Interesting Science

Steven Squyres [1], professor of astronomy and NASA's principal investigator for the Athena science packages carried by the two Mars rovers (Spirit and Opportunity), is interviewed by Jane Platt: listen to the podcast here (transcript appended below).

Watch Jake Matijevic from the Mars Exploration Project give the Flight Director's Report for January 22, 2007 (Quicktime) celebrating the third anniversary of Opportunity landing on Mars.

Transcript:

NARRATOR: Three years old, and the Mars rovers are getting even smarter. I'm Jane Platt with a podcast from JPL - NASA's Jet Propulsion Laboratory in Pasadena, California. Our guest today, Dr. Steve Squyres of Cornell University, the principal investigator for the science instruments on the twin Mars rovers, Spirit and Opportunity. The rovers are marking their third year operating on Mars this month. Steve, thanks for joining us, and it's kind of an amazing milestone.

DR. STEVE SQUYRES: Yeah, I'm frankly astonished. I mean if you had asked me three years ago, heck if you had asked me two years ago, if we were going to make it to this point I would have said no way, and they're still doing astonishingly well.

NARRATOR: So you really kind of have way bonus overtime, I mean you're getting to do a lot of things and study a lot of things and find out things that you never dreamed.

SQUYRES: We are and a key point there is that Mars keeps throwing new stuff at us. It's not like we're seeing the same things again and again. We've just seen the most spectacular vistas that the Opportunity rover has ever seen just in the past few months. Far more spectacular than anything we'd seen prior to this. So Mars keeps giving us new things to look at.

NARRATOR: The rovers will be able to do some new things, thanks to some recently uploaded software. Tell me what they'll be able to do that they couldn’t do before.

SQUYRES: Yeh, we taught them some new tricks, ya know when you spend enough time working in what used to be an unknown environment, you learn new things that you'd like to be able to do, and we've given the rovers some new capabilities. One of the ones that I love is something that, we call it "go and touch." For a long time we've done a maneuver that we call "touch and go." In "touch and go," you reach out with the arm and you make a measurement with the arm. And then you put the arm back where it stows away and you drive. But in a "go and touch," what you do is the opposite of that. Let's say there's a rock that's 10 feet away that the science team is interested in. Normally what you'd have to do is take two full days to do that, you'd have to drive to it, once you get there you take some pictures that show where the rock is, send them down to Earth, we look at the pictures, decide how do we deploy the arm onto the rock, and then we go ahead and do it on the second day. With "go and touch," we can just tell the rover, "Okay, we want to see, we want the spectrometer to be placed on that rock," and it will drive over to it and place it all in one day. Huge timesaver. Another one is, of course, there are these wonderful dust devils, right, the dust devils, these little Martian mini-tornadoes that go whirling across the plains. And the way we used to do these spectacular dust devil movies in the past is we'd just take lots of pictures and hope that a dust devil would show up. And sometimes they would, and most of the time they wouldn’t. And we'd waste all these pictures that had nothing in them. What we've done is we've taught the rovers how to find dust devils on their own, to take a picture, evaluate it, if it thinks there's a dust devil it'll send the pictures down, if not, it doesn't bother us with them. One of the new software tricks that we've got is vastly improved navigation, this thing could, the rover could actually sort of work its way through a maze now, if it had to, by kind of going down blind alleys and then figuring out how to retrace its steps and going another way.

NARRATOR: Last time we had you on one of our JPL podcasts was a year ago when the rovers were marking their second anniversary on the red planet. And here we are a year later. You at that time had kind of brought us up to speed on what the rovers had accomplished so far. Bring us up to date now, this past year, what have we learned?

SQUYRES: Okay. The big accomplishment for Spirit this past year has been that we finally reached "Home Plate." Home plate is this feature, man, we spotted that thing from orbit years ago. It's a really interesting feature within Gusev crater, it’s a plateau of layered rocks, it's the best outcrop of layered rocks the rover has ever seen. And we got a chance to explore that pretty thoroughly. What we've concluded is it was probably the result of a volcanic explosion. If volcanic lava comes into contact with water, say, that water will flash into steam, and you'll get this explosion, and you can get a deposit very much like what we see at Home Plate. The big achievement for Opportunity is we finally made it to Victoria crater. That was a 21-month drive, to drive that rover through terribly difficult terrain. It was just an unparalleled exercise in mobility on another planet. And finally after driving all those months and all those kilometers, we pulled up to the rim of the most spectacular feature that either rover has ever seen. And we're not just there for the scenery. This thing provides a deeper, broader window into the subsurface of mars and exposes more rocks than anything we could possibly hope to find with this vehicle, so we've got this geologic treasure trove that we're just barely beginning to explore now.

NARRATOR: Okay, let's take what you’ve learned in the past year and then add it to the previous two years. If you at this point had to write a little tour brochure for Mars, how would you describe the destination?

SQUYRES: The two destinations that we've been to are dramatically different from one another. The picture that we've put together of what Gusev crater, where Spirit is, long ago, what that place was like, it was a violent world . This was a place that was dominated by meteoritic impacts, effectively creating huge explosions that would throw materials into the air, volcanic explosions were going on. There was water, but it was mostly water beneath the ground, these impact craters and these volcanic vents would create explosions of steam, I mean it was a very violent place. In some respects, it had the characteristics that would have been favorable for life, there were probably hot springs, for example. But it wouldn’t have been a very nice place to be. Meridiani Planum, on the other hand, where Opportunity is, the geologic record that we see there preserved in the rocks is more quiescent, it's a place that was pretty dry most of the time. There was a lot of water beneath the ground. And when I say water, what I really mean is sulfuric acid, you wouldn't want to drink this stuff. But there was this acidic water beneath the ground, it saturated the ground, and it would occasionally come to the surface and form pools and ponds and perhaps little streams, evaporate away and when it evaporated away, it would leave salt deposits behind. And then these salt deposits would blow in the wind, and they would form dunes, and we see the record of those salty dunes preserved in the walls of Victoria crater. So it was not exactly an evolutionary paradise either, there was acid, it was dry much of the time, but it's the kind of environment that would have been definitely suitable for some simple forms of life.

NARRATOR: So there has been a lot learned, obviously, from these two rovers, which by the way, we don't know how much longer they will continue to operate.

SQUYRES: They could last another three years or they could die tomorrow, and there's no way of telling. We try to live every day with these vehicles as if it's the last. You drive them each day as if there literally is no tomorrow, because that could be the reality, so we're pushing them very hard, we're pushing ourselves very hard.

NARRATOR: And at whatever point they are no longer with us and functioning, other spacecraft up there already, more in the works.

SQUYRES: Oh, yeah, yeah. I mean, we've got this wonderful synergy going on right now among four different JPL spacecraft that are at Mars. You’ve got the two rovers on the surface. They're communicating with us daily, relaying information through the Mars Odyssey orbiter. And then at the same time, we have the newly arrived MRO, Mars Reconnaissance Orbiter, that's up there, taking incredible images where you can see the rovers on the surface, and we daily use that imaging capability and the pictures that MRO has taken of our sites to plan our operations. And, of course, the scientific discoveries that are coming out of all the instruments on the Reconnaissance Orbiter right now are just fantastic. You’ve got phoenix, the next JPL mission that's going, which is a lander.

NARRATOR: That's this summer.

SQUYRES: It's going to launch this summer, its going to land near the north pole of Mars and follow up on a discovery from Mars Odyssey that there's ice close beneath the ground at those latitudes, dig down into the ice and see what's in it. And then one of the ones that I'm really excited about, because I'm a rover guy, is you got the Mars Science Laboratory, MSL, in 2009, which is a bigger, beefier, better version of Spirit and Opportunity. It could last, it's designed to last a full Martian year, it's designed to go for very long distances, carries just a spectacular payload of scientific instruments, a lot of the things that I wish we could have had room to put on Spirit and Opportunity. So it's just gonna keep going, it's great.

NARRATOR: And just to sum up, I guess we can't reiterate enough times, the reason we're doing all this, what we want to find out is?

SQUYRES: Whether or not, Mars, which today is a cold and dry and desolate world, ever has harbored life, and find out whether or not we're alone, in the solar system and in the universe.

NARRATOR: Alright, well thank you so much for your time, Steve... You've been listening to a podcast from NASA's Jet Propulsion Laboratory.

Source: NASA 01.17.07 (Abridged)

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Steven Squyres co-authored this paper from the journal Science:

Science 5 August 1994:
Vol. 265. no. 5173, pp. 744 - 749
DOI: 10.1126/science.265.5173.744

Early Mars: How Warm and How Wet?
Steven W. Squyres and James F. Kasting (Faculty | Biblio) [2]

Early in its history, Mars underwent fluvial erosion that has been interpreted as evidence for a warmer, wetter climate. However, no atmosphere composed of only CO2 and H2O appears capable of producing mean planetary temperatures even close to 0°C. Rather than by precipitation, aquifer recharge and ground water seepage may have been enabled by hydrothermal convection driven by geothermal heat and heat associated with impacts. Some climatic warming was probably necessary to allow water to flow for long distances across the surface. Modest warming could be provided by even a low-pressure CO2 atmosphere if it was supplemented with small amounts of CH4, NH3, or SO2. Episodic excursions to high obliquities may also have raised temperatures over some portions of the planet's surface.

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[2] James F. Kasting is author of "Habitable Climates":

"One of the fundamental requirements for life as we know it is the presence of liquid water on (or below) a planet’s surface. If one is interested in detecting life remotely with Terrestrial Planet Finder (TPF), then it is important that the liquid water environment be in contact with the planet’s atmosphere, as it is only by potential biological modifications of atmospheric composition that we can can hope to do this. Possible subsurface liquid water habitats such as those that might exist on Mars or Europa are interesting with respect to our own Solar System but would be difficult or impossible to investigate on planets around other stars."

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Recent posts include:

"Microbe experiment suggests we could all be Martians"

"NASA Spacecraft En Route to Pluto Prepares for Jupiter Encounter (+ Animation)"

Technorati: steven, squyres, astronomy, nasa, athena, science, packages, podcast, mars, exploration, project, flight, director, spirit, discovery, jpl, jet, propulsion, laboratory, cornell, university, martian, earth, volcanic, victoria, crater, gusev, sulfuric, acid, evolutionary, reconnaissance, orbiter, mro, mission

Permanent Link posted by John Latter @ 5:12 PM 0 comments

Officials from the Awashima Marine Park in Shizuoka, Tokyo caught a 'living fossil' earlier this week after a fisherman from a nearby port informed them of the existence of a strange eel-like creature.

More info on Chlamydoselachus anguineus, a primitive species of shark with 6 gills instead of 5, available from Biology of Sharks and Rays:

"...body elongated and eel-like; snout blunt, jaws long and narrower at tip than at corners..."

The story was carried by many news agencies including Taiwan's The China Post: "Japanese marine park captures rare shark on film"

Another video from the National Oceanic and Atmospheric Administration (NOAA): "Ocean Explorer - A frilled shark" [Prehistoric]

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Information on the Frilled Shark from the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species*:

Justification: A generally rare to uncommon deepwater species, with a few localities where it is taken more commonly as bycatch in several fisheries. Not an important target species, but a regular though small bycatch in many bottom trawl, midwater trawl, deep-set longline, and deep-set gillnet fisheries. As bycatch, this species is variously either used for meat, fishmeal, or discarded. Occasionally kept in aquaria (Japan). There is some concern that expansion of deepwater fisheries effort (geographically and in depth range) will increase the levels of bycatch. Although little is known of its life history, this deepwater species is likely to have very little resilience to depletion as a result of even non-targeted exploitation. It is classified as Near Threatened due to concern that it may meet the Vulnerable A2d+A3d+4d criteria.

Range: Generally rare, only a few localities where it is more common. Range almost worldwide.

Population: No information on population size anywhere.

Habitat and Ecology: Marine, demersal or benthopelagic, reported as occasionally pelagic on the upper and middle continental slope, 100–1,500 m, usually 500–1,000 m. An active predator on deepwater squid and a variety of fish (including other sharks). Large mouth with sharp inwards-pointing teeth can take large prey, but this shark is not considered dangerous to man. Born 40-60 cm total length (TL). Mature 97-117 cm TL (males), 135-150 cm TL (females). Maximum approximately 196 cm TL (females). Ovoviviparous with 6-12 pups per litter, possibly a long gestation period but life cycle basically unknown.

Threats: Not a targeted fisheries species, but taken as bycatch in bottom and midwater trawls, deep-set longlines, and in deep-set gill nets. No population baseline or trends available. Some concern that increased deepwater fisheries effort (geographically and in depth range) may increase levels of bycatch. The bycatch is sometimes utilized for fishmeal and for meat. Occasionally kept in aquaria (Japan).

Conservation Measures: None known for this species. A very few states are developing or have developed shark management plans within the context of the FAO IPOA-Sharks, but few if any of these include measures for the management of deepwater fisheries bycatch.

*Citation:Paul, L. & Fowler, S. 2003. Chlamydoselachus anguineus. In: IUCN 2006. 2006 IUCN Red List of Threatened Species.

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Tanaka, S., Shiobara, Y., Hioki, S., Abe, H., Nishi, G., Yano, K. and Suzuki, K. 1990. The reproductive biology of the frilled shark, Chlamydoselachus anguineus, from Suruga Bay, Japan. Japanese Journal of Ichthyology. 37(3): 273–291.

An analysis of the reproductive biology of the frilled shark , Chlamydoselachus anguineus, was made on the basis of a collection of 264 specimens from Suruga Bay, Japan. This species is caught mainly from December to July. Almost all specimens were mature. The frilled shark appears to segregate by size and reproductive stage. Males mature below 1,100 mm total length (TL), while females reach sexual maturity between 1,400 and 1,500 mm TL. Males have active testes throughout the year. Females do not have a defined reproductive season. Ova emerge through each ovulation pore on the ovarian epithelium at a size of 230-250 g, and only enter the right oviduct. Ovarian eggs do not continue to develop during gestation. Egg capsules are shed when embryos reach between 60 and 80 mm TL.

Young are born at a size of about 550 mm TL and 380 g body weight. Litter size ranges from 2 to 10, with a mean of 6. Late stage embryos may receive nutrients from the mother. The intervals of ovulation seem to be about two weeks. The ovulation season in each female extends over a few months. The gestation period to last at least three and a half years. The encapsulated embryos maintained in artificial conditions grow at a rate of between 10 and 17 mm per month for a period up to 134 days.

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A paper presented at the 7th Indo-Pacific Fish Conference (IPFC) at Taipei, Taiwan (16-21 May 2005):

Histological Observation of Organogenesis, Especially gonadogenesis, in Frilled Shark Embryos

Sho Tanaka

(School of Marine Science and Technology, Tokai University)

The frilled shark, Chlamydoselachus anguineus, is known as one of ancient type sharks. The organogenesis in the frilled shark embryos was examined histologically. A total of 38 embryos from 15 mm to 356 mm in total length were collected from 13 pregnant sharks. The epithelium of stomach and intestines were developed abruptly in 20-30 mm TL and specialized in 100 mm TL. Rathke’s pouch was observed in 15 mm TL embryo. The ventral lobe of pituitary gland was specialized in 100 mm TL. Thyroid gland was formed in 15 mm TL embryo.

Several sizes of follicles were observed in 127 mm TL. Follicles of 219 mm TL embryo possessed a secretion in the inside. Pronephros was observed in 15 mmTL embryo and renal tubule was in 40 mm TL. Rectal gland was recognized in 30 mm TL embryo. The excretory tubules were specialized in 128 mm TL. Primordial germ cells were observed in the dorsal epithelium of abdominal cavity of 15 mm TL embryo. The germinal ridge was formed in 30-40 mm TL. The cortex of germinal ridge was developed in 56 mmTL embryo and the embryo was supposed to be female. Embryo in 108 mm TL possessed a pair of claspers and follicle-like cells in the medulla of germinal ridge.

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A recent post:

"Japan Researchers Film Live Giant Squid (Video)"

Technorati: awashima, marine, park, shizuoka, tokyo, japan, living fossil, primitive, species, shark, biology, japanese, rare, film, noaa, ocean, explorer, red, list, threatened, video, habitat, ecology, frilled, organogenesis, embryo, giant, squid, prehistoric

Permanent Link posted by John Latter @ 11:14 AM 1 comments

It has been known for some years that mother and baby exchange stem cells in the course of pregnancy, and that these may live on for many years [1], apparently tolerated by the new host. The phenomenon is known as microchimerism [2], and it is still unclear as to whether the presence of such cells can be harmful to the recipient.

A Bristol team has looked for maternal cells in children with type 1 diabetes, an immune-mediated disorder, and found that around 20 per cent of these children have unusually high levels of maternal DNA in their circulation. An even more surprising finding is that some maternal cells have entered the child's pancreas and are functioning there as insulin-producing beta cells.

The study, initially undertaken in the belief that maternal cells might trigger autoimmunity in the child, has now taken an interesting new twist, for the maternal cells might even be helping the child to repair injury.

In this study [3], published in the January 22 issue of the Proceedings of the National Academy of Sciences (PNAS), Dr Kathleen Gillespie and Professor Edwin Gale from the Department of Clinical Science at North Bristol in collaboration with Professor J. Lee Nelson and colleagues at Fred Hutchinson Cancer Research Center, Seattle, found no evidence that the mother's cells were attacking the child's insulin cells and no evidence that the maternal cells were targets of an immune response from the child's immune system.

Instead, the researchers found a small number of female islet beta cells in male pancreatic tissue (procured from autopsies) that produced insulin. Microchimerism is the term used when an individual harbors cells or DNA that originate from another genetically distinct individual. "To our knowledge a maternal contribution to endocrine function has not previously been described," the authors said. "Our findings also raise the possibility that naturally acquired microchimerism might be exploited to therapeutic benefit."

The study also found significantly higher levels of maternal DNA in the peripheral blood of 94 children and adults with Type 1 diabetes as compared to 54 unaffected siblings and 24 unrelated healthy subjects they studied.

Originally, the study of 172 individuals and pancreatic tissue from four males was designed to ask the question whether small numbers of maternal cells might be involved in any way in Type 1 diabetes. "Our initial theory was that perhaps, in some situations, too many cells cross from mother to fetus in pregnancy. Could diabetes result because the child lost tolerance to those cells because they are genetically half foreign? Our research appears to disprove this," said Professor Gale. "It is possible that the maternal cells may even be helping to regenerate damaged tissue in the pancreas."

The investigators are excited about the observation that maternal microchimerism results in cells that make insulin - these maternal stem cells could provide new insights into how insulin producing beta cells are generated. [Source: University of Bristol]

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[1] Fetal microchimerism - what our children leave behind
Michael Verneris
Blood 2003 102: 3465-3466.

"Fetal microchimerism (FMc) describes the persistence of low numbers of fetal cells in the mother after a pregnancy. A number of recent studies suggests FMc may play a role in the etiology of some autoimmune diseases. Remarkably, FMc has been demonstrated to persist for up to 38 years after pregnancy and has been found in multiple lymphocyte subsets and in early lymphoid precursors. In a single patient, FMc was demonstrated in CD34+ cells, suggesting that FMc may result from the engraftment of a long-term repopulating or stem cell."

[2] Definition from MedicineNet's Medical Dictionary:

Microchimerism: The presence of two genetically distinct and separately derived populations of cells, one population being at a low concentration, in the same individual or an organ such as the bone marrow. Microchimerism may be due to transfer of cells between mother and fetus or between two twins. Other sources of microchimerism include blood transfusions and transplants. See also: Chimera.

[3] Lee Nelson, Kathleen M. Gillespie, Nathalie C. Lambert, Anne M. Stevens, Laurence S. Loubiere, Joe C. Rutledge, Wendy M. Leisenring, Timothy D. Erickson, Zhen Yan, Meghan E. Mullarkey, Nick D. Boespflug, Polly J. Bingley, and Edwin A. M. Gale
Maternal microchimerism in peripheral blood in type 1 diabetes and pancreatic islet {beta} cell microchimerism
PNAS published January 23, 2007, 10.1073/pnas.0606169104

Maternal cells have recently been found in the circulation and tissues of mothers' immune-competent children, including in adult life, and is referred to as maternal microchimerism (MMc). Whether MMc confers benefits during development or later in life or sometimes has adverse effects is unknown. Type 1 diabetes (T1D) is an autoimmune disease that primarily affects children and young adults.

To identify and quantify MMc, we developed a panel of quantitative PCR assays targeting nontransmitted, nonshared maternal-specific HLA alleles. MMc was assayed in peripheral blood from 172 individuals, 94 with T1D, 54 unaffected siblings, and 24 unrelated healthy subjects. MMc levels, expressed as the genome equivalent per 100,000 proband cells, were significantly higher in T1D patients than unaffected siblings and healthy subjects. Medians and ranges, respectively, were 0.09 (0-530), 0 (0-153), and 0 (0-7.9). Differences between groups were evident irrespective of HLA genotypes. However, for patients with the T1D-associated DQB1*0302-DRB1*04 haplotype, MMc was found more often when the haplotype was paternally (70%) rather than maternally transmitted (14%).

In other studies, we looked for female islet {beta} cells in four male pancreases from autopsies, one from a T1D patient, employing FISH for X and Y chromosomes with concomitant CD45 and {beta} cell insulin staining. Female islet {beta} cells (presumed maternal) formed 0.39-0.96% of the total, whereas female hematopoietic cells were very rare. Thus, T1D patients have higher levels of MMc in their circulation than unaffected siblings and healthy individuals, and MMc contributes to islet {beta} cells in a mother's progeny.

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A recent post:

"Scientists create 3-D scaffold for growing stem cells"

Technorati: mother, baby, stem cells, microchimerism, maternal, cells, children, diabetes, type, 1, dna, child, pancreas, insulin, beta, study, autoimmunity, pnas, cancer, research, evidence, immune, response, system, blood, stem, diseases, pregnancy, cell, mmc, genome, x, y, chromosomes

Permanent Link posted by John Latter @ 11:46 PM 0 comments

Excerpts from an open access PLoS ONE article plus a related news report and associated PNAS paper:

Summary

Gene families are groups of homologous genes that are likely to have highly similar functions. Differences in family size due to lineage-specific gene duplication and gene loss may provide clues to the evolutionary forces that have shaped mammalian genomes. Here we analyze the gene families contained within the whole genomes of human, chimpanzee, mouse, rat, and dog. In total we find that more than half of the 9,990 families present in the mammalian common ancestor have either expanded or contracted along at least one lineage. Additionally, we find that a large number of families are completely lost from one or more mammalian genomes, and a similar number of gene families have arisen subsequent to the mammalian common ancestor. Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees, including changes likely driven by adaptive natural selection. Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic "revolving door" of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.

Introduction

Explaining the obvious morphological, physiological, and behavioral traits that separate modern humans from our closest relatives, the chimpanzees, is challenging given the low level of nucleotide divergence between the two species. More than 30 years have passed since King and Wilson ("Evolution at two levels in humans and chimpanzees") first pointed out this apparent paradox, saying that "the genetic distance between humans and the chimpanzee is probably too small to account for their substantial organismal differences". To explain the paradox, King and Wilson proposed that regulatory changes rather than protein-coding mutations were responsible for the vast majority of observed biological differences. Evidence gathered since that time demonstrates that amino acid and regulatory sequence changes have both been involved in the evolution of uniquely human phenotypes.

A third source of differentiation, necessarily overlooked in comparison of orthologous sequences, is the differential duplication and deletion of chromosomal regions. Among human segmental duplications larger than 20 kilobases, 33% are not present in chimpanzee. In total, it is estimated that at least 2.7% of the total genome has been uniquely duplicated subsequent to the human-chimpanzee split; this number does not factor either deletions or small insertions into the total amount of divergence and therefore represents a minimum estimate. Per base pair, this translates into more than twice as many nucleotides unique to each species as there are nucleotide substitutions in orthologous sequences. Without accounting for differences in the total DNA unique to each species, we cannot hope to take a proper accounting of the meaningful genetic divergence between humans and chimpanzees.

The most interesting duplication/deletion events from an evolutionary viewpoint are those that involve intact genes. Gene duplication has been hypothesized to be a powerful engine for evolutionary change in general, and gene loss has been put forward as a common, advantageous response to changes in selective regimes in human history. Recent gene duplicates are estimated to have arisen in the human genome at a rate of 0.009 /gene/million years (my). Using this rate, we would expect there to have been 1,188 new gene duplicates in the human genome since our split with chimpanzee (0.009 duplications/gene/my * 22,000 genes * 6 my). Assuming equal numbers of gene gains and losses and similar rates of turnover in chimps, the total number of genes in humans not present in chimps would be 2,376 (or approx 11% of all genes). This estimate of total genic divergence implied by rates of gene duplication has been widely overlooked due to the pervasive emphasis on nucleotide divergence between orthologous genes. Although this hypothesis assumes identical rates of gene gain and loss, and our coarse calculations have not considered that new gene duplicates are also the most likely genes to be lost, the consistency of gene number among fully sequenced mammals suggests that this is not an onerous assumption across short evolutionary time periods.

The process of differential gene gain and loss among species results in gene families that share sequence and functional homology but differ in gene number. Changes in gene family size have likely been important during human evolution and large differences in gene family size are generally ascribed to a selective advantage for either an increased or decreased gene number. While many of these differences may indeed be the result of natural selection, there has been little effort to account for the accumulation of differences due to random processes. For instance, a difference of 20 genes within a single family may be remarkable between human and chimpanzee, but not between human and mouse, or human and dog. Unlike the analysis of orthologous sequences, where there are widely accepted neutral expectations for molecular evolution, there has been no corresponding framework for the study of gene family evolution until recently.

The completed sequencing of multiple mammalian genomes provides unprecedented insight into the gain and loss of genetic material between species, and into the genomic changes exclusive to humans. In this paper we analyze gene gain and loss at a genomic scale by studying the expansion and contraction of gene families in the whole genomes of human, chimpanzee, mouse, rat, and dog. Using gene family assignments from the Ensembl project (version 41 - October 2006) we assign probabilities to the observed changes in gene family size along each mammalian lineage using a likelihood method that makes efficient use of genomic data in a phylogenetic context. Our statistical framework provides a basis for improved inferences about causative evolutionary mechanisms by providing an expectation for the extent of variation in gene family size when gains and losses occur randomly. This means that we can identify branches of the phylogenetic tree where larger-than-expected contractions or expansions potentially indicate the action of adaptive natural selection.

Our investigation suggests that random processes explain most changes in gene family size; however, we find several families with larger than expected changes, including expansions in the human lineage for families with brain-specific functions. Additionally, we find that the total number of gene differences between humans and chimps estimated by our method is similar to that predicted above from independent analyses of recent segmental duplications. In total, our results support mounting evidence that gene duplication and loss may have played a greater role than nucleotide substitution in the evolution of uniquely human phenotypes, and certainly a greater role than has been widely appreciated.

Full article available via the citation:

Demuth JP, Bie TD, Stajich JE, Cristianini N, Hahn MW (2006) The Evolution of Mammalian Gene Families. PLoS ONE 1(1): e85. doi:10.1371/journal.pone.0000085

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A BBC UK news report from September 2002:

Humans and chimps 'not so close'

...Most studies suggest that 98.5% of our genetic code can also be found in the chimp.

However, a study published in the journal Proceedings of the National Academy of Sciences says the true difference may be much larger.

In fact, say the researchers, only 95% of our DNA may be the same as the chimpanzee's.

Professor Roy Britten, of the California Institute of Technology, US, said that most studies did not take into account large sections of DNA which are not found on the genome of both man and chimp.

Based on the 2003 Proceedings of the National Academy of Sciences open access paper:

Abstract

Introduction

Mutations in the DNA are the source of variation in Darwinian evolution. Therefore it is likely that the examination of DNA differences between closely related species or among polymorphic variations in DNA of a given species will give insight into the nature of the mutations and the process of evolution. In the present paper, published and unpublished data are summarized for examples from several distantly related phylogenetic groups, and the data show that indels dominate the process of early divergence. There is a continuing problem in these data of the upper limit in the size of detected gaps and bias against larger ones. The groups sampled are apes (chimp-human DNA comparison), sea urchins (Strongylocentrotus purpuratus polymorphism), bacteria (Escherichia coli substrain comparison), insects (Drosophila polymorphism), nematodes (Caenorhabditis elegans polymorphism), and plants (Arabidopsis polymorphism). It is also noted that human genetic diseases are frequently caused by indels. The first part of the paper summarizes the results for samples of chimp DNA compared with the human genome sequence. Then an example of sea urchin polymorphism is briefly described. Initial comparison of two strains of E. coli O157:H7 is described. Finally, the published polymorphism data are reviewed and brought together with the data reported here to draw the conclusion that indel formation is a major and significant evolutionary process.

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Technorati: evolution, mammalian, gene, families, genes, lineage, genomes, human, chimpanzee, mouse, rat, dog, common ancestor, adaptive, natural selection, genetic, traits, amino acid, regulatory, divergence, duplication, history, genome, humans, code, study, dna, darwinian, mutations, bacteria, indels, rna, evolutionary, process

Permanent Link posted by John Latter @ 8:27 PM 0 comments