Saturday, December 23, 2006


Shotgun sequencing finds nanoorganisms

For 11 years, Jill Banfield at the University of California, Berkeley, has collected and studied the microbes that slime the floors of mines and convert iron to acid, a common source of stream pollution around the world.

Imagine her surprise, then, when research scientist Brett Baker discovered three new microbes living amidst the bacteria she thought she knew well. All three were so small - the size of large viruses - as to be virtually invisible under a microscope, and belonged to a totally new phylum of Archaea, microorganisms that have been around for billions of years.

What made Baker's find possible was shotgun sequencing*, a technique developed and made famous by Celera Corp., which used it to sequence the human genome in record time.

"It was amazing," said Banfield, a professor of earth and planetary science and of environmental science, policy and management at UC Berkeley since 2001. "These were totally new and very small organisms we didn't know how to culture with standard techniques. This shows the great promise of shotgun sequencing to profile a community of organisms without making any assumptions about what is there."

Nearly three years ago, Banfield employed shotgun sequencing to pick out the half-dozen bacteria and Archaea in the mine slime. It was the first successful example of community genomic analysis to profile the organisms in a drop of water - scummy water.

But Baker's discovery makes clear that shotgun sequencing can also pick out rare organisms too small to see easily, and too novel to be plucked out by other genetic techniques.

"We were essentially looking for new stuff, and we found it in all the samples studied, though at low abundance," said Baker, who is with the campus's Department of Earth and Planetary Science. "Shotgun sequencing is a better way to identify organisms than using other methods, like culturing or PCR (polymerase chain reaction), which can miss quite a lot of organisms."

Banfield, Baker and their UC Berkeley and University of Queensland, Australia, colleagues report their findings in the Dec. 22 issue of Science.

Banfield noted that the bacteria and newfound Archaea living in the highly acidic mine drainage are archetypes of the kind of life that could exist on other planets, such as in the iron- and sulfur-rich soil of Mars.

"This community of microbes is relevant to probing potential strategies for life on other planets, especially the life likely to exist on Mars," she said.

The organisms in the mine drainage, which live in a pink slick on pools of acidic green water, obtain energy by oxidizing iron - that is, generating rust - and in the process create sulfuric acid and dissolve pyrite (iron sulfide or fool's gold) to release more iron and sulfur. This self-sustaining process creates the acidic drainage that pollutes creeks and rivers, including those around the researchers' study site, the Richmond Mine at Iron Mountain, Calif. The mine is one of the largest Superfund sites in the country.

Banfield has been trying to understand how the extremophiles - microbes that live in extreme environments - live together and generate the acid drainage that makes such mines toxic hazards. The green runoff from the mine, captured and treated by the Environmental Protection Agency, is a hot 108 degrees Fahrenheit, as acidic as battery acid, and loaded with toxic metals - zinc, iron, copper and arsenic.

In 2004, Banfield collaborated with the Department of Energy's Joint Genome Institute to shotgun sequence a drop of the slime. This type of sequencing involves homogenizing the organisms in the sample, isolating the combined DNA and breaking it into lots of random strands. Each strand is then sequenced, and a powerful computer is used to find overlaps so that the pieces can be properly reordered.

This process identified five separate genomes that corresponded to five bacteria and Archaea - four of them uncultivated at that time, though closely related to known microbes.

Baker probed the gene fragments more thoroughly to turn up three Archaea from a totally unknown group, probably representing a new phylum among the several dozen known phyla of Archaea. They fall within a large class of microbes known as thermophiles, which are Archaea that live in warm and even scalding conditions. Many of these thermophiles have been recovered from hydrothermal vents in the deep mid-ocean ridges, where lava boils up between continental plates.

Once Baker had found gene segments (ribosomal RNA) from three Archaea, he was able to fish the microbes out of the slime soup and found that they were extremely small, around 200 nanometers in diameter, the size of large viruses. Bacteria average about five times this diameter.

These therefore could be the smallest organisms ever found, though Baker needs to culture them before confirming this. Because they're so small, however, they may not be free-living.

"We're not sure they can live independently, whether they have enough genes to fend for themselves, but instead are symbiotic with another organism or are feeding off another organism," Baker said.

Baker now is trying to find the right conditions for these Archaea to thrive in a culture dish. For now, he has dubbed them ARMAN-1, -2 and -3, for Archaeal Richmond Mine Acidophilic Nanoorganisms. Ted Arman is the owner of the mine.

Source: Adapted from the UC Berkeley PR "Shotgun sequencing finds nanoorganisms" December 21, 2006


Based on the journal Science paper:

"Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis"

by Brett J. Baker, Gene W. Tyson, Richard I. Webb, Judith Flanagan, Philip Hugenholtz, Eric E. Allen, Jillian F. Banfield

Science 22 December 2006:
Vol. 314. no. 5807, pp. 1933 - 1935
DOI: 10.1126/science.1132690


Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of less than 0.006 cubic micrometer.


See The New York Times (may require free registration) article "From Scum, Perhaps the Tiniest Form of Life":

"The smallest form of life known to science just got smaller.

Four million of a newly discovered microbe - assuming the discovery, reported yesterday in the journal Science, is confirmed - could fit into the period at the end of this sentence

Scientists found the microbes living in a remarkably inhospitable environment, drainage water as caustic as battery acid from a mine in Northern California. The microbes, members of an ancient family of organisms known as archaea, formed a pink scum on green pools of hot mine water laden with toxic metals, including arsenic.


Also see "Shotgun sequencing comes of age" (The Scientist):

With little fanfare, the much-debated sequencing method known as whole-genome shotgun (WGS) has become a conventional way to sequence genomes. Two studies out this month help to confirm its importance... (Written by Tabitha M. Powledge who recently authored "What is the Hobbit?")

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Researchers find novel genes critical in organ development

Researchers at the University of Minnesota have identified a group of novel genes that are critical in organ development*.

The scientists studied the roles of genes in the zebrafish secretome. This group of genes makes proteins that are located on the surface or outside of cells in the body, and are responsible for directing 'patterning' in the body, or ensuring that cells divide, differentiate and migrate to properly form vital organs in the correct places during development.

The research is published online in the current issue of the Public Library of Science journal ONE.

Continued at "Researchers find novel genes critical in organ development"


Based on the open access/free PLoS ONE paper:

"Genome-Wide Reverse Genetics Framework to Identify Novel Functions of the Vertebrate Secretome"

Citation: Pickart MA, Klee EW, Nielsen AL, Sivasubbu S, Mendenhall EM, et al. (2006) Genome-Wide Reverse Genetics Framework to Identify Novel Functions of the Vertebrate Secretome. PLoS ONE 1(1): e104. doi:10.1371/journal.pone.0000104


Understanding the functional role(s) of the more than 20,000 proteins of the vertebrate genome is a major next step in the post-genome era. The approximately 4,000 co-translationally translocated (CTT) proteins – representing the vertebrate secretome – are important for such vertebrate-critical processes as organogenesis. However, the role(s) for most of these genes is currently unknown.


We identified 585 putative full-length zebrafish CTT proteins using cross-species genomic and EST-based comparative sequence analyses. We further investigated 150 of these genes (Figure 1) for unique function using morpholino-based analysis in zebrafish embryos. 12% of the CTT protein-deficient embryos resulted in specific developmental defects, a notably higher rate of gene function annotation than the 2%–3% estimate from random gene mutagenesis studies.


This initial collection includes novel genes required for the development of vascular, hematopoietic, pigmentation, and craniofacial tissues, as well as lipid metabolism, and organogenesis. This study provides a framework utilizing zebrafish for the systematic assignment of biological function in a vertebrate genome.


*Info on Organogenesis:

In animal development, organogenesis is the process by which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. The germ layers in organogenesis differ by three processes: folds, splits, and condensation. Developing early during this stage in chordate animals are the neural tube and notochord. Vertebrate animals all differ from the gastrula the same way. Vertebrates develop a neural crest that differentiates into many structures, including some bones, muscles, and components of the peripheral nervous system. The coelom of the body forms from a split of the mesoderm along the somite axis. [More]


Also see The Center for Organogenesis:

The Center for Organogenesis (CFO) is composed of an intercollegiate and interdisciplinary group of scientists at the University of Michigan whose work is directed at a common goal: to understand the basic mechanisms by which organs and tissues are formed and maintained, and to use this knowledge to create long lasting artifical organs, stem cell therapies or organ transplantation systems that will correct genetic and acquired diseases. The mission of the Center is to establish and maintain an infrastructure for the study of organogenesis at the University of Michigan {Continued].

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Sexual Selection and the Evolution of Brain Size in Primates

An open access/free paper from the first edition of PloS ONE:

Citation: Schillaci MA (2006) Sexual Selection and the Evolution of Brain Size in Primates. PLoS ONE 1(1): e62. doi:10.1371/journal.pone.0000062

Info on Michael A. Schillaci (Department of Anthropology, University of Toronto, Canada)


Reproductive competition among males has long been considered a powerful force in the evolution of primates. The evolution of brain size and complexity in the Order Primates has been widely regarded as the hallmark of primate evolutionary history. Despite their importance to our understanding of primate evolution, the relationship between sexual selection and the evolutionary development of brain size is not well studied. The present research examines the evolutionary relationship between brain size and two components of primate sexual selection, sperm competition and male competition for mates. Results indicate that there is not a significant relationship between relative brain size and sperm competition as measured by relative testis size in primates, suggesting sperm competition has not played an important role in the evolution of brain size in the primate order. There is, however, a significant negative evolutionary relationship between relative brain size and the level of male competition for mates. The present study shows that the largest relative brain sizes among primate species are associated with monogamous mating systems, suggesting primate monogamy may require greater social acuity and abilities of deception.


Since Darwin's 1871 publication* on the evolution of humans and sexual selection, reproductive competition among males has been considered a powerful force in the evolution of primates and other mammals. The evolution of brain size and complexity in the Order Primates is widely regarded as the hallmark of primate evolutionary history. Despite their importance to understanding primate evolution, the relationship between sexual selection and brain size evolution is not well studied. With the exception of whales, primate brain evolution is unique among mammals. For primates, the evolutionary increase in brain size is often attributed to increased social complexity. Research associating increasing brain size with increasing group size and social complexity in primates predicts brain size, specifically, the size of the neocortex, will co-evolve with mating systems exhibiting social complexity. In this context, larger brains are selected for because they confer greater reproductive fitness associated with increased social acuity or the ability to manipulate others within the group. Increases in the size of the prefrontal cortex in particular, which mediates important components of complex social behavior such as planning, working memory, memory for serial order, and language may have played an important role in human brain evolution.

Recent research on mating systems and brain size in a closely related mammal, bats, predicts a negative evolutionary relationship between levels of sperm competition as measured by relative testes mass, and the development of brain size stemming from an investment trade-off between two metabolically costly tissues. The results from that study indicated that while species with mating systems that include multiple copulations by males has no evolutionary impact on relative brain size, mating systems with multiple matings by females do influence brain size evolution. Bat species with mating systems based on female promiscuity were associated with smaller brains and larger testes, while species with mating systems based on female fidelity were associated with significantly larger brains and smaller testicles.

The present research investigates the evolutionary relationship between brain size and two components of primate sexual selection in primates 1) sperm competition as measured by relative testes size, and 2) male competition for mates estimated from the level of sexual mass dimorphism.

Continued at "Sexual Selection and the Evolution of Brain Size in Primates"


*"The Descent of Man, and Selection in Relation to Sex"


The nature of the following work will be best understood by a brief account of how it came to be written. During many years I collected notes on the origin or descent of man, without any intention of publishing on the subject, but rather with the determination not to publish, as I thought that I should thus only add to the prejudices against my views. It seemed to me sufficient to indicate, in the first edition of my Origin of Species, that by this work "light would be thrown on the origin of man and his history"; and this implies that man must be included with other organic beings in any general conclusion respecting his manner of appearance on this earth. Now the case wears a wholly different aspect. When a naturalist like Carl Vogt ventures to say in his address as President of the National Institution of Geneva (1869), "personne, en Europe au moins, n'ose plus soutenir la creation independante et de toutes pieces, des especes," it is manifest that at least a large number of naturalists must admit that species are the modified descendants of other species; and this especially holds good with the younger and rising naturalists. The greater number accept the agency of natural selection; though some urge, whether with justice the future must decide, that I have greatly overrated its importance. Of the older and honoured chiefs in natural science, many unfortunately are still opposed to evolution in every form.

In consequence of the views now adopted by most naturalists, and which will ultimately, as in every other case, be followed by others who are not scientific, I have been led to put together my notes, so as to see how far the general conclusions arrived at in my former works were applicable to man. This seemed all the more desirable, as I had never deliberately applied these views to a species taken singly. When we confine our attention to any one form, we are deprived of the weighty arguments derived from the nature of the affinities which connect together whole groups of organisms- their geographical distribution in past and present times, and their geological succession. The homological structure, embryological development, and rudimentary organs of a species remain to be considered, whether it be man or any other animal, to which our attention may be directed; but these great classes of facts afford, as it appears to me, ample and conclusive evidence in favour of the principle of gradual evolution. The strong support derived from the other arguments should, however, always be kept before the mind. (Continued)


Info on Primatology:

Primatology is the study of non-human primates. It is a diverse discipline and primatologists can be found in departments of biology, anthropology, psychology and many others. It is closely related to physical anthropology, which is the primatology of the genus Homo, especially Homo sapiens. The fields cross over in the study of the hominids, which includes all ape-like ancestors of man and the other great apes (for a list of common ancestors with other living species see The Ancestor's Tale).

Modern primatology is an extremely diverse science. It ranges from anatomical studies of primate ancestors and field studies of primates in their natural habitat, to experiments in animal psychology and ape language. It has cast an immense amount of light on basic human behaviors and ancient ancestry of these behaviors.


Books on Primatology from the Science and Evolution Bookshop: UK | US

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Friday, December 22, 2006


Evolution: Winning by a neck - Giraffes avoid competition

The giraffe's elongated neck has long been used in textbooks as an illustration of evolution by natural selection, but this common example has received very little experimental attention.

In the January 2007 issue of the American Naturalist, researchers at the Mammal Research Institute* in the Department of Zoology and Entomology at the University of Pretoria tested whether foraging competition with shorter herbivores could explain why giraffes feed mostly on leaves high in trees, despite being able to feed at lower levels as well.

'This [study] provides the first real experimental evidence that the long neck of the giraffe might have evolved as a consequence of competition, which provides support for a previously untested textbook example of natural selection,' says Elissa Cameron (University of Pretoria), who coauthored the study with Johan du Toit (University of Pretoria and Utah State University).

Giraffes are well known for their unusual height, and they generally feed high in the tree canopy, above the height other herbivores can reach. Giraffes receive more leaves per bite by foraging high in the tree, but it's unclear whether this is caused by competition - smaller browsers eating some of the leaves at lower heights - or if more leaves grow at higher levels.

The researchers built low fences around trees in greater Kruger National Park to stop smaller browsers from eating leaves. After a complete growing season they found that the number of leaves on the fenced trees was roughly the same, revealing that small browsers are responsible for most of the foraging. Therefore, the researchers argue, it is competition from other herbivores, such as kudu, that appears to drive giraffes to eat leaves high in the trees.

Source: University of Chicago / PhysOrg


Based on the American Naturalist paper:

"Winning by a Neck: Tall Giraffes Avoid Competing with Shorter Browsers"

Elissa Z. Cameron and Johan T. du Toit

Cameron, E. Z. & du Toit, J. T. 2007. Winning by a neck: tall giraffes avoid competing with shorter browsers. The American Naturalist 169, 130-135.


With their vertically elongated body form, giraffes generally feed above the level of other browsers within the savanna browsing guild, despite having access to foliage at lower levels. They ingest more leaf mass per bite when foraging high in the tree, perhaps because smaller, more selective browsers deplete shoots at lower levels or because trees differentially allocate resources to promote shoot growth in the upper canopy. We erected exclosures around individual Acacia nigrescens trees in the greater Kruger ecosystem, South Africa. After a complete growing season, we found no differences in leaf biomass per shoot across height zones in excluded trees but significant differences in control trees. We conclude that giraffes preferentially browse at high levels in the canopy to avoid competition with smaller browsers. Our findings are analogous with those from studies of grazing guilds and demonstrate that resource partitioning can be driven by competition when smaller foragers displace larger foragers from shared resources. This provides the first experimental support for the classic evolutionary hypothesis that vertical elongation of the giraffe body is an outcome of competition within the browsing ungulate guild.


See "The Giraffe's Short Neck" from New York's The Nature Institute. Excerpt:

Once scientists began thinking about animals in terms of evolution, the giraffe became a welcome - and seemingly straightforward - example. It is as if the giraffe's long neck was begging to be explained by evolutionary theorists.

One of the first evolutionary thinkers, Jean-Baptist Lamarck, offered a short description of how the giraffe evolved in his major work, Philosophie Zoologique ('Zoological Philosophy'), which was published in 1809:

It is interesting to observe the result of habit in the peculiar shape and size of the giraffe: this animal, the tallest of the mammals, is known to live in the interior of Africa in places where the soil is nearly always arid and barren, so that it is obliged to browse on the leaves of trees and to make constant efforts to reach them. From this habit long maintained in all its race, it has resulted that the animal's forelegs have become longer than its hind-legs, and that its neck is lengthened to such a degree that the giraffe, without standing up on its hind-legs, attains a height of six meters. (Quoted in Stephen Jay Gould 2002, p. 188 - The Structure of Evolutionary Theory)

In Lamarck's view, we must imagine a situation in the past where the best food for browsing mammals was higher up in trees, the lower vegetation having been eaten by other animals. The ancestors of the giraffe - which we should imagine like antelopes or deer - needed to adapt their behavior to this changing environment. As Lamarck wrote, "variations in the environment induce changes in the needs, habits and modes of life of living beings ... these changes give rise to modifications or developments in their organs and the shape of their parts" (p. 179). So Lamarck imagined that over generations the habit of continually reaching for the higher browse produced in the giraffe's ancestors a lengthening of the legs and neck.

A little over sixty years later, Charles Darwin commented on giraffe evolution in the sixth edition (1872) of his seminal book, Origin of Species:

The giraffe, by its lofty stature, much elongated neck, fore-legs, head and tongue, has its whole frame beautifully adapted for browsing on the higher branches of trees. It can thus obtain food beyond the reach of the other Ungulata or hoofed animals inhabiting the same country; and this must be a great advantage to it during dearths.... So under nature with the nascent giraffe the individuals which were the highest browsers, and were able during dearth to reach even an inch or two above the others, will often have been preserved; for they will have roamed over the whole country in search of food.... Those individuals which had some one part or several parts of their bodies rather more elongated than usual, would generally have survived. These will have intercrossed and left offspring, either inheriting the same bodily peculiarities, or with a tendency to vary again in the same manner; whilst the individuals, less favoured in the same respects will have been the most liable to perish.... By this process long-continued, which exactly corresponds with what I have called unconscious selection by man, combined no doubt in a most important manner with the inherited effects of the increased use of parts, it seems to me almost certain that an ordinary hoofed quadruped might be converted into a giraffe. (Darwin 1872, pp. 177ff.) (More)

Citation: In Context #10 (Fall, 2003, pp. 14-19); copyright 2003 by The Nature Institute


*The Mammal Research Institute strives to "be internationally recognised for research and teaching on the biology and ecology of African mammals; and to maintain a focus that is relevant to Africa, and to southern Africa in particular, with regard to conserving the diversity of our indigenous mammal fauna in the context of sustainable human development."

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Turiasaurus: Giant Sauropod dinosaur found in Spain

Fossils of a giant Sauropod, found in Teruel Spain, reveal that Europe was home to giant dinosaurs in the Late Jurassic* period - about 150 million years ago. Giant dinosaurs have previously been found mainly in the New World and Africa.

This dinosaur may have been the most massive terrestrial animal in Europe.

The findings are published in the 22 December 2006 issue of the journal Science, published by AAAS, the nonprofit science society.

Researchers from the Fundacion Conjunto Paleontologico de Teruel-Dinopolis found dozens of sauropod bone fossils at the Barrihonda-El Humero site the Riodeva village, Teruel, Spain.

The new sauropod, Turiasaurus riodevensis, is named for the Teruel area (Turia) and the village where it was found.

The turiasaurus is estimated to have weighed between 40 and 48 tons (the weight of six or seven adult male elephants) and is comparable to the world's largest known dinosaurs, including Argentinosaurus and Brachiosaurus. At its estimated length, between 30 and 37 meters, the sauropod would be as long as an NBA basketball court. 'The humerus - the long bone in the foreleg that runs from the shoulder to the elbow - was as large as an adult,' said Brooks Hanson, Science's deputy editor, physical sciences.

Continued at "Giant Sauropod Dinosaur found in Spain"


Based on the Science report:

"A Giant European Dinosaur and a New Sauropod Clade"

by Rafael Royo-Torres, Alberto Cobos, Luis Alcala


Fossils of a giant sauropod dinosaur, Turiasaurus riodevensis, have been recovered from terrestrial deposits of the Villar del Arzobispo Formation (Jurassic-Cretaceous boundary) of Riodeva (Teruel Province, Spain). Its humerus length (1790 millimeters) and estimated mass (40 to 48 metric tons) indicate that it may have been the most massive terrestrial animal in Europe and one of the largest in the world. Phylogenetic analysis indicates that the fossil represents a member of a hitherto unrecognized group of primitive European eusauropods that evolved in the Jurassic.


A related internet message from 2004 - "Giant Spanish Sauropod"

"Last 26 February the discovery of a gigantic Spanish sauropod was announced to the mass media. Currently, few is know of this sauropod, which it is still in process of digging under the direction of my colleague Rafael Royo, from the Conjunto Paleontologico de Teruel (Paleontological Network Foundation of Teruel) in Teruel, Spain.

Apart from the 178 cm long humerus and the 30 (or 35) cm long claw, remains of scapular and pelvic girdles, fore and hind limbs (including a complete manus) and vertebrae are known (Moreno, 2004)...

...The sauropod comes from the village of Riodeva, in the southernmost part of Teruel Province, Aragon autonomous community, Spain. The sauropod site is one of the seventeen known in Riodeva, with stegosaurs, theropod and sauropod remains (Royo-Torres et al., 2003), all recently discovered and still unpublished.

The age of this sauropod is controversial, it comes from continental beds overlying the Upper Jurassic marine beds, Probably it comes form the same formation (El Collado formation) that produce stegosaurs (Dacentrurus) and another sauropod (Losillasaurus) in the northermost part of the Valencia Province, and its age could be Uppermost Jurassic-Lowermost Cretaceous (Tithonian-Berriasian) or Lower Cretaceous (Barremian).

The new sauropod is near (20 km north) of Losilla de Aras, the small village that originated the Losillasaurus holotype (Casanovas et al., 2001).

It seems that gigantic sauropods were common in this age in Spain." (More)


*Info on the Jurassic:

The Jurassic Period is a major unit of the geologic timescale that extends from about 199.6 plus or minus 0.6 Ma (million years ago), at the end of the Triassic to 145.4 plus or minus 4.0 Ma, at the beginning of the Cretaceous. As with other geologic periods, the rock beds that define the start and end of the period are well identified, but the exact dates are uncertain by 5 - 10 million years. The Jurassic constitutes the middle period of the Mesozoic era, also known as the Age of Dinosaurs. The start of the period is marked by the major Triassic-Jurassic extinction event.

The Jurassic was named by Alexandre Brogniart for the extensive marine limestone exposures of the Jura Mountains, in the region where Germany, France and Switzerland meet. (More)

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Genetics of eye colour unlocked

A study by researchers from The University of Queensland's Institute for Molecular Bioscience (IMB) and the Queensland Institute of Medical Research is the first to prove conclusively that there is no single gene for eye colour.

Instead, it found that several genes determine the colour of an individual's eyes, although some have more influence than others.

"Each individual has two versions of a gene, inheriting one from each parent, and these versions can be the same as each other or different," Dr Rick Sturm, the IMB researcher who led the study, said.

"It used to be thought that eye colour was what we call a simple Mendelian recessive trait - in other words, brown eye colour was dominant over blue, so a person with two brown versions of the gene or a brown and a blue would have brown eyes, and only two blues with no brown could produce blue eyes.

"But the model of eye colour inheritance using a single gene is insufficient to explain the range of eye colours that appear in humans. We believe instead that there are two major genes - one that controls for brown or blue, and one that controls for green or hazel - and others that modify this trait.

"So contrary to what used to be thought, it is possible for two blue-eyed parents to have a brown-eyed child, although this is not common."

Dr Sturm likens the system to a light bulb.

"The mechanism that determines whether an eye is brown or blue is like switching on a light, whereas an eye becoming green or hazel is more like someone unscrewing the light bulb and putting in a different one."

The study was carried out to clarify the role of the OCA2 gene in the inheritance of eye colour and other pigmentary traits associated with skin cancer risk in white populations, and examined nearly 4000 adolescent twins, their siblings and their parents over five years.

Source: University of Queensland PR "The eyes have it on multiple gene question" February 20 2007


Based on "A Three-Single-Nucleotide Polymorphism Haplotype in Intron 1 of OCA2 Explains Most Human Eye-Color Variation"

David L. Duffy, Grant W. Montgomery, Wei Chen, Zhen Zhen Zhao, Lien Le, Michael R. James, Nicholas K. Hayward, Nicholas G. Martin, and Richard A. Sturm

Am. J. Hum. Genet., 80:241-252, 2007


We have previously shown that a quantitative-trait locus linked to the OCA2 region of 15q accounts for 74% of variation in human eye color. We conducted additional genotyping to clarify the role of the OCA2 locus in the inheritance of eye color and other pigmentary traits associated with skin-cancer risk in white populations. Fifty-eight synonymous and nonsynonymous exonic single-nucleotide polymorphisms (SNPs) and tagging SNPs were typed in a collection of 3,839 adolescent twins, their siblings, and their parents. The highest association for blue/nonblue eye color was found with three OCA2 SNPs: rs7495174 T/C, rs6497268 G/T, and rs11855019 T/C (P values of 1.02 x 10-61, 1.57 x 10-96, and 4.45 x 10-54, respectively) in intron 1. These three SNPs are in one major haplotype block, with TGT representing 78.4% of alleles. The TGT/TGT diplotype found in 62.2% of samples was the major genotype seen to modify eye color, with a frequency of 0.905 in blue or green compared with only 0.095 in brown eye color. This genotype was also at highest frequency in subjects with light brown hair and was more frequent in fair and medium skin types, consistent with the TGT haplotype acting as a recessive modifier of lighter pigmentary phenotypes. Homozygotes for rs11855019 C/C were predominantly without freckles and had lower mole counts. The minor population impact of the nonsynonymous coding-region polymorphisms Arg305Trp and Arg419Gln associated with nonblue eyes and the tight linkage of the major TGT haplotype within the intron 1 of OCA2 with blue eye color and lighter hair and skin tones suggest that differences within the 5' proximal regulatory control region of the OCA2 gene alter expression or messenger RNA-transcript levels and may be responsible for these associations.


*Rick Sturm is author of the Trends in Genetics paper "A golden age of human pigmentation genetics"

Volume 22, Issue 9 , September 2006, Pages 464-468


The zebrafish golden mutation is characterized by the production of small and irregular-shaped melanin granules, resulting in a lightening of the pigmented lateral stripes of the animal. The recent positional cloning and localization of the golden gene, combined with genotype-phenotype correlations of alleles of its human orthologue (SLC24A5) in African-American and African-Caribbean populations, provide insights into the genetic and molecular basis of human skin colour. SLC24A5 promotes melanin deposition through maturation of the melanosome, highlighting the importance of ion-exchange in the function of this organelle.

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Thursday, December 21, 2006


Humans and Chimps: Close But Not That Close..

Approximately 6 percent of human and chimp genes are unique to those species, report scientists from Indiana University Bloomington and three other institutions. The new estimate, reported in the inaugural issue of Public Library of Science ONE (December 2006), takes into account something other measures of genetic difference do not - the genes that aren't there.

That isn't to say the commonly reported 1.5 percent nucleotide-by-nucleotide difference between humans and chimps is wrong, said IUB computational biologist Matthew Hahn*, who led the research. IUB postdoctoral researcher Jeffery Demuth** is the paper's lead author.

"Both estimates are correct in their own way," Hahn said. "It depends on what you're asking. There isn't a single, standard estimate of variation that incorporates all the ways humans, chimps and other animals can be genetically different from each other."

By studying "gene families" - sets of genes in every organism's genome that are similar (or identical) because they share a common origin - the scientists also provide new information about the evolution of humanness. After surveying gene families common to both humans and chimps, the researchers observed in the human genome a significant increase in the duplication of genes that influence brain functions.

"Our results support mounting evidence that the simple duplication and loss of genes has played a bigger role in our evolution than changes within single genes," Hahn said.

That finding complements reports by University of Colorado and University of Michigan researchers in the journals Science and PLoS Biology earlier this year, in which researchers showed that both gains and losses of individual genes have contributed to human divergence from chimpanzees and other primates.

Hahn and his research partners examined 110,000 genes in 9,990 gene families that are shared by humans, common chimpanzees (Pan troglodytes), mice, rats and dogs. The scientists found that 5,622, or 56 percent, of the gene families they studied from these five species have grown or shrunk in the number of genes per gene family, suggesting changes in gene number have been so common as to constitute an evolutionary "revolving door."

The researchers paid special attention to gene number changes between humans and chimps. Using a statistical method they devised, the scientists inferred humans have gained 689 genes (through the duplication of existing genes) and lost 86 genes since diverging from their most recent common ancestor with chimps. Including the 729 genes chimps appear to have lost since their divergence, the total gene differences between humans and chimps was estimated to be about 6 percent.

Hahn said any serious measure of genetic difference between humans and chimps must incorporate both variation at the nucleotide level among coding genes and large-scale differences in the structure of human and chimp genomes. The real question biologists will face is not which measure is correct but rather which sets of differences have been more important in human evolution.

"That's not for me to decide," he said.

Source: Indiana University "Human-chimp difference may be bigger" Tuesday, December 20 2006


Based on the PLoS ONE open access paper:

"The Evolution of Mammalian Gene Families"

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


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.


*From Mathew Hahn's homepage:

...Divergence in genetic networks: Proteins do not evolve in isolation, but rather as components of complex genetic networks. Therefore, a protein's position in a network may indicate how central it is to cellular function, and hence how constrained it is evolutionarily. We have examined the protein-protein interaction networks in yeast, worm, and fly, and have found that proteins with a more central position in all three networks - regardless of the number of direct interactors - evolve more slowly and are more likely to be essential for survival. By studying various types of genetic networks in a number of different genomes, we can begin to understand the determinants of sequence evolution - and therefore of phenotypic evolution.


**From Jeffery Demuth's homepage:

...There is a growing appreciation that many major morphological and functional changes in evolution result from duplications that range in size from genes to whole genomes. Furthermore, differential silencing of duplicate gene copies between populations may contribute to speciation. Unlike the analysis of orthologous sequences, where there are widely accepted neutral expectations for molecular evolution, there is no corresponding framework for the study of gene duplication and loss. While many studies attribute large changes in the size of gene families to natural selection, there is no solid theoretical foundation for what might be expected purely due to stochastic gain and loss of genes. To address this deficiency, we have developed a likelihood-based method that makes efficient use of genomic data in a phylogenetic context. The method allows us to identify gene families that are expanding or contracting significantly faster than can be explained by a random process.

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Komodo Dragon Virgin Birth Expected at Christmas

The story of the Virgin Mary is what gives meaning to Christmas.

And now, Chester Zoo has a nativity story of its own - and a dragon's tale that promises to turn the traditional concepts of the birds and the bees on its head.

In a ground-breaking paper to be published in the scientific journal Nature next week, Chester Zoo has helped to prove that Komodo Dragons - the world's largest lizard - can reproduce in the absence of a male, parthenogenetically.

The key to this discovery lies with Flora - one of the zoo's two female Komodo Dragons - and began when Flora laid a clutch of 11 eggs in May this year.

The zoo's reptile keepers placed the eggs in an incubator. Three of the eggs collapsed but, once opened, were found to contain embryos - showing that they were fertile.

Fertile dragon's eggs are not in themselves unusual, but what made this news surprising was that virgin Flora has never been mixed with, or mated by, a male dragon. Scientists at Liverpool University under the guidance of Dr Phill Watts, carried out genetic fingerprinting on the three eggs and on the adult Komodo Dragons at the zoo. This 'paternity' testing proved that Flora was indeed both the ‘mother' and the ‘father' of the fertile eggs.

Kevin Buley, Chester Zoo's Curator of Lower Vertebrates and Invertebrates and a co-author of the Nature paper, said: "Although other lizard species are known to be able to reproduce by parthenogenesis, this is the first time this has ever been reported in Komodo Dragons."

"Essentially what we have here is an imminent virgin birth and, because the eggs were laid back in May, it is not beyond the realms of possibility that the incubating eggs could hatch around Christmas time. We will be on the look out for shepherds, wise men and an unusually bright star in the sky over Chester Zoo."

The Nature paper demonstrates that, whilst the fertile eggs are not identical clones of Flora, the overall genetic make-up of the clutch reconstructs the genetic make-up of the mother exactly, and that no other Komodo Dragon could have been involved in the production of the embryos.

"This discovery has very important implications for understanding how reptiles are potentially able to colonise new areas. Theoretically a female Komodo Dragon in the wild could swim to a new island and then establish an entirely new population of dragons. The genetics of parthenogenesis in lizards means that all her hatchlings would have to be male. These would grow up to mate with their own mother and therefore, within one generation, there would potentially be a population able to reproduce normally on the new island," added Kevin. [Source: Chester Zoo]


Based on the journal Nature paper:

"Parthenogenesis in Komodo dragons"

Phillip C. Watts, Kevin R. Buley, Stephanie Sanderson, Wayne Boardman, Claudio Ciofi and Richard Gibson



Parthenogenesis, the production of offspring without fertilization by a male, is rare in vertebrate species, which usually reproduce after fusion of male and female gametes. Here we use genetic fingerprinting to identify parthenogenetic offspring produced by two female Komodo dragons (Varanus komodoensis) that had been kept at separate institutions and isolated from males; one of these females subsequently produced additional offspring sexually. This reproductive plasticity indicates that female Komodo dragons may switch between asexual and sexual reproduction, depending on the availability of a mate - a finding that has implications for the breeding of this threatened species in captivity. Most zoos keep only females, with males being moved between zoos for mating, but perhaps they should be kept together to avoid triggering parthenogenesis and thereby decreasing genetic diversity.


*Info on Komodo Dragons:

The Komodo dragon or Komodo Monitor (Varanus komodoensis) is the largest living lizard in the world, growing to an average length of 2-3 meters (approximately 6.5-10 feet). It is a member of the monitor lizard family, Varanidae, and inhabits various islands in Indonesia.

Sightings of the Komodo dragon were first reported to Europeans in 1910. Widespread knowledge came after 1912, in which Peter Ouwens, the director of the Zoological Museum at Bogor, Java, published a paper on the topic. In 1980, the Komodo National Park was founded to help protect their population. (More)


**A related news report from April 26th, 2006:

"Komodo Dragon Births Leaves Experts Foxed"

Zoologists on Monday said they were delighted and perplexed at the birth of four rare Komodo dragons, whose paternity remains a mystery. The four reptiles were born last month from a clutch laid at London Zoo by a female called Sungai.

Sungai normally lives at the Thoiry wildlife park, west of Paris, but was lent to London as part of a European breeding programme to help this badly-endangered species.

But Sungai laid the fertilised eggs before even meeting her British lover - and the last time she is known to have had intercourse was two years ago, with another Thoiry Komodo dragon called Kinaam.


***Info on Parthenogenesis:

Parthenogenesis or virgin birth (from the Greek parthenos, "virgin", genesis, "birth") describes the growth and development of an embryo or seed without fertilization by a male. Parthenogenesis occurs naturally in some species, including lower plants (called agamospermy), invertebrates (e.g. water fleas, aphids, some bees and parasitic wasps), and vertebrates (e.g. some reptiles, fish, and, very rarely, birds). (More)

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Wednesday, December 20, 2006


Oldest animal fossils may have been Giant Bacteria

The oldest-known animal eggs and embryos, whose first pictures made the cover of Nature in 1998, were so small they looked like bugs - which, it now appears, they may have been.

This week, a study in the same prestigious journal presents evidence for reinterpreting the 600 million-year-old fossils from the Precambrian era as giant bacteria.

The discovery 'complicates our understanding of microfossils thought to be the oldest animals,' said lead author Jake Bailey (homepage), a graduate student in earth sciences at the University of Southern California.

Bailey made his discovery by combining two separate findings about Thiomargarita*, the world's largest known living bacterium.

In 2005, Thiomargarita discoverer Heide Schulz, from the University of Hannover in Germany, showed that the bacterium promotes deposition of a mineral known as phosphorite**.

The fossils identified as eggs and embryos in 1998 came from southern China's Doushantuo Formation, which is rich in phosphorite.

The source for the rare mineral was unknown. Bailey wondered if an ancient relative of Thiomargarita might have been involved.

Continued at "Oldest Animal Embryos or Bacteria?"


Based on the Letter to Nature:

"Evidence of giant sulphur bacteria in Neoproterozoic phosphorites"

First Paragraph

In situ phosphatization and reductive cell division have recently been discovered within the vacuolate sulphur-oxidizing bacteria. Here we show that certain Neoproterozoic Doushantuo Formation (about 600 million years bp) microfossils, including structures previously interpreted as the oldest known metazoan eggs and embryos can be interpreted as giant vacuolate sulphur bacteria. Sulphur bacteria of the genus Thiomargarita have sizes and morphologies similar to those of many Doushantuo microfossils, including symmetrical cell clusters that result from multiple stages of reductive division in three planes. We also propose that Doushantuo phosphorite precipitation was mediated by these bacteria, as shown in modern Thiomargarita-associated phosphogenic sites, thus providing the taphonomic conditions that preserved other fossils known from the Doushantuo Formation.


*Current info on Thiomargarita:

Discovered in 1999 off the coast of Namibia, Thiomargarita namibiensis has the distinction of being the largest bacterium in the world, at a remarkable volume of 3 million times that of a normal bacterial specimen. The long string of cells, named "Sulfur pearl of Namibia" because of the reflective white globules of sulfur contained in them, was found buried in the sulfur-abundant sea floor. Each ball-shaped cell can grow up to nearly 1 milimeter in diameter - a measurement usually taken in microns. Because of some unique adaptations, Thiomargarita namibiensis is able to survive in a high-sulfur environment with little or no oxygen.


**From the journal Science:

"Large Sulfur Bacteria and the Formation of Phosphorite"

by Heide N. Schulz and Horst D. Schulz


Phosphorite deposits in marine sediments are a long-term sink for an essential nutrient, phosphorus. Here we show that apatite abundance in sediments on the Namibian shelf correlates with the abundance and activity of the giant sulfur bacterium Thiomargarita namibiensis, which suggests that sulfur bacteria drive phosphogenesis. Sediments populated by Thiomargarita showed sharp peaks of pore water phosphate (equal to or less than 300 micromolar) and massive phosphorite accumulations (equal to or greater than 50 grams of phosphorus per kilogram). Laboratory experiments revealed that under anoxic conditions, Thiomargarita released enough phosphate to account for the precipitation of hydroxyapatite observed in the environment.

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Works on screenplay for intelligent design trial movie

A feature film inspired by Dover's intelligent design trial* is in the works, but it may be a few years before the movie makes it onto the big screen.

And the words 'inspired by' will likely mean some creative liberty is taken in the retelling of the drama.

Pennsylvania native Ron Nyswaner (info), whose writing credits include 'Philadelphia,' starring Tom Hanks, and 'The Prince of Pennsylvania,' starring Keanu Reeves, has begun researching and writing the screenplay for Paramount Pictures.

The writer, who grew up in Clarksville, Greene County, said he can relate to the small-town 'characters' because they are similar to him and his relatives.

Nyswaner said he has met with several of the key players in the trial, and has read 'every word' of the court transcript, every deposition and every piece of journalism written about the trial to prepare for his writing.

He said the film will be 'inspired by true events that took place in Dover' and will incorporate 'lots of humor and lots of compelling drama.'

'I think it's a great subject for a film,' he said. 'I'm trying not to form any opinions on the issues ... but write the truth from every character's point of view. You always treat every character you're writing with respect. Assume their version of the truth is the truth.'

Continued at "Pa. native works on screenplay for intelligent design trial movie"


See A Comparison of Judge Jones' Opinion in Kitzmiller v. Dover with Plaintiffs' Proposed 'Findings of Fact and Conclusions of Law'

Executive Summary:

In December of 2005, critics of the theory of intelligent design (ID) hailed federal judge John E. Jones' ruling in Kitzmiller v. Dover, which declared unconstitutional the reading of a statement about intelligent design in public school science classrooms in Dover, Pennsylvania. Since the decision was issued, Jones' 139-page judicial opinion has been lavished with praise as a "masterful decision" based on careful and independent analysis of the evidence. However, a new analysis of the text of the Kitzmiller decision reveals that nearly all of Judge Jones' lengthy examination of "whether ID is science" came not from his own efforts or analysis but from wording supplied by ACLU attorneys. In fact, 90.9% (or 5,458 words) of Judge Jones' 6,004- word section on intelligent design as science was taken virtually verbatim from the ACLU's proposed "Findings of Fact and Conclusions of Law" submitted to Judge Jones nearly a month before his ruling. Judge Jones even copied several clearly erroneous factual claims made by the ACLU. The finding that most of Judge Jones' analysis of intelligent design was apparently not the product of his own original deliberative activity seriously undercuts the credibility of Judge Jones' examination of the scientific validity of intelligent design.

And the recent post "Intelligent Design: The God Lab":

Pay a visit to the Biologic Institute and you are liable to get a chilly reception. 'We only see people with appointments,' states the man who finally responds to my persistent knocks. Then he slams the door on me.

I am standing on the ground floor of an office building in Redmond, Washington, the Seattle suburb best known as home town to Microsoft. What I'm trying to find out is whether the 1-year-old institute is the new face of another industry that has sprung up in the area - the one that has set out to try to prove evolution is wrong.

This is my second attempt to engage in person with scientists at Biologic. At the institute's other facility in nearby Fremont, researchers work at benches lined with fume hoods, incubators and microscopes - a typical scene in this up-and-coming biotech hub.(More)


*Background info:

Tammy Kitzmiller, et al. v. Dover Area School District, et al., Case No. 04cv2688, was the first direct challenge brought in United States federal courts against a public school district that required the presentation of "Intelligent Design" as an alternative to evolution as an "explanation of the origin of life". The plaintiffs successfully argued that intelligent design is a form of creationism, and that the school board policy thus violated the Establishment Clause of the First Amendment to the United States Constitution.

Eleven parents of students in Dover, Pennsylvania, near York, sued the Dover Area School District over a statement that the school board required to be read aloud in ninth-grade science classes when evolution was taught. The plaintiffs were represented by the American Civil Liberties Union (ACLU), Americans United for Separation of Church and State (AU) and Pepper Hamilton LLP. The National Center for Science Education (NCSE) acted as consultants for the plaintiffs. The defendants were represented by the Thomas More Law Center. The Foundation for Thought and Ethics, publisher of a textbook advocating intelligent design titled Of Pandas and People, tried to join the lawsuit as a defendant but was denied.

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History-hunting geneticists can still follow familiar trail

Mitochondrial DNA* remains useful for unlocking population secrets:

As the world's first explorers branched away from humanity's birthplace in east Africa some 65,000 years ago, distinct mutations accumulated in the DNA of each population, essentially providing a genetic trail for modern researchers to follow.

Recently some scientists have raised doubts about this classic genetic system to study ancient migrations of people and to estimate the populations of people or animals as they existed tens of thousands of years ago.

But University of Florida researchers writing this month in an online edition of Science (see below) validate the approach, which involves tracking sequences of mitochondrial DNA, also known as mtDNA.

"The study of mtDNA has helped to demonstrate the African origin of our species and the relationship between living humans and the Neanderthals," said Connie Mulligan, an associate professor of anthropology in the College of Liberal Arts and Sciences and an assistant director of the UF Genetics Institute. "MtDNA data have also been used to establish the time and route of major events in human history, such as the expansion of Neolithic farmers into Europe, and the settlement of the New World."

MtDNA has made headlines recently because of initiatives such as the National Genographic Project, a multimillion-dollar endeavor to reconstruct humanity's ancient migrations, and because of well-publicized efforts to track the ancestral roots of Oprah Winfrey and other personalities.

Located within the hundreds of energy-producing mitochondria that lie outside the nucleus of our cells, mtDNA is unlike the DNA inside the nucleus of a cell that contains genes from both of our parents - in people and animals mtDNA is exclusively passed from mothers to their children.

For humans, this means that all of the mtDNA in our cells are copies of our mothers' mtDNA, which in turn were copies of their mothers' mtDNA. In this way, mtDNA progresses through the ages, springing from what many scientists believe was a common ancestral mother.

But over the eons, random mutations enter the genetic code of all species. By tracking similarities and differences of mtDNA, scientists gain insight about the size of groups and how they moved around the world.

"When you look at ancient migration, you're always asking the question, 'How big was the population, how many were there?'" said Michael Miyamoto, a professor and associate chairman of zoology in UF's College of Liberal Arts and Sciences. "The field has worked from the premise that the more mtDNA variation you saw, the larger the population was that carried that variation, just like there would be a greater diversity of T-shirts or shoes within a larger population than a smaller population."

However, the connection between mtDNA and population size was questioned this year when French scientists analyzed vast groups of gene sequences from more than 3,000 animal species. They speculated that an evolutionary tendency for species to keep helpful genes and sift out detrimental ones, called "natural selection," preferentially affects mitochondrial diversity, making mtDNA less useful for population size estimates.

"From a conservation perspective, when scientists look at census counts of animals and how the population size may be increasing or decreasing, the study of mtDNA tells us about the level of genetic diversity in a population, which is important in making conservation decisions on endangered species," Mulligan said. "If this approach were not credible, it could potentially have a bearing on future policy decisions, as well as affect literally hundreds of previous studies on humans and other mammals."

UF Genetics Institute scientists analyzed publicly available mtDNA datasets of 47 species of mammals - a subset of the animals that were in the French study - as well as associated data on protein diversity in the same species. A greater variety of proteins indicates more diverse DNA, because DNA contains a species' blueprints for manufacturing protein - and the French scientists agreed that protein diversity did correlate with population size.

All that remained for UF researchers to do to reinstate mtDNA diversity as indicative of population size was to determine that protein diversity and mtDNA diversity were correlated.

"The researchers showed a correlation between mitochondrial DNA and genetic variation in a way that has never been done before," said Marc Allard, an associate professor of biology at George Washington University who was not involved in the study. "Population geneticists have used mitochondria for all kinds of work for 20 years, and to think that mtDNA didn't correlate with population size was clearly going against the dogma. This study shows the dogma is safe in mammals and probably in vertebrates, as well."

Source: University of Florida PR Tuesday, December 19, 2006.


Based on the following two papers from the journal Science:

[1] Comment on "Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals"

Connie J. Mulligan, Andrew Kitchen, Michael M. Miyamoto

Science 1 December 2006:
Vol. 314. no. 5804, p. 1390
DOI: 10.1126/science.1132585

Bazin et al. (Reports, 28 April, 2006, p. 570) found no relationship between mitochondrial DNA (mtDNA) diversity and population size when comparing across large groups of animals. We show empirically that species with smaller populations, as represented by eutherian mammals, exhibit a positive correlation between mtDNA and allozyme variation, suggesting that mtDNA diversity may correlate with population size in these animals.

[2] Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals

Eric Bazin, Sylvain Glemin, Nicolas Galtier

Science 28 April 2006
Vol. 312. no. 5773, pp. 570 - 572
DOI: 10.1126/science.1122033

Within-species genetic diversity is thought to reflect population size, history, ecology, and ability to adapt. Using a comprehensive collection of polymorphism data sets covering approximately 3000 animal species, we show that the widely used mitochondrial DNA (mtDNA) marker does not reflect species abundance or ecology: mtDNA diversity is not higher in invertebrates than in vertebrates, in marine than in terrestrial species, or in small than in large organisms. Nuclear loci, in contrast, fit these intuitive expectations. The unexpected mitochondrial diversity distribution is explained by recurrent adaptive evolution, challenging the neutral theory of molecular evolution and questioning the relevance of mtDNA in biodiversity and conservation studies.


*Mitochondrial DNA (mtDNA) is DNA that is located in mitochondria. This is in contrast to most DNA of eukaryotic organisms, which is found in the nucleus. Nuclear and mtDNA are thought to be of separate evolutionary origin, with the mtDNA being derived from bacteria that were engulfed by early precursors of eukaryotic cells. Thus in cells in current organisms, the vast majority of proteins found in the mitochondria (approx 1500 in mammals) are encoded by nuclear DNA: some, if not most, are thought to have been originally of bacterial origin and have since been transferred to the nucleus during evolution. In mammals, 100% of the mtDNA contribution to a zygote is inherited from the mother and this is true for most, but not all, organisms. Currently, human mtDNA is present at 100-10,000 copies per cell, with each circular molecule consisting of 16,569 base pairs with 37 genes, 13 proteins (polypeptides), 22 transfer RNA (tRNAs) and two ribosomal RNAs (rRNAs). (More)


** Connie Mulligan - Research Interests:

Our lab analyzes molecular genetic variation in order to reconstruct the evolutionary history and relationships of human populations and human pathogens. Specifically, we are interested in 1) biocultural evolution of populations in the Horn of Africa and the Arabian peninsula, 2) processes of colonization and migration as revealed in East Asia and the New World, 3) identification of genetic variants involved in complex diseases using alcohol dependence as a model system, and 4) use of ancient DNA to reconstruct past genetic diversity and evolutionary history. We assay genetic variants in the mitochondrial genome, the sex chromosomes, and the autosomes in order to provide the most complete and accurate representation of human evolution. For disease studies, we focus on candidate genes and for ancient DNA studies, we assay high copy number genes or genomes, such as mitochondrial DNA. We study populations from around the world with an emphasis on Horn of Africa/Arabian, New World, and East Asian groups. Some of the current projects in the lab include: Colonization and Migration, Disease, Ancient DNA. (More)

A related post:

"Few Clues About African Ancestry To Be Found In Mitochondrial DNA"

More recent posts on this topic can be found via the searchbox

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China: Two-headed reptile fossil found

From BBC News UK: Scientists have found what is thought to be the first example of a two-headed reptile in the fossil record.

The abnormal animal, belonging to a group of aquatic reptiles, was unearthed in northeastern China and dates to the time of the dinosaurs.

The specimen reveals that it must have been very young when it died and became fossilised, says lead researcher Eric Buffetaut.

Details of the fossil appear in the UK Royal Society journal Biology Letters*.

This animal was a choristoderan**, an extinct reptile that reached a length of one metre in adulthood and was characterised by a long neck - two in this case.

Continued at "Two-headed reptile fossil found"


*Based on the paper "A two-headed reptile from the Cretaceous of China" (doi: 10.1098/rsbl.2006.0580)


A malformed embryonic or neonate choristoderan reptile from the Lower Cretaceous Yixian Formation of northeastern China is described. The tiny skeleton exhibits two heads and two necks, with bifurcation at the level of the pectoral girdle. In a fossil, this is the first occurrence of the malformation known as axial bifurcation, which is well known in living reptiles.


**Info on Choristodera:

Choristodera is an order of semi-aquatic diapsid reptiles which ranged from the Middle Jurassic, or possibly Late Triassic, to upper Eocene, or upper Oligocene. Choristoderes have been found in North America, Asia, and Europe. The most common fossils are typically found from the Late Cretaceous to the lower Eocene. Cladists have placed them between basal diapsids and basal archosauromorphs but the phylogenetic position of the Choristodera is still uncertain. It has also been proposed that they represent basal lepidosauromorphs. Most recently, workers have placed Choristodera within Archosauromorpha.


An earlier post (Wednesday, September 20, 2006):

Snake With Two Feet Appears in Shandong, China

The Epoch Times (New York): China - On September 11, 2006, Mr. Ma, a resident in Linyi city, Shandong province, displayed to the public a snake with two feet.

Ma caught the snake Sept. 10. It was about one meter long, as thick as an adult's thumb, and with a triangular shaped head. The strange thing about it was, it had two, one-centimeter-long five-toed feet on each side of its body about 30 centimeters from its head.

After seeing the snake, Professor Cao Shandong from the School of Life Science Linyi Normal University said, it was a twin-spotted rat-snake, but the feet and toes were extremely unusual. Professor Cao said it could be a case of atavism. [Evolution]

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Tuesday, December 19, 2006


Carnal Knowledge: How we evolved into male and female

According to scientists, the very first organisms to dare engage in sex were more like Adam and Steve than Adam and Eve.

That's because sex was invented before heterosexuality - before males or females for that matter.

The first sexual beings to emerge perhaps 2.5 billion years ago were what biologists call isogamous - which is a little like being gay, except everyone is somewhere between male and female.

Many organisms, including some fungi, algae and single-celled pond-swimmers, still practice isogamy*. In doing so they offer clues to the mystery of why and how the sexes ever evolved.

To understand life before the advent of males and females, you need a universal definition of each: Males produce a smaller sex cell (sperm or pollen) than their female counterparts.

Isogamous algae, on the other hand, still have sex but instead of mixing sperm and eggs they mingle sex cells of roughly the same size - generically known as gametes.

What scientists find puzzling is that most of them still use a system of two sexes - in their case plus and minus rather than male and female. Though plus and minus create the equal-sized sex cells, plus mates only with minus and minus with plus.

Such pickiness is an enormous paradox, says Laurence Hurst*, a biologist at the University of Bath. Without sexes, you wouldn't have to limit your choice of a mate to half the population. Anyone else would be fair game.

Continued at "Carnal Knowledge: How we evolved into male and female"


*From Laurence Hurst's homepage:

"It is not unusual to think in evolutionary terms about the organismic features that are easy to observe: the structure of the finch's beak or the giraffe's neck, the length of time an organism might spend foraging or the number of males a female might prefer to mate with. But can the same sort of thinking be applied to ask questions about the organisation of genetic systems? Current work in molecular genetics is providing information at an ever increasing rate about, for example, how sex is determined, how genes are transmitted, how big they are, where they are on chromosomes etc. Can there also be an evolutionary genomics to allow us to understand these features?


In a 'Presenters Article' from The Truth Will Out (BBC/The Open University UK), Laurence Hurst addresses the following questions:

What is the trend for age of reproduction and how is this affecting mutation rate?
What effect might later reproduction have on women in the long term?
What will be the effect of modern medicine on the increase of mutation and therefore on selection?
How has globalisation impacted on evolution?
What is the likelihood that humans will speciate?


*Definition from The Free Dictionary:

isogamy, in biology, a condition in which the sexual cells, or gametes, are of the same form and size and are usually indistinguishable from each other. Many algae and some fungi have isogamous gametes. In most sexual reproduction, as in mammals for example, the ovum is quite larger and of different appearance than the sperm cell. This condition is called anisogamy.


Just over a month earlier (November 12 2006) Bath University released

"Sperm proteome gives 'tantalising glimpse' towards the origin of sex":

The first ever catalogue of the different types of proteins found in sperm could help reveal the origins of sex and explain some of the mysteries of infertility, say scientists.

Research published in Nature Genetics [1] describes 381 proteins present in sperm of the fruit fly, Drosophila melanogaster. Whilst more proteins may be identified as research progresses, this study marks the first substantial 'whole-cell' characterisation of the protein components of a higher eukaryotic cell (a cell in which all the genetic components are contained within a nucleus).

This so-called 'proteome' contains everything the sperm needs to survive and function correctly, and scientists can use it to investigate the factors that make some sperm more successful than others.

Around half of the genes of the fruit fly sperm proteome have comparable versions in humans and mice, making it a useful model for studying male infertility in mammals.

By comparing the sperm proteome of the fruit fly with other species, scientists will also be able to rewind evolution and work out the core sperm proteome – the most basic constituents a sperm needs for sexual reproduction. This will shed light on how sex itself evolved.

"This is the first catalogue of sperm proteins for any organism, and it offers a tantalising glimpse into how we might begin to answer some of biology's most fundamental questions," said Dr Tim Karr from the University of Bath who led the study.

"Amazingly we know very little about what is in a sperm, which probably explains why we don't really understand sex, let alone how it evolved.

"Before we catalogued the sperm proteome, we only knew a few specific proteins in the Drosophila sperm.

"Being able to compare the structure and content of the proteomes of sperm from different species should help us understand the evolution and origin of sperm.

"We now know of at least 381, which is a greater than 50-fold increase in our knowledge base. Now that we have identified them, we should be able to study the function of all of these."

Proteins carry out an immense range of functions, from forming structural materials to catalysing chemical reactions, so knowing exactly what proteins are in sperm is a great step forward in understanding.

The research involved purifying fruit fly sperm and developing methods to study their protein content. Previous estimates for the protein content of sperm were based on counts of proteins separated into 'spots' on a special gel matrix. However, these only identify the total number of proteins in sperm - rather than identifying the specific identity of each protein constituent

"The sperm proteome provides a basis for studying the critical functional components of sperm required for motility, fertilisation and possibly early embryo development," said Dr Steve Dorus, also from the University of Bath, who collaborated with Dr Karr on the project.

"It should be a valuable tool in the study of infertility as more targeted studies can now be established in model organisms.

"Furthermore, having a comprehensive catalogue of proteins to compare between different species will reveal how natural selection has impacted sperm evolution.

"We can start to look for the 'core' sperm proteome - that is, the most basic required constituents of sperm. This will not only shed light on the evolutionary origins of sperm, but may advance our understanding of the evolution of sex itself."

The research will also help further our understanding of sperm competition – the attributes within a sperm that make one sperm more successful at reaching and fertilising the egg than its peers.

"This question of sperm competition has baffled scientists for years," said Dr Karr.

"If we can work out what makes one sperm more successful than another, we might be able to apply this knowledge to clinical therapies for the treatment of sperm that are not functioning properly."

The findings are particularly timely as a variety of research is beginning to highlight the increasingly important role of sperm.

Scientists are discovering that as well as carrying the DNA that spells out the male's contribution to a new life, sperm carries RNA and proteins which have a direct influence on fertilisation and embryo development.

Professor Geoff Parker, Derby Professor of Zoology at the University of Liverpool, said: "This paper provides a remarkable, pioneering analysis of the molecular basis of sperm form and function by identifying 381 proteins of the Drosophila melanogaster sperm proteome, including mitochondrial, metabolic and cytoskeletal proteins.

"Their work has great relevance to current debate on the evolutionary underpinnings of sperm characteristics, and may have application to mammalian sperm function. The Drosophila sperm proteins show substantial homology with the axoneme accessory structure of mouse sperm."

Professor Manyuan Long, Professor of Genetics and Evolution at the University of Chicago, said: "This is a milestone in the understanding of genomic distribution of male specific proteins. I marvel at their tremendous efforts and great successes."

The research is funded by the Royal Society and the National Science Foundation with additional support from the Biotechnology and Biological Sciences Research Council and the National Institutes of Health.

Source: Bath University PR November 12 2006


[1] Nature Genetics - 38, 1440 - 1445 (2006)
Published online: 12 November 2006; | doi:10.1038/ng1915

Genomic and functional evolution of the Drosophila melanogaster sperm proteome

Steve Dorus, Scott A Busby, Ursula Gerike, Jeffrey Shabanowitz, Donald F Hunt, and Timothy L Karr

In addition to delivering a haploid genome to the egg, sperm have additional critical functions, including egg activation, origination of the zygote centrosome and delivery of paternal factors. Despite this, existing knowledge of the molecular basis of sperm form and function is limited. We used whole-sperm mass spectrometry to identify 381 proteins of the Drosophila melanogaster sperm proteome (DmSP). This approach identified mitochondrial, metabolic and cytoskeletal proteins, in addition to several new functional categories. We also observed nonrandom genomic clustering of sperm genes and underrepresentation on the X chromosome. Identification of widespread functional constraint on the proteome indicates that sexual selection has had a limited role in the overall evolution of D. melanogaster sperm. The relevance of the DmSP to the study of mammalian sperm function and fertilization mechanisms is demonstrated by the identification of substantial homology between the DmSP and proteins of the mouse axoneme accessory structure.


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Tarbosaurus: Rare dinosaur fossil unearthed by Korea-led team

From The Hankyoreh (Korea): An international team supported by the Gyeonggi provincial government has excavated a rare dinosaur fossil in the Gobi Desert in Mongolia.

Hwaseong City in Gyeonggi Province and an international dinosaur excavation team led by Lee Yung-nam, a researcher of the Korea Institute of Geoscience and Mineral Resources, said on December 17 that they had excavated 8-kilogram fossil of the Tarbosaurus*. The Tarbosausus is an ancestor of the Tyrannosaurus.

This is the first time that an entire fossil of the Tarbosaurus, which lived during the Cretaceous** period of the Mesozoic era about 80 million years ago, has been found. The academic community thinks that with the find, it can accurately confirm for the first time what the rare dinosaur looked like. Its entire appearance has not yet been confirmed due to the fact that fossils of its pelvis and tail region have not been found until now.

In addition, the team found a gastrolith*** - a stone in the abdominal cavity that aided digestion - in the fossil, which marks the first time this stone has been found in the remains of a carnivorous dinosaur.

Continued at "Rare dinosaur fossil unearthed by Korea-led team"


The following notes on Tarbosaurus, the Cretaceous Period, and Gastroliths are taken from Wiki:

*Info on Tarbosaurus:

Tarbosaurus, meaning 'Terror Lizard' (from the Greek tarbos meaning 'fright', 'alarm', 'terror' (interestingly it can also mean 'awe' or 'reverence'[1]) and saurus meaning 'lizard'), was a member of the dinosaur family of tyrannosaurids, which flourished during the early Maastrichtian of the Late Cretaceous Period. It is closely related to the genus (and perhaps is indistinct from) Tyrannosaurus. (More)


**Info on Cretaceous:

The Cretaceous Period is one of the major divisions of the geologic timescale, reaching from the end of the Jurassic Period (i.e. from 145.5 +- 4.0 million years ago (Ma)) to the beginning of the Paleocene epoch of the Tertiary Period (about 65.5 +- 0.3 Ma). As the longest geological Period, the Cretaceous constitutes nearly half of the Mesozoic. The end of the Cretaceous defines the boundary between the Mesozoic and Cenozoic eras.

The Cretaceous (from Latin creta meaning 'chalk') as a separate period was first defined by a Belgian geologist Jean d'Omalius d'Halloy in 1822, using strata in the Paris basin and named for the extensive beds of chalk (calcium carbonate deposited by the shells of marine invertebrates, principally coccoliths), found in the upper Cretaceous of the continental Europe and the British Isles (including the White Cliffs of Dover). (More)


***Info on Gastroliths:

Gastroliths ('stomach stones' or 'gizzard stones') are rocks, which are or have been held inside the digestive tract of an animal. Among living vertebrates, gastroliths are common among herbivorous birds, crocodiles, seals and sea lions. Domestic fowl, for instance, require access to 'grit', for the purpose of food-grinding. Gastroliths are retained in the very muscular gizzard and serve the masticatory function of teeth, in an animal without suitable grinding teeth. The grain size of the gastrolith depends upon the size of the animal and its special needs. Particles as small as sand and stones the size of cobbles or greater have been found.

Some extinct animals, such as bird-like theropod dinosaurs, appear to have used stones to grind tough plant matter. Gastroliths have only rarely been found in association with fossils of sauropod dinosaurs and a trituration of their food with the stones is not plausible. Aquatic animals, such as plesiosaurs, may have used them as ballast, to help balance themselves or to decrease their buoyancy, as crocodiles do. More research is needed, to understand the function of the stones in aquatic animals. While some fossil gastroliths are rounded and polished, many stones in living birds are not polished at all. Gastroliths associated with dinosaur fossils can be several kilograms in weight. Stones swallowed by ostriches can also reach a length of more than 10 cm. (More)

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