Potluck--Behavioral genetics and postgenomics

Hey guys -- 

Here is an awesome paper by a cool guy named Evan Charney from Duke (the place I still love, by the way). 

Anyways, the paper is super lengthy, but does an awesome job tying in much of what we've talked about this semester from the scope of behavioral genetics. He examines the role of epigenetics, environmental factors, heritability, genetic variability, etc. in shaping human behavior. 

-Travis

Microbiome in chimps and humans

Hey guys -- 

Not sure if y'all saw the recent study by Ochman and colleagues about comparing the enterotypes between chimps and humans ... The paper came out the day after we talked about it in class. They basically find that humans and chimps share similar enterotypes, which was a crucial factor in human evolution. 

Here's the Yale News link and here's the link for Nature paper. 

cheers, 
travis

Evolutionary Medicine- Clonal Competition in Cancer

Hey everyone,

I was interested in the chemotherapy strategies suggested when cancer is studied from an evolutionary medicine perspective. I couldn't find a popular news source on the topic, but am curious to hear how doctors/patients feel about using lower doses of chemotherapy. Here's a link to an article that studied the clonal competition in patients with multiple myeloma.

-Abi

The Epigenetics of Motherly Love in Rats

Hey everyone!

Here's a link to an interactive (and adorable!) site explaining how early parental care strategies in rats play a role in personality development via epigenetics.

If you're not tempted by the strangely endearing rat pup simulations, here's a link to the original article in Nature.

-Abi

Hey all,

     Here's a pretty light Times article that does some simple explanations of epigenetics but more interestingly brings in some other examples of epigenetic observations in vivo, its connection to Lamarck's theories, and a little bit about possible drug creation to effect the epigenetic conditions!

Best,
Jimmy

Evolutionary Genomics of Olfaction

Hi all --

Here is an interesting article about olfaction recently published by Yoshihito Niimura in Current Genomics: "Olfactory Receptor Multigene Family in Vertebrates: From the Viewpoint of Evolutionary Genomics." Niimura gives a general overview of the evolution of olfaction in vertebrates. Importantly, he finds that higher primates and other mammals with well-developed vision systems have a smaller number of olfactory receptor (OR) genes.  He also notes that there are about 400 OR genes in the human genome, forming the largest multi gene family.

-Travis

From the Science Table of Contents

A pretty interesting news article was published last week in Science, and I wanted to briefly share it. Michael Balter wrote the article entitle "Why are our brains so big?" and points out a few theories about the evolutionary basis of the size of human brains.

Balter notes that humans have the largest brain among all species when adjusted for body weight. The "social brain hypothesis" is the most leading theory of our brain size and attributes our large brain size to a large neocortex, which is linked to sociality. Balter points out that this is likely a large contributor to our brain size, but must we must also factor in other hypotheses and possibilities. 

-Travis

Potential Explanation for Human Dichromacy

Hey all,

Here's a link to an interesting and frequently-cited article concerning human dichromacy. There is a remarkably high incidence of dichromacy in the human population (up to 2%). The authors examine a potential explanation for this trend and show that dichromats can detect color-camouflaged texture patterns more quickly than trichromats. They explain that trichromats turn first to color differences when 'segmenting' visual inputs, a strategy that can impede their recognition of texture patterns that lie beneath the color differences. This article introduces interesting ideas about whether benefits such as camouflage-detection help to maintain visual polymorphism in the human population, or whether non-adaptive genetic factors such as unequal crossing-over at the red-green locus are responsible for the high incidence of dichromacy in humans.

-Abi

New perspectives on old samples

Hey all -- 

Here is an interesting paper that was just published that does a good job linking two of the papers for our class -- the Neandertal mtDNA paper with the recent draft sequence of the Neandertal genome. 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390907/ 

Thanks, 
Travis

The "Language Gene" (FOXP2) in Neanderthals

Hello everyone,

Here's a link to a really interesting NPR interview/article discussing the discovery of FOXP2 changes in the Neanderthal genome, changes previously known only in humans. This gene has been associated with speech and language development, leading to some very interesting questions about the appearance of language in the hominid lineage. Alternatively, if the claims of critics are correct and Neanderthals did not have language, what might this discovery say about our understanding of the polygenic nature of language? Here's a link to the original article in Current Biology.

-Abi

Archaic admixture in Africa?

Hey all,

      I liked this argumentative piece in the times that brings back some of the geneticists vs. paleoanthropologists disagreement we talked about earlier. Basically, Lachance and Tishkoff are arguing that there are signs of archaic human interbreeding with certain African populations but don't have a fully integrated fossil argument/record, only genetic analysis. Their full paper is here. 

See y'all Monday!

Jimmy

Why Fathers Matter

Here's a link to the article that was brought up in class today:

http://www.nytimes.com/2012/09/09/opinion/sunday/why-fathers-really-matter.html?_r=3pagewanted=1&emc=eta1&

Advances in sequencing technologies

Hi All -

I wanted to share the technical perspective of genome-wide sequencing with a review of the advances of sequencing. It gives an overview of the stepping stones in DNA sequencing from Sanger sequencing to various modern methods.

Here is the link to the article, published in Biotechnology Journal a few months ago. Enjoy ..

PS here is another link if the one above doesn't work.

-Travis

This is a pretty interesting ethical/logistical question! I was originally searching for something about the European-ancestry bias in genetic databases, but found this instead--similar concept of something that will become more of an issue as we continue to increase the pace of genome sequencing and medical genetics becomes more of a commonplace element of daily life.

Whole Genome Sequencing and Cancer Treatments

Hi all,

I want to share a really interesting story about how whole genome sequencing was used to treat a patient's case of unresponsive leukemia. After a young cancer researcher discovered that he had unresponsive leukemia, he was able to use his medical connections to fully sequence the genomes of his cancer cells, his healthy cells, and his RNA. These sequences revealed that he had a mutation in his FLT3 gene that was causing an overproduction of a particular protein. He took a drug intended to treat kidney cancer that shuts town FLT3, and his cancer has since gone into remission. This is a very cool story with interesting implications about using increasingly accessible genome sequencing to individually tailor medical treatments.

The NYT article:
http://www.nytimes.com/2012/07/08/health/in-gene-sequencing-treatment-for-leukemia-glimpses-of-the-future.html?pagewanted=all

A related New England Journal of Medicine article:
http://www.nejm.org/doi/full/10.1056/NEJMoa074306

-Abi

The Role of "Junk DNA" in Disease

Hi everyone,

Recently there was a huge amount of news coverage on the international Encode research project results, which showed that "junk DNA" has a large and previously unknown role in disease. Here's a link to the New York Times' coverage of the story:

http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?_r=1&pagewanted=all

There are 574 comments on this NYT article alone; clearly, a huge amount of public interest was generated by this story. A brief scan reveals that many of the commenters focus on the apparent arrogance of scientists in labeling a segment of the genome 'junk DNA'. Further exploration led me to the link below, in which a biological anthropologist explains the origin of the term 'junk DNA', usefully clarifying that scientists are not quite so arrogant as the public may like to believe.

http://www.genomicron.evolverzone.com/2007/09/junk-dna-let-me-say-it-one-more-time/

-Abi

Interesting tie-in of Language to analysis of human evolution!

Here's a couple of different studies on the matter:

http://www.pnas.org/content/85/16/6002.short

Jimmy

Own Justin Bieber DNA? A question of bioethics.

I don't really know how I came across this article, but it is interesting in terms of genetic privacy.  Basically this company gets (probably steals) genetic samples from celebrities and then clones and sells this DNA.http://www.radaronline.com/exclusives/2012/05/justin-bieber-dna-necklaces-celebrity-gene

Integrative analysis of the African bushbuck

This paper used an integrative approach to understand pan-african biodiversity at the genetic and biogeographic level, with generalizable implications for African conservation biology. They started by identifying haplogroup the African bushbuck (Tragelaphus scriptus) by sequencing a 516 bp sequence from the control region of the mitochondrial genome. When they matched the haplogroup diversity with phenotypic data, they found poor correlation between present taxonomic delineations and their own molecular data. They then looked at the relationship between haplotype structure and 58 previously described biogeographic regions. By integrating these data and testing a number of previously proposed models, they came up with 28 ecoregions that are ecologically heterogeneous and defined by genetic similarity of the bushbuck that inhabit them. By targeting these regions, it will be possible to conserve the entirety of bushbuck diversity. The authors posit that targeting these regions will be suitable for conserving most afro-tropical animals, especially generalist species.
















Don't YOU want to save this bushbuck baby?!

Loud-call structure and molecular phylogeny agreement in leaf monkeys

A recent study looked at the acoustic structure of loud-calls and molecular phylogeny in surilis (leaf monkeys, Presbytis) of Sumatra and Java. The taxonomy of this group has been disputed over the years, largely due to over 50 described color variants in this genus. Surilis emit loud, acoustic vocalizations that have several functions (defend resources, mate competition, intragroup cohesion, etc.). In order to delineate the phylogeny of this diverse genus, this study combined the results from a previous phylogenetics study (same research group) with their analysis of 100 acoustic vocalizations emitted from 68 male surili individuals across 19 locations. They demonstrated that the structure of acoustic calls reliably maps onto phylogenetic relatedness, thus indicating a tool for identifying species and providing a robust example of integrative taxonomy.

A multidimensional approach for detecting species patterns in Malagasy vertebrates

This paper sets out to make an inventory of the vertebrate species that inhabit Madagascar. Of interest to the primatologist is the section on long-tailed shrew tenrec (Microgale) and mouse lemurs (Microcebus). The number of species in both of these groups has increased substantially in the past few decades. The authors atribute this increase to "a notable increase in museum specimens from previously unsurveyed portions of the island, and to a better understanding of patterns of intra- and inter-population variation." They also credit the ability of molecular methods for uncovering cryptic species in these groups. In the tenrecs, they cite the example of the sympatry to two cryptic species, M. majori and M. longicaudata, which they claim are two species based on both molecular and morphological analyses. The mouse lemurs have quadrupled in species number in the past decade, and according to this paper, are the most specious of the Lemuriformes. This paper highlights the behavioral and morphological mechanisms (auditory and chemosensory) that support the biological (and mate recognition) species concepts that, when paired with the mtDNA data, support the species diversity of the mouse lemur.

Primate communication in the pure ultrasound

This study published last month sheds new light on ultrasonic communication. Frequencies above 20 kHz, the human boundary for hearing, are classified as ultrasonic. While some primates have been known to emit partially ultrasonic vocalizations, there has been little evidence of purely ultrasonic primate communication. In the study, the auditory brainstem response (ABR) method was used to estimate auditory sensitivity in six Philippine tarsiers (T. syrichta). Additionally, the calls of 35 wild tarsiers were recorded with an ultrasound recording unit. The tarsiers' high frequency auditory limit was estimated to be 91 kHz, shattering the primate record of 65 kHz in the bush baby. Moreover, eight individuals' vocalizations were determined to be purely ultrasound. These results suggest that T. syrichta can communicate purely in the ultrasound, which may allow for private communication undetectable to predators, prey, or competitors.

Taste clustering in humans and primates

Are there relationships between types of human taste thresholds? This study looked at previously recorded impulses on isolated taste fibers during tongue stimulation of primates to see if there was a correlation between electrophysiology in primates and humans. The highest correlations between tastes were for the sugars and quinine hydrochloride/tannins. These two taste classes, which were grouped into “pleasant” and “unpleasant” clusters, are common to humans, chimpanzees, macaques, and marmosets. The various salts and acids cluster found in this study was not found to be shared by previously recorded primate species.

These two broad clusters of pleasant and unpleasant tastes are thought to represent major selective pressure on the primate gustatory system. The low thresholds for sugars and high thresholds for quinine and tannin could indicate the evolution of optimal feeding strategies to maximize nutritional intake and avoid toxic substances.

Flavor trip level: salad

This group of researchers figured out how to express miraculin in transgenic lettuce. Miraculin is the protein produced by Richadella dulcifica, the West African shrub that grows our flavor-tripping berries. They were able to place a synthetic gene coding for miraculin under constitutive promoter control, and then transferred the package to lettuce. This made the transgenic lettuce express miraculin protein in its leaves! They didn't say whether it also made everything else you eat taste sweet also. My bet is yes. Talk about GMOs, can't wait to hear the food co-op's official take on these babies!

Olfactory senescence

Ah, the joys of senility. Apparently, this now includes eating spoiled food and the inhalation of toxic vapors. A study comparing olfactory sensory neurons (OSN) in subjects 45 or younger and 60+ found that OSNs in younger subjects exhibited highly specific responses to two distinct odours, while those in the elderly subjects were more likely to respond to multiple odor stimuli indicating a loss of specificity. Interestingly, OSN density was comparable between the two groups. This means that loss of specificity in OSNs from older subjects may contribute to smell loss and the inability to differentiate between smells. Since smell is so intimately linked to taste, this could also result in decreased tasting abilities.

Using parasites to infer social networks of Microcebus

A fresh article on the use of parasites in studying social structure and behavior in a wild population of mouse lemurs! This study tagged parasitic louse on captive lemurs using colored nail varnish and analysed transferance rates as a proxy for frequency of social interactions. Very cool. Here's the ScienceDaily snack-size version: http://www.sciencedaily.com/releases/2012/03/120326112923.htm

Major taste loss in carnivorous mammals

This article, which came out today, is a follow-up on work done on the pseudogenization of the Tas1r2 gene in felines. The authors expanded their study to 12 other species in the order Carnivora. The pseudogenization of Tas1r2 gene, which codes for the Tas1r2 receptor, causes organisms to lose the ability to taste sweet compounds. Seven out of the 12 species studies had also independently pseudogenized this gene. All seven of these species are also strict carnivores, including species as diverse as sea lions and otters. The authors conclude that this loss in taste receptor function is an adaptive response to feeding behavior.

A relationship between neocortex size and tactical deception in primates

The “Machiavellian intelligence” hypothesis states that intense social living, which is exhibited in certain species of primates, leads to selection for increased social skill, which is a function of neocortical enlargement. Neocortex size has been found to vary with different types of mating systems and social group size, and thus it is hypothesized that there is a social origin for the neocortical enlargement of primates dependent on the degree of social manipulation and inter-group competition.

This study looked at absolute neocortex volume and the ratio of neocortex volume to the remainder of the brain in 18 species of the major primate groups. Social cognition was measured as “tactical deception,” in which primates exhibited manipulative behavior of others within the social group without the use of force. Absolute neocortex volume was found to be a reliable predictor of the use of deception; however, there was no significant correlation between the use of deception and social group size, in contrast to the results of previous studies. The authors concluded that primate tactical deception is generally a function of rapid and extensive learning in monkeys and prosimians, and is only based on understanding of mechanism in a few records of great apes. Thus, the learning ability of primates seems to be dependent on neocortical enlargement, which is subject to the selective pressures of social sophistication.

Genetics of Physical Activity and Physical Inactivity in Humans

Recent studies have suggested that physical activity (PA) and physical inactivity (PI) may not only be affected by psychosocial and environmental factors, but also may be two phenotypes with genetic mechanisms. This review published online just last week in Behavior Genetics compiles such data available to date from 45 previous studies, including twin, family, linkage and association studies as well as one GWA study. In order to be included in the review, the studies needed to provide information on heritability estimates, linkage results, or identified genes and markers. The most significant finding associated Gln223ARrg, MC4R and DRD2 genes with the PA phenotype.

OXTR and Trust

This study looking at 108 adult (human) males found a reliable association between a SNP (G) in the OXTR gene and trust behavior. Individuals homozygous (G/G) for the SNP exhibited greater trust behavior as compared to heterozygous (G/A) or homozygous for A (A/A). It's unclear what functional effect this SNP may have and more research on how OXTR interacts with other genes/environment will be necessary to make this a robust relationship.

Non-invasive conservation genetics of the golden-crowned sifaka (Propithecus tattersalli)

In January 2009 Conservation Genetics published an article titled Non-invasive conservation genetics of the critically endangered golden-crowned sifaka (Propithecus tattersalli): high diversity and significant genetic differentiation over a small range  on a study led by French researcher Erwan Quéméré. Tatterall's sifaka, or the golden-crowned sifaka, is a critically endangered species of lemur found in the Daraina region of Madagascar. The only behavioral study published on P. tattersalli (Meyers 1993; see Vargas 2002) found that the lemurs live in social groups of 3-10 individuals in a territories 9-10 hectares large. Quéméré et al. undertook the study in response to conservation concerns that human deforestation, gold mining initiatives and the paving of a national road could bring significant ecological changes to the region. The study had four goals: (a) to identify genetically differentiated populations, (b) to determine diversity of P. tattersalli populations, to discuss resistance of the populations against forest fragmentation and (d) to identify specific conservation methods. 

Quéméré et al. sampled feces from 82 individuals over a period of three months during the summer of 2006. The DNA samples were then genotyped at 13 microsatellite loci to determine levels of diversity among the three areas of forrest fragmentation. The study found that a high level of genetic diversity in P. tattersalli populations despite high levels of habitat defragmentation and a narrow population distribution. Results indicate the P. tattersalli groups are able to successfully use small forest patches between the three larger forest fragments to migrate, in spite of the national road. In conclusion the authors stress a greater need to maintain such corridors and forest patches between forest fragments, in addition to the need of research teams to explore genetic diversity outside of the three observed zones of forest fragmentation. 

DNA methylation and mercury in Polar Bears

This study used a LuMA-based approach to look at DNA methylation and mercury levels in polar bear brains. Mercury is a pollutant that gets amplified up the food chain, making animals like the endangerred polar bear highly susceptible to detrimental effects. Looking at mercury's effects on genetic expression, however, is impeded because the polar bear genome is unresolved. The LuMA approach uses methyl-sensitive restriction enzymes followed by bioluminometric PCR (a quantitative method). This yields information about relative methylation of the genome between "experimental" groups, but yields no functional information. These researchers found that brain stem mercury had an inverse relationship with global DNA methylation in male bears, but no effect was found in female bears. Global hypomethylation of the genome has been linked to genomic instability, and could render these animals even more at risk to the effects of climatic instability and habitat degradation.

Genetic Diversity and Distinctiveness of the Proboscis Monkeys of the Klias Peninsula, Sabah, Malaysia

Proboscis monkey populations have declined in recent decades due to agricultural practices. In Sabah, the easternmost state of Malaysia located in northern Borneo, four clusters of proboscis monkey populations can be found among eastern waterways while one western cluster persists on the Klias Peninsula. The goal of this study was to assess genetic diversity within the Klias Peninsula, and to compare the Klias populations to those of the eastern waterways for which previously generated data exists. Researchers collected fecal samples and obtained 21 mtDNA control region sequences representing a central and a southern Klias group. Nine haplotypes and three haplogroups were identified, indicating that the Klias proboscis monkeys have maintained a decent level of diversity. The researchers pointed out that such diversity is consistent with primates with high female transfer between groups, but limited mitochondrial structure within Klias suggests such transfer has occurred only recently. Additionally, haplotype diversity and nucleotide diversity were greater in the southern Klias group compared to the central, and little evidence was found for regional genetic structure across Sabah. The authors argue that conservation efforts should aim to restore and maintain connectivity between the central and southern Klias groups.

Using genomics to test for a genetic bottleneck in Ring-tailed Lemurs

Increasing rates of deforestation, resource extraction, and bushmeat consumption have negatively impacted the endemic flora and fauna of Madagascar. This study sampled ring-tailed lemurs (L. catta) in two southwestern Madagascar sites to see if they had undergone a recent population bottleneck due to anthropogenic activities. They collected blood samples from 45 specimens, and tested for reductions in population size using an M-ratio test, and evaluated three mutation models for heterozygosity excess tests (stepwise, two-phase, and infinite allele). Analyses were conducted on samples containing both males and females, and then females only, as males are primarily the dispersing sex in L. catta.

Both populations showed reduction via the M-ratio test as well as significant heterozygosity excess via the infinite allele model, especially for one of the two populations, but the other analyses did not yield overall significant results.

The authors hold that their results are indicative of a recent genetic bottleneck in L. catta, and point to anthropogenic activities as the main cause of this genetic shift. They highlight the negative effects of a bottleneck, such as inbreeding depression and fixation of deleterious alleles, and conclude that accounting for human- and climate-founded perturbations are an important inclusion in genomics-based conservation assessments.

BBC eDocumentary on the Slow Loris

In January 2012 BBC Natural World released an eDocumentary titled Jungle Gremlins of Java in response to the YouTube video The Cutest Slow Loris Ever!!!!! that went viral months earlier. All five loris species are currently listed by the IUNC Red List as "Endangered" or "Vulnerable" and comments left on the youtube video such as "sooooo cute!!! where can I get one?" demonstrate the increasing threat of the illegal trade, along with habitat loss, to all species' extinction.

The hour length documentary features beautiful cinematography and chronicle the adventures of researcher Anna Nekaris, who believes the Slow Loris to be her "spirit animal." Nekaris and BBC have constructed a very informative piece, meant to deter those who want to illegally buy a Slow Loris for a pet. At certain points the exaggerated musical arrangements and the narrator's dramatic portrayal of the Slow Loris as a "Jackle and Hyde" of the forest are a bit laughable. However, on the whole I felt that the video is informative and provocative to potential viewers who know nothing about the ecology, behavior or conservation of Loris populations. The BBC eDocumentary has even inspired a rapping sock monkey Slow Loris video called The Slow Loris--Jungle Poet! The video contains such sensational lyrics as: "It's with regret / that you would get / a loris pet / this trade is illegal / so get a gerbil!" For optimal viewing pleasure, I highly recommend watching all three videos (Cute Slow Loris, Documentary, Rap) in succession!

Unhealthy travelers present challenges to sustainable primate ecotourism

This article, whose lead author is Mike Muehlenbein, details a survey of visitors to the Sepilok Orangutan Rehabilitation Centre, Sabah, Malaysia. The survey's goal was to illuminate the amount and type of illnesses carried by human visitors to the Centre, and to stress the threat of human-borne illnesses on great ape conservation. 15% of the visitors reported current cold symptoms. The article ends with several suggestions for minimizing the transmission of diseases from visitors to the animals and park personell.

Experimental viral evolution to specific host MHC genotypes reveals fitness and virulence trade-offs in alternative MHC types

This study tests the requirements of the antagonistic coevolution hypothesis for MHC variability. If frequency-dependent selection on MHC alleles is occurring, then the pathogens must be more fit in "familiar" (ie more common) MHC host types, verses unfamiliar (ie rare) host types, and this fitness must be correlated with virulence. The researchers test this hypothesis by infecting mice of various MHC profiles with a mouse-specific retrovirus. The study presents positive results: the more common the MHC type, the more fit and virulent the pathogen. They conclude that this study is unique in confirming the necessary conditions for the antagonistic coevolution model of MHC evolution.

Chimpanzee mothers at Bossou, Guinea carry the mummified remains of their dead infants

Summary

The forests surrounding Bossou, Guinea, are home to a small, semi-isolated chimpanzee community studied for over three decades [1]. In 1992, Matsuzawa [2] reported the death of a 2.5-year-old chimpanzee (Jokro) at Bossou from a respiratory illness. The infant's mother (Jire) carried the corpse, mummified in the weeks following death, for at least 27 days. She exhibited extensive care of the body, grooming it regularly, sharing her day- and night-nests with it, and showing distress whenever they became separated. The carrying of infants' corpses has been reported from a number of primate species, both in captivity and the wild [3], [4], [5], [6] and [7] — albeit usually lasting a few days only — suggesting a phylogenetic continuity for a behavior that is poignant testament to the close mother-infant bond which extends across different primate taxa. In this report we recount two further infant deaths at Bossou, observed over a decade after the original episode but with striking similarities.


http://www.sciencedirect.com/science/article/pii/S0960982210002186

A follow-up to the Wedekind study: MHC-correlated odour preferences in humans and the use of oral contraceptives

This study contests Wedekind’s experimental design for the hypothesis that women using oral contraceptives preferred MHC-similar men by stating that the pill-using sample size was a) too small b) between-subjects rather than within-subjects. The authors adhered to Wedekind’s initial design, but accounted for the previous “flaws” by increasing the pill-using group to 97 and comparing preferences before and after initiating pill use.

There was no significant effect of MHC dissimilarity on odor pleasantness regardless of pill use, indicating a lack of general preference for MHC dissimilarity. Similarly, females did not display a preference when men were considered as the unit of analysis (MHC-similar or dissimilar). This experiment was essentially unable to replicate the results of Wedekind’s study, but does support the hypothesis that the use of oral contraceptives disrupts adaptive female mate preference by shifting it in favor of MHC-similar males.

Parasite-mediated evolution of the functional part of the MHC in primates

In this study published last year in the Journal of Evolutionary Biology, authors L.Z. Garamszegi and C.L. Nunn set out to test how parasite burden affects MHC polymorphisms with the largest sample size yet for such a comparison. (The authors pulled MHC data from 51 studies and parasite data from 447 studies, ultimately representing data for 41 primate species and 629 different parasites.) First, the relationship between MHC polymorphisms and total parasite richness was examined. MHC polymorphisms were described in terms of nonsynonymous substitution rate at the antigen-binding site (dN-ABS). No relationship was detected between species richness and MHC traits. A second analysis replaced total parasite richness with nematode species richness and actually revealed a positive correlation (between nematode richness and dN-ABS). After controlling for confounding variables such as population size and geographic range, this positive association remained. The authors did however provide a disclaimer, stating that drawing inferences about the strength of such effects would be premature.

Parasite Burden, MHC & the Malagasy Mouse Lemur

In the February 2005 issue of the International Journal of Evolution there is a study published by Schad et al. that analyzes the role of parasite burden and the major histocompatability (MHC) complex in the Malagasy mouse lemur (Microcebus murinus). The study is notable as the first to examine the relationship between parasite burden and MHC variation in a free-ranging primate. Schad et al. hypothesized that pathogen-driven selection acting by frequency-dependent selection maintains MHC polymorphisms in M. murinus. The team examined four littoral forest fragments in southeastern Madagascar and found that "fourteen different MHC class II DRB-exon 2 alleles were found in 228 individuals with high levels of sequence divergence between alleles." Nematode infection status (either infected or not) differed between the four forest areas, with heterozygosity not statistically correlated to the number of nematode morphotypes nor to the fecal egg count values per individual. 


A positive relationship though, was found between specific parallel loads and three specific alleles that had unique amino acide motifs in the antigen binding sites; supporting the team's original hypothesis. Schad et al. conclude that further investigation is needed to support selection hypotheses and that allele frequencies and that parasite burdens need to be followed through time in order to better unsterstand the role of parasite selection and MHC diversity in free-ranging populations.

Compatibility counts: MHC-associated mate choice in a wild promiscuous primate

This study looked at the diversity of MHC-based constitution n a wild population of grey mouse lemurs. Grey mouse lemurs are highly promiscuous, which is perhaps expected given that they are only receptive for one night per year. Behavioral studies show that females mate indiscriminately during this night, implying that there is no evidence of pre-copulatory mate choice. However, the authors expected that female post-copulatory mating choices should be based on the disassortative or diverse MHC hypotheses.

They found that fathers of offspring had a higher number of MHC supertypes different from the mother than the females’ other partners that did note sire offspring, indicating that a post-copulatory mechanism could take place based on preference for MHC dissimilarity, and thus more beneficial immunocompetence, in offspring. The study supports the hypotheses of MHC-associated post-copulatory mate choice in wild lemurs, with sperm competition and female cryptic choice highlighted as the primary mechanisms for increased diversity in immune genes.

Comparison of Human and Chimp MHC molecules

Despite chimps being the older species, their MHC genes are less polymorphic than humans. To quantify this reduced polymorphism, Can Kesmir's group from the Netherlands compared the protein binding repertoire of MHC genes between chimps and humans. They utilized the proteomes of over 900 mammalian viruses and showed that binding efficiency at two chimp loci (A and B) show different degrees of reduction. Specifically, class A molecules have 36% lower binding than the human analogues, whereas class B molecules only show a 15% reduction. They further found that class A molecules are much more similar to each other than class B molecules, supporting the idea that class A molecules show signs of a selective sweep in chimps. The agent causing this sweep is thought be an ancestral HIV-like virus, and their results do indeed show high binding efficiency of the HIV virus to chimp class A molecules. However, they found two other viruses in their library with binding efficiencies greater than the HIV virus. Unfortunately, their experiment was inconclusive as to whether or not these newly identified viruses could have caused the selective sweep.

Aye-Ayes Warm Up Specialized Middle Digit During Foraging

In the January 2012 issue of the International Journal of Primatology there is a fascinating article by Moritz and Dominy, a graduate student at Dartmouth and her advisor, who used infrared thermography (IRT) to visualize the surface temperatures of Aye-Ayes (Daubentonia madagascariensis) in order to answer questions about dynamic vascular supply during percussive and probative foraging. Aye-Ayes are the world's largest nocturnal primate, known for their use of a specialized middle digit to find and extract nutritious bettle larvae from tree trunks (see video). During foraging the Aye-Aye implements the digit by tapping it against a tree trunk up to 8 times/second, listening for the tiny change in resonance that indicate a hollow space within. Additionally, the finger contains many sensitive nerve endings that allow the Aye-Aye to sense the vibrations of beetle larvae through the trunk. These specialized sense receptors make the digit costly in terms of energy. Researchers hypothesized that the physiology of the digit might play an equally important role in foraging as auditory and sensory clues for "it [the digit] is a vital sensory tool that is expected to feature a high density of dermal mechanoreceptors that radiate heat and impose thermal costs under cool temperatures."

The team acquired IRT images of 8 Aye-Aye engaged in a variety of passive and probative behaviors. Findings are that the prominent middle digit of the Aye-Aye warms its surface temperature up to 6°C hotter in contrast to invariant surface temperatures of other digits during foraging. One explanation for the change in heat is constriction or dilation of the blood vessels that supply the digit. A second less likely explanation is that the creature might mitigate temperature changes through the flexibility of the digit. Moritz and Dominy acknowledge that the mechanisms behind these temperature fluctuations are unknown, through they indicate a unique, dynamic vascular supply that highlight the "thermal costs of a highly specialized sensory structure."

Non-random mate choice in humans

Are there other genetic factors that contribute to mate choice other than MHC dissimilarity? This paper published in Molecular Ecology performed a genome-wide scan of three populations of different origin (from the HapMap 3 project) - European American (CEU), Mexican (MEX), and African (YRI) - for regions of extreme similarity or dissimilarity between spouses. For the CEU and YRI populations, immunity genes exhibited excess similarity and dissimilarity; the CEU population looked to be extremely dissimilar at these loci, while the YRI sample appeared significantly similar. Additionally, two olfactory receptors were excessively similar between spouses in the MEX and YRI populations. HLA genes were not significant in this study, although they only considered 31 SNPs in comparison to over 9,000 SNPs incorporated into studies that had previously found non-random mating in relation to this locus.

Interestingly, when a functional category of genes (e.g. epidermis development) showed a strong signal in two populations, different genes were actually involved, suggesting the possibility of sexual selection occurring for the same traits in these populations, but recruiting different genes.

Company Unveils DNA Sequencing Device Meant to Be Portable, Disposable and Cheap

This NYTimes article reports that British company Oxford Nanopore Technologies has announced it will begin selling a disposable gene sequencing device by the end of the year. This device, no larger than a USB stick, would be capable of using nanopore sequencing and will only cost $900.

The technology is projected to have benefits for wildlife biologists, enabling them to sequence DNA in the field.

West Nile Virus Immunity in Macaques and Humans

Aged humans have almost a 10-fold higher risk of encephalitis due to West Nile Virus than younger humans. In order to study this age-dependent susceptibility, the authors used rhesus macaques as a model for investigating primate immune responses to WNV. The authors infected macaques of different age classes and levels of adaptive cellular immunity with WNV under simulated “natural” conditions. They found that sensitivity of both “adult” and “old” macaques to WNV is actually low, and that they rapidly resolve the circulating viral RNA infection. This suggests evidence of a heightened innate immune system response in macaques, and the authors finally conclude that macaques might not be the best model for vaccine testing against WNV. The authors hope that a different model system will lead to a better understanding of older primates’ greater susceptibility to WNV-based encephalitis. A proper model system is critical, as it will allow us to effectively study the age-based decline of protective immunity, as well as improvements in vaccination strategies and other preventative immune system treatments.

Vaccinating the great apes

Immunity gene evolution just can't keep up! Many of the great ape populations (chimpanzees, gorillas) are currently at risk for extinction due to infectious disease transmission. Ecologists are now considering vaccination as a possible route to prevent a catastrophic outbreak (like Ebola) that could decimate ape populations. The other alternative is enforcing hygienic standards in areas of ape tourism and research, but this is extremely difficult to do. Major vaccination priorities are measles, mumps, and influenza. Other possibilities may be an Ebola vaccine (currently under trial in group of captive chimps).

For more info check out VaccinApe or the PloS One article recently published

Intradermal smallpox DNA vaccine

In January 2011 a research team lead by first author Lauren A. Hirao at the University of Pennsylvania School of Medicine published an article in The Journal of Infectious Diseases that enumerates a recent study to test the success rate of multivalent smallpox DNA vaccine, delivered via an interadermal device, to provide immunity in nonhuman primates against a lethal strain of monkeypox. The research was sparked in part by the threat of a human monkeypox outbreak but also in response to the aftermath of the September, 11 2001 World Tower terrorist attack that lead government officials to fear the feasibility of a smallpox-based bioterrorist attack. Simple recombinant vaccine development is technologically difficult for poxviruses, such as Monkeypox, due to their large, complex nature.

Hirao et al. hypothesized that a multicomponent mixture of vaccines is most likely important for protection. The team inserted a synthetic, highly concentrated DNA vaccine to 14 captive macaques by a minimally invasive novel skin electroporation. The vaccine offered protection fromt he highly pathogenic monkeypox challenge producing a diverse, high-titer antibody response against 8 different DNA-encoded antigens administrated simultaneously in microvolumes that have not been previously described. Further study of this combination of technologies is likely to enhance efficacy of vaccine potency, in addition to informing vacine areans where antibody responses are important.

Rapidly Evolving Immunity Loci

This article identified 18 new TRIM genes (Tripartite Motif): regions that code for ubiquitin ligases and are an innate immunity response to viruses. They found 11 new regions unique to humans and African apes, and 7 that are human-specific. They all seem to have derived from segmental duplications, and mostly from a single locus on chr 11. They are also copy number variable within the human population, and Han chines women have 12 additional copies. The locus they derived from has been identified as a "hotspot" in chimpanzee and macaque genomes. They conclude that this "recombinationally volatile locus" is important for the host-virus arms race, and provides immune defenses to new pathogens through rapid segmental duplication and CNV.

Sexual selection by female immunity against paternal antigens can fix loss of function alleles

Humans lack the Neu5Gc molecule because of the loss of function of the gene CMAH. Neu5Gc is a sailic acid molecule that is involved in cellular recognition during infection, development, and immune regulation. In humans, the CMAH gene was switched off about 3 million years ago and quickly driven to fixation. The authors of this paper test whether pathogen-driven fixation would be the sole cause of the prevalence of this pseudogenization. They are interested in an alternative hypothesis of sexually-selected change because of reproductive compatibility. In order to test this, they use transgenic and wild type mice to test the immune response to Neu5Gc in CMAH (-/-) females, and by testing if human anti-Neu5Gc antibodies and would attack chimpanzee sperm in vitro. Both tests produced positive results, indicating that selection due to female immunity against foreign antigens can fix loss-of-function alleles from moderate initial frequencies. Interestingly, Neandertals also have a loss-of-function CMAH gene, supporting the idea that they could easily hybridize with Homo sapiens.

Hair and adaptation by-products!

In light of our recent conversation on Wednesday about "putative-adaptations", here's a great example of an explicit adaptation by-product: iridescent hair in the blind golden mole. Iridescence is fairly rare in mammals, so researchers were interested in characterizing the hair of four golden mole species that have a purple/green iridescent sheen. Thorough analyses revealed that the hairs are broader and flatter than usual allowing for increased surface area to react with light. "Scales" on the hairs were also quite small, and iridescence was likely a product of light traveling through multiple layers of hairs, hitting these scales, and producing green-purple colors (a phenomenon called thin-film interference). The authors explicitly stated that iridescence was likely a by-product of some other adaptation such as "durable, low-friction pelts" (rather than a sexually selected trait...you know, because moles are blind...).

Ultrasonic communication in Tarsiers

In the New York Times yesterday, I found this article on a recently published piece in Biology Letters. A group of researchers in the Philippines captured several tarsiers and measured auditory sensitivity and also recorded vocalizations. Tarsiers best auditory sensitivity regions are 1.4 and 16 kHz and their audible range extends to 91 kHz (the ultrasonic range - inaudible to humans) - that's the highest recorded value for any primate and on par with only a few mammals such as bats and cetaceans. Additionally, they also recorded vocalizations that were pure ultrasound (approx. 70 kHz). In summary, tarsiers can receive ultrasonic signals (for instance, from the insects they eat) or send ultrasonic signals to conspecifics.

Regulatory changes and primate evolution

What influences gene regulation in primates? The authors of this article employed a multi-species array within and between humans, chimpanzees, and macaques to estimate variation in liver, kidney, and heart tissue. They discovered a significant overlap across tissues of genes whose regulation evolved under stabilizing selection. Additionally, they found a correlation between selection on gene regulation and constraints at the protein sequence level, which suggests that adaptation through changes in evolutionarily constrained genes can occur by altering their regulatory patterns. Finally, there was evidence of directional selection between human and chimpanzee metabolic pathways, supporting the idea that human pathways have been remodeled in a way that is indicative of the life-style and dietary shift between humans and non-human primates.

Genetic regulation of parasite infection in wild primates: the functional significance of an IL4 gene SNP on nematode infections

The authors of the above study, published last spring in Frontiers in Zoology, examined fecal samples collected from a wild population of red-fronted lemurs (Eulemur fulvus rufus) in western Madagascar to better determine the association of IL4-gene promoter polymorphisms with nematode infections and the possible functional role of the IL4-polymorphism on male reproductive success. Sequence analysis of lemur DNA showed a new SNP in the IL4 gene promoter area. Out of the three genotype--T/T, C/T and C/C--the genotype T/T showed higher rates of nematode infection intensities (see graph above). Yet, genetic population analyses collected over a period of ten years suggested a higher overall reproductive success of T/T males than expected. Results suggest that the intensity of parasite infections is linked to the regulatory effect of an IL4 gene promoter polymorphism. Despite limits of the study, such as low frequencies of T/T genotypes, Clough et al. assert that the IL4 polymorphism contributes to a better understanding of the immune response in red-fronted lemurs against gastro-intestinal parasites.

Bitter Taste Receptor Evolution in Primates

Bitter taste receptors are important for detecting toxins in the environment, particularly in the leaves of plants. To explore the selection pressures on bitter taste receptor genes, Wooding sequences the TASR38 gene from 40 phylogenetically disparate primate taxa. He found considerable variation (more than expected), but still an overall theme of purifying selection. Notably, signatures of selection were variable based on domain; for instance, the second external loop of the receptor (extracellular region) underwent strong positive selection indicating changes in ligand targeting. Cool stuff!

Open-Sourcing our Articles

(Not necessarily related to 420/820--but very relevant to researchers in YMAL). A nice article about the problem of academic publishing and the push for open-source.

Network-level analysis of a metabolic pathway across primates

The authors of this study published last year in Mol. Bio. Evol. analyzed the evolutionary constraints on the N-glycosylation metabolic pathway across humans, gorillas, chimps, orangutans, and macaques. Glycosylation attaches a glycan, or a chain of sugars known to mediate biological functions in the cell, to a protein. Multiple alignments were obtained of the CDS of each of 52 orthologous genes involved in the N-glycan biosynthesis pathway. The structure of the pathway was derived and represented graphically in order to compare the selection acting on genes with respect to their connectivity, their position in the nearly-linear network, and the rates of evolution of their neighboring genes. The genes involved in glycan synthesis were found to be highly conserved with no evidence of positive selection since the divergence of primates. Additionally, the gene products that were highly interactive with others were found to be more highly constrained and to evolve more slowly, suggesting that connectivity within networks influences evolutionary constraints.

Extensive X-linked adaptive evolution in central chimpanzees

This article is brand new this week! The autosomes and X chromosomes of 12 chimpanzees were tested for protein-coding polymorphisms. The researchers found that on the X chromosome, as many as 30% of the amino acid substitutions are adaptive. They compared this level of substitution with the autosomes and found that the autosomes had much fewer adaptive substitutions, with the exception of selective sweeps on immunity genes. They then compared their results to those of humans and found stronger purifying selection in the chimpanzee, especially on the X chromosome.

The other side of the coin: nonadaptive processes in primate evolution

This week we are investigating various examples of functional genetic changes that have played a role in the adaptive evolution of primates. By moving in to the "age of -omics", we are better able to find these loci, and compare them across species. Another emergent property of the genomics revolution, however, is an increased understanding of non-functional molecular change. By better understanding the regulatory and intergenic regions of the genome, it has become evident that nonadaptive molecular processes (i.e. drift and mutation) have also played an appreciable role in the evolution of primates. This review, published in 2010 in The Yearbook of Physical Anthropology does a nice job of summarizing these effects and their potential evolutionary consequences.

Native Americans share a recent common ancestor with Altaians

This article used Y-chromosome and mtDNA variation to determine that all Native Americans had a single recent ancestor shared with indigenous Altaians. Genetic variation was characterized in northern and southern populations of the Altai region (south-central Russia bordering on Mongolia, China and Kazakhstan). The bulk of the work in this paper attempted to quantify genetic structuring in the Altai region. This was contrasted to known Native American mtDNA and Y chromosome haplogroups. They did not find exact mtDNA matches between the two groups, but conclude that the two are closely related sister group sharing a recent common paternal ancestor.

Genetic Evidence for the Origins of Human Sexual Systems

How did human sexuality evolve? Researchers are undecided as to whether our sexual basis lies in monogamy, polygamy, or polyamory. Some fossil remains tend to indicate monogamy, while many genetic analyses support polygamy. A group of scientists from University of Arizona compared X-chromosome data against autosomes of six different human societies to determine male vs. female effective population size. The genetic evidence suggests that the male-female ratio is biased in favor of multiple women, supporting the idea that polygyny was the dominant mating system during the past 10,000 years of human evolution. However, some anthropologists argue that polygyny could have been the result of the emergence of agriculture, which favors patrilocal societies. The jury is still out on whether or not this genetic data can be used to infer the origins of human sexual systems.

Determinants of Paternity Success in a Group of Captive Vervet Monkeys

In 2011 The International Journal of Primatology published the aforementioned paper* by Weingrill et al. that examined the reproductive skew in a group of captive vervet monkeys (Chlorocebus aethiops sabaeus) over a period of 2-3 years in Strasbourg. Researchers hypothesized that increased tenure length of Alpha males would decrease reproductive success. Vervet monkeys present a unique case study, as they are the only cercopithecines that live in multimale groups, in which females show no conspicuous reproductive signals. A long mating period combined with a lack of conspicuous signals suggests that ovulation in vervet monkeys is concealed. Findings by Weingrill et al. are that fertile periods do not equate to paternity success, nor do housing conditions (indoor versus outdoor sanctuary). Paternity success decreased as a function of time in alpha males, leading researchers to hypothesize that female choice played a role in their study. Also, contrary to predictions reproductive success of alpha males was among the highest found in cercopithecines, with the alpha males siring 78% of all offspring.

*Please click title for link to article.

Please don't watch!

This paper that just came out in the March 2012 issue of American Journal of Primatology: Sneaky Monkeys: An Audience Effect of Male Rhesus Macaques (Macaca mulatta) on Sexual Behavior. This study was conducted on captive group-living macaques in the Netherlands. The "audience effect" is essentially when female sexual behavior is influenced by the presence of bystander males (usually the alpha male). The findings indicated that females were more likely to copulate with subordinate males when the alpha male was absent, and this was also true for when nonalpha male bystanders were absent. The reason for this may be that interventions initiated by males present during copulation usually result in the female receiving the brunt of the punishment. Therefore, it's advantageous for females to solicit copulations without an audience. The general consequences of this are that a male monopolizing a female in estrus may be undermined by the female soliciting frequent matings with subordinate males in his absence. Additionally, he may experience less copulations with receptive females if nonalpha male bystanders are present.

Gelada follower males

Here is the abstract of brand-spanking-new research showing different reproductive strategies for adult gelada males. Geladas live in a social structure that is "harem-like", with one male mating with multiple females. However some harems have "follower males", old leader males who stuck around or younger males who didn't have what it takes to take over the unit for themselves. These potentially lower-quality follower males get some benefit, though. 18% of paternity in the unit! In return, leader males tolerate this because the presence of follower males increases leader males' tenure by 61%. This paper is presently under review.

Testing adaptive hypotheses of male reproductive cooperation

This study published last summer in Animal Behavior explores the potential for direct and/or indirect fitness benefits from reproductive cooperation among polyandrous males in Sanguinus geoffroyi (Geoffroy's tamarin). As observed in Geoffroy's tamarins, a single female mates with all adult males unrelated to her, and in turn the males cooperate to rear the young. Researchers studied six groups from two tamarin populations over 2-3 years, and determined that the polyandrous males were consistently more highly related to each other than expected by chance, and they often shared paternity both within litters and across the 2-3 year period. Groups with a single sire were also observed, which may be attributed to sperm competition. These findings suggest that both indirect and direct fitness benefits may play a role in the evolution of male reproductive cooperation.

Hsp90 stress potentiates rapid cellular adaptation through induction of aneuploidy

Researchers investigated how yeast responds to stressful environments and discovered that it adapts by gaining or discarding chromosomes. Aneuploidy, or an uneven number of chromosomes, is often seen as deleterious, as in cancers. However, many yeasts are aneuploid and it is hypothesized that this uneven number of chromosomes allows yeast DNA to mutate more readily, thus providing novel genetic material during unstable, stressful environments. This would then allow more rapid phenotypic evolution. In this study, the yeast became drug resistant.