Evaluating the Evidence of Genome Downsizing

Flowering plants  recurrently undergo whole genome duplications, which in theory should create an increasing tendency of genome sizes. When lookingImageGST+GD at genome size distributions across more than 5,0000 taxa, the average genome size for polyploids remains constant at increasing ploidies. In the past this constancy has been attributed to a phenomenon called genome downsizing which in principle reduces the size of genomes. However, genome downsizing is not the only mechanism that could recreate the constancy in the polyploid genome sizes. I proposed different  simulations that recreate this pattern  assuming that  large genome taxa, or taxa with large chromosome numbers are not undergoing or surviving whole genome duplications due to physiological, ecological, or maladaptive restrictions. With these simple simulations I estimated that we only expect from 0.3% to 17% genome downsizing when  large genomes do not undergo or survive whole genome duplications, that is genome downsizing does not have to be large in order to maintain a constant genome despite multiple whole genome duplications.
The full article is published in the American Journal of Botany and can be found here.

 

Phyloseminar with Brian O’Meara at UTK

This Fall 2015 I have the opportunity to teach with Dr. Brian O’Meara a diversification seminar as part of his Phyloseminar series. It is a mix of articles and R tutorials about use of models and statistical tools to estimate speciation and extinction rates in a phylogenetic context.

Tutorials

  1. Birth-Death Stochastic Process. Estimation of speciation and extinction. 
    Week2-08312015Tutorial

 

Statistical Ecology in R. Thailand workshop

Thailand was wonderful and we had a great time teaching basic concepts iP1040515n statistical Inference. The class material can be found here:
workshop website

This workshop was organized thanks to funding from QSE3 IGERT at University of Florida and

King Mongkut’s University of Technology Bangkhuntien support. This workshop was jointly taught with

Mollie Brooks http://www.popecol.org/team/mollie-brooks/

Trevor Caughlin.  Postdoc at University of Florida 

Jake Ferguson. Postdoc at NIMBios 

Vertebrate blood cell volume

In collaboration with Dr. Jamie Gilloly.

We have analyzed  the functional relationship between red blood cells and body temperature across vertebrates, and found some interesting positive correlation.
Screen Shot 2015-07-04 at 4.46.07 PM

The publication link here

Gillooly, James F., and Rosana Zenil-Ferguson. “Vertebrate blood cell volume increases with temperature: implications for aerobic activity.” PeerJ 2 (2014): e346.

Green Turtles and Their Lost Years

Collaboration with Melania Lopez Castro
PostDoc at Texas A&M

Melania sampled green turtles from many different beaches along the Atlantic ocean and performed a trace element experiment. The goal was to detect a possible location for the young green turtles  in the ocean during their lost years. We wanted to know which trace elements were relevant for distinguishing groups of turtles, but also how many clusters those important trace elements were determining. We used Bayesian Model clusters and calculated their BIC to choose the best trace elements and clusters using the  High  Performance Cluster at UF.

Publication can be found heremelaniacluster

López-Castro, Melania C., Karen A. Bjorndal, George D. Kamenov, Rosana Zenil-Ferguson, and Alan B. Bolten. “Sea turtle population structure and connections between oceanic and neritic foraging areas in the Atlantic revealed through trace elements.” Mar. Ecol. Prog. Ser 490 (2013): 233-246.

Birds in Amazonia. Alarm Responses

Collaboration with Ari Martinez
PostDoc at San Francisco State University

Profile Likelihood Responses for foragersAri was interested in how different foraging patterns affect the length of latency responses in birds. He perform a very detailed field work in Peru, with different species of birds belonging to three main foraging groups.  We analyzed his data using likelihood functions and we obtained relevant differences in alarm responses that depend on foraging behavior.

You can find the publication here

Martínez, Ari E., and Rosana T. Zenil. “Foraging guild influences dependence on heterospecific alarm calls in Amazonian bird flocks.” Behavioral Ecology 23.3 (2012): 544-550.