Identifying Dependencies in Auditory Stimuli: Squirrel Monkeys

I came across another interesting article on primate behavior this morning, and thought I'd share! This article published in Biology Letters focuses on Saimiri sciureus (squirrel monkeys) and their capability to detect dependencies in auditory stimuli. The process of being able to identify dependencies, in the context of this article, is defined as identifying two (or more) separate sensory stimuli as related. This process also has significant relevance in human cognition. The study found that squirrel monkeys can differentiate between tone sequences that contain a dependency and tone sequences that lack a dependency. The researchers conclude that the capability to identify dependencies had already evolved in the common ancestor between humans and squirrel monkeys.

Sima de Los Huesos Hominins

Exciting article! In a recent Nature study, researchers sequenced the mitochondrial genome of a hominin linked to the Sima de Los Huesos ("Pit of Bones" in Northern Spain). They found that this hominin lived approximately 400,000 years ago, and also shared a common ancestor with Denisovans. These results were unexpected, as the fossilized remains from the Sima de Los Huesos shared morphological characteristics with the Neanderthals. The researchers propose that another hominin group may have carried Denisovan-like mtDNA (via gene flow) to the Sima de Los Huesos hominins. Taking these results into account, the researchers emphasize that this study opens the door to further work with hominins from the Middle Pleistocene.

A New Altai Mountains Neanderthal Genomes and Insights into Archaic Population History

An article published in today's nature discusses the sequencing of the genome of an unknown hominin, which was determined to be a Neanderthal, from the Altai mountains. The authors also performed a low-coverage genome-sequencing of a Mezmaikaya Neanderthal (Caucuses) and were thus able to do some interesting reconstructions of archaic population history. This study was full of interesting findings!
Including:
-Very low genetic diversity for the Altai population, suggesting high levels of inbreeding
-Neanderthal gene flow into Eurasians most similar to the Mezmaikaya Neanderthal.
-evidence of admixture between Neanderthals and Denisovans, with greatest gene flow in genomic regions related to immunity and spermatogenesis (HLA and CRISP gene families)
-evidence of admixture between Denisovans and a as-of-yet-unidentified archaic hominin (!)
-a high resolution list of human-specific genetic changes (conserved in Neanderthals, Denisovans, and chimps) which includes a measly 96 fixed amino acid changes!

Hello Everyone!

I chose to keep an eye on PLOS Genetics in the past few weeks. Below I’ve summarized my favorite articles that popped up during that time. Overall it was eye-opening looking at studies on so many different organisms. It really reinforced the idea that we’re all essentially made of the same stuff :) Check out the pieces and enjoy!

Best,

Emi

Dynamics of DNA Methylation in Recent Human and Great Ape Evolution

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003763

Hernando-Herraez et al

September 05, 2013

Hernando-Herraez et al explored the differences in methylation patterns of humans vs. apes in order to find information that could account for the huge phenotypic differences between human beings and “our closest relatives”. Nine humans and 23 primates were used in the study and all species of great apes—chimpanzee, bonobo, gorilla and orangutan— were included. The researchers analyzed methylation patterns at CpG (Cytosine—phosphate—Guanine) sites and found about 800 genes with altered methylation patterns among the primates including 170 genes with a methylation pattern specific to humans. After finding that many of these genes are essential to developmental and neurological processes, they suggested that epigenetic changes have occurred frequently during recent human and non-human primate evolution. The study concluded that epigenetic alterations influence primate evolution and thus should be explored thoroughly in the context of comparative genomics.

Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003735

N. Renzette et al

September 26, 2013

Human cytomegalovirus (HCMV) is relatively common in the US and asymptomatic in healthy human beings. Unfortunately, in individuals with a compromised immune system or one that is not fully developed (i.e. infants) HCMV can cause permanent nerve damage or lead to death. This study posited that HCMV’s extremely high rate of evolution within human hosts can be attributed to the virus’s high genetic variability. The study longitudinally collected HCMV samples from the urine and plasma of 5 infected infants and analyzed the genetic variability of the viral populations. The study found that the virus was relatively stable over time in each sample, but variation from one sample to another within a host was comparable to variation between samples of unrelated hosts. Not only did the study confirm the high rate of variation within the HCMV species, but it also provided the most detailed map of DNA virus evolution in human hosts to date.

Evolutionary Change within a Bipotential Switch Shaped the Sperm/Oocyte Decision in Hermaphroditic Nematodes

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003850

Y. Guo et al

October 03, 2013

The transcription factor TRA-1 controls sexual development in nematodes. According to this study, TRA-1 works with part of another complex (TRR-1) to initiate spermatogenesis but a truncated form of TRA-1 blocks spermatogenesis. Since the truncated and normal forms of TRA-1 have opposite roles, researchers conclude that TRA-1 is bipotential, meaning it can repress or activate the same locus. The study then compared related species of nematodes and found that, in one species, mutations on TRR-1 lead germ cells to become oocytes while mutations that affect 3 FEM proteins (which also work with TSA-1 in a regulatory role) do not. In another nematode species, the roles were switched. Analysis of this data led the study to conclude that the roles of the two types of TRA-1 (truncated and whole) have been altered during recent evolution.

The Meiotic Recombination Checkpoint Suppresses NHK-1 Kinase to Prevent Reorganisation of the Oocyte Nucleus in Drosophila

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001179

O. M. Lancaster et al

October 28, 2010

Haploid gametes are made from diploid cells via meiosis. A crucial step in meiosis is the recombination checkpoint where cells that have not properly completed recombination (the first portion of the process) are barred from proceeding to the rounds of segregation needed to complete meiosis. This study focused on the role of protein kinase NHK-1 on formation of the karyosome- a meiosis-specific arrangement of chromosomes that occurs once segregation can proceed. In Drosophila, formation of the karyosome is suppressed by activation of the recombination checkpoint. The study found that despite this link, mutations in the karyosome directly resulting from mutations in NHK-1 occur independently of the recombination checkpoint. The study also found that DNA breaks formed during recombination lead to activation of the recombination checkpoint which in turn suppresses the activity of NHK-1, preventing it the formation of the karyosome. This led the researchers to conclude that protein kinase NHK-1, in Drosophila, plays an essential regulatory role in meiosis and is controlled by the recombination checkpoint.

Recurrent Tissue-Specific mtDNA Mutations Are Common in Humans

J. H. Samuels et al

November 07, 2013

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003929

DNA mutations taken form randomly which implies that any replicated patterns of DNA somatic mutations in unrelated individuals or in multiple organs within one individual are highly unlikely. Since variation in mitochondrial DNA (mtDNA) can affect phenotypic variation, understanding the distribution of mtDNA mutations can aid in understanding many human diseases. Samuels et al used next-generation sequencing to compare mtDNA variation in ten tissues among un-related individuals. They found that in un-related individuals certain tissues display the same mutations which were all found extremely close to sites that regulate mtDNA replication. The study used 4 sequenced individuals (two in which they successfully replicated mutations found in the first pair) to reach the conclusion that the observed variations can alter the replication in the mutated mtDNA genome which suggests that tissue-specific positive selection is present for these mutations.

Reconstructing the Population Genetic History of the Caribbean

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003925

Moreno-Estrada et al

November 14, 2013

Latinos are often combined into a single group/category, even in biomedical contexts. In order to debunk the assumption that Latinos can be taken as one heterogeneous group, the study compared patterns of genome-wide variation in 330 individuals in various populations of the Caribbean comprising mainland, Antilles, and Native American communities. They then compared the genomic data of these individuals to that in a database of genomic variation among over 3,000 individuals from various European, African, and Native American populations. The study was able to use this information to characterize the intricate population genetic history of this region. Their findings distinguished insular populations from mainland Caribbean populations and from other Hispanic/Latino populations as well.

Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003380

M. Sasai et al

December 12, 2013

M. Sasai et al constructed a model to represent the genetic network of mouse embryonic stem cells in order to better understand the presence of extreme phenotypic variation in individual cell expression of an important regulatory protein, Nanog. Nanog plays a key role in maintaining the pluripotency of mouse embryonic stem cells, yet riation in vexpression level of the protein don’t seem to affect the function of embryonic stem cells. The model constructed successfully models cell differentiation by taking into account processes of gene regulation such as histone-code modification and binding of transcription factors. Although the study did not fully characterize the process by which the embryonic stem cell heterogeneity remains, it did create a model that can be used to represent the fluctuation of cells and their differentiation processes.

In the spirit of my (soon to be completed) paper

Epigenetic Regulation

A recent article in the American Journal of Human Genetics explored the connection between lincRNA (large intergenic noncoding regions) and epigenetic regulation.  They found that methylation in gene regulation regions had effects similar to the effects of protein coding genes.  They also found correlation between methylation and expression, although both positive and negative correlation was observed.

http://www.sciencedirect.com/science/article/pii/S0002929713004795

Atapuerca mt genome in this week's Nature!

Analysis of the ancient (~300ka) mtDNA from a hominin fossil of Sima de Los Huesos was published today in Nature. Notably, phylogenetic analysis suggests a close relationship between the Atapuerca hominins and Denisovans.

What We Know Currently about Mirror Neurons

This is an interesting minireview in Current Biology about mirror neurons.  If you didn’t already know, a mirror neuron is a neuron that fires when an animal acts and also when the animal observes this same action performed by another animal.  They were first discovered in macaques about 20 years ago.  This discovery was exciting because it led to a new way of thinking about how we act and its relationship to the actions of others.

One example of when a mirror neuron is fired is when (1) a primate picks up an object or (2) the primate watches a human pick up the same object.  What is interesting is that this neuron will not be fired if the primate watches a machine pick up the object.  Although this field of studying mirror neurons is quite novel and we certainly don’t know its functional significance, it is interesting to think about their implications and also the questions we should be asking in this field. 

http://download.cell.com/current-biology/pdf/PIIS0960982213013262.pdf?intermediate=true

Ancient DNA suggests European hunters tamed the first dogs

http://www.nbcnews.com/science/ancient-dna-suggests-european-hunters-tamed-dogs-2D11591252

A new ancient DNA study that came out on Friday helps clarify the origin of domestic dogs.  Researchers used ancient wolf and dog-like specimens dating from 1,000 to 36,000 years ago as well as DNA from modern dogs and wolves  to create a phylogeny of these species.  They found that modern dogs are most closely related to an ancient type of wolf now extinct that lived in Europe.  This suggests that dog domestication was begun by European hunter-gatherers between 18,000 and 32,000 years ago. These results were unexpected as previously, based solely on modern DNA a team comprising some of the same researchers claimed a Middle Eastern origin for domestic dogs.

FDA orders 23andMe to cease marketing

On November 22nd the FDA issued an order for the genetics company 23andMe to immediately cease marketing for their home DNA screening kits after several warnings about "misleading claims." The FDA argues that the company "has not analytically or clinically validated the personal genome service for its intended uses." The original FDA letter can be found here, and a CNN article can be found here. 

Ancient Siberian genome publication out in Nature

The 42,000 year old genome of the Siberian child earlier announced in Science News is now officially published in this week's Nature. When compared with various living human groups, researchers found the individual to be most closely related to Native Americans, but also that a portion of the genome was most closely related to western Europeans. This week's Nature Podcast features an interview with the lead author.

Genetic Adaptation Potluck: Climate

This article published in Plos Genetics focuses on genetic variation due to climate pressures. The researchers used a bioinformatics approach to genotype 873 SNPs in genes involved in energy metabolism across 54 worldwide populations. They found the strongest signals in LEPR R109K, FABP2 A54T, genes that are known to be involved with cold intolerance. Thus, overall this study suggests that climate has been one of many important selective pressures affecting genes implicated in metabolism.