June 8, 2017 Unique mutational fingerprints in each of 6 environments. Credit: Maharajan and Ferenci graphic in PLOS Biology

Starvation for essential elements determines the pattern of genetic variation.

Evolution is rather simple in outline; plentiful biological variation allows natural selection to pick the fittest variant that reproduces and out-competes the other variants in a population.

Since Darwin, we have learned a lot about how selection and fitness determine evolutionary outcomes but a lot less about the variation part of evolution.

The neglect of variation as a determinant of evolution was common in the 20th century, largely because the common belief was that genetic variation through mutations was random and common so unlikely to limit evolutionary outcomes.

In this research, Maharjan and Ferenci discovered that genetic variation is not uniform in different environments and that nutritional factors provide a strong influence on what variation is available to organisms.

To resolve the randomness of mutations in different environments, M&F used tightly controlled cultures of a bacterium whose growth was limited by each of the most important essential elements for life (i.e. hunger for carbon, oxygen, nitrogen, phosphorus and iron). One of these elements was limiting in each culture, the others being in excess. In chemostats, the organisms were grown at the same rate so the level of nutritional stress was the same, even though the limiting nutrient was different.

The detailed analysis of mutations in these nutritionally distinct environments provides an entirely new perspective on the nature of mutation and genetic variation in evolution. Even at the same growth rate (i.e. similar fitness levels), some, but not all, nutritional limitations significantly increase the number of mutations. Other environments do not have increased total mutations but we find that the proportions of 16 different types of mutation are all environment-specific.

Remarkably, there were over 100-fold differences in the availability of some types of mutation between, say oxygen and phosphorus limitation.

Phosphorous and carbon starvation induced a four- to nine- fold increase in the total mutation rate (per locus per generation), whereas nitrogen, oxygen and iron starvation had no impact on the mutation rate. Interestingly, regardless of the total mutation rates, the mutation spectra differed substantially across all stresses (see Figure attached). For instance, IS mutations (Insertion Sequence transpositions) were higher in Fe and O starvation compared to C and N, and lowest under P limitation. P limitation also induced a large overproduction of BPS (Base Pair Substitutions), primarily due to GC?AT transitions and GC?TA transversions. Thus, each stress produced a unique set of mutations that were then available for subsequent evolution.

The conclusions are that evolutionary dynamics may be shaped by exposure to specific nutritional stresses; nutrition determines mutations! Furthermore, organisms exposed to a repeated, specific nutritional stress may accumulate distinct mutations over long periods, potentially solving some previously unexplained patterns of genome architecture over time. Mutation availability in different environments is thus a fundamental feature of evolution.

The study is published in PLOS Biology.

Explore further: Ongoing natural selection against damaging genetic mutations in humans

More information: PLOS Biology (2017). DOI: 10.1371/journal.pbio.2001477

Journal reference: PLoS Biology

Provided by: University of Sydney

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The road not taken: Do stress-specific mutations lead down different evolutionary paths? - Phys.Org

Biologist Jonathan Wells, author of Zombie Science, slices up the fairy tale of whale evolution. He describes three massive acts of re-engineering under the general headings of breathing, swimming, and reproduction that would need to be accomplished inturning a land creature into a fully marine one like a whale:

If we wanted to turn a land mammal into a whale, these are a few of the changes we would have to implement. Could the changes have happened accidentally, without design?

People who believe in Darwinian evolution point out that fossils have been found of animals that might have been transitional between fully terrestrial mammals and fully aquatic cetaceans. The fossil animals had legs but probably spent much of their time in the water. Darwinian paleontologists call them walking whales because they have a particular ear bone that had previously been found only in cetaceans (though the bone has now been found in an extinct land mammal, Indohyus, that is not classified as a cetacean). But the supposedly transitional animals are anatomically more like amphibious sea lions and otters than whales, and the transition from amphibious to fully aquatic must have happened in a geological blink of an eye.11

Even if the transition were perfectly documented with intermediate forms, however, it would not answer the how questions. How did the features needed for a fully aquatic lifestyle originate? How would the hind limbs of a sea lion turn into a fluke (which is very different)? How would a males testicles become simultaneously internalized and surrounded by countercurrent heat exchange systems? How would a female develop specialized nursing organs to inject milk forcibly into her calf? Indeed, why would any of these changes occur? Sea lions are already well adapted to their amphibious lives.

An intelligence could have planned to make fully aquatic mammals and designed these features to actualize the plan. But Darwinian theory says no design is allowed, and that leaves us with little more than a fairy tale about how natural selection could turn swimming bears into whales.

The rest is over at Salvo. Read it there.

Darwin thought the ancestral land beast was something like a bear. Even after scrubbing this from updated editions of the Origin of Species, stung by mockery for the suggestion, he continued to hold the view privately. Current theories are hardly more credible.

Photo: Fluke of a sperm whale, by Vilmos Vincze via Flickr.

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Jonathan Wells on the Fairy Tale of Whale Evolution - Discovery Institute

Knowledge Waits is a feature where I just share some bit of comic book history that interests me.

I thought it would be interesting to look to see how Wonder Womans Invisible Jet had evolved over the years.

We first saw the plane in Wonder Womans first full story (after her preview debut in All-Star Comics #8) in Sensation Comics #1 (by William Marston and H.G. Peter).

Awesomely, there is no explanation given for why Wonder Woman has an invisible plane.

We see in Wonder Woman #20 (by Joye Hummell and H.G. Peter) that the plane responds to her thoughts

And in Wonder Woman #26 (by Hummell and Peter), we see that it can go into the stratosphere!!

As Robert Kanigher took over the series, in Wonder Woman #45 he revealed that the plane no longer had propellers, so it was basically a jet

But when Ross Andru and Mike Esposito took over from H.G. Peter with Wonder Woman #98, the very next issue they revealed the new design of the invisible jet (making it look like the jets that they had been drawing for years in DCs war comics) and this was the look that would last pretty much from this point forward

A few different versions of the invisible jet were used on the Wonder Woman TV series

In Wonder Woman #261 (by Gerry Conway, Jose Delbo and Vince Colletta), the plane can now travel faster than the speed of light!!

And in Wonder Woman #312 (by Dan Mishkin and Don Heck), it is now sentient!!!

Then Crisis on Infinite Earths happened and George Perez just gave Wonder Woman the ability to fly, so she didnt need the jet, so it was not part of Wonder Womans Post-Crisis history until John Byrne introduced some characters who had an invisible jet in Wonder Woman #115

And then two issues later, they gave the special crystal to Wonder Woman, which would respond to her thoughts to create whatever she wanted

It eventually gained sentience and became a wonderful Dome for Wonder Woman, but in Wonder Woman #201 (early in Greg Ruckas first run), the Dome sacrificed its life to save Paradise Island.

Initially, the invisible jet really wasnt part of the New 52, but in Rebirth, Greg Rucka has made it so that when Steve Trevor crashed on Paradise Island, the Amazons fixed his ship and made it invisible, so now it is Steve Trevor who has an invisible plane.

I think you can make an argument that having Wonder Woman not have the ability to fly is a bit of a slight to her (thats surely what Perez was thinking when he gave her the power), but damn, man, the invisible jet is so cool!

If anyone else has a cool piece of comic book history that theyd like to see featured, feel free to drop me a line at brianc@cbr.com!

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The Evolution of Wonder Woman's Invisible Jet! - CBR (blog)

Are the red and eastern wolves separate species, or hybrids with coyotes? And what has that got to do with climate change? Actually a lot, in illustrating what scientific inquiry is and what it isnt.

COMPARING CANID GENOMES

A report in this weeks Science Advancesquestions conclusions of a 2016 comparison of genome sequencesfrom 28 canids. The distinction between species and hybrid is of practical importance, because the Endangered Species Act circa 1973 doesnt recognize hybrids. But DNA information canrefine species designations or muddy the waters.

At first, genetic marker (SNP) studies hinted at a mixing and matching of genome segments among coyotes, wolves, and dogs. Then came full-fledged genome sequencing.

Last yearBridgett M. vonHoldt, head of Evolutionary Genomics and Ecological Epigenomics at Princeton and colleagues, scrutinized the 28 full genome sequences for signs of lack of unique ancestry. They compared the genomes of 3 domestic dog breeds (boxer, German shepherd, and Basenji), 6 coyotes, a golden jackal from Kenya, and various wolves to 7 reference genomes from 4 Eurasian gray wolves (to minimize recent mutations) and 3 coyotes. The conclusion: lots of genes have flowed from coyotes and gray wolves into the genomes of the animals that became what we call red and eastern wolves, in different proportions.

A bit of background. Red wolves were declared endangered in 1973. A dozen animals, selected by appearance and absence of coyote traits in their young, were captively bred to establish a population in North Carolina that is now several hundred strong. The 3 red wolf genomes evaluated in the 2016 study came from NC. Historically the animals are from the southeastern US. Gray wolves and coyotes, according to the 2016 study, are very close relatives with a recent common ancestry, although theres about as much genetic variability between the two species as within each. Eastern wolves are from the Great Lakes and the Algonquin Park region of Ontario, moving eastward.

Classifying these animals based on geography and visible traits gets confusing, with all the overlaps and shared DNA sequences. Apparently various pairings can successfully mate but probably dont do so very much in the wild when populations are large. Tracking genomes reveals a classic cline, in the parlance of population genetics, with coyote gene introgression into wolf genomes rising from Alaska and Yellowstone (8-8.5%), to the Great Lakes (21.7-23.9%), to Ontario (32.5%-35.5%), and to Quebec (>50%). (BTW the Basenji, the barkless dog, is 61% gray wolf.)

Paul A. Hohenloheof the University of Idaho and colleagues maintain that the 2016 findings actually support 2 hypotheses: recent admixture (hybridization) or that red and eastern wolves are distinct species. Actually its 3: hybridization might have happened a long time ago, something that following genes with known mutation rates might reveal.

The new paper challenges the 28-genome comparison:

The 7 reference genomes were chosen based on the animals physical characteristics and home turf not on some standard coyote or gray wolf genome. So the genomes to which the 28 were compared might not have been pure anything. Two reference coyote genomes were pooled from animals from Alabama and Quebec which might have had some gray wolf genes. Gene flow when animals mate is, after all, a two-way street, sending wolf genes back into coyotes as well as the other way around. The 2016 paper hypothesizes that red wolves are distinct due to genetic drift chance sampling from an ancestral genome but unique ancestry is an alternate explanation. The lack of unique ancestry from the 2016 study doesnt mean it isnt there.

Dr. vonHoldts team respondedto Dr. Hohenlohes teams comments, reiterating that the results show red wolf and eastern wolves are genetically very similar to coyotes or gray wolves, reflecting recent hybridization.

Discussion of wolf classification goes back a quarter century, and this trio of papers is only a recent glimpse of the debate. But I love the respectful back-and-forth of the efforts to extract a compelling narrative from the data that might be what actually happened. Multiple interpretations of the same data and amending interpretations as new data accumulate is the very essence of the scientific process.

ANTI-SCIENCE RHETORIC

Lets reframe the wolf papers using the language of the popular climate change discussion.

Are Hohenlohe and his co-workers coyote deniers?

Do vonHoldt and her colleagues believe in wolf-coyote couplings and Hohenlohe et al dont?

The science of wolf origins is clearly not settled for science is NEVER settled. Facts arent proven, but instead evidence demonstrated and assessed, from both experimentation and observation. The information from tested hypotheses may be so consistent and compelling that it eventually builds to gestate a theory, or even a law, that then explains further observations. But to get there, science is all about asking questions. As Ive written in all 35 or so editions of my various textbooks, science is a cycle of inquiry.

In fact the history of genetics is a chronicle of once-entrenched dogma changing with new experiments and observations. I was in grad school when Walter Gilberts famed Why Genes in Pieces? was published. The classic paper introduced introns, the parts of genes that arent represented in the encoded protein. It was an astonishing idea circa 1978, but with compellingevidence. Yet even Mendels pea crosses sought an alternate explanation for the prevailing notion that traits simply disappear between generations.

Before Im hurled insults, let me assert that although my expertise isnt in climate science, I think that the evidence very strongly supports the hypothesis that the planet is warming at an accelerated rate compared to some other times. And fossil fuel use is likely a partial cause, not just a correlation or association, because the relationship is linear and a mechanism plausible. But I dont believe in global warming as if it is the tooth fairy or a deity.

I cringe when politicians and celebrities appoint and anoint themselves experts on climate change, then use language that illustrates profound unfamiliarity with the ways of science.

Why did Eddie Vedderbegin his speech at the Rock and Roll Hall of Fame induction ceremony for Pearl Jam with climate change is real? Hes a musician, not a meteorologist. Why not, semi-conservative DNA replication is real? Or hydrogen bonds are real? Noble gases are real?

Ive long had a problem with the term climate change, because of course climate changes! Why would it ever be static, given weather ups and downs?

Climate dynamics are a little like the composition of blood, or any other manifestation of biological homeostasis. Have a complete blood countat various times and, if youre healthy, results are likely to be within a narrow normal range. Ditto blood sugar, liver enzymes, serum cholesterol level. But steady blood counts dont mean that the same blood cells hang out forever. Bone marrow stem cells continually pump out blood cell progenitors as the older specialized cells die off. Natural systems change over time, with fluctuations large and small.

Climate always has and always will change.

We can learn about normal blood circulationby studying off-kilter situations leukemia, infection, anemia without fear of being labeled a denier. Its not only a scientifically inappropriate term, but one that is offensive to some, with its echoes of the Holocaust.

Im interested in other times deep, geologic time, not the presidents simplistic reference to the next century when the climate warmed at the rate that it is doing so now. How long did the warming escalate and persist? What forces or events might have precipitated warming? What factors accompanied its ultimate reversal as ice ages neared? By asking questions we can learn what we can expect from nature, so that perhaps we can better understand what we can do to counter the warming trend.

And so those who claim to believe in climate change and vilify those who ask questions might learn a lesson in what science actually is from the elegant discussion of wolf origins.

(Mini book review: for a compelling look at a fictional U.S. embroiled in a second civil war circa 2074-2095 that erupts over fossil fuel use, when Florida is a sea and much of humanity has fled underwater coastal cities for the former midwest, read American War, by Omar El Akkad. I am a voracious reader of dystopian fiction, and this book is hauntingly terrific.)

Read more here:

Wolf Evolution and Settled Science - PLoS Blogs (blog)