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

Friday, April 27, 2018

Non-potluck post: Intelligence and genetics.

The study of intelligence has previously been considered controversial, however, Plomin and von Stumm (2018) state that the scrutiny has had a positive effect on the quality of the research produced. Plomin and von Stumm (2018) suggest the use of genome-wide polygenic scores (GPS), that take into account multiple regions of variation within the genome, are beneficial as an investigative tool in understanding the genetic basis of intelligence. 

The heritability of intelligence is noted by Plomin and von Stumm (2018) to be about 50% based on previous studies, particularly those looking at twins. When specifically looking at SNPs the heritability of intelligence is stated to be around 25%, whereas GPS heritability is stated to be about 10% (Plomin and von Stumm, 2018). It is suggested by Plomin and von Stumm (2018) that the discrepancy between the heritability values for SNPs and GPS could be ameliorated through increasing the GWAS sample size as well as looking at the interaction between genes and the environment amongst other considerations.

It is also noted by Plomin and von Stumm (2018) that this particular area of research has many ethical, legal, and social considerations. Particularly the issues associated with stigmatisation, as seen in the misuse of IQ data in the 1900’s as a way of separating out individuals, as well as the potential use of biological determinism (Plomin and von Stumm, 2018).

Click here to see the article.

Third post from Nature Reviews Genetics.

Plomin, R., and von Stumm, S., 2018. The new genetics of intelligence. Nature Reviews Genetics. 19: 148-159.

Victoria Lockwood

Non Potluck: aDNA from tropical environments?

The authors of this recent study in AJPA compared the performance of two different methods for extracting aDNA, specifically from hot, humid environments.  Samples came from several
archaeological sites and from a chimpanzee tooth collected in Tanzania in 1966.  Their results indicated that both the creatively named Method D and Method H were similarly effective in recovering aDNA.  However, Method H produced sequences with both higher endogenous content and clonality, while Method D produced shorter fragments.  The authors argue that because aDNA is highly fragmented in these environments, that Method D (the simpler one) is preferred.  They do acknowledge that these results are only from teeth, and that other material may yield different results.  Interesting nontheless.

(AJPA post 3/3)

Non Potluck: DNA methylation/demethylation

We didn't get into epigenetics much this semester, but a recent AJPA article on the topic caught my attention.  The authors investigated ten genes related to DNA methylation/demethylation in the context of stress and overall health. 25 mother-infant dyads from Goma, DRC were studied.  Genetic and epigenetic data were combined with surveys and interviews on perinatal stress.  Stressors included everything from in-law stress to war trauma.  Results indicated that most genes in question did not affect genome-wide methylation or birthweight.  However, DNMT1, DNMT3A, TET3, and MBD2 were found to correlate with maternal methylation and birthweight.  The authors suggest that these genes may be part of a molecular mechanism underlying the human biological response to stress.

Read the full article here.

(AJPA post 2/3)

Non Potluck: aDNA study of pre-Hispanic South American populations

A recent study in AJPA used aDNA to examine haplotype composition in Andean populations.  They compiled autosomal, mitochondrial and Y-chromosome data from 8 groups identified during the Regional Developments Period (900-1430 AD). 19 individuals across 7 archaeological sites were compared.  This was a very interesting phylogeographic study that found individuals clustering into pre-Inca and Inca groups, regardless of geographic location.  It was also intriguing because both maternal and paternal lineages were predicted using the mitchondrial and Y-chromosome data.

Read the full article here.

(AJPA post 1/3)

Non Potluck: Anthropogenic pressures and the loss of species genetic diversity

Humans have been known to drastically alter the environment that they are in and this usually has a negative impact for native species living in the area. A recent study sought to examine changes in genetic diversity within two species of gorillas, whose habitats have been altered due to human activity. Using both museum and modern fecal samples, they looked at over 100 complete mitochondrial genomes. The results showed that there was a significant decline in haplotype and nucleotide diversity when comparing modern samples to the historic ones. Furthermore, this decline in diversity has been attributed to the loss of the peripheral populations (ones most impact by anthropogenic pressures) rather than the core range of the species. This study shows the importance of species conservation and preservation as it has been studied that genetic diversity is important for a species long-term survival and with the genetic diversity of gorilla’s declining, it makes it all the more vital for increase conservation efforts.

The article can be found in Nature here


(Nature review 3/3)

Non Potluck: A Systems approach to Understanding gut microbial in relation to colon cancer

Previous studies on the human microbiome (the collective genomes of the microbiota) have shown that gut dysbiosa (imbalance) is associated with increased incidences of colon cancer. However, there is still a lot of unknown about the correlation between the two. A new data drive- computational approach has been taken to better understand the gene-environment interaction in carcinogenesis to find the possibility of colon cancer (CRC) diagnosis, treatment, and prevention. Data was pulled for CRC associated genes from three databases and  also from Molecular signature databases.  While there were some limitations to this study, the  data driven computational method  was used to show association. For instance, a disease name or a list of associates genes are inputted and the output is a resulting list of associated microbial metabolites. It’s an interesting start for micro biome-gene interaction.

The article from Nature can be found here


(Nature review 2/3)

Non Potluck: Adaption to unfavorable conditions

The Maipo River in Chile is considered to be highly polluted. Within the river lives a species of fish known as Basilichthys microlepidotus in which different populations occupy either polluted or non polluted areas of the river. A study was done to investigate if environmental pollution is related to phenotypic or genotypic selection. To find this, a transcriptomics approach based on RNA seq was used to determine differentially expressed genes from the populations living in polluted areas versus non polluted areas. The results showed that in one population from a polluted site there was an unregulated gene found related to suppression and progression of tumors, while in another population from a polluted site there was an unregulated gene related to function of apoptotic was over expressed. These results showed a plastic response in expression due to anthropogenic pollution.

The article from Nature can be found here


(Nature review 1/3)

Non Putluck Post- Carly Johnson #3

Ageing-associated DNA methylation dynamics are a molecular readout of lifespan variation among mammalian species

Mammals have a wide and varied lifespan, but recent studies have established ageing- associated differently methylated positions in human and mouse.  After studying mammals such as a mouse, human and whale that vary greatly in size and lifespan and determining an association, they tested the theory on dogs, in which this is not the case. In all, this study identified six negative relationships between rate of change of methylation levels a DMPs and lifespans, this study is hopeful that aDMPS will be a sound molecular tool for out future understanding of the biological factors that determine lifespan in mammals.

Robert LoweEmail author,
Carl Barton,
Christopher A. Jenkins,
Christina Ernst 
Oliver Forman,
Denise S. Fernandez-Twinn, 
Christoph Bock, 
Stephen J. Rossiter, 
Chris G. Faulkes,
Susan E. Ozanne,
Lutz Walter,
Duncan T. Odom,
 Cathryn Mellersh and
 Vardhman K. RakyanEmail author
Contributed equally
Genome Biology201819:22
©  The Author(s). 2018
Received: 27 September 2017
Accepted: 19 January 2018
Published: 16 February 2018

Non Potluck Post 2 Carly Johnson

Non Potluck Post 2 Carly Johnson

Glioblastoma multiforme (GBM) is one of the most aggressive tumors to the central nervous system, giving the afflicted patients on average only about 5 year survival rate and only 5% recovery prognosis. This paper highlights a  new view into the treatment of gliblastoma tumors, by using cultured neural stem cells in the mammalian CNS. This study hopes for the invention of novel therapeutic targets and pathways for GBM based on the development of single cell-transcription and epigenmone analysis by way of epigenmonic change delineation associated with GMB tumors. 

Bing Yao, Peng Jin
Genome Biology201819:51
©  The Author(s). 2018
Published: 10 April 2018

Journal update 3/3: DNA mass spectrometry to improve sensitivity of newborn screening for Fabry disease.

Fabry disease is likely to cause mortality in many female carriers. The aim of this study was to develop an improved cost-effective screening method that would be able to detect Fabry disease among female newborns. Their study found that the Agena iPLEX assay is powerful for detecting females with Fabry disease. With this study, they were able to detect many disease-onset adult family members who were originally undiagnosed for Fabry disease and the screening for this study helped them to receive treatment in time before severe and irreversible cardiac damage occurred.

Link: here


Journal update 2/3: Alcohol consumption may influence the development and progression of epithelial ovarian cancer.

This study suggests that certain epigenetic factors and consumption of alcohol which have been previously found to suppress DNA methylation may influence the development and progression of epithelial ovarian cancer. They however note that there is no clear understanding whether these factors interact to affect the EOC risk. They performed a causal inference test (CIT) and the VanderWeele and Vansteelandt multiple mediator model to examine CpG sites that mediate the association between alcohol consumption and EOC risk. They found that decreased methylation at both CpGs was more common in cases who drank alcohol at the time of enrollment vs. those who did not.

Link: here