New clues to evolution dug up from world’s largest human fossil collection

The skulls of a modern human (Cro-Magnon 1, far left) and a Neandertal (La Ferrassie 1, center left) Credit: SciencE Mag/FOSSIL SKULLS AND CHIMPANZEE/J.-J. HUBLIN; BONOBO/ROYAL MUSEUM FOR CENTRAL AFRICA, TERVUREN, BELGIUM

The Sima de los Huesos (pit of bones) is a cave in northern Spain from which 6500 human fossils from at least 28 individuals have been recovered to date. Analysis of skulls from the earliest humans with Neandertal-like features reassigned the age of the fossils to about 430 000 years ago.

Dr Lee Arnold, from the Environment Institute at Adelaide University, was one of the lead authors on the research paper published in the journal Science. The research addresses controversy associated with human evolution during the Middle Pleistocene period, in particular the origin of Neandertals and modern humans.

Previous studies of fossils in the cave in the Atapuerca Mountains reported the age of the skulls at more than 530 000 years old. Dr Lee Arnold is a geochronologist and led the dating part of the study. He conceded that “This age range is one of the most difficult to date”. However, Arnold says that to arrive at the new date range: “rather than relying on a single dating technique, we used six different techniques to produce a robust chronological study which would not have been possible a few years ago”.

At the Sima de los Huesos. Credit: Science Mag/JAVIER TRUEBA/MADRID SCIENTIFIC FILMS

The result is more compatible with morphological and genetic evidence for human evolution of the time. “We’ve resolved the age of the fossils at 100,000 years younger than previously reported, which makes them the oldest reliably-dated humans to show clear Neandertal morphology.” Dr Arnold and Dr Martina Demuro, geochronologists from Adelaide University’s Environmental Luminescence group, conducted dating of the site while at Spain’s National Research Centre for Human Evolution (CENIEH).

Along with a more accurate age of the fossils, studies of the specimens cranial, facial, and dental features of the Atapuerca hominins allows more precise evolutionary positioning of these Neandertal ancestors. The analysis has allowed for testing of the “accretion” model which proposes that Neandertal features appeared separately rather than at the same time. For example the facial features evolve at a different time to the neocranium.

The skulls from this population show jaws and teeth which are more typically Neandertal and upper cranial features more like Homo heidelbergensis, suggesting the fossils may belong to a new species or sub-species. “A picture is emerging of human evolution which is way more complex than has been considered over the past couple of decades,” says Dr Arnold.

More skulls of extinct human species have been found at the Sima archaeological site than anywhere else in the world. “This collection of bones, which is expected to continue growing in the coming years, is becoming increasingly important for the study of human evolution.” says Professor Juan Luis Arsuaga, from Madrid’s Complutense University and the ISCIII Joint Centre for Evolution and Human Behaviour in Spain.

Obtaining the fossils is difficult, with access limited to a 500 metre crawl through underground caves and a 13 metre abseil down a deep vertical shaft. A career as a research scientist really can take you to some amazing places!

Hear Dr Lee Arnold speak on ABC Radio National or read the transcript.

New Zealand claims back the Kiwi after ancient DNA testing

Almost 20 years ago, Alan Cooper from the Australian Centre of Ancient DNA found that the Kiwi might actually originate from Australia.

Given that the emu and cassowary are the Kiwis closest living relatives and that New Zealand split off from Australia when Gondwana broke up, this was a logical suggestion.

Alan Cooper is from New Zealand himself and says: “This was a huge psychological blow in New Zealand and extremely unpopular”.

Photo: Kyle Davis and Paul Scofield

A new paper published today in Science sets the record straight. Alan Cooper and his team have been able to analyse the ancient DNA of two extinct birds from Madagascar and have found the Kiwis to be their closest relatives.

The emu, cassowary, ostrich, rhea and kiwi are known as “ratite birds” they can’t fly because they have lost the bone that wing muscles can attach to. The fact that the DNA of the kiwi closely matches the DNA of the extinct elephant bird from Madagascar means that birds of kiwi lineage must have flown at some point to get from Madagascar.

The connection between these birds undermines the idea that ratites evolved from ancestors that didn’t fly.

“Twenty years later it’s great to be able to show using ancient DNA that the kiwi is not an Australian bird. In fact its closest relative is the elephant bird from Madagascar,” he says.

“The New Zealanders will be much more comfortable with that. It’s their worst nightmare to be a derivative of Australia.”

Find out more about this story and flightless birds in Kieren Mitchell and Alan Cooper’s Conversation article and also in New Scientist, Science News and ABC Science Online articles.

From Birdsong Metrics to Ancient Arctic DNA: Selected Publications from the 1st Quarter, 2014

In the first quarter of 2014, researchers at The Environment Institute have published on a vast array of topics, from Ancient DNA in the Arctic, to birdsongs to  recommendations for improvements to guidelines such as the Ecological Footprint in order to better inform policy makers.

A selection of these publications is listed below.

1. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature
Research into the type of vegetation present during the last 50 thousand years in the Arctic is presented. Rather than using fossilised pollen as the main source of data as has been the case for previous studies, this study used plant and nematode DNA from sites across the Arctic. This data brings into question the diet of megafauna such as the woolly mammoth.

2. Distribution and Diversity of Soil Microfauna from East Antarctica: Assessing the Link between Biotic and Abiotic Factors. PLOS ONE
An investigation into soil microfauna composition, abundance, and distribution in East Antarctica. The study found that where a population exists is likely to be determined by soil geochemistry.

3. Higher Levels of Multiple Paternities Increase Seedling Survival in the Long-Lived Tree Eucalyptus gracilis. PLOS ONE
Data from populations of Eucalyptus gracilis (white mallee or yorrell) across the Murray-Darling Basin in southern Australia was collected in order to gain an understanding of how local environments affect seed quality.

4. Rapid deforestation threatens mid‐elevational endemic birds but climate change is most important at higher elevations. Biodiversity Research
The effect of deforestation and climate change on bird communities in Lore Lindu National Park, Sulawesi, Indonesia was investigated. The National Park is a globally important hotspot of avian endemism, and has lost almost 12% of its forest in the decade of 2000-2010.

5. Does the Shoe Fit? Real versus Imagined Ecological Footprints. PLOS BIOLOGY
This article seeks to demonstrate that “Ecological Footprint” measurements as currently constructed and presented misleading and cannot be used effectively in any serious science or policy context. Outlined are a set of principles that any ecological indicator should be based on in order to be scientifically sound and relevant for use in decision making.

6. Historical changes in mean trophic level of southern Australian fisheries. Marine and Freshwater Research
It is suggested that care in interpretation of mean trophic level (MTL) of catches should be taken because reductions do not necessarily reflect change in species high on the food chain by fishing pressure. They found that the change in MTL is mainly attributable to large catches of sardines.

7. Ecology Needs a Convention of Nomenclature. BioScience
A convention of ecological nomenclature as well as a transnational institution to manage it is proposed, in order to overcome the synonymy and polysemy across disciplines, which currently handicaps the progress of ecology.

8.Emerging Challenges for the Drinking Water Industry Environmental Science & Technology
Three principles that underpin alternative water source choices are introduced: Reliability, thresholds and future projections of water quality and quantity.

9. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature
The first large-scale evolutionary study of long noncoding RNA (lncRNA) repertoires and expression patterns in eleven tetrapod species is presented. About 400 highly conserved lncRNA’s (of more than 10 000 identified) probably originated an astonishing 300 million years ago at least.

10. Direct evidence for organic carbon preservation as clay-organic nanocomposites in a Devonian black shale; from deposition to diagenesis Earth and Planetary Science Letters
The temperature and oxygenation of the oceans are influenced by one of the most fundamental biogeochemical processes on Earth-the burial of organic carbon in marine sediments. This buried organic carbon also comprises the primary source of hydrocarbons. This paper presents research into the composition of Woodford Shale.

11. A guide to southern temperate seagrasses (Book, CSIRO Publishing)
A reference guide to the diverse seagrasses present in the ocean of the temperate parts of the southern hemisphere. Evolution, biology and ecology of the seagrasses is introduced. This book allows readers to rapidly identify a particular species, including those often confused with others.

12. A Potential Metric of the Attractiveness of Bird Song to Humans. Ethology
Bird species such as the common nightingale and European blackbird have songs that are known to have inspired classical music. Developing a metric for these songs might help identify birds that are present in international bird trade which could contribute to studies of invasion and conservation biology.

13. Genetics in conservation management: Revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biological Conservation
A review of recent theoretical and empirical evidence concludes that the population rules for minimising inbreeding and for maintaining evolutionary potential in perpetuity need to be at least doubled and sections of the IUCN Red List criteria require revision, to be more effective conservation tools.

Quenching the curiosity of everyday Australians.

Environment Institute members Corey Bradshaw and Barry Brook were part of a hand-picked group of 27 academic experts and science writers from across Australia who contributed to a very interesting publication released late last year by the Chief Scientist of Australia.

The book, available for download as a pdf or to e-readers is entitled “The Curious Country“. This collection of essays is the result of asking Australians directly what were the important issues that they wanted science to address.

What were their concerns about science? What inspires them? 1186 Australians were surveyed, men and women ages 18 to 65, from all education levels and locations around Australia. Climate along with heath issues topped the list for 30% and 32% of Australians, respectively. Pollution and water were the environmental issues of greatest concern.

The book is designed to bridge the gap between heavy scientific papers for specialists, and those wanting more accurate, up-to-date information about science than what currently filters through the mainstream media.

There is no need to read the book from start to finish. Flip and flick until you find a story that piques your curiosity. Perhaps there is some scientific phenomena that you always wondered about, but haven’t yet come across a reliable and accessible source.

“Powering the Future” by Barry Brook

 

Barry Brook explains in his contribution Powering the Future that Australia must use science and technology innovations to move away from a dependence on coal and seek lower carbon alternatives.  Brook notes that: “Australia has been a world leader in the development of lower-cost and more-efficient crystalline solar photovoltaics” and support for this type of research should continue. Along with this, he urges Australia to embrace the exploration of new frontiers such as engaging in multi-lateral collaborations- he uses the large hadron collider project as an example.

 

 

“Biowealth: all creatures great and small” by Corey Bradshaw

 

In Biowealth: all creatures great and small, Corey Bradshaw explains how all people depend on absolutely every other species for their own survival. Take for example the very air we breathe every day, which is provided to us free of charge by other species, mostly plants and marine algae. Biodiversity is extremely important to the human race, and yet it is being lost at an alarming rate. Corey discusses his involvement in the project on his own blog ConservationBytes.com.

New Review: Parasites as biological tags to assess host population structure: Guidelines, recent genetic advances and comments on a holistic approach

A new review involving Environment Institute member Bronwyn Gillanders, as well as Sarah Catalano, Ian Whittington and Stephen Donnellan of the Australian Centre for Evolutionary Biology and Biodiversity has recently been published in the International Journal for Parasitology: Parasites and Wildlife.

This review, titled “Parasites as biological tags to assess host population structure: Guidelines, recent genetic advances and comments on a holistic approach“ includes a summary of the population studies that have used parasites as biological tags for marine fish and cephalopods. The new ways that parasite genetic data can be incorporated into population structure studies is discussed.

Hundreds of dicyemid parasites (white, fuzzy strands) attached to the renal appendage (in red) of a cuttlefish individual.

Download the review to find out more.

New clues to evolution dug up from world’s largest human fossil collection

The Environment Institute blog has moved! Please see this post on the new blog here. 

Ancient DNA unravels Europe’s genetic diversity

Image – Flickr/leted

Ancient DNA recovered from a time series of skeletons in Germany spanning 4,000 years of prehistory has been used to reconstruct the first detailed genetic history of modern-day Europeans.

The study, published today in Science, reveals dramatic population changes with waves of prehistoric migration, not only from the accepted path via the Near East, but also from Western and Eastern Europe.

The research was a collaboration between the Australian Centre for Ancient DNA (ACAD), at the University of Adelaide, researchers from the University of Mainz, the State Heritage Museum in Halle (Germany), and National Geographic Society’s Genographic Project. The teams used mitochondrial DNA (maternally inherited DNA) extracted from bone and teeth samples from 364 prehistoric human skeletons – ten times more than previous ancient DNA studies.

“This is the largest and most detailed genetic time series of Europe yet created, allowing us to establish a complete genetic chronology,” says joint-lead author Dr Wolfgang Haak of ACAD. “Focussing on this small but highly important geographic region meant we could generate a gapless record, and directly observe genetic changes in ‘real-time’ from 7,500 to 3,500 years ago, from the earliest farmers to the early Bronze Age.”

“Our study shows that a simple mix of indigenous hunter-gatherers and the incoming Near Eastern farmers cannot explain the modern-day diversity alone,” says joint-lead author Guido Brandt, PhD candidate at the University of Mainz. “The genetic results are much more complex than that. Instead, we found that two particular cultures at the brink of the Bronze Age 4,200 years ago had a marked role in the formation of Central Europe’s genetic makeup.”

Professor Kurt Alt (University of Mainz) says: “What is intriguing is that the genetic signals can be directly compared with the changes in material culture seen in the archaeological record. It is fascinating to see genetic changes when certain cultures expanded vastly, clearly revealing interactions across very large distances.” These included migrations from both Western and Eastern Europe towards the end of the Stone Age, through expanding cultures such as the Bell Beaker and the Corded Ware (named after their pots).

“This transect through time has produced a wealth of information about the genetic history of modern Europeans,” says ACAD Director Professor Alan Cooper. “There was a period of stasis after farming became established and suitable areas were settled, and then sudden turnovers during less stable times or when economic factors changed, such as the increasing importance of metal ores and secondary farming products. While the genetic signal of the first farming populations becomes increasingly diluted over time, we see the original hunter-gatherers make a surprising comeback.”

Dr Haak says: “None of the dynamic changes we observed could have been inferred from modern-day genetic data alone, highlighting the potential power of combining ancient DNA studies with archaeology to reconstruct human evolutionary history.” The international team has been working closely on the genetic prehistory of Europeans for the past 7-8 years and is currently applying powerful new technologies to generate genomic data from the specimens.

Ecological Armageddon in forest fragments

Malaysian rainforest. Image – jswakins/Flickr

An international team of scientists including the University of Adelaide’s Professor Corey Bradshaw has found that species living in rainforest fragments could be far more likely to disappear than was previously assumed.

Published today in the leading journal Science, the researchers outlined a study spanning two decades in which they witnessed the near-complete extinction of native small mammals on forest islands created by a large hydroelectric reservoir in Thailand.

“Tropical forests remain one of the last great bastions of biodiversity, but they continue to be felled and fragmented into small ‘islands’ around the world,” says co-author Professor Corey Bradshaw, Director Ecological Modelling at the University of Adelaide’s Environment Institute.

“This study shows we need to be even more concerned than we thought – the speed at which there was near-total loss of native small mammals was alarming and shows that leaving fragments of forest behind is not nearly enough to protect these species.”

“It was like ecological Armageddon,” says Luke Gibson from the National University of Singapore, who led the study. “Nobody imagined we’d see such catastrophic local extinctions.”

The study was motivated by a desire to understand how long species can live in forest fragments. If they persist for many decades, then this gives conservationists a window of time to create wildlife corridors or restore surrounding forests to reduce the harmful effects of forest isolation.

However, the researchers saw native small mammals almost vanish at great speed, with just a handful remaining – on average, less than one individual per island – after 25 years.

As well as suffering the effects of population isolation, the small mammals also had to deal with a devastating invader – the Malayan field rat. In just a few years, the invading rat virtually displaced all native small mammals. The field rat normally favours villages and agricultural lands, but will also invade disturbed forests.

“This tells us that the double whammy of habitat fragmentation and invading species can be fatal for native wildlife,” says Dr Antony Lynam, from the US-based Wildlife Conservation Society. “And that’s frightening because invaders are increasing in disturbed and fragmented habitats around the world.”

“The bottom line is that we must conserve large, intact habitats for nature,” says Luke Gibson. “That’s the only way we can ensure biodiversity will survive.”

Near-complete extinction of native small mammal fauna 25 years after forest fragmentation is published in Science and is available at www.sciencemag.org.

Predicting publishing success in scientists.

Men with printing press circa 1930s
Image – Flickr/ Seattle Municipal Archives.

A provocative new study suggests it is straightforward to predict which academics will succeed as publishing scientists.

Those who publish earlier and more often while young are typically the long-term winners.

“We were really surprised,” said Professor William Laurance of James Cook University in Cairns, Australia, who led the study.

“It doesn’t matter if you go to Harvard or a low-ranked university. If you begin publishing scientific articles when you’re still a graduate student, you are far more likely to succeed in the long run.”

Laurance’s team scrutinized more than 1400 biologists on four continents, and then selected 182 to study intensively.

They found the researchers varied greatly – by almost a hundred-fold – in the number of scientific articles they published during their careers.

“For reasons that are not totally clear, some people just ‘get’ the publishing game early in their careers, and it’s these scientists who are most likely to keep on publishing strong research,” said Professor Corey Bradshaw of the University of Adelaide’s Environment Institute in South Australia.

Another finding was that women faced some disadvantages in publishing research, even those who overcame the well-documented attrition of senior female academics.

“Women have to jump a lot of hurdles in science,” said Carolina Useche of the Humboldt Institute in Colombia. “Family responsibilities weigh heavily on them, and they don’t seem to promote themselves as aggressively as some men do.”

Language also plays a role, according to Ms Useche. “Those who grow up speaking and writing English have an advantage, because most scientific journals are in English,” she said.

The research team reached two key conclusions.

First, far too few women make it to the top in science, in large part because they do not, on average, publish as often as men.

“For women scientists, it’s just not a level playing field, and we need to find ways to help them advance professionally,” Professor Bradshaw said.

Second, those who publish early and often are most likely to become scientific superstars, regardless of the international standing of the universities where they obtained their PhD.

“We need to pay a lot of attention to the early training of scientists,” Professor Laurance said. “If we do a good job, we can give them a head start that will last their whole lives. This research gives us a good evidence base for our efforts.”

 

Predicting publication success for biologists by William F. Laurance, D. Carolina Useche, Susan G. Laurance, and Corey J. A. Bradshaw was just published online in BioScience: http://www.jstor.org/discover/10.1525/bio.2013.63.10.9?uid=3737720&uid=2129&uid=2134&uid=2&uid=70&uid=4&sid=21102642299977

 

Further evidence on human global warming

Professor Tim Wigley

A team of international climate scientists including University of Adelaide’s Professor Tom Wigley has today reported further strong evidence of the human influence on climate change.

Published today in the Proceedings of the National Academy of Sciences of the USA (PNAS), the researchers have detailed a comprehensive study investigating the causes of temperature changes in Earth’s atmosphere.

They have analysed satellite temperature data over 34 years and compared these data with results from more than 20 different climate models, focussing on the vertical structure of atmospheric temperature change (from the troposphere or lower levels of the atmosphere through to the stratosphere or upper reaches of the atmosphere).

The study was led by scientists from the Lawrence Livermore National Laboratory in the United States and builds on work published in 1996 by the same group. The 1996 Nature paper, ‘A search for human influences on the thermal structure of the atmosphere’, was the first published work to clearly identify the human fingerprint in observed temperature changes.

“With this paper we have built on our earlier work with another 20 years of data that adds further strong evidence for the human impact on our climate,” says Professor Wigley, ARC Fellow with the University of Adelaide’s Environment Institute.

Professor Wigley says the study is more much comprehensive than other published studies and has been able to better define the human ‘signal’ in atmospheric temperature change. There is a clear pattern of warming temperatures in the troposphere and cooling temperatures in the stratosphere, changes that are the characteristic signature of human activity.

“The main thing is that we can identify what is called a human fingerprint, or a distinctive pattern of change in the observational record, and that pattern is derived from climate modelling experiments,” he said.

“We look at patterns of change that can be attributed to other things, such as changing output of the sun for example, and we show that those cannot be identified in the observational record. 

“We can see the human fingerprint, we can’t see the fingerprint of any other cause, and so it’s pretty obvious that the only explanation is there’s been a very distinctive human influence on the patterns of climate change.”

The scientists said more had been done to tackle ozone depletion than the effects of greenhouse gases.

“Greenhouses gases trap the warmth in, they allow radiation from the sun to penetrate to the lower layers of the atmosphere, but they don’t allow as much outgoing radiation and that’s what’s called the greenhouse effect,” Professor Wigley said.

“One of the standard skeptic ‘arguments’ is that all the observed changes are caused by natural variability, and often supposed to be due to solar activity,” says Professor Wigley.

“What we have shown beyond a shadow of doubt is that the climate changes we are observing cannot be due to the Sun or any other natural factors.

“There is simply no other way to explain the changes that have occurred since 1979 (when special research satellites were introduced by the US National Oceanic and Atmospheric Administration) other than as a result of human influences – primarily greenhouse gases and related pollutants like sulphur dioxide emissions and gases that affect the atmospheric concentrations of ozone.

“Other published work has already shown a convincing and growing pile of pebbles of evidence for the dominant role of humans in climate change. Our paper adds a huge boulder to that pile.”

Find the paper here. 

Read a longer interview with Professor Wigley here.