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DNA Surveillance

Species identification with DNA

What Rat is That? Home About How to Use The Science Links and Publications Data Ownership
Search Cluster (Simple) Cluster (Advanced) Maximum Likelihood Example Data

What Rat is That?

This site provides phylogenetic tools for the identification of rats (Rattus spp.) from the region of southeast Asia and the Pacific.

See the specific details on how to use this site.

In general, you submit a sequence from one of three mitochondrial DNA regions, and the system builds a phylogenetic tree. You then infer the identity of your query sequence on the basis of its placement in the tree.

We have operationally defined species as phylogenetic clades on the basis of sequences from three mitochondrial DNA regions: control region (=D-loop), cytochrome b, and cytochrome oxidase I (COI). More details are available.

Some of these clades coincide with taxonomic species, defined using morphological characters. Other clades contain representatives of two or more nominal species. Some nominal species are present in two or more clades.

It's complicated! This is very much a work in progress.

Shane Lavery
Bioinformatics Institute and School of Biological Sciences
University of Auckland