This is the blog for GW students taking Human Evolutionary Genetics. This site is for posting interesting tidbits on: the patterns and processes of human genetic variation;human origins and migration; molecular adaptations to environment, lifestyle and disease; ancient and forensic DNA analyses; and genealogical reconstructions.

GWHEG figure

GWHEG figure

Tuesday, December 4, 2018

Epigenetics found in Single-Cell Archaea, not just Eukaryotes










By; Maria Groussis

In a study by the University of Nebraska-Lincoln, epigenetics was found in single-celled archaea, meaning that they are not only present in eukaryotes as previously thought. Evidence of epigenetics was found in Sulfolobus solfataricus, a sulfur-eating species that live in the boiling, acidic springs of Yellowstone National Park. Through previous studies where they increased levels of acidity through the years, scientist developed three independent and genetically different strains. These super acid-resistant derived strains were named Crenarchaeota (SARC) and they showed a resistance 178 times greater than that of their Yellowstone ancestors. This heritable acid-resistance trait was believed to be resulted from a mutation, but this later was proven to be a false assumption. By sequencing the genomes of the three strains of SARC (SARC-C, SARC-O, and SARC-I) and comparing it to the parental genome the mutations were found. SARC-C had 5 mutations and SARC-O had 29, while SARC-I had none. This implies SARC-I must have a different non-mutation mechanism. The scientists then disrupted proteins that are thought to control the expression of resistant-relevant genes and left no change in the DNA. This immediately stopped the resistance in future generations. Therefore, it can be concluded that SARC-I has an epigenetic-like mechanism.


This new evidence of Archaea having epigenetics indicates that it is not as relatively ‘new’ thing to the Earth. It also raises the question whether the shared common ancestor of Archaea and Eukaryotes had this mechanism, or did each evolve epigenetics independently through coevolution. This also raises the question if epigenetics is the reason why no known archaea cause disease or are antibiotic like bacteria. This finding could accelerate the study of epigenetics in Humans. The differentiation of eukaryotic cells and the occurrences of cancer makes it difficult to study in eukaryotes, but the simplicity of archaea and the structural similarity to eukaryotes make it easier to study. Using archaea to study epigenetics is also faster and cheaper. This may finally help scientists determine how to reverse epigenetics and learn how to switch it on and off.
https://www.eurekalert.org/pub_releases/2018-12/uon-nit113018.php
https://news.unl.edu/newsrooms/today/article/not-in-the-dna-evolution-sans-mutation-discovered-in-single-celled-archaea/
http://www.pnas.org/content/115/48/12271.full

Monday, December 3, 2018

According to an article titled "Coffee or Tea? The Answer Might Be In Your Genes" written by Nicola Davis, a genetic predisposition to perceiving the bitterness of particular substances is key in our selection of beverages. This study involves two sets of data. The first study shows that particular genetic variants are linked to the strength of perception of different tastes: one specific variant was associated with slightly higher ratings of bitterness for caffeine and another to great bitterness for quinine and a third to greater bitterness for a drug known as propylthiouracil, or prop. The team found people with a greater genetic predisposition to perceiving the bitterness of caffeine drank a little more coffee but an increase perception of the bitterness of quinine and prop were linked to a small reduction in coffee drinking. The team also found that greater perception of the bitterness of prop was linked to a lower chance of being a heavy drinker of alcohol. Their findings also lead to the conclusion that people who prefer to drink tea, drink it as it contains a lower concentration of bitter substances meaning that it might prove more acceptable than coffee to those with a heightened perception of bitterness. It has also been reported that the preference towards tea can be seen as a consequence of abstaining from coffee because our genes might have made coffee a little bitter for our palates to handle.

Nana Evison

Wednesday, November 28, 2018

First Genome-Wide Significant Loci Associated with ADHD Identified

this article published by the Guardian on Monday the 26th states that a major breakthrough has been made in regards to the genetic variants that increase the risk of ADHD. The original study The study the first genome-wide significant risk loci and indicates an important role for common variants in the polygenic architecture of ADHD. Future work is going to be needed to find the strong source of association in each loci, but this is a breakthrough nonetheless. In the past it was hard to really pinpoint any source of ADHD because many of the genes thought to be involved increased the risk by a small degree. This is the first time that genome wide significant loci associated with ADHD has been identified. Some of the revelations of the study were already predicted such as the association with ADHD and other neurological conditions such as insomnia to schizophrenia. So in a GWAS meta-analysis of over 55,000 individuals over 12 study cohorts they were able to identify 12 locus that could be deemed significant risk loci. The results of this study not only hope to shed light on the biological factors associated with ADHD and hopefully be able to develop new drugs for ADHD (which is largely trial and error) and to encourage a dimensional view of ADHD and some argue that this could help destigmatize it too.

Ritalin is used to treat ADHD. Scientists say their findings could potentially aid the development of new drugs.

Seeran Enayet

Wednesday, November 14, 2018

Did humans domesticate themselves?

This article presents new genetic evidence from a study showing that humans probably self-domesticated themselves to select for pro-social traits. The original journal article compared the genomes of anatomically modern humans to genomes of other domesticated species (i.e. cows and dogs) and their wild types (i.e. wolves and Neanderthals). It claims that AMH and domesticated species do share overlapping genes that are associated with domestication traits. Such domestication traits are associated with docile phenotypes and behaviors. There was also no significant overlapping between AMH and Neanderthals. In case of random overlapping, researchers made sure to also compare human and domesticated species genomes to greater apes and found that this wasn't the case, which is positive evidence for self-domestication. They also looked at nearly fixed ancestral or derived SNPs in archaic lineages that have variants in AMH that would represent "under-domesticated" traits. Using other literature sources, they found that there's an ancestral mutation related to symptoms of aggressiveness and developmental delays in certain AMH diseases. Lastly, they noticed there were changes in genes associated with neural crest development in AMH from Neanderthals/Denisovans that were the same changes seen in neural development of self-domesticated species. This study can improve our understanding of why social cooperation so clearly defines modern human cognition.

Paulette Ma

Monday, November 12, 2018

Early Human Dispersals within the Americas



A new study entitled, “Early Human Dispersals within the Americas” was published in Science on November 8th by researchers from the University of Copenhagen and University of California schools summarized in Science Daily.  The researchers sequenced the genome of 15 ancient humans found in North America (ranging from Alaska to Patagonia), including some that had not been analyzed previously and compared them to genomes from nearly 400 contemporary humans as well as to SNP panels of nearly 200,000 SNPs. They found that Native Americans did not migrate out of Beringia until about 12,000 years ago and once they did engaged in a rapid expansion and split into many different populations. They also found that these early Native Americans first reached South America about 11,700 years ago and found they mixed with an Australasian population around this time. In the middle to late Holocene another wave of migration came from Mesoamerica into South America. Finally, they were able to discern that two samples from Lagao Santa and Spirit Cave that were initially labelled to be “paleoamericans” that predated the presence of Native Americans in the Americas due to their unusual cranial morphology were, in fact, Native Americans that likely had unusual skulls as a result of population isolation.

Ancient DNA and Migratory Patterns

Original Article: https://www.cell.com/cell/fulltext/S0092-8674(18)31380-1
News Article: https://www.eurekalert.org/pub_releases/2018-11/cp-ade110118.php
IMAGE

New genome-wide ancient DNA data is being utilized to revise the history of the peopling of Central and South America. This history of migratory patterns in the Americas has long been the focus of archeogeneticists, geneticists, and biologists of many different fields.  The history is constantly being revised as new date presents itself. Now, new genome-wide ancient DNA data has being utilized by an international research team to revise the history of the peopling of Central and South America.

Many recent studies have come to the same conclusion as this particular study, which involves co-senior author David Reich.  The researchers involved used DNA from 49 individuals from Central and Southern America.  Their DNA suggests that within the ancestral lineage of migrants that originally populated these areas there are two previously unknown migrant lineages.  One of these migrants waves was displaced by a new wave of migrants 9 kya.  The descendants of these new migrants are very closely related to peoples in modern who are located in the same region.

Additionally, the study found that certain groups of individuals in Central and South America were closely related to the Clovis peoples who were mainly located in North America.  Prior to this, it was not known that Clovis peoples had succeeded in spreading beyond North America.

Hannah Jacobson

Civil War POW study finds a father's stress can alter a son's genetics


A new study of the offspring of Union soldiers adds to a growing body of evidence that suggests traumatic events experienced by one generation can have profound effects on the next. This all concerns the growing field of epigenetics, the ability for our DNA to be affected by and interact with the environment. The study, based on an analysis of National Archives records of Civil War prisoners of war and their families, turned up stories of surviving captivity in the notorious Andersonville prison in Georgia, where crowding, starvation, and poor sanitation were rampant. To see how these conditions affected or did not affect POWs and their offspring, click here.

For the full study, click here.