Closing Remarks and Overall Summary

Closing Remarks: 
Epigenetics investigates changes in the phenotype of organisms without a change in the underlying genotype. DNA methylation and histone modification do not directly change the DNA's genetic code but do allow for heritable changes in gene expression. This allows animals to adapt to situations and environments in a more rapid manner than other evolutionary methods of improving traits through direct DNA modification. Epigenetics clearly affects behavior of animals and allows animals to rapidly adapt to their environment. 

Summary of the 9 types of epigenetic implications on behaviors and the relation of this mechanism to evolution:

1. Implications of neglectful mothering: Rat pup's phenotypic behavior was physically altered due to the environmental upbringing. This epigenetic effect was also proven to be reversible utilizing enzymes (Weaver et al., 2004).
2. Cocaine creates an epigenetic change in the genome: Increases a rats' behavioral yearning for a next dose. This is due to epigenetic suppression of a particular histone, and the suppression causes creation of extra dendritic spines (Miller, 2010).
3. Nearly 500 gene sequences are specific to humans for epigenetic modification: These epigenetic modifications specific to humans and not our ancestors could be the cause of our human-specific traits and behaviors. Much of our evolution may be thanks to epigenetics (Shula et al., 2012), (Zeng et al., 2012).
4. Twins Studies: Decisions individuals make will lead to epigenetic changes in their genome which impact future behaviors & the next generation: Epigenetics also causes silencing or expression of genes that could lead to cancer or disease susceptibility. Epigenetics thus is vital to understanding our behavior, behavior of cancerous cells, and evolution of these mechanisms which are all the result of our epigenetic tags (PBS.org, 2009).
   
5. Evolution and epigenetics is also demonstrated through the study of the Linaria vulgaris. The methylation of the Lcyc gene in the Linaria vulgaris causes an advantageous change in the phenotype, this behavior allows the plant to adapt to its environment and potential pollinators (Cubas et a., 1999).
6. Epigenetics allows for plasticity of sex traits: Sex traits and behaviors have evolved to improve likelihood of achieving a mate, and epigenetics has allowed animals to continue extravagance in order to achieve this goal as well as survive (Geary et al., 2012). 
7. Captive environment and limited mating selection impacts diversity of livestock: Agrigulture specialists will utilize epigenetics to enhance the environment and behaviors of animals as well as impact the evolution of these animals through future generations (Goddard et al., 2014), (Zeric, 2012), (Gonzalez-Recio, 2012).
   
8. Research demonstrates that mice can epigenetically pass down a particular fear through the mechanisms of epigenetics: In this way epigenetics is aiding in the survival behaviors of animals allowing them to have an evolutionary leg-up against competition and predators (Diaz et al., 2013).
9. Bees and ants rely on epigenetic changes to thrive and change behavioral castes for the good of their population. Bees are able to change between nurses and foragers, while ants are able to become a queen from a worker. All is due to epigenetic changes that result in a behavioral and physical change in phenotype which evolutionarily allows the species to survive and adapt rapidly (Herb et al., 2012), (Boasio et al., 2010).  

All images accessed on 25/05/15 and referenced from appearing top to bottom of blog:

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References:

(2009) PBS.org/nova/sciencenow. https://www.youtube.com/watch?v=wFsxVkuChdU

Bonasio, R., Zhang, G., Ye, C., Mutti, N. S., Fang, X., Qin, N., . . . Liebig, J. (2010). Genomic Comparison of the Ants Camponotus floridanus and Harpegnathos saltator. Science, 329(5995), 1068-1071. doi: 10.1126/science.1192428

Cubas, P., Vincent, C., & Coen, E. (1999). An epigenetic mutation responsible for natural variation in floral symmetry.Nature, 401(6749), 157-161. http://www.nature.com/nature/journal/v401/n6749/full/401157a0.html

Dias, B. G., & Ressler, K. J. (2013). Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat Neurosci, 17(1), 89-96. doi: 10.1038/nn.3594

Geary, D., Jašarević, E., Rosenfeld, C.,  (2012). Sexually Selected Traits: A Fundamental Framework for Studies on Behavioral Epigenetics. ILAR J,  53 (3-4), 253-269. doi: 10.1093/ilar.53.3-4.253

Goddard, M. E., & Whitelaw, E. (2014). The use of epigenetic phenomema for the improvement of sheep and cattle.Frontiers in Genetics, 5. doi: 10.3389/fgene.2014.00247

Gonzalez-Recio, O. (2012). Epigenetics: a new challenge in the post-genomic era of livestock. Frontiers in Genetics, 2. doi: 10.3389/fgene.2011.00106

Herb, B. R., Wolschin, F., Hansen, K. D., Aryee, M. J., Langmead, B., Irizarry, R., . . . Feinberg, A. P. (2012). Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat Neurosci, 15(10), 1371-1373. doi: http://www.nature.com/neuro/journal/v15/n10/abs/nn.3218.html#supplementary-information

Miller, G. (2010). The Seductive Allure of Behavioral Epigenetics. Science Magazine, 329 (5987), 24-27. doi: 10.1126/science.329.5987.24

Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, et al. (2012) Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons. PLoS Biol 10(11): e1001427. doi:10.1371/journal.pbio.1001427

Weaver IC, C. N., Champagne FA, D'Alessio AC, Sharma S, Seckl JR, Dymov S, Szyf M, Meaney MJ (2004). Epigenetic Programming by Maternal Behavior. Nature Neuroscience, 7(8), 847-854. 

Zeng, J., Konopka, G., Hunt, B. G., Preuss, T. M., Geschwind, D., & Yi, S. V. (2012). Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution. American Journal of Human Genetics, 91(3), 455–465. doi:10.1016/j.ajhg.2012.07.024

Zeric, D. (2012). Importance of Epigenetics in Animal Breeding: Genomic Imprinting. Swedish University of Agricultural  Sciences. http://stud.epsilon.slu.se/3888/1/zeric_d_120221.pdf

Epigenetics and Animal Caste Behavior

Many behaviorally social animals depend on a certain individuals to complete certain tasks. This specialized organization is referred to as a caste system in biology. Two examples of animals that thrive utilizing a caste system are ants and bees. Typical caste groups could include a queen, workers, and soldiers. These castes are anatomically and morphologically distinct. Although in bees, subcastes of worker bees exist such as foragers which gather food and nursers which feed and care for other bees. Both groups are a part of the worker caste but each carry out different duties. Typically there is no interchanging between castes, a queen bee's behavior is fixed and will never become a worker. However research has found that bees are able to change between the worker subcastes of foragers and nursers.



In Nature Neuroscience, Herb et al. published their research on the epigenetics of honeybees Apis mellifera (Herb et al., 2012). The scientists found over 150 methylated regions that were different between nurses' and foragers' DNA. Following this discovery the researchers designed an experiment to observe the two subcastes. All forager bees were sent out of the hive to gather food, and the researchers removed all nurse bees from the hive so that all which remained was larvae and the queen. Once the foragers returned half of the group changed to become new nurses and the other half remained foragers. The results showed that this drastic phenotypic "U-Turn" was the result of epigenetic switches in the methylation of the epigenome. In a follow-up experiment 45 particular reversible methylation sites were identified when the researchers looked a region in the genome when a bee changed from nurse to forager and back again from forager to nurse.
(Herb et al., 2012)

This study exemplifies that phenotypic behavior is able to be regulated by epigenetic changes, it is not only the DNA that solely modulates behavior but epigenetic changes as well.

This type of notion is not solitary to bees. Epigenetics also plays a role in the caste system in ants as well. The full genomic sequence of two types of ant species, Jerdon's jumping ant Camponotus floridanus and the Florida carpenter ant Harpegnathos saltator, proved to unveil epigenetic differences in castes as well. Bonasio et al. published their research on this concept in Science Magazine  in 2010 (Bonasio et al., 2010). The two types of ants are socially different, carpenter ants rely on the queen and once she dies the colony will likely perish as well although in Jerdon's jumping ant worker ants can battle to become queen. (Harmon, 2010). The Jerdon's jumping worker ant that becomes queen is called a gamergate queen and it will change physically and behaviorally to maintain its duties. Importantly though, in both species the queen ant lives longer than workers.

Camponotus floridanus (left) & Harpegnathos saltator (right)

According to Bonasio et al., "Telomere shortening is a hallmark of cellular senescence in multicellular eukaryotes, and the enzyme telomerase (TERT), which counteracts telomere shortening, prolongs life span upon overexpression. TERT RNA levels were highest in eggs and lower in adults in both C. floridanus and H. saltator, but they were up-regulated in H. saltator gamergates" (Bonasio et al., 2010). This is a particular finding that proves in gamergate ants epigenetic changes occur to increase the lifespan of the ant as it switches from worker to queen. It is epigenetic changes that allow a worker ant to behaviorally and physically change its characteristics within its lifetime. This epigenetic ability is an evolutionary important advantage because it allows the ant colony to continue quickly and easily once a queen dies. 

Both bees and ants rely on epigenetic changes to thrive and change behavioral castes for the good of their population. 

References:

Bonasio, R., Zhang, G., Ye, C., Mutti, N. S., Fang, X., Qin, N., . . . Liebig, J. (2010). Genomic Comparison of the Ants Camponotus floridanus and Harpegnathos saltator. Science, 329(5995), 1068-1071. doi: 10.1126/science.1192428

Harmon, K. (2010). First Ant Genomes Promise Insight into Epigenetics and Longevity. Scientific American. http://www.scientificamerican.com/article/first-ant-genomes-epigenetics/

Herb, B. R., Wolschin, F., Hansen, K. D., Aryee, M. J., Langmead, B., Irizarry, R., . . . Feinberg, A. P. (2012). Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat Neurosci, 15(10), 1371-1373. doi: http://www.nature.com/neuro/journal/v15/n10/abs/nn.3218.html#supplementary-information

All images accessed on 23/05/15 and are referenced from appearing top to bottom of blog:

http://antark.net/wp-content/uploads/2014/09/ants-pests-argentine1.jpg
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http://www.nature.com/neuro/journal/v15/n10/images/nn1012-1329-I1.jpg
http://holykaw.alltop.com/wp-content/uploads/2013/10/ant_bee_1170-770x460.jpg
http://ucanr.edu/blogs/bugsquad/blogfiles/1574.jpg

Epigenetics and Olfactory Experience

Traumatic experiences dramatically effect neurological functioning and memories of the person that experienced the specific trauma. Although, how does this effect future generations? Surely a mother that experiences a trauma will nurture her children differently since she will likely have different behavior than a mother not exposed to a trauma. As mentioned earlier in this blog, a mother rat's parenting style greatly impacts the epigenome of her children such that neglected pups will have distinctly different epigenetic markers than rats with caring mothers. In turn the neglect causes anxious behaviors and that behavior is often passed down. In this way it is the nurture that effects the rats epigenome. However, it is also possible that the traumatic experience can cause a naturally hereditable fear in the epigenome.

Molecular formula for acetophenone

Researchers Brian Dias and Kerry Ressler investigated the idea of a fear in mice that could be hereditable, and published their results in Nature Neuroscience. Dias and Ressler subjected male mice to "odor fear conditioning" of the smell acetophenone. They paired the fruity smell along with a slight shock on the foot. The next two generations of mice, smelling the odor for the first time in their lives, "had an increased behavioral sensitivity to the F0-conditioned odor, but not to other odors" (Dias & Ressler, 2013). Upon looking at the brains of the subsequent generations the researchers found increased amounts of neurological receptors in the olfactory system that detect the smell of acetophenone.

In order to prove that this was epigenetically inherited rather than by how the pups were nurtured, the scientists harvested the sperm of the first generation and conducted in vitro fertilization, only to find the following generations still had the same odor fear as the father or grandfather. Therefore the sperm was determined to be the cause. Investigation showed an altered epigenetic methylation signature at the Olfr151 (M71) locus in the sperm to be the particular location for the heritable olfactory fear.

It seems strange that it might be evolutionarily deleterious to inherit the fears of a parent. In an interview with a National Geographic journalist Dias explains his supposition, "And why, evolutionarily, would a parent pass down such specific information? “So that when the offspring, or descending generations, encounter that environment later in life, they’ll know how to behave appropriately,” Dias said" (Hughes, 2013).  


Indeed, it seems that epigenetics is working as a plastic mechanism for evolutionary change. Olfaction is a key sense that humans as well as a myriad of animals rely on for awareness of their surroundings. This research identifies that epigenetics is the cause for a heritable fear and poses questions as to what other types of fears or information can be passed to future generations via the senses. Epigenetics is aiding in animals survival behaviors by allowing animals to give their children heightened awareness toward particular objects or surroundings. A recognition of a negative smell by mechanisms other than nurture enhances animals abilities to quickly adapt to situations in an instinctual manner. 



References:

Dias, B. G., & Ressler, K. J. (2013). Parental olfactory experience influences behavior and neural structure in subsequent generations. Nat Neurosci, 17(1), 89-96. doi: 10.1038/nn.3594

http://www.nature.com/neuro/journal/v17/n1/abs/nn.3594.html#supplementary-information

Hughes, V. (2013). Mice Inherit the Fears of Their Fathers. National Geographic Magazine(Only Human). 

Picture References: All pictures accessed on 21/05/15 and are referenced appearing from top to bottom of blog

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Epigenetics and Livestock

The field of epigenetics is rapidly evolving and people other than scientists are taking note. Agriculture researchers are now considering how the industry can exploit epigenetic mechanisms. Understanding how epigenetics can be utilized in agriculture can also lead to understanding the importance epigenetics plays in animal heredity and evolution. 

Epigenetic changes often occur due to various environmental factors. Goddard et al. explains, "If an environmental treatment of a male affected his progeny’s performance that would be more surprising and more valuable because the treatment would be applied to only a small number of males but benefit the whole herd or flock. This might occur as a result of an inherited epigenetic mark or by RNA attached to sperm" (Goddard et al. 2014). 
Therefore a male would pass his epigenetic changes down and in a species that tends to have multiple mates and copious children this could impact an entire population or more. As mentioned in a previous post, mice with neglectful maternal care react to stress in a more negative fashion, thus if a male passes on a negative epigenetic trait it could result in a detriment to the fitness of the offspring and population. This process impacts the evolution of species especially in captivity such as livestock where the environment is unchanging and mating likely limited.


Thankfully, scientists have utilized epigenetics positively in the hopes of improving livestock environments. Recognizing the influence environment has on the expression of genes, scientists claim,
"A variety of imprinted genes have been found in livestock that affect traits such as milk yield, growth and carcass traits, fat and meat deposition and fetal development… More focus on the maternal contribution will be needed [in breeding programs]" (Zeric, 2012).
Agricultural specialists have also begun mapping the epigenome of livestock in order to identify disease susceptible methylation patterns. Further, studies have also attempted to compare diets and grazing behaviors, "animals with concentrate and uni-feed diet systems are expected to be differently methylated than animals in a less intensive system based on a pasture feeding systems" (Gonzalez-Recio, 2012). 

Epigenetics is impacting our agricultural industry in various ways and will hopefully bring about positive changes. The environment and behavior of one can epigenetically impact the future generation and incorporating more maternal care will likely bring about healthier livestock. 

References:

Goddard, M. E., & Whitelaw, E. (2014). The use of epigenetic phenomema for the improvement of sheep and cattle. Frontiers in Genetics, 5. doi: 10.3389/fgene.2014.00247

Zeric, D. (2012). Importance of Epigenetics in Animal Breeding: Genomic Imprinting. Swedish University of Agricultural Sciences. http://stud.epsilon.slu.se/3888/1/zeric_d_120221.pdf

Gonzalez-Recio, O. (2012). Epigenetics: a new challenge in the post-genomic era of livestock. Frontiers in Genetics, 2. doi: 10.3389/fgene.2011.00106

All photos accessed 14/05/15 and referenced from top to bottom of blog
http://oklahomafarmreport.com/wire/news/2012/07/media/00390_Poulty-Chickens-House053020.jpg
http://upload.wikimedia.org/wikipedia/commons/5/59/2789694551_37beafc438_b_-_Grass_Fed_Beef_-_Ryan_Thompson_-_Flickr_-_USDAgov.jpg
http://environmentagriculture.curtin.edu.au/local/images/res_agriculture.jpg
http://analyzemycareer.com/Careers/ooh/life-physical-and-social-science/agricultural-and-food-scientists.htm

Epigenetics: Sexually Selected Traits and Behaviors

Differences between females and males has always intrigued scientists. Pre and post-natally, individuals are subjected to hormones that greatly affect development. Geary et al. published an article in 2012 examining epigenetic influences on sexually selected traits and behaviors. The researchers discovered that many sexually dimorphic traits are due to epigenetic mechanisms. These mechanisms are induced by sex steroids and are more dynamic than other naturally selected traits.

This dynamism allows for fluctuation in hormones such as testosterone. Male animals often invest significant energy in expressing sexually selected traits to attract female partners both anatomical and behavioral. For example bright plumage in birds or male-male aggression in deer which helps various species achieve the reward of a female mate. Although these features or behaviors could potentially increase predation risk (Geary et al. 2012).

Geary et al. discovered that epigenetic regulation of sex-traits vary due to factors such as season. Regulating these characteristics evolutionarily can improve the survival and success of an animal so that the animal can spend energy elsewhere rather than always on their sexual traits or behavior. 

Geary et al. explains, "Serum testosterone concentrations in such males declines after the breeding season, and these traits are thus confined only prior to and at the time the animals seek out mates, suggesting again that sexually selected traits are tightly regulated by environmental cues, including daylight and other factors, operating through the endocrine system." This plasticity would not be possible if not for epigenetic mechanisms. Sex traits and behaviors have evolved to improve likelihood of achieving a mate, and epigenetics has allowed animals to continue extravagance in order to achieve this goal. 


All pictures accessed 10/05/15 and referenced from top to bottom of articlehttp://www.clker.com/cliparts/4/K/G/V/J/7/boy-and-girl-stick-figure-red-md.pnghttp://www.uecthai.com/wp-content/uploads/boy-girl-sterotypes.jpg
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Reference:
Geary, D., Jašarević, E., Rosenfeld, C.,  (2012). Sexually Selected Traits: A Fundamental Framework for Studies on Behavioral Epigenetics. ILAR J,  53 (3-4), 253-269. doi: 10.1093/ilar.53.3-4.253