Population structure is the core of ecological genetics, as it’s practiced today. Genetic differentiation between populations in different places is our null hypothesis and one of our most widely used indirect signals that environmental factors are impacting the evolution of those different populations. Oh, and it’s also a first step to the origin of new species.
The huge body of published datasets testing for population structure is a great resource for synthetic work, that identifies broad general patterns about population genetic processes. Last year we saw one such study link locomotion mode and genetic differentiation — confirming that bird populations are less likely to differentiate, given a particular geographic distance, than populations of land-bound vertebrates. Now, freshly out in Molecular Ecology, we have a similar project in a more specific taxonomic scope: bees.
Climate change threatens to land many, many species in conditions for which they’re not adapted — too warm, too dry, too stormy, too flood-prone — and traditionally the ways that living things might respond to this are framed as a choice between moving to more suitable habitat elsewhere, adapting to the new conditions in the current habitat, or dying out. These are a false choice, of course; it’s possible to move and adapt, and it’s possible that even doing both won’t be enough to avoid extinction. A new study of one rare chipmunk in the Sierra Nevada mountains pinpoints exactly such a case.
The 2019 Molecular Ecology prize has been awarded to Scott Edwards for an illustrious career that has combined rigorous scientific achievement with a long and consistent record of mentoring and promoting early-career scientists. Proficient at both empirical and theoretical studies, Edwards has made important contributions to coalescent modeling, phylogeographic inference, immunogenetics and other connections between genotype and phenotype, and the often-misunderstood difference between gene trees and species trees in nature, as well as many more specialized contributions to ornithology. Countless people from around the world have benefited from his work over many decades to support junior scientists and to promote diversity at all levels of the scientific enterprise.
The editorial board of the journal Molecular Ecologyis seeking nominations for the Harry Smith Prize, which recognizes the best paper published in Molecular Ecologyin the previous year by graduate students or early career scholars with no more than five years of postdoctoral or fellowship experience. The prize comes with a cash award of US$1000 and an announcement in the journal and in the Molecular Ecologist. The winner will also be asked to join a junior editorial board for the journal to offer advice on changing research needs and potentially serve as a guest editor. The winner of this annual prize is selected by the junior editorial board.
The prize is named after Professor Harry Smith FRS, who founded Molecular Ecology and served as both Chief and Managing Editor during the journal’s critical early years. He continued as the journal’s Managing Editor until 2008, and he went out of his way to encourage early career scholars. In addition to his editorial work, Harry was one of the world’s foremost researchers in photomorphogenesis, where he determined how plants respond to shading, leading to concepts such as “neighbour detection” and “shade avoidance,” which are fundamental to understanding plant responses to crowding and competition. More broadly his research provided an early example of how molecular data could inform ecology, and in 2008 he was awarded the Molecular Ecology Prize that recognized both his scientific and editorial contributions to the field.
Please send a PDF of the paper you are nominating, with a short supporting statement (no more than 250 words; longer submissions will not be accepted) directly to Nick Fountain Jones (firstname.lastname@example.org) by Friday 31 May 2019. Self-nominations are accepted.
One obvious effect of climate change will be the spread of
invasive species and the subsequent ecological, commercial, and health
repercussions. Therefore, studies that
address the patterns of colonization and possible underlying genetic mechanisms
that may lend to being a successful invader are worth paying attention to
IMHO. Three papers have come out
recently that each focus on genetic components of invasive species in either
the terrestrial, marine, or freshwater realm.
First up, Sherpa et al.
examined the role genetic admixture plays in the invasion biology of the Asian
tiger mosquito, Aedes albopictus, the
most invasive mosquito species in the world, with established populations now
on every continent save Antarctica. It
is a vector for dengue, zika, and other nastiness so understanding where host invasions
originated, how fast they can spread, and adaptive advantages of founder
populations has important implications for epidemiology and vector and disease
biology. The authors looked at A.
albopictus populations from Reunion Island and Europe. Tropical Reunion Island, with both a wetter
and a drier coast represents an older invasion (>100 years). Europe was first colonized by A. albopictus 40, then 30 years ago and
some populations established only within the last dozen years. The authors were
interested in knowing if populations from Reunion Island and Europe are
connected (previous studies suggested maybe) and how genetic diversity levels
compared between Europe and Reunion Island and among populations within each
region. Using standard methods (de novo assembly
of loci via Stacks, population clustering via STRUCTURE, maximum likelihood
tree building via RAxML, genetic distances, and pairwise FST), they
show that there is no genetic connectivity between Reunion Island and Europe, though
there are daily movements of people and cargo between those two regions. The genetic distinctiveness between these two
regions indicate that the mosquito invasions happened independently (as the
historical record states) from independent sources. Genetic patterns among
Reunion Island conform to the isolation-by-distance (IBD) model of
differentiation, which suggests that these populations have been stable long
enough to reach migration-drift equilibrium.
Furthermore, there was no evidence of differentiation between the wetter
and drier coasts (a result that contradicted previous studies with different
markers). Strikingly, the FIS
values were consistent with those expected from a species with low dispersal
ability. Conversely, European populations showed no IBD signal and the oldest
populations (Italy, Albania) were not different from the edge of the invasion
(France, Slovenia). Genetic patterns in Europe suggested that Albania was
colonized first but that bottlenecked population remained isolated from the
rest of the European invasion while maintaining a low level of genetic
diversity. An introduction of A.
albopictus in Italy in 1990 led to subsequent expansions into the rest of
Europe via a bridgehead effect where an introduced population becomes the
source of secondary introductions begetting a chain reaction of sorts. A
horrifying feature of human-mediated spread of invasive species is how they
undergo rapid, long-distance jumps as opposed to a diffusion pattern of
spreading. This brings genetically
different populations into contact where admixture occurs, thus providing a
pool of novel genetic combinations to continue to the reign of terror, as
exemplified in the Asian tiger mosquito.
[As an aside, I was struck by the clear methods section in
this paper. The analyses were
straightforward and easy to follow. The authors took extra space to explain
what would be expected or why they chose one methodology over the other. Frankly, I’m surprised there wasn’t pushback
to trim the methods of anything remotely extraneous, but I’m grateful it got
included. In the age of increasingly
reductionist methods, I applaud extra detail that does not require the reader
to infer or extrapolate.]
Next we have a study that focused on the formidable lionfish. Anyone who’s been scuba diving in the Gulf of Mexico or Caribbean in the last decade or so knows that these aggressive aquarium fish native to the Indo-Pacific are swiftly staking claim to many coral reef habitats and outcompeting/consuming pretty much every fish in sight. Can we all just agree to not dump our unwanted pets into the outdoors, especially if they are VENOMOUS?
Along with the typical demographic hypotheses, this paper
sought to identify a gene or set of genes under selection in the invading
population, which may be conferring adaptive advantage to lionfish that have
found themselves in novel niches. Along with population patterns, Bors et al. searched for loci by looking for
sections of the genome with larger FST values as compared to their
neighbors. Of the 24 loci identified as
putatively under selection, seven were identified by BLAST and three were
flagged as particularly interesting due to their function: learning and memory,
gamete maturation, and cell division and growth. As with most studies on non-model organisms,
the results were hampered by what little genomic resources there are available
to facilitate identification of genes.
Nevertheless, it’s an intriguing result and sets the stage for future
studies targeting those specific genes. The demographic patterns were not
surprising – genetic diversity was inversely correlated with geographic
distance from the point of initial introduction in Florida. However, an important insight from this paper worth
mentioning is the attention to sampling needed in invasive species
studies. In situations where the
invasion happened very recently, and many age classes may be present, which may
confound interpretations of when and how the invasion is progressing. This study also introduced me to the term
allele surfing, which is the process of a rare allele rising to high
frequency/fixation near the edge of the expansion of a population due to
repeated founder effects. Learning!
My favorite example of interesting biological invasions, though, is the marbled crayfish. These anomalous creatures have gotten much attention of late (see here and here and especially McSWEENEY’S take here, which coins the phrase “asexual Aphrodite” (stellar band name)). The prevailing theory is that about 25 years ago, two distantly related slough crayfish (native to Florida) mated in an aquarium in Germany. However, one of the two had an autopolyploid gamete, resulting in a triploid offspring. Under most circumstances, this would be an evolutionary dead end lost to the annals of time, but this genomic duplication conferred an advantageous adaptation: obligate parthenogenesis. Voila! Much like Dr. Frankenstein flipping a switch in his lab, a new, all female, clonal evolutionary trajectory was created instantaneously. Since their genesis in 1995, marbled crayfish have spread across Europe and Africa eating everything in sight (detritus, fish, insects). First introduced in Madagascar in 2005, they now occupy 100,000km2 and threaten several native crayfish species. Oh, and they can be carriers of the dreaded crayfish plague as well. This genome is one of the only decapod crustacean genomes to be sequenced (!!), one of the few from asexually reproducing animals, and perhaps the only one from an asexual reproducer with the evolutionary history of a quarter century. As the marbled crayfish persists, the evolution of its genomic architecture will be fascinating to track. Unfortunately, it will be at the expense of native crayfish.
Bors, EK, Herrera, S, Morris, JA, Shank, TM. Population genomics of rapidly invading lionfish in the
Caribbean reveals signals of range expansion in the absence of spatial
population structure. Ecol Evol.2019; 9: 3306– 3320. https://doi.org/10.1002/ece3.4952
Gutekunst J, Andriantsoa R, Falckenhayn C, Hanna K, Stein W, Rasamy JR,
Lyko F. Clonal genome evolution and rapid invasive spread of the marbled
crayfish. Nat Ecol Evol. 2018;2:567–73.
Sherpa, S. , Blum, M. G., Capblancq, T. , Cumer, T. , Rioux, D. and
Després, L. (2019), Unraveling the invasion history of the Asian tiger mosquito
in Europe. Mol Ecol. Accepted Author Manuscript. doi:10.1111/mec.15071
A textbook example of predator-prey coevolution could need revision, if the conclusions of a recently posted pre-print hold up more broadly. The manuscript, lead-authored by Michael Hague with Amber Stokes, Chris Feldman, and Ed and “Butch” Brodie, calls into question whether poisonous rough-skinned newts (Taricha granulosa) and the garter snakes (Thamnophis sirtalis) that prey on them truly exert reciprocal selection on each other. The data in the manuscript are consistent with newts creating selection for greater toxin resistance in the snakes — but not with the snakes selecting for more toxic newts.
Rough-skinned newt populations in Western North America are distinguished by one of the most over-the-top defenses against predation seen in a vertebrate: they secrete tetrodotoxin, the same neurotoxin produced by pufferfish and blue-ringed octopuses. Tetrodotoxin disables the molecular channels that allow nerve cells to generate electrical signals, which paralyzes just about any predator with nerves. Some populations of garter snakes (and other snakes that feed on tetrodotoxin-defended amphibians) have mutations to the channels that let them resist the paralyzing effect — and this should set the stage for a coevolutionary arms race between newts’ production of the poison and snakes’ ability to cope with it.
Some tiny microbes are making a pretty big splash, and not just in the hot springs they call home in Yellowstone National Park. Recently, there was an interesting article published in Nature Microbiology about some amazing archaea, which are generally famous for inhabiting diverse extreme environments on the planet, including hot springs, hypersaline waters, and anoxic muds.
The first author of the paper, Luke McKay, wrote a succinct ‘Behind the Paper’ summary on the work reported in the study. In the article, the authors report the findings of a metagenomic analysis from samples collected from the Washburn Hot Springs in Yellowstone, which, as far as I can tell, looks like a beautiful place to hike. In 1870, an expedition led by General Washburn explored and mapped the land that eventually became Yellowstone National Park, and named one of the more famous geysers you might be familiar with, Old Faithful.
I am trying to keep this short. You might remember my recent blog post on data sharing. I basically wanted to point out that data acquisition can be an art on its own. It can take months of planning, applying for permits, securing money, coming up with an elegant sampling design, and finding what you had been looking for. This is usually followed by weeks in the laboratory extracting the right molecules and preparing them for sequencing. Some people are really good at this and they should get credit for it. How can we make this happen?
I’ve been talking myself into and out of writing this post
since the 12th day of the government shutdown. It temporarily ended after a record breaking
35 days. My delay has partly to do with
procrastination (because of course), but also was impossible to predict when
the legislature would actually mobilize to open the government, then prevent
the next one. The results were that the negotiations
went down to the wire, again, (which is incredibly disruptive and harrowing for
government scientists) and, bewilderingly, there is increased
funding for a select few science-related activities in the continuing resolution…
along with a national emergency.
There’s an emergency all right, but it’s not a groundswell
of immigrants clambering across bulldozed butterfly
sanctuaries in southern Texas.
It’s the negligent if not disdainful regard for the role of basic
research in government agencies and the role of science in informing policy
decisions by the very leaders appointed to uphold the missions of those
agencies. This “partial” shutdown affected only about 25% of the government,
but disproportionately affected science agencies such as the Department of the
Interior that houses the USGS, the National Park Service, and the Bureau of Land Management; the Department of
Commerce that houses NOAA and the National Marine Fisheries Service; The
Department of Agriculture, the EPA, and of course, the National Science
Foundation. Noticeably absent from the list of science agencies impacted were
the CDC and the NIH – those focused on human health. Others that predict where earthquakes and
hurricanes will hit and if volcanos will erupt weren’t funded, but were deemed
essential and so worked without pay through the furlough. But those that work
on the natural world outside of human health? Those that work at the world class Smithsonian
museums or Water Science Centers and study invertebrates, early hominid
evolution, or fish disease and taxonomy? Not funded and not essential. However,
it is inherently valuable and worthwhile to study our natural world. Even if we can’t grind it up and cure cancer
with it. I worry about the fate of this basic
Even though the second 2019 shutdown has been averted, I am still compelled to write this because I was a contractor for one year and a temporary government scientist for seven years. Though I am no longer a federal worker, I took this last shutdown rather personally. I missed being one of those furloughed workers by two months, though I did experience the 15 day shutdown in 2013. I know what it feels like to an extent – to file for unemployment even though you HAVE a job, to be uncomfortable with charity, again, because you have a job and will likely to get paid eventually, to not be able to work when you want to work, to feel completely marginalized. And of course, if I had remained a contractor, doing the same work, I would not have been compensated (and it’s not looking good for them this time around either). Imagine going to work knowing your coworkers just got back pay for a month of furlough and you didn’t. For the same work. IMAGINE. THAT. As a PI, imagine being banned from work in the crucial planning time of extensive field seasons. How about if you have expensive equipment that’s supposed to be formally shutdown when it’s idle. Do you fire it up in the three weeks of reprieve, or delay experiments until you know there won’t be another shutdown? Just like a car, starting and stopping some lab equipment can be more costly than having them run. Furthermore, with a month of standing idle in refrigerators and freezers, I imagine there was a purge of expired reagents upon the return to work, but also a hesitation of ordering more until the future looked more stable. So you have to make a choice to sit on your hands and delay for three weeks or scramble like mad in the window you know you have. Thankfully, now our governmental colleagues will be able to exhale and plan for the future (up until September) after the major disruption in productivity.
Cherry picking to keep some governmental parts functioning
and other parts shuttered is damaging to natural science research, because
that’s the part that we’ve historically
invested in for the long game.
And it’s becoming painfully obvious how myopic and forgetful our society
is. Apparently, we need waves of small
pox and measles to move through our ranks every decade or so to remind us as a
whole that vaccines work really, really well.
We need to strip our parks and monuments of their employees and stewards
to grasp that, without them, we are savages
that cannot be trusted to act like mindful parts of a larger community. Also, because the detrimental effects of
marginalizing government science won’t be immediately felt by most US citizens,
future games of chicken could extend for months. What catalyzed the temporary reopening was the air traffic
controllers flexing at La Guardia airport, thereby causing a ripple of delayed
and cancelled flights throughout the US. The government was reopened the same
day. Here I was, entertaining the notion
that the government may be shut down for MONTHS, but all it took was one day of
flight disruption. Do government
scientists hold that same sway?
HAHAHAHA! What if this happens
again, only this time TSA and air traffic controllers have the funding and are
If you are reading this, you probably have a love of science
and if you have kids, it’s going to
permeate in some volume to them – from the books you read them, to what tv
programs you watch, what museums you drag them to, the summer camp, the
backyard activities, what you talk about while cooking dinner. They will be exposed. And some of them will be inspired to consider
being a person in STEM when they grow up.
It’s what we encourage in kids, right?
An astronaut! A marine biologist! How are they going to do that? Why
would they want to? What is this nonsense doing to the very
foundations of science in the US?
To add insult to injury, the rollcall of the leadership that
scientists faced upon return was and is, especially bleak. Our EPA colleagues returned to Andrew
Wheeler, the ex-lobbyist for fossil fuel and energy companies who has been a
critic of limiting greenhouse gases.
Over at the Department of the Interior, after the recent resignation of
Ryan Zinke as Secretary, the former oil lobbyist ( and endangered
delta smelt nemesis) David Bernhardt has been appointed to succeed
him (as an aside, when I was a Department of the Interior employee, I was not
allowed to hold stocks in oil, gas, or mining companies. You know, conflict of interest.). And who
could forget the champion of the working class, Secretary of Commerce Wilbur
Ross, whose net worth is $700 million, expressing befuddlement
at unpaid government workers resorting to food banks when they could simply
apply for loans.
I feel like I should end this with a call to action or some concrete solutions. I don’t have those. I’m still feeling panicked, helpless, and enraged. It is truly unfortunate that this kneecapping of government scientists came at a pivotal time when our research and policy should be strongest as a nation. Now, when the world is looking for strong, swift innovations to combat a truly international state of emergency: CLIMATE CHANGE. If I had suggestions they would be to elect people to ALL tiers of government (pay attention to local elections too!) that are from diverse backgrounds and science backgrounds – people who have the guts to draft a document like the New Green Deal and then TALK about it, people who won’t bring a snowball into the Senate as proof global warming isn’t real, is a good start. Vote for representatives who talk about science and prioritize climate change in their platforms. And crucially, don’t forget about your federal government colleagues (AND CONTRACTORS) and give them a voice when they are silenced next time. MAGA.