The Great London:
Evolution

Mammals immortalise their genes through eggs and sperm to ensure future generations inherit good quality mitochondria to power the body's cells, according to new UCL research.

Before now, it was not known why mammals rely on dedicated sex cells that are formed early in development (a germline) to make offspring whereas plants and other simple animals, such as corals and sponges, use sex cells produced later in life from normal body tissues.

In a new study, published today in >PLOS Biology and funded by Natural Environment Research Council, Engineering & Physical Sciences Research Council and the Leverhulme Trust, UCL scientists developed an evolutionary model to investigate how these differences evolved over time and discovered that the germline in mammals developed in response to selection on mitochondria (the powerhouses of cells).

First author and UCL PhD student, Arunas Radzvilavicius, said: "There have been many theories about why mammals have a specialised germline when plants and other ancient animals don't. Some suggest it was due to complexity of tissues or a selfish conflict between cells. The distinction between sex cells and normal body tissues seems to be necessary for the evolution of very complex specialised tissues like brain.

"Surprisingly, we found that these aren't the reason. Rather, it's about the number of genetic mutations in mitochondrial DNA over time, which differs between organisms, and the variation between cells caused by the mitochondria being randomly partitioned into daughter cells at each division."

In plants, mitochondrial mutations creep in slowly, so a germline isn't needed as mutations are corrected by natural selection. Mitochondrial variation is maximised by forming the next generation from the same cells used to make normal tissue cells. When the cells divide to form new daughter cells, some receive more mutant mitochondria than others and these cells are then removed through natural selection, preserving the reproductive cells containing higher quality mitochondria.

In mammals, genetic errors in mitochondria accumulate more quickly due to our higher metabolic rate so using cells that have undergone lots of division cycles would be a liability. Mitochondria are therefore only passed along to the next generation through a dedicated female germline in the form of large eggs. This protects against errors being introduced as eggs undergo many fewer replication cycles than cells in other tissues such as the gut, skin and blood.

The germline ensures that the best quality mitochondria are transferred but restricts the genetic variation in the next generation of cells in the developing embryo. This is corrected for by mammals generating far too many egg cells which are removed during development. For example, humans are born with over 6 million egg-precursor cells, 90% of which are culled by the start of puberty in a mysterious process called atresia.

Senior author, Dr Nick Lane (UCL CoMPLEX and Genetics, Evolution & Environment) added: "We think the rise in mitochondrial mutation rate likely occurred in the Cambrian explosion 550 million years ago when oxygen levels rose. This was the first appearance of motile animals in the fossil record, things like trilobites that had eyes and armour plating - predators and prey. By moving around they used their mitochondria more and that increased the mutation rate. So to avoid these mutations accumulating they needed to have fewer rounds of cell division, and that meant sequestering a specialized germline."

Co-author, Professor Andrew Pomiankowski (UCL Genetics, Evolution & Environment), concluded: "Without a germline, animals with complex development and brains could not exist. Scientists have long tried to explain the evolution of the germline in terms of complexity. Who would have thought it arose from selection on mitochondrial genes? We hope our discovery will transform the way researchers understand animal development, reproduction and aging."

Source: University College London [December 20, 2016]

Placental mammals consist of three main groups that diverged rapidly, evolving in wildly different directions: Afrotheria (for example, elephants and tenrecs), Xenarthra (such as armadillos and sloths) and Boreoeutheria (all other placental mammals). The relationships between them have been a subject of fierce controversy with multiple studies coming to incompatible conclusions over the last decade leading some researchers to suggest that these relationships might be impossible to resolve.

There are thus many outstanding questions such as which is the oldest sibling of the three? Did the mammals go their separate ways due to South America and Africa breaking apart? And if not, when did placentals split up?

"This has been one of the areas of greatest debate in evolutionary biology, with many researchers considering it impossible to resolve," said lead author Dr Tarver of Bristol's School of Earth Sciences. "Now we've proven these problems can be solved -- you just need to analyse genome-scale datasets using models that accurately reflect genomic evolution."

The researchers assembled the largest mammalian phylogenomic dataset ever collected before testing it with a variety of models of molecular evolution, choosing the most robust model and then analysing the data using several supercomputer clusters at the University of Bristol and the University of Texas Advanced Computing Centre. "We tested it to destruction," said Dr Tarver. "We threw the kitchen sink at it."

"A complication in reconstructing evolutionary histories from genomic data is that different parts of genomes can and often do give conflicting accounts of the history," said Dr Siavash Mirarab at the University of California San Diego, USA. "Individual genes within the same species can have different histories. This is one reason why the controversy has stood so long -- many thought the relationships couldn't be resolved."

To address the complexities of analysing large numbers of genes shared among many species, the researchers paired two fundamentally different approaches -- concatenated and coalescent-based analyses -- to confirm the findings. When the dust settled, the team had a specific family tree showing that Atlantogenata (containing the sibling groups of African Afrotheria and the South American Xenarthra) is the sister group to all other placentals.

Because many conflicting family trees have already been published, the team then gathered three of the most influential rivals and tested them against each other with the same model. All of the previous studies suddenly fell into line, their data agreeing with Tarver and colleagues.

With the origins of the family tree resolved, what does this mean for placental mammals? The researchers folded in another layer -- a molecular clock analysis. "The molecular clock analysis uses a combination of fossils and genomic data to estimate when these lineages diverged from each other," said author Dr Mario Dos-Reis of Queen Mary London, UK. "The results show that the afrotherians and xenarthrens diverged from one another around 90 million years ago."

Previously, scientists thought that when Africa and South America separated from each other over 100 million years ago, they broke up the family of placental mammals, who went their separate evolutionary ways divided by geography. But the researchers found that placental mammals didn't split up until after Africa and South America had already separated.

"We propose that South America's living endemic Xenarthra (for exmaple, sloths, anteaters, and armadillos) colonized the island-continent via overwater dispersal," said study author Dr Rob Asher of the University of Cambridge, UK.

Dr Asher suggests that this isn't as difficult as you might think. Mammals are among the great adventurers of the animal kingdom, and at the time the proto-Atlantic was only a few hundred miles wide. We already know that New World monkeys crossed the Atlantic later, when it was much bigger, probably on rafts formed from storm debris. And, of course, mammals repeatedly colonised remote islands like Madagascar.

"You don't always need to overturn the status quo to make a big impact," said Dr Tarver. "All of the competing hypotheses had some evidence to support them -- that's precisely why it was the source of such controversy. Proving the roots of the placental family tree with hard empirical evidence is a massive accomplishment."

The findings are published in Genome Biology and Evolution journal.

Source: University of Bristol [February 15, 2016]

A new UCL study examines how the baculum (penis bone) evolved in mammals and explores its possible function in primates and carnivores—groups where many species have a baculum, but some do not.

The baculum has been described as "the most diverse of all bones", varying dramatically in length, width and shape in the male mammals where it is present.

The research, published today in the Royal Society journal >Proceedings of the Royal Society B, shows that the ancestral mammal, like humans, did not have a baculum - but both ancestral primates and carnivores did. The work uncovers that the baculum first evolved in mammals between 145 and 95 million years ago.

The study found that prolonged intromission - defined as penetration for longer than 3 minutes - was correlated with baculum presence across the course of primate evolution. Prolonged intromission was also found to predict a longer baculum in primates and carnivores.

High levels of postcopulatory sexual competition between males also predicted longer bacula in primates.

First author, Matilda Brindle (UCL Anthropology), said: "Our findings suggest that the baculum plays an important role in supporting male reproductive strategies in species where males face high levels of postcopulatory sexual competition. Prolonging intromission helps a male to guard a female from mating with any competitors, increasing his chances of passing on his genetic material."

The findings of the study may also provide clues as to why humans do not have a baculum.

When any cultural aspects of sex are removed and a male's aim is solely to ejaculate, humans have a short intromission duration.

In species where mating occurs between multiple males and multiple females (known as polygamy), there is acute competition between males to fertilise a female. However, human mating systems are not like this. Instead humans tend to be monogamous or, more rarely, polygynous (where one male mates with multiple females). In these circumstances, only one male has access to a female and postcopulatory competition between males is absent or very low level.

Brindle added: "Interestingly, humans have neither prolonged intromission durations, nor high levels of postcopulatory sexual competition. Given the results of our study, this may help to unravel the mystery of why the baculum was lost in the human lineage."

Chimpanzees and bonobos, humans' closest relatives, have very small bacula (between about 6-8mm) and short intromission durations (around 7 seconds for chimpanzees and 15 seconds for bonobos). However, they are characterised by polygamous mating systems, so they experience high levels of postcopulatory competition between males. The researchers suggest that this may be why these species have retained a baculum - albeit a small one.

Co-author, Dr Kit Opie (UCL Anthropology), commented: "After the human lineage split from chimpanzees and bonobos and our mating system shifted towards monogamy, probably after 2mya, the evolutionary pressures retaining the baculum likely disappeared. This may have been the final nail in the coffin for the already diminished baculum, which was then lost in ancestral humans."

Source: University College London [December 14, 2016]

It took 100 million years for oxygen levels in the oceans and atmosphere to increase to the level that allowed the explosion of animal life on Earth about 600 million years ago, according to a UCL-led study funded by the Natural Environment Research Council.

Before now it was not known how quickly Earth's oceans and atmosphere became oxygenated and if animal life expanded before or after oxygen levels rose. The new study, published today in Nature Communications, shows the increase began significantly earlier than previously thought and occurred in fits and starts spread over a vast period. It is therefore likely that early animal evolution was kick-started by increased amounts of oxygen, rather than a change in animal behaviour leading to oxygenation.

Lead researcher, Dr Philip Pogge von Strandmann (UCL Earth Sciences), said: "We want to find out how the evolution of life links to the evolution of our climate. The question on how strongly life has actively modified Earth's climate, and why the Earth has been habitable for so long is extremely important for understanding both the climate system, and why life is on Earth in the first place."

Researchers from UCL, Birkbeck, Bristol University, University of Washington, University of Leeds, Utah State University and University of Southern Denmark tracked what was happening with oxygen levels globally 770 - 520 million years ago (Ma) using new tracers in rocks across the US, Canada and China.

Samples of rocks that were laid down under the sea at different times were taken from different locations to piece together the global picture of the oxygen levels of Earth's oceans and atmosphere. By measuring selenium isotopes in the rocks, the team revealed that it took 100 million years for the amount of oxygen in the atmosphere to climb from less than 1% to over 10% of today's current level. This was arguably the most significant oxygenation event in Earth history because it ushered in an age of animal life that continues to this day.

Dr Pogge von Strandmann, said: "We took a new approach by using selenium isotope tracers to analyse marine shales which gave us more information about the gradual changes in oxygen levels than is possible using the more conventional techniques used previously. We were surprised to see how long it took Earth to produce oxygen and our findings dispel theories that it was a quick process caused by a change in animal behaviour."

During the period studied, three big 'snowball Earth' glaciations - Sturtian (~716Ma), Marinoan (~635Ma) and Gaskiers (~580Ma) - occurred whereby the Earth's land was covered in ice and most of the oceans were frozen from the poles to the tropics. During these periods, temperatures plummeted and rose again, causing glacial melting and an influx of nutrients into the ocean, which researchers think caused oxygen levels to rise deep in the oceans.

Increased nutrients means more ocean plankton, which will bury organic carbon in seafloor sediments when they die. Burying carbon results in oxygen increasing, dramatically changing conditions on Earth. Until now, oxygenation was thought to have occurred after the relatively small Gaskiers glaciation melted. The findings from this study pushes it much earlier, to the Marinoan glaciation, after which animals began to flourish in the improved conditions, leading to the first big expansion of animal life.

Co-author Prof. David Catling (University of Washington Earth and Space Sciences), added: "Oxygen was like a slow fuse to the explosion of animal life. Around 635 Ma, enough oxygen probably existed to support tiny sponges. Then, after 580 Ma, strange creatures shaped like pizzas lived on a lightly oxygenated seafloor. Fifty million years later, vertebrate ancestors were gliding through oxygen-rich seawater. Tracking how oxygen increased is the first step towards understanding why it took so long. Ultimately, a grasp of geologic controls on oxygen levels can help us understand whether animal-like life might exist or not on Earth-like planets elsewhere."

Source: University College London [December 17, 2015]

Photosynthesis is the process by which plants, algae and cyanobacteria use the energy from the Sun to make sugar from water and carbon dioxide, releasing oxygen as a waste product. But a few groups of bacteria carry out a simpler form of photosynthesis that does not produce oxygen, which evolved first.

A new study by an Imperial researcher suggests that this more primitive form of photosynthesis evolved in much more ancient bacteria than scientists had imagined, more than 3.5 billion years ago.

Photosynthesis sustains life on Earth today by releasing oxygen into the atmosphere and providing energy for food chains. The rise of oxygen-producing photosynthesis allowed the evolution of complex life forms like animals and land plants around 2.4 billion years ago.

However, the first type of photosynthesis that evolved did not produce oxygen. It was known to have first evolved around 3.5-3.8 billion years ago, but until now, scientists thought that one of the groups of bacteria alive today that still uses this more primate photosynthesis was the first to evolve the ability.

But the new research reveals that a more ancient bacteria, that probably no longer exists today, was actually the first to evolve the simpler form of photosynthesis, and that this bacteria was an ancestor to most bacteria alive today.

"The picture that is starting to emerge is that during the first half of Earth's history the majority of life forms were probably capable of photosynthesis," said study author Dr Tanai Cardona, from the Department of Life Sciences at Imperial College London.

The more primitive form of photosynthesis is known as anoxygenic photosynthesis, which uses molecules such as hydrogen, hydrogen sulfide, or iron as fuel -- instead of water.

Traditionally, scientists had assumed that one of the groups of bacteria that still use anoxygenic photosynthesis today evolved the ability and then passed it on to other bacteria using horizontal gene transfer -- the process of donating an entire set of genes, in this case those required for photosynthesis, to unrelated organisms.

However, Dr Cardona created an evolutionary tree for the bacteria by analyzing the history of a protein essential for anoxygenic photosynthesis. Through this, he was able to uncover a much more ancient origin for photosynthesis.

Instead of one group of bacteria evolving the ability and transferring it to others, Dr Cardona's analysis reveals that anoxygenic photosynthesis evolved before most of the groups of bacteria alive today branched off and diversified. The results are published in the journal PLOS ONE.

"Pretty much every group of photosynthetic bacteria we know of has been suggested, at some point or another, to be the first innovators of photosynthesis," said Dr Cardona. "But this means that all these groups of bacteria would have to have branched off from each other before anoxygenic photosynthesis evolved, around 3.5 billion years ago.

"My analysis has instead shown that anoxygenic photosynthesis predates the diversification of bacteria into modern groups, so that they all should have been able to do it. In fact, the evolution of oxygneic photosynthesis probably led to the extinction of many groups of bacteria capable of anoxygenic photosynthesis, triggering the diversification of modern groups."

To find the origin of anoxygenic photosynthesis, Dr Cardona traced the evolution of BchF, a protein that is key in the biosynthesis of bacteriochlorophyll a, the main pigment employed in anoxygenic photosynthesis. The special characteristic of this protein is that it is exclusively found in anoxygenic photosynthetic bacteria and without it bacteriochlorophyll a cannot be made.

By comparing sequences of proteins and reconstructing an evolutionary tree for BchF, he discovered that it originated before most described groups of bacteria alive today.

Author: Hayley Dunning | Source: Imperial College London [March 15, 2016]

A relationship that has lasted for 100 million years is at serious risk of ending, due to the effects of environmental and climate change. A species of spiny crayfish native to Australia and the tiny flatworms that depend on them are both at risk of extinction, according to researchers from the UK and Australia.

Look closely into one of the cool, freshwater streams of eastern Australia and you might find a colourful mountain spiny crayfish, from the genus Euastacus. Look even closer and you could see small tentacled flatworms, called temnocephalans, each only a few millimetres long. Temnocephalans live as specialised symbionts on the surface of the crayfish, where they catch tiny food items, or inside the crayfish's gill chamber where they can remove parasites. This is an ancient partnership, but the temnocephalans are now at risk of coextinction with their endangered hosts. Coextinction is the loss of one species, when another that it depends upon goes extinct.

In a new study, researchers from the UK and Australia reconstructed the evolutionary and ecological history of the mountain spiny crayfish and their temnocephalan symbionts to assess their coextinction risk. This study was based on DNA sequences from crayfish and temnocephalans across eastern Australia, sampled by researchers at James Cook University, sequenced at the Natural History Museum, London and Queensland Museum, and analysed at the University of Sydney and the University of Cambridge. The results are published in the >Proceedings of the Royal Society B.

"We've now got a picture of how these two species have evolved together through time," said Dr Jennifer Hoyal Cuthill from Cambridge's Department of Earth Sciences, the paper's lead author. "The extinction risk to the crayfish has been measured, but this is the first time we've quantified the risk to the temnocephalans as well -- and it looks like this ancient partnership could end with the extinction of both species."

Mountain spiny crayfish species diversified across eastern Australia over at least 80 million years, with 37 living species included in this study. Reconstructing the ages of the temnocephalans using a 'molecular clock' analysis showed that the tiny worms are as ancient as their crayfish hosts and have evolved alongside them since the Cretaceous Period.

>A symbiotic relationship that has existed since the time of the dinosaurs is at risk of ending,> as habitat loss and environmental change mean that a species of Australian crayfish >and the tiny worms that depend on them are both at serious risk of extinction >[Credit: David Blair/James Cook University]
Today, many species of mountain spiny crayfish have small geographic ranges. This is especially true in Queensland, where mountain spiny crayfish are restricted to cool, high-altitude streams in small pockets of rainforest. This habitat was reduced and fragmented by long-term climate warming and drying, as the continent of Australia drifted northwards over the last 165 million years. As a consequence, mountain spiny crayfish are severely threatened by ongoing climate change and the International Union for the Conservation of Nature (IUCN) has assessed 75% of these species as endangered or critically endangered.

"In Australia, freshwater crayfish are large, diverse and active 'managers', recycling all sorts of organic material and working the sediments," said Professor David Blair of James Cook University in Australia, the paper's senior author. "The temnocephalan worms associated only with these crayfish are also diverse, reflecting a long, shared history and offering a unique window on ancient symbioses. We now risk extinction of many of these partnerships, which will lead to degradation of their previous habitats and leave science the poorer."

The crayfish tend to have the smallest ranges in the north of Australia, where the climate is the hottest and all of the northern species are endangered or critically endangered. By studying the phylogenies (evolutionary trees) of the species, the researchers found that northern crayfish also tended to be the most evolutionarily distinctive. This also applies to the temnocephalans of genus Temnosewellia, which are symbionts of spiny mountain crayfish across their geographic range. "This means that the most evolutionarily distinctive lineages are also those most at risk of extinction," said Hoyal Cuthill.

The researchers then used computer simulations to predict the extent of coextinction. This showed that if all the mountain spiny crayfish that are currently endangered were to go extinct, 60% of their temnocephalan symbionts would also be lost to coextinction. The temnocephalan lineages that were predicted to be at the greatest risk of coextinction also tended to be the most evolutionarily distinctive. These lineages represent a long history of symbiosis and coevolution of up to 100 million years. However they are the most likely to suffer coextinction if these species and their habitats are not protected from ongoing environmental and climate change.

"The intimate relationship between hosts and their symbionts and parasites is often unique and long lived, not just during the lifespan of the individual organisms themselves but during the evolutionary history of the species involved in the association," said study co-author Dr Tim Littlewood of the Natural History Museum. "This study exemplifies how understanding and untangling such an intimate relationship across space and time can yield deep insights into past climates and environments, as well as highlighting current threats to biodiversity."

Source: University of Cambridge [May 24, 2016]

Hot vents on the seabed could have spontaneously produced the organic molecules necessary for life, according to new research by UCL chemists. The study shows how the surfaces of mineral particles inside hydrothermal vents have similar chemical properties to enzymes, the biological molecules that govern chemical reactions in living organisms. This means that vents are able to create simple carbon-based molecules, such as methanol and formic acid, out of the dissolved CO2 in the water.

The discovery, published in the journal Chemical Communications, explains how some of the key building blocks for organic chemistry were already being formed in nature before life emerged - and may have played a role in the emergence of the first life forms. It also has potential practical applications, showing how products such as plastics and fuels could be synthesised from CO2 rather than oil.

"There is a lot of speculation that hydrothermal vents could be the location where life on Earth began," says Nora de Leeuw, who heads the team. "There is a lot of CO2 dissolved in the water, which could provide the carbon that the chemistry of living organisms is based on, and there is plenty of energy, because the water is hot and turbulent. What our research proves is that these vents also have the chemical properties that encourage these molecules to recombine into molecules usually associated with living organisms."

The team combined laboratory experiments with supercomputer simulations to investigate the conditions under which the mineral particles would catalyse the conversion of CO2 into organic molecules. The experiments replicated the conditions present in deep sea vents, where hot and slightly alkaline water rich in dissolved CO2 passes over the mineral greigite (Fe3S4), located on the inside surfaces of the vents. These experiments hinted at the chemical processes that were underway. The simulations, which were run on UCL's Legion supercomputer and HECToR (the UK national supercomputing service), provided a molecule-by-molecule view of how the CO2 and greigite interacted, helping to make sense of what was being observed in the experiments. The computing power and programming expertise to accurately simulate the behaviour of individual molecules in this way has only become available in the past decade.

"We found that the surfaces and crystal structures inside these vents act as catalysts, encouraging chemical changes in the material that settles on them," says Nathan Hollingsworth, a co-author of the study. "They behave much like enzymes do in living organisms, breaking down the bonds between carbon and oxygen atoms. This lets them combine with water to produce formic acid, acetic acid, methanol and pyruvic acid. Once you have simple carbon-based chemicals such as these, it opens the door to more complex carbon-based chemistry."

Theories about the emergence of life suggest that increasingly complex carbon-based chemistry led to self-replicating molecules - and, eventually, the appearance of the first cellular life forms. This research shows how one of the first steps in this journey may have occurred. It is proof that simple organic molecules can be synthesised in nature without living organisms being present. It also confirms that hydrothermal vents are a plausible location for at least part of this process to have occurred.

The study could also have a practical applications, as it provides a method for creating carbon-based chemicals out of CO2, without the need for extreme heat or pressure. This could, in the long term, replace oil as the raw material for products such as plastics, fertilisers and fuels.

This study shows, albeit on a very small scale, that such products, which are currently produced from non-renewable raw materials, can be produced by more environmentally friendly means. If the process can be scaled up to commercially viable scales, it would not only save oil, but use up CO2 - a greenhouse gas - as a raw material.

Source: University College London [April 27, 2015]

The horticulturist who came up with the concept of ‘evolution by natural selection’ 27 years before Charles Darwin did should be more widely acknowledged for his contribution, states a new paper by a King’s College London geneticist.

The paper, published in the Biological Journal of the Linnean Society, argues that Patrick Matthew deserves to be considered alongside Charles Darwin and Alfred Russel Wallace as one of the three originators of the idea of large-scale evolution by natural selection.

Furthermore, Matthew’s version of evolution by natural section captures a valuable aspect of the theory that isn't so clear in Darwin's version – namely, that natural selection is a deductive certainty more akin to a ‘law’ than a hypothesis or theory to be tested.

Patrick Matthew (1790-1874) was a Scottish landowner with a keen interest in politics and agronomy.  He established extensive orchards of apples and pears on his estate at Gourdie Hill, Perthshire, and became adept in horticulture, silviculture and agriculture.

Whilst Darwin and Wallace’s 1858 paper to the Linnean Society, On the Origin of Species, secured their place in the history books, Matthews had set out similar ideas 27 years earlier in his book On Naval Timber and Arboriculture. The book, published in 1831, addressed best practices for the cultivation of trees for shipbuilding, but also expanded on his concept of natural selection.

“There is a law universal in nature, tending to render every reproductive being the best possibly suited to its condition that its kind, or that organized matter, is susceptible of, which appears intended to model the physical and mental or instinctive powers, to their highest perfection, and to continue them so. This law sustains the lion in his strength, the hare in her swiftness, and the fox in his wiles.”  (Matthew, 1831: 364)

In 1860, Matthew wrote to point out the parallels with his prior work, several months after the publication of On the origin of species.  Darwin publically wrote in 1860 “I freely acknowledge that Mr. Matthew has anticipated by many years the explanation which I have offered of the origin of species”, while Wallace wrote publically in 1879 of “how fully and clearly Mr. Matthew apprehended the theory of natural selection, as well as the existence of more obscure laws of evolution, many years in advance of Mr. Darwin and myself”, and further declared Matthew to be “one of the most original thinkers of the first half of the 19th century”.  However, both asserted their formulations were independent of Matthew’s.

Even if Matthew did not influence Darwin and Wallace, his writings provide a valuable third point of reference on the notion of macroevolution by natural selection, argues the paper’s author, Dr Michael Weale. Dr Weale has created a public website to act as an online repository of the writings by Patrick Matthew, including some of his lesser-known work.

Dr Michael Weale, from the Department of Medical and Molecular Genetics at King’s College London, said: ‘Whilst Darwin and Wallace both deserve recognition for their work, Matthew, the outsider who deduced his idea as part of a grand scheme of a purposeful universe, is the overlooked third man in the story. Matthew’s story is an object lesson in the perils of low-impact publishing. Despite its brevity, and to some extent because of it, Matthew’s work merits our renewed attention.’

Source: King's College London [April 20, 2015]

Scientists have developed the largest ever family tree of a major group of flowering plants called monocots, which could help protect their diversity.

Monocots account for a quarter of all flowering plants. They are among the most diverse and economically important plants on the planet, but their evolutionary lines have never been properly mapped. Monocots include staples such as corn, rice, wheat and barley; many tropical fruits such as pineapples and bananas; and other foods such as dates and sugarcane. Monocots such as grasses, bamboo, palms, and their derivations including fibres, are used as key building materials in many countries such as in China.

Now, researchers at Imperial College London have created the most up-to-date family tree or phylogenetic tree, which traces the lines of evolutionary descent of monocots. The researchers analysed DNA samples from across the globe, aiming to determine what factors affected the diversity of monocot species.

Their work could help scientists to conserve the biodiversity of monocots and lead to new types of uses for these plants, such as in the development of new medicines.

Professor Vincent Savolainen, study co-author from the Department of Life Sciences at Imperial College London, said: "Monocots are so important in our lives, providing us with essential food and building materials. Our study is not only the most detailed family tree of monocot species ever developed, it is also importantly helping us to understand what factors affect their diversity. This could lead to better methods for conserving and protecting them.

"It may also lead to new uses for them such as in medicines. Sometimes the best active compound to use in medicine is found in a different species to the one in which it was initially discovered. Therefore, testing close evolutionary relatives may reveal a slightly different molecule that has a stronger effect in combatting one particular disease."

As expected, the team in today's study found that biological factors - such as the way different monocots evolved to take advantage of their environment - played a part in their diversity. However, the researchers discovered that the most important factors in the diversity of monocots in any given region were geographical factors such as the habitat size, its latitude, and altitude.

In particular, they found that the size of the habitat accounted for a third of the species diversity. They suggest this is likely because a bigger habitat means that there are generally more resources and less competition, which enables more species to thrive together rather than compete against each other. They also found that species diversity was reduced at higher altitudes. This may be because temperatures are lower and there is less water available, which causes fiercer competition among monocots for fewer resources.

The researchers were also able to verify previous findings that monocot species are most varied around the equator, and that the closer monocots are to the poles, the fewer species are available. This might be due to higher UV radiation at the equator, causing more genetic mutations and species variation in equatorial regions as a result.

This research analyses 1,987 of the 2,713 types of monocot worldwide. Researchers in this field will now look to increase their sampling to ultimately encompass the roughly 400,000 plant species, to create the entire botanical 'tree of life'.

The study was published in >Botanical Journal of the Linnean Society.

Author: Caroline Brogan | Source: Imperial College London [November 09, 2016]

Species across the world are rapidly going extinct due to human activities, but humans are also causing rapid evolution and the emergence of new species. A new study published today summarises the causes of humanmade speciation, and discusses why newly evolved species cannot simply replace extinct wild species. The study was led by the Center for Macroecology, Evolution and Climate at the University of Copenhagen.

A growing number of examples show that humans not only contribute to the extinction of species but also drive evolution, and in some cases the emergence of entirely new species. This can take place through mechanisms such as accidental introductions, domestication of animals and crops, unnatural selection due to hunting, or the emergence of novel ecosystems such as the urban environment.

Although tempting to conclude that human activities thus benefit as well as deplete global biodiversity, the authors stress that extinct wild species cannot simply be replaced with newly evolved ones, and that nature conservation remains just as urgent.

"The prospect of 'artificially' gaining novel species through human activities is unlikely to elicit the feeling that it can offset losses of 'natural' species. Indeed, many people might find the prospect of an artificially biodiverse world just as daunting as an artificially impoverished one" says lead author and Postdoc Joseph Bull from the Center for Macroecology, Evolution and Climate at the University of Copenhagen.

The study which was carried out in collaboration with the University of Queensland was published in >Proceedings of Royal Society B. It highlights numerous examples of how human activities influence species' evolution. For instance: as the common house mosquito adapted to the environment of the underground railway system in London, it established a subterranean population. Now named the 'London Underground mosquito', it can no longer interbreed with its above ground counterpart and is effectively thought to be a new species.

"We also see examples of domestication resulting in new species. According to a recent study, at least six of the world's 40 most important agricultural crops are considered entirely new" explains Joseph Bull.

Furthermore, unnatural selection due to hunting can lead to new traits emerging in animals, which can eventually lead to new species, and deliberate or accidental relocation of species can lead to hybridization with other species. Due to the latter, more new plant species in Europe have appeared than are documented to have gone extinct over the last three centuries.

Although it is not possible to quantify exactly how many speciation events have been caused through human activities, the impact is potentially considerable, the study states.

"In this context, 'number of species' becomes a deeply unsatisfactory measure of conservation trends, because it does not reflect many important aspects of biodiversity. Achieving a neutral net outcome for species numbers cannot be considered acceptable if weighing wild fauna against relatively homogenous domesticated species. However, considering speciation alongside extinction may well prove important in developing a better understanding of our impact upon global biodiversity. We call for a discussion about what we, as a society, actually want to conserve about nature" says Associate Professor Martine Maron from the University of Queensland.

Researchers do agree that current extinction rates may soon lead to a 6th period of mass extinction. Since the last Ice Age, 11.500 years ago, it is estimated that 255 mammals and 523 bird species has gone extinct, often due to human activity. In the same period, humans have relocated almost 900 known species and domesticated more than 470 animals and close to 270 plant species.

Source: Faculty of Science - University of Copenhagen [June 28, 2016]

Scientists from Wageningen UR and other institutes are proposing a new research model - the turnover model - as a way of answering the question why there are always so many plant species in tropical rainforests.

In their publication in New Phytologist magazine, the Dutch, British and Swiss scientists show that major evolutionary changes, such as the origin of large groups of species, occur with a reasonably constant frequency while the origin of new species is an explosive process.

Various models

Darwin’s contemporary Alfred Russel Wallace already argued that the Tropics are, in essence, a museum of biodiversity. As tropical climates are stable, Wallace suggested that species would gradually increase in number over longer time periods, the so-called museum model. More recently, however, it was suggested that the Pleistocene ice ages, and the impact thereof on the climate in the Tropics, resulted in recent explosions of speciation, the so-called cradle model.

Both models are supported by previous research into patterns of diversification in tropical plants. This research is performed by means of reconstructed ‘phylogenetic trees’; genealogical trees that show the interrelated  descent of plant species. Where analyses of plant families focused on studying as many evolutionary lines as possible from the family, diversity was shown to increase gradually. For instance, the development of diversity in important tropical plant groups such as palm trees, the leguminous family and the soursop family, appear to follow the museum model. However, within these large plant families there are also plant genera that seem to follow the cradle model: so-called radiations in which many different species developed recently and over a short period of time.

Equatiing seems impossible

Equating these two models seems an impossible task. How can a large plant family that presents an explosive increase in the number of species diversify as an entire family following the museum model? The answer lies in analysing more species per family, and better modelling speciation over long periods in evolution via the computer.

Mahogany trees

Scientists from Wageningen UR, Kew (London) and Zürich compiled the largest amount of data so far for the Meliaceae , or mahogany family. This family mainly grows in the Tropics, and is known for valuable wood such as mahogany and Spanish cedar. Parts of the nuclear and chloroplast genome of approximately 35% of the species were sequenced; a technology in which all the building blocks of the DNA are mapped.

The analysis of evolutionary diversification showed that the diversity of larger groups, such as plant genera and families, does develop in accordance with the museum model, i.e., with a certain constant frequency in the origin of new branches. The scientists showed that, in addition to this ‘museum fundament’, the origin of individual species is an explosive process which occurs in accordance with the cradle model.

‘Young’ species

The research shows that the mahogany family developed approximately 68 million years ago. The circa 200 mahogany species that grow in the South American rainforests are largely the result of two explosions in speciation (radiations) that occurred independently in two evolutionary lines in the late Miocene epoch, which was less than 10 million years ago.

An interesting aspect of this explosive origin of large numbers of species within the mahogany family is that it involves two different groups within the family which independently evolved the same ecological adaptations, such as plant height and an adaptation of seeds to the same animal species that distribute them. In addition, the two groups show a similar speed of speciation. These abrupt increases in speciation speed occurred after the mahogany family had left its original habitat (tropical dry forests and seasonal forests) and colonised the rainforests, where they were faced with different climate conditions.

New model for evolution

The results of the study show that most mahogany species in the Tropics are relatively recent. It can be assumed that this also applies to other families. The authors propose a new model, the turnover model, in which the number of evolutionary lines increases with a more or less constant speed, while speciation occurs separately and in a more explosive way.

Source: Wageningen University [June 19, 2015]

The first eukaryote is thought to have arisen when simpler archaea and bacteria joined forces. But in an Opinion paper published in >Trends in Cell Biology, researchers propose that new genomic evidence derived from a deep-sea vent on the ocean floor suggests that the molecular machinery essential to eukaryotic life was probably borrowed, little by little over time, from those simpler ancestors.

"We are beginning to think of eukaryotic origins as a slow process of growing intimacy--the result of a long, slow dance between kingdoms, and not a quick tryst, which is the way it is portrayed in textbooks," says Mukund Thattai of the National Centre for Biological Sciences in India.

The eukaryotic cells of plants, animals, and protists are markedly different from those of their single-celled, prokaryotic relatives, the archaea and bacteria. Eukaryotic cells are much larger and have considerably more internal complexity, including many internal membrane-bound compartments.

Although scientists generally agree that eukaryotes can trace their ancestry to a merger between archaea and bacteria, there's been considerable disagreement about what the first eukaryote and its immediate ancestors must have looked like. As Thattai and his colleagues Buzz Baum and Gautam Dey of University College London explain in their paper, that uncertainty has stemmed in large part from the lack of known intermediates that bridge the gap in size and complexity between prokaryotic precursors and eukaryotes. As a result, they say, the origin of the first eukaryotic cell has remained "one of the most enduring mysteries in modern biology."

That began to change last year with the discovery of DNA sequences for an organism that no one has ever actually seen living near a deep-sea vent on the ocean floor. The genome of the archaeon known as Lokiarchaeum ('Loki' for short) contains more "eukaryotic signature proteins" (ESPs) than any other prokaryote. Importantly, among those ESPs are proteins (small Ras/Arf-type GTPases) critical for eukaryotes' ability to direct traffic amongst all those intercellular compartments.

The authors consider the available data to explore an essential question: what might the archaeal ancestor of all eukaryotes look like? "If we could turn back the clock and peer inside this cell, would its cellular organization have been like that of an archaeal cell or more eukaryote-like?" Dey says.

As the closest known archaeal relative of eukaryotes, Loki helps to answer that question. The researchers say that the ESPs found in Loki are unlikely to work in the same way they do in eukarytoes. That's because Loki doesn't appear to have enzymes required for ESP association with membranes or key building blocks of the membrane trafficking machinery.

"However," Baum says, "the genome can be seen as 'primed' for eukaryogenesis. With the acquisition of a number of key genes and lipids from a bacterial symbiont, it would be possible for Loki-type cells to evolve a primitive membrane trafficking machinery and compartmentalization."

The researchers predict that, when Loki is finally isolated or cultured, "it will look more like an archaeon than a proto-eukaryote and will not have internal compartments or a vesicle-trafficking network." But its morphology and/or cell cycle might have complexities more often associated with eukaryotes.

Baum and Dey say they now plan to explore the basic cell biology of the related archaea Sulfolobus acidocaldarius, first isolated from an acidic hot spring in Yellowstone National Park.

"We believe it will be very difficult to crack the mysteries of eukaryogenesis without first understanding the archaeal cell biology," Dey says. "We are currently developing tools in the lab to study the cell cycle and cellular morphology of Sulfolobus at the single-cell level under the microscope. We would also love to catch a glimpse of Loki."

Source: Cell Press [June 16, 2016]

In tropical climes, animals and plants aren't adapted to surviving freezing temperatures - and why would they be? It's never all that cold near the Equator, even at altitude. But in places like the Rocky Mountains, where temperatures can climb into the 100s and dip below freezing, species are hardier and more equipped to deal with such fluctuations.

These divergent climate tolerances play crucial roles in how species evolve. Colorado State University research offers new insight into this long-held understanding of species diversity.

A study led by CSU biologists shows that insect populations in the tropics exhibit a higher number of distinct species than in the Rockies. But the distinctions between those species consist of subtle, genetic differences that aren't readily visible. These are called cryptic species - by the looks of things identical, but actually genetically distinct.

The study supports a classic theory dating back to the 1960s. The saying goes that "mountain passes are higher in the tropics" - that is, tropical mountain passes are stronger barriers to the dispersal of organisms than temperate-zone passes of equivalent altitudes. That's indeed true, and the CSU researchers have now found that that species differentiation is more subtle - cryptic - than previously understood.

The study, published in >Proceedings of the Royal Society London B - Biological Sciences will be featured on the journal's printed cover. The lead author is Brian Gill, a graduate student co-advised by Chris Funk in the College of Natural Sciences' Department of Biology and Boris Kondratieff in the College of Agricultural Sciences' Department of Bioagricultural Sciences and Pest Management. Gill led a field team that traversed watersheds in the wilds of Colorado's Rocky Mountains and in the remote Ecuadorean Andes to collect and analyze thousands of mayflies at comparable elevations. Mayflies are common aquatic insects that play key roles in stream food webs and other ecological processes.

Comparing mayfly specimens between the Rockies and the Andes, the researchers identified higher species richness in Ecuador than in Colorado - a disparity rooted in high levels of cryptic tropical diversity. They used a genetic analysis called DNA barcoding to parse out these subtle species differences, which would not be apparent using standard taxonomy.

In fact, by standard taxonomic methods, it would appear that Colorado had a greater abundance of mayfly species. But the subtle, molecular-level differences unveiled by the DNA analyses tipped the scale well in favor of species richness for tropical mayflies.

"Since there is this high climatic zonation in the tropics and narrow thermal tolerances, there are more opportunities for populations to become divergent and isolated, which is what you need for speciation to happen," Gill explained. By comparison, temperate species and their tolerance to a wider range of conditions leads to more gene flow, which limits the number of distinct species that can evolve.

"We think our results can contribute to the discussion about species vulnerability and how it varies across the planet," Gill said.

The next step is to provide better support for latitudinal differences in physiology, and more insight into how species disperse. For those follow-up studies, the researchers will continue to work with collaborators at CSU, Cornell University, University of Nebraska Lincoln, Universidad San Francisco de Quito, and Universidad Tecnológica Indoamérica.

Source: Colorado State University [June 15, 2016]

A new study from researchers at Uppsala University shows that variation in genome size may be much more important than previously believed. It is clear that, at least sometimes, a large genome is a good genome.

'Our study shows that females with larger genome lay more eggs and males with larger genome fertilize more eggs', says research leader Goran Arnqvist, Professor of Animal Ecology at Uppsala University.

The amount of nuclear DNA per cell, or the size of the genome, varies by orders of magnitude across organisms. Our understanding of the evolutionary forces that are responsible for this variation is very limited. For unknown reasons, there are simple plants with a genome almost 50 times as large and grasshoppers with a genome 5 times as large as our own! In fact, the insects with the smallest and largest genomes differ by a factor of 200, yet they all look and act like typical insects.

Biological explanations for these dramatic differences come in two flavours:

The first suggests that variation in genome size is made up by "junk" DNA that has little bearing on organismal function and that random processes determine genome size.

The second instead suggests that the amount of DNA matters and that natural selection shapes genome size. The study of seed beetles now present evidence suggesting that natural selection may be more important.

The study is published in the scientific journal Proceedings of the Royal Society of London. Their results show that variation in genome size may be much more important than previously believed. It is clear that, at least sometimes, a large genome is a good genome.

Source: Uppsala University [September 14, 2015]

From skeletal remains found among ancient owl pellets, a team of scientists has recovered the first ancient DNA of the extinct West Indian mammal Nesophontes, meaning "island murder." They traced its evolutionary history back to the dawn of mammals 70 million years ago.

The authors, including Selina Brace, Jessica Thomas, Ian Barnes et al., published their findings in the advanced online edition of >Molecular Biology and Evolution.

The insect-eating creature existed in the Caribbean islands until the 16th century when, perhaps, they were outcompeted as the first Spanish ships arrived—-introducing rats as stowaways. "Nesophontes was just one of the dozens of mammals that went extinct in the Caribbean during recent times," said Professor Ian Barnes, Research Leader at London's Natural History Museum.

Scientists used a 750-year-old specimen to generate many thousands of base pairs of DNA sequence data. This allowed the research team to uncover its evolutionary origins and finally resolve the relationships between its closest relatives, the insectivores, a group including shrews, hedgehogs and moles. Phylogenetic and divergence time scenarios clearly demonstrate that Nesophontes is a deeply distinct sister group to another group of living native Caribbean insectivores, the solenodons. The time of the split between these two correlates with an era when the northern Caribbean was formed of volcanic islands, well before the origins of the islands we see today.

Obtaining DNA from tropical fossils is notoriously difficult, and the team made use of the latest developments in ancient DNA technology to conduct the study.

"Once we'd dealt with the tiny size of the bone samples, the highly degraded state of the DNA, and the lack of any similar genomes to compare to, the analysis was a piece of cake," said Natural History Museum scientist Dr. Selina Brace.

The findings will be of considerable interest for evolutionary biologists studying mammalian biogeography, and the significant role that humans may have played in a recent extinction.

Source: Oxford University Press [September 13, 2016]

Looking different to your parents can provide species with a way to escape evolutionary dead ends, according to new research from Queen Mary University of London (QMUL).

The work by researchers at the School of Biological and Chemical Sciences looked at polyploid hybrids in the genus Nicotiana, the group that includes tobacco.

Unlike humans, which are diploids -- with two copies of each of their 23 chromosomes (one from each parent), - polyploids can have three, four or more copies of each chromosome. This makes them particularly prone to producing hybrids and, - in contrast to better-known hybrids such as the mule which is (the sterile product of a cross between a male donkey and a female horse), means that crosses between polyploids are often fertile.

While hybrids might be expected to be a blend of the two parent species, the researchers found that they tended to have shorter and wider flower openings than both of the parent species which means that a wider range of pollinators can enter the flowers.

By allowing a wider range of insects to pollinate them, hybrids make themselves much less vulnerable to the extinction of a single pollinator.

Dr Elizabeth McCarthy, who carried out the work as part of her PhD at QMUL but who is now at University of California Riverside, said: "Some plants evolve increasingly specialised relationships with the species that pollinate them. A classic example is Darwin's Madagascan orchid, first discovered in 1798. Its exceptionally long nectar spur led Charles Darwin to propose that it was pollinated by a moth whose proboscis -- the organ that extracts the nectar -- was longer than that of any moth known at the time. Darwin's prediction was spectacularly verified 21 years after his death when just such a moth was discovered."

The problem with this sort of specialised relationship -- which we now term coevolution -- is that if one of the two species involved becomes extinct, the other is also doomed.

The findings are >published in Nature Plants.

Source: Queen Mary University of London [August 08, 2016]

An intriguing study involving walking stick insects led by the University of Sheffield in England and the University of Colorado Boulder shows how natural selection, the engine of evolution, can also impede the formation of new species.

The team studied a plant-eating stick insect species from California called Timema cristinae known for its cryptic camouflage that allows it to hide from hungry birds, said CU-Boulder Assistant Professor Samuel Flaxman. T. cristinae comes in several different types -- one is green and blends in with the broad green leaves of a particular shrub species, while a second green variant sports a white, vertical stripe that helps disguise it on a different species of shrub with narrow, needle-like leaves.

While Darwinian natural selection has begun pushing the two green forms of walking sticks down separate paths that could lead to the formation of two new species, the team found that a third melanistic, or brown variation of T. cristinae appears to be thwarting the process, said Flaxman. The brown version is known to successfully camouflage itself among the stems of both shrub species inhabited by its green brethren, he said.

Using field investigations, laboratory genetics, modern genome sequencing and computer simulations, the team concluded the brown version of T. cristinae is shuttling enough genes between the green stick insects living on different shrubs to prevent strong divergent adaptation and speciation. The brown variant of the walking stick species also is favored by natural selection because it has a slight advantage in mate selection and a stronger resistance to fungal infections than its green counterparts.

"This is one of the best demonstrations we know of regarding the counteractive effects of natural selection on speciation," said Flaxman of CU-Boulder's Department of Ecology and Evolutionary Biology, second author on the new study. "We show how the brown population essentially carries genes back and forth between the green populations, acting as a genetic bridge that causes a slowdown in divergence."

A paper on the subject appeared in a recent issue of the journal Current Biology. Other study co-authors were from the University of Sheffield, Royal Holloway University of London, Utah State University, the University of Nevada, Reno and the University of Lausanne in Switzerland.

"This movement of genes between environments slows down the genetic divergence of these stick insect populations, impeding the formation of new species," said Aaron Comeault, a former CU-Boulder graduate student and lead study author who conducted the research while at the University of Sheffield. Comeault is now a postdoctoral researcher at the University of North Carolina at Chapel Hill.

The new results underscore how combining natural history and cutting-edge genetics can help researchers gain a better understanding of how evolution operates in nature. It also shows how natural selection can sometimes promote but other times hinder the formation of new species, according to the research team.

Walking sticks are one of nature's oddest insect groups and range in size from the half-inch long T. cristinae to species in Borneo and Vietnam that are more than a foot long. Most walking sticks rely on plant mimicry to protect them from predators.

Source: University of Colorado at Boulder [August 06, 2015]