iMapGenes: An Anthropocene map of genetic diversity – University of Copenhagen

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An Anthropocene map of genetic diversity

Understanding what determines biodiversity is a major scientific challenge for the 21st century, especially in the light of global change.

Biodiversity encompasses diversity at all levels of biological organization, from genetic diversity within populations, to species diversity within communities and the diversity of ecosystems in a landscape. However, most of the studies to date on the global patterns of Biodiversity have been conducted at the species and ecosystem diversity levels.

Despite recent rapid advances in sequencing technology and the availability of an ever-increasing amount of genetic sequence data in public repositories, We still lack crucial baseline information on genetic diversity, such as a global map of its distribution.

We present the the first global map of genetic diversity

Our research is published in Science and free access is available to the abstract, full text reprint and full text online.

Video: This study provides the first global distribution map of intraspecific genetic diversity for terrestrial mammals and amphibians.

Method

To achieve this we took advantage of the immense wealth of publicly available genetic sequences in GenBank and BOLD Systems repositories. We then developed bioinformatic tools to attach geographic coordinates to a total of 92,801 mitochondrial sequences (31,029 for amphibians and 61,772 for terrestrial mammals) and adapted a widely-used genetic diversity metric, nucleotide diversity, to explore how this diversity is distributed across the globe.

Results

The study shows that genetic diversity is generally higher in the tropics (i.e., tropical Andes, Amazonia and the tropics of East Asia) than in higher latitudes, a pattern that follows the global pattern of species richness. It also shows that areas more impacted by humans, as urban areas and croplands, have reduced genetic diversity when compared to wilder regions - a pattern that is especially evident in amphibians.

A global distribution map of genetic diversity for combined taxa of amphibians and terrestrial mammals. Any use of the map must be credited Journal Science / AAAS

iMapGenes

For a more detailed exploration of the data used and the patterns detected in our study check our iMapGenes browser below:

iMapGenes: Diversity Explorer

In the website users can select their species of interest and see how genetic diversity is distributed across its geographical range. The website will also automatically calculate genetic diversity for a selected group of species in an interactive way. Finally users can also download sequence accession numbers used and their respective geographic coordinates.

Check this document to see all the functionality of the webpage.

Citation:

Andreia Miraldo, Sen Li, Michael K. Borregaard, Alexander Flórez-Rodríguez, Shyam Gopalakrishnan, Mirnesa Rizvanovic, Zhiheng Wang, Carsten Rahbek, Katharine A. Marske & David Nogués-Bravo (2016): An Anthroppocene map of genetic diversity. Science 353 (6307), p1532-1535, published online on September 30th, 2016 (DOI: 10.1126/science.aaf4381).