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‘Micro snails’ we scraped from sidewalk cracks help unlock details of ancient Earth’s biological evolution

Scientists discovered microbes that have lived on Earth for millions of years.

Every step you take, you're likely walking on a world of unseen and undescribed microbial diversity. And you don't need to head out into nature to find these usually unnoticed microscopic organisms.

As biologists, we know this firsthand. A meetup for coffee several years ago ended with our using makeshift sampling tools – actually a coffee stirrer and a coffee cup lid – to collect some of the black gunk from between the sidewalk's concrete slabs. In this mundane space on the Mississippi State University campus, we discovered microbes that have lived on Earth for millions of years.

Finding these charismatic organisms in the environment, while exciting, is just the first step. Our mutual interest is to better understand how organisms are related to one another. We're using DNA to reveal their relationships in the very distant past.

By sampling organisms that are alive today, we can ask deeper questions about the evolution that happened millions of years ago in now extinct ancestors.

Piecing together the tree of life

Our simple act of collection after our 2015 coffee date started a fruitful collaboration between our labs in the field of molecular protistology. Our focus is on the microscopic single-celled organisms called protists, particularly ones that move around using tiny tentacles called pseudopodia.

Amphizonella – identified in the authors' sidewalk sample – has a soft protective layer.

Matthew W. Brown, CC BY-ND

One elusive critter we identified in our sidewalk sample is an amoeba named Amphizonella; we joke that it makes its own “leather jacket" in the form of a soft, protective outer layer.

Despite what other scientists had previously thought, we had a hunch that this organism wasn't closely related to other amoebae that have tougher outer coverings. This other much larger group, called testate amoebae, have shells – imagine microscopic snails – instead of leather jackets.

Because testate amoebae make a hard shell, they have the potential to fossilize. In fact, their vivid fossil record represents some of the oldest unequivocal fossils of eukaryotes – the category of life whose members hold their DNA within their cells' nuclei. Why is this important? Human beings are also eukaryotes, as are plants, fungi, other animals, kelps and protists. Because these amoebae are some of the oldest eukaryotic fossils, they can in turn tell researchers like us something about our own species' origins.

Since the advent of DNA sequencing in the early 2000s, biologists have used a small piece of the genome, even a single gene, to examine the relationships between organisms, though with limited success. Through similarity of DNA sequences between living organisms, one can infer relationships using complex computational approaches that model evolution change over time from empirically derived data. Simply put, scientists try to piece together who's related to whom in order to reconstruct the evolutionary tree of life, or what we call a phylogenetic tree.

The first step of single-cell transcriptomics is isolating a single organism. Here, a micropipette picks up one Amphizonella cell. Credit: Matthew W. Brown.

In most cases the testate amoebae are quite difficult to cultivate in the laboratory, making it very hard to obtain enough material to sequence their DNA with the usual methods.

To overcome these challenges, we're using a cutting-edge technique that allows us to take an organism directly from the environment and sequence its entire transcriptome – that's the blueprint of all the proteins that it makes. This way, we're able to bypass sequencing the whole genome (with its extraneous information) and sequence only the protein-coding regions. We end up with high-quality data of billions of base pairs of DNA that we can directly compare with similar data from other organisms.

This method provides better resolution by sampling hundreds of genes, rather than a single one. Then we use the data to build a phylogenetic tree of life that organizes our amoebae by how closely related they are to each other based on the similarity of their DNA. With these data, we can go further and compare our testate amoebae to other eukaryotes and identify what makes them unique and similar at a genomic level.

Connecting today's life to ancient ancestors

Because life evolved over billions of years from a last universal common ancestor, all organisms, both living and extinct, must be related to each other in a single family tree.

But fossils don't preserve DNA information. While it's true that some ancient DNA sequencing is possible, in general it's only been done with frozen samples like the woolly mammoth or ancient human beings like mummified remains. These ancient DNA samples have not really fossilized, and in comparison to fossils, they're significantly more recent – for instance, the oldest human-related DNA to have been sequenced was from a Denisovan person's tooth, which is about 110,000 years old.

In contrast, the fossil of Archaeopteryx, one of the most ancient relatives of birds, is about 150 million years old. That means that, today, we are about 100,000 times more distant to Archaeopteryx than we are to the Denisovan remains. That's an immense amount of time.

A scanning electron micrograph of a fossilized Ciclocyrillium torquata, sampled from the Urucum formation in central Brazil.

Luana Morais, CC BY-ND

The fossils that seem to relate to today's testate amoebae are about 750 million years old, from a time period called the Neoproterozoic. Scientists know very little about what was happening on Earth in that very distant past. Researchers have identified these tiny fossils in rocks collected in the Grand Canyon and central Brazil.

In order to compare the tree we created based on DNA from living species with the fossilized shells of the Neoproterozoic, we had to somehow extrapolate our data. Using the rates of evolution calculated in our tree, we were able to apply these rates using how the shells look today, to estimate what they might have looked in the past. This way, we can create a hypothetical ancestor that we can then compare to the actual fossils.

A family tree of testate amoebae linking the fossil record (left) to present day testate amoebae (right).

Lahr et al. 2019, Current Biology https://doi.org/10.1016/j.cub.2019.01.078., CC BY-ND

Our results were impressive. We calculated seven hypothetical ancestors based on a few million possibilities. When we compared them to the fossil record, previously described in the literature, we found five fossil species that were incredibly similar to our predictions. This allowed us to confidently determine that those Neoproterozoic fossils are indeed very ancient testate amoebae, and that this group has been around since before 750 million years ago. And even by then, they had already considerably diversified.

Showing that these creatures were around and diverse at such deep time scales is important because they're complex organisms, with complex ecologies and behaviors. They provide an inside look into what life might have been like in those ancient eras. The amoebae can be predators, but they can also be grazers, or even harbor symbiotic algae that produce their food, making them primary producers.

The fact that many diverse types of testate amoebae were around by this stage implies that complex food webs had already developed, which in turn has implications for what the environment might have been like. Now, geochemists will compare their notes to our biological insights, and our understanding of ancient earth will continue to improve.The Conversation

Matthew Brown, Assistant Professor of Biological Sciences, Mississippi State University and Daniel Lahr, Assistant Professor of Zoology, Universidade de São Paulo

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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What can 3D printing do for medicine? The "sky is the limit," says Northwell Health researcher Dr. Todd Goldstein.

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Sponsored by Northwell Health
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A recent study gives new meaning to the saying "fake it 'til you make it."

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  • Results consistently showed that high-class people tend to overestimate their abilities.
  • However, this overconfidence was misinterpreted as genuine competence in one study, suggesting overestimating your abilities can have social advantages.
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Maps show how CNN lost America to Fox News

Is this proof of a dramatic shift?

Strange Maps
  • Map details dramatic shift from CNN to Fox News over 10-year period
  • Does it show the triumph of "fake news" — or, rather, its defeat?
  • A closer look at the map's legend allows for more complex analyses

Dramatic and misleading

Image: Reddit / SICResearch

The situation today: CNN pushed back to the edges of the country.

Over the course of no more than a decade, America has radically switched favorites when it comes to cable news networks. As this sequence of maps showing TMAs (Television Market Areas) suggests, CNN is out, Fox News is in.

The maps are certainly dramatic, but also a bit misleading. They nevertheless provide some insight into the state of journalism and the public's attitudes toward the press in the US.

Let's zoom in:

  • It's 2008, on the eve of the Obama Era. CNN (blue) dominates the cable news landscape across America. Fox News (red) is an upstart (°1996) with a few regional bastions in the South.
  • By 2010, Fox News has broken out of its southern heartland, colonizing markets in the Midwest and the Northwest — and even northern Maine and southern Alaska.
  • Two years later, Fox News has lost those two outliers, but has filled up in the middle: it now boasts two large, contiguous blocks in the southeast and northwest, almost touching.
  • In 2014, Fox News seems past its prime. The northwestern block has shrunk, the southeastern one has fragmented.
  • Energised by Trump's 2016 presidential campaign, Fox News is back with a vengeance. Not only have Maine and Alaska gone from entirely blue to entirely red, so has most of the rest of the U.S. Fox News has plugged the Nebraska Gap: it's no longer possible to walk from coast to coast across CNN territory.
  • By 2018, the fortunes from a decade earlier have almost reversed. Fox News rules the roost. CNN clings on to the Pacific Coast, New Mexico, Minnesota and parts of the Northeast — plus a smattering of metropolitan areas in the South and Midwest.

"Frightening map"

Image source: Reddit / SICResearch

This sequence of maps, showing America turning from blue to red, elicited strong reactions on the Reddit forum where it was published last week. For some, the takeover by Fox News illustrates the demise of all that's good and fair about news journalism. Among the comments?

  • "The end is near."
  • "The idiocracy grows."
  • "(It's) like a spreading disease."
  • "One of the more frightening maps I've seen."
For others, the maps are less about the rise of Fox News, and more about CNN's self-inflicted downward spiral:
  • "LOL that's what happens when you're fake news!"
  • "CNN went down the toilet on quality."
  • "A Minecraft YouTuber could beat CNN's numbers."
  • "CNN has become more like a high-school production of a news show."

Not a few find fault with both channels, even if not always to the same degree:

  • "That anybody considers either of those networks good news sources is troubling."
  • "Both leave you understanding less rather than more."
  • "This is what happens when you spout bullsh-- for two years straight. People find an alternative — even if it's just different bullsh--."
  • "CNN is sh-- but it's nowhere close to the outright bullsh-- and baseless propaganda Fox News spews."

"Old people learning to Google"

Image: Google Trends

CNN vs. Fox News search terms (200!-2018)

But what do the maps actually show? Created by SICResearch, they do show a huge evolution, but not of both cable news networks' audience size (i.e. Nielsen ratings). The dramatic shift is one in Google search trends. In other words, it shows how often people type in "CNN" or "Fox News" when surfing the web. And that does not necessarily reflect the relative popularity of both networks. As some commenters suggest:

  • "I can't remember the last time that I've searched for a news channel on Google. Is it really that difficult for people to type 'cnn.com'?"
  • "More than anything else, these maps show smart phone proliferation (among older people) more than anything else."
  • "This is a map of how old people and rural areas have learned to use Google in the last decade."
  • "This is basically a map of people who don't understand how the internet works, and it's no surprise that it leans conservative."

A visual image as strong as this map sequence looks designed to elicit a vehement response — and its lack of context offers viewers little new information to challenge their preconceptions. Like the news itself, cartography pretends to be objective, but always has an agenda of its own, even if just by the selection of its topics.

The trick is not to despair of maps (or news) but to get a good sense of the parameters that are in play. And, as is often the case (with both maps and news), what's left out is at least as significant as what's actually shown.

One important point: while Fox News is the sole major purveyor of news and opinion with a conservative/right-wing slant, CNN has more competition in the center/left part of the spectrum, notably from MSNBC.

Another: the average age of cable news viewers — whether they watch CNN or Fox News — is in the mid-60s. As a result of a shift in generational habits, TV viewing is down across the board. Younger people are more comfortable with a "cafeteria" approach to their news menu, selecting alternative and online sources for their information.

It should also be noted, however, that Fox News, according to Harvard's Nieman Lab, dominates Facebook when it comes to engagement among news outlets.

CNN, Fox and MSNBC

Image: Google Trends

CNN vs. Fox (without the 'News'; may include searches for actual foxes). See MSNBC (in yellow) for comparison

For the record, here are the Nielsen ratings for average daily viewer total for the three main cable news networks, for 2018 (compared to 2017):

  • Fox News: 1,425,000 (-5%)
  • MSNBC: 994,000 (+12%)
  • CNN: 706,000 (-9%)

And according to this recent overview, the top 50 of the most popular websites in the U.S. includes cnn.com in 28th place, and foxnews.com in... 27th place.

The top 5, in descending order, consists of google.com, youtube.com, facebook.com, amazon.com and yahoo.com — the latter being the highest-placed website in the News and Media category.
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Mother bonobos, too, pressure their sons to have grandchildren

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