I, microbe: Sequencing the bugs in our bodies
20 May 2010 by Caitlin Stier
People are more microbe than human, with microbes outnumbering our cellsby 10 to 1. But strangely, scientists know more about the microbes that inhabit the soil and sea than those that call us home. Now, the genetic sequencing of 178 of these microbes will help close that gap.
Scientists have long known that our microbial inhabitants, collectively known as the microbiome, can contribute to disease. But culturing the cells outside of the human body can be difficult, complicating efforts to identify many of them, particularly rare species.
Read the rest of this entry here.
O noes! Another species of human in Eurasia?
http://whyevolutionistrue.wordpress.com/2010/05/13/o-noes-another-species-of-human-in-eurasia/
The story of Homo keeps getting weirder and weirder. Just as I was getting used to the idea that Neandertals may have tossed the salad with more modern Homo sapiens, somebody calls my attention to yet anotherlineage of Homo that may have coexisted with both “modern” humans and Neandertals. This conclusion comes from DNA extracted from a single bone and described in a paper by Krause et al. (and, of course, Svante Pääbo) in the April 8 issue of Nature.
(Why Evolution Is True, May 13, 2010)
NEANDERTALS LIVE!
at 7:54 am on Saturday, 8 May 2010
I, for one, welcome my Neandertal ancestry.
It may not sound like a lot — between 1 and 4 percent. But that’s the equivalent of one great-great-great grandparent’s DNA contribution. In the case of the Neandertal contribution, more than 1500 generations ago, it’s an enduring legacy of an ancient group of people, spread across many lines of the genealogies of living people. Beyond their genealogical interest, Neandertal genes might have made a big difference to our evolutionary potential.
In case you wonder what the heck I’m talking about, here’s the story: Two new papers in Science describe the full draft sequence of the Neandertal genome, and perform additional analyses to understand the pattern of adaptive evolution in the population ancestral to living people.
(John Hawks Weblog, May 6, 2010)
Signs of Neanderthals Mating With Humans
http://www.nytimes.com/2010/05/07/science/07neanderthal.html?emc=tnt&tntemail1=y
Neanderthals mated with some modern humans after all and left their imprint in the human genome, a team of biologists has reported in the first detailed analysis of the Neanderthal genetic sequence.
The biologists, led by Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have been slowly reconstructing the genome of Neanderthals, the stocky hunters that dominated Europe until 30,000 years ago, by extracting the fragments of DNA that still exist in their fossil bones. Just last year, when the biologists first announced that they had decoded the Neanderthal genome, they reported no significant evidence of interbreeding.
(New York Times, May 6, 2010)
Cracking the Genetic Code of a Frog
Unless your father was a prince with a shady past, you probably haven’t thought much about how related you are to a frog lately. But it turns out that about 80 percent of the genes known to cause diseases in humans have counterparts in the genome of Xenopus tropicalis—the western clawed frog native to sub-Saharan Africa.
Scientists at the Joint Genome Institute in California revealed the Xenopus genome in the April 30 issue of Science. It’s the first frog to have its genetic code cracked and the first amphibian.
(Scientific American, May 4, 2010)
Do chimps say “no” by shaking their heads?
at 8:02 am on Friday, 7 May 2010
http://whyevolutionistrue.wordpress.com/2010/05/06/do-chimps-say-no-by-shaking-their-heads/
When people study primate behavior with the idea of relating it to human behavior, standards of evidence often seem quite low. There’s a lot of publicity and attention to be gotten by detecting the roots of our behavior in the other apes that are our relatives. Who among us hasn’t been fascinated by going to the zoo, watching a chimp, and saying, “Wow–they’re so much like us!”
This is not to deny that some of our behaviors descend from those of apey ancestors. They do, of course, and Darwin was the first to write about it. But we also have culture that can rapidly transmit un-apelike behaviors across diverse groups (e.g., dancing and making music).
(Why Evolution is True, May 6, 2010)
Close encounters of the weird kind: Quick guide to the Neandertal genome
http://whyevolutionistrue.wordpress.com/2010/05/07/quick-guide-to-the-neandertal-genome/
The genome of Neandertals was just sequenced (reference below).
For those of you who don’t want to plow through the long (but informative!) explanatory about the Neandertal genome that have appeared on several science websites, here’s a quick guide:
- What’s the deal? A large group of scientists from several countries have determined the DNA sequence of most of the Neandertal genome.
- Is it “Neandertal” or “Neanderthal”? Either is correct. “Neanderthal” is most common but the new Science paper uses “Neandertal.” The name is taken from the German “Neander Tal”, or “Neander Valley,” where the first bones of these individuals were found.
(Why Evolution is True, May 7, 2010)
New australopithecine described
at 1:06 pm on Saturday, 10 April 2010
http://whyevolutionistrue.wordpress.com/2010/04/08/new-australopithecine-described/
Lee Berger of the University of the Witwatersrand and several colleagues will be describing a new species of Australopithecus, A. sediba, from 1.78 to 1.95 million-year-old deposits in South Africa, intomorrow’s issue of Science. The issue will also have a geological article on the find by Paul H.G.M. Dirks of James Cook University, Queensland, and colleagues, and a news item, all available now atScience’s website (plus a podcast and video). The description is based on two partial skeletons, including a well preserved juvenile skull, most of the right arm and shoulder girdle, parts of the hip and leg, and various other bits.
(Why Evolution is True, April 8, 2010)
Fossil skeletons may belong to an unknown human ancestor
at 12:24 pm on Saturday, 10 April 2010
http://www.guardian.co.uk/science/2010/apr/08/fossil-skeletons-unknown-human-ancestor
Fossilised skeletons recovered from a deep underground cave in South Africa belong to a previously unknown species of human ancestor, scientists claim.
The partial skeletons of an adult female and a young male, aged 11 or 12, were found lying side by side in sediments that first covered their remains an estimated 1.9m years ago.
The individuals are thought to have fallen into the cave network through a fissure before being carried a few metres by mud or water into a subterranean pool, where they were gradually encased in rock.
(guardian,co.uk, April 8, 2010)
New Hominid Species Discovered in South Africa
at 12:17 pm on Saturday, 10 April 2010
http://www.nytimes.com/2010/04/09/science/09fossil.html?pagewanted=2&tntemail1=y&emc=tnt
CRADLE OF HUMANKIND, South Africa — Nine-year-old Matthew Berger dashed after his dog, Tau, into the high grass here one sunny morning, tripped over a log and stumbled onto a major archaeological discovery. Scientists announced Thursday that he had found the bones of a new hominid species that lived almost two million years ago during the fateful, still mysterious period spanning the emergence of the human family.
Dad, I found a fossil!” Matthew said he cried out to his father, Lee R. Berger, an American paleoanthropologist, who had been searching for hominid bones just a hill and a half away for almost two decades. Fossil hunters have profitably scoured these rolling grasslands north of Johannesburg since the 1930s.
(NY Times, April8, 2010)
Gut bacteria are what we eat
http://www.the-scientist.com/blog/display/57272/
Gut microbes, which help humans degrade otherwise indigestible plant material, acquire some crucial digestive enzyme genes from the bacteria in the food we eat, according to a study published this week inNature. This new finding provides an example of horizontal gene transfer by which diet can influence the genetic diversity and functionality of the human gut microbiome.
“It’s a fascinating story,” said microbiologistJeffrey Gordonof Washington University School of Medicine in St. Louis, who did not participate in the study. “It shows that there’s a dimension to human evolution that’s occurring at the level of our gut microbiome.”
(The-scientist.com, April 7, 2010)
Close to Homo? – The announcement of Australopithecus sediba
http://scienceblogs.com/laelaps/2010/04/close_to_homo_-_the_announceme.php
A little less than two million years ago, in what is now South Africa, a torrential downpour washed the bodies of two humans into the deep recesses of a cave. Just how their remains came to be in the cave in the first place is a mystery. Perhaps they fell in through the gaping hole in the cave roof just as hyenas, saber-toothed cats, horses, and other animals had, but, however the humans entered the cave, their bones ultimately came to rest in a natural bowl carved into the rock. This mode of preservation would keep their remains in good condition until their discovery in 2008, and today in the journal Science a team of researchers has described them as the latest addition to our family tree, Australopithecus sediba.
(Laelaps, April 8, 2010)
New hominin found via mtDNA
http://www.the-scientist.com/blog/display/57254/
A previously unknown human ancestor may have coexisted with Neanderthals and early modern humans, German researchers report online inNaturetoday (March 24).
| For the first time, the scientists identified the novel hominin using mitochondrial gene sequencing of bone fragments, not fossils. The genomic analysis also revealed a hitherto-unknown migration from Africa to Eurasia just under one million years ago. “It’s such a surprise,” said Terence Brown, a biomolecular archaeologist at the University of Manchester, who was not involved in the study. “You start to think, how complete is our knowledge of ancient human ancestors?” |
(NewScientist.com, March 24, 2010)
Famous Footprints Yield New Insights Into How Fossil Humans Walked
at 10:25 am on Wednesday, 24 March 2010
http://scienceblogs.com/laelaps/2010/03/famous_footprints_yield_new_in.php
About 3.6 million years ago, at a spot now in Laetoli, Tanzania, a pair of hominins trudged through the ashfall dumped onto the landscape by a nearby volcano. We don’t know for certain what they looked like (it is generally believed that they were Australopithecus afarensis from the presence of fossils found at the site), but the fossil trackway they left behind has provided scientists with a narrow glimpse into the life and behavior of these individuals. The big question has been what these tracks say about how the prehistoric humans moved. Did they walk like us, like apes forced to stand up, or in an entirely different fashion?
According to a new study published this week in PLoS One, the famous Laetoli trackway preserves the footprints of upright, bipedal hominins that walked in a manner extremely similar to us. . . .
(Scienceblogscom, March 23, 2010)
New Finding Puts Origins of Dogs in Middle East
http://www.nytimes.com/2010/03/18/science/18dogs.html?emc=tnt&tntemail1=y
Borrowing methods developed to study the genetics of human disease, researchers have concluded that dogs were probably first domesticated from wolves somewhere in the Middle East, in contrast to an earlier survey suggesting dogs originated in East Asia.
The dingo was one of the breeds studied to determine where dogs were first domesticated from wolves.
This finding puts the first known domestication — that of dogs — in the same place as the domestication of plants and other animals, and strengthens the link between the first animal to enter human society and the subsequent invention of agriculture about 10,000 years ago.
(New York Times, March 18, 2010)
“Ida” not a missing link
at 12:22 pm on Sunday, 7 March 2010
http://whyevolutionistrue.wordpress.com/2010/03/06/ida-not-a-missing-link/
On May 20 of last year, at a remarkable press conference in New York, a group of researchers announced—with much ballyhoo—that they’d found a 47-million-year-old primate fossil named Darwinius masillae(nicknamed “Ida”). Ida, the finest fossil primate in existence, was touted loudly as the missing link between the two major branches of primates, the Haplorhini (anthropoids [apes and monkeys] and tarsiers), and the Strepsirrhini (lemurs and lorises; see figure below). Concurrent with the press conference was a History Channel documentary and a book about Ida, Colin Tudge’s The Link, that proclaimed, with much heavy breathing, that Ida was, as one of the earliest primate ancestors of our own species, an earthshaking discovery (see my review of the book here).
Surprising mtDNA diversity
http://www.the-scientist.com/blog/display/57199/
Mitochondrial genomes are not uniform across cells of the body as previously believed, but vary between different tissue types, according to a study published online today (March 3) inNature.
The findings may affect forensics and the search for biomarkers, both of which utilize mitochondrial DNA.
(more…)
Human Culture, an Evolutionary Force
http://www.nytimes.com/2010/03/02/science/02evo.html?em
As with any other species, human populations are shaped by the usual forces of natural selection, like famine, disease or climate. A new force is now coming into focus. It is one with a surprising implication — that for the last 20,000 years or so, people have inadvertently been shaping their own evolution.
The force is human culture, broadly defined as any learned behavior, including technology. The evidence of its activity is the more surprising because culture has long seemed to play just the opposite role. Biologists have seen it as a shield that protects people from the full force of other selective pressures, since clothes and shelter dull the bite of cold and farming helps build surpluses to ride out famine.
Evolution by the Grassroots
http://opinionator.blogs.nytimes.com/2010/03/02/evolution-by-the-grassroots/?hp
Imagine the Earth without grasses.
There would be no lawns or meadows. No prairies. No savannahs or steppes. No wheat fields or rice paddies. No sugar cane.
No sheep, elephants or horses.
No people.
We live in the age of grass. Indeed, from our point of view, the evolution of grasses was one of the most momentous events in the history of the Earth. Which is why I’m nominating them for Life-form of the Month: March.
(New York Times, March 2, 2010)
Morality and religion: are they genetic adaptations?
In a new paper, “The origins of religion: evolved adaptation or byproduct?”, Ilkka Pyysiäinen from the University of Helsinki and Marc Hauser from Harvard discuss the evolution of religion and morality (The paper was highlighted by Philip Ball in Nature News and by P.Z. at Pharyngula.) The paper is divided roughly into two parts: . . .
(Why Evolution Is True, February 14, 2010)
Ancient humans more diverse?
at 2:21 pm on Wednesday, 10 February 2010
http://www.the-scientist.com/blog/display/56279/
Researchers have delved back further than ever into the genetic history of humans, and found that the ancient population that gave rise to modern humans may have been nearly twice as genetically diverse than humans today, according a study published this week in Proceedings of the National Academy of Sciences.
 |
| Scientific reconstruction of a Homo erectus Image: Wikimedia commons, Lillyundfreya |
While most studies on the genetics of ancient humans have focused on the last half million years, this study looks at particularly old areas of the genome, allowing the researchers to look at the more distant past, said molecular geneticist Prescott Deininger of the Tulane Cancer Center in New Orleans, LA, who was not involved in the research. “This [study] is a little window to look back a little bit further,” he said.
(The Scientist.com, January 11, 2010)
First ancient human sequenced
at 1:58 pm on Wednesday, 10 February 2010
http://www.the-scientist.com/blog/display/57140/
For the first time researchers have sequenced an ancient human genome, revealing characteristics of Greenland’s first inhabitants and providing evidence of a previously unknown human migration, according to a study published in this week’s Nature.
 |
Artist rendition of ancient Saqqaq Image: Nuka Godfredtsen |
Past studies have sequenced partial genomes or mitochondrial DNA, which only codes for the mother’s side of the genome, said David Lambert, an evolutionary biologist from Griffith University who was not involved in the study. “But this is really the first complete ancient human genome.”
(The Scientist.com, February 10. 2010)
THE COEVOLUTION OF HUMAN HANDS AND FEET
(Evolution: International Journal of Organic Evolution, January 29, 2010)
Becoming Human
The Institute of Human Origins provides this site dedicated to human evolution.
The Ancestor Hunter
http://www.miller-mccune.com/science_environment/the-ancestor-hunter-1372
The University of Arizona’s Michael Hammer is using advanced DNA techniques to figure out where we came from. Which, apparently, is not just one place, or even one species.
Maybe it’s the scooter propped in the corner of his office, or the fact that he’s wearing a T-shirt and denim cargo shorts while sporting a gold hoop in his left ear, but Michael Hammer definitely looks more like a surfer than one of the world’s leading gene detectives. The maps are a giveaway, though.
(Miller – McCune, August 31, 2009)