Final Reflection

     I don't think overall my perspective of evolution has changed from this class, but most certainly my understanding of the mechanisms of evolution have grown considerably. Especially in understanding those mechanisms in an empirical and mathematical way e.g. how different starting frequencies affect fixation of alleles, visualizing mutation-selection balance, looking at genetic drift over generations, etc. Although I never saw evolution as an aimed track of nature, I now more better see how statistical probabilities play into how evolution unfolds. Sexual selection has been especially influential in helping see this more accidental, purely competitive side of evolution. I've grown into that idea that evolution serves to benefit individual after individual, not necessarily populations and definitely not necessarily communities. I still do not discount mutualism in nature, however. Even if evolution generally is a very selfish process, I still think there is an integrity in the way natural systems evolve together and generate a mostly self-sustaining balance.

    Most importantly from this course I have bettered my skill of data pondering and interpreting. In the past data has felt at times esoteric or otherwise confusing but working with R and seeing "raw" data that we then processed ourselves to generate communicative models...this helped develop the ability to see data as numerical realizations of hypotheses rather than just numbers collected. I've gotten a better sense at taking a question and brainstorming what data is needed to provide support/critique of that question. As a future wildlife biologist I feel that I can much more confidently walk out into a natural community and go through the process of developing answerable, mathematical hypotheses and addressing them accordingly. I do however need to learn how to not overthink data that I'm confronted with interpreting: in many of my self-assessments this was a common theme. I think this could be helped by seeking to fully understand the study before trying to understand the data, which I often neglected to do because of rushing through assignments. With R, I feel like I've just begun to understand it and to continue growing that skill I need to be more resourceful and practice varying tasks.

    I started off my blogs by giving a scientific and poetic definition to evolution, which I now would like to revise. With the technical side of the coin, I now see that evolution is more about the change of genetics of populations over generations through the survival and reproductive success of well-adapted individuals, rather than just species changing to fill the space of available niches (though I certainly would say this plays an important role, still). Poetically, I still see evolution as "Life" seeking to express itself in as many ways as possible, but within that ideology I'd like to add the notion of chance success and capitalizing upon it, rather than natural communities "working together" to develop that sustainable web of interconnectedness. I still think the beauty of that interconnectedness is a beautiful ~chance~ result of all those lucky breaks, of course. 

Speed of Speciation

     I'd like to start this out by saying that I think defining a speed at which speciation can occur may inevitably be futile. Not just in the fact that it most certainly depends on the context of each genus/ancestral species in question, but also in that our defining of species is arbitrary even in our most specific of definitions. Because, as always, nature doesn't give a flying hoot about what is a species and what isn't. But of course, our conceptualizations of species is important in the way that we as humans steward and manage populations and communities of organisms, so while it may be arbitrary it certainly can serve a pragmatic use.

   Anyways, this discussion on speciation speed will be something of a paper review, A paper by Hendry, Nosil, and Rieseberg from 2007 did a review seeking to understand an ecological perspective of evolution involving both contemporary evolution and ecological speciation. Most importantly, I think, they examine how adaptive divergence causes reproductive isolation (their definition of ecological evolution); this being a cornerstone to understanding species in a most objective way possible. An important note is that this study doesn't consider reproductive isolation to be zero gene flow between two populations but rather a significant reduction in gene flow. Just as a comment, I think this is very important because it goes back to how we as humans can't seem to solidly define reproductive isolation, at least most of the time.

    They first note how speciation seems to occur very first when their is a single locus or group of pleiotropic loci determining mating between individuals: a so called "magic trait." In these cases ecological separation can occur within well less than 100 generations. Dispersal rates of populations also seems to play a potentially important role: new populations colonizing new habitats are likely to experience bursts of adaptation. Selection against migrants in these newly colonized environment is also important as it significantly reduces inter-population gene flow.

    The next major thing looked at is mate choice. Disruptive selection can encourage assortative mating which can lead to reproductive isolation within a couple hundred generations. Likewise, adaptive speciation, where competition for limited resources forces evolutionary branching, can cause a similar mechanism of reproductive isolation. Reinforcement, where two divergent populations come into secondary contact, can also rapidly evolve mating preference to avoid maladaptive assortment of mating. Hybrids are looked at in this paper, although it seems that at the time the way they interacted with gene flow wasn't very well documented and didn't prove useful to this paper's goal, as the results don't seem very conclusive.  They do mention how hybrid species can quickly become reproductively isolated when they colonize new habitats and quickly adapt to it.

    Plants, especially, seem to have an immense capacity for speciation through dispersal of hybrids. A certain species of sunflower, Helianthus anomalus, based on genomic evidence, seems to have evolved within about 60 generations. Invertebrates, specifically insects, may also have a quick divergence due to hybrids as shown by a fly species, Rhagoletis sp. The authors claim that reproductive isolation may be almost immediate when a hybridization introduces a phenotype that automatically separates potential mates. In a certain species of salmon, Oncorhynchus nerka, after only 14 generations significantly reduced gene flow had occurred between two locally adapted populations.

    So, all in all, it seems that the rate of speciation can be quite rapid in the grand-scale of things, especially at a more microlevel and with certain softened qualifications for reproductive isolation. At the very least, within 100 or so generations seems to be somewhat of an "average" consistent across all the examples looked at in this review. I think it's also worth noting, that once reproductive isolation occurs (after 100 generations or what have you), then a more "recognizable" speciation is apt to take place as new selective pressures and lack of gene flow create ideal conditions to reproductively diverged populations to adapt and evolve different characteristics.

Resource:

(Hendry, Nosil, and Rieseberg, 2007): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605086/

Antibiotics vs Disinfectants

 I personally think that antibiotics are an interesting case study of both modern ingenuity and, alternatively, hubris. Antibiotics are highly specific in the way that they kill bacteria, which is both their glory and their downfall. This specificity makes them very effective in deactivating whatever metabolic pathway they target but also places a selective pressure on the bacteria that allows them to quickly evolve a resistance. Thus, while antibiotics can be very effective in curing bacterial ailments, the medical community must be very careful about the prescription of antibiotics to patients to prevent the potential evolution and spread of hyper-resistant strains.

Disinfectants, on the other hand, do not pose this same threat. Heat, alcohol, ultraviolet light... these things do not target specific metabolic pathways that bacteria can evolve around. They produce environments that are highly intolerable to the bacteria to the point where they are simply obliterated, rather than just biochemically interfered with. This is extremely useful in the medical world for keeping pathogen exposure as minimal as possible without generating selective pressures on bacteria that allow for them to become something like MRSA, which is a considerable threat. A drawback to these things is that they are not so easily implemented upon the human body: you can't apply hundreds of degrees of heat to a human to rid them of bacterial infection nor use highly concentrated alcohol (although, has anyone with strep throat tried day-drinking absinthe?).

Hopefully we are able to find a way to use disinfectant-like techniques to internally fight bacterial infections so that antibiotic usage doesn't eventually create a superpowered bacteria monster that wipes out Western civilization! Marvel supervillain idea, maybe?

Mental Disorders as Diseases of Civilization

 For this blog post, I will be discussing how depression and anxiety are diseases of civilization.

In this modern day world, we live with a lot of stress. Our jobs, school, toxic family dynamics, social expectations, and so much more can all bring potentially daily stress-triggering moments. We evolved our stress response as wild animals, not civilized individuals; our stress response is meant to be activated, save us from danger, and end until needed the next time the mammoth you were trying to kill turns tries to stomp on you. With the advent of modern civilization, we began to be exposed to stressors that were drawn out in ways very contrary to how this biological stress-response system wishes to operate. 

The result of this? You name it. To my understanding, stress is linked to a myriad of problems: heart disease, IBS, hypertension, and what I will focusing on, depression and anxiety. 

Because of our disconnect from our evolutionary past, us moderners are deprived of the kind of exercise that keeps our bodies and brain stimulated, cut off from the diets that built our species, and exposed to exacerbated social pressures (in the workplace, and especially on social media). Miller and Raison (2016) point out a connection between stress-induced inflammation and molecular patterns from the gut microbiome with anxiety and depression. They also mention that depression is a sort of convalescent evolutionary response to fighting pathogens, and whether this is true or not, it certainly is an interesting idea to ponder. In our more sanitary and high-stress modern world, does that mean that depression is a self-defense mechanism of the body against pressures of civilized life? The long-term stress exposure that we experience can disrupt our sleep, damage our brains, and disrupt our immune systems, so potentially that makes depression our body trying to escape from stress and force ourselves to convalesce. 

Stephen Ilardi, a doctor of clinical psychology, recommends rewilding your life style as much as possible to try and combat the tension between the modern lifestyle and your brains ability to deal with stress. These include exercising (like walking and hiking), getting healthy sleep, sunlight, and social connection. 

I think by now because of self-wellness trends and such, we all know quite a bit of this information. However, I think this delve into depression from an evolutionary perspective rather than from a purely chance disease one is very helpful in thinking about how to reflect upon the way that the way we think we're "supposed" to live nowadays may hinder our wellbeing. 

Resources:

https://www.filmsforaction.org/articles/depression-is-a-disease-of-civilization-huntergatherers-hold-the-key-to-the-cure-return-to-now/

https://www.psychotherapynetworker.org/blog/details/456/anxiety-a-modern-phenomenon

https://www.nature.com/articles/nri.2015.5

Hybrids

    Hybridization seems to be a tricky concept in evolutionary biology. It's an inarguable fact of nature but frameworks like the biological species concept force us to deny it in order to create artificial, human-serving categories. But why is it important? Even though it makes things messy for us, there should be some sort of sense to why it occurs in the first place, right? A beneficial mechanism of communities or perhaps just a happy coincidence of probability and biochemistry?

    While we maybe can't say whether it "exists for a reason" or not, we can definitely see that it has an impact on biological processes. It also presents some challenges in the conservation world (i.e., if you don't know what things constitute a species, how do you protect that species?). In terms of population genetics, hybridization can fix beneficial alleles and it can also dispose of detrimental ones (Quilodrán et al, 2020). So evolutionary, if another "species" has a good line of genetic coding that could benefit another closely related, geographically overlapping species, then when two individuals (or more) decide to make some babies then you instantly have children with a new beneficial allele (or dozens!), assuming they're not reproductively isolated by sterility. If these genes are beneficial enough, then they could quickly spread into the target "species" population via these interbreeding events and reproduction of the alleles by hybrids rearing more and more diluted-hybrid offspring. In simple terms I feel that this could act as a sort of evolutionary springing board: a slew of new genetic material is thrown out into the pool to be acted upon by selection, and if it's good enough, it explodes in the population. A quote from the same paper: "hybrids have the potential to exploit a unique ecology that is intermediate between those of the parental species." While this is in reference to a speciation of yeast, I think that if you extrapolate the information from that quote you can find the gold nuggets of interspecies breeding. Sometimes, it could actually be ecologically beneficial to lose the extremities of two parental species and instead act within an intermediate habitat. If this habitat is novel and made accessible by hybridization, then there's an instead potential for colonization and utilization of that resource the diversifies an ecological community. 

    Interestingly enough, this article also stresses how hybridization can be detrimental to biodiversity. More interesting, it seems to be when it's specifically "forced" anthropogenically, rather than coming about through natural overlap of allopatry. It seems that demographic decline (presumably from habitat loss) and interspecies breeding interact in a negative way to expedite extinction. Radically different allopatric species can bring maladaptive alleles into populations that are on an unwanted genetic extreme, if you will, as opposed to before when geographically related populations could offer genes that were beneficial because of their relatedness. Something known as "speciation reversal" can occur when these maladaptive traits effectively reverse local adaptations and eliminate ecological opportunity.

All in all, it appears that hybridization, like most things, is not good or bad in and of itself. Rather, depending on the context of the hybridization events, biodiversity can either be benefited or damaged according to the background of the interspecies breeding. 

Resources:

Harmonizing hybridization dissonance in conservation; Quilodrán et al. 2020

https://www.nature.com/articles/s42003-020-1116-9

Snail Sex

 Molluscs are fun, in my honest opinion.

Awh, they're hugging!

    They have a range from lil clams to big ass octopuses that are horrifyingly smart. And right in the middle are the wonderful garden snails that leave behind fantastic lil shells for you to collect as a little kid, albeit at the cost of maybe eating your parents' hostas. Quick anatomy rundown on snails: most importantly, they're hermaphrodites, and also, they form special sexy-time swords forged from calcium carbonate and other hard compounds to encourage fertilization of their partners. Love darts, they're called. You may have heard of these in the many popscience platforms that exist. They aren't really "darts" per se, as they aren't fired like projectiles but rather wielded like the lance of a jousting knight.  Why am I talking about this? Well, pipefish seemed fun and cool but I think in terms of sexual evolution and conflict, snails stabbing each other with bone swords is cooler. 

Hm, less cute

    

    I won't go into the physiology of the love dart itself, but I will say that it is developed in the "dart sac" (or bursa teloris) which is part of the snail genital apparatus. It is more or less pushed out from the body like the tongue from the mouth when you're teasing someone, except in this case it falls off. A new love dart must then be formed by the snail. In action, the love dart serves the purpose of secreting hormones that influence the spermoviduct of the opposing snail, which helps to neutralize the recipient's ability to digest sperm cells. This little violent trick can double the fertilization of the recipient snail. Oh, it can also lead to death of the other snail if the other snail has been stabbed by love one too many times.

    My best hypothesis about why this involved has everything to do with the innate truth of sexual conflict: males have to put in less than females. With snails, since they're majority hermaphrodites, then snails in mating essentially compete for who is the acting "male" and "female," thereby competing for who has to devote more energy after the mating ritual. Having a competition of jousting allows for one snail to potentially get the upper hand in insemination and spread more of its genes rather than its opposition/lover. So, perhaps the love dart exists simply to create a gentleman's duel for the sexless snails to decide who must bear the fate of pregnancy and egg-laying. 

    Anyways, you're welcome for sharing everything about snail sex you probably didn't want to know.

Resources:

http://www.molluscs.at/gastropoda/index.html?/gastropoda/morphology/love_dart.html

https://en.wikipedia.org/wiki/Reproductive_system_of_gastropods#:~:text=Gastropods%20are%20capable%20of%20being,the%20opportunity%20to%20self%2Dfertilize. 

Plants that eat... plants?

There's a good chance that you've heard of Rafflesia spp. plants. They're often cited as having the largest flowers in the world, which is true depending on the perspective you're taking. They're also known for smelling like a dead possum you'd pull out from under you deck after wondering what that smell was for 3 days, yummy! Oh, and if you were a nerdier kid you'd probably recognize that the Pokémon Vileplume was inspired by their enormous petals:

Rafflesia arnoldii on its host vine,  Tetrastigma sp.

Vileplume from Pokémon

Now, even if you knew about Rafflesia, you probably didn't know that it's actually a holoparasite, i.e., it exclusively receives its nutrients from a host. In other words, this is a plant that forgot how to be a real plant: it cannot photosynthesize. They exist, rather, more like fungal mycelium nestled amongst the fibers of host Tetrastigma vines (which are in the same family as grapes) in thin strands of cells that are quite lackluster. That is, until they decide to bloom. 

    Jeanmaire Molina, an evolutionary plant biologist, was the one to find out that these plants in the Rafflesiaceae family have completely ditched any functional chloroplast genes. A team at Harvard uncovered in a closely related species, Sapria himalayana, that these plants have shed all photosynthetic capacities in order to be more efficient parasites, outsourcing the labor of metabolic processes to their hosts. Hauntingly, 1.2% of Sapria's genome comes from hosts of Christmas past and present (which is bigger than it sounds given these are complex eukaryotes here). Their genome has been described as a "huge graveyard of DNA" by Liming Cai, a systematic biologist postdoc. Also, like 60% of these things' genome is repeating retrotransposons, but no one really knows what that's about yet. All in all, they have evolved exclusively to get really good at schmoozing their hosts out of their hard-made food and then making one hell of a scene when they're ready to get some.

To summarize, some of the largest flowers in the world are made by plant vampires. Sleep well! :)

Thanks for reading!

P.S. if you're interested in more parasitic plants, One-Flower Indian Pipe (Monotropa uniflora) are native (albeit, rare) to the Eastern part of Kansas :)

Resources:

Article by Quanta Magazine: https://www.quantamagazine.org/dna-of-giant-corpse-flower-parasite-surprises-biologists-20210421/