Evolutie. Deel XV

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Wheeler, D.A. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.

The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome1, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2–40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual2 by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.

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Gregory, T.R. (2008) Understanding evolutionary trees. Evolution: Education and Outreach, 1, 121-137.

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

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Islan, M. et al. (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature, 452, 840-845.

Sequencing DNA from several organisms has revealed that duplication and drift of existing genes have primarily moulded the contents of a given genome. Though the effect of knocking out or overexpressing a particular gene has been studied in many organisms, no study has systematically explored the effect of adding new links in a biological network. To explore network evolvability, we constructed 598 recombinations of promoters (including regulatory regions) with different transcription or sigma-factor genes in Escherichia coli, added over a wild-type genetic background. Here we show that approx95% of new networks are tolerated by the bacteria, that very few alter growth, and that expression level correlates with factor position in the wild-type network hierarchy. Most importantly, we find that certain networks consistently survive over the wild type under various selection pressures. Therefore new links in the network are rarely a barrier for evolution and can even confer a fitness advantage.

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Op woensdag 16 april 2008 23:41 schreef ATuin-hek het volgende:

[..]

Daar zitten zo te zien interessante dingen tussen Enig idee hoe moeilijk ze doen over bestellingen van buiten de US?

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Italian wall lizards introduced to a tiny island off the coast of Croatia are evolving in ways that would normally take millions of years to play out, new research shows.

In just a few decades the 5-inch-long (13-centimeter-long) lizards have developed a completely new gut structure, larger heads, and a harder bite, researchers say.

In 1971, scientists transplanted five adult pairs of the reptiles from their original island home in Pod Kopiste to the tiny neighboring island of Pod Mrcaru, both in the south Adriatic Sea.

Genetic testing on the Pod Mrcaru lizards confirmed that the modern population of more than 5,000 Italian wall lizards are all descendants of the original ten lizards left behind in the 1970s.

Lizard Swarm

While the experiment was more than 30 years in the making, it was not by design, according to Duncan Irschick, a study author and biology professor at the University of Massachusetts, Amherst.

After scientists transplanted the reptiles, the Croatian War of Independence erupted, ending in the mid-1990s. The researchers couldn't get back to island because of the war, Irschick said.

In 2004, however, tourism began to open back up, allowing researchers access to the island laboratory.

"We didn't know if we would find a lizard there. We had no idea if the original introductions were successful," Irschick said.

What they found, however, was shocking. "The island was swarming with lizards," he said.

The findings were published in March in the journal Proceedings of the National Academy of Sciences.

Fast-Track Evolution

The new habitat once had its own healthy population of lizards, which were less aggressive than the new implants, Irschick said.

The new species wiped out the indigenous lizard populations, although how it happened is unknown, he said.

The transplanted lizards adapted to their new environment in ways that expedited their evolution physically, Irschick explained.

Pod Mrcaru, for example, had an abundance of plants for the primarily insect-eating lizards to munch on. Physically, however, the lizards were not built to digest a vegetarian diet.

Researchers found that the lizards developed cecal valves—muscles between the large and small intestine—that slowed down food digestion in fermenting chambers, which allowed their bodies to process the vegetation's cellulose into volatile fatty acids.

"They evolved an expanded gut to allow them to process these leaves," Irschick said, adding it was something that had not been documented before. "This was a brand-new structure."

Along with the ability to digest plants came the ability to bite harder, powered by a head that had grown longer and wider.

The rapid physical evolution also sparked changes in the lizard's social and behavioral structure, he said. For one, the plentiful food sources allowed for easier reproduction and a denser population.

The lizard also dropped some of its territorial defenses, the authors concluded.

Such physical transformation in just 30 lizard generations takes evolution to a whole new level, Irschick said.

It would be akin to humans evolving and growing a new appendix in several hundred years, he said.

"That's unparalleled. What's most important is how fast this is," he said.

While researchers do know the invader's impact on its reptile brethren, they do not know how the species impacts local vegetation or insects, a subject of future study, Irschick said.

Dramatic Changes

The study demonstrates that a lot of change happens in island environments, said Andrew Hendry, a biology professor at Montreal's McGill University.

What could be debated, however, is how those changes are interpreted—whether or not they had a genetic basis and not a "plastic response to the environment," said Hendry, who was not associated with the study.

There's no dispute that major changes to the lizards' digestive tract occurred. "That kind of change is really dramatic," he added.

"All of this might be evolution," Hendry said. "The logical next step would be to confirm the genetic basis for these changes."

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Op woensdag 23 april 2008 21:37 schreef wijsneus het volgende:
Erg benieuwd of ze nog genetisch compatible zijn, de ouder populatie en de nieuwe.

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The relatively large fraction of leaves included into the diet of lizards in the introduced population of Pod Mrcˇaru has apparently also resulted in the evolution of cecal valves, a structure previously unreported for this species and rare in this family and scleroglossan lizards in general (13, 14, 18). Our data also add to the growing number of studies suggesting that the inclusion of plant matter into the diet of small temperate lizards may be more common than previously thought (21, 22). Moreover, our data show not only rapid, directional changes in quantitative phenotypic traits related to the inclusion of plant matter into the diet, but also the evolution of novel morphological structures on extremely short time scales. Although the presence of cecal valves and large heads in hatchlings and juveniles suggests a genetic basis for these differences, further studies investigating the potential role of phenotypic plasticity and/or maternal effects in the divergence between populations are needed.

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Op woensdag 23 april 2008 22:04 schreef wijsneus het volgende:
Nee - maar zoals Darwin al opmerkte: variaties kunnen fenotypisch enorm verschillen, maar toch perfect vruchtbaar zijn. De vraag is: is er speciatie opgetreden?

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Op woensdag 23 april 2008 23:18 schreef barthol het volgende:

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5 volwassen paartjes als founder population.... Hier zal genetische drift zeker ook een rol gespeeld hebben bij de snelle fenotypische veranderingen.

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In the first analysis of proteins extracted from dinosaur bones, scientists say they have established more firmly than ever that the closest living relatives of the mighty predator Tyrannosaurus rex are modern birds.

The research, being published Friday in the journal Science, yielded the first molecular data confirming the widely held hypothesis of a close dinosaur-bird ancestry, the American scientific team reported. The link was previously suggested by anatomical similarities.

In fact, the scientists said, T. rex shared more of its genetic makeup with ostriches and chickens than with living reptiles, like alligators. On this basis, the research team has redrawn the family tree of major vertebrate groups, assigning the dinosaur a new place in evolutionary relationships.

Similar molecular tests on tissues from the extinct mastodon confirmed its close genetic link to the elephant, as had been suspected from skeletal affinities.

“Our results at the genetic level basically agree with what has been seen in skeletal data,” John M. Asara of Harvard said in a telephone interview. “There is more than a 90 percent probability that the grouping of T. rex with living birds is real.”

Dr. Asara and Lewis C. Cantley, both of Beth Israel Deaconess Medical Center and Harvard Medical School, processed the proteins from tissue recovered deep in bones of a 68 million-year-old T. rex excavated in 2003 by John R. Horner of Montana State University. Mary H. Schweitzer of North Carolina State University discovered the preserved soft tissues in the bones.

For the molecular study, Dr. Asara and Chris L. Organ, a researcher in evolutionary biology at Harvard, compared the dinosaur protein with similar protein from several dozen species of modern birds, reptiles and other animals.

Dr. Organ was the lead author of the journal report, which concluded that the molecular tests confirmed the prediction that extinct dinosaurs “would show a higher degree of similarity with birds than with other extant vertebrates.” The researchers said they planned to extend their investigations to include comparisons of T. rex protein with more species of birds, reptiles and other dinosaurs.

Dinosaur paleontologists were not surprised by the findings. An accumulation of fossil evidence in recent years had given them increasing confidence in their contention that birds descended from certain dinosaurs.

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Op dinsdag 29 april 2008 22:40 schreef barthol het volgende:
Even een mooie foto die ik jullie niet wil onthouden.
Een Orang-Oetan die een speer gebruikt om te vissen.
[ afbeelding ]
De foto is uit een artikel op primatology.net
In dat artikel staan ook links naar een aantal wetenschappelijke rapporten over het gebruik
van tools door Orang-Oetans.

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We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

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The 18,527 protein-coding genes predicted from the platypus assembly fall within the range for therian genomes. Of particular interest are families of genes involved in biology that links monotremes to reptiles, such as egg-laying, vision and envenomation, as well as mammal-specific characters such as lactation, characters shared with marsupials such as antibacterial proteins, and platypus-specific characters such as venom delivery and underwater foraging. For instance, anatomical adaptations for chemoreception during underwater foraging are reflected in an unusually large repertoire of vomeronasal type 1 receptor genes. However, the repertoire of milk protein genes is typically mammalian, and the arrangement of milk protein genes seems to have been preserved since the last common ancestor of monotremes and therian mammals.

Since its initial description, the platypus has stood out as a species with a blend of reptilian and mammalian features, which is a characteristic that penetrates to the level of the genome sequence. The density and distribution of repetitive sequence, for example, reflects this fact. The high frequency of interspersed repeats in the platypus genome, although typical for mammalian genomes, is in contrast with the observed mean microsatellite coverage, which appears more reptilian. Additionally, the correlation of parent-of-origin-specific expression patterns in regions of reduced interspersed repeats in the platypus suggests that the evolution of imprinting in therians is linked to the accumulation of repetitive elements.

We find that the mixture of reptilian, mammalian and unique characteristics of the platypus genome provides many clues to the function and evolution of all mammalian genomes. The wealth of new findings and confirmation of existing knowledge immediately evident from the release of these data promise that the availability of the platypus genome sequence will provide the critically needed background to inspire rapid advances in other investigations of mammalian biology and evolution.