Grad Core- Week 2: Thoughts on body size and/or extinction ?
Hi all. The topics for our section in paleoecology this week are body size and extinction. Please post comments on the papers assigned and/or things said in lecture.
p.s. Jonathan Payne responded to your posts - his replies are in the comments
Ok, so maybe I'm behind everyone else on 'getting it', but after reading "Body Size, Eneregetics, and Evolution" I finally started to understand what we've been talking about.
ReplyDeleteThe way the article was worded helped me finally understand the basis of the metabolic ecology equations we have been talking about for weeks now. It was very beneficial (to me, at least) that the concepts & equations in the paper were stated very clearly, simply, and had clear examples of their basis/application.
After weeks of struggling to understand something that just looked like a bunch of random math with pie-in-the-sky reasoning that got so frustrating that I pretty much gave up on it, I'm actually looking forward to reading more about the subject now-- which is a significant improvement over the last few weeks.
I kind of wish I had seen this paper weeks ago-- I think I would have gotten more out of everything else. :-/
I am sure the analysis has been done, but in class today I was wondering if humans (well maybe not today) follow Bergmann's rule. Size of European vikings vs South American natives for example?
ReplyDeleteI agree, this paper should have been read a long time ago. I have been keeping up pretty well with what Felisa Smith has been discussing, but this would have certainly helped put Jim Brown's lectures into perspective.
ReplyDeleteIn the article, "Body size, energetics, and evolution" Smith wrote, "True deviations from predicted values can provide important insights into evolutionary history and adaptation."
I would like to comment on this by saying that I was initially stuck on the notion that the trend line and the proportionality constants had to perfectly and accurately account for the data. I initially viewed the scatter plots that did not have consistent, tight fit to the trendline as flawed and as evidence of the lack of practicality modeling had. I have since become more interested in what causes that variation- what is it about a particular animal that allows it to have traits outside a predicted value?
Payne & Finnegan 2007: Seeing that geographic range is selected upon during extinction events, I wonder what the underlying mechanism could be. That is, is it selectively eliminating those organisms that do not have a pelagic lifestyle, or at least pelagic larvae? If so, how does having a more complex life-cycle alter ecology?
ReplyDeleteRaup & Sepkoski: This paper also got me thinking about what is under selection during extinction events. The paper presented extinction quantities based on families, but I wonder how that would look if “families” were changed to trophic level (very coarse: producer, herbivore, carnivore), or age of family?
Payne et al. 2009: I really liked this paper –it infers a mechanism behind the trend towards larger body size in the fossil record.
Smith et al. 2010: How fun! I find it interesting that biotic methane additions rival those of abiotic methane levels (post-Younger Dryas
Alyssa, I don't know if work has been done on humans following Bergmann's rule, but some cool work has been done looking at adaptation of humans to colder climates. For instance, Inuits have fat in their fingers to keep them warm and useable!
ReplyDeleteAn anthropologist, Christopher Ruff, has conducted a number of studies of Bergmann's and Allen's rules in humans; he finds they conform quite well. He uses these findings to make inferences about ancient human morphologies. Look for him on Google Scholar
ReplyDeleteSmith, Body Size...:
ReplyDeleteAlyssa, I felt the same way you did at first, back when Jim was first getting into scaling. It seems like a macroecological perspective takes a little getting used to because it is working on such a large scale of investigation--a bit different than what we're used to. I thought Jim did a great job of reminding us often that it isn't necessarily the pursuit of THE factor, but the most important factor among many that is most directly responsible for patterns we may find. And I'm beginning to be a believer in body size as perhaps the most important phenotypic variable with regard to an organisms' ecology.
I didn't realize Bergmann's Rule was originally framed in terms of species within a genus and over time rather than latitude. I think it makes good sense to think of it in a phylogenetic and historical context rather than purely phenotypic plasticity over a gradient. I wasn't sure which interpretation of Bergmann's Rule Figure 4 was using, though. A question I had related to this is if larger body size is favorable in cold climates, then why are there so many more small animals than large in the arctic? Perhaps considering the fossil record would resolve the issue?
Payne et al. 2009:
I thought the coolest thing about this paper was the idea of body size as an adaptive trait, a way to diversify. However, it seems like this fact was overlooked somewhat in the discussion of Figure 2. While I realize it wasn't the direct focus of the article (maximum body sizes), Figure 2 shows that not all groups keep on increasing in body size over time. This suggests other factors like competition or perhaps selection for smaller size play a major role in determining the size of organisms. Not that the article denies this point, I just think it could have been emphasized to show the importance of size in general, besides simply maximum size.
Also, where do clonal organisms fit into the calculation of "World's largest" living things? I have been told that there is a clonal aspen tree somewhere that is technically the single largest organism because it's clonal root sprouts cover more than a square kilometer or something enormous...
I also wanted to share this relevant link to an NPR.org story...Watch the video for a body size scaling surprise!
ReplyDeletehttp://www.npr.org/blogs/thetwo-way/2010/10/22/130758623/scientists-reveal-how-fast-dogs-must-shake-to-dry-their-fur
Thanks for the comments on human body size and adaptations, I will look into those ideas.
ReplyDeletePayne and Finnegan; Raup and Sepkoski. What caught my attention was the idea of how the rates of both extinction and speciation must be considered. Is a rise in the number of families, genuses, etc due to a decrease in extinctions, an increase in origination, or a combination. While scientists may be focused on what extinction event caused a particular decrease in families over time, maybe some attention should be payed to what caused speciation to decrease.
Also, I am curious about how extinction and origination rates vary between marine, freshwater, and terrestrial habitats.
I like Meghan's idea about the geographic range depending on life cycle- Great point!
Smith et al. 2010;
ReplyDeleteWhat an interesting paper! Figure 1 was convincing enough for me, but they really put a lot of effort in making sure they had complete data sets and rigorous statistical support.
I recently read a pop science article that said researchers have genetically modified some grasses to have less lignin which would make it easier for cattle to digest, thus resulting in less methane production. This made me wonder what was the natural vegetation the mega-herbivores were eating, and how does the lignin and cellulose content compare to what mega-herbibores ate previously and modernly. Is plant community and composition somehow related aswell? (maybe a little far-fetched, but it had me wondering).
Payne et al. 2009;
ReplyDeleteI found figure 2B very interesting in that nearly all of the plant clades have at some point in the rise and fall of their size approached a similar maximum threshold. It is interesting to compare it to 2A, where the chordata line increased rapidly, but stays near the upper bound. What is it about plant physiology and/or ecology that would lead to such variability in size over time and across clades? Why is the same trend not observed in animals?
Smith, Body Size:
ReplyDeleteThis paper summed it all up. The discussion on endothermy was intriguing. It makes perfect sense that this is one of the most important factors in limiting body size in mammals. Endotherms have a competitive advantage yet have size limitations that are defined by being able to keep a constant body temperature.
Matt
I like the paper "Body size, energetics, and evolution" too. This is the "basic" one for people of weak ecological background just like me. There are helpful concepts and definitions, as well as the explanation for roots.
ReplyDeleteI find the island rule interesting. And I wonder if it will also affect plants. Since there's less competition on island, I assume they don't need to grow as high as those in mainland to get more sunshine.
Smith, Body Size...
ReplyDeleteOut of curiosity, I am wondering what the ~100kg endothermic aquatic organism is? Also, as aquatic organisms don't have to deal with this gravity nonsense, why has there not been several events in which a really large aquatic organism (like a blue whale) has evolved? Or has there been? Shouldn't our blue whale have some big friends to play with?
Additionally, I am wondering whether all of these metabolic scaling data are corresponding to adults? How does scaling differ between species through ontogeny? For example, Fig.2 graphs mass to metabolic rate. Is this relationship constant throughout ontogeny for all these organisms? Particularly for organisms that do not exhibit exogenous feeding for their entire life cycle...(there's my nod to fishes)
Fig.4- I have to wonder about the reliability of this data. The number of species tested seems to be inadequate to make this type of assertion. The fish data, for example, is based on 18 sp! This is appx. 0.0006% of extant fishes.
Payne and Finnegan 2007.
ReplyDeleteSummary: Having a large geographic range reduces your risk of extinction during "business as usual" background extinction; however, it doesn't seem to help much during mass extinctions.
I can rationalize this in my own mind because the causes of the big five were "global catastrophies". In contrast, run of the mill extinction appears to work on more regional scales.
I know the paper addressed this, but I would be wary of their interpretation of some of those negative log-odds values because of problems in the rock record. Using the number of named rock formations as a proxy for completeness of the rock record is okay, but has some problems.
The proxy dataset they used comes from Peters and Foote 2001 and is a dataset for North America alone, and Payne and Finnegan 2007 are discussing global phenomena. I also question whether this long term trend holds up under shorter geologic intervals, specifically the Frasnian-Famenian of the late Devonian. This time period has a particularly depauperate rock record, and an even worse fossil record. The log-odds value they calculate for the end Devonian is also among the most negative calculated. I find this suspect 1) because it has such a lousy record anyway and 2) Raup and Sepkoski 1982 were only sort of able to identify it as a "mass" extinction in the first place without massaging the data.
I'll just point out that the end Devonian is weird, so that might be all the explanation you really need. The extinction may be fundamentally different from the others, and probably is.
I can logically work out in my head what would cause positive and zero log-odds values in Payne and Finnegan 2007; either range size helps you (+) or it doesn't matter (0). But, I have a hard time imagining a mechanism that would lead to an increase in probability of extinction with greater range size (-). Without a proposed mechanism, I'm less convinced that the negative values are "real". But past experience tells me that if you can't imagine something, you need to think harder.
In response to Alyssa, Payne et al. 2009
ReplyDeleteI don't know that it's really fair to directly compare plants and animals. They're two entirely different things in this sense. They are responding to the same laws/variables (gravity etc.) but have two functionally different ways of doing so. Where we have bones, exoskeletons etc, they have lignin and cellulose. Where we have blood and veins and guts, they have xylem and phloem.
Perhaps it's just that we have yet to see a serious decline in animals like that shown for plants. Animals might just be operating on a different time scale since they are altogether more complex organisms.
Payne and Finnegan, 2007
ReplyDeleteSummary:
Having a large geographic range reduces your risk of extinction during business as usual background extinction. However, it doesn't help you during mass extinctions.
Log-odds values of 0 make sense for mass extinctions because these events are global catastrophies. By contrast, background extinction seems to work on more localized to regional scales.
Payne and Finnegan, 2007
ReplyDeleteCaveats:
1. Rock formation names are a good proxy for “rock record completeness”; however, the data for this proxy from Peters and Foote, 2001 is for North America alone. Payne and Finnegan, 2007 is addressing global phenomena.
2. The above stated proxy may not hold up for all geologic intervals, I’m specifically referring to the end Devonian (Frasnian-Famenian).
3. The Frasnian-Famenian has a lousy rock record; and an even worse fossil record.
4. The most negative log-odds value calculated by Payne and Finnegan, 2001 is for... the Famenian.
5. Raup and Sepkoski, 1982 were only able to identify the end Devonian extinction as being a statistically different from background extinction after ignoring the other big 4 and running their analyses again. So why the big negative log-odds value?
Payne et al., 2009
ReplyDeleteA quantitative analysis and synthesis of what paleontologists have been be casually observing via "visual inspection" for a long time.
Smith, F.A. 2007. Body size, energetics and evolution.
ReplyDeleteI think this article provides many reasonable understanding of the basic concepts in ecology. I like the way to explain words by breaking them into prefix/suffix and root. Especially it gives reasonable deductions about body size, energy and food acquisition. The explanation for “each gram an animal the size of a mouse uses 20 times more energy than a gram of elephant ” describes that different animals have different ways (better digestion enzyme or longer digestion pipes) to deal with low quality food such like plants. This gives a critical understanding of the evolution of herbivore animals.
I am curious about a question: is there any genomic analysis or molecular evolution work done about body size related or determine genes, or energy generating/consuming genes or gene network?
Payne et al. 2007 (Geographic range & extinction risk)-- The modeling used benthic marine species. Could this same concept be applied to land-based organisms? (plants, animals, etc)
ReplyDeleteLiow et al. 2008 -- I found it surprising that large mammals had a lower taxa 'survival' rate. Again, since it was a particular order they studied (Mammalia) I am curious as to if the same pattern will hold in other orders, especially in the plants-- pre- & post- the rise of the angiosperms.
Smith et al. 2010-- Cool take on an issue that is relevant to current affairs. The rationale & math/stats are well reasoned & well demonstrated.
Jablonski 2008-- I liked that they were quick to point out what they used for a model, why and that it most likely wouldn't work in other systems.
Payne and Finnegan 2007
ReplyDeleteThough I don't have nearly the knowledge base that Melissa has, I'm with her on this one! Just reading the paper it didn't seem very definitive in the assertion that having a large geographic range reduces the risk of extinction during background extinctions. I know little about the actual data, but the wording in the paper, and the weakness pointed out by Payne and Finnegan of the fossil record at certain times makes me rather suspect of such a broad hypothesis. After reading Mel's comments, the flaws become more evident!
Payne et al 2009
Though we talked about this in class, this paper really drove the point home. How cool is it that such huge jumps in size occurred over such short periods of time. The tie-in to "biological potential and environmental opportunity" at the closing of the paper is a great phrasing of a concept that I think many people have a hard time grasping. I think that many people focus on either the environment or changes in biological processes when discussing evolution, and I think Payne et al did a beautiful summarizing of the importances of both in regards to the huge jumps in size.
Raup and Sepkoski 1982
For me, this paper raised the question of what is the driving force? Why would there be a change from extinctions to increasing diversity from the Early Cambrian? I wish they would have expanded on this question.
Smith 2008
I'm with everybody else on this one! This paper would have been great to read earlier, because it made it all seem more relevant. I do agree with Brooks, in that Jim did a really good job of making the connections, but I think this paper would have been great at the very beginning of his section because it took me a few classes of him saying it mattered for it to really sink in! It also made the math a lot less scary. Also, the readability of this paper makes the topic very approachable.
Smith et al 2010
This paper was really interesting. While people often talk the anthropogenic effects on methane production, by cattle ranches in particular. I had never thought about the effects of losing huge numbers of methane producers in the mega-herbivore extinction. One thing that I'm not quite understanding is how did the methane levels reach such a high concentration at the end of the Youger Dryas?
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ReplyDeleteHi all - I'll try to address a few of the comments regarding the Payne and Finnegan 2007 paper.
ReplyDelete1. Rock formation names are a good proxy for “rock record completeness”; however, the data for this proxy from Peters and Foote, 2001 is for North America alone. Payne and Finnegan, 2007 is addressing global phenomena.
Two points here. First, the Peters and Foote data are N. America, but they track quite well with global diversity. This is in part because most of the well-sampled marine fossil record derives from N. Am. and Europe. Second, and perhaps more importantly, we're not interested in variation in absolute geographic range. Rather, we're asking how differences in geographic range are associated with extinction probability. Thus, unlike studies of diversity, there expectation for the influence of change in sampling on selectivity is not obvious.
2. The above stated proxy may not hold up for all geologic intervals, I’m specifically referring to the end Devonian (Frasnian-Famenian).
3. The Frasnian-Famenian has a lousy rock record; and an even worse fossil record.
I understand the impulse to mistrust poorly sampled intervals. But, what is the expectation for selectivity of a poorly-sampled record? Because the analysis is about differential effect of range on survival, all we are assuming is that genera with larger sampled ranges had larger true ranges, regardless of the absolute values involved. This makes the approach relatively insensitive to variation in rock record quality.
4. The most negative log-odds value calculated by Payne and Finnegan, 2001 is for... the Famenian.
This value is very close to, and indistinguishable from, zero. I don't think we'd want to call it negative.
When we ran the initial analyses, we did get negative values for parts of the Mesozoic when we included ammonoids. This makes sense when you think about it. Ammonoids have a pelagic adult habitat, broad geographic range, and rapid turnover rates (perhaps in part because they are used for biostratigraphy). Consequently, they create a dataset where the broadest-ranging taxa had the highest extinction rates. However, we feel that this analysis is mixing apples and oranges due to the differences in ecology between benthic and planktic organisms. Overall, I think the biggest question about our analysis is the extent to which we are combining taxa with such different ecologies that the results could come from unexpected mixing effects.
I hope this is helpful!
Jon
Very helpful. I'm glad we have the chance to think about rocks and fossils critically.
ReplyDeleteMethane Emissions from Extinct Megafauna - 2
ReplyDeletethis paper was so computational that the purpose and outcome were deeply shaded. In the first paragraph there is an indication of a potential hypothesis for humans being the reason for the 80% drop out of large-bodied mammals. I felt the purpose was stated a bit late in the paper, to evaluate the influence on the methane cycle of the sudden loss of all of these mammals. The method was to estimate their annual enteric methane production. I liked how the authors used a new method for evaluation. Turns out there was a big drop in the methane levels and is was correlated with the extinction of New World megafauna. It was also predicted that novel mechanisms were at play during this particular methane decrease because it was so fast.
Mass Extinctions in the Marine Fossil Record - 2
ReplyDeleteThis paper is full of statistics, assumptions, and speculation. The purpose was to gather fossil data and investigate major extinctions, this paper found four to be qualitatively distinct in the marine realm as compared to background extinction levels. I liked how the paper states problems with extinction records from the beginng; precise timing and magnitude are hard to measure, fossil records are fragmented, comprehensive and accurate data are unobtainable, there are sampling limitations and taxanomic uncertainty. This data was more complete as it took into account all taxanomic and stratigraphic investigations to date. Data was assessed at the level of family.
Two-phase increase in the max size of live over 3.5 bil yrs reflects biological innovation and environmental opportunity - 2
ReplyDeleteThis paper determined a pattern and timing for the 16 orders of magnitude body size increase over the last 3.5b yrs. The authors describe Bonners first attempt, and note that he had no fossil records to base his findings on. One of the future goals of this paper was to shed light on the constraints on the evolution of body size. I thought it was a neat approach to change mass into volume for comparative analysis. The pattern was found to be two ‘jumps,’ one in the Paleoproterizoic Era, and the other in the Neoproterozoic Era. I thought it was cool that the largest living organisms are not much bigger than the largest known fossils.