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Humans have had a definite effect upon a diverse array of species. In his paper entitled, “Loss of speciation rate will impoverish future diversity”, Michael Rosenzweig discusses the effects of human presence upon the macroevolution of species. One of the papers arguments is rooted in the idea that human intervention and development is directly contributing to a lower speciation rate. Rosenzweig claims that this can be traced to the reduction of natural areas which has caused species with naturally wide geographical ranges to consolidate into smaller areas, reducing isolation due to potential geographical barriers, and genetic variability. Both of these factors contribute to speciation events, and when disrupted due to human activity their absence could severely limit such diversification events.

However, the very notion that humans act as the world’s greatest evolutionary force in one of swollen egocentrism.

Life on earth has been estimated to have been developing for the last 3.7 billion years. Humans reached full behavioral modernity merely 50,000 years ago. The majority of the human impact upon nature has occurred within the past 150 years with the advent of technology. Currently, the extinction rates are 100 to 1000 times the background extinction rates previously observed in earth’s evolutionary history.

While this is obviously no small feat, it encompasses a minute dimple in the time scale of the earth and it’s biological diversity; compared to the Permian- Triassic extinction event which is believed to have caused the extinctions of approximately 96% of all marine species and over 70% of all land species, human influence pales in comparison.

While the human impact upon evolution is certainly grandiose in our own eyes, it is by no means the greatest force to hold sway over the intricacies of evolution.

 

References:

For more information regarding the human impact on evolution, please refer to: Rosenzweig, M., 2001. Loss of speciation rate will impoverish future diversity. PNAS. 98(10): 5404-5410.

The study of the evolution of human traits such as behavioral characteristics and culture is a difficult task. Unlike morphological features, such traits present no direct physical relics of their previous forms, causing extrapolations and educated conjecture to dominate the field of study.

Thus, the argument that cultural evolution possess Darwinian properties, though intriguing, is debatable. In their paper,  Mesoudi, Whiten and Laland argue that human cultural evolution can be assessed by the same basic principles cemented by Darwin in his theory of natural selection. The research group defined culture as the collection of beliefs, values and knowledge that was “inherited through social learning”. Elments of culture

However there are certain behaviors integrally tied with culture that depreciate the fitness of an individual. Smoking tobacco and consuming unhealthy foods are both prime examples of cultural activates that lead to a reduction in individual health and reproductive abilities.

Suicidal practices are also an interesting cultural component to assess in terms of Darwinian selection. Seppuku is a term describing the ritual suicide practices of samurai. The ritual disembowelment was viewed as a way to honorably submit to death. Today, Japan has one of the highest suicide rates in the world and culturally, suicide is often portrayed as morally acceptable and honorable, though the recent upsurge in suicide packs has sparked media and public discourse over the proliferation of such practices.

The paper briefly addressed this phenomena, stating that “cultural traits will not necessarily promote the inclusive fitness of the humans expressing them (Cavalli-Sforza and Feldman 1981). In the same way that parasites can manipulate behavior to their own ends (Moore 2002), cultural variants that exhibit high rates of (nonvertical) transmission (such as smoking) can spread whether or not they enhance fitness and promote adaptation in the individuals who adopt them.” Yet it goes no further to address the reasons behind the self induced fitness depreciating behaviors.

References

For more information regarding the evolution of human cultural variants, please refer to: Mesoudi A., Whiten A., Laland K., 2004. Perspective: Is human cultural evolution Darwinian? Evidence reviewed from the perspective of the Origin of Species. Evolution. 58(1):1-11.

The inclusive fitness of an individual organism is comprised of two components:

1. The successfulness of reproduction and thus the organism genetic contribution and proliferation in the next generation.

2. The number of equivalents of the organism offsrping that share genetic similarities and thus impart the genetic mark of individual into the next generation. Such offspring are gleaned by cooperative behaviors.

Kin selection is a term coined regarding the apparent prioritization of the survival and reproduction of an individual organisms relatives even at the cost of the individuals own survival. The evolution of such a seemingly “altruistic” behavior in different species has puzzled evolutionary biologists and still remains a subject of great debate.

I believe that the model system proposed by Nowak, Tarnita, and Wilson does an adequate job at describing some of the behaviors observed in certain species such as honey bees or certain types of wasps, however there is still probably many components of the behavior mechanisms which we do not yet understand. Thus the model probably will be expanded upon in the near future.

The alternative model proposed in the paper has its merits and potential, and did a good job at ascribing reasons and a evolutionary force behind social species groups. The authors explained that kin selection and inclusive fitness are advantageous to species that survive in close knit environments where cooperation and group living is a staple in life.

References:

For more information please refer to: Nowak, Tarnita, and Wilson, 2010. The Evolution of Eusociality. Nature.  466: 1057-1062.

Male redback spiders place their bodies near the mouth of their female mating partner, in an act of apparent tacit compliance regarding the female’s post-copulation cannibalistic practices. In her paper, Andrade argues that such actions are evidence of an adaptation amongst male spiders that excites a willingness to undergo such predation as it increases their chances of successfully mating.  This observed behavior is especially interesting as it most likely has little impact upon the gestation of the female; the male spider’s small size limits the amount of nutrients his body could provide, thus severely limiting any paternal effort effects upon the female.  The paper suggests that the longer copulation time available to a male that commits suicide results in a higher paternity rate.

I believe that such behavioral characteristics could potentially be an adaptation that has been naturally selected for throughout generations. Male spiders that committed suicide had higher paternity rates, and thus a greater relative fitness compared to those that did not. I believe it would be interesting to discover if there is a genetic basis to this behavior.

Another particularly striking example of sexual selection is the reproductive practices of ducks. Male ducks have large phalluses, typically ranging around 40 centimeters in length, which are supported by lymph. Additionally, unlike most birds, whose oviducts a tubular in structure, the female duck has a complex winding vaginal track, comprised of spirals, branches, and crevices.

The present theory behind these strange morphological characteristics is the forced copulation practices among waterfowl.  In a study conducted by Dr. Patricia Brennan in affiliation with the Department of Evolutionary Biology at Yale University, male ducks that had been selectively bred to have larger phalluses, were able to penetrate an artificial vaginal tract, while wild type ducks were unable to copulate. The study provided supportive evidence that the male duck phallus size is directly related to individual fitness.

References:

For more information regarding redback spider sexual cannibalism, please refer to: Andrade, M., 1996. Sexual Selection for Male Sacrifice in the Australian Redback Spider. Science. 272(5245):70-72.

For more information regarding duck reproductive habits, please refer to: Laskin, M. 2010. Unraveling the Mysteries of Duck Mating. Yale Scientific Magazine. http://www.yalescientific.org/2010/09/unraveling-the-mysteries-of-duck-mating/

 

Review of Literature

 

  1. Introduction the viral relics in the human genome. What they are and where they came from-

 

  • 8% of the human genome is composed of retroviral relics.

 

  • It has been estimated that the human genome contained roughly 31 different families of virus.

 

  • Retroviruses replicate a DNA intermediate, called a provirus, that becomes integrated in the host organism’s genome. If such integration occurs in a cell that gives rise to gametes, the retroviral insert DNA can be inherited.

 

  • Some groups have been able to analyze retroviral insertions, such as those originating from the Hepadnaviridae family and determine the time at which the insertion occurred. In their paper, Gilbert and Feschotte examined Hepadnaviridae insertions within the zebra finch genome.

 

  • The determined that the Hepadnaviridae insertion was at least 19 million years old.

 

  • The Hepadnaviridae family is composed of small viruses with genomes that are partially double stranded DNA. Hepatitis B virus is within the Hepadnaviridae family.

 

  • Additionally, some viruses that contain DNA genomes and replicate within the host cell nucleus also have been known to leave “fossil” relics.

 

  • The pararetroviruses have left numerous copies of viral DNA segments within plant genomes

 

  • Similar activities have also been reported in  flaviviruses with the mosquito host, totovirus-like and M2-killer-like viruses in fungi, and gemini-like viruses in tobacco. “Conservation of integrated sequences in plant genomes might indicate benefits for the host during evolution.” (Staginnus, 2006).

 

  • “The recent discovery of multiple endogenous bornaviruses and filoviruses in diverse mammals showed that these single-stranded RNA viruses were able to infiltrate repeatedly the germline of distant mammalian species over at least the past 40 My” (Gilbert, 2010),

 

  1. Introduce the study of paleovirology. What it is and why it is useful and problems within the field-

 

  • Paleovirology is an emerging field which examines exogenous ‘fossil’ virus insertions within the host genome. It allows researchers to examine the evolutionary history of such viruses, as well as further the understanding between the selective pressures behind the evolution of host immune systems.  In a study regarding foamy viruses within sloth species,  “our analysis highlights the role of evolutionary constraint in maintaining viral genome structure and indicates that accessory genes and mammalian mechanisms of innate immunity are the products of macroevolutionary conflict played out over a geological time scale.” (Katzourakis, 2009).

 

  • It is also useful for understanding the long-terms evolutionary tendencies of extant viruses.

 

  • Though the field is new, its potential is multifaceted and could have many implications in the study of evolution. Currently researchers are working to answer several questions, such as the role of prehistoric viruses in evolutionary transition events, the role of mutation rates on population dynamics, as well as determining whether correlated positive selection for specific antiviral genes within the primate phylogeny depicts responses to the same viral pathogen.

 

  • It is often difficult to estimate the age of different viral lineages, due to their absence in the fossil record. The fossil record refers to DNA samples taken from prehistoric human specimens, as well as the viral fossil relics within the modern human genome. Natural selection plays a definite role in cleansing potentially problematic exogenous DNA insertions.

 

  • It has also proved difficult to study viruses that have left relatively no trace of their existence within the human genome. However, researchers have recently discovered traces of a bornavirus gene that inserted itself into mammalian hosts several times throughout evolutionary history.

 

  1. Proposal.

 

  • One of the prevailing questions within the field of paleovirology is how prehistoric viruses shaped modern life. The proposed project will investigate the potential relation between viral pressures and immune system development, as well as potential viral influence over evolutionary transitional events.

 

Methodology

 

  • Different groupings of species will be chosen based upon commonalities between immune systems.

 

  • Such commonalities will be assessed by sequence and functional similarity of specific cytokines, cytokine receptors, MHC I receptors, antimicrobial peptides secreted within the mucus and lymphocytes.

 

  • The genomes of such organisms will then be examined in attempt to detect similarities between retroviral elements as well as any other viral relics maintained within the DNA.

 

  • Studies such as the one conducted by Gilbert and Feschotte utilize an array of techniques to determine the point in evolutionary history in which the viral insert emerged.  They utilized “cross-species analysis of orthologous insertions, molecular dating, and phylogenetic analyses to demonstrate that hepadnaviruses infiltrated repeatedly the germline genome of passerine birds” (Gilbert 2010). Such techniques could be similarly applied to the proposed project.

 

  • The admission of such elements will then be dated, so as to estimate at which point the insertion originated. This will then be compared to known evolutionary history as well as the known development of immune system characteristics.

 

Expected Results

 

The expected results could vary. It would not be unreasonable to assume that certain pathogenic pressures helped shape immunity. However, whether or not this will be depicted through the retroviral elements present within host genomes is uncertain.

It would be interesting if such pressures also helped trigger the development of specific morphological features that protect against infection, such as mucus membranes, and impermeable barriers such as skin.

 

Bibliography

 

For more information on the conflict between species definitions, please refer to:  Hey, J., 2001. The mind of the species problem. Trends in Ecology and Evolution. 16 (7 ): 326-329.

 

“Paleovirology Expanded: Non-Retroviral Virus Fragments Found in Animal Genomes.”ScienceDaily. ScienceDaily, 18 Nov. 2010. Web. 02 Apr. 2012.

 

Katzourakis, A., Gifford, R., 2010. Endogenous Viral Elements in Animal Genomes. PLoS Genetics. 6(11): e1001191.

Gilbert, C., Feschotte, C., 2010. Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses. PLoS Biology. 8(9): e1000495.

Duffy S, Shackelton L. A, Holmes E. C, 2008. Rates of evolutionary change in viruses: patterns and determinants. National Review Genetics. 9: 267–276.

Holmes E. C, 2003. Molecular clocks and the puzzle of RNA virus origins. J Virol 77: 3893–3897.

Bannert N, Kurth R, 2006. The evolutionary dynamics of human endogenous retroviral families. Annu Rev Genomics Hum Genet 7: 149–173.

Staginnus C, Richert-Pöggeler K. R., 2006. Endogenous pararetroviruses: two-faced travelers in the plant genome. Trends Plant Sci 11: 485–491

Katzourakis A, Gifford R. J, Tristem M, Gilbert M. T. P, Pybus O. G, 2009.  Macroevolution of complex retroviruses. Science 325: 1512.

 

Scientists have been disagreeing regarding the true definition of a species for decades. The biological species concept claims that a species is defined as a population that is capable of interbreeding and producing fertile offspring. However, sometimes a more precise definition is required, and thus species is defined by similarities in DNA, ecological niche’s or morphological traits.

Image from: Gómez, J., Verdú, M., Perfectti, F., 2010. Ecological interactions are evolutionarily conserved across the entire tree of life. Nature. 465: 918–921

Hey discusses the reasons behind the ‘species conflict’, providing several observations on his opinions as to why such an issue regarding definition persists in the scientific community. He claims that taxonomical classification is a subjective science; the patterns and devices scientists utilize to place different taxa vary depending on individual perception. He also claims that, “The patterns of similarity that we recognize are the remnants of former evolutionary groups that might have long since shifted and splintered.” Additionally, when describing said evolutionary groups, due to science’s obsession with precision and quantification, many try to delineate between different groups, and draw clear cut boundaries between them. However, this is ineffective, as such boundaries may not exist in nature; “real evolutionary groups need not be distinct”.

Hey’s points regarding our failures of describing a species indicate an important point; a precise definition may be impossible to create and furthermore, unnecessary. Due to the aforementioned underlying problems, we might never fully grasp what truly defines a species, however as long as we describe what it means in the context of a particular study, such a shortcoming should not prove inhibitory.

References:

For more information on the conflict between species definitions, please refer to:  Hey, J., 2001. The mind of the species problem. Trends in Ecology and Evolution. 16 (7 ): 326-329.

Quantitative trait loci (QTL) mark sections of an organism’s genome, either specific sequences of DNA or chromosomal segments, which are believed to be responsible for trait variation.

I found Barton and Keightley’s discussion regarding variation and mutation throughout natural populations particularly interesting, especially in references to topics which we have already discussed in class. They state that in order for a variation in an allele to remain circulating within a population for a prolonged period of time, its actual effect upon an organism must be small and it must be present at a number of different loci. This abundance then increases the chances of the trait being inherited as it would be included within several gametes.

In regards to mutation, the paper states that “it is now clear that mutation rates for quantitative traits are high enough to make a substantial contribution.” Barton and Keightley continue on, explaining that mutations of small effect take a long time to become fixed within a population; however mutations that contribute a large effect “contribute to the selection response” within the population in a much shorter time span. Furthermore, the authors claim, “Mutations of large effect are expected to contribute even more in bigger populations, because the total number of mutations available to selection is proportional to the population size.” However, these mutations if they have a large effect upon the fitness of the organism, will only be present in the population for a small number of generations.

This discussion of QTL variation and mutation lends itself to the topic of punctuated equilibrium. Only small changes remain circulating within the population, contributing to a net stasis. Conversely, mutations in QTL’s that produce large effects and vary greatly from the established trait, will be have a large selection response, however they will only last amongst the population for a short time period, hindering the idea of phyletic gradualism supported by such continuous changes.

References:

For more information regarding QTL, please refer to: Barton, N., Keightley, P., 2002. Understanding Quantitative Genetic Variation. Nature Reviews, Genetics. 3: 11-21.

Grant Topic

Paleovirology is the study of viral fossils, DNA insertions of viral origin found within a modern host organism. For instance, the human genome contains a vast array of retroviral relics, which combined comprise approximately 8% of the human genome (Emerman, 2010). Additionally, it has been estimated that the human genome contained roughly 31 different families of virus. While such endogenous remnants offer direct windows to the primitive viruses they once composed, paleoviruses can also be inferred through examining the selective evolutionary pressures on modern immune systems.

It would be interesting to amass an array of genomes from varying species and examine their genomes from similar retroviral elements. If similarities were present, it could mean that some ancestral organism was infected by the paleovirus which it then incorporated into its genetic code. If such relations existed it could provide additional framework for phylogenetic relationships, as well as potential interesting insight into the pressures upon the developing immune systems within the different species.

Additionally, it would be interesting to investigate any effect highly pathogenic viruses have upon populations. Outbreaks that demolished large portions of a population would result in rapid evolutionary changes or allopatric speciation.

The grant proposal addresses decent with modification and molecular environmental pressures that shape modern populations.

 

References:

Emerman M, Malik HS (2010) Paleovirology—Modern Consequences of Ancient Viruses. PLoS Biol 8(2): e1000301. doi:10.1371/journal.pbio.1000301

 

Dark Fly

I found an interesting paper.

“Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. Using next-generation sequencing technology, we determined the whole genome sequence of Dark-fly and identified approximately 220,000 single nucleotide polymorphisms (SNPs) and 4,700 insertions or deletions (InDels) in the Dark-fly genome compared to the genome of the Oregon-R-S strain, a control strain. 1.8% of SNPs were classified as non-synonymous SNPs (nsSNPs: i.e., they alter the amino acid sequence of gene products). Among them, we detected 28 nonsense mutations (i.e., they produce a stop codon in the protein sequence) in the Dark-fly genome. These included genes encoding an olfactory receptor and a light receptor. We also searched runs of homozygosity (ROH) regions as putative regions selected during the population history, and found 21 ROH regions in the Dark-fly genome. We identified 241 genes carrying nsSNPs or InDels in the ROH regions. These include a cluster of alpha-esterase genes that are involved in detoxification processes. Furthermore, analysis of structural variants in the Dark-fly genome showed the deletion of a gene related to fatty acid metabolism. Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation.”
Abstract from: Izutsu M, Zhou J, Sugiyama Y, Nishimura O, Aizu T, et al. (2012) Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment. PLoS ONE 7(3): e33288. doi:10.1371/journal.pone.0033288

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0033288.

My first proposal idea is to examine the evolution of the virus. I believe this would be a topic because there is a sizable amount of research regarding the retro-viral involvement in the evolution  of life. The genomes of several different species would be analyzed, searching for relics of retro-viral DNA.  These would then be compared in an attempt to date when they originated. This would fall under the category of a “dream proposal”.

My second idea would be researching the evolution of intelligence. This would involve examining relics of prehistoric man and changes in the cranial structure of different humanoid transitional fossils.

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