Researchers sequence complete genomes of extinct and living elephants

An international team of researchers has produced one of the most comprehensive evolutionary pictures to date by looking at one of the world's most iconic animal families - namely elephants, and their relatives mammoths and mastodons-spanning millions of years.

Crushed dentine from a Woolly Mammoth for DNA extraction [Credit: JD Howell, McMaster University]

The team of scientists-which included researchers from McMaster, the Broad Institute of MIT and Harvard, Harvard Medical School, Uppsala University, and the University of Potsdam-meticulously sequenced 14 genomes from several species: both living and extinct species from Asia and Africa, two American mastodons, a 120,000-year-old straight-tusked elephant, and a Columbian mammoth.

The study, published in the Proceedings of the National Academy of Science, sheds light on what scientists call a very complicated history, characterized by widespread interbreeding. They caution, however, the behaviour has virtually stopped among living elephants, adding to growing fears about the future of the few species that remain on earth.

"Interbreeding may help explain why mammoths were so successful over such diverse environments and for such a long time, importantly this genomic data also tells us that biology is messy and that evolution doesn't happen in an organized, linear fashion," says evolutionary geneticist Hendrik Poinar, one of the senior authors on the paper and Director of the McMaster Ancient DNA Centre and principal investigator at the Michael G. DeGroote Institute for Infectious Research.

"The combined analysis of genome-wide data from all these ancient elephants and mastodons has raised the curtain on elephant population history, revealing complexity that we were simply not aware of before," he says.

Graduate student Emil Karpinski holds a tibial cross section from a Siberian Woolly Mammoth. This permafrost
preserved sample still contains fat entombed marrow [Credit: JD Howell, McMaster University]

A detailed DNA analysis of the ancient straight-tusked elephant, for example, showed that it was a hybrid with portions of its genetic makeup stemming from an ancient African elephant, the woolly mammoth and present-day forest elephants.

"This is one of the oldest high-quality genomes that currently exists for any species," said Michael Hofreiter at the University of Potsdam in Germany, a co-senior author who led the work on the straight-tusked elephant.

Researchers also found further evidence of interbreeding among the Columbian and woolly mammoths, which was first reported by Poinar and his team in 2011. Despite their vastly different habitats and sizes, researchers believe the woolly mammoths, encountered Columbians mammoths at the boundary of glacial and in the more temperate ecotones of North America.

Strikingly, scientists found no genetic evidence of interbreeding among two of the world's three remaining species, the forest and savanna elephants, suggesting they have lived in near-complete isolation for the past 500,000 years, despite living in neighbouring habitats.

These are African savanna elephants in the San Diego Zoo. In the middle is Swazi, the female elephant from
which the reference genome was sequenced [Credit: San Diego Zoo Global]

"There's been a simmering debate in the conservation communities about whether African savannah and forest elephants are two different species," said David Reich, another co-senior author at the Broad Institute who is also a professor at the Department of Genetics at Harvard Medical School (HMS) and a Howard Hughes Medical Institute Investigator. "Our data show that these two species have been isolated for long periods of time - making each worthy of independent conservation status."

Interbreeding among closely related mammals is fairly common, say researchers, who point to examples of brown and polar bears, Sumatran and Bornean orangutans, and the Eurasian gold jackal and grey wolves. A species can be defined as a group of similar animals that can successfully breed and produce fertile offspring.

"This paper, the product of a grand initiative we started more than a decade ago, is far more than just the formal report of the elephant genome. It will be a reference point for understanding how diverse elephants are related to each other and it will be a model for how similar studies can be done in other species groups," said co-senior author Kerstin Lindblad-Toh, a senior associate member of the Broad Institute and Director of the Science for Life Laboratory at Uppsala University in Sweden.

"The findings were extremely surprising to us," says Eleftheria Palkopoulou, a post-doctoral scientist in at HMS. "The elephant population relationships could not be explained by simple splits, providing clues for understanding the evolution of these iconic species."

Researchers suggest that future work should explore whether the introduction of new genetic lineages into elephant populations-both living and ancient-played an important role in their evolution, allowing them to adapt to new habitats and fluctuating climates.

Source: McMaster University [February 26, 2018]

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Geological change confirmed as a factor behind the extensive diversity in tropical rainforests

The tropical rainforests of Central and South America are home to the largest diversity of plants on this planet. Nowhere else are there quite so many different plant species in one place. However, the entire region is increasingly threatened by human activity, which is why researchers are stepping up their efforts to record this astonishing biodiversity and find out how it developed. In a project undertaken by Johannes Gutenberg University Mainz (JGU) in collaboration with Dutch research institutions, the causes of this plant diversity were investigated by studying two closely related groups of trees of the Annonaceae family.

Cremastosperma brevipes, French Guiana [Credit: Paul J. M. Maas]

The researchers identified three relevant factors: the formation of the Andes mountain range, the disappearance due to natural causes of the extensive Pebas wetlands system that once existed in the Amazon region, and the formation of a land bridge between Central and South America in the form of the Panama Isthmus.

Cremastosperma and Mosannona are two genera of the Annonaceae or custard apple family the habitat of which is neotropical rainforests, where they extend from the lowlands up to elevations of 2,000 meters. They are primarily found in the Andes region of South America, but also as far north as Central America.

Mosannona costaricensis, Costa Rica [Credit: Reinaldo Aguilar]

The team of botanists led by Dr. Michael Pirie, who joined JGU as a researcher in 2013, looked at the distributions of the various species of both genera and their phylogenetic history in order to determine the influence of the geological upheavals on the continent.

For this purpose they compiled a time-calibrated phylogenetic tree based on DNA data, using the so-called molecular clock technique which is calibrated using the ages of the available fossils. In total, they analyzed 11 species of the genus Mosannona and 24 species of the genus Cremastosperma.

Formation of the Andes, the Isthmus of Panama, and the drying-out of the Pebas wetland system all promoted diversification

The research has produced a biogeographical scenario that confirms in this context the significance of the geological history of north-western South America during the late Miocene and early Pliocene periods about 5 to 10 million years ago.

Cremastosperma yamayakatense, Peru [Credit: Michael Pirie]

"We have actually discovered that the diversification of these two plant genera took place in parallel with major geological events, namely the formation of the Andes, the drying-out of the Pebas system, and the development of a land bridge to Central America," explained Pirie. Cremastosperma species, for example, were able to spread into what is today the Amazon basin and diversify, once the wetlands had silted up due to the deposition of material from the rising Andes.

One way in which diversification can be stimulated is by migration into a new ecosystem while another is adaptation to new conditions. "Natural changes over longer periods provide plants with a chance to adapt," added Pirie. On the other hand, rapid changes, such as those that have occurred in the recent past, do not give plants sufficient time to evolve.

Cremastosperma leiophyllum, Bolivia [Credit: Lars W. Chatrou]

While the development of the two genera in line with geological conditions could be said to be more or less as might be expected, the biologists did find one clear difference between them. Although their distribution patterns mostly overlap, Cremastosperma species and Mosannona species to some extent dispersed along differing routes. In the case of Cremastosperma, colonization of an area in what is now Guyana began from north-western South America at a time before the last parts of the Andes developed and could form a barrier. Mosannona, on the other hand, began to spread here at a far later date from its base in the Amazon basin.

Taxonomic update to include five new species

Dr. Michael Pirie will be continuing his research work in 2018 with the aid of a grant from the Heisenberg Program of the German Research Foundation (DFG). This will also involve publication of an extensive monograph in which a total of 34 Cremastosperma species will be described, including five new species that Pirie and his colleagues have recently discovered.

The study is published on Royal Society Open Science.

Source: Universitat Mainz [Febraury 26, 2018]

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Why are there so many types of lizards?

Lizards have special superpowers. While birds can regrow feathers and mammals can regrow skin, lizards can regenerate entire structures such as their tails. Despite these differences, all have evolved from the same ancestor as lizards.

The Anolis auratus is one of several lizard species studied as part of new research comparing lizard genomes - their entire
DNA code - to those of other animals [Credit: Kenro Kusumi]

Spreading through the Americas, one lizard group, the anoles, evolved like Darwin's finches, adapting to different islands and different habitats on the mainland. Today there are more than 400 species.

Constructing a family tree for three lizard species collected in Panama at the Smithsonian Tropical Research Institute (STRI) and a fourth from the southeastern U.S., scientists at Arizona State University compared lizard genomes -- their entire DNA code -- to those of other animals.

The researchers discovered that changes in genes involved in the interbrain (the site of the pineal gland and other endocrine glands), for color vision, hormones and the colorful dewlap that males bob to attract females, may contribute to the formation of boundaries between species. Genes regulating limb development also evolved especially quickly.

"While some reptiles such as tortoises changed remarkably little over millions of years, anole lizards evolved quickly, generating a diversity of shapes and behaviors," said Kenro Kusumi, corresponding author and professor at ASU School of Life Sciences. "Now that sequencing entire genomes is cheaper and easier, we discovered molecular genetic evidence for rapid evolution that may account for striking differences between bodies of animals living in different environments."

Kusumi's lab, working with colleagues at the University of Arizona College of Medicine-Phoenix, is especially interested in how reptiles' genomes shape their ability to regenerate and to develop a diversity of body forms.

"This is the first time the complete genetic code -- the genome -- of any vertebrate species from Panama has been sequenced and analyzed," said Oris Sanjur, co-author and Associate Director for Science Administration at STRI. "Information from these three species is an important contribution to our understanding of biodiversity and the evolution of new species."

The Anolis apletophallus is one of several lizard species studied as part of new research comparing lizard genomes - their
entire DNA code - to those of other animals [Credit: Kenro Kusumi]

Scientists estimate that there are 40 species of anolid lizards living in Panama, compared to only one in the U.S. A team from ASU collected three species with permission from the Ministry of the Environment, MiAmbiente: the Central American giant anole, Anolis frenatus, lives high on tree trunks; the grass anole, A. auratus, perches on bushes or on grassy vegetation and the slender anole, A. apletophallus, found only in Panama, hangs out lower on tree trunks or on the ground.

Researchers at ASU's School of Life Sciences lined up the DNA sequences of the lizards with the DNA sequences of 31 other animals: the lobe-finned fish and the four-legged animal groups that evolved from them. They also took a careful look at genes that code for proteins: more than 22,000 genes in the green anole, A. carolinensis, versus approximately 20,000 identified each in A. auratus and A. frenatus and 13,000 in A. apletophallus.

One obvious explanation for a faster rate of evolution is the anole lizards' faster rate of reproduction. Anoles typically mate in their first year of life, while other reptiles take much longer to reach sexual maturity. They also breed with many other individuals so mutations that make it difficult for individuals to survive are eliminated fairly quickly.

The first and only other anole lizard to be sequenced previously was the green anole, A. carolinensis, the only anole species resident in the U.S. In that study from MIT, the A. carolinensis genome held evidence of more recent evolution and the loss of ancient repeated elements in the part of the DNA that does not code for proteins. In this sense, it was important to sequence the three Panamanian species, because the U.S. species may not be the most representative of the diverse anole group.

"For 15 years, an impressive amount of time and money poured into discovering the genomes of mammals, motivated by our drive to understand human evolution and to look for cures for disease. Even though the squamate reptiles include more than 10,000 species -- almost double the number of mammal species -- a single genome was not enough to understand the variability within this group," said the first author of the report, Marc Tollis, a post-doctoral fellow at ASU.

"By comparing these four anole lizard genomes, we're beginning to understand how one of the most diverse groups of vertebrates regenerate, develop and diversify," he added.

The study is published in Genome Biology and Evolution.

Source: Arizona State University [February 23, 2018]

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Playing both ends: Amphibian adapted to varied evolutionary pressures

Caecilians are serpent-like creatures, but they're not snakes or giant worms. The limbless amphibians, related to frogs and salamanders, favor tropical climates of Africa, Asia and the Americas. Most live in burrows of their own making; some are aquatic.

A limbless amphibian, known as Caecilian, Siphonops annulatus, widely distributed in Brazil. Scientists from Utah State
University in the United States and Brazil’s Butantan Institute report skin gland concentrations adapted
to different evolutionary pressures in the head and posterior regions of the amphibian
[Credit: Carlos Jared, Butantan Institute]

With colleagues from Brazil, Utah State University ecologist Edmund "Butch" Brodie, Jr. reports caecilians feature greatly enlarged poison glands at each end of their bodies, which appear to have evolved from different selective pressures - the ability to tunnel into the ground and to defend oneself from predators.

Brodie, along with Carlos Jared, Pedro Luiz Mailho-Fontana, Rafael Marques-Porto, Juliana Mozer Sciani, Daniel Carvalho Pimenta, and Marta Maria Antoniazzi of São Paulo's Butantan Institute, published the findings in Scientific Reports.

The team's research, supported by the Brazilian National Council for Scientific and Technological Development, focuses on Siphonops annulatus, a caecilian species found throughout Brazil.

"My Brazilian colleagues noticed the burrows made by this species were lined with a shiny, slick substance," says Brodie, professor in USU's Department of Biology and the USU Ecology Center. "We didn't think it was a secretion from the poison glands, so we decided to investigate."

The Brazilian caecilian, grayish in color and measuring about 18 inches in length, is a surprisingly rapid burrower, he says.

Magnified image of connective tissue matrix forming honeycomb structure surrounding glands on the head of Caecilian,
Siphonops annulatus. Scientists from Utah State University in the United States and Brazil’s Butantan Institute report skin
gland concentrations adapted to different evolutionary pressures in the head and posterior regions of the amphibian
[Credit: Carlos Jared, Butantan Institute]

"When caecilians burrow, they force their snouts into the ground and essentially dive into the soil," Brodie says.

As suspected, the team discovered all the skin glands in the serpentine creatures' head region were greatly enlarged, tightly packed mucous glands - not poison ones. The slippery lubrication enables the caecilians' rapid, subterranean escape from predators, especially coral snakes.

"We know of no other amphibian with this high concentration of mucous glands," Brodie says. "In other terrestrial amphibians, mucous is mainly related to the uptake of oxygen. Here, in caecilians, it's obviously used in locomotion."

Examination of the caecilians revealed further information. The mucous glands extend throughout the amphibians' body, in gradually reduced concentration, and give way to poison glands concentrated in the tail.

"The poison glands, resulting from a different selective pressure, provide another defense from predators," Brodie says. "In addition to chemical defense, the tail acts as a 'plug,' blocking the tunnel and further deterring predators."

The eccentric amphibian, Brodie and colleagues write, is "really a box of surprises."

Author: Mary-Ann Muffoletto | Source: Utah State University [February 23, 2018]

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A protein that self-replicates

ETH scientists have been able to prove that a protein structure widespread in nature – the amyloid – is theoretically capable of multiplying itself. This makes it a potential predecessor to molecules that are regarded as the building blocks of life.

Lakes in volcanic surroundings could have been the breeding ground for the first biochemical compounds
around 4 to 4.5 billion years ago [Credit: Dhilung Kirat/Wikimedia, ETH Zurich]

Long regarded as a biological aberration, amyloids are fibrous aggregates of short protein fragments. Amyloids have a bad reputation because they are thought to be the cause of multiple neurodegenerative diseases, including Alzheimer’s, Parkinson’s and Creutzfeldt–Jakob disease.

It was only recently that researchers discovered that amyloids appear as structural and functional building blocks in a wide range of life forms, from bacteria, yeast and fungi to humans. In vertebrates, they play a role in the production of the pigment melanin, while yeast cells use amyloid aggregates to form a kind of molecular memory.

Catalysts in prebiotic evolution

Composed of short peptides, amyloid fibres can accelerate chemical reactions in a similar way to enzymes; they have thus been viewed for several years as candidates for the first precursor molecules of life. Until now, however, an important chemical property was lacking in the theory of amyloids role in abiogenesis: self-replication.

Left: electron micrograph of an amyloid fibre. In green is a diagram of the sheet structure characteristic
for amyloids, consisting of multiple short peptide chains [Credit: Jason Greenwald/ETH Zurich]

Early proponents of the amyloid hypothesis include ETH Professor Roland Riek and his senior assistant Jason Greenwald, from the Laboratory of Physical Chemistry. In an experiment, they have now been able to show that amyloids can serve as a chemical template for the synthesis of short peptides. And the critical point: “This ability also potentially applies to the amyloid itself – meaning the molecules can self-replicate,” says Riek. The researchers reported their findings in a study in Nature Communications.

Template for self-replication

The ability to self-replicate is regarded as an essential prerequisite for every early form of life. By proving that amyloids self-replicate, Riek and his team have not only highlighted another amazing aspect of this commonly underestimated protein, but also filled in a previously missing link in the amyloid hypothesis’ argument.

Almost two years earlier, the ETH scientists had already proven in an experiment that amyloid structures can spontaneously form with astounding ease – from simple amino acids that probably already existed when the Earth was still lifeless, and under reaction conditions that appear very plausible for the primordial soup.

The self-replication mechanism of amyloid fibres depicted schematically: piece by piece, specific amino acids (coloured
building blocks) settle at the right site and chemically combine. During the process, the growing amyloid serves
as a template for itself [Credit: Lukas Frey/ETH Zurich]

The same is true for the newly discovered peptide synthesis: “The reaction mechanism seems to be of a general nature. It is stable over a wide range of temperatures and salt concentrations, in both acidic and alkaline environments,” explains Greenwald.

This discovery strengthens the researchers’ opinion that early in evolutionary history, amyloids could have played a central role in the development of early life forms as information carriers and catalytic units.

Not just an RNA world

Until now, however, the most widespread idea for the molecular beginnings of life has been the RNA hypothesis, which sees ribonucleic acid (RNA) as the only key player in the prebiotic primordial soup. This is because, like the genetic material DNA, RNA molecules can code information, and are also able to self-replicate.

The ETH researchers are now picking away at the prevailing dogma of an RNA-based world. They think that the amyloid hypothesis is more plausible; firstly, because RNA molecules with a biological function are much larger and more complex, so they are unlikely to form spontaneously under prebiotic conditions. “Additionally, amyloids are much more stable than early nucleic acid polymers, and they have a much simpler abiotic synthesis route compared to the complexity of known catalytic RNAs,” says Greenwald.

Riek adds: “We will never be able to prove which is true – to do so, we would have to turn back the last 4 to 4.5 billion years of evolution. However, we suspect that it was not one, but multiple molecular processes with various predecessor molecules that were involved in the creation of life.”

Author: Michael Keller | Source: ETH Zurich [February 22, 2018]

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Loops, loops, and more loops: This is how your DNA gets organised

It’s so impressive: a living cell is able to neatly package a big jumble of DNA, over two meters in length, into tidy, tiny chromosomes while preparing for cell division. For over a century, it has been clear that a cell can do so, but scientists have been puzzled for decades on how the process works.

Artist impression of a condensin protein complex creating a loop in DNA
[Credit: Cees Dekker Lab TU Delft/Scixel]

Researchers from the Kavli Institute of Delft University and EMBL Heidelberg now managed for the first time to isolate and film the process, and witnessed—in real time—how a single protein complex called condensin reels in DNA to extrude a loop. By extruding many such loops in long strands of DNA, a cell effectively compacts its genome so it can be distributed evenly to its two daughter cells. The scientists published their findings online in Science.

Spaghetti

This major discovery resolves a heated debate in the field, as it finally answers a question that has been discussed in biology for over a century: Before dividing in two, DNA in a cell is comparable with spaghetti – a messy mixture of intermingled strands. The cell needs to organise this jumble in chromosomes to be able to divide its DNA neatly over both daughter cells.

For many years, it has been clear that a protein complex called ‘condensin’ plays a key role, but until now, biologists were divided on exactly how. One theory stated that condensin works like a hook that can grasp and connect DNA within the jumble of DNA, thus tying it together. Another theory suggested that the ring-shaped condensin pulls the DNA inwards to create a loop.

Motor function

In a cover article in Science last November, scientists from Delft and collaborating labs showed that condensin indeed has the motor function needed for such loop extrusion. This added an important new piece to the puzzle, but as Kim Nasmyth from Oxford University—one of the leading scientists in the field of DNA organisation—noted in the accompanying perspective in Science, “the discovery that condensin is a DNA translocase is certainly consistent with the idea that it functions as a loop extruder, but by no means proves it. The challenge will be to observe extrusion as well as translocation, to establish whether it is a property of individual or multimeric complexes, and to elucidate the molecular mechanism.”

Resolving the mystery

And this is exactly what has now been accomplished. Scientists from the Cees Dekker group at the Kavli Institute of Delft University, together with the Christian Haering group from EMBL Heidelberg who established the purification and fluorescence labeling of the protein, managed to make actual movies that caught the action of the condensin complex in the act – that is, while it was extruding a loop of DNA.

“We’ve simply proved it by filming it,” says Mahipal Ganji, a postdoc in the group of Cees Dekker at Delft. “DNA is such an entangled mishmash, that it is very difficult to isolate the process and study it in cells. In our study, the first step was to fix the two ends of a DNA molecule onto a surface and put colour dyes on the DNA and condensin. By then applying a flow in the fluid perpendicular to the molecule, we oriented the DNA in a U-shape and brought it into the focal plane of our microscope. Amazingly, we could then see a single condensin bind and start extruding a loop.”

Fuel

Prof. Cees Dekker adds, “This settles the debate. These data provide compelling evidence that condensin indeed reels in DNA to form loops. Our novel imaging approach also allows measurement of all kinds of quantitative data: the symmetry of the loop extrusion, the speed at which the loop is formed, what happens when you pull on the DNA.”

The looping speed was found to be remarkably high: up to 1500 base pairs of DNA can be reeled in by condensin per second. And it does so while consuming only a modest amount of ATP—the ‘fuel’ of the condensin motor—indicating that condensin does not step along the DNA base by base, but pulls it in large steps. When slightly pulling on the DNA, the looping process slows down. Apparently, with tension, condensin seems to struggle more to create a loop.

Unexpectedly, the loop extrusion is asymmetric: “We saw that condensin docks onto DNA and anchors itself there, and then starts reeling in DNA from one side only.” Dekker adds, “Yet another interesting finding.”

Medical relevance

The research represents a significant step in the fundamental understanding of DNA in our cells, but it is also relevant for medical research. Problems with the protein family to which condensin belongs—the SMC proteins—are related to hereditary conditions such as Cornelia de Lange Syndrome. Condensin is also crucial in the organisation of the chromosomes during cell division, and errors in the process can result in cancer. A better understanding of these processes is vital for tracking down the molecular origins of serious illnesses.

Source: Delft University of Technology [February 22, 2018]

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The conflict between males and females could replace the evolution of new species

New research shows that males and females of the same species can evolve to be so different that they prevent other species from evolving or colonising habitats, challenging long-held theories on the way natural selection drives the evolution of biodiversity.

Image showing variations between male and female Liolaemus nigriceps [Credit: Dr Daniel Pincheira-Donoso,
School of Life Sciences, University of Lincoln]

According to Darwin's theory of natural selection, first introduced in his book On the Origin of Species (1859), new environments such as mountains and islands with abundant food and habitats, offer species the 'ecological opportunity' to colonise an area using those resources.

New research from the UK has shown that exactly the same mechanism of evolution that creates new species also operates within the same species when males and females compete for the ecological resources available in different habitats, such as bushy areas or stony patches with abundant food. The conflict between the sexes can lead to one sex becoming bigger, more colourful or adapting to eat different food, just like a traditional process of evolution by natural selection can lead an ancestor to split into two different species.

This process of evolution between the sexes expands the biodiversity of the area - a development that evolutionary biologists previously thought only occurred when the number of different species using different resources or 'niches' increases. This new research challenges that assumption, showing that different species and different sexes of the same species can occupy these niches.

Image showing variations between male and female Liolaemus tenuis [Credit: Dr Daniel Pincheira-Donoso,
School of Life Sciences, University of Lincoln]

This new research which explored the evolution of lizards in the Chilean Andes Mountains and Argentinean Patagonia, shows that different sexes of the same species can fill niches as well, meaning new species are actively prevented from evolving. This is because there is no new environment for them to occupy - a necessary condition for new species to evolve under Darwin's theory of natural selection.

Conducted by academics from the Universities of Lincoln, Exeter and Sheffield, the study demonstrated that biodiversity can now be seen as the formation of new, different species, or, as the formation of different sexes which are distinct enough to be equivalent to different species in the way they 'saturate' ecological niches.

Dr Daniel Pincheira-Donoso, Senior Lecturer in Evolutionary Biology at the School of Life Sciences at the University of Lincoln and lead researcher on the study, said: "Our research reveals evidence for this intriguing phenomenon that the evolution of sexes within a species could replace the evolution of new species, which begins to add a new layer to our understanding of the evolution of biodiversity.

"It is important to stress that the diversity of life on our planet applies not only to the evolution of different species, but also to the independent evolution of males and females within the same species, which potentially has very important implications."

The findings have been published in the scientific journal Global Ecology and Biogeography.

Source: University of Lincoln [February 21, 2018]

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