Recent Lab News:
A new version of Wallace is now available on CRAN. Wallace v.188.8.131.52 provides options to turn clamping on/off when using the maxent.jar modeling module. This option was previously only available for the maxnet package.
In November 2020 Gonzalo Pinilla-Buitrago talked about Wallace in two ecological modelling courses in Colombian universities (Universidad de Pamplona and Universidad Militar Nueva Granada).
In September 2020 CCNY graduate students participated in the Humboldt Day celebration by making Science Communication videos. Lab member, Gonzalo Pinilla-Buitrago participated with the video “Rodents in the sky-with-island. See YouTube video here.
In October 2020, lab members participated in a virtual workshop to gain feedback on the development version of Wallace software and extensions of it for conservation biology. The workshop was led by Dr. Mary Blair at the American Museum of Natural History in New York and Dr. Elkin Noguera of the Instituto Humboldt in Bogota Colombia. Via a NASA grant to Dr. Blair, this project is developing new tools for estimating species geographic ranges and quantifying indicators of biodiversity change, supporting the goals of the international Group on Earth Observations Biodiversity Observation Network (GEO-BON).
Robert Anderson et al. (2020) published a new paper in Frontiers of Biogeography. "Optimizing biodiversity informatics to improve information flow, data quality, and utility for science and society". Access the full text here.
In July 2020, the Anderson lab began a new NSF biogeography project, studying colonization and extinction for mammals of Mexican 'sky islands' based on environmental history and species traits. We are applying the Constraint-based model of Dynamic Island Biogeography (C-DIB) to predict and then test community composition on isolated patches of montane forests. Our collaborators include J. Robert Burger, Lazaro Guevara, Ella Vazquez-Dominguez, and Elizabeth Arellano.
Camilo Sanín and Robert Anderson published a new paper in The American Naturalist. "A framework for simultaneous tests of abiotic, biotic, and historical drivers of species distributions: empirical tests for North American wood-warblers based on climate and pollen". pdf
There is new version of Wallace on CRAN and Github (v1.0.6). Wallace now has two options for running Maxent: maxnet (default) and maxent.jar. The exciting thing: no more rJava dependency". See on CRAN.
Rob Anderson gives Wallace webinar in Spanish for Modelado de Distribuciones Potenciales series: "El software Wallace para modelar nichos y distribuciones: Un coche con motor R, volante de ratón y cerebro de humano." Broadcast from the City College of New York, City University of New York. Watch on You Tube.
Jamie Kass hosts Wallace webinar including tutorial and live demonstration: "WALLACE: A flexible platform for reproducible modeling of species niches and distributions built for community expansion." Broadcast from the City College of New York, City University of New York. Watch on You Tube.
Gonzalo Pinilla-Buitrago publishes his master's work on Mexican biogeography. "Areas of endemism persist through time: A palaeoclimatic analysis in the Mexican Transition Zone" by Pinilla-Buitrago et al. is published in the May 2018 issue of Journal of Biogeography. pdf
Editor's Choice: Peter Galante et al. explore the challenges of modeling niches and distributions for data-poor species. "The challenge of modeling niches and distributions for data-poor species: a comprehensive approach to model complexity" by Galante et al. is Editor's Choice in the May 2018 issue of Ecography. pdf
Cover! Beth Gerstner et al. revise distributional estimates for a recently discovered carnivoran. "Revised distributional estimates for the recently discovered olinguito (Bassaricyon neblina), with comments on natural and taxonomic history" by Gerstner et al. is featured on the cover of the April 2018 issue of Journal of Mammalogy. pdf
Jamie Kass et al. release and document new biodiveristy software Wallace. "Walace: a flexible platform for reproducible modeling of species niches and distributions built for community expansion" by Kass et al. is published in the April 2018 issue of Methods in Ecology and Evolution. pdf
Lázaro Guevara et al. demonstrate the importance of assessing variation among GCMs when reconstructing geographic distributions. "Variation among Global Circulation Models for reconstructions of geographic distributions at the Last Glacial Maximum: relevance for phylogeography" by Guevara et al. is published in the January-April 2018 issue of Ecosystemas. pdf
Lázaro Guevara et al. illustrate recommendations for estimating species range shifts in Global Change Biology. "Toward ecologically realistic predictions of species distributions: A cross-time example from tropical montane cloud forests" by Guevara et al. is published in the April 2018 issue of Global Change Biology. pdf
In August 2017, the lab commenced a three-year grant from the National Science Foundation to expand the Wallace biodiversity software (“ABI Innovation: Wallace: a flexible platform for reproducible modeling of species niches and distributions built for community expansion”). In collaboration with Dr. Cory Merow (Yale University) and Dr. Matthew Aiello-Lammens (Pace University), the grant is funded by the Advances in Biological Informatics program, Division of Biological Infrastructure.
"When and how should biotic interactions be considered in models of species niches and distributions?" by R. P. Anderson is published in Journal of Biogeography. pdf
"A single-algorithm ensemble approach to estimating suitability and uncertainty: cross-time projections for four Malagasy tenrecs" by Boria et al. is published in Diversity and Distributions. pdf
"Opening the black box: an open–source release of Maxent" by Phillips et al. is published in Ecography. pdf
In August 2016, the lab began a one-year NSF EAGER grant “Making code-based analyses widely accessible for modeling species niches and distributions” from the Advances in Biological Informatics program (Division of Biological Infrastructure) to produce the first full release of Wallace, a user-friendly and modular web application for advanced niche/distributional modeling.
Beth Gerstner wins the CCNY Professor Martin Sacks/Sylvia F. Rubin Award for the graduating student demonstrating the greatest proficiency in research in Environmental Science.
Jamie Kass will be supported by Grant-in-Aid of Research (American Society of Mammalogists: $1500) to extend field work in 2017 for study on invasive raccoons in Japan.
Jamie Kass was selected for the Provost’s Digital Innovation Grant (CUNY Graduate Center: $10,000). This grant for the academic year 2016-2017 will allow him to continue the development of Wallace, a user-friendly and modular web application for advanced niche/distributional modeling.
Jamie Kass received a grant from CUNY Doctoral Student Research Grant Program to fund one of his dissertation projects: research on the spread of the invasive North American raccoon in Japan, and its interactions with the native raccoon dog (which belongs to a different family of carnivorans).
Beth Gerstner's data collection on bats at the American Museum of Natural History has been used for a study spearheaded by Laurel Yohe, a Ph.D. student at Stony Brook University. The resulting multi-authored paper has been published in Biology Letters and is titled "Bayesian hierarchical models suggest oldest known plant-visiting bat was omnivorous". A link to the article can be found here.
Jamie Kass and Rob Anderson were part of a team selected as Finalists in the Global Biodiversity Information Facility (GBIF) Nielsen Challenge (GBIF press release) for their development of the beta software "Wallace" -- which combines data from the GBIF network with two recently developed R packages (spThin and ENMeval).
Maria Gavrutenko was awarded the 2015 Ward Medal and Stratford Prize from the Department of Biology at CCNY (Stratford Prize, for the graduating senior demonstrating the greatest proficiency in both coursework in zoology and zoological research).
Recent Lab Visitors:
Olivier Broennimann (Univ. of Lausanne), 3-12 January 2018
- Olivier spent two weeks in the lab collaborating with Jamie Kass and Rob Anderson to expand the functionality of Wallace, and
worked to develop multi-species modeling capabilities.
Sara Varela (Leibniz Institute for Research on Evolution and Biodiversity), 4-17 November 2017
- Sara spent two weeks in the lab collaborating with Jamie Kass and Rob Anderson on the development
of Wallace. Her contributions include helping to re-engineer Wallace in order to streamline the process of adding new modules.
Thank you Sara for your informal talk on mammal extinction events during the Quaternary.
Joseph R. Burger (Univ. of North Carolina at Chapel Hill), 13 November 2017
- Robbie gave a presentation, "Metabolism sets the pace of life: implications for life history, population constraints, and insular
biodiversity" as part of the Biology Fall 2017 Colloquium series.
Israel del Toro (Univ. of Copenhagen), 16-17 May 2016.
- Isreal gave a presentation, "The heat is on! Climate change impacts on the biogeography and ecology of ecosystem engineers"
as part of the Biology Spring 2016 Colloquium series at CCNY.
Trishna Dutta (Columbia University), 20 April 2016
Town Peterson (Univ. of Kansas), 10 November 2015
- Town gave a talk on his group's work examining niche evolution in a phylogenetic context
Enrique Martínez-Meyer (Univ. Nacional Autónoma de México), 9-10 November 2015
- Enrique gave a talk relating abundance data to modeled niche suitability
Thomas Albright (Univ. of Nevada), 5 October 2015