Category Archives: Transhuman News

Imagine attempting to trace your genetic history using only information from your mother's side. That's what scientists studying the evolution of the red fox had been doing for decades. Now, University of California, Davis, researchers have for the first time investigated ancestry across the red fox genome, including the Y chromosome, or paternal line. The data, compiled for over 1,000 individuals from all over the world, expose some surprises about the origins, journey and evolution of the red fox, the world's most widely distributed land carnivore.

"The genome and the information it contains about our ancestry and evolution is huge," said lead author Mark Statham, an assistant project scientist with the UC Davis Veterinary Genetics Laboratory. "If you're only looking at what your mother's mother's mother did, you're only getting a small portion of the story."

The study, published in the latest issue of the journal Molecular Ecology, represents the most globally comprehensive work yet on the red fox.

Conventional thinking based on maternal genetics suggested that red foxes of Eurasia and North America composed a single interconnected population across the Bering land bridge between Asia and Alaska. In contrast, this new research shows that the red foxes of North America and Eurasia have been almost entirely reproductively isolated from one another for roughly 400,000 years. During this time, the North American red fox evolved into a new species distinct from its Old World ancestors.

The previous view was distorted by the maternal picture because a single female line transferred from Asia to Alaska about 50,000 years ago.

The new genetic research further suggests that the first red foxes originated in the Middle East before beginning their journey of colonization across Eurasia to Siberia, across the Bering Strait and into North America, where they eventually founded the North American population.

"That small group that got across the Bering Strait went on to colonize a whole continent and are on their own evolutionary path," Statham said.

During the red foxes' journey over millennia, ice sheet formation and fluctuating temperatures and sea levels offered periods of isolation and reconnection, impacting their global distribution. Statham said understanding the evolutionary history of the red fox can provide insight into how other species may have responded to climate change and those same environmental shifts.

The research effort, headed by Statham and Ben Sacks, associate adjunct professor and director of the UC Davis Mammalian Ecology and Conservation Unit, involved a network of collaborators and contributors from around the world and relied heavily on specimens in natural history museums.

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Around the world in 400,000 years: Journey of the red fox

PUBLIC RELEASE DATE:

8-Oct-2014

Contact: Edyta Zielinska edyta.zielinska@jefferson.edu 215-955-5291 Thomas Jefferson University @JeffersonUniv

(PHILADELPHIA) Transfer RNAs (tRNAs) are ancient workhorse molecules and part of the cellular process that creates the proteins, critical building blocks of life that keep a cell running smoothly. A new discovery suggests that the number of human genomic loci that might be coding for tRNAs is nearly double what is currently known. Most of the newly identified loci resemble the sequences of mitochondrial tRNAs suggesting unexpected new links between the human nuclear and mitochondrial genomes, links that are not currently understood.

Transfer RNAs (tRNAs) represent an integral component of the translation of a messenger RNA (mRNA) into an amino acid sequence. TRNAs are non-coding RNA molecules and can be found in all three kingdoms of life i.e., in archaea, bacteria and eukaryotes.

At the DNA level, a triplet of consecutive nucleotides known as the "codon" is used to encode an amino acid. Frequently, a given amino acid can be encoded by more than one codon: in fact, there are 61 distinct codons encoding the 20 standard human amino acids. During translation, each of the codons contained in the coding region of the mRNA at hand is recognized by its matching tRNA and the corresponding amino acid added to the nascent amino acid sequence. It has been known for many years that each of these 61 tRNAs has multiple copies spread throughout the genome that is found in the human nucleus. The presence of multiple genomic loci from which the same molecule can be made is a fairly standard trick of genomic organization: processing these loci in parallel can ensure that adequate amounts of each tRNA can be generated quickly enough to meet the high demand that the amino acid translation process imposes on the cell. In addition to the 61 tRNAs that are found in the human nuclear genome, 22 more tRNAs are encoded in the genome of the cellular organelle known as the mitochondrion: the mitochondrion, originally a bacterium itself, uses these 22 tRNAs to make proteins out of the just-over-a-dozen mRNAs that are encoded in its genome.

Recent research efforts have shown that tRNAs can have other roles, which go beyond their involvement in protein synthesis. For example, tRNAs can affect the physiology of a cell, they can modulate the abundance of important molecules, etc. These and other unexpected findings have revived interest in looking at tRNAs, this time under a different prism. But, how many tRNAs are actually encoded by the human genome and could be potentially involved in amino acid translation and other processes?

A team led by Isidore Rigoutsos, Director of the Computational Medicine Center at Thomas Jefferson University (TJU), set out to tackle this question and they have reported their findings in a study that was just published in the journal Frontiers in Genetics. "What we found, frankly, surprised us," said Rigoutsos.

The team searched the 3 billion base pairs of the human genome for DNA sequences that resembled the 530 known nuclear and mitochondrial tRNAs. Even though they used very stringent criteria in their searches, they found 454 "lookalike" loci, i.e., sequences that look like tRNA, but haven't yet been experimentally confirmed as such. The researchers found nearly as many as the known ones with which they started: 81% of these tRNA-lookalikes had not been reported previously. Rather unexpectedly, the team found that most of these new loci resembled some of the 22 mitochondrial tRNAs.

Interestingly, the discovered tRNA lookalikes are not spread uniformly across the 24 chromosomes. Instead, they have penetrated preferentially some chromosomes and have avoided others. For example, chromosomes 1, 2, 7, 8 and 9 claim the lion's share of the discovered tRNA-lookalikes. On the other hand, chromosome 18 contains no lookalikes. Also, some of the codons are particularly over-represented among the lookalikes whereas other codons are absent.

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Conspicuous tRNA lookalikes riddle the human genome