A New Species of Great Ape

Scientists have confirmed that a group of great apes discovered nearly 20 years ago is indeed a different species from all the other known great apes, according to a BBC news report. It's the first documented new ape species in more than 100 years.

First discovered in 1997 in remote forests of Sumatra, the Tapanuli orangutan (genus/species Pongo tapanuliensis) is distinctly different from Bornean and Sumatran orangutan species. DNA evidence indicates that it split from a common ancestor of the Sumatran orangutan about 700,000 years ago. In addition, its skull structure is different from either of the other two orangutan species, and it vocalizes differently. A research paper documenting the new species is published in the journal Current Biology.

Now for the bad news. There are only an estimated 800 individuals of this new species, meaning that it is in danger of extinction.

When Did Humans Reach the Americas?

Until now, the best available evidence had indicated that humans probably reached the Americas about 20,000 years ago.  But now a new paper published in Nature raises the possibility that humans reached the Americas as early as 130,000 years ago.  The new findings could force a re-thinking of when, how, and by whom the Americas were colonized.

The new paper focuses on an archaeological site in California, where smashed and broken bones of a mastodon were found intermingled with what are reported to be crude stone tools.  Uranium/thorium dating shows that the bones are a whopping 130,000 years old.  The authors propose that the bones were deliberately smashed, leading to the conclusion that humans must have been in California at least as early as 130,000 years ago.

The findings are intriguing, but we'll probably have to wait for corroborating evidence before everyone accepts the new date.  For starters, it would help if we could find human bones that old; so far, no human bones older than about 20,000 years have ever been found in the Americas.  And then there's the question of how they could have gotten to the Americas in the first place.  The humans who colonized the Americas about 20,000 years ago crossed over from Asia via a land bridge that existed at the time between current-day Russia and Alaska.  That land bridge probably didn't exist 130,000 years ago.  They could have arrived by boat, but that would presume a higher degree of sophistication than implied by primitive stone tools.

Finally, there's the question of who these people were, if indeed they ever existed.  DNA evidence indicates that Native Americans can trace their ancestry back to a common ancestor who lived about 20,000 years ago.  If a band of humans arrived more than 110,000 years before that, they must have died out without leaving a continuous line of descendants.

Many Primate Species Face Extinction

Our closest living relatives in the animal kingdom, the primates, are in trouble. According to a comprehensive review of primate populations around the world by some 31 scientists from 11 countries, nearly 60% of all primate species are in danger of extinction, and many of the others are in decline. That includes every species of apes and nearly all species of lemurs. The one primate species that still appears to be doing extremely well is humans.

The causes are multiple and predictable. Reduction in habitat due to an expanding human population, changes in primate's habitat due to logging, agriculture, and mining, predation (hunting) by humans, and even climate change are all thought to be contributing factors.

Unfortunately, there aren't any easy solutions on the horizon. Unless action is taken soon, it becomes increasingly likely that some of our primate relatives will disappear from planet Earth, if not within the next few decades, most certainly within the next few centuries. And that would be sad.

Purposefully Causing the Extinction of a Species

Question: If it were technically possible, should we deliberately cause the extinction of species that we perceive as harmful (to us)? If we could actually eliminate forever the species of mosquitoes that carry certain human diseases such as yellow fever, malaria, and the Zika virus, should we do it?

Think hard on this question, because one day it may be possible. Right now, we know how to modify mosquitoes so that the males are sterile; when these sterile males are released into the wild there is a sharp drop in the mosquito population in the local region, but not a complete extinction because there are still plenty of wild normal males to ensure the survival of the species. But what if you could modify mosquito genes so that they could only produce male offspring? Such a change would wipe out the entire species in short order.

The ides of deliberately causing the extinction of certain species may be morally repugnant to some. But even if its not, we need to be aware of that there may be risks. Time and time again we've seen how the introduction of an invasive species disrupts an ecosystem. What might be the unintended consequence of the opposite scenario; eliminating a species from its ecosystem? If we were to eliminate a species in the wild, it might be wise to keep colonies of the species in captivity so that they could be re-introduced if necessary.

On the political front, who would be responsible for giving consent for a species extinction? Mosquitoes know no political boundaries. Any plan to eliminate a species, even one so universally unloved as a mosquito, should require nearly universal international approval. Don't count on that any time soon.

Neanderthals Interbred with Modern Humans

What happened to the Neanderthals, that now-extinct group of stocky, big-boned ancient humans who lived in Europe and Asia until about 30,000 years ago? Were they wiped out by conflict with modern humans who arrived later in Europe or by some other unfavorable environmental condition? Did they interbreed with modern humans, ultimately "disappearing" as a distinct group because their genes were incorporated into a much larger gene pool of modern humans?

Several years ago I reported (this blog May 12, 2010) that Neanderthals shared a number of genetic variations with modern Europeans that they did not share with modern Africans. These findings at least suggested, but did not prove, that interbreeding occurred when Neanderthals met modern humans.

More recently, DNA analysis reveals that up to 3% of the DNA of modern Eurasians is similar to the DNA of the Neanderthals. And according to a paper published this week in Nature, DNA analysis of a bone of a modern human who lived in present-day Romania around 40,000 years ago revealed that 6-9% of his genes were from Neanderthals. In other words, he may have had a great, great-grandparent who was a Neanderthal.

Of course, this does not prove that interbreeding was the cause of the disappearance of the Neanderthals. Interbreeding can occur between groups in conflict, as the behavior of modern-day humans clearly shows. But at least it indicates that interbreeding did occur, at least occasionally.

Global warming, climate change, and species extinctions

In the latest study of the effect that global warming and climate change may have on species extinctions, a study from the University of Connecticut concludes that up to one in six species may be at risk of extinction, depending in the amount of global warming that actually occurs. The study is what is called a meta-analysis; it combined and summarized the data from all of the available global warming -species extinction studies available that met certain criteria of relevance and quality - 131 studies in all.

The results of the study suggest that only 5% of species would become extinct if global warming could be kept to the international agreed-upon target of just 2 degrees centigrade above pre-industrial levels. But virtually no one believes now that we can keep global warming to that limit, given our failure to curb global warming so far. Many of the individual studies summarized in the present meta-analysis predict global warming of more than 4 degrees centigrade, leading to the higher estimate of 1 in 6 species at risk of extinction (about 16%). Most of the extinctions will occur in the tropics, according to the analysis.

Current climate change models predict only what might happen in the time period of decades or centuries. Extinctions might be much higher if higher global temperatures were to persist for tens of thousands of years. Indeed, some scientists think we may be entering a prolonged period that will become the sixth mass extinction experienced by Earth over its 4 billion life span so far.

Many species are likely to be affected by global warming and climate change, even if they do not become extinct. Species may undergo substantial changes in populations, range, and interactions with other species, for example. The good news is that over prolonged periods of time (thousands to millions of years), evolution will continue and species will adapt and change. Life will go on, though whether humans will still be here is anybody's guess.

Horizontal Gene Transfer in Humans

People who worry about genetic modification of organisms by the transfer of genes from another species should know that it happens naturally, even in humans.  The transfer of genes from one species to another in nature is called horizontal gene transfer.  It's rare, but it does happen.

What's the evidence for interspecies gene transfer?   In a paper published recently in Genome Biology, researchers at Cambridge University examined currently available genetic databases of primates (including humans), fruit flies, and nematode worms (the groups were chosen because their genetics are fairly well-known).  They then searched the world's known genetic databases for all other organisms for exact matches to specific genes within each group.  Matches within a group (e.g. all primates), are most likely to descent from a common ancestor.  On the other hand, matches between completely unrelated species (e.g. humans and bacteria), are most likely due to horizontal gene transfer at some time in evolutionary history.

The findings suggested all three groups have picked up genes from totally unrelated species over the long time course of evolution, including genes from algae, fungi, and bacteria.   Humans, for example, have picked up more than 145 genes from other species.  That's not a lot out of the 20,000 or so in the human genome, but its at least evidence that horizontal gene transfer does occur.  Most of these horizontally transferred genes in humans were acquired from bacteria early in human evolution.

Are we better off for it or not?  That remains an open question.  In terms of the current debate over the safety of genetic engineering, it's worth noting that the natural process is glacially slow compared to the modern purposeful transfer of genes.   Still, it's interesting that the process does occur in nature.

Earth’s Largest Mass Extinction Occurred Quickly

Planet Earth has experienced at least five mass extinctions over the past 500 million years or so. The largest mass extinction, marking the boundary between the Permian and Triassic periods, resulted in the loss of close to 95% of all species of organisms living at the time.

Until recently it has not been possible to determine exactly when the mass extinction occurred or how long it lasted. But now, using better dating techniques, scientists have pinpointed the Earth’s largest mass extinction more precisely, to between 251.88 and 251.94 million years ago. That’s a duration of just 60,000 years (0.06 million years); much shorter than previously thought. What could have caused such a rapid and devastating die-off? Scientists don’t know for sure, but it’s worth noting that the extinction coincided with a massive rise in atmospheric CO2 levels to over 2,000 parts/million (ppm), perhaps due to a period of increased volcanic activity. That in turn may have caused a substantial global warming, including warming of the oceans.

Some people think that as a result of human activity (the release of CO2 into the atmosphere as the result of the burning of fossil fuels) we may be at the beginning of a new period of mass extinction. Its worth noting that atmospheric CO2 levels are currently around 390 ppm, clearly up from 280 ppm before the industrial revolution but nowhere near the levels seen in the last extinction. Is that good news, or bad? No one knows for sure. In another 60,000 years we might know the answer, but by then it would be too late.

You and I will be long gone by then….

New Clues to Archaic Human Evolution

The evolutionary history of humans just gets more interesting every day.

Last month (see "How Many Species of Primitive Humans Were There?") I reported on an anatomical analysis of a series of archaic human skulls that challenged the “multiple species” theory of archaic human evolution. The authors of the study concluded that despite marked anatomical differences between the skulls, they could in fact all have belonged to one species.

New evidence using DNA analysis seems to support the notion of interrelatedness of seemingly distinct groups of archaic humans. The oldest sample of human DNA ever analyzed comes from a fossil of an ancient human ancestor who lived in Spain nearly 400,000 years ago. As expected, this DNA shares many features with the DNA of the Neanderthals who lived on the same continent. However (and surprisingly), it most closely resembles the DNA of a group of ancient humans called the Denisovans, who lived in Siberia nearly 4,000 miles away and more than 300,000 years later.

In light of the new DNA findings, scientists are going to have to think seriously about how far archaic humans might have traveled, and about how much they might have interbred when they came in contact with each other. If in fact they did come in contact with each other and interbreed, it may be time to consider that archaic humans all belonged to one species, and not the multiple species generally described by most paleoanthropologists.

How Many Species of Primitive Humans Were There?

Based on structural differences between a few skulls and some partial skeletons, the prevailing thought among paleoanthropologists has been that once humans left Africa for the first time they evolved into at least five or six distinct species of primitive humans, including Homo erectus, H. georgicus, H. ergaster, H. heidelbergensis, H. rudolfensis, and H. neanderthalensis. Historically, paleontologists were quick to assign a new species name to nearly every unique skull or skeleton discovered. In part, that’s because discovering a new species generally advances the discoverer’s career. But were all these alleged species really all that different? Were they even different species?

As more skulls and skeletons are discovered, the “multiple-species” argument is beginning to be challenged. The discovery of the most complete Homo skull yet in the Georgia region of Russia brings the controversy to a head (no pun intended). The discoverers compared the newest skull to four others found previously in the same region. They note that there are substantial structural differences between them, even though they presumably belonged to the same species. Indeed, there are just as many differences between the skulls of currently living humans, all of whom belong to just one species (Homo sapiens). Based on these findings, the researchers hypothesize that all of the known skulls of primitive Homo belong to a single evolving lineage (a single species)

Generally speaking, a species is loosely defined as a group of organisms that under natural conditions tend to breed within that group. A key question, then, is whether individuals of the so-called different species could (or did) interbreed. So far we don’t know the answer. Absent that critical information, we can expect the “multiple species” versus “single species” controversy to remain with us for a while.

Were the Flores People a Separate Species?

Ever since they were first discovered in 2004, the skeletal remains of a diminutive group of humans found on the island of Flores in Indonesia have been at the center of a controversy. Did the Flores people belong to a previously undiscovered species of the genus Homo, or were they simply modern humans (Homo sapiens) who suffered from some sort of growth disorder?

New evidence strongly supports the new-species hypothesis. In a paper published in PLOS One, researchers used CT scans to compare the brain shape of the one available skull of a Flores person to primitive species of Homo, to modern humans, and to modern humans with various growth disorders. They conclude that the Flores people are most closely related to the primitive human species known as Homo erectus. Furthermore, the evidence did not support the hypothesis that the Flores people were modern humans with a growth disorder, and so it seems appropriate to consider the Flores people a separate species of primitive Homo. Scientists have named the new species Homo floresiensis in honor of where they were discovered.

That’s where we stand today, at least. But the fact is that all this talk of a new species is based on just one skull and a partial skeleton, plus a bunch of bones of other individuals of the same group. It would be nice to have a few more skulls to really nail this thing down. Perhaps in time….

The Human Hand Makes a Good Fist

One of the defining features of humans is that the shape of our hands and fingers allows us to touch the tips of our fingers with our thumbs. As a result, we are able to pick up and manipulate very small objects – something other primates can’t do. Textbooks describe this human anatomical feature as having “opposable thumbs”. Allegedly it is a feature that has given us an evolutionary advantage.

Now researchers report that there’s another unique feature of the human hand that also confers an evolutionary advantage. According to a recent paper published in the Journal of Experimental Biology, the structural arrangement of the bones in the hand and the wrist allow us to make a very effective fist, for use as a weapon. The report demonstrates rather convincingly that when we curl the four fingers into the palm and then position the thumb over the index and second finger, the unique shape of the human fist allows the palm to buttress and support the fingers when we strike a blow. As a result, more force is transmitted by the knuckles than would be possible with the hand anatomy of other primates.

The authors of the study suggest that being able to use the fist as a weapon confers an evolutionary advantage. In other words, our hand evolved not only to be able to manipulate small objects easily, but also to fight effectively.

Austalopithecus afarensis Definitely Climbed Trees

Analysis of the partial skeleton of “Lucy”, the best-known skeleton of Australopithecus afarensis discovered in 1974, revealed that the species was capable of standing and walking upright.  Many scientists presumed, based on the probable shape of her shoulder bones (some bones were missing) that she also still climbed trees, like her ancestors.  Others disagreed, arguing that the shape of her shoulder was just a vestigial retention from her ancestry, no longer of any real functional value.

To resolve this issue, researchers compared the anatomy of the scapula bone of a partial skeleton of a recently-discovered juvenile A. afarensis to the growth patterns of scapula bones of humans and modern apes.  They concluded that A. afarensis, like modern apes, used its upper limbs to climb and move through trees, at least part of the time.  Perhaps they slept in trees as a protective strategy, or climbed trees to harvest food.

The unique shoulder anatomy that permits overhead use of the upper limbs to climb and swing from trees disappeared in Homo erectus, a later transitional species in the human lineage.

Origin of the Australian Aborigines

Where did the native peoples of Australia (the Aborigines) come from? To find out, scientists analyzed the DNA genomic sequence of a lock of hair from an Australian Aborigine that was collected over 100 years ago, in which there is no evidence of contamination or mixture with Europeans’ genes. The results, published Science, show that the Australian Aborigines descended from humans who migrated out of Africa to Eastern Asia around 62,000 – 75,000 years ago, well before a second dispersion from Africa of the current modern Asians (25,000 – 38,000 years ago). In other words, the Aborigines did not diverge from the current population of Asians, but from a group that left Africa much earlier, settled in Australia, and then remained isolated from and unaffected by later migrations. If this is true, then the Australian Aborigines may be the oldest human population to continuously occupy a region outside of Africa.

Reference: Rasmussen, Morton et al. An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Science 334:94-98, Oct. 7, 2011.

Australopithecus sediba – A Close Relative?

Newly discovered skeletons of a 2-million-year old member of the human family called Australopithecus sediba have piqued the interest of paleontologists. Some are suggesting that A. sediba may be a closer relative of modern humans than Australopithecus afarensis – the most famous skeleton of which is “Lucy”, who lived about 3.2 million years ago. Others are not so sure.

In five articles in the September 9 issue of Science, scientists describe some of the primitive and modern features of the brain, pelvis, hands, and feet of this transitional archaic human. The brain shows signs of reorganization, including an enlarged frontal lobe. The hand looks like that of a modern human’s, but it is attached to a long arm typical of species that still swing from trees. The pelvis has some, but not all, of the features of an upright-walker. And the lower leg, ankle, and foot are an odd mixture of primitive and modern features. A. sediba probably could walk upright, though it’s gait would have been significantly different from our own.

Regardless of where paleontologists ultimately choose to place A. sediba in the human ancestral tree, further analysis of the species will almost certainly add significantly to our understanding of the transition to modern humans.

The Origins of Language

Where and when did human language originate? One way to tell is to analyze changing patterns in the number of phenomes – the distinct sounds that are used to form words - in languages around the world. According to recent research, the largest numbers of phenomes occur in languages in Africa, while the smallest are found in South America and Oceania. Coupled with knowledge of how and when human populations changed and migrated, the data are consistent with an African origin of language.

No surprise there, I guess. Modern humans originated in Africa, according to current thinking. This new data would imply that language developed before modern humans migrated from Africa more than 50,000 years ago. In fact the acquisition of language may have been what gave modern humans a distinct evolutionary advantage, ultimately allowing us to colonize the entire world.

Redefining Evolutionary Relationships

The evolutionary tree of life may undergo a makeover in the next decade or so.

In the past, the primary sources of information about the evolutionary relationships between organisms came from the fossil record or from comparative anatomy, physiology, or biochemistry. But now a new scientific field called phylogenomics (the study of the evolutionary history of organisms based on genetics) has emerged, thanks to the increased availability and cheap cost of sequencing DNA.

How does comparative DNA sequence data tell us anything? By tracing specific differences in the nucleotide sequences of the genes of closely related species, phylogeneticists can tell just how closely related two species are and when they most likely split from a common ancestor. That’s because when a mutation (a change in nucleotide sequence) occurs by random chance in a common ancestor, that mutation should still be present in all subsequent descendants of that ancestor. So when exactly the same mutation appears in the same gene in two species, the mutation most likely occurred before the two species split from a common ancestor – i.e. the two species are related to each other by a common ancestor.

The DNA sequences of a wide variety of species are now known, and more are being determined every day. We can expect challenges to the current tree of life (also called the phylogenetic tree) as the data are analyzed and debated.

The Sixth Mass Extinction

Over about 3.5 billion years, evolution (descent of species over time, with genetic modification) has produced the astonishing variety and number of life forms found on Earth today. Punctuating this natural evolutionary process of speciation have been five mass extinctions – periods characterized by the rapid (compared to evolutionary processes) loss of over 75% of all species. Past causes of mass extinctions include major changes in ocean and atmospheric chemistry, changes in climate, periods of volcanic activity, and an impact with an asteroid.

According to a recent review article in Nature, we may be about to enter a sixth mass extinction, meaning that over the next 300 to several thousand years we can expect that over 75% of all current species will become extinct. Somewhat disturbing is the suggested cause – humans. Won’t THAT be an interesting and contentious debate over the next 300 years or so!

This is a well-referenced review in a high-quality journal. It’s worth reading if you’re interested in this subject. The notion that the next mass extinction may be caused by humans is only a small part of it.

Dinosaur Proteins Found in Fossils

Paleontologists have generally assumed that the only useful information that could be obtained from ancient fossils was in the sizes and shapes of the organism’s bones. The prevailing view has been that the soft tissues and any organic molecules or cellular structures within the bones themselves would have long since disappeared, leaving behind only fossils comprised of the same minerals found in rocks.

That view is slowly changing. It now appears that under the right conditions of fossilization, organic molecules may still remain in some fossils. So far, researchers have identified molecules that appear to be collagen and even fossilized osteocytes (bone-forming cells) and red blood cells, from the bones of dinosaurs as old as 80 million years.

No one is suggesting that we could ever resurrect dinosaurs from these ancient materials – cloning dinosaurs is still in the realm of science fiction. However if we could identify the precise sequences of certain ancient proteins, we’d have a better understanding of the function of these proteins within the organism. We might also be able to more accurately map out the evolutionary relationships between organisms, both ancient and living.

Reference: Schweitzer, Mary. Blood From Stone. Scientific American Dec. 2010, pp. 62-69.

A New (Extinct) Human Ancestor

Scientists have discovered two partial skeletons of a new species of the genus Australopithecus near Johannesburg, South Africa, which they named Australopithecus sediba. The new australopithecines, nearly 1.95 million years old, appear to be closely related to both A. Afarensis and A. africanus.

Of course, paleoanthropologists are already debating where to place A. sediba in the human family tree; direct human ancestor, or evolutionary dead end? Regardless of the outcome, the new find is significant in that it fills some gaps in our understanding of evolutionary processes leading to humans. For instance, it appears that changes in the shape of the pelvis occurred before brain enlargement, and that the legs underwent adaptive changes for upright walking before the arms took on smaller, more human-like proportions.