Recent reading: 21 Jan 2022

Rose Main Reading Room, New York Public Library (Flickr: saebaryo)

The period between semesters is supposed to be quiet. I’ve been mentally dumping things to do into this one — paper revisions, reviewing service, analysis of long-awaited new data, a first draft of a new grant, writing my (eek) application for tenure — since at least October. But SARS-CoV-2 had other plans.

I spent the first week after campus reopened in the New Year watching the number of COVID exposure alerts sent to faculty mount up until the number of buildings on campus with a reported case was greater on the first workday after the break than the peak we hit during fall Finals Week, when students flocked back for in-person exams. Pretty soon after that we got word (via the University’s Twitter and then an all-campus email sent with no prior alert to faculty) that the first three weeks of Spring 2022 would be “primarily remote instruction” … but maybe not all of it? And so in between all the other stuff I’ve been trying to figure out how to teach a botany lab from my home office. It’ll be fine, I am telling myself.

In the midst of all that, here’s what I’ve read recently:

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Molecular Ecology and Molecular Ecology Resources are recruiting new Associate Editors

Molecular Ecology and Molecular Ecology Resources are looking for new Editorial Board members to join the journals as Associate Editors in the key subject areas below:

  • Broad genomic resources including genome assembly. Experience with plant genomes would be advantageous
  • Microbial ecology/community ecology
  • Microbiome research/coevolution
  • Epigenetics

Nominations and personal applications are welcome, and whilst scientific qualifications are paramount, we would particularly appreciate nominations and applications from suitably qualified researchers in underrepresented groups, including women, ethnic minority scientists, and scientists with disabilities, among others. Please email nominations/applications by February 15th, 2022 to manager.molecol@wiley.com with the following items:

  • Cover letter stating the reasons for your nomination, of if applying for yourself, your interest in the role and familiarity with the journals,
  • Abbreviated CV (Education, Publications, Outreach) if you have it.
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Recent reading: 7 Jan 2022

“Library” (Flickr: Stewart Butterfield)

It’s a new year, and while many of the challenges of 2020 and 2021 don’t show any sign of letting up, I’m trying to pick up some habits that fell by the wayside while I juggled fully online semesters and social distancing via fieldwork. One of those is good old fashioned blogging. Writing briefly about the papers I’m reading and the scientific concepts I’m mulling has been part of my scholarly process since graduate school. Over two years of the COVID-19 pandemic I’ve alternated between feeling like I had no spare time for blogging and feeling like I had no capacity for blogging — but I’ve felt the absence of the practice.

So, here’s one starting point: I’m going to begin posting roundups of the preprints and papers I’ve recently read, with brief reactions. Expect these every other week or so, with adjustments in frequency depending on my personal bandwidth. A paper’s inclusion in these posts will not constituted any kind of endorsement other than “this caught my attention long enough to download the PDF”, as perhaps this first batch will demonstrate.

Without further ado, here’s what I’ve read recently:

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These worms develop differently depending on their parents’ genes — even the ones they don’t inherit

(A) A small, plankton-hunting larva, also known as a planktotroph; (B) A large larva or lecithotroph, that has no appendages; (C) and (D) are two examples of larvae with intermediate phenotypes between (A) and (B). Photographs taken at 20X magnification by Conor Gilligan, a graduate student in the Rockman lab.

The following is a guest post by Ornob Alam, a graduate student in Michael Purugganan’s lab at New York University. Ornob’s PhD projects examine the demographic and evolutionary history of domesticated Asian rice in the context of past climate change and human migrations; he is on Twitter as @genomeinquirer.

Female ocean sunfish release up to 300 million eggs into the water during spawning to be met by similarly large numbers of sperm released by the males. This marks the end of their parental investment, leaving newly fertilized offspring to fend for themselves and mostly die. The ocean sunfish reproductive strategy stands in stark contrast to our own, where the offspring first develops inside the mother and parents pour extensive resources into raising a small number of offspring to adulthood.

How did animals come to have such divergent life histories? This question is deeply entwined with inquiries into the evolution of novel modes of post-fertilization development, and at the heart of a recent study in Evolution that explored the genetic bases of different modes of development occurring in a single species of marine worms.

Matt Rockman, a co-author of the study, first began studying these worms – called Streblospio benedicti – in his lab at New York University in 2008. It is one of many species of worms he studies to address various evolutionary questions. 

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The forest, the trees, and the fungal ties that bind

A view up a forested mountain valley to clear skies dotted with clouds
Forested mountainsides in the Mount Baker-Snoqualmie National Forest (Photo by Jeremy Yoder)

The following is a guest post by Erin Zess, a Postdoctoral Researcher with the MOI Lab in the Department of Plant Biology at the Carnegie Institution for Science. Erin is on Twitter at @ZessingAround.

The Molecular Ecologist uses affiliate links for books discussed on our site, which means that we may get a small referral commission for purchases made via those links.

The Menominee Tribe of Wisconsin, whose ancestral lands extended over 10 million acres across the Great Lakes region, call themselves “Maeqtekuahkíhkíw Kew Kanâhwíhtahquaq,” which translates to “The Forest Keepers.” The land ethic of the Tribe — articulated by Chief Oshkosh over two centuries ago, before the arrival of professional forestry in North America — is to: “Start with the rising sun and work towards the setting sun, but take only the mature trees, the sick trees, and the trees that have fallen. When you reach the end of the reservation, turn and cut from the setting sun to the rising sun and the trees will last forever.” Living by this dictum, the Menominee Tribe has sustainably managed their remaining Tribal lands, 235,560 acres, for over 150 years. In that time, they have harvested the entire volume of the forest twice over and, today, the forest volume is greater than when timber harvesting began. 

Suzanne Simard, a professor of forest ecology in the University of British Columbia’s Faculty of Forestry, is another kind of forest keeper. Simard’s research focuses on the function, distribution, and ecological impact of the belowground fungal networks that connect trees in robust forests, and her work has helped shift the mainstream Western perspective on forest systems towards understanding them as cooperative and connected. In her new book, Finding the Mother Tree: Discovering the Wisdom of the Forest (Knopf, $28.95 in hardback), Simard recounts her journey from her family’s homestead in British Columbia, through her early career at a timber company and in the Canadian Forest Service, to her current position in academia, describing how her work has brought her, “full circle to stumble onto some of the indigenous ideals: diversity matters.” 

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2021 Harry Smith Prize awarded to Yann Dorant, for considering CNVs in the lobster

Female (top) and male American lobsters, drawn by F.H. Herrick (Flickr: Biodiversity Heritage Library)

The Harry Smith Prize, which recognizes the best paper published in Molecular Ecology by an early career scholar within a given year, has been awarded to Yann Dorant at the Université Laval in Québec. Dorant led the 2020 paper “Copy number variants outperform SNPs to reveal genotype-environment association in a marine species,” an examination of local adaptation to climate in the American lobster, Homarus americanus. As the award committee, Alison Nazreno and Katrina West, noted in their decision letter,

Although CNVs are a major component of genotypic and phenotypic variation in genomes, their adaptive role has been largely neglected in wild populations. In this context, Dorant’s approach presents a new, cost-effective approach for reduced- representation sequencing data sets, which enables the joint analysis of sequence and structural variation. The work by Dorant and colleagues highlights the extent to which CNVs are overlooked in population genomics studies, thus underscoring the missed opportunities to reveal subtle population genetic structures and identify loci associated with local adaptation.

Dorant’s winning article is available online at the Molecular Ecology website. The award committee also recognized two graduate students at the University of British Columbia, Kaichi Huang and Tom R. Booker as second and third runners’ up, respectively. Huang and her coauthors demonstrated the role of chromosomal inversions in the adaptive divergence of a sunflower ecotype, and Booker et al. used simulations and empirical data to show that low-recombination genome regions may have unusually long-tailed distributions of FST, complicating interpretation of genome scans for locally adapted loci.

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#NewPI in the time of Covid – A recap

Whew. The spring semester has wound down for most of us or will in the next couple of weeks, and summer research (and recovery!) time has begun. I’m now 9 months into being a #newPI at the University of Cincinnati and given the wild ride that being a #newPI generally is, plus the clusterf*ck that was 2020-2021, it felt like time for reflection and checking in with my Pre-NewPI Summer To Do List. The first thing I want to note for postdocs who are about to transition to a faculty position or are planning to transition in the future: On our CVs, these positions have discrete start and end dates but in reality, they overlap for months. When I mentioned this to other #newPIs, they all commiserated with this issue. In the last 2-3 months of my postdoc, I was spending 5-10 hours a week on preparing to start my position – everything from planning my move to getting my institutional email set up to attending faculty meetings or orientation events, participating in discussions of who is teaching what, discussing possible lab renovations or purchases, making plans for transitioning data/grants/samples/etc. And since most positions start the same month that teaching begins, if you teach that first semester, I suggest you start working on that class material earlier than your start date. Then I moved and the situation was reversed – unless you’re extremely lucky (I was not), you’ll still be working on postdoc papers at least your first semester if not for the next couple of years. I assumed the postdoc work would bleed into the faculty work but did not realize how much the faculty work would bleed into the last few months of my postdoc.

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The 2021 Molecular Ecology Prize goes to Fuwen Wei, for pioneering panda genomics

A sleepy panda (Flickr: Rob Schlieffert)

The Molecular Ecology Prize Committee has announced the 2021 recipient of the award, which recognizes an outstanding scientist who has made significant contributions to the still-young field of molecular ecology:

The Molecular Ecology Prize Committee is pleased to announce that the 2021 Molecular Ecology prize has been awarded to Dr. Fuwen Wei, Professor of Animal Ecology and Conservation Biology in the Institute of Zoology, Chinese Academy of Sciences. Dr. Wei is a pioneer in conservation genomics and metagenomics of endangered animals, focusing mainly on giant and red pandas. He has applied genetic and genomic techniques to assess the past, present and future of giant panda populations, infer their evolutionary and demographic processes, and reveal their adaptive mechanisms for feeding on their specialized bamboo diet. He also has proposed and elaborated targeted strategies for the long-term survival of pandas, which were featured in Science as “Hope for Wild Pandas”. With 5 books and over 270 peer-reviewed journal articles, he is a global leader in molecular ecology and conservation genomics.  He has also trained numerous students and postdocs, and fostered international cooperation among zoologists and conservation biologists. His impressive accomplishments have earned him numerous awards and recognition, for instance, the Lifetime Achievement Award for Giant Panda Research and Conservation and the Outstanding Science and Technology Achievement Prize of Chinese Academy of Sciences.

Dr. Wei joins the previous winners of the Molecular Ecology Prize: Godfrey Hewitt, John Avise, Pierre Taberlet, Harry Smith, Terry Burke, Josephine Pemberton, Deborah Charlesworth, Craig Moritz, Laurent Excoffier, Johanna Schmitt, Fred Allendorf, Louis Bernatchez, Nancy Moran, Robin Waples, Scott Edwards, and Victoria Sork.

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Genomic windows into ancient climate change

An infructescence of domestic rice, Oryza sativa. (Flickr: Matt Lavin)

The following is a guest post by Ornob Alam, a graduate student in Michael Purugganan’s lab at New York University. Ornob’s PhD projects examine the demographic and evolutionary history of domesticated Asian rice in the context of past climate change and human migrations; he is on Twitter as @genomeinquirer.

While modern, anthropogenic climate change threatens to be unprecedented in rapidity and scale, humans have always lived at the whim of an unpredictable planet. For decades, paleoclimatologists have been using tree ringsice coreslakebed sediments, and other natural records to reconstruct ancient climates, revealing a dynamic tapestry of global weather patterns through time. This has allowed archaeologists, paleontologists, and others concerned with understanding the past to place historical events within their climatic context, notably implicating climate change as having helped to drive the Neolithic shift from hunter-gatherer to agricultural societiesthe rise and fall of civilizations, and megafaunal extinctions.

Recently, this alliance between archaeology and paleoclimatology has welcomed genomics into the fold, with the emergence of studies that incorporate all three. As any single kind of historical record is incomplete at best and misleading at worst, such interdisciplinary collaboration strengthens our ability to make inferences about the past. Whole genome sequencing, ancient DNA extraction technologies, and population genetics methods allow us to not only study the demographic history of humans using modern and ancient human DNA, but also many aspects of their behavior and culture by exploring their biotic environments. Two studies published in 2020 used non-human genomes to show long-lasting effects of ancient climate change on human societies in different parts of eastern Asia.

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Fieldwork in the pandemic springtime

Western Joshua trees, Yucca brevifolia var. brevifolia, within sight of the snow-dusted eastern Sierras in Kern County, California. (Photo by jby)

The first thing I did after getting my first dose of the Moderna vaccine against SARS-CoV-2 was to drive from the City of Los Angeles mass vaccination clinic at Pierce College to my home campus, California State University Northridge, to print out a sheaf of field collecting permits.

I’d planned fieldwork well before anyone had any firm idea when the vaccine roll-out would reach college faculty and staff, and it was sheer silly luck that I landed the appointment at Pierce the day before I drove into the desert. That was more than a month and thousands of miles of road travel ago; since then I’ve had my second dose and seen very nearly every kind of habitat where Joshua trees grow.

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