Sunday, September 30, 2018

Tomiya 2013

Body Size and Extinction Risk in Terrestrial Mammals Above the Species Level

 Blog Author: Devra Hock

Author:
Susumu Tomiya—Currently postdoc at Department of Anatomy, Des Moines University. PhD at Dept. of Integrative Biology, UC Berkeley. 
            Research Interests: Dr. Tomiya studies evolution and extinction of mammals at various scales of time (hundreds to millions of years) and space (local to continental) to better understand the trajectory of mammalian diversity and place the modern extinction crisis in a historical context.


Summary/Main Points:
1. Main Question:
            Background—Large body size has long been considered to increase the risk of extinction in mammals through long generation time, small population size, and susceptibility to reduction in geographic sizes. Author points to late Pleistocene extinction events, in which large-bodied mammalian species disproportionately disappeared from multiple continents
            Assumptions—There are more large-bodied mammals than small on the IUCN Red List 
-Body size governs many aspects of ecology and  life-history of organisms.  
-Cladograms used are hypotheses proposed by taxonomic experts and are not directly supported by numerical analyses.
            Main Questions—1. Address the relationship between body size and the probability of genus-level extinction, using the rich fossil record terrestrial mammals in North America and focusing on the durations of taxa that became extinct between 28 and 1 million years ago. 
-2. Heterogeneity in extinction selectivity across body-size spectra reported by previous studies can be accommodated by extinction pressures operating at different scales of space, time, and phylogeny. 

2. Methods: 
            Database—North American fossil occurrence data from the Oligocene to present (34 Ma – 0 Ma) compiled from MioMap and FaunMap databases. Genus Homo, volant and aquatic groups, and taxonomic occurrences of unknown or uncertain generic identities, generic occurrences from localities lacking maximum or minimum age estimates, and genera that are represented by a single occurrence were trimmed from the datasets. 
            Methods—Dental measurements for 901 fossil taxa were compiled from the Paleobiology Database and author original data. 
-Comparative analyses were conducted within the framework of generalized least squares regression to accommodate the possible phylogenetic correlations among generic durations. 50% confidence interval estimates for the first appearance dates were adopted as the ages of terminal nodes on the composite phylogeny. 

3. Results:
            -Significantly lower range-through sampling probability was observed for small mammals compared to large mammals in North America during much of the Miocene Epoch (23-5.3 Ma)
            -Large mammalian genera were better sampled during much of the Miocene
            -Sampling in the post-Miocene is roughly comparable between large and small body sizes
            -Values in the latest Oligocene are difficult to compare because of poor fossil records 
            -Western Eurasian mammals show opposite patterns to North America, with the range-through sampling probability smaller for large mammals
            -Phylogenetic signals in genus durations is generally very weak
            -In North America, body size was not included in the best survival model, same survival probability was inferred for large and small mammals
            -In western Eurasia, best supported survival models include body size, indicating higher extinction probabilities of large-bodied mammals

4. Discussion/Summary:
            -Closely related genera do not necessarily share similar extinction probabilities. No single organismal traits, population properties, or ensemble of traits that follow similar patterns of change across phylogeny is likely to have a dominant influence over the persistence of genera. 
            -Estimated boy size of fossil genera were found to be poor predictors of generic durations in most cases
            -Animalivores are the only group for which weak but significant negative correlation was detected between body mass and durations. Correlation becomes nonsignificant when group is split into lipotyphlans and carnivorans for separate analyses. 
            -Size-biased extinctions of animalivores are reflecting generally short durations of carnivorans. Elevated extinction risk of carnivora may be due to lower population densities, lower reproductive rates, and greater geographic range requirements
            -A moderate but clear deviation from the general phylogenetic signals is the elevated signals for the reverse cohort of taxa that became extinct 9 and 5 ma. Principally driven by the loss of closely related ungulates that are broadly united by the timing of their originations and extinctions. Extinctions have been tied to spread of open, arid, grasslands. 
            -The disappearance of large herbivores in the late Miocene accompanied by loss of small mammalian genera
            -Size selectivity hinges on biogeographic and environmental contexts
            -Size biased extinction of mammalian genera do not constitute a general feature of Holarctic faunas in the Neogene. 
                        -Differences in biological properties of North America and western Eurasian taxa
                        -Rapid movement of large mammals out of wester Eurasia
                        -Differences in environmental histories of the two continents relating to biomic heterogeneity and geographic range reduction


Questions:
            I had problems understanding the methods of the phylogenetic analyses. His discussion of the implications and what the results mean was much easier to understand. 
            Overall, I think Tomiya did a good job explaining the results and the data. However, I think there could have been more discussion on the traits that body size influences and how those encourage or discourage extinction. There is some of this broadly in the introduction, but given the results that during the Miocene small mammals were more prone to extinction, a discussion on what traits small body sizes influence. Tomiya talks about larger geographical ranges , low population density, and lower reproductive rates seen in large mammals, but a similar discussion for small mammals is lacking and I thought would have brought some additional implications for paleontology and conservation to the paper. 

Wednesday, September 26, 2018

Paper 18

Brown J.H. and P. H. Nicoletto. 1991. Scaling of species composition -body masses of North American land mammals. American Naturalist 138-1478-1512. 

Blog Author:  Altangerel Tsogtsaikhan

(We have already introduced Dr. Brown's biography)

Background
Biological diversity compositions are varied in different regions. Biotic compositions in different scales caused and affected by different biological processes such as colonization, extinction, and speciation. As we zoomed in, more micro-ecological processes affect in small patches of homogeneous habitats and species interaction and abiotic environmental effects influence species coexistence, and microevolutionary processes such as natural selection and genetic drift in a population level. Both macro and microscopic ecological and evolutionary processes composite the continental and regional community. This paper analyses the North American terrestrial mammal composition using body size and spatial scale.

The main question: what is the macro compositional pattern of the North American terrestrial mammal based on the body mass across different spatial scale?

Methods: Three different spatial scales of terrestrial North American mammals were used including the entire NA continent with Mexico, 21 biomes (Dasman, 1975) and 24 small patches of homogeneous habitats. The North American and Mexican species list was obtained from Hall 1981 and Ramirez-Pulido et al. 1968. Species list of local habitats were collected from the variety of sources including some unpublished work. Bats were not included. Single body mass was assigned for each species (obtained from field guides (Burt and Grossenheider 1976, Whitaker 1980). Kolmogorov-Smirnov Dn statistic was used.

Results/discussions: Body mass frequency distribution of the entire continent was highly modal and skewed right (465 species median size was 45g). Comparing to the larger distribution, local communities have similar sizes because of competitive exclusion, differential extinction of species of large size with small geographic range, and specialization of energy use and dietary constraints. 24 small patches have a uniform body size. 19-37 species ranged from 100g to 2,500 g. 21 biomes were intermediate which indicated that 20 to 250 g body sized species would not coexist.

Discussion question, why is this pattern useful and how can we use this to deal with current species extinction in North America?

Tuesday, September 25, 2018

Yom-Tov and Geffen, 2011

Yom-Tov, Y., and Geffen, E. 2011. Recent spatial and temporal changes in in body size of terrestrial vertebrates: probable causes and pitfalls. Biological Reviews 86: 531-541.

Blog author: Maria Goller

1st author: Dr. Yoram Yom-Tov 
Bachelors, Masters, PhD at Tel Aviv
Emeritus zoology professor at Tel Aviv University
Also was curator of terrestrial vertebrates at the museum as well as academic director of zoological garden

2nd author: Dr. Eli Geffen
Professor at Tel Aviv University
Has worked on a lot of different things, including visual communication in chameleons, sociality in carnivores, and parasite loads in rodents...
Studies vocal communication in rock hyraxes and tries to understand song syntax (which is what I do, yay!)

This is a review paper of how variation in various abiotic and biotic factors shapes changes in body size.

Overview and Major Points
1. Body size varies with space and time
·     In some taxa, food availability during development plays a major role in determining body size
·     Food availability changes with weather/climate, and from season to season
·     Climate proxies for food availability - such as ambient temperature - are used because food availability is difficult to measure
·     Both year and latitude affect body size indirectly
·     Competition also affects body size
·     Resource rule = mammal body size variation depends on resource fluctuation

·     Species may vary widely in the pattern of change in body size 
·     Lumping body size patterns across species may mask variation

·     Depending on the spatial or temporal scale of sampling, you may see different patterns in changes in body size

2. Rate of change
·     Body size trends are fluid, even at short temporal scales

3. Time span, sample size, and the possibility of detecting a trend
·     As number of samples increases, likelihood of detecting a trend in body size increases
·     Also, as time of sampling increases, the likelihood increases
·     So just because you don't see a trend, doesn't mean there isn't one

4. Sources of variation
·     Not useful to measure body mass because it changes daily/seasonally/etc...
·     Both body length and skull length vary annually
·     Wing length is thought to be the best measure of avian body size, but it doesn't yield clear-cut results
·     Birth year of sampled organisms matters due to differences in food availability/climate/etc…
·     Continuous data are better than discrete
·     Need to test climatic variables separately because they're all interrelated and lead to messy trends

5. Linear, non-linear, and cyclic effects on body size
·     Environmental predictors vary cyclically
·     Have found linear trends in body size with change in temperature
·     Different trends in migratory and nonmigratory birds
·     Body size changes correlated with precipitation, food availability, and biomass productivity, which are all influenced by temperature
·     Temperature fluctuates among years, so taking a one-year snapshot isn't very revealing

6. Food supply and body size
·     Climate and short-term changes in food availability (due to weather) shape body size patterns
·     Various relationships between temperature and body size based on local conditions
·     Climate change also may cause an increase/decrease in competition => changes in body size
·     Also, humans may shape food availability and influence body size patterns
·     Body size may change over short time periods if habitats change

7. Phenotypic and genetic variation
·     A lot of the recent trends seem phenotypic in nature
·     Genetics may play a role in some cases

Main Message:
·     Body size is variable and fluctuates across time and space
·     Although many predictors are correlated with body size, it is difficult to untangle which factors directly, and which indirectly, drive changes in body size 

I like review papers because they give an overview of the state of the field.


I think this review reiterates the trend in the papers we’ve read this semester about everything being much more complicated than one might at first assume.

Monday, September 24, 2018

Paper 5

Paper 5- Hutchinson and MacArthur 1959

Blog Author: Angel Sumpter

Hutchinson, G.E. and R.H. MacArthur. 1959. A theoretical ecological model of size distributions among species of animals. American Naturalist 93:117-125.
Blog Author: Angel Sumpter

Blurb author: S.K. Morgan Ernest
  • University of Florida; Department of Wildlife Ecology and Conservation
    • Interdisciplinary Ecology
    • Associate Professor
  • Runs the Portal Project long term ecological research site.

Paper Author 1:G.E. Hutchinson
  • The Father of Ecology
  • Primary Field of Research was limnology; the study of the physical, chemical, geological and biological aspects of lakes and other bodies of freshwater.
  • One of the most influential biologists of the 20th century and was a beloved professor at Yale for 43 years.
Paper Author 2: Robert H. MacArthur
  • His PhD thesis became the renowned 1958 Ecology paper on the coexistence of five species of warblers in northeastern coniferous forests
  • MacArthur will be remembered as one of the founders of evolutionary ecology
  • With Edward O. Wilson, he developed the view that an island flora or fauna could be viewed as a potential equilibrium between the arrival of new species and the extirpation of residents

Paper Summary:
  1. Main Question
    1. Background History
      1. Small animals comprise a large portion of groups with the largest number of species in an area. Though this logic follows the Eltonian pyramid closely, using the expression to explain how this happens in any area you choose to examine, seems unbelievable. An environment ideally does not seem able to provide enough room and usable resources to house such a large number of species all at once. Simple things that herbivores may need to survive (water and food) may be home to other animals.
    2. Goal
      1. To determine why there is more abundance in smaller animals compared to larger animals using an equation.
  2. Methods
    1. Examine/ consider  fauna found in different areas of the world. Determine a contagious element within the environment and determine how it interacts with the environment. Conduct probabilities of the how the element will correspond to a niche. Determine how different elements correspond to environment and how the it affects the organisms that are within the environment.
      1. All of these are placed as variable into an equation/ model.
  3. Results
    1. Information- Theoretic Interpretation
      1. If niches are put into mixed group sizes, there is more diversity within the niches.
    2. Empirical Interpretation
      1. Three assumptions to keep in mind
        1. If each niche can only support one species than the quantity is an unsatisfactory measure of the function.
        2. If a single species is present, then there is a limiting probability.
        3. The number of available niches will increase to some sort of maximum and eventually a plateau of some size will decline to unity.
      2. Graph Results
        1. Mammal fauna of a certain kind can be built with a small amount of diversity if given sufficient range size.
        2. Large mammals going extinct may actually be due to human randomization of the habitat.
  4. Conclusion
    1. In brief, the data gained from actual application of the theory serve no actual importance to answering the main question. The results matched what information was known prior to the application and did very little to bring new knowledge to light. Based off information found, this theory could lead to modeling terrestrial faunas. Efforts in modeling such data will require much higher efforts in data collection with a new level of difficulty overall. Though very trivial, the theory might be able to possibly explain part of the reasons whole faunas have sizes dispersed the way they are. Data collected from this theory does not suffice as an answer, but as a stepping stone to other ideas.
  5. Question/ Comments
    1. What is a mosaic element? Google keeps telling me its an acoustic guitar...
      1. Mixed elements?
    2. I like how this entire math equation is based off of probability and assumptions. I know there is a lot more to it but wow, he made a lot of good educated guesses  for him to be named a founder of ecology.

Gorman and Hone 2012

Body Size Distribution of the Dinosaurs
 Blog Author: Sebastian Botero
Authors:

Eoin J. O’Gorman. PhD in Marine Ecology from Cork University College.
Currently a faculty of Natural Sciences at the Imperial College London. His main research interest is on “understanding the role of trophic interactions in mediating ecosystem-level responses to global change”. He works on the effect of anthropogenic disturbances on trophic networks properties across terrestrial, freshwater and marine realms.

David W. E. Hone. Ph.D. in Vertebrate Palaeontology with a thesis titled “The phylogenetics and macroevolution of the Archosauromorpha”
Currently alecturer at the School of Biological and Chemical Sciencesin the University of London. He works on dinosaur biology, with special emphasis on gaining understanding of the ecology and behavior of theropods and pterosaurs. Has written several popular science books about paleontology and has an interesting blog on science and paleontology (https://archosaurmusings.wordpress.com/publications/

Background:

It is well stablished that for many extant groups of organisms at large spatial and taxonomic scales the body size frequency distribution presents a right skewed shape, with most species being small. Nonetheless, more research on this is needed for extinct faunas. This is especially true for non-avian dinosaurs, a very interesting group from this perspective given that it includes the largest terrestrial animals that have existed. It is of interest to assess if this distribution differs from current distributions, reflecting unique evolutionary pressures and adaptations. With this, the questions asked by the authors are: i) what is the body size frequency distribution of dinosaurs? ii) How it compares to that of other groups and iii) what are the differences among dinosaur groups, Mesozoic eras and sites?

Methods:

-      Assemble a database of maximum femur length for 329 dinosaur species using literature reports and measurements from museum specimens.
-      Evaluate the relation between femur length and body mass and use this relation to estimate body mass for all the dinosaurs in the database.
-      Get body mass information on for all major extant vertebrate groups, Cenozoic mammals and Pterosaurs from literature and published databases.
-      Create the body mass distribution (BMD) for dinosaurs as well as the abovementioned groups and compare them using the Kolmogorov-Smirnov test. Here, it was especially important to compare the distribution of body size of dinosaurs against that of the other extinct groups to assess the possible effect of preservation bias of large animals over the results. 
-      Finally, they compared the distribution among Theropod, Ornithischia and Sauropodomorpha to see if different groups with contrasting ecologies differ in the distribution of body sizes. The mass distribution for different periods, as well as different formations were also evaluated.
-       
Results

-      The body mass distribution of dinosaurs is significantly different from that of the other vertebrate groups analyzed. The distribution is skewed to the left, with most of the species being large. 
-      Cenozoic mammals and Pterodactyls showed different BMDs from dinosaurs, suggesting that the observed pattern is not the result of taphonomic bias.
-      When dinosaurs were analyzed by group, only the herbivores Ornithischia and Sauropodomorpha showed the skewed pattern towards higher body size.
-      It seemed that this size distribution pattern appeared toward the end of geological eras during the Mesozoic.
-      No difference between formations.

Discussion
-      Significant difference in the BMD of dinosaurs against other vertebrate groups indicate differences in the biology of these animals.
-      As the pattern is apparent only for herbivore dinosaurs, it is hypothesized that the large size provided an advantage in more effective digestion of plant materials.
-      Young large dinosaurs could have occupied the niches of small animals.
-      The hypothesis of positive effect of extended stability periods on body size increase is supported by the fact that BMD is left skewed at the end of the Mesozoic periods.

Comments:

I enjoyed reading this paper. It is compelling how from this “simple” analysis, the authors are able to provide that amount of information and provide support for some of the theories explaining the evolution of large bod size not only in dinosaurs, but also in other groups. 
The authors don´t talk much about this, but do you think that the more normally distributed body sizes for the dinosaurs at the beginning of