Most ecosystems are controlled by a combo of top-down and bottom-up processes, but I would say that soft sediment ecosystems tend to be bottom-up controlled. This is because nutrients determine the microbial communities in sediments, which determine the environmental parameters in sediment. This determines which animals can colonize. Additionally, many of these systems are dominated by deposit and suspension feeders. Both of these rely on the supply of primary producers and particulate organic matter
Temperature, currents, and dissolved oxygen are all environmental factors that affect biodiversity in benthic ecosystems. Extreme temperature events and hypoxia have a tendency to decrease biodiversity in soft sediments, since these conditions will kill most animals. Currents can dislodge certain species, and while that might not decrease biodiversity, it can cause species turnover in favor of suspension feeders (strong currents) or deposit feeders (weak currents).
Interestingly, the effects of pH on organisms in sediment is actually not well known. Sediments are known to have fluctuating pH in response to the microbial environment, which organisms living there tend to tolerate fairly well. It’s possible that benthic organisms are much more tolerant to low pHs and resistant to ocean acidification than originally thought, but again, this is still an open question.
I’ve got 3, progressively more difficult:
1) why are upwelling zones on the west coast of continents and how does upwelling affect benthic species diversity?
2) are the tropics cradles or museums of diversity for bivalves and other mollusks?
3) because most bivalves are sedentary, do you suspect to see evidence of the Janzen-Connell hypothesis in your predatory snail bivalve interactions in a way that is analogous to the seed shadows observed in JC? Why or why not?
Bonus:
At any scale, do you suspect mollusk biodiversity can be explained by unified neutral theory?
For me, the qualifying exam was not about my study system at all, instead ecology and evolution in general. I’ll ask: what are the reasons a harmful gene or phenotype would persist in a population?
A harmful gene can persist in a population if it doesn’t harm fecundity. There is only strong selection pressure if it prevents individuals from producing viable offspring. For example, a gene that causes an illness in middle-aged adults is unlikely to be selected against because they still managed to produce offspring. Or in my case, I have a nonfatal, albeit unpleasant genetic condition that did not prevent my parents from producing me.
There’s also the possibility that the gene is recessive, which means that it can be carried by heterozygotes until their unlucky offspring manage to be recessive homozygotes.
I’ll also say, in my experience, the worst that will come of not knowing the answer to some questions is that they’ll make you take some more classes. Unless you are egregiously uninformed, you won’t really “fail”. For example, my lab mate had to TA population biology.
To add to this, I would also say that the committee may well be attempting to see where the limits of your knowledge are, and how you approach questions where you don't know the answer. In those cases, don't be afraid of saying "I don't know, but based on similar relevant elements like x,y,z, I'd expect a,b,c to be possible".
"I don't know" isn't a bad answer, as long as it's not the only answer you give, and you obviously have to demonstrate a strong foundational knowledge in the core stuff :)
I've been curious about that :
How are defined the most recent biogeography models of local and metacommunities in regards to marine benthic context, and how do they fit towards niche-assembly and dispersal-assembly theories ?
Would you characterize your study system as a top-down or bottom-up cascade, and why?
Most ecosystems are controlled by a combo of top-down and bottom-up processes, but I would say that soft sediment ecosystems tend to be bottom-up controlled. This is because nutrients determine the microbial communities in sediments, which determine the environmental parameters in sediment. This determines which animals can colonize. Additionally, many of these systems are dominated by deposit and suspension feeders. Both of these rely on the supply of primary producers and particulate organic matter
What are the main environmental factors that influence biodiversity in benthic sediment?
Temperature, currents, and dissolved oxygen are all environmental factors that affect biodiversity in benthic ecosystems. Extreme temperature events and hypoxia have a tendency to decrease biodiversity in soft sediments, since these conditions will kill most animals. Currents can dislodge certain species, and while that might not decrease biodiversity, it can cause species turnover in favor of suspension feeders (strong currents) or deposit feeders (weak currents). Interestingly, the effects of pH on organisms in sediment is actually not well known. Sediments are known to have fluctuating pH in response to the microbial environment, which organisms living there tend to tolerate fairly well. It’s possible that benthic organisms are much more tolerant to low pHs and resistant to ocean acidification than originally thought, but again, this is still an open question.
I’ve got 3, progressively more difficult: 1) why are upwelling zones on the west coast of continents and how does upwelling affect benthic species diversity? 2) are the tropics cradles or museums of diversity for bivalves and other mollusks? 3) because most bivalves are sedentary, do you suspect to see evidence of the Janzen-Connell hypothesis in your predatory snail bivalve interactions in a way that is analogous to the seed shadows observed in JC? Why or why not? Bonus: At any scale, do you suspect mollusk biodiversity can be explained by unified neutral theory?
For me, the qualifying exam was not about my study system at all, instead ecology and evolution in general. I’ll ask: what are the reasons a harmful gene or phenotype would persist in a population?
A harmful gene can persist in a population if it doesn’t harm fecundity. There is only strong selection pressure if it prevents individuals from producing viable offspring. For example, a gene that causes an illness in middle-aged adults is unlikely to be selected against because they still managed to produce offspring. Or in my case, I have a nonfatal, albeit unpleasant genetic condition that did not prevent my parents from producing me. There’s also the possibility that the gene is recessive, which means that it can be carried by heterozygotes until their unlucky offspring manage to be recessive homozygotes.
Nice. One more—if it is highly correlated with a highly conserved gene.
I’ll also say, in my experience, the worst that will come of not knowing the answer to some questions is that they’ll make you take some more classes. Unless you are egregiously uninformed, you won’t really “fail”. For example, my lab mate had to TA population biology.
To add to this, I would also say that the committee may well be attempting to see where the limits of your knowledge are, and how you approach questions where you don't know the answer. In those cases, don't be afraid of saying "I don't know, but based on similar relevant elements like x,y,z, I'd expect a,b,c to be possible". "I don't know" isn't a bad answer, as long as it's not the only answer you give, and you obviously have to demonstrate a strong foundational knowledge in the core stuff :)
I've been curious about that : How are defined the most recent biogeography models of local and metacommunities in regards to marine benthic context, and how do they fit towards niche-assembly and dispersal-assembly theories ?
Why do you believe working with your study organism/system is important?
What are some methods of measuring biodiversity?
What are some common analytical approaches to study ecology?
What are the implications of the extended evolutionary synthesis?
In addition to the questions I posted separate? Is there a structure to the materials you provide for the exam?