BIO 345
Design a hypothetical experiment to determine whether greater virulence is advantageous in a horizontally transmitted parasite or in a vertically transmitted parasite.
Greater virulence will be advantageous to a parasite despite its mode of transmission if increased virulence also increases fitness. Generally, greater virulence will increase the reproductive rate of a horizontally transmitted parasite but at the cost of increased risk of mortality for the host (and thus the parasite). The key to a successful experiment to determine advantage is to measure whether reproductive rate or risk of mortality increases faster.
Which species in the genus, Homo, was resemble humans more than earlier hominins? why?
Homo habilis resembled modern humans more than earlier hominins, with a flatter face, shorter tooth row, humanlike hand, and greater cranial capacity. Although its limbs suggest an ability to climb, its legs and feet show that its walk was nearly human. H. habilis made stone tools (habilis means "handy man"), and animal bones with cut marks have been found with its fossils. Homo erectus in many respects, erectus had the anatomy and behavior of modern humans. Its skull was rounded, its face projected less than in earlier species, and its teeth were smaller. Importantly, its cranial capacity was larger, about 1000 cc (see the figure above and below).
What might account for decline in extinction rates?
Species become better adapted by natural selection over time, and so should become less vulnerable to changing environments. The average number of species per genus and per family seems to be greater in the Cenozoic than in earlier eras. Another explanation is that some clades are more volatile than others: they have a higher turnover rate, evolving new families and losing others before the entire clade becomes extinct.
Explain how ascomycete fungus Ophiocordyceps infect Camponotus leonardi ants?
Parasitic fungi manipulate ant behavior to complete their own reproductive cycle.
Parsimony, maximum likelihood, and Bayesian inference are different analytical techniques for developing phylogenies from DNA sequence data. Why would a researcher choose one method over another? What are the advantages and disadvantages of the three methods?
Parsimony-based methods are computationally simple, compute rapidly, and usually produce good results. Methods like bootstrapping and other resampling techniques allow one to calculate statistical support for nodes. However, they do not allow more sophisticated analysis, such as estimating rates of sequence evolution. Parsimony methods can give erroneous results easily as homoplasy is rampant. Parsimony would be favored when computation time or ability is limited and finding a single "best" tree is the goal. Maximum likelihood (ML) can incorporate explicit models of sequence evolution (including changing rates), yield precise branch lengths, and support predictions of ancestral character states. However, it is computationally intensive, so the processing can be slow, especially for large data sets. It also can be biased when incorporating non-random data like morphology. ML would be used by researchers with small data sets or for whom computation power is not a constraint, who need explicit estimation of the likelihood of ancestral character states, and who require branch lengths and statistical support for each node. Bayesian approaches use the Bayes equation to explore "parameter" space rapidly; it can evaluate many models similarly to maximum likelihood. It also has the advantage of the use of "prior probabilities" which allow a research to use existing evidence (such as morphological data) to weight resulting trees. However, Bayesian results can be heavily influenced by model choice and the prior probabilities (for that reason, many researchers choose to forgo prior probabilities and begin with an assumption of equal probability for all possible trees). Because Bayesian algorithms randomly explore parameter space, they need a lot of time to run and there still may be uncertainty as to whether the best possible trees were considered in the analysis. Bayesian methods can produce multiple trees, with each tree's relative probability.
What were the conclusions from studies about cognitive ability?
All the evidence says that people of different ethnicities do not differ genetically in cognitive ability.
How can Outgroups be helpful?
An outgroup can give you a sense of where on the bigger tree of life the main group of organisms falls. It is also useful when constructing evolutionary trees.
What characteristics of a meme would enhance its fitness (its reproduction or survival)?
Any characteristic that motivates a human host to communicate it, enhances its reproduction. Some memes do this through humor - we are more likely to spread a funny joke than a non-funny joke. Other memes do this through outrage or being interesting. Also, some features of memes help or hinder us from remembering them and faithfully replicating them. Simple, clear memes survive better than complicated, subtle memes. Memes that play to our evolutionary psychology, and appear to be relevant to human reproduction and survival, tend to be better remembered than memes that have nothing to do with sex and death.
Why do we use bootstrapping in phylogenies? When do we often use it?
Bootstrapping is often used with parsimony, to randomly discard some of the data and then reestimate the phylogeny. Bootstrapping is often used to assess the degree of confidence in the individual branches of a tree.
Why did the same changes not evolve in the chimpanzee lineage?
Chimpanzees have likely lived in forest habitats during all of their evolutionary history, and so they have not experienced selection that decreases their ability to climb.
What factor of phylogenies enable us to determine that all terrestrial mammals are quadrupedal (walk on all four legs) except humans, the one bipedal twig on the many branches of the mammalian tree?
Common ancestor/inferring the state in each common ancestor/trace the evolution of organisms' characteristics
Which of the major events in the evolutionary history of memes involved an increase in the reproduction rate of memes? Which involved an increase in the survival of memes?
Communication The invention of written language
Explain reinforcement of reproductive isolation
The evolution of stronger prezygotic isolation because of selection against low fitness hybrids is called reinforcement. Not all types of isolating mechanisms can evolve this way. Alleles that strengthen prezygotic isolation gain an advantage because individuals with them have higher fitness than do those that hybridize. But stronger postzygotic isolation usually cannot evolve by natural selection.
Discuss the two hypotheses of the evolution of the human brain.
The first is ecological. This hypothesis suggests that selection favored learning how to function in complex environments, for example while hunting. A second, proposed by anthropologist Robin Dunbar, is the social brain hypothesis. Dunbar reasoned that living in complex social groups selected for large brains, particularly enlargement of a region called the neocortex, which is responsible for learning, memory, and cognition.
How does fossil record help in Phylogenetic studies?
The fossil record, enable biologists to piece together the evolutionary history of organisms and their characteristics, ranging from DNA sequences to geographic distributions. They document patterns of evolution—aspects of change that are common to many groups of organisms.
Explain one example of zombie in human.
Toxoplasma gondii is a well known mindsucking parasite which is infected the brain of its host and has the ability to modify the brain and behavior of its host. It widespread by infecting its rodent host. Research confirms that the infected rat by Toxoplasma loses their fear of cat because for the next step of their life cycle they have to get inside the gut of a cat, then they will be hunting by the cat and this parasite is transferred to the human by having contact with a cat. The association between parasite-brain interaction and movement disorders, epilepsy, cancer, and Alzheimer's disease has been identified through "disease-deconvolution"
What are evolutionary trade-offs?
Traits that confer a fitness advantage may also have a fitness cost relative to another environmental factor.
Neanderthal fossils were first discovered in the nineteenth century. Study of their morphology suggested that Neanderthals were more closely related to humans than any living species of primate. Much later, it became possible to sequence DNA from Neanderthal fossils and compare the sequences to those from other primates. Did the results confirm or refute the earlier conclusions based on morphology? Explain.
Comparison of DNA sequences from chimpanzees, Neanderthals, and living humans confirms the earlier conclusions based on fossils. Sequences from Neanderthals are much more similar to those from humans than either is to sequences from chimpanzees.
What is ecological speciation?
is the process by which ecologically based divergent selection between different environments leads to the creation of reproductive barriers between populations.
In situations when DNA sequences are not available, which source can be used as a phylogenetic data?
morphological data
Why many taxa continued to dwindle long after the main extinction events while others, often members of previously subdominant groups, diversified?
During mass extinction events, taxa with otherwise superb adaptive qualities succumbed because they happened not to have some critical feature that might have saved them from extinction under those circumstances. Both abiotic and biotic environmental conditions were probably very different after mass extinctions than before.
What changes in environmental conditions in Africa might have selected for a less arboreal lifestyle in the human lineage?
During the evolution of hominins, the landscape in East Africa became increasingly open (dominated by savannah), which may have selected increasingly for walking upright at the expense of the ability to climb.
estimates of species diversity on a worldwide basis
Estimates of species diversity are likely to change if the PSC is used. In particular, one would expect the number of species to increase. This is because individuals from divergent allopatric populations that can potentially interbreed would belong to the same species under the BSC. These same organisms would be classified as members of different species under the PSC.
Rates of evolutionary change measured overshort time intervals are often very high. However, rates of evolutionary change measured over long time intervals are generally much lower. For example, see the discussion of body mass in mammals. Should we expect this pattern to hold true for most characters? Does this pattern imply that the evolution of major new characters, such as the wings of bats, should occur very rapidly?
Evolutionary histories are rife with change, stasis, and reversals. The pattern described is commonly seen in many organisms and will apply to many organismal features. Comparisons of two points of a lineage may show a change, but in between there will certainly also be periods of stasis. The evolution of novel characteristics might occur rapidly. A new trait that provides a benefit will likely have immediate impact and refinement through natural selection. Once it arrives at a local fitness maximum, we would expect to see stasis.
Why are the direct and indirect applications of evolutionary biology so important?
For medicine and public health than in any other area.
What evidence shows the most recent common ancestor of chimpanzees and humans was much more arboreal than are modern humans?
Fossils of early hominins such as Ardipithecus had features (e.g., opposable big toes, arms long relative to legs) that are adaptations to climbing. These features are shared with chimpanzees, showing that the ancestor of humans and chimpanzees also had these features.
What is the 'hygiene hypothesis'?
A hypothesis that suggests the environments of Western children are unnaturally clean, dramatically decreasing their exposure to routine microorganisms.
What is the difference between a passive and an active trend?
A passive trend is strong constraint in one direction An active trend is "bias" in direction
What happened to The brain volume of hominins through time?
Average brain size increased throughout hominin history.
Behavioral expression depends on what factors?
Human behaviors are affected both by our genetic evolutionary heritage and by culture.
When conditions change, what determines whether a species can adapt fast enough to avoid extinction?
If a new trait that helps the species survive is heritable favorable then the species can evolve towards the new optimum value that maximizes survival.
Some pathogens, such as HIV, can be transmitted both vertically and horizontally. How do you expect their virulence to compare with that of pathogens that are transmitted only horizontally or only vertically?
If all else is equal, we generally expect pathogens that are only transmitted vertically to be less virulent (or even benign), and those that are only transmitted horizontally to be more virulent. Pathogens that are transmitted both horizontally and vertically are expected to have virulence that is intermediate between those extremes. In fact, HIV does show intermediate virulence: it makes its host sick, but typically only after a period of months to years.
studies of species diversity in ecological communities
If the PSC is used, phenotypic and DNA sequence data would be sufficient to identify the species that make up a community. Comparisons of species differences among communities, or among samples from different localities, might be affected because more allopatric populations might be called different species, hence lower species overlap between regions would be recognized.
discourse on the evolutionary mechanisms of speciation
In contrast to the biological species concept (which focuses on reproductive isolation), the phylogenetic species concept focuses on clusters of diagnostically distinct organisms that share common ancestry. Mechanisms of reproductive isolation are important to the BSC (such as whether isolating barriers are premating, prezygotic, or postzygotic). If the PSC were used, there would be less focus on reproductive isolation and greater emphasis on the identification of clades. Research on mechanisms of speciation would be focused on how population differences arise by mutation, drift, and selection.
What do you understand by the term "complexity"?
Organisms taken together show a passive trend toward greater complexity, no characteristic displays a consistent driven trend among all, or even most, branches of the tree of life.
Briefly discuss the evolutionary time machine.
It is now possible to sequence the ancient DNA from skeletons unearthed by archeologists. By comparing them with sequences from people still living in the same place, we can see for the first time directly how gene frequencies changed in time.
What is a memeplex?
Memes band together in mutually reinforcing communities, and begin reproducing as a unit.
What are the differences between cultural and genetic inheritance?
Most important, cultural traits can spread quickly by horizontal transmission, that is, between individuals of the same generation. Horizontal transmission does occur rarely with genes, but it can be orders of magnitude faster with cultural traits.
Between Neanderthals and Denisovans which of them has contributed the advantageous alleles to the human gene pool that affect the skin and immune traits?
Neanderthals
Distinguish between the rate of speciation in a higher taxon and its rate of diversification. What are the possible relationships between the present number of species in a taxon, its rate of speciation, and its rate of diversification?
Rate of diversification is a function of both origination (speciation) and extinction. Rate of speciation is only a measure of origination. The present number of species we observe in a taxon could be the result of either high or low rates of speciation, combined with high or low rates of extinction. Thus, the present number of species we observe in a taxon reflects that group's overall diversification rate.
conservation practices under such legal frameworks as the U.S. Endangered Species Act
The choice of species concept affects conservation biology. Distinct populations that belong to the same species under the BSC can belong to different species under the PSC. Each of these populations could potentially be classified as an endangered species. Also, hybridization between populations has different ramifications, depending on which species concept is used. Because individuals that belong to divergent populations are not considered part of the same species under the PSC, conservation efforts that involve introducing individuals from different populations are less likely to be utilized. The U.S. Endangered Species Act actually provides for protection of "distinct populations," so in many cases it is used to protect organisms that might be considered "sub-species" under the BSC, but would be classified as separate species under the Endangered Species Act.
Briefly describe the concept of "progress"?
The sense of context-dependent adaptive improvements in species
Heritability is one key criterion for natural selection, but for memes to evolve and adapt what factor is necessary to be in the population? And in what environments they can evolve?
There also must be variation in the population, and that variation must affect the reproduction and survival of the memes.
Some infectious diseases evolve to be less virulent over time (and some more virulent). Here virulence means the amount of damage (and likelihood of death) that the disease causes to its host. Under what conditions would you predict that an infectious disease would become less virulent?
There are two major selective pressures on infectious diseases: survival within the host and transmission to a new host. Some (virulent) diseases destroy their host in the process of transmitting. Others need their hosts to be relatively healthy - it is those that are under selective pressure to evolve to be less virulent. For example, sexually transmitted diseases only get rare changes to transmit, and their host must be capable of attracting a mate. Other examples, like the common cold, require people to be healthy enough to be out of bed and moving around in order to transmit (through sneezing, coughing or touching). This also probably explains why the common cold is not very virulent.
Provide another example of an extended phenotype, aside from a beaver's dam.
When a parasite zombifies its host, it changes the host's behavior to benefit the fitness of the parasite. That modified host behavior is part of the extended phenotype of the parasite.
How does antibiotic resistance develop?
When mutation occurs in the DNA of a gene it could change the protein and cause a different characteristic meaning it is not affected by a particular antibiotic any more
Can there be more copies of a meme in the world than the number of living humans?
Yes
Do memes control our behavior? Are we zombies?
Yes and yes
Which factor affects more on homosexuality?
a largely biological basis
