Tuesday, January 31, 2012

Testing adaptive hypotheses of male reproductive cooperation

This study published last summer in Animal Behavior explores the potential for direct and/or indirect fitness benefits from reproductive cooperation among polyandrous males in Sanguinus geoffroyi (Geoffroy's tamarin). As observed in Geoffroy's tamarins, a single female mates with all adult males unrelated to her, and in turn the males cooperate to rear the young. Researchers studied six groups from two tamarin populations over 2-3 years, and determined that the polyandrous males were consistently more highly related to each other than expected by chance, and they often shared paternity both within litters and across the 2-3 year period. Groups with a single sire were also observed, which may be attributed to sperm competition. These findings suggest that both indirect and direct fitness benefits may play a role in the evolution of male reproductive cooperation.

Monday, January 30, 2012

Hsp90 stress potentiates rapid cellular adaptation through induction of aneuploidy

Researchers investigated how yeast responds to stressful environments and discovered that it adapts by gaining or discarding chromosomes. Aneuploidy, or an uneven number of chromosomes, is often seen as deleterious, as in cancers. However, many yeasts are aneuploid and it is hypothesized that this uneven number of chromosomes allows yeast DNA to mutate more readily, thus providing novel genetic material during unstable, stressful environments. This would then allow more rapid phenotypic evolution. In this study, the yeast became drug resistant.

Tuesday, January 24, 2012

For Those With a Sweet Tooth & Good Sense of Humor!

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

The authors of this new study aimed to shed some light on endangered primate species lacking genome-level data, as such data will be crucial to future conservation efforts. As we've learned, chimps, orangutans, and rhesus macaques have gotten lots of attention in the genomics department, but there remain several primates, many endangered, for which little genomic data is available. Researchers analyzed genetic diversity, which is associated with risk of extinction, after sequencing RNA from liver samples taken from humans, chimps, rhesus macaques, vervets, common marmosets, five lemur species, and two lorisoids. They found no correlation between diversity and endangered status. Furthermore, the two most endangered species included in the study (both lemur species) actually had the highest diversity, offering new hope to future conservation efforts.

Three Monkeys a Genetic Mishmash

Is reality mirroring mythology? Scientists have created rhesus monkey chimeras, whose cells contain the DNA of up to six different embryos. Although chimeric mice are common in biological research, scientists found that working with monkeys was much more trying--implying that creating a human chimera might be similarly difficult. How do you think that this finding could impact regenerative medicine?

Global discovery of primate-specific genes in the human genome

In order to discover single-copy primate-specific genes, the authors of this paper screened a catalog of 38,037 human transcriptional units (TUs) and found 131 TUs that were primate-specific insertions across 9 different primate species. They estimate that 46% of these TUs might be protein coding. They also discovered that most of these primate-specific insertions were in organs specific to reproduction; supporting the hypothesis that the order primates arose through biological speciation.

CNV variation in the great apes

An awesome comparison made possible by having the great ape genomes! These researchers looked at copy number variations (CNVs) in the great apes and in this way compared genomic structural variation across chimps, bonobos, gorillas and orangutans. They found signatures of different, species specific selection pressures as follows: purifying selection in the gorilla, positive selection for the fixation of structural variants in the orangutan, and relaxed purifying selection with high mutation rates in chimpanzees and bonobos. A surprising result is that chimpanzees and bonobos share more CNVs with gorillas than they do with each other (figure shown below). This is explained by homoplasy. This analysis was done on a total of 51 individuals from the four species by applying a comparative genomic hybridization of their samples onto the reference genome for each species. *Discussion question: I wonder what this same analysis would look like in 10 years after we get higher quality reference genomes for each of these species! How much does everyone trust this result given the state of the genomes today? Brenda, maybe you can comment on this better than any of us can....*

Friday, January 20, 2012

3D Fruitfly Genome

Genomics era - so 10 years ago! We're now entering into the 3D Genomics Era. Yup, researchers have mapped the fruitfly genome in 3D to better understand how nucleotide changes can affect structure and function of the genome. The 3D folding of chromosomes could provide insight into how genomic neighborhoods can affect interactions between genes and thus gene expression. The creation of more 3D genomes will help shed light on basic questions about genome organization.

Thursday, January 12, 2012

The 24-hour Genome!

Announced in Nature News. This "nanofluid" chip can't be used for de novo sequencing, but is a very quick way to screen certain SNPs (at least that's what I got from a qick read of this news piece). Should be interesting!

Tuesday, January 3, 2012

Genome Study Points to Adaptation in Early African-Americans

Just thought this was a cool article that discussed genomic admixture studies like some we discussed in class last semester about selective advantages in early African American slaves.