#NewPI chat: Third (or maybe fourth) time's the charm edition

(Flickr: jby)


Following up on last fall’s group-chat discussion of life as a new(is) professor, three *Molecular Ecologist contributors who are in our first years on faculty recently reconvened on the TME Slack channel to talk about that #NewPI life for an hour. What follows is a transcript of our chat, lightly edited for clarity and grammar and with the odd hyperlink added for context. Enjoy!*
— Jeremy
Jeremy Yoder: Good (Pacific Time) morning, fellow new PIs! Let’s have a quick round of re-introductions, and then dig in. Who’s on the chat?
Stacy Krueger-Hadfield: Well me, Stacy Krueger-Hadfield, newish PI at the University of Alabama at Birmingham
Arun Sethuraman: Arun Sethuraman, newish PI at CSU San Marcos
JBY: And I’m Jeremy Yoder, no-longer-completely-new PI at CSU Northridge. I’m now a couple months (!) into my second semester, and I think both Arun and Stacy are sailing through year two?
AS: “Sailing” would be an overstatement haha
SKH: Sailing through … oh Jeremy you jest
JBY: Well, I have the year right, at least?
AS: Yup, class of Fall 2016
SKH: Yes, class of fall 2016!
JBY: Okay, so my role in this is to draw on that extra year of experience you each have, and find out whether things do get … well, not better, because they’re honestly pretty great, but let’s say less frantic?
I feel like the place we have to start is scheduling, because by my count it took about three tries to get us all together for this chat. One of which was an appointment that I totally blew through.
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Genomic signatures of ancient rendezvous and separation in elephant evolution

Evidence from various levels of the tree of life is showing that we’ve been picturing ancient encounters between related species all wrong and admixture events are probably more common than expected. Even rendezvous among primates, caniforms, and majestic proboscideans often turned from afternoon tea to a wild party, and the outcomes are clearly written in the genetic code.
Or maybe not so clearly. Only now, with complete nuclear genomes, we are beginning to understand the extent of admixture in evolutionary history.
Obviously, great excitement was provoked by the discoveries of Neanderthal introgression into modern humans (Green et al. 2010), as well as by admixture in our primate relatives, chimpanzees and bonobos (de Manuel et al. 2016). However, analyses of admixture in non-primate species also revealed intriguing patterns.
The ancestry of two species of North American wolves, representing admixture between grey wolves and coyotes (vonHoldt et al. 2016), has been stirring up questions about how admixed species should be treated in conservation policies. The admixed populations might play an important role in changing environments, for example in times of rapid climate change. This was likely the case with polar bear admixture into brown bears, which seems to be linked with climate fluctuations at the end of the last ice age (Cahill et al. 2018).

“Thus admixture resulting from climate-related habitat redistribution is likely to have long-term and widespread evolutionary consequences, and may be an important mechanism for generating and maintaining diversity.” (Cahill et al. 2018)

Admixture and isolation in elephants and their relatives

Straight-tusked elephant. Source: Wikimedia Commons/DFoidl


Now proboscideans joined the party and a new study by Palkopoulou et al. (2018) showed that “both gene flow and isolation have been central in the evolution of elephantids”.
Palkopoulou and colleagues generated new high-coverage genomes for the Asian elephant, African savanna and forest elephants, and low- to medium-coverage genomes for the woolly mammoth, American mastodon, and Columbian mammoth. Moreover, they generated first data, including one low-coverage and one 15X-coverage genome, of the straight-tusked elephant (Palaeoloxodon antiquus), which lived ~120,000 years ago in Europe.
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What’s in a name? A review of cryptic species and species concepts

It is a contentious can of worms. Species concepts are both essential to understand and at the same time incredibly difficult to define. Species names allow us to discuss fundamental units of biodiversity in any ecosystem and study genome evolution, but jeeze, they’re hard to agree on. Multiple decades of disagreements on the topic have essentially led to a diversification event and landed us with dozens of currently used definitions.
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Meet the new Molecular Ecologists

This month we’re excited to welcome a bunch of new voices to *The Molecular Ecologist, from all over the world and with all sorts of research interests. Say hello to the 2018 cohort of TME contributors!*

Katharine Coykendall

Katharine Coykendall


Who are you?
I grew up at the back door of the Great Smoky Mountains National Park in East Tennessee. Oddly, this rural, mountainous, landlocked childhood lit a fire in me to be a … marine biologist. Go figure. As an undergraduate I started working in a conservation genetics lab to bide the time, got a marine science undergraduate degree and went on to get a PhD in genetics. I’ve managed to cobble together a meandering career path that has genetics and marine science as the main threads. I’m also taking bioinformatics classes at Hood College because I can’t help myself.
Where are you?
For now, I’m in Shepherdstown, West Virginia working in a federal lab doing marine science. Again, go figure.
What do you study?
A fair bit of the science we do is concerned with the deep sea ecosystems off the US coast, where leasing blocks for oil and gas exploration occur. We use genetic and genomic techniques to characterize patterns of connectivity between populations of cold water corals and chemosynthetic communities. We participate in many deep sea expeditions for our research, which typically result in finding organisms new to science. We document and characterize this biodiversity as a baseline for future studies.
What do you do when you’re not studying it?
Listen to live music, hill-avoidance road biking when the weather is nice, occasionally walk around outside, visit far-flung friends, voraciously consume podcasts.

Kathryn Turner

Kathryn Turner


Who are you?
I’m originally from Austin, Texas, PhD at the University of British Columbia. I recently started as an Eberly Postdoctoral Fellow at Pennsylvania State University, in the in the labs of Dr. Jesse R. Lasky (Biology) and Dr. George H. Perry (Biology/Anthropology). I’m an ethnobotany nerd, fixated on invasive species. Everywhere I go, I recognize some of the flora, so there’s that.
Where are you?
The very literally named town, State College, Pennsylvania, located in lovely wooded Centre County (cuz it’s in the middle of the state of course). It is, I’m told, a Lyme disease hot spot, so that’s exciting.
What do you study?
I’m interested in introductions, range expansions, and biological invasions. What happens when humans move plant species around all willy nilly? How do some species manage to succeed in the face of near-total environmental change? What are the impacts of human selection, intentional or unintentional, in ‘natural’ populations? Invasive species are the Moriarty to my Sherlock Holmes. Species I particularly love and/or hate include: diffuse knapweed (Centaurea diffusa), blue mustard (Chorispora tenella), and Texas bluebonnet (Lupinus texensis).
What do you do when you’re not studying it?
Grow things. Eat them, pickle them. Brew and/or judge beer. Trivia. Hike, slowly, with a field guide, looking everything up.

Alex Twyford

Alex Twyford (and an Arisotolochia)


Who are you and where are you?
I’m an independent Research Fellow at the University of Edinburgh, and a Research Associate at the Royal Botanic Garden Edinburgh.
what do you study?
My research focus is on the ecology and evolution of plants, and in particular on the genetic basis of speciation and adaptation. My work combines genomic approaches with experiments and field observations, and I tend to work on whichever plant group is best suited to a particular research question. I’ve studied tropical begonias, widespread monkeyflowers, and Chilean conifers, amongst other groups. Lately I’ve been drawn to parasitic plants, with recent projects studying population dynamics and genome evolution of British native parasitic eyebrights (Euphrasia).
What do you do when you’re not studying it?
When I’m not working, I like to get out and botanise or travel, and I’m also quite a wine enthusiast having completed the periodic table of wine in 2016.

Sophie von der Heyden

Sophie von der Heyden


Who are you?
My name is Sophie von der Heyden.
Where are you?
I live in the most beautiful part of the world, between mountains, vines and the sea, in Stellenbosch, South Africa.
What do you study?
The research of the von der Heyden lab is by necessity very broad (there are not many molecular ecologists in Africa), but mainly focusses on using genetic and genomic tools to study the evolutionary processes that shape marine populations in southern Africa. My particular interests lie in the applicability of molecular ecological and genomics tools to inform marine spatial planning, understanding MPA connectivity patterns and resilience and adaptation of marine species to ongoing and future change, as well as the impacts of changing marine communities on society.
What do you do when you’re not studying it?
I run after three very busy kids and a crazy dog, swim and row whenever I can, bake cakes, read a lot, clean the chickens and then remember that I am also a molecular ecologist. And we love to travel as a family.

Laetitia Wilkins

Laetitia Wilkins, in Panama


Who are you and where are you?
I am a postdoctoral research scholar originally from Switzerland who lives now in California. I work at UC Berkeley sponsored by Prof. Stephanie Carlson and at UC Davis sponsored by Prof. Jonathan Eisen.
What do you study?
I study host-microbe interactions and their co-evolution. My study hosts include fishes, porcelain crabs and Sierra Nevada yellow-legged frogs. I run projects in Switzerland, California and Panama. I love people, care about diversity and critical thinking, and I help researchers with families to thrive in academia.
What do you do when you’re not studying it?
I love the outdoors and try to spend a lot of time with my husband and children.

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Book review: Jonathan Losos' Improbable Destinies

The Molecular Ecologist receives a small commission for purchases made on Bookshop.org via links from this post.

Is evolution predictable? This is one of the Big Questions, as much philosophy as it is biology and no less important for not really having an answer. You’re probably familiar with it as the rhetorical peg for countless talks on convergent evolution; I’ve already seen two this year to use it, and it’s only February. So it’s somewhat surprising that Jonathan Losos’ new book Improbable Destinies is, to the best of my knowledge, the first broadly framed exploration of the topic for a general audience. If I’m right about this, it was probably worth the wait–Destinies is pleasingly readable, and a mostly deft blend of science with explanations of why we should care about it.

Improbable Destinies: Fate, Chance, and the Future of Evolution
By Jonathan B. Losos
Illustrated by Marlin Peterson
Buy it on Bookshop.

The bulk of the book is a well-curated catalog of case studies spanning Anolis lizards in the Bahamas to E. coli in incubators in Michigan. These examples broadly trend from the descriptive to the experimental, from vertebrates to the microbes. Avoiding the missteps of other scientist-memoir-cum-manifestos, Losos strikes a judicious balance between focusing on his own work (which he of course knows best) and the work of others; and between the obscure (Russel 1982??) and the canonical (Schluter et al. 1985). In a few instances, big names became real people: the history behind Endler’s guppy research is delightful, and I was pleased to learn Rowan Barrett is a backcountry skier. The glue that holds these chapters together, though, is the way in which the broad themes of evolutionary biology are tied together by the yin and yang of the historical accident and the deterministic force of selection. From morphological novelty in the platypus to the pace of diversification, Losos makes a compelling argument that most research topics can be viewed through the lens of convergent evolution. If you’re anything like me, you’re left with the suspicion that you might be unknowingly studying it, too.

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Exploring the genomic diversity of tubeworm endosymbionts

Tubeworms are cool. (To be read only in your best (eleventh) Doctor Who voice). Although, depending on how close they are to a hydrothermal vent, they might be more on the hot side….Regardless, if you’re on the fence about how nifty these creatures are, you could check out this educational video by Ed Yong published last November, and then read this recently published article by Reveillaud and colleagues.

In this study, the authors report the characterization of the endosymbionts from the giant tube worm genera Lamellibrachia and Escarpia from the Caribbean Sea. This study is the first to take a swing at characterizing the endosymbionts from tubeworms outside of the Pacific Ocean as well as from these two lesser studied genera.
Escarpia sp. tubeworms. Image credit: The Chemo III project, BOEM and NOAA OER
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How Molecular Ecologists Work: Sean Hoban on Google Docs and time-per-task calculations

Welcome to “How Molecular Ecologists Work”, the interview series that asks scientists how they get stuff done. In the final installment of this second season of interviews, we welcome Dr. Sean Hoban from The Morton Arboretum.

Location: The Morton Arboretum, a botanical institute in Lisle Illinois (30 minutes west of Chicago)
Current Position: Tree Conservation Biologist, Department: Center for Tree Science (equivalent to Assistant Professor)
Current mobile device(s): iPhone SE (remarkably, my first smart phone!)
Current computer(s): custom built workstation from Puget Systems– 32 core Xeon processors with 128 GB RAM, 8 TB HD, running Kubuntu; a Toshiba laptop; a basic Windows desktop
What kind of research do you?
I like empirical, applied, and theoretical work, so my research program spans three elements. (1) Interpreting genetic data to understand population ecology, in particular contemporary dispersal and mating patterns as well as longer time-scale (Quaternary) changes in species’ distributions.  I also investigate the evolutionary impact of disease and fragmentation; adaptation in new environments; and hybridization.  (2) Conservation of rare species via planning ex situ seed collections and in situ population prioritization, primarily using genetic data but increasingly using non-genetic data.  The goal is to ensure the long term survival of species with effective intervention (such as our current IMLS funded project).  (3) Developing and improving statistical methods and software in population genetics and conservation; I particularly like to test methods in situations for which they weren’t designed as well as evaluate sampling strategies.  This area of work is crucial because misapplication of methods or misinterpretation of results can lead an entire field in the wrong direction.
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Retrieving a million sequences and avoiding primer bias, a new method that might have it all

We have come a long way since the early days when sequencing was a breakthrough method initially used to identify uncultured microbes from the environment. It is now been almost three decades, in fact, since the first microbial 16S rRNA gene sequences were reported directly from environmental samples. As Soren M Karst and colleagues point out in a recent article in Nature Biotechnology, we are now in an era where sequencing has become an integral part of microbial ecology centered research.
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How Molecular Ecologists Work: Hanna Kokko on tending her literature garden and learning by reviewing


Location: University of Zurich
Current Position: professor of evolutionary ecology
What kind of research do you?
Evolutionary ecology
Can you use one word to describe the way you work?
Multitaskingly. Is that a word?
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How Molecular Ecologists Work: Kathryn Hodgins on one liners and the beautiful drone of construction work

Welcome to “How Molecular Ecologists Work”, the interview series that asks scientists how they get stuff done.
This week, we are headed to Australia to talk to Dr. Kathryn Hodgins. Her work focuses on understanding rapid local adaptation, especially in the context of invasive/weedy plants. I asked her how she gets it done.
Location: Monash University, Melbourne Australia
Current Position: Lecturer (Teaching and Research position)
Current mobile device(s): Samsung S8, iPad
Current computer(s): MacBook Pro, iMac
What kind of research do you?
I study the genetic basis of adaptation in invasive and foundation plant species. I am interested in how species evolve during colonization and invasion. I am also particularly concerned with the factors that facilitate gene reuse during adaptation to similar environments. My research involves a mix of genomic data analysis, common garden experiments and field work.
Can you use one word to describe the way you work?
Tenacious
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