Applying evolutionary medicine to clinical practice will not be straightforward
We still need to understand the full depth and breadth of our genome. This won't happen, conservatively for at least a century, but as we grow what we do know, there will be a lot we can do with personalized medicine, as well as advancing our knowledge of evolutionary medicine.
caused by single gene mutation
These diseases will be the target diseases for gene editing technology to potentially treat/eliminate first.
Genomics has also been used for tracing the evolutionary history of pathogens as they transmit within populations
Very relevant right now. If there is a way to knock down the spread of covid-19 that exists in other animals, then maybe it could be applied to our current condition.
that occur faster than the genome is able to adapt
...For now...
n addition, characteristic changes in the microbiome have been correlated with a variety of diseases
I have a friend who went through a bad infection, then after the medicine needed, their microbiome was all but wiped out. its so powerful, it limits the use of antibacterial medicine for life.
he most varied microbiome is found in the gastrointestinal tract
I believe the most varied of any creature we've studied.
menopause and longevity
These are interesting attributes to our species as they don't necessarily contribute to increased reproductive success, but can contribute to species success. Could antagonistic pleiotropy be a genetic trademark of societal species?
this selection can favour genes that are beneficial in youth but detrimental in old age.
This makes me think about scar tissue. it is not made to replace a problem and "heal" it. Instead it just glues local tissues together, and hopes for the best. Then, once there, the old tissue can never be replaced.
“It’s something we concluded from the complex archaeological record, but for which we couldn’t directly link with the genetic populations.”
Using both genetics and archaeology to confirm each-other's findings is going to be huge for putting together a true analysis of pre-record history.
To explain this, the researchers point to a fortuitous mutation among the highlanders—an immune gene correlated with smallpox, which may have conferred a protective effect.
The fact that this gene seems to have evolved before the arrival of small pox to the continent is amazing!
quashing a longstanding theory that a group of Paleoamericans existed in North America prior to Native Americans.
I'm sorry, but doesn't that make the Fallon Paiute-Shoshone tribe the paleoamericans? the first tribe to inhabit the area?
Meltzer and Willerslev don’t know if this population arrived before or after the ancestors of Native Americans
If it was after, that might explain why they didn't stay for very long, or leave much of a trace. If it was before, I might speculate that the climate of this ice age era might have been a motivator to drive them south.
Mesoamerica (what is today Mexico and Central America) toward both North and South America.
This is something that seems like it should be obvious, but we've always assumed that migration was minimal after initial colonization of the Americas. Based on no real evidence. And migration does really seem to be an integral part of human population behavior, so it really doesn't make sense that that was a conclusion.
Many of the examples of urban genetic driftdescribed above result from barriers, particularlyimpervious surfaces suchas roads and buildings,that restrict gene flow between urban habitatfragments.
This "Island effect" of urban animal populations may devolve into their eventual extirpation if city planners don't consider native wildlife needs when designing city sprawl..
Many urban populations are newly establishedby immigration from surrounding rural areas.Although studies have tested for evidence ofreduced genetic variation within urban pop-ulations as outlined above, few have examinedthe consequences of founder effects associatedwith the establishment of new populations
What happens to the genetic diversity of those rural areas? Will those populations be sustainable for long-term population survival? Urbanization could be the loss of many small human cultures, as well as the creation of new cultures. The same may happen to the genetic diversity of the human populations as a whole.
lower di-versity, and abundance of some native species(8,9), and a loss of phylogenetic diversity withincommunities
These changes are going to be important more and more as we lose species at faster rates. Additionally, Invasive species are a trademark of the modern era, and the corona epidemic is the perfect example of that. We travel more and more, and other forms of life come with us.
He also never produced a clear picture of why some lineages seem to be experiencing stronger sexual selection than others.
Genotype variation? Cheetahs would be a good species to explore this on, because of their "Super Mom" phenomenon.
quantitative genetics and formal selection theory, which resulted in quantitative techniques for the measurement of selection in natural populations
This kind of approach is great to find the gene = behavior mechanisms that drive sexual selection, IMO.
pipefish, Syngnathus scovelli, is extremely sexually dimorphic with secondary sexual traits appearing only in females
Interesting that the Syngnathidae family seems to reverse the roles with females showing sex traits, and the males choosing.
seahorses (genus Hippocampus) tend to be sexually monomorphic
The males tend to select based on large female body size. Today you learned.
Nevertheless, definitive tests of these models are difficult to find, and the subject remains controversial
Until we learn to accept that individuality of every species studied will in some way influence mating behavior, yes, we won't have definitive tests. Go ahead and describe exactly what an opposite sex member of your species make selection based off of.
We really can only use averages to measure these kinds of decisions, and accept that biology is almost completely grey, not black-and-white. Variations exist.
Although Darwin appreciated the importance of mating preferences in sexual selection, he did not cleanly identify the evolution of mate choice as a key topic in its own right
It is likely that 1) He did not know how to go about proving this with the resources he had on hand, remembering that most of his work had to be done in England, but he didn't have any living Galapagos finches with him, and 2) He was limited by ability (legal, technological, ideological, etc.) about how he could have approached it. It is also possible that he just didn't think to, or decided not to based on difficulty to provide evidence of it.
the peacock’s tail
This really is the best visual evidence for the condition-dependent indicator model. When male peacocks are in better health, and have great access to nutrition, the tails grow longer, larger, and more full of feathers. Limited access to food, or illness will wilt and shrink the feathers of the tail, and attract less mates.
Natura non facit saltum.
Nature does not create omissions.
In other words, adaptations will occur in small degrees.
For instance, a swim-bladder has apparently been converted into an air-breathing lung. The same organ having performed simultaneously very different functions, and then having been in part or in whole specialised for one function; and two distinct organs having performed at the same time the same function, the one having been perfected whilst aided by the other, must often have largely facilitated transitions.
Divergent evolution
We have seen that a species under new conditions of life may change its habits, or it may have diversified habits, with some very unlike those of its nearest congeners. Hence we can understand, bearing in mind that each organic being is trying to live wherever it can live, how it has arisen that there are upland geese with webbed feet, ground woodpeckers, diving thrushes, and petrels with the habits of auks
Behavioral diversity, and habit adaptation.
When two varieties are formed in two districts of a continuous area, an intermediate variety will often be formed, fitted for an intermediate zone; but from reasons assigned, the intermediate variety will usually exist in lesser numbers than the two forms which it connects; consequently the two latter, during the course of further modification, from existing in greater numbers, will have a great advantage over the less numerous intermediate variety, and will thus generally succeed in supplanting and exterminating it.
Rarity of transitional varieties.
We have seen that in two beings widely remote from each other in the natural scale, organs serving for the same purpose and in external appearance closely similar may have been separately and independently formed; but when such organs are closely examined, essential differences in their structure can almost always be detected; and this naturally follows from the principle of natural selection. On the other hand, the common rule throughout nature is infinite diversity of structure for gaining the same end; and this again naturally follows from the same great principle
Convergent evolution
Thirdly, when two or more varieties have been formed in different portions of a strictly continuous area, intermediate varieties will, it is probable, at first have been formed in the intermediate zones, but they will generally have had a short duration. For these intermediate varieties will, from reasons already assigned (namely from what we know of the actual distribution of closely allied or representative species, and likewise of acknowledged varieties), exist in the intermediate zones in lesser numbers than the varieties which they tend to connect. From this cause alone the intermediate varieties will be liable to accidental extermination; and during the process of further modification through natural selection, they will almost certainly be beaten and supplanted by the forms which they connect; for these, from existing in greater numbers will, in the aggregate, present more varieties, and thus be further improved through natural selection and gain further advantages. Lastly, looking not to any one time, but at all time, if my theory be true, numberless intermediate varieties, linking closely together all the species of the same group, must assuredly have existed; but the very process of natural selection constantly tends, as has been so often remarked, to exterminate the parent forms and the intermediate links. Consequently evidence of their former existence could be found only among fossil remains, which are preserved, as we shall attempt to show in a future chapter, in an extremely imperfect and intermittent record.
Two vital ideas represented here: 1) There were/are transitional beings, but they don't survive as well, and will quickly die off. And 2) Fossil records are unreliable to ascertain the existence of these transitional states.
In the higher Vertebrata the branchiae have wholly disappeared--but in the embryo the slits on the sides of the neck and the loop-like course of the arteries still mark their former position.
These three passages show important ideas in transitional evolution. Organs forming new different special purposes that differentiate species also offer evidence of former common ancestry (especially in developmental embryology).
Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory.
To restate: The eye didn't just happen in all its complexities. It formed over millennia, in multiple different generational evolutions of different species'. Each time it changed, and those it changed in thrived, it offered a new an beneficial adaptation.
Science in general and evolutionary science in particular are often politicized, exactly because of their fundamental importance to human society.
Politicizing is, regrettably, unavoidable. But the issues I take are with the education of science being restricted or ignored because of this politicizing. That hurts society, when we have less informed citizens.
THIS is why this paper, and others like it are important to the future of evolutionary biology, and science in general. We have to observe why this information is important, how it will affect us, individually and as a whole, what biases may affect its conclusions, and what forces would seek to ruin it.
We strongly support the movement toward open access for the scientific literature to accelerate research and allow more investigators to participate. We also encourage provision of open software, data and databases, as well as their computational reuse and distillation, as outlined by Lathrop et al. (2011) [99]. These individual and community efforts will be increasingly necessary for development of new research programs and insights.
Two things need to be removed from the scientific community for this to happen: egos, and profits. I'm just saying, while I would love for this to occur, I'm skeptical that it will.
Beyond the challenge of understanding the capacity of species to respond (e.g., [51],[87]) and the potential for dramatic state-shifts in the biosphere [17] lies the daunting problem of understanding the many interactions between community-scale ecological dynamics and evolution of traits within populations
I wonder. We have billions of years of evolution, and evolution is a one-way stream of changes. We can't flow backward, and neither can anything else. If this biosphere were to be destabilized enough by us, would we see an end to all life? Even the microorganisms have evolved the whole time, and they can't change their genetics backward any more than we can. Have we specialized enough that if it all kicks off again, is that it?
Linking spatial data on phenotypes, genomes and environments in a phylogenetic context allows us to identify and name Earth's diverse life forms
Additionally, this new genomic area of study has also highlighted organisms that we haven't yet discovered, or have gone extinct, by leaving blank spaces in the "tree of life" that we suspect had to have been filled by some type of organism. https://www.the-scientist.com/news-opinion/sequencing-the-tree-of-life-37604
discovery, design, and enhancement of drugs and vaccines (e.g., [34])
In addition to protecting food sources, this type of drug enhancement can now start using your own specific genome to design an optimal medical treatment for your body when you are ill. So Kewl!!
In particular, engineering and design processes have incorporated evolutionary computation, leading to improvements in design of cars, bridges, traffic systems robots, and wind turbine energy, among other applications
One conservation advancement that I like are the wildlife bridges used to prevent roads from being boundaries for life forms, but even it had drawbacks. Hopefully, one day, advancements using these technologies can overcome those modern pitfalls.
genotypes across environments
This is an interesting phrase to me, because while the reality is many, many organisms will travel to multiple different environments in their lifetimes (even over relatively small habitats), there are just as many different types of life that can't travel. They are stuck in just one environment, even though that environment isn't static. Those organisms are the ones that will benefit the most from phenotypic plasticity, and acclimatization. Those genomes are going to be the hardest hit from drastic change in environment that epigenetics can't protect them from. Dandelion seeds may scatter to new places on the wind, or hitchhiking, but mama dandelion is stuck where she dug roots.
Thedocumentation of environmental variation was historically a centralarea of research, and evaluating how well experimental environmentsmimic or simulate natural environments, particularly the relativefrequency of each component of the environment, is still relevanttoday in assessing variation in evolutionary responses among popula-tions (for example, Jacobs and Latimer, 2012)
This may become important in the future, and even today in conservation of endangered species to be able to allow co-habitation of endangered animals, and humans in a new anthropogenic environment.
The reliability of environmental cues is of criticalimportance for plasticity to be favored within and across generations(Scheiner and Holt, 2012). With reliable cues and machinery to sensethe environment, phenotypic plasticity can reduce mismatches, andthereby enhancefitness
This is important, even in historically Heterogeneous environments, as humans are instituting the same types of massive environmental changes over enormous landscapes that don't even follow natural boundaries. Even in phenotypically plastic species, the types of changes humans are creating (like toxicity, or loss of habitat) may not be surmountable.
A possible approach to the complexity of the human microbiome variability and disease risks is to obtain longitudinal data from multiple cohorts in global studies from which subjects developing any diseases throughout their lifespan are excluded, and only the healthy subjects (lacking a disease phenotype) are considered.
I really don't know how I'd feel about excluding the diseased from such a study. What if healthy and unhealthy people share extremely similar microbial communities? It's impossible to know without gathering the data. That being said, seeing if healthy individuals have similar ratios of similar microbial communities at similar locations could open the door on understanding probiotics in the human gut a little wider.
he idea of freezing healthy stools and using them to restore after antibiotic treatment has not been implemented but seems ecologically plausible.
While this is a promising treatment, and the ^ article above is a very specific circumstance, as we develop new treatments based on new science, one must always try to consider the blowbacks. Every technology has the potential for harm.
6 months under the selective pressure of milk shaping the gut microbial communities, whose metabolites promote peripheral regulatory T-cell generation.51 Bacteria given to germ-free mice induce germinal centres (lymphoid cells) to produce IgA+ B cells.52Bacterial molecules also induce mucosa-associated lymphoid tissue of the intestine, via Toll-like receptors, and shape the intes-tinal Th-cell mediated immunity.53 Thus, antigen-driven priming/activation, polarisation and expansion of naïve T cells yield Th1 and/or Th17 effector cells,54 which enter the systemic circula-tion and home to the gut to help destroy the invading patho-gens.55
So, wait a minute, is this saying the the microbes are promoting new white blood cells in the infant's immune system? The next question I have is, Does the transmitted immunity of the mother stay in the gut, or circulate systemically in the baby?
Crazy thought that can't be correct: The antibodies in the mother's milk are used to stimulate B-cell specialization in the infant's circulatory system via microbial prompting.
Herbivory did not affect the number of inflorescences (Figure S1; GLMM: χ2 = 2.20, df = 5, P = 0.821) nor the number of flowers (Figure S1; GLMM: χ2 = 1.47, df = 5, P = 0.916). Flowers had an average display area of 1.0 cm2 and length and width of 1.2 × 1.0 cm. Herbivory affected the display size of flowers (Figure S2; generalized linear model [GLM]: χ2 = 46.3, df = 5, P < 0.001), and flowers of plants infested with P. xylostella were 18% larger than flowers of uninfested plants (Tukey's post hoc tests, P < 0.001). Herbivory affected several shape characteristics of flowers (Figure S2), such as major chord length (GLM: χ2 = 36.5, df = 5, P < 0.001), minor chord length (GLM: χ2 = 25.3, df = 5, P < 0.001), aspect ratio (GLM: χ2 = 11.7, df = 5, P = 0.039), solidity (GLM: χ2 = 14.9, df = 5, P = 0.011), and convexity (GLM: χ2 = 12.7, df = 5, P = 0.026). Herbivory did not affect flower eccentricity (LM: χ2 = 5.4, df = 5, P = 0.368).
All figures presented here are useful to my proposed experiment, even if they did not show herbivore-correlated changes.
Herbivory affected the surface area of petals (Figure S3; GLM: χ2 = 40.9, df = 5, P < 0.001), and petals of plants infested with L. erysimi or D. radicum were 7% larger than uninfested plants (Tukey's post hoc tests, P = 0.008 or P = 0.010, respectively). Herbivory affected several shape characteristics of petals (Figure S3), such as major chord length (GLM: χ2 = 79.0, df = 5, P < 0.001), minor chord length (GLM: χ2 = 37.3, df = 5, P < 0.001), aspect ratio (GLM: χ2 = 52.3, df = 5, P < 0.001), and eccentricity (GLM: χ2 = 59.0, df = 5, P < 0.001). Overall, petals of herbivore‐infested plants had smaller aspect ratios and eccentricity than had uninfested plants, caused by shorter (A. rosae and B. brassicae) or broader (P. xylostella, L. erysimi, D. radicum) petals. Despite changes in petal size caused by all herbivores, only flowers of plants infested with P. xylostella had larger display size and smaller solidity than had uninfested plants.
Again, all relevant to my proposal.
gene–culture co-evolution
Sometimes called dual-inheritance evolution. Basically, this theory applies to human behavior in culture. It states that the genomics of a population can be dependent on cultural biases rather than strict evolutionary behaviors. For example: If being a green-eyed red-head became the most prized possession of traits (though both are the rarest) then over time, cultural breeding for these traits will shift our gene pool in their favor.
niche construction
This is where the behavior of a species creates an ecological niche where it can flourish. Beavers that block rivers with a dam is a perfect example of niche construction.
This establishes the gut microbiota–brain axis as an essential regulator of neurodevelopment, acting bidirectionally: the gut microbiota produces neuroac-tive compounds that influence the brain, and the brain acts on gut and immune functions that help to shape the gut’s microbial population
There have been studies done on mice that look at changes in preference for types of food in developing pups. I wonder if the bacteria present in the gut used this mechanism to lead some of them to alter their food preference away from their mother's food type to a different type made available to the pups. And if it happens in mice, does it happen to us?
Thus, the innate immune system may have evolved not only for defence, but also because of the need to recognize complex communities of beneficial microor-ganisms and to maintain homeostatic relationships with them
I wonder if any studies have been done to see if bacterial cell membrane proteins can alter after anchoring in a developing intestine to become "immune" to the host's defense system.
SchulzandcollaboratorsstudiedpatternsofgeneticandDNAmethylationdiversityanddifferentiationbetweenwildpopulationsfromadjacenthabitattypeswithrespecttolightavailability(i.e.floodplainmeadowvs.alluvialwoodlandfringe).TheyfoundastronggeneticstructurebetweenV.eliatorpopulationsirrespectiveofthegeographicaldistances(i.e.noIBDpattern)mostlikelyduetohighselfingratesandsmallpopulationsizes,bothfactorspromotingge-neticdrift.Conversely,differentiationinDNAmethylationpatternsbetweenpopulationswassignificantlylowerandbetterrelatedtohabitatconditions,whichstronglysuggestsanenvironmentallyin-ducedepigeneticconvergencebetweenpopulations.Inaconserva-tioncontext,thesepopulationsshouldbeconsideredasdifferentESUsthatcanbeecologicallyexchang
This is fascinating. So, even though there is high conservation of the genome in this species, there is very little difference in the epigenomes of these two populations of plants, despite the different environments. This may show that genetics plays at least as strong a factor in the epigenome as the environment.
Althoughageneticbasisun-derlyingsuchadaptivechangeinshellmorphologycannotcompletelyberuledout,thesefindingsstronglysupporttheemergingideathat,insomecases,variationinDNAmethylationpatternscancompensateforalackofgeneticvariationandmayprovidenon-negligiblesupportforadaptation(Verhoeven&Preite,2
This clonal DNA study is perfect for the inspection of epigenetic mechanism on phenotype in different environments. This study (if done with corresponding DNA alteration studies) supports how fast phenotype can be altered in different environments. It can happen in just one generation; and if it will happen with animals, seeing this type of adaptive transformation in plant life as well could be explained via the same mechanism.
Inthesamevein,Sheldonetal.(2018)foundsimilardegreesofgeneticandDNAmethylationdifferentiationbetweenthreeinvasivepopulationsofhousesparrow(Passer domesticus)inAustraliaoriginatingfromthreeindependentintroductionevents
This is very fascinating for epigenetics as a field, and for my use in discovering the phenotypic fallout of different stimuli via the epigenome. Here, there are ostensibly the same species of bird entering the same environment, but from different paths. This one difference seems to be all that is needed to alter and vary the epigenetic difference in these sub-populations.
Geographicallyisolatedandgeneticallydifferentiatedpopulationsinhabitdifferentecologicalhabitats.BothgeneticdifferentiationandDNAmethylationdifferentiationareexpectedbetweenpopu-lations.PatternsofgeneticandDNAmethylationdifferentiationcancoincideifthevarianceinDNAmethylationprofilesisunderstronggeneticdeterminismorifpotentiallocaladaptationinvolvedtheco-segregationofsomegeneticandDNAmethylationpatterns
This may be an incredible factor in the future. We are on the cusp of an anthropogenic mass extinction, and the transplantation of species (especially Island species) may determine their fate. With this piece of information, conservationists can theoretically better predict the outcome of the epigenetics of that species in a new environment.
Integrative approaches offer much that current practices do not. Integration facilitates the generation of new hypotheses and new questions because representatives with an array of expertise communicate with one another about general but complex issues.
Another potential advantage that should be listed here is the ability to contrive of future problems before they occur. Imagine if Silent Spring was anticipated from DDT before it actually occurred. How many future environmental disasters could this approach stave off?
One example of integrative efforts that bears a different label is that of “systems biology.”
Systems biology is the holistic studying of biological system, or organisms as larger wholes. This is in contrast to reductionism, which is studying the larger biological system or organism by breaking it down to it's smaller, individual functioning components (organism->organ system->organ->tissue->cells, etc.).
This type of study might be seen as a precursor or forerunner to integrative biology. In my opinion, it seems to be on a much smaller scale, however.
Read more at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3067528/#__sec3title Under the section titled: Emergence of Systems Biology.