evolution

our-oldest-microbial-ancestors-were-way-ahead-of-their-time

Our oldest microbial ancestors were way ahead of their time

Biology, eukaryotes, evolution, paleontology, Science / /

Going Golgi —

Specialized internal structures were present over 1.5 billion years ago.

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computer generated image of membrane structures inside a cell

Enlarge / The Golgi apparatus, shown here in light green, may have been involved in building internal structures in cells.

ARTUR PLAWGO / SCIENCE PHOTO LIBRARY

Before Neanderthals and Denisovans, before vaguely humanoid primates, proto-mammals, or fish that crawled out of the ocean to become the first terrestrial animals, our earliest ancestors were microbes.

More complex organisms like ourselves descend from eukaryotes, which have a nuclear membrane around their DNA (as opposed to prokaryotes, which don’t). Eukaryotes were thought to have evolved a few billion years ago, during the late Palaeoproterozoic period, and started diversifying by around 800 million years ago. Their diversification was not well understood. Now, a team of researchers led by UC Santa Barbara paleontologist Leigh Ann Riedman discovered eukaryote microfossils that are 1.64 billion years old, yet had already diversified and had surprisingly sophisticated features.

“High levels of eukaryotic species richness and morphological disparity suggest that although late Palaeoproterozoic [fossils] preserve our oldest record of eukaryotes, the eukaryotic clade has a much deeper history,” Riedman and her team said in a study recently published in Papers in Paleontology.

Really, really, really old tricks

During the late Palaeoproterozoic, eukaryotes most likely evolved in the wake of several major changes on Earth, including a drastic increase in atmospheric oxygen and shifts in ocean chemistry. This could have been anywhere from 3 billion to 2.3 billion years ago. Riedman’s team explored the layers of sedimentary rock in the Limbunya region of Australia’s Birrindudu basin. The fossils they unearthed included a total of 26 taxa, as well as 10 species that had not been described before. One of them is Limbunyasphaera operculata, a species of the new genus Limbunyasphera.

What makes L. operculata so distinct is that it has a feature that appears to be evidence of a survival mechanism used by modern eukaryotes. There are some extant microbes that form a protective cyst so they can make it through harsh conditions. When things are more tolerable, they produce an enzyme that dissolves a part of the cyst wall into an opening, or pylome, that makes it possible for them to creep out. This opening also has a lid, or operculum. These were both observed in L. operculata.

While splits in fossilized single-cell organisms may be the result of taphonomic processes that break the cell wall, complex structures such as a pylome and operculum are not found in prokaryotic organisms, and therefore suggest that a species must be eukaryotic.

Didn’t know they could do that

Some of the previously known species of extinct eukaryotes also surprised the scientists with unexpectedly advanced features. Satka favosa had a vesicle in the cell that was enclosed by a membrane with platelike structures. Another species, Birrindudutuba brigandinia, also had plates identified around its vesicles, although none of its plates were as diverse in shape as those seen in different S. favosa individuals. Those plates came in a large variety of shapes and sizes, which could mean that what has been termed S. favosa is more than one species.

The plated vesicle of S. favosa is what led Riedman to determine that the species must have been eukaryotic, because the plates are possible indicators that Golgi bodies existed in these organisms. After the endoplasmic reticulum of a cell synthesizes proteins and lipids, Golgi bodies process and package those substances depending on where they have to go next. Riedman and her team think that Golgi or Golgi-like bodies transported materials within the cell to form plates around vesicles, such as the ones seen in S. favosa. The hypothetical Golgi bodies themselves are not thought to have had these plates.

This sort of complex sorting of cellular contents is a feature of all modern eukaryotes. “Taxa including Satka favosa… are considered [eukaryotes] because they have a complex, platy vesicle construction,” the researchers said in the study. These new fossils suggest that it arose pretty early in their history.

Eukaryotes have evidently been much more complex and diverse than we thought for hundreds of millions of years longer than we thought. There might be even older samples out there. While fossil evidence of eukaryotes from near their origin eludes us, samples upwards of a billion years old, such as those found by Riedman and her team, are telling us more than ever about their—and therefore our—evolution.

Papers in Paleontology, 2023.  DOI: 10.1002/spp2.1538

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big-evolutionary-change-tied-to-lots-of-small-differences

Big evolutionary change tied to lots of small differences

Biology, eggs, evolution, live birth, Science, snails / /

Cracking the eggs —

Lots of genes changed as a species of snail went from laying eggs to live births.

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Image of a dark, grey-black snail shell.

Enlarge / An example of a Littorina species, the common periwinkle.

The version of evolution proposed by Charles Darwin focused on slow, incremental changes that only gradually build into the sort of differences that separate species. But that doesn’t rule out the potential for sudden, dramatic changes. Indeed, some differences make it difficult to understand what a transitional state would look like, suggesting that a major leap might be needed.

A new study looks at one major transition: the shift from egg-laying to live births in a set of related snail species. By sequencing the genomes of multiple snails, the researchers identified the changes in DNA that are associated with egg-laying. It turns out that a large number of genes are associated with the change despite its dramatic nature.

Giving up eggs

The snails in question are in a genus called Littorina, which are largely distributed around the North Atlantic. Many of these species lay eggs, but a number of them have transitioned to live births. In these species, an organ that coats eggs with a protein-rich jelly in other species instead acts as an incubator, allowing eggs to develop until young snails can crawl out of their parent’s shells. This is thought to be an advantage for animals that would otherwise have to lay eggs in environments that aren’t favorable for their survival.

The egg laying species are so similar to their relatives that they were sometimes thought to just be a variant of an egg-laying species. All of which suggests that live birth has evolved relatively recently, giving us a good opportunity to understand the genetic changes that enabled it.

So, a large international team of researchers sequenced the genomes of over 100 individual snails, both egg-laying and live birth. The resulting data was used to analyze things like how closely related different species are, and what genetic changes are associated with live birth.

The results suggest that there are two separate clusters of species that reproduce through live births. Put differently, on an evolutionary tree of these snail species, there’s a branch full of egg-laying species separating two groups that give birth to live snails. Typically, this structure is viewed as an indication that live births evolved twice, once for each of the two clusters.

But that doesn’t seem to be the case here, for reasons that we’ll get into.

Lots of variations

Separately, the researchers looked for regions of the genome that are associated with giving live births. And they found lots of them—88 in total. These 88 regions were identified in both clusters of live-birth species, and the DNA sequences within them were very similar. This suggests that these regions had a single origin and were maintained in both these lineages.

One possibility to explain this is that a population of live-birth animals reverted to egg-laying at some point in their evolution. Alternatively, hybridization between egg-layers and live-birthers could have let these variations spread within an egg-laying population and ultimately re-enable live births when enough of them were present in individual animals, producing a separate live-birth lineage.

The 88 regions identified as underlying live births have very little genetic diversity, suggesting that a specific genetic variant in each region is so advantageous that it swept through the population, displacing all other versions of the stretch of DNA. They have, however, picked up some distinct variations that are rare outside the egg-laying populations—enough to allow the researchers to estimate the age when these pieces of DNA came under evolutionary selection.

The answer varies depending on which of the 88 segments you’re looking at, but it ranges from about 10,000 to 100,000 years ago. That range suggests that the genetic regions that enable live births were put together gradually over many years—exactly as the traditional view of evolution suggests.

The researchers acknowledge that at least some of these regions are likely to have evolved after live births were already the norm and simply improve the efficiency of the internal incubation. And there’s no way to know how many variants (or which) need to be present before live births are possible. However, the researchers now have an extensive list of genes to look into to understand things better.

Science, 2024. DOI: 10.1126/science.adi2982  (About DOIs).

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