimes tears, that is available wherever you listen to podcasts.

 

heather AstleyJoe Ortiz herstory host

Women of HERstory: A Podcast is a twice weekly podcast dedicated to celebrating women who have made, or are making, their mark on society. Each Tuesday, hosts Heather Ashley and Joe Ortiz, discuss women of the past with a researched biographical episode showcasing the contributions of a woman who has left her stamp on our world. From the ancient Celtic Warrior Queen, Boudicca, to NASA coder, Margaret Hamilton, they explore the lives of doctors, artists, activists, engineers, and everyone in between.

One episode a week is just not enough, so the HERstory team decided to kick your weekends off on the right foot with interview episodes every Friday. Heather sits down with women of today who are making moves in their fields, no matter where in their respective careers they are currently situated. In these interviews, that feel much more like a conversation, they discuss questioning themselves, their successes, failures, second favorite colors, and anything else that seems to come to mind. Women of HERstory: A Podcast takes great care in crafting their interviews to showcase the incredible guests.

In upcoming interviews, Heather talks with a woman entering her second year of med school. Her entire life she was on track to become a professional ballerina when an injury sidelined her. She went back to school, became a dietician, and then went back to school once again to further her medical education. There was another conversation with an epilepsy researcher. She discusses what it’s like to be a woman of color in the field, and what her female mentors have meant to her development.

 

Women are significantly under-represented in the sciences, a trend that seems to be changing, and Heather and Joe excitedly lift these women up, and amplify their voices.

From those still in school, to established researchers well into their career, the conversations are relatable and eye-opening.

There is not one single definition of success. It can feel daunting when the only people you are constantly hearing about are the same 35, or someone, somewhere, said “you’re only a REAL actor if..” “you’re only a REAL chef if..” “you’re only a REAL scientist if..” and so on. We should not have to quantify the validity of our existence, careers, or personal lives. Over, and over again, Heather has heard “Are you sure I’m who you want for this podcast?”  or “I might not be successful enough to be featured.”

Women especially, are taught to downplay their achievements, particularly if they are about their career and not their family, so as not to make the people around them uncomfortable. Women of HERstory is about reversing that mindset.

Your experiences and the resulting lessons you learned through them, are worth sharing. You deserve to celebrate everything it is that you have accomplished, and there is no reason to feel guilty about it.

Women of HERstory is more than a podcast. They are striving to create a community that inspires people to push boundaries. To not only be enlightened with the knowledge of the women that paved the way, but to also be equipped with insights of the women out there now.

 

http://www.ofherstory.com – find episodes and how to connect on social media 

herstory twitter.png

 

 

s7 -ICB issue 2- a “scientist’s playlist”- there’s a little something for everyone…

2020 s7 Millighan Myhre pic .jpgphoto- Dr. Kathryn Milligan-Myre

In January of 2020, in Austin Texas,  symposia (s7) was held entitled-” Building Bridges from Genome to Phenome: Molecules, Methods and Models”.

The papers from this symposia will be published in issue 2 and in issue 6 of ICB this year.

Dr. Kathryn (Kat) Milligan-Myhre took part with her paper/ presentation :

“Early life exposure to an enteric pathogen affects organ development in threespine stickleback raised in germ-free conditions”

by Lucas Kirschman, Anastasia Khadjinova, Kelly Ireland and Kathryn Milligan-Myhre (to be published) 

**other papers from this grouping already in Advanced

Unique Genomic and Phenotypic Responses to Extreme and Variable pH Conditions in Purple Urchin Larvae by Garrett et al 

https://doi.org/10.1093/icb/icaa072

Recommendations for Advancing Genome to Phenome Research in Non-Model Organisms by Durica et al 

https://doi.org/10.1093/icb/icaa059

Here is Kat’s Scientist’s “playlist” below 

*science podcasts:

Ologies,
Ologies .jpg
Period with Kate Clancy,
PhDivas
Science for the People
Science History
Spark Science
The Effort Report
This Podcast will Kill You
this podcast will kill you
This week in….series, Tiny Vampires

*science publications :

The Immortal Life of Henrietta Lacks by Rebecca Skloot,   
(@RebeccaSkloot)
henrietta .jpeg
I Contain Multitudes by Ed Yong,
Braiding Sweetgrass by Robin Kimmerer,
Biohazard by Ken Alibek,
The Lives of a cell by Lewis Thomas,
Your Inner fish by Neil Shubin

*workshop or conference I don’t miss (even online) :

Beneficial Microbes

microbes.png@BenMicrobesMtg

*my scientist social media faves

@NeedhiBhalla,
@NeedhiBhalla,
@SarahMackAttack,
@1NativeSoilNerd,
@_Astro_Nerd_,
@AFro_Herper,
@hood_naturalist,
@hood_naturalist .png
@ivanividivici,
@ACasadvall1,
@shrewshrew,
@DNLee5,
@microbiomdigest,
@microbiomdigest
@KimTallBear,
@drkatclaw

Connect with Dr. Kat Milligan -Myhre via

milligan myrhre s7 blog

Starting a new job during the pandemic? You are not alone.

By Noah Bressman, Kelly Diamond, Sarah Friedman, and Joe Heras.

            The COVID-19 Pandemic has disrupted so many of our lives. Some have become ill and/or helped care for sick family members. Some of us are experiencing unemployment. Those of us who are parents have had to watch children while also doing their jobs from home, online learning rapidly becoming the norm, and then the entire field season has pretty much been cancelled. It is not easy for anybody to try to continue with some semblance of life, let alone go through big life changes like moving or starting a new job. 

I (Noah Bressman) learned this firsthand when I defended my PhD at Wake Forest University alone via Zoom, moved (four times) across the country with everything either shut down or dangerously open along the way, and started a new job as a postdoc at Chapman University this spring, all during the height of the pandemic. With campus closed, my orientation was abbreviated at best.

Because I have not been able to meet anyone in person or interact with other postdocs, I have no in-person social circle and I still do not really know what my role as a postdoc is—I am not quite a student but not quite a professor? Through social media, I realized that I am not alone; there are plenty of other people going through something similar to what I am going through.

We may not have an in-person cohort, but we can form an online one to share experiences and learn from each other.

With the fall semester approaching, many others out there who are going to be starting new positions and will be struggling with the same issues. To help build a sense of community in this time, some members of my “cohort” shared their thoughts, fears, and difficulties of starting their new positions during the pandemic, but also offer some words of hope:

 

Introduce Yourself:

Kelly Diamond: In January 2020 my partner and I moved from South Carolina, where I had finished my PhD, to Seattle, Washington, for my current postdoc fellowship. My dissertation focused on biomechanics and ecomorphology while my postdoc work is exploring how machine learning can be used in 3D image analysis. While both are focused on morphology, the techniques I’m currently implementing are entirely new to me. These new methods are simultaneously exciting and infuriating, especially in the current reality of remote work and layers of communication challenges. 

Sarah Friedman: I am currently finishing up my Ph.D. at UC Davis and am preparing to move across the country to start a postdoctoral fellowship position at Yale University in September 2020. Suffice it to say, the pandemic has complicated nearly every aspect of starting my new position from moving logistics to the fellowship program design to the research I had proposed to work on.

Joe Heras: In the midst of this pandemic, I’m in the middle of transitioning from my postdoctoral appointment at University of California, Berkeley to an assistant professor position in the Department of Biology at California State University, San Bernardino.

Kelly Diamond recently gained her PhD from Clemson University and started a postdoc at Seattle Children’s Research Institute.

 

How is your orientation/settling in impacted?

Kelly: Fortunately, I was able to do all of my orientation training before everything shut down. However, Seattle didn’t stay open long enough to develop any kind of social support, which is definitely the biggest challenge so far. My partner and I got married right before everything shut down, we joke we are honeymooning on our own private Pandemic Island in the middle of our new city!

Sarah: Moving to a new place is challenging in the best of times. During a pandemic, even simple tasks are monumentally more complex. It has become an exercise in navigating basic city services, like obtaining a residential parking permit, while bureaucratic offices are indefinitely closed. Additionally, without being able to meet new people or explore my surroundings, it’s clear that the pandemic will delay feeling “at home” in my new city for quite some time.

 

What are you most uneasy about? 

Kelly: I’m most uneasy about finding my next job. My goal has always been to love my job and live in a place my partner and I can enjoy our time off.  I was planning to restrict future job/postdoc searches to the southeastern US to be closer to our families, but now we just want stability more than anything else.

Sarah: I am most immediately concerned about getting sick nearly a continent away from all of my friends and family. Additionally, my partner, an academic on the west coast, and I are now forced to navigate the two body problem while trying to minimize potential exposure travelling to see each other. 

Sarah Friedman recently graduated from the University of California, Davis with her PhD and is about to start a postdoc at Yale University.

 

What’s been the biggest challenge you’ve faced starting a new position during the pandemic?

Sarah: I would say the biggest challenge so far has been figuring out moving logistics. Pre-pandemic, I had imagined a fun road trip across the country with stops at various National Parks along the route. Those grand plans vanished pretty quickly once the shutdowns began. Now, the plan is to get across as quickly as possible while minimizing potential exposure. We have decided that avoiding large cities and camping wherever possible are safer bets, but the complete lack of information has made planning into an unfortunate guessing game. 

Joe: There are plenty of challenges that I face at the moment and patience is truly a virtue.  With all California State Universities moving forward with a remote teaching plan for the Fall, I am preparing all of my materials from home, and I have invested in a nice pair of Sony headphones (to reduce any audio difficulties that I may face).

 

How have your future plans/ goals changed because of the pandemic? 

Sarah: The position I am starting is somewhat unique because I am one of 10 postdocs participating in a new fellowship program designed to foster interdisciplinary collaborations. Unfortunately, that specific framework depended heavily on personal interactions, which are significantly hindered for obvious reasons. I am concerned about missing out on these opportunities as well as those that come from interacting with the broader scientific community at my new university. Considering most of my past research experience has been computational, I was also looking forward to the opportunity to diversify my skill set with lab-based work that I had proposed in my fellowship application. Now, I will have to rethink my postdoctoral research program, taking time out of an already limited two year position. 

Noah: I was supposed to co-teach a marine biology field course this summer, which would have been my first instructor experience for a full course. However, this is no longer happening. This course was one of the things that drew me to my current postdoc position because I thought it would help me gain the teaching experience that my CV lacks, ultimately helping me get a professor position. Instead, to increase my teaching experience, I developed a Ted-Ed lesson and guest lectured (via Zoom) for a few courses. As part of my postdoc, I was also supposed to mentor undergraduates and guide them through research projects. In all likelihood now, I probably will never meet some of these students in person before they graduate, let alone provide them with in-lab mentorship. Instead, I will encourage them to take up projects using open-source and previously-collected data while remotely teaching them the analytic skills necessary to do so.

Noah Bressman recently received his PhD from Wake Forest University and started a postdoc at Chapman University.

 

What are the most creative or best solutions to pandemic-related issues in academia that you have seen or implemented?

Kelly: Many of the most creative solutions to pandemic related issues that I’ve seen are related to outreach and child care. While this may not seem like a strictly academic issue, professors and postdocs are parents too. I love that my neighborhood has turned into a village where the kids are always outside laughing and playing. I started an outreach project where neighborhood kids could ask me questions about animals and answering those questions is often the highlight of my week!

Sarah: My current lab has been bringing in different early-career scientists to speak about their research in our weekly Zoom lab meetings. Since we’re all attending virtually, there is no reason to keep meetings limited to just local researchers. I think it’s a very creative way to meet new researchers and keep up with cutting edge science with the current limitations. 

Joe: This Fall, I am teaching an upper division Evolution course, which entails a mixed strategy of synchronous (real-time) and asynchronous (self-paced) methods to keep students engaged in the material.  My plans are to use zoom for synchronous activities, which includes live lectures and breakout sessions for discussions.  For asynchronous activities, I’ll use a mixture of surveys (Google Forms), discussion board posts (Slack), and pre-recorded videos (YouTube) to explain difficult concepts and assess students’ progress throughout the course.  Also, I’m thinking of ways to conduct research during this difficult time, which will be mostly in silico.  I’m an evolutionary geneticist and I intend to have students extract candidate genes from online genetic databases (e.g. GenBank and Ensembl) to look for patterns of adaptive evolution.  My hopes are to have students in the field and in the lab by next summer 2021.  This is my COVID-19 pandemic plan for my first year as an assistant professor. 

Joe Heras recently finished a postdoc at the University of California, Berkeley and is starting as an assistant professor at California State University, San Bernardino.

 

What’s one good thing about starting a job in the middle of a pandemic?

Kelly: As an introvert, the best part of starting a job in the middle of a pandemic are the new online learning and networking opportunities. Personally, the hardest part of networking at conferences is actually walking up to the person I want to talk to. But in zoom there’s no need to psych yourself up to try to breach the social circle! You can just ask your question because you’re already in the conversation! Hopefully these interactions will help me get a job when all of this is over! If nothing else I get to learn new things I would not have had time for without the pandemic! 

Sarah: I think everyone has been incredibly flexible and understanding of the difficult circumstances. Though I know it is far from universal, my experience interacting with other academics at this time has been largely positive.

Joe: I’m fortunate to have a position in science under these difficult circumstances.  My new colleagues in the biology department at California State University, San Bernardino have reached out to me to say hello and offer support through answering my questions related to starting my position as an assistant professor.

Noah: I have a lot of time to revise and publish manuscripts from my graduate program without tons of new work piling up. I am also doing a lot more #SciComm outreach than I normally would be doing, which is always great! Whether its through Skype a Scientist, blogs, or social media, I am trying to stay productive/sane through educating others.

 

            Though the pandemic is scary, difficult, overwhelming and isolating, remember, you are not alone. Billions of people are affected by these unprecedented circumstances, which means there are undoubtedly others having the same shared experiences even in academia.

Some may even be struggling more than others. Together, they are coming up with creative solutions and learning from each other. By helping each other, and sharing these experiences together, we will build a supportive community to get through this.

 

We have created a Google group for people starting new positions or have advice for those starting new positions during the pandemic. If you would like to join a Google group of such people to share advice, form a cohort, and learn new solutions for your issues, please email NoahBressman@gmail.com.

Shark Week Special: You’re Swimming with Thousands of Sharks and that’s Awesome!

By Noah Bressman

In 2018, I took a trip to Charleston, SC to catch sharks from the beach. When I caught a sandbar shark (Carcharhinus plumbeus) from the surf, many of the beachgoers got out of the water, not out of fear, but out of curiosity. For many of them, it was their first time seeing a shark in the wild, so they had had many questions about the shark (and wanted to touch it).

I told them that summer is the perfect time of year to catch sharks from beaches in the Carolinas because that’s where blacktips (Carcharhinus limbatus) and other shark species migrate.

Then, I let the shark go, most of the onlookers cheered at the safe release of this beautiful animal, and then promptly returned to the water. While most people had no issue swimming with many small-medium sharks mixed in with the swimmers, one woman came up to me, saying how I am attracting all of the sharks to the beach and that I am going to get all of the swimmers killed. This post is to address the concerns of that woman, as well as others who are not familiar with the annual east coast shark migration or are scared of going in the water because of sharks.

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Noah with sandbar shark and curious beachgoers.

Each winter, tens of thousands of blacktip sharks (as well as other similarly-sized species, like sandbar sharks, but most research focuses on the blacktips) aggregate along the beaches of Palm Beach County, Florida, where the Gulf Stream comes in close proximity to the shore.

This giant aggregation of sharks signals the beginning of their annual spawning migration to the Carolinas. According to Dr. Stephen Kajiura, professor of biology at Florida Atlantic University, their migration is strongly tied to water temperature.

The ideal water temperature for blacktip sharks is 21-25˚C (70-77˚F), which is approximately the water temperature off southeast Florida during late January-March. When the water begins to warm up in April, 99% of the sharks migrate north to cooler waters (Kajiura and Tellman, 2016). The blacktips finish their migration around the Carolinas in the summer, where their nursery grounds occur. There, the sharks give birth just off the beaches, and feed on spawning aggregations of baitfish like menhaden.

noah beach pic

Hundreds of blacktip sharks sharing a beach with hundreds of people in Palm Beach County, Florida. (Photo courtesy of Dr. Stephen Kajiura)

So, there are tons of sharks at the beach in Florida in the winter and the Carolinas in the summer, but why are shark attacks still extremely rare?

There are two main reasons, according to Dr. Kajiura: 1) humans are not on the menu for these relatively small sharks (typically no more than 2 meters/6 feet). They have small teeth that are optimized for grabbing little fish, not for cutting thick bones or tearing off large chunks of flesh. 2) We give off different sensory signals than their prey.

Even in murky water where the sharks can’t see well, humans give off different vibrational and electrical signals than small baitfish. We come off as enormous, sloppy, noisy beasts to them, which actually scares them away from us. However, shark attack frequencies do increase during the migration, particularly in north Florida to the Carolinas, where the water is murky. The sharks may mistake hands and feet for small fish, and bite out of mistaken identity. To reduce your (already low) chances of getting bitten by a shark during the migration, simply avoid wearing shiny jewelry in the water, don’t swim at dawn and dusk, and stay away from schools of bait. These sharks are fairly small though, so while blacktip sharks are responsible for the most shark attacks in the country, none of these attacks are fatal.

Now, is it safe to fish for sharks from the beach with swimmers around? More-or-less, the answer is yes! If you are using a single piece of bait on a hook, that would be a very discrete sensory cue to sharks, so it would be easy to localize on the bait. However, DO NOT CHUM if there are people in the water. Chumming puts non-discrete scents in the water that can stir the sharks up into a frenzy, and it can make the swimmers smell like baitfish. If you are using a single bait, though, as long as you don’t cast your bait right next to swimmers, there won’t be any additional shark threat. I recommend finding a gap between swimmers in the water, wading out a bit (about to waist-depth, unless you wiped your hands covered in bait scent on your shorts, then walk out to shin-depth), and casting just behind the breaking waves, where there probably won’t be any swimmers or surfers. Many of the sharks will be waiting there to ambush prey that gets stunned in the surf, so it’s also the best place to put your bait.

One fisherman on the beach is not going to attract thousands of sharks to the area; the sharks are already there, and that fisherman will just show you what’s already in the water. Consider the huge number of people in the water, the huge number of sharks in the water, and the extremely low number of shark attacks. You’re more far more likely to choke to death on a hot dog at the beach than get killed by a shark, even during the migration. “Don’t sweat it,” says Dr. Kajiura, shark biologist, “and just enjoy the beach!” You were having a great time until you saw the shark (which was harmlessly there all along), so instead of letting it ruin your beach day, see it as a highlight, a chance to observe a beautiful animal in the wild!

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Noah Bressman is a Postdoctoral Fellow at Chapman University studying hagfish slime and fish biology. Above is Noah with a Sandbar Shark (Carcharhinus plumbeus), caught on a dead menhaden shad with 30 lb. test steel leader and a circle hook from a beach in Charleston, SC.

IG: noahwithfish

Twitter: noahwithfish

References

Kajiura, S. M., & Tellman, S. L. (2016). Quantification of massive seasonal aggregations of blacktip sharks (Carcharhinus limbatus) in Southeast Florida. PloS one11(3), e0150911.

S7- Genome-to-Genome-to-Phenome: Understanding the Sources of Mitochondrial Functional Variation

Image 1

Potamopyrgus antipodarum. Photo credit Bart Zjilstra 2013.

I think many of us first entered into genomics with the idea that we’d just find the gene that controls our phenotype of interest, only to find out it’s not so simple. Indeed, one of the most consistent conclusions from the genomics era has been that genetic variation rarely maps to phenotypic variation in a simple, one-to-one relationship. Rather, we see that mutation, drift, selection, epistasis, recombination, reproductive mode and mating system, TEs, gene expression, development, and perhaps most importantly, the environment, all modulate organismal phenotypes in myriad and complex ways. As is so often the case in science, our newfound ability to observe data at unprecedented resolution and throughput (i.e., whole genome sequencing) also opened our eyes to axes of variation that we did not previously appreciate.

image 2

Figure 1. OXPHOS complexes are comprised of subunits encoded by nuclear (blue) and mitochondrial (red) genomes, adapted from Rand et al., 2004.

Mitochondrial genomes, the products they encode, and their intimate biochemical interactions with nuclear-encoded gene products, are a prime example of the complexity of genome to phenome mapping. In particular, the enzymes responsible for aerobic respiration (i.e., oxidative phosphorylation – “OXPHOS”) are comprised of subunits encoded by two distinct and separately inherited genomes (Figure 1). Research over the past two decades into the evolution and genetics underlying these so-called “mito-nuclear” interactions has revealed that co-evolution between nuclear and mitochondrial genomes is essential for proper mitochondrial function and organismal health across a diverse slew of eukaryotes. Thus, when evolutionary forces perturb the nuclear genome, the mitochondrial genome, must, perforce, co-evolve to compensate and vice versa. We can therefore take advantage of genomic perturbations (e.g., changes in reproductive mode, whole genome duplications, changes in environmental conditions, etc.) to identify rules governing the translation of genomic and inter-genomic variation to phenotypic variation.

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Figure 2. Nuclear (lines) and mitochondrial (circles) inheritance under sexual vs. asexual reproduction.

Potamopyrgus antipodarum offers a useful system in which to evaluate how mito-nuclear genotypic variation shapes mitochondrial function and organismal health because it features multiple separate transitions from obligate sexual to obligate asexual reproduction. Transitions in reproductive mode are expected to have profound consequences for both nuclear and mitochondrial genomes. First, mitochondrial genomes are typically swapped across different nuclear genomic backgrounds via sexual reproduction, such that mutations that occur in one genome can be selected independently from mutations present in the other genome(s) (Figure 2). Asexually reproducing taxa do not share that luxury, as nuclear and mitochondrial genomes are co-inherited and thus effectively linked, such that selection acts at the level of mito-nuclear genotype, rather than at the level of individual mutations. Selection acting at this higher level of organization is expected to have two primary and opposing consequences. First, nuclear and mitochondrial genomes are expected to accumulate deleterious mutations more rapidly in asexual lineages than in comparable sexual lineages. Second, selection can act relatively efficiently on the highly heritable mito-nuclear genotypes of asexual lineages compared to sexual lineages in which mito-nuclear genotypes are broken apart each generation.

Previous work evaluating mutation accumulation in mitochondrial genomes of sexual vs. asexual lineages has so-far supported the hypothesis that mitochondrial genomes experience reduced efficacy of selection in asexual vs. sexual lineages. For example, asexual P. antipodarum accumulate amino acid changing mutations more rapidly than sexuals and radical amino acid changes persist longer in mitochondrial genomes of asexual lineages of P. antipodarum than in sexual lineages. Evaluating whether accelerated mutation accumulation in mitochondrial genomes of asexual lineages actually results in reduced mitochondrial function compared to closely related sexual lineages is therefore critical to understanding how genomic and inter-genomic variation translate into variation in mitochondria-related phenotypes. We sought to test this hypothesis in wild-caught sexual and asexual lineages of P. antipodarum by assaying mitochondrial function at the organellar, organismal, and behavioral levels in sexual vs. asexual individuals from six New Zealand lake populations.

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Figure 3. Mitochondrial genomes (circles) occur on different nuclear genomic backgrounds (chromosomes) and are found in different New Zealand lakes in asexual P. antipodarum, an ideal scenario for genome-to-phenome mapping.

Based on earlier work demonstrating heritable variation in mitochondrial function among lineages, we weren’t altogether surprised that lake-of-origin proved to be the major predictor of mitochondrial function in wild P. antipodarum. However, the lakes from whence these snails originated exhibited such large effects that they obscured those, if any, of reproductive mode on mitochondrial function. For better or worse, determining reproductive mode in P. antipodarum requires snail sacrifice, meaning that we cannot know whether sexual and asexual individuals were sampled from each lake until after assaying mitochondrial phenotypes. Sadly, in this case, most lake samples were comprised entirely of sexual or asexual individuals, not a mix, making it difficult to compare across reproductive modes while also taking into account lake-of-origin. We can say that when the lakes are pooled together, there are no global differences in mitochondrial function across reproductive modes, nor when we restrict our comparisons to the few lakes from which we sampled both sexual and asexual individuals.

With our genome-to-phenome appetite sufficiently whetted, we are thus left with an unabated thirst for more data. Do these results reflect large lake effects that hide reduced mitochondrial performance in asexuals? Or those of nuclear compensation for mitochondrial mutation accumulation resulting from efficient co-adaptation between genomes in asexual lineages?

Testing genome-phenome relationships is tricky, isn’t it?!

All hope is not lost, though. One of the cool aspects of using asexual lineages to tease apart genome-to-phenome connections is the very thing we are interested in studying (i.e., faithful co-inheritance of mito-nuclear genotype). It turns out that there exists extensive mito-nuclear discordance among asexual P. antipodarum such that nuclear genotype is a relatively poor predictor of mitochondrial haplotype. We can use this to our advantage by testing mitochondrial function of various mitochondrial genomes in similar vs. different nuclear backgrounds and vice versa, and even by testing the same mito-nuclear genotype across different lake populations (Figure 3). In collaboration with Kristi Montooth and Omera Matoo at the University of Nebraska – Lincoln, we aim to do just that, so stay tuned for more on how inter-genomic variation relates to phenotypic variation in our beloved “Potamos.

Guest Blog Post by Joel Sharbrough

Book chat – Feats of Strength (& at long last ectotherms in minks get their due)

 

feats lailvaux book rev

 

I’m always on the lookout for books by one of our former ICB authors and or SICB members. Luckily my search was made easier when one of our Twitter followers directed me to this one. Thankfully the author carved out some time to talk.

Something I love about talking with authors is that you never quite know what to expect. My recent book chat below with Dr. Simon Lailvaux about his awe-inspiring book, Feats of Strength: How Evolution Shapes Animal Athletic Abilities was no different. The most surprising bits of information involved lizards wearing minks and the title having derived from one of my (and Simon’s apparently) favorite episodes of Seinfeld. Go figure!

 

You noted in your intro that you changed your research focus. Why did you feel locomotor performance was more important to focus on than metabolism?

Performance is a more direct target of selection. It’s more proximate to fitness, and it’s also involved in almost everything. The TARDIS is a great mechanic for stories because it can go anywhere in time and space, which means the Doctor Who writers can write about whatever they like. Performance is like the TARDIS of evolutionary ecology, because there’s a performance angle on most areas of evolution. So working on performance, and writing about it, allows me to indulge my Dirk Gently-esque interest in the interconnectedness of all things. 

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You also mention that non biologists have difficulty understand the necessity of this type of research. What would you say to one of those non biologists in a sort of elevator pitch synopsis of sorts to help them best understand why whole organism performance/locomotor performance is vital to us all? 

In my experience when people ask why is this vital or why they should care about it, they’re wondering about the economic value. “Because it’s interesting” never goes over well. All scientific innovation rests upon a foundation of basic science, yet one can’t always predict what will lead to a breakthrough. Those benefits are tangible, but often invisible to a non-scientist watching you put a beetle on a racetrack and wondering what on earth the point is.  

 So I would say that understanding the natural world teaches us about ourselves as well. Humans are animals, and if we take what we’ve learned about animal performance and apply it to ourselves, it’s very revealing.

That’s what the last chapter of the book is about. For example, there’s evidence supporting a potential performance-based explanation for why ~10% of humans are not strictly right-handed, and an evolutionary reason for why humans are such amazing endurance runners.

What affects do you feel climate change will have had and will continue to have on animal’s performance? 

Thermal physiology was once thought to be very evolutionarily conservative, but there is increasing evidence that it does indeed respond to selection. So adaptation is a possibility for some species, as is using their performance abilities to relocate; but for those that can’t move, their prospects will hinge on their capacity either to acclimate or to mitigate thermal challenges through behavior.  

 

In this recent blogpost about Creative Mornings, entomologist, Adrian Smith, talked about maintaining curiosity and continuing to have moments of wonder as he calls them.

https://integrativeandcomparativebiology.wordpress.com/2020/06/23/being-social-while-being-physically-distanced-creative-mornings/

Adrian’s example was involved a small speck of a bug on his trash can and how it added on a whole new section to his research.

That being said, what is a recent moment of wonder you have had and what implications might it have for research? 

The downside of running your own research group is that you find yourself with less time for watching animals than you once had. Now it’s my students who get to do the fun stuff! So these days my moments of wonder come from experiments and data.

            For example, several years ago Catriona Condon, at the time a Ph.D. student in Australia, visited my lab and we designed an experiment where we made crickets fight each other to test how performance pertains to the “loser effect”. She found that that male crickets who lost a fight showed an immediate decrease in their bite forces, despite no injuries or changes in morphology. With the help of collaborators, we were later able to connect this directly to neuropharmacology, and now my lab is working on how biogenic amines affect performance motivation! I never would have expected to be doing this, and those data were like finding a missing piece of a puzzle you didn’t know you were looking for. 

            It’s hard enough keeping up with important research in just one area, but I like making connections between fields, and I enjoy working with others with the same mindset.
Is there any area, now looking back, that you did not feel you were able to spend adequate time on in your book, and how has it informed your choice of what your researching currently? 

I knew that I was never going to be able to cover everything, nor to acknowledge everyone who has made important contributions to our understanding of performance. So I developed a plan early on as to what specifically I wanted to talk about and then ruthlessly cut anything that didn’t fit in that framework. Which turned out to be a lot!

The publisher nixed one thing I really wanted to include. Back in the day, Raymond Cowles did an experiment testing why ectotherms don’t have furry insulation, and he took a picture of a chuckwalla in a little bespoke mink coat. He gave that picture to Ray Huey, who later gave it to someone else, and now it is lost. I could only obtain a reprint, and the quality wasn’t good enough for publication. But it’s fantastic and everyone should see it, so here it is. Enjoy!

 

Lailvaux blog pic

Do you have other interests that are not science related per say, that you feel lend themselves to your work, and or your being a better biologist? 

I once thought that learning martial arts would give me some insights into male combat. It did not. But it’s fun! I’ve trained eskrima for the last 10 years, and recently began learning silat as well.

           I think a lot of my interest in science stems from my love of comic books as a kid. A huge percentage of superheroes/supervillains are scientists or products of science. Comic book science is obviously insane, but I sometimes wonder if I might have done something different with my life if I hadn’t been such a massive comic book nerd!

 

 Connect with Simon via Twitter

 

@SLailvaux

 

and through http://www.fs.uno.edu/slailvau/people.html

 

Purchase Feats of Strength via

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yalebooks.yale.edu  (Hardcover)

or on Amazon.com (Kindle or Hardcover )

 

Check out some of Simon’s other ICB publications below

An Individual-Based Simulation Approach to the Evolution of Locomotor Performance

Ann M. CespedesSimon P. Lailvaux

 

 

https://doi.org/10.1093/icb/icv082

 

 

Predicting LifeHistory TradeOffs with WholeOrganism Performance

Simon P. LailvauxJerry F. Husak

 

 

https://doi.org/10.1093/icb/icx073

 

 

How Do We Measure the Cost of Whole-Organism Performance Traits?

Jerry F. HusakSimon P. Lailvaux

 

 

https://doi.org/10.1093/icb/icx048