Evo Devo

Evolutionary Developmental Biology (a.k.a Evo Devo) is a growing field of biology that stands at the interface between evolutionary biology and developmental biology. With an ever increasing knowledge base, the literature on the topic is becoming increasingly difficult to wade through. I hope this blog can highlight the important findings in the field that anyone, scientist or layperson, may find interesting and enjoyable.

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sagansense:

Quick, in ten words or less, how does evolution work? The old phrase “survival of the fittest” quite likely sprung to mind, and you’d (mostly) be on the right track. But that phrase, coined by Herbert Spencer, is a gross oversimplification of Darwin’s theory of natural selection.

The key is how we define “fitness.” In the evolutionary sense, fitness refers to an organism’s ability to not just survive, but reproduce. And if an organism can successfully produce offspring—in essence, copies of itself—it will propagate faster than one that can’t.

Seems obvious, right? Well, again, this is another oversimplification. If one creature is better at reproducing itself than another creature, the first one is going to eventually win out. But how does a creature become “better” in the first place, and how does this drive evolution?

Watch the video by Bjørn Østman and Randy Olson of Michigan State, which features fitness landscapes, a method of visualizing evolution that was first proposed by Sewall Wright in a 1932 paper. Personally, I love them because they show how evolution is like an ever-morphing puzzle.

A fitness landscape from Sewall Wright’s 1932 paper.

A peak in the chart represents a highly-fit genotype, or the set of genes that makes an organism what it is; you might also think of it as the “ideal” genotype for a specific ecological niche. The dots are individuals; the closer together they are, the more similar their genotypes are.

As Østman and Olson explain in the video, over time, organisms move towards higher ground on the chart—becoming more fit—because as they get closer to that “peak,” they’re able to reproduce more, and some of their offspring will produce more, and so on.

It helps show how evolution isn’t an active process on the part of organisms—despite what you may have heard, chimps didn’t just decide one day that they wanted to become humans. Instead, it’s a matter of probability: when an opportunity opens up, those organisms best suited to take advantage of it will produce more of themselves than competitors, and the most successful of those offspring will produce even more, and so on as the population climbs up the fitness mountain.

Source: EvoSysBio

Now, if everything in the world was completely static, we’d eventually see organisms evolve towards a single solution for their specific environment. You can imagine this if you take a mental snapshot of the world right now; a polar bear is pretty highly suited for its environment, food sources, competition, and so on. But the world isn’t static at all. The environment, geography, animal behavior, biodiversity, and competition—both intra- and interspecies—are all continually in flux, meaning the “peaks” on the fitness landscape of the world are always shifting.

And as they shift, so do the successful genotypes that are able to climb up them. In essence, that’s how evolution works on a very macro scale: Because the rules of success for a specific ecological niche are always changing, the ideal solution also must change.

One interesting case is when fitness peaks change rapidly—because the population doesn’t have time to shift fully towards one or the other, organisms that are suited to both might arise, or the population might drift towards one peak and not the other. That’s often when you’ll get new species.


From the journal paper “Microbial laboratory evolution in the era of genome‐scale science" via Molecular Systems Biology

In another case, where fitness is density-dependent—having too large a population makes the whole population less successful—you see populations becoming more specialized quickly, like that of Darwin’s famous finches, which evolved beaks to deal with very specific food types.

When you look at a fitness landscape on a broad scale, like Wright’s original diagram above, you can start to see that there are plenty of fitness peaks in the world, and that those genotypes closest to the peak will most likely continue to evolve in that direction as they continue to get more and more fit. And when populations split and shift to this ever-changing landscape of fitness peaks, the end result is the ever-changing mosaic of species that have evolved on Earth.

Source:  MOTHERBOARD; Main Image: “Mental Model: Fitness Landscapes" via FutureBlind

sagansense:

Quick, in ten words or less, how does evolution work? The old phrase “survival of the fittest” quite likely sprung to mind, and you’d (mostly) be on the right track. But that phrase, coined by Herbert Spencer, is a gross oversimplification of Darwin’s theory of natural selection.

The key is how we define “fitness.” In the evolutionary sense, fitness refers to an organism’s ability to not just survive, but reproduce. And if an organism can successfully produce offspring—in essence, copies of itself—it will propagate faster than one that can’t.

Seems obvious, right? Well, again, this is another oversimplification. If one creature is better at reproducing itself than another creature, the first one is going to eventually win out. But how does a creature become “better” in the first place, and how does this drive evolution?

Watch the video by Bjørn Østman and Randy Olson of Michigan State, which features fitness landscapes, a method of visualizing evolution that was first proposed by Sewall Wright in a 1932 paper. Personally, I love them because they show how evolution is like an ever-morphing puzzle.

imageA fitness landscape from Sewall Wright’s 1932 paper.

A peak in the chart represents a highly-fit genotype, or the set of genes that makes an organism what it is; you might also think of it as the “ideal” genotype for a specific ecological niche. The dots are individuals; the closer together they are, the more similar their genotypes are.

As Østman and Olson explain in the video, over time, organisms move towards higher ground on the chart—becoming more fit—because as they get closer to that “peak,” they’re able to reproduce more, and some of their offspring will produce more, and so on.

It helps show how evolution isn’t an active process on the part of organisms—despite what you may have heard, chimps didn’t just decide one day that they wanted to become humans. Instead, it’s a matter of probability: when an opportunity opens up, those organisms best suited to take advantage of it will produce more of themselves than competitors, and the most successful of those offspring will produce even more, and so on as the population climbs up the fitness mountain.

imageSource: EvoSysBio

Now, if everything in the world was completely static, we’d eventually see organisms evolve towards a single solution for their specific environment. You can imagine this if you take a mental snapshot of the world right now; a polar bear is pretty highly suited for its environment, food sources, competition, and so on. But the world isn’t static at all. The environment, geography, animal behavior, biodiversity, and competition—both intra- and interspecies—are all continually in flux, meaning the “peaks” on the fitness landscape of the world are always shifting.

And as they shift, so do the successful genotypes that are able to climb up them. In essence, that’s how evolution works on a very macro scale: Because the rules of success for a specific ecological niche are always changing, the ideal solution also must change.

One interesting case is when fitness peaks change rapidly—because the population doesn’t have time to shift fully towards one or the other, organisms that are suited to both might arise, or the population might drift towards one peak and not the other. That’s often when you’ll get new species.

image
From the journal paper “Microbial laboratory evolution in the era of genome‐scale science" via Molecular Systems Biology

In another case, where fitness is density-dependent—having too large a population makes the whole population less successful—you see populations becoming more specialized quickly, like that of Darwin’s famous finches, which evolved beaks to deal with very specific food types.

When you look at a fitness landscape on a broad scale, like Wright’s original diagram above, you can start to see that there are plenty of fitness peaks in the world, and that those genotypes closest to the peak will most likely continue to evolve in that direction as they continue to get more and more fit. And when populations split and shift to this ever-changing landscape of fitness peaks, the end result is the ever-changing mosaic of species that have evolved on Earth.

Source: MOTHERBOARD; Main Image: “Mental Model: Fitness Landscapes" via FutureBlind

New theory uncovers cancer's deep evolutionary roots

pitchforking:

A new way to look at cancer – by tracing its deep evolutionary roots to the dawn of multicellularity more than a billion years ago – has been proposed by Paul Davies of Arizona State University’s Beyond Center for Fundamental Concepts in Science in collaboration with Charles Lineweaver of the Australian National University. If their theory is correct, it promises to transform the approach to cancer therapy, and to link the origin of cancer to the origin of life and the developmental processes of embryos.

Davies and Lineweaver are both theoretical physicists and cosmologists with experience in the field of astrobiology – the search for life beyond Earth. They turned to cancer research only recently, in part because of the creation at Arizona State University of the Center for the Convergence of Physical Science and Cancer Biology. The center is one of twelve established by the National Cancer Institute to encourage physical scientists to lend their insights into tackling cancer.

The new theory challenges the orthodox view that cancer develops anew in each host by a series of chance mutational accidents. Davies and Lineweaver claim that cancer is actually an organized and systematic response to some sort of stress or physical challenge. It might be triggered by a random accident, they say, but thereafter it more or less predictably unfolds.

Their view of cancer is outlined in the article “Exposing cancer’s deep evolutionary roots,” written by Davies. It appears in a special July issue of Physics World devoted to the physics of cancer.

“We envisage cancer as the execution of an ancient program pre-loaded into the genomes of all cells,” says Davies, an Arizona State University Regents’ Professor in ASU’s College of Liberal Arts and Sciences. “It is rather like Windows defaulting to ‘safe mode’ after suffering an insult of some sort.” As such, he describes cancer as a throwback to an ancestral phenotype.

The new theory predicts that as cancer progresses through more and more malignant stages, it will express genes that are more deeply conserved among multicellular organisms, and so are in some sense more ancient. Davies and Lineweaver are currently testing this prediction by comparing gene expression data from cancer biopsies with phylogenetic trees going back 1.6 billion years, with the help of Luis Cisneros, a postdoctoral researcher with ASU’s Beyond Center.

But if this is the case, then why hasn’t evolution eliminated the ancient cancer subroutine?

“Because it fulfills absolutely crucial functions during the early stages of embryo development,” Davies explains. “Genes that are active in the embryo and normally dormant thereafter are found to be switched back on in cancer. These same genes are the ‘ancient’ ones, deep in the tree of multicellular life.”

The link with embryo development has been known to cancer biologists for a long time, says Davies, but the significance of this fact is rarely appreciated. If the new theory is correct, researchers should find that the more malignant stages of cancer will re-express genes from the earliest stages of embryogenesis. Davies adds that there is already some evidence for this in several experimental studies, including recent research at Harvard University and the Albert Einstein College of Medicine in New York.

“As cancer progresses through its various stages within a single organism, it should be like running the evolutionary and developmental arrows of time backward at high speed,” says Davies.

This could provide clues to future treatments. For example, when life took the momentous step from single cells to multicellular assemblages, Earth had low levels of oxygen. Sure enough, cancer reverts to an ancient form of metabolism called fermentation, which can supply energy with little need for oxygen, although it requires lots of sugar.

Davies and Lineweaver predict that if cancer cells are saturated with oxygen but deprived of sugar, they will become more stressed than healthy cells, slowing them down or even killing them. ASU’s Center for the Convergence of Physical Science and Cancer Biology, of which Davies is principal investigator, is planning a workshop in November to examine the clinical evidence for this.

“It is clear that some radically new thinking is needed,” Davies states. “Like aging, cancer seems to be a deeply embedded part of the life process. Also like aging, cancer generally cannot be cured but its effects can certainly be mitigated, for example, by delaying onset and extending periods of dormancy. But we will learn to do this effectively only when we better understand cancer, including its place in the great sweep of evolutionary history.”

rhamphotheca:

Fossil Fish With “Limbs” Is Missing Link, Study Says

by James Owen, Apr., 2006

Fossil hunters may have discovered the fish that made humans possible.

Found in the Canadian Arctic, the new fossil boasts leglike fins, scientists say. The creature is being hailed as a crucial missing link between fish and land animals—including the prehistoric ancestors of humans.

Researchers say the fish shows how fins on freshwater species first began transforming into limbs some 380 million years ago. The change was a huge evolutionary step that opened the way for vertebrates—animals with backbones—to emerge from the water.

“This animal represents the transition from water to land—the part of history that includes ourselves,” said paleontologist Neil Shubin of the University of Chicago.

Shubin was co-leader of a team that uncovered three nearly complete fossils measuring up to nine feet (3 m) long on Ellesmere Island in 2004. The new species, Tiktaalik roseaehad a flattened, crocodile-like head and strong, bony fins…

(read more: National Geo)                  

(image: T - Shawn Gould, Nat. Geo.; BL - Univ of Chicago; BR - Graham Roberts, NY Times)

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read more:

http://en.wikipedia.org/wiki/Tiktaalik

http://tiktaalik.uchicago.edu/index.html

http://evolution.berkeley.edu/evolibrary/news/060501_tiktaalik

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Aspiring Biologist: Mammals evolved to survive the dinosaurs...

imprettymuchabiologist:



Recent studies of jaw and ear function in primitive mammal-like reptiles indicate that the larger angular bone, which later became the tempanic ( bone of the skull, partially enclosing the middle ear and supporting the eardrum ) may have supported an eardrum while still part of the…

Iqbal Selvan: Chimpanzee geniuses also exist

iqbalselvan:

A perfect storm of abilities seems to come together to create the Einsteins of the animal kingdom. While testing intelligence, one chimp, named Natasha, had scores that were off the charts in comparison to other chimps. Is she like an ape genius?

Certain apes appear to be much smarter…

(via iqbalselvan-deactivated20130111)

goforgold93:

Bill Nye “Creationism isn’t for kids”

"Biologists tracing the roots of a global pandemic will take samples in multiple locations, sequence the DNA and map how the virus has evolved through time by looking at how its genes have been modified.
“Once they’ve got the family tree… they can trace back along the branches of the tree all the way back to the origin,” Atkinson said in a telephone interview.
“What we did was apply the same kind of approach to languages.”
The team built a database of cognates such as mother, which is moeder in Dutch, madre in Spanish, mat in Russian, mitera in Greek and mam in Hindi."

Turkey the birthplace of Hindi, English: study

I always assumed the word for mother was similar in most languages because going from a closed mouthed “M” sound to an open mouthed vowel is the simplest vocalization (and babies generally learn words for mother first).

(via slartibartfastibast)

(via slartibartfastibast)

neurosciencestuff:

A new UCLA study pinpoints uniquely human patterns of gene activity in the brain that could shed light on how we evolved differently than our closest relative. Published Aug. 22 in the advance online edition of Neuron, these genes’ identification could improve understanding of human brain diseases like autism and schizophrenia, as well as learning disorders and addictions.
Read more
(Image by Michael Nichols)

neurosciencestuff:

A new UCLA study pinpoints uniquely human patterns of gene activity in the brain that could shed light on how we evolved differently than our closest relative. Published Aug. 22 in the advance online edition of Neuron, these genes’ identification could improve understanding of human brain diseases like autism and schizophrenia, as well as learning disorders and addictions.

Read more

(Image by Michael Nichols)

rhamphotheca:

Drivers of marine biodiversity: Tiny, freeloading clams find the key to evolutionary success

by PhysOrg staff

What mechanisms control the generation and maintenance of biological diversity on the planet? It’s a central question in evolutionary biology. For land-dwelling organisms such as insects and the flowers they pollinate, it’s clear that interactions between species are one of the main drivers of the evolutionary change that leads to biological diversity.

But the picture is much murkier for ocean dwellers, mainly because the scope of ecological interactions remains poorly characterized for most marine species. In one of the first efforts to examine how species interactions drive diversification of ocean-dwelling organisms, two University of Michigan researchers and an Australian colleague looked at the lifestyle choices within an exceptionally diverse superfamily of tiny clams, the Galeommatoidea.

They found that the fingernail-size-and-smaller clams’ propensity to shack up with much larger, burrowing creatures such as sea urchins, shrimp and worms was a key adaptation that led to the evolutionary success of the superfamily, as measured by its “megadiverse” status among marine bivalves. There are about 500 described species of galeommatoidean clams and many more undescribed species…

(read more: PhysOrg)       (images: Kevin Lee/diverkevin.com)

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Journal reference: PLoS ONE

Provided by University of Michigan