How did we get where we are? Genetically speaking, that is. A few posts ago, that whole genotype-phenotype question was discussed, how do genomes make plants and animals (and don’t forget the microbes!) look and act how they do. Another broader question linked to this topic involves trying to understand how genomes have evolved over time, clearly no small task.
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(Flickr: Paul Gorbould)
This is how much the US undervalues K-12 teachers: When we file taxes, we expect them to claim personal funds spent on teaching supplies.
— Terry McGlynn (@hormiga) February 9, 2017
Donors Choose lets us help teachers save their none-too-generous paychecks by pitching in money for individual projects or classroom resources. You can easily search for biology-specific requests, or for schools in your own neighborhood, but here’s a few good options to get you started:
For bonus #resistance points, maybe add a memo to dedicate your donation to the new Secretary of Education.
Recently, one R package which I like to use for visualizing phylogenetic trees got published. It’s called ggtree, and as you might guess from the name it is based on the popular ggplot2 package. With ggtree, plotting trees in R has become really simple and I would encourage even R beginners to give it a try! When you’ve gotten the hang of it, you can modify and annotate your trees in endless ways to suit your needs.
ggtree supports the two common tree formats Newick and Nexus. It also reads outputs from a range of tree-building software such as BEAST, EPA, HYPHY, PAML, PHYLDOG, pplacer, r8s, RAxML and RevBayes.
library("ape")
library("Biostrings")
library("ggplot2")
library("ggtree")
nwk <- system.file("extdata", "sample.nwk", package="ggtree")
tree <- read.tree(nwk)
tree
After you’ve loaded your tree in R, visualization is really simple. The ggtree function directly plots a tree and support several layouts, such as rectangular, circular, slanted, cladogram, time-scaled, etc.
Continue readingThe multi-species coalescent model (MSCM) is the biggest name in the game (if the game is genetic species delimitation). But a new paper from Proceedings of the National Academy of Sciences asks: is the MSCM really doing what we think it’s doing?
Some background: The MSCM, usually implemented in the program BPP (Yang & Rannala 2010), models speciation as an instantaneous event under the birth-death process.
But we know that the biological reality is more complex. Within most species there is some amount of gene flow restriction (e.g., due to environmental or geographic barriers), not all of which will eventually lead to speciation. Depending on the extent and duration of isolation and the strength of selection, speciation can be a gradual and stochastic process.
Sukumaran & Knowles (2017) tested the performance of the MSCM using data simulated under the “protracted speciation model,” which includes a few more biologically relevant parameters compared to the simpler birth-death model. Two key components of the protracted speciation model are the species conversion rate (c, the rate at which incipient species develop into true species), and another parameter that accounts for incipient species going extinct or merging back into their parent species.
Figure 1 from Sukumaran & Knowles 2017. The multi-species coalescent model may over-estimate the “true” number of species on a phylogeny.
Figure 2 from Sukumaran & Knowles 2017. The multi-species coalescent model infers more than the true number of species, under a variety of simulation conditions (A). However, it does correctly estimate the number of lineages (B).
This study also served as a call for new methods for genetic species delimitation, and the researchers have already tweet-hinted at a new method that may be coming down the pipe soon. I imagine the new method will have some basis in protracted speciation model? I’m looking forward to reading it.
Modified from Figure 1 (Belleghem et al., 2017). Sample of diversity among H. erato.
Modified from Figure 1 (Belleghem et al., 2017). Geographical distribution, phylogeny and color pattern diversity among H. erato individuals
The March for Science champions publicly funded and publicly communicated science as a pillar of human freedom and prosperity. We unite as a diverse, nonpartisan group to call for science that upholds the common good, and for political leaders and policymakers to enact evidence-based policies in the public interest.
Scientists are often politically minded — we’re people, just like everyone else — but we don’t like to think of the work we do in the lab and field as political. (In fact, it’s arguable that the worst misuses of the scientific method have happened when scientists couldn’t see past prevailing social attitudes.) Still, we’re not the ones who have decided that the facts of climate change, medecine, and basic biology are politically charged. As meteorologist and climate journalist Eric Holthaus lays out in his ringing call to the March for Science, the independence of empirical fact itself is what we now must defend:
We are now living in a country where our head of state routinely utters falsehoods about even mundane things — about things that can’t possibly have happened the way he says they did. As a scientist and journalist and someone who has dedicated my life to pursuing truth, it is deeply, deeply offensive to me that the idea of truth itself is being called into question. How are we supposed to carry on as normal? The answer is that we don’t. The answer is that we march.
So that’s your action item at the end of this grueling introduction to the new normal: sign up for updates, and start planning your trip to Washington or pick a satellite march closer to you. We’ll see you on Earth Day.
You don’t have to get very far into an evolution textbook before you bump into Darwin’s finches, the birds descended from South American finches that colonized the Galapagos Islands and “radiated” into an array of different species, each with a beak adapted to different food sources across the archipelago. Another, equally interesting case of avian adaptation is found in North America, on a different sort of archipelago. It’s found in patches of lodgepole pine forest that cloak the slopes and foothills of the Rocky Mountains, in the hooked beaks of red crossbills.
In the Rockies, crossbills feed on lodgepole pine seeds, using the tips of those hooked beaks to prise open the scales of seed cones. You might think that the trees would object to this, and they do, so to speak — but across most of the area where lodgepole pines face off with crossbills, they’re also under attack by an even more pernicious threat, red squirrels. Unlike crossbills, which get into pine cones while they’re attached to the tree, squirrels gnaw whole cones free from the branches, and they target larger cones, which contain more seeds. The result is that most lodgepole pine populations have evolved small, squat cones with thickened bases that protect against harvesting squirrels. However, in the South Hills of Idaho, some patches of lodgepole pine are free of squirrels — and in those sites, the pines’ cones are longer and narrower, with thickened scales at the tip, where crossbills prefer to start their prying. Those differences make an effective defense against the birds, and South Hills crossbills have evolved deeper beaks to cope.
This situation is a classic “geographic mosaic of coevolution”, a landscape of populations in which crossbills and lodgepole pine have the potential to shape each others’ evolution, but only do so in the right kind of (squirrel-free) environment. The details of the crossbill-lodgepole mosaic have been studied extensively, but it’s not been clear whether South Hills crossbills are genetically isolated by coevolution with pine in that one tile of the mosaic. If they are, the birds’ adaptation to the tree’s defenses might be setting the South Hills crossbills on the road to the origin of a new species.
Continue readingWhile the current administration is in office we’re posting small, concrete things you can do to help make things better, every Friday. (And, when it’s urgent, on other days too.) Got a suggestion for an Action Item? E-mail us!
This morning, news broke that the US Environmental Protection Agency (EPA) has been instructed to freeze all current contracts and grants. The contracts used by the EPA provide a multitude of benefits to Americans, from funding waste cleanup to monitoring drinking water quality. The EPA also funds a wide array of research projects that allow them to make science-based decisions on environmental regulations.
This extensive spending freeze has interrupted and endangered millions of dollars in scientific research — jeopardizing data that could influence the health of current and future generations and the people who devote their careers to collecting and sharing it.
Importantly, as one of the pillars of federal science funding, the EPA provides an example of what could happen at any moment to other funding bodies. Without warning or oversight, the President can halt the progress of science.
Do you care about science funding? Do you care about basing public policy on sound science? Then now is the time to contact those who represent you in Washington. Here are some specific EPA points you can mention:
Find out amount & purpose of EPA grants awarded in your congressional district. Then call your Rep to tell them… https://t.co/raymwg9NoV
— Emilio M. Bruna (@BrunaLab) January 24, 2017
As a reminder, calling the local office of a Member of Congress is effective even if you think you already know the Member’s position. If they’re on the wrong side, it’s good for them to hear directly from constituents who disagree. If they’re on the right side, it still helps them to know you think this is a priority and they have your support to take action.
The Molecular Ecologist receives a small commission for purchases made on Bookshop.org via links from this post.
On September 7, 1936, at the Beaumaris Zoo in Hobart, Tasmania, a wolf-like creature named Benjamin paced up and down in his cage. As night fell, temperatures grew cooler. The keepers, underpaid and struggling themselves, had forgotten to open the sliding wooden door that would allow Benjamin to move from the outside enclosure into his protected nighttime pen. Benjamin, dehydrated, exhausted, and neglected, died during the night.
The story might sound like a sad but typical event during the Great Depression: with limited resources, many zoos had trouble tending to their creatures. Benjamin’s story was especially tragic, though, because he was the final thylacine—also called a Tasmanian wolf or Tasmanian tiger—on Earth.
But what if we could resurrect him?
The thylacine’s story is just one of the many that Helen Pilcher delves into in her new work, Bring Back the King: The New Science of De-Extinction (Bloomsbury Sigma, $27 in hardback). Alternating between captivating stories about the loss of some of Earth’s most majestic species, and the details of how we could bring them back to life, the book is both a thoughtful analysis of the revolutionary science of “de-extinction” and a consideration of our moral responsibilities towards the ghosts of our past.
While the current administration is in office we’re posting small, concrete things you can do to help make things better, every Friday. Got a suggestion for an Action Item? E-mail us!
Today was the inauguration. Tomorrow, millions of people around the U.S. and across the world will say what they think about that. The Women’s March started as a Facebook post proposing a post-inauguration protest in Washington, DC, and it’s now grown to hundreds of sister marches worldwide. As the name suggests, the March was particularly motivated by the new president’s unapologetic sexism and the new vice president’s astonishingly poor record on women’s rights — but the March’s vision brings together the myriad objections people of goodwill have to the new administration, and its many partners range from the Natural Resources Defense Council to GLAAD to the AFL-CIO to the ACLU.
So make a poster featuring your favorite science, pick out a geeky tee-shirt (may we suggest?) and find a sister march close to you to attend tomorrow. We’ll see you in the streets.
