Thursday, October 31, 2013

New method for determining Identity by Descent

This article describes a method for determining Identity by Descent using sequencing data instead of SNP array data.  The method targets specific known IBD segments and calculates a genotype error rate for that segment.  Genotype error rate is calculated using a ratio of the observed rate and expected rate of homozygotes or heterozygotes.

Monday, October 28, 2013

The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q

A recent study published in PLOS examines Y-chromosome data from more than 400 Native Americans to shed further light on the peopling of the Americas. This study focuses on Y-chromosome data from Native American individuals belonging to haplogroup Q -- the only Y-chromosome haplogroup observed in Central and South Native Americans. The study reveals two main founding lineages, one of which is observed in Far East Asia and a subclade of the other in southern Siberia. Results support a Y-chromosome based conclusion of a Siberian origin of founding populations in the Americas, and indicates two main lineages descending down into the Americas from Beringia.

Original Article Here. 

A European population in Minoan Bronze Age Crete

An article published in Nature this past spring discusses the genetic origins of the ancient Minoans.  DNA taken from some of the archaeological sites there, and the haplotypes of the mitochondrial DNA was examined. Previously, archaeologists thought that the Minoans might have been related to a range of other populations including those from North Africa, the Middle East, the Balkans based on their material culture.  The results of this study showed that the Minoans were related most closely to North and Western Europeans.  They share a much of their genetic make up with other ancient finds from Iberia, Sardinia, France and Scandanavia.  Additionally, the article stated that the modern inhabitants of Crete are direct descendants, at least matrilineally, from the Minoans.  

Biology Letters: October

This article published in Biology Letters focuses on a topic pertinent to animal behavior and evolutionary anthropology. Disruptive coloration is a common mechanism used by organisms (i.e. moths) to avoid detection by predators. However, the researchers brought up the point that there has not been experimental evidence relating disruptive coloration and decreased likelihood of detection. From this, the researchers designed an experiment in which human subjects were asked to search for computer-generated moth targets; eye movement of the human subjects was measured. The researchers found that an increase in the number of edge-intersecting patches (simulating disruptive coloration) on the moth decreases the probability of it being detected. From these results, the researchers discussed that there is a strong evolutionary basis for disruptive coloration and provided experimental evidence for this adaptation.

Using Whole-Genome In-Solution Capture (WISC) for aDNA Libraries

In a study recently published in the American Journal of Human Genetics, researchers applied a technique (whole-genome in-solution capture: WISC) to enrich ancient DNA libraries. Specifically, the researchers used RNA “baits” that were produced through transcription from genomic DNA libraries. These RNA “baits” were hybridized to ancient DNA libraries, and subsequently the RNA "baits" and bound aDNA were pulled down with magnetic streptavidin-coated beads. After the unbound (non-human) DNA was washed away, the captured endogenous human aDNA was amplified for further sequencing. The researchers emphasize that further work is needed; however, their results offer a promising outlook. WISC resulted in an increase from 1.2% (from shotgun sequencing) up to 59% of reads mapped to the human genome.

Sunday, October 27, 2013

Oldest Full Modern Human Genome Holds Big Surprise for Native American Ancestry

Michael Balter of Science reports in this week's issue on the announcement at a recent conference of the sequencing of the whole genome of a Siberian individual living 24,000 years ago (also currently in press at Nature). This is the oldest genome of a modern human ever sequenced to date, at almost five times the antiquity of the next most ancient modern human genome. But even more interesting was the research team's findings with regard to the individual's ancestry. This ancient Siberian was found to be most closely related to living Native Americans. However, approximately one third of the of the genome showed an affinity to living Europeans. This may suggest that Native Americans had European ancestry prior to admixture following European colonization of the New World after 1492. It will be extremely interesting to see the forthcoming Nature paper, especially given the challenges of sequencing modern human ancient DNA, and considering that the researchers involved were likely themselves of European descent!

Additionally, you can listen to the Science podcast interview with Michael Balter on this research.

Wednesday, October 23, 2013

This Wednesday's Nature: An opinion on "Skull Five" plus Transcription and Epigenetics supplement

Last week, a paper in Science announced the discovery of the most complete hominin cranium ever found from the Early Pleistocene. The Dmanisi fossils, the earliest known hominins outside of Africa, have long been remarked upon for their apparent inter-individual morphological diversity, as well as retention of seemingly "primitive" traits like small relative brain size. The individual that the newly-described Dmanisi "Skull Five" belonged to lived at the same time as Homo erectus, but as is clear from this latest publication, possessed a remarkably small braincase and a large, prognathic lower face. The contrast between this specimen's features with those of its known Homo coevals prompted its discoverers to advocate for the collapse of all early Homo taxa into a single, variable species.

In a cleverly-named opinion piece in this week's nature, Fred Spoor argues that this conclusion is premature. He finds fault with Lordkipanidze et al.'s phenetic analysis of the specimen's morphology, and argues that a character-based cladistic approach is necessary. He further points out that the fossil shows a combination of primitive and derived traits. This suggests that Skull Five is not best lumped in with other primitive Homo, but rather that it exhibits a relatively primitive Homo erectus-specific morphology, as has been observed and may, under certain models of speciation, be expected on the periphery of the Homo erectus range.

This issue of nature also contains a special supplement on Transcription and Epigenetics, which may be of interest.

Tuesday, October 22, 2013

Coupled Oscillator Dynamics of Vocal Turn-Taking in Monkeys

Attached is an interesting publication in Current Biology regarding vocalization patterns of Marmoset monkeys.  These monkeys were used to determine whether non-human primates exhibit cooperative vocal communication by taking turns speaking.  Results of these studies showed that they do indeed take turns in extended sequences and that the pattern is characteristic of a coupled oscillator (similar to humans).  Since marmosets are on a different branch of the evolutionary tree, this could very well be convergent evolution of vocal cooperation.

Monday, October 14, 2013

Genetic Makeup and Diet Interact with the Microbiome to Impact Health


A new study conducted at the Mayo Clinic investigates the interactions between host genome and the microbiome of the gut.  The study used mice models that were meant to mimic a condition found in 20% of humans.  These people cannot process the sugar metabolite fucose, which many bacteria rely on as a source of energy.  The researchers found that in environments lacking this sugar, bacteria that normally processed it were forced to adapt and take on new functions.  Researchers thought that conditions such as these could lead to different digestive disorders like Crohn's disease as the bacteria adopt new roles. The study showed though that the genetic makeup of the mammalian host can directly impact and shape the microbes found in its gut.

Using Microbiome for Forensics Applications

In a paper titled "A Microbial Clock Provides an Accurate Estimate of the Postmortem Interval in a Mouse Model System," which appeared in a September issue of eLIFE (online science and biomedical journal), researchers used a sequencing-based method to determine postmortem interval time of death in criminal investigations. Current forensic means of diagnosing the time of death are variable in their success rate and include: corpse temperatures, insect coverage on a cadaver, and extent of rigor mortis. Researchers tracked the changes in microbial communities on the head, torso, body cavities, and grave soil of 40 mice over a period of 48 days. At regular intervals (8 different points equally distributed across those 48 days), the researchers used complementary sequencing technology (Illumina High Sequence Platform and Pacific Biosciences RS Platform used to sequence rRNA) to characterize microbial environment on different parts of the body. The results showed that the microbial patterns were consistent among individual mice at each time-interval. This genomic research has interesting forensic applications.

Brewer's Yeast implicated in Gut Fermentation Syndrome

This research article chronicles the bizarre case of a man who appeared to suddenly become intoxicated without consuming any alcohol. The man frequently reported feelings of intoxication at inappropriate times and in response his wife bought a breathalyzer to document the occurrences. While doctors initially disregarded his condition as a case of closet drinking, experimentation proved that his gut actually was fermenting carbohydrates into alcohol, and to very high levels. Stool cultures showed that the man had an unusual growth of Saccharomyces cerevisiae in his gut -- Brewer's Yeast. Because of its use in biofuels, the Saccharomyces cerevisiae genome has been published. The man underwent successful treatment to rid his gut of Saccharomyces cerevisiae, which proved to be the causative agent for his sudden intoxication. This occurrence has been documented before but has never been formally proved in a clinical setting.

Original article here. 

Monday, October 7, 2013

Biology Letters Article

Journal: Biology Letters (Sept 2013)
This article focuses on animal behavioral adaptations to human intervention; it also expands upon potential natural selection reasonings in the discussion section of the paper.

This Biology Letters article focuses on the relationship between speed limit in regions of a road in western France (the human intervention) and a bird’s flight-initiation-distance or FID (behavioral adaptation). The main variable the researchers measured was FID on four road sections with speed limits of 20, 50, 90, and 110 km/hr. To differentiate between the variables of car speed and speed limit, three scenarios were set for each road section: a car would travel first under the speed limit, second at the speed limit, and third above the speed limit. The landscape was kept constant across these various road sections.

The researchers measured the following variables from each road section: speed limit, car speed, season, bird position, and bird mass. Linear mixed models showed that there was an increase in bird FID in response to increasing speed limit (see attached graph in link above). However, they found that the car speed (entering the road section) did not have any direct or indirect relationship with FID. The researchers thus concluded that birds are able to associate certain road sections with speed limits as a means to measure the risk of a collision. The researchers also found that increasing body mass index correlated with increasing FID; birds with larger body mass index are less agile and thus require a larger FID to escape collision.