This is another good example of a limit to phenotypic plasticity. This states that novel conditions have the ability to prevent an adaptive response. This is due to being developed through a threshold for phenotypic switch. With conditions that have been experienced during evolution there are phenotypes present that have been adapted to a wide range of environments. This is particularly concerning because extremely novel environments will continue to be very difficult to adapt to.

This is a perfect example of a hypothesized limit to plasticity. The authors are proposing that with a higher adaptive response to environmental shifts comes a slower life history and population level response. When I think about phenotype plasticity I think of an inherently good survival mechanism, often overlooking the implications that such a response can entail. A certain level of fitness is required in order for plastic responses to take place, which in turn limits the overall ability for a population level plastic response. The implications of a plastic response are not always positive.

These factors are pertinent to the limit and extent of plasticity because they are all environmental factors that can severely affect the survival of wild populations. These factors also have the potential to shift dramatically over time, forcing the relative plasticity of an individual to adapt with it. As urbanization and climactic shifts increase in frequency, so will the level of plasticity found among wild species. Studies such as the ones we are proposing now are extremely important for predicting how these environmental changes will affect plasticity.

I think that this is a very interesting point. I don't think that I had ever thought that the costs of plasticity would ever be so significant that they would be lost through selection. This is an important point to show the limit for rarely used plasticity. This makes me want to understand more about how/why these types of species were originally plastic at all.

This is an excellent example that really helped me understand the difference between a "cost of plasticity" vs a "cost of phenotype". When looking into this it explains that the least beneficial phenotype (short spines in high pred. environment) clearly has the greater cost of phenotype. What helped me understand "cost of plasticity" explained that G2 (long spines) was more beneficial to the plastic genotype (G3 long spines w pred. short with abs of pred.) This would therefore mean that G3 had a cost of phenotype when in an environment with pred. present. I thought that this was a key idea in understanding the limits of plasticity.

I think looking at mutations when trying to find the limits of plasticity is vital. It only make sense to look at mutations when determining limits because a presence or absence of a mutation could be the determining factor of an organisms limit to plasticity.

I think it is important to note that even though there are many limits to plasticity wild species have the ability to overtime over come such limits which makes it hard to pinpoint limits to plasticity of wild species if they have the ability to change.

I have always heard that breast-feeding a child is better for them than bottle feeding, though I had never really understood why. I suppose people are speaking on the beneficial microbes that are present in breast milk, or even the microbes that can be transmitted from the mothers epithelium. I am eager to look into studies comparing the immune health of a child that was breast-fed vs. bottle fed.

This makes me wonder if all mammalian breast milk contains generally the same beneficial microbes? If not, I wonder if there is an affect on the gut microbiota of humans that consume cows milk vs. that of a vegans. I'm sure the overall makeup of the gut microbiota would be vastly different, but I wonder if that plays a role in other micro-scale functions.

Are the authors suggesting that this aspect of mammalian evolution was in part to reduce the risk of infection that comes with a single canal? It certainly makes sense given that prolonged labour increases the risk for infection. I wonder if there is a correlation between longer the exposure to maternal vaginal and fecal microbes and the overall immune health of the infant.

This would be a fascinating concept of phenotypic plasticity to explore. Perhaps further comparisons of maternal and non-maternal microbiota during gestation would lead to new information on its potential adaptive value. I believe that it must yield a certain level of adaptive value, whether that is effieciency of nutrient uptake or an immune protective "barrier". It would also be facinating to know what triggers this colony-wide microbiota change during gestation. Perhaps an increase in estrogen or progesterone plays a role in signaling.

1) I never understood how much the microbiome has an affect on an organism 2) I didn't know that the microbiome could be so sensitive to change--- accidentally swallowing chlorinated water and can result in a change in your microbiome blows my mind!

I know a lot of women in today's world that freeze their extra breast milk and give it to mothers who cannot breastfeed, for various reasons, to give to their own babies. I don't really know how I feel about this process, but maybe it could help solve the problem of synthetic milk for infants that is not so synthetic. I had no idea that breast milk has any role in the microbiome and it would be interesting to read up more on how breast milk and different formulas affect infants .

This is an interesting thought. I would like to know more about how this process would work. Would this actually be beneficial? Would reintroducing the microbiota actually work to be a "self-transplant". I understand the concerns with the regulations among the FDA, but I would like to know if tests have been conducted and more information has been recorded on this idea.

I am still super interested in the comparative effects of being born vaginally v.s. c-section on the microbiome. I did a quick search on the differences and some researches say that there is an impact on the immune system later in life if born by c-section (weaker immune system). It is also known that c-section babies lack Bacteroides phylum that vaginal babies are exposed to when being born. C-section babies are also more prone to allergies, asthma, and obesity which blows my mind being a c-section baby myself. haha

In this excerpt where it says “bacteria acquired during labor...” I assume this refers to vaginal births. With that assumption made this makes sense to a connection I can make in my own life. I was born via C section and when I was a baby I could not drink milk of any kind and was placed on a soy formula. If this passage is referring to the idea that bacteria required to digest lactose, etc. are acquired through vaginal birth that makes sense as to why as a baby my body could not! Interesting connection!

This is an interesting point explaining that there is still much that is unknown about the topic. This excerpt goes on to explain that we understand that maternal strains colonize with different parts of the infants body yet we are still unsure of all of their functions as well as if there is more that contributes to what it may be. It is also and interesting point to mention that there may be a difference in outcomes when comparing a vaginal birth to a C section birth due to the fact that with a C section birth they would not have that exposure to the microbes in the vagina. I would be very interested in seeing what the differences in these two are.

This sentence is huge! As humans continue to increase in population and build outward, sadly we increase the risk of destroying biodiversity. It is important to look at how other species have adapted epigentically to the increasing anthropocentric world to try and come up with new conservation strategies.

I don't know if you could tell but I am definitely 100% towards the conservation side of things haha. I think looking at the underlying epigenetics of species should be a major step when determining a conservation plan because it is important to look at how the environment has an affect on certain species and how plastic a species is. I don't think it's possible to try an conserve a species without looking at epigenetic variation.

This is further explaining the goal of how an epigenetic conservation perspective can be beneficial (see box 1 for more) but this is a nice conclusion to have come to as well as an important goal to establish.

This is explaining how epigenetics can play a crucial role in development as well as be influenced by the environment.

This right here explains a key reason why an epigenetics based perspective is useful in the field of conservation biology. It is understood that these "epimutations"play a role in determining phenotype (morphology, behavior, etc.) that can lead influence natural selection as well as sexual selection.

With this knowledge more studies and experiments can be conducted to truly understand the relevance of epigenetics and biodiversity, and their symbiosis. Not only does this encourage integrative biology for field research, this also includes environmental law for conservation and sustainability efforts.

This is an extremely pertinent concept. This not only encompassed the importance of epigenetic influence on biodiversity, but it also includes the importance of these factors in relation to human society. As humans we are hugely reliant on this natural world that we largely take for granted. Epigenetics can allow us to optimize crop yields, which in turn influences the food industry and medicinal development. By maximizing ecosytem biodiversity, we can increase overall plant productivity. This gives us a new and improved model for agriculture.

How common are these spontaneous and random modification in methylation patterns? Does this result in a more broad mean phenotype than that of standard changes in methylation patterns due to changing environment?

This is a new concept for me. I hadn't heard of this, and wow, this is super cool. This is an interesting conservation effort.

This is incredibly exciting news for conservation efforts across the globe. It is certainly a new concept to approach conservation through the lens of epigenetics. This concept promotes an integrative and fresh approach to problems that we have been facing for countless years. Though it seems as if the hardest part of conservation on any front is legislative support, perhaps new methods will elicit an overall change in mentality as well as new discoveries.

Yes, exactly... furthermore, this can help scientists decide which species are in dire need of assistance and conservation efforts.

Interesting way to look at it... epigenetic modifications can definitely assist in increasing and advancing intraspecific diversity.

... and epigenetic mutations are therefore a very important driver of adaptation, which in turn corresponds with an organism's ability and likelihood to adapt to environmental changes & pressures. Hence why it is crucial that mutations at the epigenetic level receive just as much attention as those that occur at the genetic level.

By using genetic tools, is it possible to come up with a solution for the current extinction or will it end at helping us understand it better

This has certainly become apparent to me in taking both Genetics and Eco Devo at the same time. I believe its fascinating to compare and contrast the differences between the relatively set in stone mechanisms of genetic inheritance vs the largely unexplored realm of epigenetic mechanisms and its relation to phenotypes. The sheer amount of variability in phenotypic expression relating to environment is immense and truly interesting to explore.

Mechanism isn’t a “silver bullet” to explain variation because phenotypic traits are not necessarily going to be presented with epigenetic modifications. The relationship between mechanism and variation is not direct, meaning the correlation is loose and contains variability in and of itself. For example, an organism can be more likely to develop a certain phenotype, but not positively going to. There are no direct patterns to this relationship.

Epigenetic modifications are generally considered non-genetic because they tend to not be as “cut and dry” as DNA mutations. These modifications can elicit phenotypes without affecting the genetic makeup of an organism, often resulting in an outcome that could otherwise not be achieved from genetic variation alone. I believe the main distinction between epigenetics and mechanisms of genetic variation is that epigenetics is highly unpredictable. With the methods of karyotyping and gene sequencing we have today, it is far easier to predict the genetic makeup of an organism, rather than the result of epigenetic modifications.

This is an excellent spot to discuss Q1 Why do we care as well as Q5 how this is relevant for both conservation bio as well as human health. The information learned in this article, leads me to believe that there is a lot that we do not currently understand about the concept of epigenetics. Gathering a better understanding of this would help conserv bio in ways that we have discussed in class as well as what the majority of the paper discusses. A better understanding of the world around us and how to enact the 5 main goals of conservation biology. This understanding would also help in the human health field by better aiding in understanding human genetics and how to care for those. Epigenetics can help us understand diseases for example cancer. Knowing what genes are "turned on" and "turned off" can help connect the missing points as to why are some people susceptible to things that others, especially in the same family, are not.

1... Even though the main focus is phenotypic traits there is a whole lot more to a change in phenotype than what can be seen on the surface. Epigentics underpins a lot of the variation/ plasticity of the phenotypic traits that are observed. To understand why some of the traits continue to get passed down through generations or why a not so advantageous trait persists you need to take into account the epigentic markers that are responsible to genes being turned off or on.

2: Epigeneitcs links to phenotype here because epigenetic markers can be passed down through generations and effect the phenotype of a generation that may not fit the environment that that organism is developing in but the markers are still within the genes or amino acids and have the power to affect the phenotype. There are more examples further down the paper that explain more in depth how the relationship of epigentics effects the phenotype (methylation in Linaria vulgaris affects the flower symmetry which is also heritable)

This is an example where epigenetic modifications link to phenotype in A..thaliana, or what we know as a mustard plant. In short, it is depicting how the same species is altered in different locations throughout Europe. Data of methylation polymorphisms was also investigated along with their flowering times.

First of all, super interesting. Definitely an avenue of invasive species that I hadn't thought of prior to reading this. Second, this is a great example of why we care about ecological epigenetics when our focus is on phenotypic traits. Through the regulation of epigenetics, various phenotype, some of which may be better/more beneficial for the organism, can be achieved.

In other words, phenotype is achieved not only through genetic variation, but also through epigenetics, and the phenotypic traits that result from epigenetics can differ from those that result from genetic variation. Is it correct to say that epigenetics can potentially provide a segway to a string of phenotypic traits that cannot be achieved through genetic variation?

With respect to the 4th bullet point, this is yet another reason why epigenetics is "non-genetic."

With respect to bullet point #4, epigenetic modifications are considered "non-genetic" because when put simply, epigenetic modifications result in phenotypic changes without making any changes to genetics sequences.

As a ESP major, this reminded me of some of the concepts that we have studied throughout our policy classes. This selectiveness regarding which principles and guidelines to follow is a common occurrence throughout many business, organizations, universities, etc., and quite frankly, it has the potential to be an issue. When a concept is as slippery as this one, individuals/groups do not feel the need to adopt all features and principles that make up such concepts, and thus their efforts may not be as effective, nor as successful.

To me this is what school systems are already doing and have been doing in every level of education.

Expanding on this idea and giving an example would be helpful in understanding the statement made. How far from the central discipline should educational curricula stretch?

This statement, to me, sums up the paper as a whole. Integrative biology is science for the 21st century because of the fact that humans are continually looking for faster and more efficient ways to problem solve and without collaboration across multiple fields of expertise this is not possible.

I believe that there are more challenges than just expertise that a person or organization face when trying to integrate other fields of study into their own. For example, communication and funding can affect the amount of integration a person or organization are able to incorporate into research.

I'm not sure if I'm not reading this statement correctly, but I don't understand how integrative biology is an "...attitude about the scientific process...". I agree that integrative biology can be a "...description of a way of doing science...", but I don't think I would call it an attitude.

This is an interesting point because it is saying that educators must be aware of integrative sciences. This would be helpful because they can spread their knowledge of the science to their students making the change to integrative methods of science much quicker and easier for the next generation.

This is really interesting because it says that we have not reached a point where biologists start to not just focus on one aspect of Biology, they combine them.

I think Wake's ideas about integrative biology are the way that science needs to be heading and hopefully already is since this article was published. Looking at a problem or research question through only one type of lens will never produce the same results as having people from many different disciplines looking at the same problem and attacking it from all different angles.

After working at an environmental education camp for the duration of my summer I can certainly attest to the importance of making those visually tangible scientific connections at a young age. Something as seemingly minuscule as sweep netting in a meadow can initiate a discussion of biodiversity.

In addition to these advantages, integrative research may also spark up a passion that was previously not realized and may have remained undiscovered. Integrative research not only benefits the advancement of various scientific fields, but also the blossoming of bright minds and the potential for a life of deeply enjoying your career.

Sound like the definition of ecology to me.

Outreach IS integrative when it allows a back-and-forth among stakeholders. Maybe outreach is what should be added to all sciences in order to make them integrative, as long as it's not a one-way street approach, like disseminating research findings to the public/other disciplines and not taking feedback or taking feedback seriously.

This is interesting because I usually see "expertise" as something that becomes narrower and more specific.