GenGIS: A geospatial information system for genomic data.

@article{Parks2009GenGISAG,
  title={GenGIS: A geospatial information system for genomic data.},
  author={Donovan H. Parks and Michael S. Porter and Sylvia Churcher and Suwen Wang and Christian Blouin and Jacqueline L. Whalley and Stephen Brooks and Robert G. Beiko},
  journal={Genome research},
  year={2009},
  volume={19 10},
  pages={
          1896-904
        }
}
The increasing availability of genetic sequence data associated with explicit geographic and ecological information is offering new opportunities to study the processes that shape biodiversity. The generation and testing of hypotheses using these data sets requires effective tools for mathematical and visual analysis that can integrate digital maps, ecological data, and large genetic, genomic, or metagenomic data sets. GenGIS is a free and open-source software package that supports the… 

Figures from this paper

GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework

GenGIS version 2 is introduced, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes and implements a recently published method for biomonitoring reference condition analysis (RCA).

PolyLens: software for map-based visualisation and analysis of genome-scale polymorphism data

PolyLens is a Java-based, integral visual analytical toolkit which can systematically process population genomic data, visualise geographic distributions of genealogical lineages, and display allele distribution patterns.

PGT: Visualizing temporal and spatial biogeographic patterns

  • X. Xia
  • Environmental Science, Biology
    Global Ecology and Biogeography
  • 2019
PGT is simpler, more elegant, and of much higher quality than alternatives for plotting phylogenetic trees over geographic regions for visualizing distribution of biodiversity over space and time.

SVAMP: sequence variation analysis, maps and phylogeny

The utility of SVAMP is demonstrated in tracking a methicillin-resistant Staphylococcus aureus outbreak from published next-generation sequencing data across 15 countries and the scalability and accuracy of the software on 245 Plasmodium falciparum malaria isolates from three continents.

Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases

Genomic and epidemiological monitoring have become an integral part of our response to emerging and ongoing epidemics of viral infectious diseases. Advances in high-throughput sequencing, including

Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense

The dispersal corridors and historical gene flow detected here suggested that the mountains acted as a bridge, facilitating gene flow between the eastern and western populations, suggesting the presence of multiple refuges in multiple mountainous regions in China.

Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis

The purpose of this review is to present the most common and emerging DNA‐based methods used to generate data for biodiversity and biomonitoring studies, with particular attention to the DNA metabarcoding method.

GPT: a web-server to map phylogenetic trees on a virtual globe

GPT (Global Positioning Trees) is a web-server that maps phylogenetic trees on a virtual globe and will be useful for phylogeographical and spatial epidemiological studies.

Understanding the processes of diversification along the speciation continuum in a recent evolutionary radiation of grasshoppers

This study highlights the power of coalescent-based approaches to delimit taxa boundaries when handling large genomic datasets and indicates that integrating a broad suite of traits for the two sexes could be beneficial when aiming at determining species limits, particularly at early-stages of divergence where conflicting inferences are more prone to appear.
...

References

SHOWING 1-10 OF 85 REFERENCES

Phylogeographic information systems: putting the geography into phylogeography

This paper aims to stimulate the resurgence of geography as an equal partner in the symbiosis that is phylogeography as well as advertise some benefits that can be obtained from the application of GIS practices and technologies.

Megx.net—database resources for marine ecological genomics

This work introduces Megx.net, a set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts that will help researchers to generate a better understanding of the functioning of marine ecosystems.

Spatial analysis and visualization of genetic biodiversity

The features of the first release version of GenGIS, a free and open source GIS package that provides tools for spatial visualization and analysis of microbial genome data, are described and used to test questions about microbial biodiversity in the world’s oceans.

Micro-Mar: a database for dynamic representation of marine microbial biodiversity

The Micro-Mar database aims to integrate molecular data and taxonomic affiliation with biogeographical and ecological features that will allow to have a dynamic representation of the marine microbial diversity embedded in a user friendly web interface.

Integrating GIS-based environmental data into evolutionary biology.

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

The results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.

Toward a More Robust Assessment of Intraspecies Diversity, Using Fewer Genetic Markers

It is shown here that phylogenies of closely related organisms based on the average nucleotide identity (ANI) of their shared genes correspond accurately to phylogenies based on state-of-the-art analysis of their whole-genome sequences.

Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus).

This work demonstrates the ease and utility of using spatial analyses of environmental data and phylogenetics in species delimitation, especially for groups displaying fine-scaled endemism and cryptic species.

Phylogenetic approaches in coevolution and biogeography

Parsimony analysis in coevolution and biogeography should be based on identification of different types of events, each of which is associated with a specific cost, as well as in the mapping of gene trees onto organism trees.

Combining data sets with different phylogenetic histories.

A simple methodology for dealing with the possibility that two data sets may have different underlying phylogenetic histories is proposed, and computer simulations suggest that the accuracy of combined analysis for recovering the true species phylogeny may exceed that of either of two separately analyzed data sets under some conditions.
...