Study of ancient dog DNA traces canine diversity to the Ice Age

A global study of ancient dog DNA, led by scientists at the Francis Crick Institute, University of Oxford, University of Vienna and archaeologists from more than 10 countries, presents evidence that there were different types of dogs more than 11,000 years ago in the period immediately following the Ice Age.

Veretye dog image [Credit: E.E. Antipina]

In their study, published in Science, the research team sequenced ancient DNA from 27 dogs, some of which lived up to nearly 11,000 years ago, across Europe, the Near East and Siberia. They found that by this point in history, just after the Ice Age and before any other animal had been domesticated, there were already at least five different types of dog with distinct genetic ancestries.

This finding reveals that the diversity observed between dogs in different parts of the world today originated when all humans were still hunters and gatherers.

Pontus Skoglund, author and group leader of the Crick's Ancient Genomics laboratory, says: "Some of the variation you see between dogs walking down the street today originated in the Ice Age. By the end of this period, dogs were already widespread across the northern hemisphere."

This study of ancient genomics involves extracting and analysing DNA from skeletal material. It provides a window into the past, allowing researchers to uncover evolutionary changes that occurred many thousands of years ago.

The team showed that over the last 10,000 years, these early dog lineages mixed and moved to give rise to the dogs we know today. For example, early European dogs were initially diverse, appearing to originate from two highly distinct populations, one related to Near Eastern dogs and another to Siberian dogs. However, at some point this diversity was lost, as it is not present in European dogs today.

Anders Bergström, lead author and post-doctoral researcher in the Ancient Genomics laboratory at the Crick, says: "If we look back more than four or five thousand years ago, we can see that Europe was a very diverse place when it came to dogs. Although the European dogs we see today come in such an extraordinary array of shapes and forms, genetically they derive from only a very narrow subset of the diversity that used to exist."

The researchers also compared the evolution in dog history to changes in human evolution, lifestyles and migrations. In many cases comparable changes took place, likely reflecting how humans would bring their dogs with them as they migrated across the world.

But there are also cases when human and dog histories do not mirror each other. For example, the loss of diversity that existed in dogs in early Europe was caused by the spread of a single dog ancestry that replaced other populations. This dramatic event is not mirrored in human populations, and it remains to be determined what caused this turnover in European dog ancestry. 

Greger Larson, author and Director of the Palaeogenomics and Bio-Archaeology Research Network at the University of Oxford, says: "Dogs are our oldest and closest animal partner. Using DNA from ancient dogs is showing us just how far back our shared history goes and will ultimately help us understand when and where this deep relationship began."

Ron Pinhasi, author and group leader at the University of Vienna, says: "Just as ancient DNA has revolutionised the study of our own ancestors, it's now starting to do the same for dogs and other domesticated animals. Studying our animal companions adds another layer to our understanding of human history."

While this study provides major new insights into the early history of dog populations and their relationships with humans and each other, many questions still remain. In particular, research teams are still trying to uncover where and in which human cultural context, dogs were first domesticated.

Source: The Francis Crick Institute [October 29, 2020]

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The order of life

At first glance, a pack of wolves has little to do with a vinaigrette. However, a team led by Ramin Golestanian, Director at the Max Planck Institute for Dynamics and Self-Organization, has developed a model that establishes a link between the movement of predators and prey and the segregation of vinegar and oil. They expanded a theoretical framework that until now was only valid for inanimate matter. In addition to predators and prey, other living systems such as enzymes or self-organizing cells can now be described.

Particles of two types (red and green) interact with each other. While particles of the same type
inevitably experience reciprocal attraction or repulsion, particles of different types can interact
 non-reciprocally. Here the green particles chase the red particles. On a large scale, the highly
compressed bands of the green particles chase the bands of the red particles. This creates
order and movement in the system [Credit: MPIDS/Novak, Saha,
Agudo-Canalejo, Golestania]

Order is not always apparent at first glance. If you ran with a pack of wolves hunting deer, the movements would appear disordered. However, if the hunt is observed from a bird's eye view and over a longer period of time, patterns become apparent in the movement of the animals. In physics, such behaviour is considered orderly. But how does this order emerge? 

The Department of "Living Matter Physics" of Ramin Golestanian is dedicated to this question and investigates the physical rules that govern motion in living or active systems. Golestanian's aim is to reveal universal characteristics of active, living matter. This includes not only larger organisms such as predators and prey but also bacteria, enzymes and motor proteins as well as artificial systems such as micro-robots. "When we describe a group of such active systems over great distances and long periods of time, the specific details of the systems lose importance. Their overall distribution in space ultimately becomes the decisive characteristic", explains Golestanian.

From inanimate to living system

His team in Gottingen has recently made a breakthrough in describing living matter. To achieve this, Suropriya Saha, Jaime Agudo-Canalejo, and Ramin Golestanian started with the well-known description of the behaviour of inanimate matter and expanded it. The main point was to take into account the fundamental difference between living and inanimate matter. In contrast to inanimate, passive matter, living, active matter can move on its own. Physicists use the Cahn-Hilliard equation to describe how inanimate mixtures such as an emulsion of oil and water separate.

The characterization developed in the 1950s is considered the standard model of phase separation. It is based on the principle of reciprocity: Tit for tat. Oil thus repels water in the same way as water repels oil. However, this is not always the case for living matter or active systems. A predator pursues its prey, while the prey tries to escape from the predator. Only recently has it been shown that there is non-reciprocal (i.e. active) behaviour even in the movement of the smallest systems such as enzymes. Enzymes can thus concentrate specifically in individual cell areas - something that is necessary for many biological processes. Following this discovery, the Gottingen researchers investigated how large accumulations of different enzymes behave. Would they mix together or form groups? Would new and unforeseen characteristics arise? With the aim of answering these questions, the research team set to work.

Suddenly waves appear

The first task was to modify the Cahn-Hilliard equation to include non-reciprocal interactions. Because the equation describes non-living systems, the reciprocity of passive interactions is deeply embedded in its structure. Thus, every process described by it ends in thermodynamic equilibrium. In other words, all participants ultimately enter a resting state. Life, however, takes place outside the thermodynamic equilibrium. This is because living systems do not remain at rest but rather use energy in order to achieve something (e.g. their own reproduction). Suropriya Saha and her colleagues take this behaviour into account by expanding the Cahn-Hilliard equation by a parameter that characterizes non-reciprocal activities. In this way, they can now also describe processes that differ from passive processes to any extent.

Saha and her colleagues used computer simulations to study the effects of the introduced modifications. "Surprisingly, even minimal non-reciprocity leads to radical deviations from the behaviour of passive systems", says Saha. For example, the researcher observed the formation of travelling waves in a mixture of two different types of particles. In this phenomenon, bands of one component chase the bands of the other component, thereby resulting in a pattern of moving stripes. In addition, complex lattices can form in particle mixtures in which small clusters of one component chase groups of the other component. With their work, the researchers hope to contribute to scientific progress in both physics and biology. For example, the new model can describe and predict the behaviour of different cells, bacteria, or enzymes. "We have taught an old dog new tricks with this model", says Golestanian. "Our research shows that physics contributes to our understanding of biology and that the challenges posed by studying living matter open up new avenues for fundamental research in physics."

The findings are published in Physical Review X.

Source: Max-Planck-Gesellschaft [October 29, 2020]

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Models for potential precursors of cells endure simulated early-Earth conditions

Membraneless compartments--models for a potential step in the early evolution of cells--have been shown to persist or form, disappear, and reform in predictable ways through multiple cycles of dehydration and rehydration. Such wet-dry cycles were likely common conditions during the early development of life on Earth and could be a driving force for reactions important for the evolution of life.

Membraneless compartments, called complex coacervates, which form micrometer-sized droplets
(center), are widely studied as models of protocells, a potential step in the evolution of life on
Earth. New research shows that the droplets behave as predicted by an experimentally derived
phase diagram (left) in response to a proposed early-Earth environmental process, the wet-dry
cycle as could be seen as small ponds or puddles evaporate and reform. The preference for
RNA molecules (fluorescently labeled red in the right panel) to accumulate inside the
droplets decreases as the solution dries [Credit: Hadi Fares, Penn State]

Understanding how the compartments--known as complex coacervates--respond to wet-dry cycling also informs current applications of the droplets, which are found in many household items, such as adhesives, cosmetics, fragrances, and food, and could be used in drug delivery systems. A paper describing the research, led by Penn State scientists, appears in the journal Nature Communications.

"Wet-dry cycling has gotten attention recently in attempts to produce molecules that could be the precursors to life, things like the building blocks of RNA, DNA, and proteins," said Hadi Fares, a NASA Postdoctoral Program Fellow at Penn State and the first author of the paper. "We are looking into a possible step further in the evolution of life. If these building blocks form compartments--the precursors of cells--what happens if they undergo the same type of wet-dry cycling?"

The researchers make membraneless compartments, which form through liquid-liquid phase separation in a manner akin to oil droplets forming as a salad dressing separates, by controlling the concentrations of reagents in a solution. When the conditions--pH, temperature, salt and polymer concentrations--are right, droplets form that contain higher concentrations of the polymers than the surrounding solution. Like oil drops in water, there is no physical barrier or membrane that separates the droplets from their surroundings.

Dehydrating the solution, like what could happen during dry periods on a pre-life Earth where small ponds or puddles might regularly dry up, changes all of these factors. The researchers, therefore, wanted to know what would happen to the membraneless compartments in their experimental system if they recreated these wet-dry cycles.

"We first mapped out how the compartments form when we alter the concentrations of the polymers and the salt," said Fares. "This 'phase diagram' is experimentally determined and represents the physical chemistry of the system. So, we know whether or not droplets will form for different concentrations of polymers and salt. We can then start with a solution with concentrations at any point on this phase diagram and see what happens when we dehydrate the sample."

If the researchers start with a solution with concentrations that favor the formation of droplets, dehydration can change the concentrations such that the droplets disappear. The droplets then reappear when the sample is rehydrated. They can also start with a solution in which no droplets form and dehydration could bring the concentrations into the range that droplets begin to form. The behavior of the droplets during dehydration and rehydration match the predictions based on the experimentally derived phase diagram and they continue to do so through several iterations of the wet-dry cycle.

As mixtures of membraneless compartments, called complex coacervates, are dried, the concentrations
 of all components increase as the total volume decreases. The preference of an added RNA molecule
 to locate within the coacervate droplets decreases with drying while its mobility increases. These
results emphasize the importance of carefully considering the environment in studies of
membraneless coacervate compartments as models of protocells in the early
evolution of life on Earth [Credit: Hadi Fares, Penn State]

Next, the researchers addressed the ability of droplets to incorporate RNA molecules inside of the membraneless compartments. The "RNA world" hypothesis suggests that RNA may have played an important role in the early evolution of life on Earth and previous experimental work has shown that RNA in these solutions becomes concentrated inside of the droplets.

"As we dry droplets that contain RNA, the overall concentration of RNA in the solution increases but the concentration of RNA inside the droplets remains fairly stable," said Fares. "The preference of RNA molecules to be inside the droplets seems to decrease. We believe that this is because as they dry the composition inside the droplets is changing to look more like the composition outside the droplets."

The research team also looked at the ability of RNA to move into and within the droplets during dehydration. As they dry the sample the movement of RNA into and out of the droplets increases massively, but movement within the droplets increases only modestly. This difference in RNA mobility could have implications for the exchange of RNA among droplets during dehydration, which could in turn be functionally important in protocells.

"What we are showing is that as the membraneless compartments dry, they are able to preserve, at least to some extent, their internal environment," said Fares. "Importantly, the behavior of the coacervates, or protocells, whether they persist or disappear and reappear through the wet-dry cycle, is predicable from the physical chemistry of the system. We can therefore use this model system to think about the chemistry that might have been important for the early evolution of life."

Beyond early life scenarios, the research has implications much closer to home.

"People underestimate how important coacervates are beyond their role as a model for protocells," said Christine Keating, Distinguished Professor of Chemistry at Penn State and leader of the research team. "Many of the things that you have in your house that appear cloudy have coacervates in them. Any time you want to compartmentalize something, whether it's for drug delivery, a fragrance, a nutrient, or food product, coacervates may be involved. Understanding something new about the physical chemistry of the process of droplet formation will be important for all of these things."

Author: Sam Sholtis | Source: Pennsylvania State University [October 28, 2020]

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Scientists discover new organic compounds that could have helped form the first cells

Chemists studying how life started often focus on how modern biopolymers like peptides and nucleic acids contributed, but modern biopolymers don't form easily without help from living organisms. A possible solution to this paradox is that life started using different components, and many non-biological chemicals were likely abundant in the environment. A new survey conducted by an international team of chemists from the Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology and other institutes from Malaysia, the Czech Republic, the US and India, has found that a diverse set of such compounds easily form polymers under primitive environmental conditions, and some even spontaneously form cell-like structures.

A new study by scholars based at the Earth-Life Science Institute at Tokyo Institute
of Technology showed that non-biological chemicals produce polymers
and cell-like structures under primitive Earth-like settings
[Credit: Kuhan Chandru]

Understanding how life started on Earth is one of the most challenging questions modern science attempts to explain. Scientists presently study modern organisms and try to see what aspects of their biochemistry are universal, and thus were probably present in the organisms from which they descended. The best guess is that life has thrived on Earth for at least 3.5 billion of Earth's 4.5 billion year history since the planet formed, and most scientists would say life likely began before there is good evidence for its existence. Problematically, since Earth's surface is dynamic, the earliest traces of life on Earth have not been preserved in the geological record. However, the earliest evidence for life on Earth tells us little about what the earliest organisms were made of, or what was going on inside their cells. "There is clearly a lot left to learn from prebiotic chemistry about how life may have arisen," says the study's co-author Jim Cleaves.

A hallmark of life is evolution, and the mechanisms of evolution suggest that common traits can suddenly be displaced by rare and novel mutations which allow mutant organisms to survive better and proliferate, often replacing previously common organisms very rapidly. Paleontological, ecological and laboratory evidence suggests this occurs commonly and quickly. One example is an invasive organism like the dandelion, which was introduced to the Americas from Europe and is now a common weed causing lawn-concerned homeowners to spend countless hours of effort and dollars to eradicate. 

Another less whimsical example is COVID-19, a virus (technically not living, but technically an organism) which was probably confined to a small population of bats for years, but suddenly spread among humans around the world. Organisms which reproduce faster than their competitors, even only slightly faster, quickly send their competitors to what Leon Trotsky termed the "ash heap of history." As most organisms which have ever existed are extinct, co-author Tony Z. Jia suggests that "to understand how modern biology emerged, it is important to study plausible non-biological chemistries or structures not currently present in modern biology which potentially went extinct as life complexified."

This idea of evolutionary replacement is pushed to an extreme when scientists try to understand the origins of life. All modern organisms have a few core commonalities: all life is cellular, life uses DNA as an information storage molecule, and uses DNA to make ribonucleic RNA as an intermediary way to make proteins. Proteins perform most of the catalysis in modern biochemistry, and they are created using a very nearly universal "code" to make them from RNA. How this code came to be is in itself enigmatic, but these deep questions point to their possibly having been a very murky period in early biological evolution ~ 4 billion years ago during which almost none of the molecular features observed in modern biochemistry were present, and few if any of the ones that were present have been carried forward.

Drying, followed by rehydration, of a glycolide/glycine mixed monomer solution results in polymers
which self-assemble into macromolecular aggregates, as observed by light microscopy
[Credit: Jim Cleaves, ELSI]

Proteins are linear polymers of amino acids. These floppy strings of polymerised amino acids fold into unique three-dimensional shapes, forming extremely efficient catalysts which foster precise chemical reactions. In principle, many types of polymerised molecules could form similar strings and fold to form similar catalytic shapes, and synthetic chemists have already discovered many examples. "The point of this kind of study is finding functional polymers in plausibly prebiotic systems without the assistance of biology, including grad students," says co-author Irena Mamajanov.

Scientists have found many ways to make biological organic compounds without the intervention of biology, and these mechanisms help explain these compounds' presence in samples like carbonaceous meteorites, which are relics of the early solar system, and which scientists don't think ever hosted life. These primordial meteorite samples also contain many other types of molecules which could have formed complex folded polymers like proteins, which could have helped steer primitive chemistry. 

Proteins, by virtue of their folding and catalysis mediate much of the complex biochemical evolution observed in living systems. The ELSI team reasoned that alternative polymers could have helped this occur before the coding between DNA and protein evolved. "Perhaps we cannot reverse-engineer the origin of life; it may be more productive to try and build it from scratch, and not necessarily using modern biomolecules. There were large reservoirs of non-biological chemicals that existed on the primeval Earth. How they helped in the formation of life-as-we-know-it is what we are interested in," says co-author Kuhan Chandru.

The ELSI team did something simple yet profound: they took a large set of structurally diverse small organic molecules which could plausibly be made by prebiotic processes and tried to see if they could form polymers when evaporated from dilute solution. To their surprise, they found many of the primitive compounds could, though they also found some of them decomposed rapidly. This simple criterion, whether a compound is able to be dried without decomposing, may have been one of the earliest evolutionary selection pressures for primordial molecules.

The team conducted one further simple test. They took these dried reactions, added water and looked at them under a microscope. To their surprise, some of the products of these reaction formed cell-sized compartments. That simple starting materials containing 10 to 20 atoms can be converted to self-organised cell-like aggregates containing millions of atoms provides startling insight into how simple chemistry may have led to complex chemistry bordering on the kind of complexity associated with living systems, while not using modern biochemicals.

"We didn't test every possible compound, but we tested a lot of possible compounds. The diversity of chemical behaviors we found was surprising, and suggests this kind of small-molecule to functional-aggregate behavior is a common feature of organic chemistry, which may make the origin of life a more common phenomenon than previously thought," concludes co-author Niraja Bapat.

The findings are published in Scientific Reports.

Source: Tokyo Institute of Technology [October 28, 2020]

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Answer to Darwin's question

How do new species arise, and how quickly does this happen? Evolutionary biologist Professor Axel Meyer from the University of Konstanz and his team have come one decisive step closer to answering fundamental questions in biology. Upon evaluation of an extensive data set collected during extensive research on extremely young species of cichlids in crater lakes in Nicaragua, empirical evidence suggests that the evolutionary divergence of a population in the same geographical area into a new species is more likely to occur when many genes across the genome are involved in producing species-distinguishing characteristics. 

Credit: Ad Konings

And, what is more, new species can emerge within only a few hundred years This contradicts the hitherto established theory that speciation is a slow process and that ecologically important interspecies differences with simple, genetically locally limited architecture are more likely to result in the formation of a new species than those on a so-called polygenic basis are. Ultimately, it is about the question that Darwin already asked: What is a species, and how and why do new species arise? The results of this large-scale multidisciplinary study have been published in Nature.

Which genes and how many of them are involved in speciation?

In genetics, the question of emergence of new species translates into: What is the pattern of changes in the genome that leads to the emergence of new species? What happens genetically during the continuum from initially no differences within a population up to the completed speciation of reproductively separate species? Since his doctoral thesis in the 1980s at the University of California, in Berkeley, USA, and since the end of the 1990s at the University of Konstanz, Axel Meyer has been researching the question of which and how many genes or genetic loci - i.e. regions on the genome - are involved in the development of adaptations and new species. 

Here, the focus is on the study of very young species of cichlids, often only a few hundred generations old, living in crater lakes in Nicaragua. Although all these fishes descended from the same older original populations in the two large lakes of Nicaragua, Lake Managua and Lake Nicaragua, there are fish populations or even small species complexes of several species in each of the crater lakes that live exclusively in the respective lake, with specific phenotypic differences that are sometimes found in very similar fashion in several lakes, i.e. seem to have developed independently several times.

Multiple phenotypes in the same crater lake There are fishes with pronounced lips and such without lips, gold-coloured and black-and-white fishes, fishes that differ from others by having particularly slender bodies or certain delicate or robust tooth shapes. These phenotypes originated within the crater lakes, thus in the same geographical area ("sympatric speciation"), without external barriers such as rivers or mountains favouring this by limiting gene flow by gene exchange through reproduction. This is, thus, no "allopatric speciation".

The variations regarding the lips, colour, body and tooth shape of the fishes are genetically rooted in the original population, as Axel Meyer and his team (especially Dr Andreas Kautt, Dr Claudius Kratochwil and Dr Alexander Nater) were able to show after analysing complete genomes of a total of almost 500 fishes from each of the small lakes. 

Thus, these represent not independently originated new mutations, but rather the sorting out and selective choosing of the same original gene variants, which have re-assorted themselves in the individual lakes. Previously, it was unclear whether these are new species that have individually evolved through adaptation to new ecological conditions. In fact, the phenotypically different populations in the lakes also prefer to mate among themselves.

Many genes have a large effect

For Ernst Mayr - known by his contemporaries as the "Darwin of the 20th century" who helped to develop the biological species concept - this would be an indication that this is a species in its own right. (Mayr, who was Axel Meyer's mentor from Harvard University, was awarded an honorary doctorate by the University of Konstanz in 1994 before passing away in 2005). However, the new results of genome sequencing suggest otherwise. 

After the sequencing of more than 450 piscine genomes, crossbreeding experiments and genome-wide association (GWA), it was found that the conspicuous differences, such as lip size and colour, in the genomes of these populations are determined by only one or two locally very limited genome regions via Mendelian inheritance. Fish with the same type of lips or colour reproduce almost exclusively with each other. These genes did not lead to genome-wide genetic differences as would be expected between species. In contrast, surprisingly, the other sympatric species with the phenotypically far less conspicuous differences in body shape and special tooth shape showed much greater genome-wide genetic differences.

This means that many genes at many positions in the genome each make a small contribution to genetic differentiation with the effects effectively adding up over the entire genome and leading to the emergence of new species. The number of mutations in the entire genome between these young species is ten times higher than in the physically very different polymorphisms of the large-lipped or golden versus black and white striped fishes, for example, that do not represent unique species. The combined effect of many genes thus has a stronger effect on the development of new species. 

"This is not what we expected. It also contradicts large parts of the theory according to which individual loci with a great effect on the appearance of species, such as pronounced lips or colouration, should cause new species to develop more quickly," said Axel Meyer. And, it is especially surprising here, where the loci impact both the ecology and the choice of partners. "At least according to the criterion of the average difference in the entire genome, fishes with such conspicuous phenotypical differences are nevertheless not different species, but are at the level of mere polymorphisms (diversity) on the speciation continuum."

Crater lakes constitute a natural experiment

The geographical situation makes the crater lakes studied a "natural experiment". The original fish populations originate from two much older neighbouring lakes, to which there is no connection. This chain of crater lakes has been colonised by the fish populations independently of each other. When and how specimens from the original population got into each of the seven smaller lakes can only be calculated by simulation. 

It took place, however, somewhere between just a few hundred and a few thousand generations ago, and there were not very many fish that colonised the crater lakes. The emergence of new species can thus, as demonstrated here, take place much faster than previously thought. Meyer compares the lakes with Petri dishes, all inoculated with the same initial genetic situation, which evolve independently over generations: "There are very few systems in the world, such as the Galapagos Islands or the crater lakes in Nicaragua, that are a natural experiment for evolutionary research."

Source: University of Konstanz [October 28, 2020]

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Yeast study yields insights into longstanding evolution debate

In the past two decades, researchers have shown that biological traits in both species and individual cells can be shaped by the environment and inherited even without gene mutations, an outcome that contradicts one of the classical interpretations of Darwinian theory. But exactly how these epigenetic, or non-genetic, traits are inherited has been unclear.

Charles Darwin and Jean-Baptiste Lamarck
[Credit: Yale University]

Now, in a study published in the journal Cell Reports, Yale scientists show how epigenetic mechanisms contribute in real time to the evolution of a gene network in yeast. Specifically, through multiple generations yeast cells were found to pass on changes in gene activity induced by researchers.

The finding helps shed light on a longstanding question in evolutionary biology; scientists have long debated whether organisms can pass on traits acquired during a lifetime.

"Do genetic mutations have to be the sole facilitator of gene network evolution or can epigenetic mechanisms also lead to stable and heritable gene expression states maintained generation after generation?" asked Yale's Murat Acar, associate professor of molecular, cellular & developmental biology, a faculty member at the Yale Systems Biology Institute, and senior author of the paper.

During much of the last half of the 20th century, biology students were taught that mutations of genes that helped species adapt to the environment were passed on through generations, eventually leading to tremendous diversity of life. However, this theory had a problem: advantageous mutations are rare, and it would take many generations for physiological changes caused by the mutation to take root in a population of any given species.

Scientists in the last century have found that certain regions of DNA do not code for genes but regulate gene activity in the face of environmental change. The concept of passing on stable gene expression states to offspring resurrected the once widely discredited theories of 18th century French scientist Jean-Baptiste Lamarck, who first proposed inheritance of traits acquired during a lifetime.

For the new study, Acar lab graduate students and co-first authors Xinyue Luo and Ruijie Song wanted to investigate the role of epigenetic inheritance in the evolution of gene network activity in individual yeast cells, which reproduce asexually about every 100 minutes. As their experimental model, they investigated a gene network known as the galactose utilization network, which regulates use of the sugar-like molecule galactose, in the yeast. Through daily cell-sorting, they segregated the cells that had lowest levels of gene expression in the population and grew these cells in the same environment over a period of seven days.

Ultimately, they found expression level reductions persisted for several days and multiple generations of reproduction after the 7-day segregation period. Genetic causes alone could not explain the expression reduction; inheritance of epigenetic factors contributed to the observed change, the Yale team found.

Acar said the findings show a clear Lamarckian epigenetic contribution to gene network evolution and the classic Darwinian interpretation of evolution alone cannot explain our observations. "The findings support the idea that both genetic and epigenetic mechanisms need to be combined in a 'grand unified theory of evolution,'" he said.

Author: Bill Hathaway | Source: Yale University [October 27, 2020]

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Timeline of early eukaryotic evolution unveiled

One of the most important and puzzling events in the evolution of life has been the origin of the first complex eukaryotic cells. Almost all lifeforms that we can perceive with the naked eye, such as algae, plants, animals and fungi, are made up of complex cells known as 'eukaryotes'. A collaborative study between the groups of Toni Gabaldon, ICREA researcher at the Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Supercomputing Center (BSC-CNS), and Berend Snel at the University of Utrecht, has concluded that the first cell to incorporate a mitochondrion (considered the key step to the increased complexity of eukaryotic cells) already presented eukaryote-like complexity in structure and functions. This scenario serves as a bridge between the signs of complexity observed in some archaeal genomes and the proposed role of mitochondria in triggering eukaryogenesis.

Timeline of early eukaryotic evolution unveiled the mitochondrial acquisition occurred
in a scenario of increasing complexity [Credit: Utrecht University, IRB Barcelona]

"The acquisition of mitochondria was considered either to be the crucial first step or the last step in the development of eukaryotic cell complexity," explains Gabaldon, "our findings show that it was indeed a crucial event, but that it happened in a scenario where cell complexity had already increased."

Complexity as a prelude to the diversity of life

For roughly the first half of the history of life on Earth, the only forms of life were the relatively simple cells of bacteria. "Eukaryotic cells are larger, contain more DNA and are made up of compartments, each with their own task," explains first author Julian Vosseberg. "In that sense, you could compare bacterial cells with a tent, while eukaryotic cells are more like houses with several rooms."

How and when organisms traded the tent for a house is still a mystery, as there are no intermediate forms. One important moment in evolution was the origin of mitochondria, a component of eukaryotic cells that function as their 'power plants'. Mitochondria were once free-living bacteria, but during evolution, they were absorbed by the ancestors of today's eukaryotic cells. As gene duplication probably drove the increase in cell complexity, the researchers attempted to reconstruct the evolutionary events based on these genetic changes.

Bioinformatics for evolutionary path reconstruction

"We can use the DNA of contemporary species to reconstruct evolutionary events. Our genes were formed over aeons of evolution. They have changed dramatically over that time, but they still hold echoes of a distant past." Vosseberg adds, "We have a vast quantity of genetic material available, from a variety of organisms, and we can use computers to reconstruct the evolution of thousands of genes, including ancient gene duplications. These reconstructions have enabled us to uncover the timing of important intermediate steps."

The co-corresponding author, Berend Snel, from the University of Utrecht, says, "Scientists did not have a timeline of these events. But now we've managed to reconstruct a rough timeline." To achieve this, the researchers adapted an existing method developed at Gabaldon's lab to create a new protocol, which has resulted in novel insights. These indicate that a lot of complex cellular machinery had evolved even before the symbiosis with mitochondria, including the development of transport within the cell and the cytoskeleton. "The symbiosis wasn't an event that served as the catalyst for everything else. We observed a peak in gene duplications much earlier in time, indicating that cell complexity had already increased before that moment," says Snel.

"Our study suggests that the ancestral host that acquired the mitochondrial endosymbiont had already developed some complexity in terms of a dynamic cytoskeleton and membrane trafficking" says Gabaldon "this might have favoured the establishment of symbiotic associations with other microorganisms, including the mitochondrial ancestor, which eventually became integrated".

Source: Institute for Research in Biomedicine (IRB Barcelona) [October 26, 2020]

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Tracking the Himalayan history from the evolution of hundreds of frogs, lizards and snakes

The Himalaya are among the youngest and highest mountains in the world, but the exact timing of their uplift and origins of their biodiversity are still in debate. Generally, there are two hypotheses about the uplift process of the Himalaya. The "Stepwise Hypothesis" states that the Himalaya rose slowly from 1000-2500 m during 56-23 million years ago (Ma), before an additional rapid uplift to 4000 m during 23-19 Ma, and a final rise to the current average elevations (~5000 m) at around 15 Ma. Alternatively, recent hydrological and thermal evidences support that this region was probably not elevated to current elevation till mid-Pliocene ("Late Orogeny Hypothesis").

The Himalaya and representative amphibians and reptiles
[Credit: Science China Press]

Time-based records of biological processes can be informative about montane histories and environmental changes. Various hypotheses about Himalayan origins can be tested using phylogenetic information and estimates of the timing of biological speciation events. To address the question about the timing of the Himalaya uplift, we carried out field work across the Himalaya to collect samples of amphibians and reptiles. The Himalayan region encompasses multiple countries and has many access challenges, so sampling across the entire region is difficult, which has inhibited integrative studies of the origin of the Himalayan biota.

Combining 14 time-calibrated phylogenies of Himalayan-associated amphibian and reptile families involving 85 genera and 1628 species, we estimated times of divergence among 183 species that occur in the Himalaya. We identified 230 biogeographic events related to the Himalayan species. The dynamics of in situ diversification and dispersal rates remained essentially parallel across the Cenozoic. Both the in situ diversification rate, as well as the dispersal rate into the Himalaya, fit the Stepwise Hypothesis for the origin of this mountain range. In contrast, our estimates of origination and peak diversification are not consistent with the late-uplift hypothesis.

Biotic assembly through time of herpetofauna in the Himalaya. (a): The rates of in situ diversification
 and dispersal of the Himalayan herpetofauna through time (smoothed across 5 Ma windows).
Dispersal indicates "dispersal into the Himalaya." MDivE = maximal number of observed
 in situ diversification events per Ma. MDisE = maximal number of observed dispersal events
per Ma. Ambiguous events are separately listed. (b): Dispersal events from adjacent regions
 into the Himalaya (smoothed across 5 Ma windows). MDisE = maximal number
of observed dispersal events per Ma [Credit: Science China Press]

The rapid Himalayan uplift and associated intensified South Asia Monsoon not only promoted a pulse of uplift-driven in situ diversification, but also affected the rates of biotic interchange. Biotic interchange was restricted by the lack of a moist environment that is required by many reptiles and amphibians. In contrast, an expanded tropical forest belt is thought to have persisted between the Himalaya and Southeast Asia since the middle Miocene, which likely accounts for the high dispersal rates between these two regions.

This work has important implications about the assembly process of Himalayan herpetofauna and its conservation. Our analyses show a deep-rooted origin of Himalayan herpetofauna originating in the Paleocene, but with rapid diversification in the Miocene.

The study is published in the National Science Review 2020.

Source: South China Press [October 26, 2020]

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