Evolution as a web (Introduction)
by David Turell 
, Tuesday, April 05, 2022, 19:24 (961 days ago)
The latest interrelationships show a web, not a bush:
https://aeon.co/essays/why-evolution-is-not-a-tree-of-life-but-a-fuzzy-network
"The hypothesis of reticulate evolution is that species are not as isolated from each other as Haeckel’s branching trees propose. Instead, species both diverge and merge together. The tree of life doesn’t look like a tree so much as the reticulated pattern of a python’s skin.
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"Veron argues that today’s corals are a product of Darwin’s classical natural selection when currents are slack, and of hybridisation when they are strong. Species separate and merge, and more so over long expanses of time and space. That’s why it was so hard for Veron to nail down what a ‘species’ is across an area as big as the Pacific Ocean.
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"Since Veron’s eureka moment, genetic tools have become more widespread and sophisticated. Does data support the hypothesis that species don’t just separate, they also merge? The answer is a resounding yes.
"It’s not just rare freaks or accidents, it’s happening all the time. And in quite divergent species too,’ said Nielsen. Roving genes have been found in every branch of the tree of life where geneticists have looked. Today, the technical terms for the process of genes moving between populations are introgression or admixture.
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"‘I think that process of splitting up and merging back together again, and getting a bit of DNA from here to there, that’s happening all the time, in all of the tree of life,’ Nielsen said. ‘And it’s really changing how we’re thinking about it, that it really is a network of life, not a tree of life.’
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"‘The reality is that a single tree to represent the entire species isn’t possible,’ Kirkpatrick told me. ‘Different pieces of DNA have different gene trees, and you just can’t represent all of that in a single diagram.’
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"...Cui, Schumer and their colleagues analysed 160 different genes in 24 different species, and built trees for each gene. Then, they overlaid all 160 gene-trees on top of each other. The branches of the gene trees flowed together and apart. Where they separated, genes meandered from one species to another.
"‘Look at that. They’re all fuzzy because they don’t agree because of hybridisation,’ Kirkpatrick said. ‘So that’s a visualisation of, I think, what [Veron] was struggling with.’
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Re-envisioning evolutionary trees as fuzzy networks raises another question: if genes rove so much, why do we see species at all? Why don’t species just lump together like so many paint pigments into a genomic version of brown?
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"Bateson surmised that if multiple genes could work together to influence a trait, it was just as likely they could not work together too. Such genetic incompatibilities would compromise hybrid health.
"While the idea is easy enough to think about theoretically, it’s tough to find practically. That’s largely because the evidence – an unviable individual – won’t have much of a presence. But recently geneticists have begun to discover gene incompatibilities that look like they keep species from merging together.
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"What we do know is that the tree of life is much more complicated and twisty than we believed it to be just a generation ago.
"I imagine having the chance to speak to my students again. I would place Haeckel’s tree on the screen and tell them that it is an anachronism. I would explain how species are not isolated on the ends of branches, that there are many more interconnections and opportunities for innovation. I would say that only by recognising its inherent fuzziness can we begin to understand evolution more clearly."
Comment: a very new view. Hybridization and gene transfer are very active processes. Humans are an interconnected part of the web at its endpoint. Let's hope dhw doesn't try to slice it up.
Evolution as a process: ancient DNA found two mya
by David Turell , Wednesday, December 07, 2022, 19:10 (715 days ago) @ David Turell
In Greenland:
https://www.newscientist.com/article/2350324-dna-from-2-million-years-ago-is-the-oldest...
"DNA from 2 million years ago recovered from sediments in Greenland is the oldest preserved DNA found to date, blowing past the previous benchmark of 1 million years set in 2021.
“The age of the DNA is twice as old approximately compared to what has been retrieved previously,” says Eske Willerslev at the University of Cambridge.
"The DNA comes from a host of different organisms, enabling Willerslev and his colleagues to reconstruct the ecosystem that existed in northern Greenland 2 million years ago, at a time when the climate was warmer than it is today. Today, the area is Arctic desert and has few organisms, but back then it was a forest inhabited by hares, reindeer and perhaps even mastodons, elephant-like animals that once lived in North America.
"The find suggests that it will be possible to uncover DNA from much more ancient time periods than previously suspected. “I wouldn’t be surprised if it turned out that in the north [the Arctic], we could go twice as far back in time,” says Willerslev.
"He and his team obtained ancient DNA from the Kap København Formation, a series of layers of sand, silt and mud more than 90 metres thick in total. These were laid down 2 million years ago.
"The DNA didn’t come from fossilised organisms, but was instead bound to mineral particles in the sediment layers. This helped preserve the DNA, because enzymes couldn’t get to it to break it down, says team member Karina Sand at the University of Copenhagen in Denmark. (my bold)
"This environmental DNA came from the whole range of organisms living in the area. The team detected 102 genera of plants. Some still grow in northern Greenland today, like the shrubs Dryas and Vaccinium. But others no longer live there, like spruce (Picea) trees, hawthorn (Crataegus) and Populus flowers. “It is, in fact, a forest,” says Willerslev.
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"If free-floating DNA can survive this long by binding to mineral particles in cold conditions, it suggests there is truly ancient DNA to be found, says Laura Parducci at Sapienza University of Rome in Italy, who wasn’t involved in the research."
Comment: our ingenuity is reaching back into time. My bold again demonstrates life's molecules can only work with other of life's molecules
Evolution as a process: current adaptability brings stasis
by David Turell , Wednesday, January 24, 2024, 22:07 (302 days ago) @ David Turell
A study showing adaptability is stabilized:
https://www.scientificamerican.com/article/living-fossil-lizards-are-constantly-evolvin...
"Scientists have long wondered how these species withstand the pressures of natural selection. The prevailing hypothesis for this “stasis paradox” has been that natural selection keeps some species unchanged by selecting for moderate or average traits (so-called stabilizing selection) rather than selecting for more extreme traits that would cause a species to change (directional selection). But a study published in the Proceedings of the National Academy of Sciences USA contradicts this idea, showing that evolution constantly favors different traits in seemingly unchanging animals that improve short-term survival. In the long term, though, “all that evolution cancels out and leads to no change,” says the study's lead author, James Stroud, a biologist at the Georgia Institute of Technology.
"Stroud and his colleagues studied four anole lizard species, all relatively unchanged for 20 million years, living on a small island in Florida's Fairchild Tropical Botanic Garden. The researchers captured members of these populations every six months for three years... Stroud expected to observe stabilizing selection at work preserving moderate traits. Instead he saw clearer evidence of directional selection: some lizards with unique traits, such as stickier toes, survived better in the short term.
"In each generation, though, the “best” traits changed—for instance, long legs aided survival in some years and short legs in others. The direction and strength of selection fluctuated so much that sometimes there was no clear pattern. Such changes are probably happening “back and forth on a micro scale with no net directional change,” says Rosemary Grant, a Princeton University evolutionary biologist, who has studied stabilizing selection in Darwin's finches." (my bold)
Comment: "Because the new study shows that natural selection favored extreme traits from year to year rather than moderate ones, its results don't support the theory of stabilizing selection. Instead they offer “a good explanation for why we see what we think is stabilizing selection,” says Tadashi Fukami, an ecologist studying evolution at Stanford University. Many new traits are evolving in the short term, but they don't provide a crucial advantage over the long term. In other words, species in stasis may simply have found the best possible combination of traits for lasting success in their environment."
https://mail.google.com/mail/u/0/#inbox/FMfcgzGwJvfPTvJKWQWBWxFDZgrNHLrS
My comment: This is playing word games. The species is static, just adapting back and forth to a changing environment. Calling it stabilized selection simply tries to fit it into Darwin theory. Also presented here: Tuesday, January 02, 2024, 18:16
Evolution as a process: constant convergence
by David Turell , Friday, March 01, 2024, 19:04 (265 days ago) @ David Turell
Chitons demonstrate it:
https://www.quantamagazine.org/mollusk-eyes-reveal-how-future-evolution-depends-on-the-...
"A new paper published today in Science describes a rare and important test case... which is fundamental to understanding how evolution and development interact. A team of researchers at the University of California, Santa Barbara happened upon it while studying the evolution of vision in an obscure group of mollusks called chitons. In that group of animals, the researchers discovered that two types of eyes — eyespots and shell eyes — each evolved twice independently. A given lineage could evolve one type of eye or the other, but never both.
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"Chitons, small mollusks that live on intertidal rocks and in the deep sea, are like little tanks protected by eight shell plates — a body plan that’s remained relatively stable for some 300 million years. Far from being inert armor, these shell plates are heavily decorated with sensory organs that enable the chitons to detect possible threats. (my bold)
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“'Independently, chitons evolved eyes — and, through them, what we think is likely something like spatial vision — four times, which is really impressive,” Varney said. “They also evolved that incredibly quickly.” The researchers estimated that in the neotropical genus Chiton, for example, the eyespots evolved within just 7 million years — a blink of an eye in evolutionary time. (my bold)
"Varney saw that twice, independently, lineages with 14 or more slits in the head plate evolved eyespots. And twice, independently, lineages with 10 or fewer slits evolved shell eyes. She realized that the number of slits locked into place which kind of eye type could evolve: A chiton with thousands of eyespots needs more slits, whereas a chiton with hundreds of shell eyes needs fewer. In short, the number of shell slits determined the evolution of the creatures’ visual systems."
Comment: an ancient organism develops eyes by itself. This is what is called convergence, that is, the same organ appearing in many new places in evolution independently. It is as if the organisms reach into a box for a readymade tool and grab it. If that is the case, how did that naturally occur? A chance event is highly improbable as it requires many hundreds of new integrated mutations. This is where Simon Conway Morris, quite an authority, steps in and offers a designer.