User:Oberlin.24/sandbox

Topic

 * How has the evolution of eye morphology progressed in convergent ways among genetically disparate species? – Cephalopods, et al

Reference Summaries
 * This article provides the example of convergent evolution between octopi and trout eyes in their morphological functions. The article then continues with additional information on how ecological environments could have swayed selection for these convergent eyes.
 * This article is an overview of the evolution of the camera eye in coleoid cephalopods compared to other molluscs as well as explaining the convergent evolution present with the camera eye and the eyes of several vertebrates. It first starts by referring to the information known about common ancestors in order to identify genes which may be involved in the process of the formation and function of the coleoid cephalopod camera eye. An experiment was then conducted to expound on this information through the use of a transcriptomic analysis to determine the genes involved in the evolution of the camera eye.
 * A discussion on the gene expression of octopus and human eyes within a comparative context which was conducted in order to understand the molecular basis of the convergent evolution shared between them. The experiment within the study on their similarity established that 729 non-redundant gene ESTs of the octopus eye match with commonly expressed human eye ESTs. The authors then suggest that a large amount of conserved genes and similar gene expression may be the link to their convergent evolution.
 * This article states that it is important to study Mollusca in order to gain a better-rounded understanding of the eye and how different diseases affect it rather than ceding to the traditional Drosophila model for each study. Molluscan optical systems display a similarity in their “basic visual processes, physiology of vision, development of the visual system, and evolution.” It is easily inferred then, that studies such as these should occur because of the convergent evolution present between the Mollusca and humans.
 * This article begins as a general overview of differentiation between various molluscan eye types. It then goes on to describe how these eye types fit into a general step-wise evolutionary pattern that results in a convergent eye with many other species through example cases.

Assignment 2 - October 1st
https://en.wikipedia.org/wiki/Cephalopod_eye Suggestions
 * 1) While the article discusses how the cephalopod eye vs. the vertebrate eye forms, it doesn’t discuss why this is a comparable analysis – information should be added that this is a comparison due to their similarity of adapting to have the camera-eye trait which would be the example of their convergent evolution.
 * 2) There is almost absolutely zero information on the morphology of the eye of the cephalopod. In conjunction with this problem, the diagram showing the internal structure of the eye and the dialogue which accompanies it is only informative on the vertebrate eye and includes no true information about the octopus eye next to it. The diagram should be corrected and should include more information about the cephalopod eye, or be replaced with a better diagram and description. There should be more information included concerning the morphology of the eye in the article itself, such as what parts are included in a cephalopod eye and what are not. An example of this would be that several cephalopods, including octopuses, lack a cornea.
 * 3) As the cephalopod eye is a common example of convergent evolution there should be more information added about how it is representative of a convergent evolution on the page, including a link back to the convergent evolution page. More examples of vertebrates which show convergent evolution could also be added to enhance the article such as a convergent evolution of cephalopod and trout or other fish eyes, as well as information on the convergent evolution of cephalopod and human eyes.

Sentence + Citation
 * For the past 140 years, the camera-type cephalopod eye has been compared with the vertebrate eye as an example of convergent evolution, where both types of organisms have independently evolved the camera-eye trait and both share similar functionality.
 * Serb, J., & Eernisse, D. (2008). Charting Evolution's Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution. Evolution: Education & Outreach, 1(4): 439-447.

Final Draft
'''How has the evolution of eye morphology progressed in similar or convergent ways among genetically disparate species, cephalopods et al.? – A discussion of parallel vs. convergent evolution'''


 * From Darwin to modern day, evolutionary types, including convergent evolution, have been a hot topic due to the confusing and difficult matter of understanding the phylogenetic relationships between taxa, leaving a greater amount of polytomies within phylogenies unresolved. Depending on the methodology accepted for a study, a taxon’s relationship could be much closer in relative time to another taxon than what would have been accepted with a separate methodology. In the past, this phylogenetic taxonomy was limited to traits such as morphological features, behavioral, and reproductive patterns to determine absolutely the ‘closeness’ of taxa in evolutionary time, but with the advent of genomic sequencing through the study of DNA sequences, this process has become much more effective in dealing with uncertainty between taxa while creating more uncertainty between others. This is due to the recognition that while species may not be related by lineage with a common ancestor, they may independently acquire an analogous (similar according to form and/or function) part due to natural selection affecting them in a similar way according to their similar environments; a convergent evolution (Bergstrom et al., 2012).


 * While many studies have benefitted from this new information, none of the studies have been as crucial to the understanding of convergent evolution as what has been revealed within the study of ocular morphology through evolutionary time between cephalopods and vertebrates. While the exact form may be dissimilar, both of these types of organisms are bilaterally symmetrical and possess the same basic assemblage of parts in what is known as a ‘camera eye,’ although not all bilateral organisms possess a camera eye (Kozmik et al., 2008). The camera eye consists of an iris, a circular lens, vitreous cavity (eye gel), pigment cells, and photoreceptor cells that translate light into nerve signals which travel along the optic nerve to the brain (Serb 2008). Some small differences between the structures exist, such as differing types of photoreceptors as well as cephalopods lacking a cornea (Serb & Eernisse, D. 2008). Overall, the comparison of this morphology between cephalopods and vertebrates is remarkably similar. This morphological evidence begs the question: how has the evolution of eye morphology progressed in convergent ways among these genetically dissimilar species? What is the evidence that this is a matter of convergent evolution?


 * These questions are important to keep in mind when considering the ocular traits, as some scholars believe the evolution of these commonalities is due to a parallel evolution rather than a convergent evolution. Even with genetic information concerning developmental genes which affect the eye being applied, the justification of whether ocular morphology evolution as seen between cephalopods and vertebrates is truly a convergent evolution remains murky. Whereas convergent evolution was stated as an independent evolution of traits where natural selection affected the taxa in a similar way in their similar environments, parallel evolution is defined as an evolution of traits of similar taxa toward a similar endpoint, at a similar sequence of events, sometimes after diverging from a common ancestor, and is generally associated with closely related lineages (Fernald 2006; Serb & Eernisse, D. 2008).


 * The main problem between the distinction of these two concepts deals with how the phylogeny is constructed and understood. Confusion regarding the relationships between taxa over a long stretch of evolutionary time can make it ambiguous whether a trait arose due to parallel or convergent evolution. This confusion is present in determining whether the evolution of the camera eye between cephalopods and vertebrates is truly convergent or if it is parallel evolution.


 * Despite the large majority of researchers believing that the evolution of the camera eye is a convergent evolution, there is an ever-present collection of researchers that believe that it is in fact an example of parallel evolution. A representative study of this would be Gehring’s study of Pax genes in 2004 where the study of modern and ‘ancestral’ Pax genes was used to determine whether an ancestral linkage was present to both cephalopods and vertebrates today. The discovery that the development of the eye in bilateral organisms is almost entirely initiated from the gene, Pax6, lead more researchers to believe that all eyes of all bilateral organisms came from a common ancestor with this related genetic path (Gehring 2004; Nilsson 2004), especially after seeing that a phylum which many taxa have branched off from, cnidarians, also possessed Pax regulatory genes.


 * Nilsson (2004) explains that the controversy between parallel and convergent evolution of eyes can be easily picked apart when looking at the problem from a comparative physiology of the eye vs. developmental genetics of the trait perspective. Although this genetic link exists (the presence of Pax genes in earlier evolved phyla such as cnidarians), Nilsson states that this cannot refute the evidence of other regulatory/developmental genes which, while common between species, differ in how they regulate the development of the eyes in the organism (Gehring 2004; Nilsson 2004). The example given is the homologue of the hh signal in Drosophila, the Shh signal in zebrafish. While both signals turn off Pax6, hh is crucial to eye formation in Drosophila while Shh is only needed for the spacing of ganglion cells in zebrafish, suggesting that rather than a parallel sequence of evolution toward the same endpoint, a convergent evolution is most probably what is occurring (Nilsson 2004). Considering how these signals affect developmental genes such as Pax6’s expression is an important step in determining homologous cell-types for eyes vs. analogous cell-types for eyes. Even this evidence cannot be absolutely certain to determine a convergent evolution, although there may never be enough evidence for such certainty to occur.


 * A study of acquisition of Pax6 splicing variants by Yoshida et al. in 2014 concurs with the previous idea that the evolution of the camera eye among cephalopods and vertebrates occurred through convergent evolution. “In bilaterian animals, the presence of splicing variants or duplicated loci of the Pax6 gene is known to be important for eye formation,” and these variants are often created through the addition of exons into the genetic code (Yoshida et al. 2014). Through the use of multiple types of PCR testing on sample DNA of cephalopods, and by then comparing it to vertebrate splicing variants, Yoshida et al. found that the 5 variants of Pax6 discovered must have arose independently in cephalopods as compared to vertebrates due to their differential evolution of variation (Yoshida et al. 2014). The splicing variants of both cephalopods and vertebrates were then placed in a lineage-specific manner to cross-check, and it could be seen that the Pax6 variants evolved according to the insertion of exons into the PST domain (the transactivation region of Pax which is enriched with proline, serine, and threonine) until both reached analogues of Pax6 as seen in modern vertebrates and cephalopods (Yoshida et al. 2014; Singh et al. 2001).


 * This type of independent evolution can also be seen through a gene expression profile of ESTs (expressed sequence tags) based on frequency of occurrence of mRNAs in an octopi camera eye study, where 1,052 non-redundant genes of the eye itself had a match within the protein database (Ogura et al. 2004). To get a better scope of this, Pax6’s homolog six3 would have been one such gene within this large amount. Six3 is the expressed gene in octopi, while Pax6 is conserved, unlike in other cephalopods. By having these genes listed within a known parameter for function within the protein database, they were then able to be used to compare with 13,303 pre-known ESTs of the human eye to determine a commonality of ESTs between the two, of which there were 729. When comparing ESTs of the octopi eye with human ‘tissues other than eye’ ESTs to check for other homologies, the results were significantly low. These results mean that the similarities between these two kinds of organisms stem only from the analogous camera eye, and there is no significant genetic similarity in other ways (Ogura et al 2004). At this point in the study by Ogura et al. it was crucial to understand the genetic commonality of ESTs of octopi camera eyes with the last common ancestor between octopi and humans. Depending on the significance of the similarity, this value determines the mechanism of the evolution: namely if it was convergent or parallel. While it was confirmed in the study that the ESTs for camera eyes between octopi and humans were conserved within the genome of their last common ancestor (which would signify a parallel evolution) the way the conserved genes were expressed as the camera eye was wholly natural selections pressure on the two discrete taxa, as the conserved genes could have likely been expressed in any number of other ways, confirming that the evolution of the camera eye of cephalopods and vertebrates was through convergent evolution (Ogura et al 2004).


 * While the study of the convergent evolution of the camera eye is interesting to study for knowledge’s sake, there are many crucial benefits to society that studying this evolution presents as well. While typically a laboratory setting uses Drosophila for most experiments concerning eyes because of the significantly shared genetics for development they share with humans, Serb puts forth the idea that species or taxa with convergent, analogous traits should be used in such settings, with cephalopod analysis replacing the Drosophila analysis. Studies of analogous traits could give a more accurate evaluation by considering how evolutionary time has shaped the trait, especially concerning important medical studies of the human eye such as disease occurrence, prevalence, and protection. Despite the limited amount of data per species of cephalopod available, the study of cephalopod eyes provides an evolutionary outlook for the study of the human eye; to see at a genetic level what determines the phenotype of the eye (Serb 2008). Another boon of experimenting with cephalopod eyes is that cephalopods can regenerate their eyes due to their ability to re-enable their developmental processes, allowing studies of the same cephalopod to continue past one trial sample as well as allowing a more complex study of how regeneration may be conserved in the genome alongside the genes expressing for camera eye (Serb 2008).


 * It has been concluded that although there was once a common ancestor between cephalopods and vertebrates where common genes and proteins may have at one time arose, which would underlie a parallel evolution, this common ancestor was significantly older than the discrete taxa now presented. This organism has since been found to have preceded the evolution of the camera-eye in cephalopods by 270 million years, as well as preceded the evolution of camera eye in vertebrates by 110 to 260 million years ago, which represents a significantly varied evolutionary gap (Fernald 2006). Other contributions to this would be the varied ways in which natural selection would have acted upon the conserved and expressed genes of the two taxa throughout evolutionary history. Similar environments would introduce similar pressures, culminating in the convergent expression of camera eyes in cephalopods and humans. This progression of convergent evolution in cephalopods and vertebrates has allowed for a better understanding of convergent evolutions in general and has provided society with a beneficial representative example for future medical use.

References Cited

Bergstrom, C. T., and L.A. Dugatkin 2012. Evolution. New York: Norton. G-1—G-8.

Fernald, R. D. 2006. Casting a genetic light on the evolution of eyes. Science, New Series 313(5795):1914-1918.

Gehring, W. J. 2004. Historical perspective on the development and evolution of eyes and photoreceptors. Int. J. Dev. Biol. 48:707-717.

Kozmik, Z., J. Ruzickova, K. Jonasova, Y. Matsumoto, P. Vopalensky, Iryna Kozmikova, H. Strnad, S. Kawamura, J. Piatigorsky, V. Paces, and C. Vlcek 2008. Assembly of the cnidarian camera-type eye from vertebrate-like components. Proc Natl Acad Sci U S A 105(26): 8989–8993.

Nilsson, D-E 2004. Eye evolution: a question of genetic promiscuity. Current Opinion in Neurobiology 14(4): 407-414.

Ogura, A., K. Ikeo, T. Gojobori,, M. L. Sogin, and G. J. Olsen 2004. Comparative analysis of gene expression for convergent evolution of camera eye between octopus and human. Genome Research 14(8):1555-1561.

Serb, J. M. 2008. Toward Developing Models to Study the Disease, Ecology, and Evolution of the Eye in Mollusca*. American Malacological Bulletin 26:3-18.

Serb, J., and D. Eernisse 2008. Charting Evolution's Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution. Evolution: Education & Outreach 1(4): 439-447.

Singh S., L. Y. Chao, R. Mishra, J. Davies, and G. F. Saunders 2001. Missense mutation at the C-terminus of PAX6 negatively modulates homeodomain function. Human Molecular Genetics 10(9):911-918.

Yoshida, M.-a., K. Yura, and A. Ogura  2014. Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants. Scientific Reports 4(4256).

Additions to article
https://en.wikipedia.org/wiki/Cephalopod_eye Additions

Preview

 * They have a camera-type eye which consists of an iris, a circular lens, vitreous cavity (eye gel), pigment cells, and photoreceptor cells that translate light from the light-sensitive retina into nerve signals which travel along the optic nerve to the brain.
 * Contention exists on whether this is truly convergent evolution or parallel evolution.

Research and medical use

 * The main medical use emerging in this field is for research on eye development and ocular diseases. New research studies on ocular gene expression are being performed using cephalopod eyes due to the evidence of their convergent evolution with the analogous human eye. These studies replace the previous Drosophila studies for gene expression during eye development as the most accurate, although Drosophila studies remain the most common. The conclusion that they are analogous lends credibility to their comparison for medical use in the first place, since the trait in both would have been shaped through natural selection by similar pressures in similar environments; meaning there would be similar expression of ocular disease in both organisms’ eyes.
 * An advantage of cephalopod eye experimentation is that cephalopods can regenerate their eyes due to their ability to re-enable their developmental processes, which allows studies of the same cephalopod to continue past one trial sample when studying the effects of disease. This also permits for a more complex study concerning how regeneration may be conserved in the cephalopod genome and if it may be somewhat conserved in the human genome alongside the genes expressing for the camera eye.

Evolutionary debate

 * Disagreement on whether the evolution of the camera eye within cephalopods and within vertebrates is a parallel evolution or a convergent evolution still exists, although is mostly resolved. The current standing is that of a convergent evolution for their analogous camera-type eye.
 * Those maintaining that it is a parallel evolution state that there is evidence that there was a common ancestor containing the genetic information for this eye development. This is evidenced by all bilaterian organisms containing the gene Pax6 which expresses for eye development.
 * In contrast, those supporting a convergent evolution state that this common ancestor would have preceded both cephalopods and vertebrates by a significant margin. The common ancestor with the expression for camera-type eye would have existed approximately 270 million years before the evolution of camera-type eye in cephalopods and approximately 110 to 260 million years before the evolution of camera-type eye in vertebrates. Another source of evidence for this is the differences of expression due to independent variants of Pax6 arising in both cephalopods and vertebrates. Cephalopods contain five variants of Pax6 in their genome which independently arose and are not shared by vertebrates, although they allow for a similar gene expression when compared to the Pax6 of vertebrates.