Evolutionary Surprise: Eight Percent of Human Genetic Material Comes from a Virus

ScienceDaily (Jan. 8, 2010) — About eight percent of human genetic material comes from a virus and not from our ancestors, according to researchers in Japan and the U.S.

The study, and an accompanying News & Views article by University of Texas at Arlington biology professor Cédric Feschotte, is published in the journal Nature.

The research showed that the genomes of humans and other mammals contain DNA derived from the insertion of bornaviruses, RNA viruses whose replication and transcription takes place in the nucleus. Feschotte wrote on recent research led by Professor Keizo Tomonaga at Osaka University in Japan. Feschotte said this virally transmitted DNA may be a cause of mutation and psychiatric disorders such as schizophrenia and mood disorders.

In his article, Feschotte speculates about the role of such viral insertions in causing mutations with evolutionary and medical consequences.

The assimilation of viral sequences into the host genome is a process referred to as endogenization. This occurs when viral DNA integrates into a chromosome of reproductive cells and is subsequently passed from parent to offspring. Until now, retroviruses were the only viruses known to generate such endogenous copies in vertebrates. But Feschotte said that scientists have found that non-retroviral viruses called bornaviruses have been endogenized repeatedly in mammals throughout evolution.

Bornavirus (BDV) owes its name to the town of Borna, Germany, where a virus epidemic in 1885 wiped out a regiment of cavalry horses. BDV infects a range of birds and mammals, including humans. It is unique because it infects only neurons, establishing a persistent infection in its host's brain, and its entire life cycle takes place in the nucleus of the infected cells. Feschotte said this intimate association of BDV with the cell nucleus prompted researchers to investigate whether bornaviruses may have left behind a record of past infection in the form of endogenous elements. They searched the 234 known eukaryotic genomes (those genomes that have been fully sequenced) for sequences that are similar to that of BDV. "The researchers unearthed a plethora of endogenous Borna-like N (EBLN) elements in many diverse mammals, " Feschotte said.

The scientists also were able to recover spontaneous BDV insertions in the chromosomes of human cultured cells persistently infected by BVD.Based on these data, Feschotte proposes that BDV insertions could be a source of mutations in the brain cells of infected individuals.

"These data yield a testable hypothesis for the alleged, but still controversial, causative association of BDV infection with schizophrenia and mood disorders," Feschotte said. The research in Feschotte 's laboratory, which largely focuses on transposable elements, the genetic elements that are able to move and replicate within the genomes of virtually all living organisms, is representative of the research under way at UT Arlington, an institution of 28,000 students on its way to becoming a nationally recognized, top-tier research university.

http://www.sciencedaily.com/releases/2010/01/100107103621.htm

New Theory on the Origin of Primates

ScienceDaily (Jan. 20, 2010) — A new model for primate origins is presented in Zoologica Scripta, published by the Norwegian Academy of Science and Letters and The Royal Swedish Academy of Sciences. The paper argues that the distributions of the major primate groups are correlated with Mesozoic tectonic features and that their respective ranges are congruent with each evolving locally from a widespread ancestor on the supercontinent of Pangea about 185 million years ago.

Michael Heads, a Research Associate of the Buffalo Museum of Science, arrived at these conclusions by incorporating, for the first time, spatial patterns of primate diversity and distribution as historical evidence for primate evolution. Models had previously been limited to interpretations of the fossil record and molecular clocks.

"According to prevailing theories, primates are supposed to have originated in a geographically small area (center of origin) from where they dispersed to other regions and continents" said Heads, who also noted that widespread misrepresentation of fossil molecular clocks estimates as maximum or actual dates of origin has led to a popular theory that primates somehow crossed the globe and even rafted across oceans to reach America and Madagascar.

In this new approach to molecular phylogenetics, vicariance, and plate tectonics, Heads shows that the distribution ranges of primates and their nearest relatives, the tree shrews and the flying lemurs, conforms to a pattern that would be expected from their having evolved from a widespread ancestor. This ancestor could have evolved into the extinct Plesiadapiformes in north America and Eurasia, the primates in central-South America, Africa, India and south East Asia, and the tree shrews and flying lemurs in South East Asia.

Divergence between strepsirrhines (lemurs and lorises) and haplorhines (tarsiers and anthropoids) is correlated with intense volcanic activity on the Lebombo Monocline in Africa about 180 million years ago. The lemurs of Madagascar diverged from their African relatives with the opening of the Mozambique Channel (160 million years ago), while New and Old World monkeys diverged with the opening of the Atlantic about 120 million years ago.

"This model avoids the confusion created by the center of origin theories and the assumption of a recent origin for major primate groups due to a misrepresentation of the fossil record and molecular clock divergence estimates" said Michael from his New Zealand office. "These models have resulted in all sorts of contradictory centers of origin and imaginary migrations for primates that are biogeographically unnecessary and incompatible with ecological evidence."

The tectonic model also addresses the otherwise insoluble problem of dispersal theories that enable primates to cross the Atlantic to America, and the Mozambique Channel to Madagascar although they have not been able to cross 25 km from Sulawesi to Moluccan islands and from there travel to New Guinea and Australia.

Heads acknowledged that the phylogenetic relationships of some groups such as tarsiers, are controversial, but the various alternatives do not obscure the patterns of diversity and distribution identified in this study.

Biogeographic evidence for the Jurassic origin for primates, and the pre-Cretaceous origin of major primate groups considerably extends their divergence before the fossil record, but Heads notes that fossils only provide minimal dates for the existence of particular groups, and there are many examples of the fossil record being extended for tens of millions of years through new fossil discoveries.

The article notes that increasing numbers of primatologists and paleontologists recognize that the fossil record cannot be used to impose strict limits on primate origins, and that some molecular clock estimates also predict divergence dates pre-dating the earliest fossils. These considerations indicate that there is no necessary objection to the biogeographic evidence for divergence of primates beginning in the Jurassic with the origin of all major groups being correlated with plate tectonics.

Chimp and Human Y Chromosomes Evolving Faster Than Expected

ScienceDaily (Jan. 15, 2010) — Contrary to a widely held scientific theory that the mammalian Y chromosome is slowly decaying or stagnating, new evidence suggests that in fact the Y is actually evolving quite rapidly through continuous, wholesale renovation.

By conducting the first comprehensive interspecies comparison of Y chromosomes, Whitehead Institute researchers have found considerable differences in the genetic sequences of the human and chimpanzee Ys -- an indication that these chromosomes have evolved more quickly than the rest of their respective genomes over the 6 million years since they emerged from a common ancestor. The findings are published online this week in the journal Nature.

"The region of the Y that is evolving the fastest is the part that plays a role in sperm production," say Jennifer Hughes, first author on the Nature paper and a postdoctoral researcher in Whitehead Institute Director David Page's lab. "The rest of the Y is evolving more like the rest of the genome, only a little bit faster."

The chimp Y chromosome is only the second Y chromosome to be comprehensively sequenced. The original chimp genome sequencing completed in 2005 largely excluded the Y chromosome because its hundreds of repetitive sections typically confound standard sequencing techniques. Working closely with the Genome Center at Washington University, the Page lab managed to painstakingly sequence the chimp Y chromosome, allowing for comparison with the human Y, which the Page lab and the Genome Center at Washington University had sequenced successfully back in 2003.

The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content. The chimp Y, for example, has lost one third to one half of the human Y chromosome genes--a significant change in a relatively short period of time. Page points out that this is not all about gene decay or loss. He likens the Y chromosome changes to a home undergoing continual renovation.

"People are living in the house, but there's always some room that's being demolished and reconstructed," says Page, who is also a Howard Hughes Medical Institute investigator. "And this is not the norm for the genome as a whole."

Wes Warren, Assistant Director of the Washington University Genome Center, agrees. "This work clearly shows that the Y is pretty ingenious at using different tools than the rest of the genome to maintain diversity of genes," he says. "These findings demonstrate that our knowledge of the Y chromosome is still advancing."

Hughes and Page theorize that the divergent evolution of the chimp and human Y chromosomes may be due to several factors, including traits specific to Y chromosomes and differences in mating behaviors.

Because multiple male chimpanzees may mate with a single female in rapid succession, the males' sperm wind up in heated reproductive competition. If a given male produces more sperm, that male would theoretically be more likely to impregnate the female, thereby passing on his superior sperm production genes, some of which may be residing on the Y chromosome, to the next generation.

Because selective pressure to pass on advantageous sperm production genes is so high, those genes may also drag along detrimental genetic traits to the next generation. Such transmission is allowed to occur because, unlike other chromosomes, the Y has no partner with which to swap genes during cell division. Swapping genes between chromosomal partners can eventually associate positive gene versions with each other and eliminate detrimental gene versions. Without this ability, the Y chromosome is treated by evolution as one large entity. Either the entire chromosome is advantageous, or it is not.

In chimps, this potent combination of intense selective pressure on sperm production genes and the inability to swap genes may have fueled the Y chromosome's rapid evolution. Disadvantages from a less-than-ideal gene version or even the deletion of a section of the chromosome may have been outweighed by the advantage of improved sperm production, resulting in a Y chromosome with far fewer genes than its human counterpart.

To determine whether this rapid rate of evolution affects Y chromosomes beyond those of chimps and humans, the Page lab and the Washington University Genome Center are now sequencing and examining the Y chromosomes of several other mammals.

This research was funded by the National Institutes of Health (NIH) and the Howard Hughes Medical Institute (HHMI).

http://www.sciencedaily.com/releases/2010/01/100113131505.htm