Tuesday, April 30, 2013

Evolutionary Anthropology

January/February 2013

This article looks at how microwear patterns on teeth can shed light on the dietary habits of primates because they conserve information about the items that primate consumed before death.

This article discusses how endocasts, or fillings of the endocranial cavities can provide a lot of information about morphology. We can start understanding how the brain structure and strange pattern of ontogeny evolved in modern humans.

March/April 2013

This news article talks about the findings presented at the meeting of the Society for Integrative and Comparative Biology. A few presentations that seem particularly interesting have to do with energy of primates, in different areas such as locomotion and the correlation between energy and obesity.

This study is really interesting because it looks at the human social structure in order to gain insight into the evolution of the system, rather than the individual parts that build the system.  The author's five-stage sequence about the human social structure's evolutionary history points to constraints as well as areas for future research.

This paper argues that two very different arguments about post-fertile lifespan in humans both contain correct arguments, but the failure to distinguish between two different traits has perpetuated the misconceptions. I think this paper is a good read because it highlights how interdisciplinary evolutionary research needs to be.

Tuesday, April 16, 2013

WEE1 tyrosine kinase, a novel epigenetic modifier

I’ve been monitoring newly released papers in Trends in Genetics this semester, and there hasn’t been too much activity regarding primate genomics.  However, there was an interesting paper released relevant to epigenetics (an important topic throughout the class).

WEE1 is a receptor (specifically, a tyrosine kinase receptor) on the plasma membranes of cells that was found to be an important regulator of epigenetic modifications during the DNA synthesis phase of mitosis.  Specifically, it regulates histone synthesis and genome stability by regulating the activity of many factors involved in replication.  For example, it regulates the phosphorylation of the H2B complex, which is a histone protein that organizes DNA in the nucleus.  It is believed that the function of WEE1 is critical for preventing aneuploidy.

The link to the somewhat relevant article is below:

Wednesday, April 10, 2013

Sugar cancer vaccines


Tumor cells tend to display unique carbohydrates on the surfaces of their cells which are not recognize by the immune system as targets for destruction. 
The idea here is that by creating a vaccine with these particles, a general immune response could be triggered near the clusters of sugars to eradicate the cancer.
This response would not be particular specific though, so how would this affect the patient?

Social stress changes immune system gene expression in primates


This article discusses a study linking social status and gene regulation in female primates.  By comparing the expression of 1,000 genes between high and low ranking rhesus macaque females, the study found significant differences in genes tied to immune response.  They also found that when a female's rank improves, her gene expression would change within a few weeks.  The results suggest that primates with low rank, and therefore chronic stress of survival, compromise their immune system. These results hold interesting implications for the link between human health and stress, as well as the link between socioeconomic status and elevated disease risk.

Age-Related Macular Degeneration

study published a few months ago reveals that age-related macular degeneration may be caused by changes in how the genes in the immune system function. The study found that this disease associated with vision impairment in the elderly could have strong epigenetic influences.  Researchers tested levels of DNA methylation and found that different expressions of certain genes heavily correlated with AMD. They also tested identical and fraternal twins to determine if these patterns were genetic or environmental and found that epigenetics could play a large role in AMD.

Primate Immunity Pot Luck

A study done in 2010 shows that humans are more susceptible to some various than non-human primates. This finding explains where there are some diseases that can only effect humans. One example in with HIV. Humans see worse effects than chimpanzees do in terms of HIV. WHat I found to be most interesting is the fact that this infection actually originated in non-human primates. This idea could show the possibility that evolution could help lead to a cure or future disappearance of such disease. While the 'core' response was the same throughout the three species used in this example, the regulatory response was shown to be different. This difference shows that there must have been some adaptation in certain primates that was not transferred to different species through evolution.

These Weeks in Science

Hey All!
Here are the last two weeks worth of interesting articles from Science. (4 and 7 are particularly interesting in light of today's topic)
1) This article on scientist's attempts to bring back a new species of pigeon that has the same characteristics as the passenger pigeon.
2)This article showing that pseudoenzymes (or dead enzymes) cannot catalyze reactions, but that they may have other functions.
3)This really interesting policy forum article on the ethics of bringing species back to life from extinction.  
4)THIS super applicable article on the role of HLA-C expression level on HIV control (it also had a deleterious effect on Crohn's disease).
5)This bioethics paper that urges the notification of individuals with abnormal DNA results who participate in studies.
6)This article on genetic causes for premature aging syndromes.
7)THIS super applicable article on multiple instances of ancient balancing selection shared between chimps and humans besides MHC.

Primate Immune Genomics Potluck

Hey guys!
This is a really interesting landmark paper (Ober et al 1997) of MHC in humans. It was one of the first studies to show MHC dependent mate choice in humans, which it did among the Hutterite population (which is also just really interesting as a great human experimental model).  The Hutterites have a limited number of MHC haplotypes, have large sibships, mate only within the community, and do not have divorce.  Because of these factors, they were a great population to show human preference for mates with different MHC alleles from them.

Month of Birth Impacts Immune System Development

Hey guys, for my potluck on primate immunology I have an article of a study done in the UK that shows how a baby’s birth month can affect the development of its immune system.  The study provides a biological basis for why individuals born in May have a greater chance of developing multiple sclerosis than those born in November.  Multiple sclerosis (MS) is a disorder where the immune system damages the central nervous system through ways such as autoreactive T-cells, cells that attack your own body’s cells.  MS is also associated with low levels of Vitamin D.  Samples of blood from the umbilical cord were extracted from 50 babies born in the month of November and 50 from the month of May, and levels of autoreactive T-cells and Vitamin D were measured.  They found that babies born in May had double the level of autoreactive T-cells and about 20% less Vitamin D than babies born in November.  More long-term studies need to be carried out to prove causation.

Tuesday, April 9, 2013

Primates, Immune Function, and Biomedicine

This article deals with one of the central issues driving comparative primate genomics: the impact of primate genomics and immune studies on the field of biomedicine.


The authors discuss the benefits of studying immune function and disease through the lens of our closest relatives. However, the assumptions underlying this article's construction and thesis may be worth revisiting. Should it be true that our studies of comparative primate genomics be so heavily driven by biomedicine in particular? How can science for the sake of science be justified in comparative primate genomics and immune studies? Are there moral issues at stake here?

Anthropoid Immune System Evolution (Royal Society B)

This is a really interesting article about how the evolution of the anthropoid immune system might be responsive to environmental factors, using baseline leucocyte concentrations as a proxy.


The authors conclude that while group size and population dynamics are less tightly associated with parasitism and leucocyte concentration, annual rainfall (due to wetness and increased presence of parasites) and body mass (due to relatively higher or lower proportion of surface area available for damage/injury) are related. These conclusions are interesting especially in light of our discussions on adaptive immune response in the readings this week.

Wednesday, April 3, 2013

Galapagos Tortoise Bottleneck with Surprising Results

Recovery of a nearly extinct Galapagos tortoise despite minimal genetic variation
This article discusses a study of a dramatic bottleneck after a reduction of a species of Galapagos tortoise to 12 remaining females and 3 males.  They were then bred in captivity for over 30 years and produced over 1,700 offspring, which were then reintroduced to the island in the early 1990s.  The species successfully continued to reproduce, indicated by the growth in the percentage of juveniles hatched on the island (0% in 1994, 3% in 2004, and 24% in 2007).  Furthermore, there was a high level of size distribution of the tortoises, the population was surprisingly heterogeneous. This result was interesting because the original population brought into captivity was very small (an estimated population size less than 8) and theoretically, very low levels of genetic diversity should correlate with low levels of long-term persistence and adaptation.  The study concluded that some endangered species seem capable of successful and rapid recovery despite a low level of genetic variation.  They do note, however, that these results can't be confidently extrapolated to any long-term conclusions because, despite the 40 year length of this study, the long life span of tortoises mean that there have not been many generations yet.

Peeking into the Sex Lives of Endangered Turtles

In a recently published study in Molecular Ecology, scientists were able to shed some light on the relatively unknown mating habits of hawksbill turtles.  By studying the DNA of the mothers and of the offspring, they were able to construct paternal genotypes that provided an incredible amount of information about the mating systems of hawksbill turtles, including that more than 90% of females only mate with a single male. This study also provides an optimistic look at the preservation of these turtles, because scientists found a lot of genetic diversity in their samples, which indicates that there are a lot of genetically viable male hawksbill turtles. These could indicate that this species may not be as endangered as scientists had previously thought.

Forest Corridors and Conservation Genetics

Here are two related articles focusing on the importance of forest corridor maintenance for genetic diversity. Populations of two species (Panthera pardus fusca and Panthera tigris) were studied in India. "Meta-populations" composed of fragmented populations living in protected areas which were connected by corridors were analyzed for genetic diversity via faecal  genetic analysis. In both species, the sub-populations were found to have high genetic variation, low genetic subdivision, and highly admixed genetic populations. This kind of research shows that forest corridors are successful tools in conservation genetics and have relevance to many primate conservation efforts. (For example, "living fence" initiatives are quite interesting!) 

Leopard: http://onlinelibrary.wiley.com/doi/10.1111/ddi.12024/abstract

Tiger: http://onlinelibrary.wiley.com/doi/10.1002/ece3.432/abstract

Conservation genetics potluck

This article is a quick science news article that brings of the really interesting idea of species resurrection   Currently in development for amphibians, the Lazarus tries to resurrect extinct species.  I found this very interesting.  In terms of future conservation efforts, will this project's success help or hinder the conservation mission.  Some of the mission is driven by the idea that we don't know everything about the species and that in the future, they may prove useful so we cannot let them go extinct now.  If we have the technology to bring species back if, in the future they prove to be useful, will this divert from efforts to keep species from going extinct in the first place, essentially creating a system where we have a genomic biobank but no species in their natural environments.  

Forensics Genetics


The conservation genetics lab at University of Arizona uses genetics to identify whether or not certain species are likely of soon becoming endangered. There are several reasons such as urbanizations that can lead to a species becoming extinct, but the one most focused on here is inbreeding. As members of a species disperse and becoming isolated, there is a greater likelihood that inbreeding will occur. This study allows researchers to to see how the different animals of a species are related to one another. By studying different segments of the DNA, whether dealing with individuals, groups, or species, the researchers are able to notice to genetic diversity or lack of. With this information, the researchers are able to intervene where they can see inbred is occurring.

The forensics genetics has been able to help also stop wildlife crime,  identify species is no area around the world, as well as notify when endangered species need to become captive.

Three species of Aye-Ayes' genomes sequenced in conservation effort

This article discusses the work of researchers at Penn who, in conjunction with other researchers from many institutions, set about identifying population patterns in Aye-Ayes in order to better understand their population histories and glean information about Aye-Aye genomic diversity to aid in conservation efforts.  By sequencing 12 individuals from different populations, they were able to both gain a sense of the genetic diversity among the populations as well as to determine how long these populations have been independent.  Their work highlights the amount of diversity between Aye-Aye populations in Madagascar and emphasizes the importance of protecting this species.

This week in Nature

This week in Nature, one of the featured Research Highlights is pretty relevant to today's discussion of Conservation Genomics.

The research featured suggests that the hunting of primates needs to be controlled not only for the sake of the dwindling primate populations, but for the ecology and growth of the forest itself. 

Conservation Genetics in Cote d'Ivoire

The first link is a really interesting article about the interplay among conservation genetics, conservation biology, poaching, and politics. The authors performed surveys of eight species of monkey in the Tai National Park (Cote d'Ivoire) in order to target locations particularly impacted by hunting. Most compelling for conservation politics is the fact that their data clearly indicated that species closest to tourist sites and research stations were least affected by hunting. The authors also discuss the impact of hunting for bushmeat on wild populations. Conservation genetics, especially DNA barcoding techniques, is a particularly useful tool for targeting hotspots for poaching. The second article listed below discusses a more explicitly genetic approach to conservation, targeting a part of the mitochondrial cytochrome b region as a species identification tag for wildlife forensics. It is an interesting method in conjunction with the discussion in the first article of how to best address primate conservation issues.



Tuesday, April 2, 2013

Body Mass, Extinction, and Conservation Status (Royal Society B)

The following article is not explicitly genetic in nature but is very related to this week's topic. The authors of this article use phylogenetic Bayesian and Maximum Likelihood (ML) statistics to explore the hypothesis that larger body mass is positively correlated with extinction rates in primates. This assumption has been a key tenet underlying analyses on extinction of past primate species, especially in deep time, and relies on the idea that larger bodied primates reproduce less frequently and have lower speciation rates. The extent to which this relationship is corroborated by statistical data has implications for how decisions are made on which extant species warrant special conservation status (e.g. on the IUCN Red List of Threatened Species). The authors' data suggest that there is, in fact, no statistical correlation between body size and extinction or speciation, indicating that other factors are better suited to understanding primate species' proneness to extinction or relative population threat in the wild.