The results underwent a manual consistency check and cleaning across the dataset: (1) occurrence data for different entity names that refer clearly to one entity were merged (e.g., Google Corporation and Google), (2) all locations were clustered according to region, (3) named entities occurring in less than four articles were ignored in further analysis.
The dataset of occurrence localities (described below) was divided into subsets for two- and three-populations from the inferred genetic structure shown by Mitchell et al. [ 27].
Cluster 2 contains sequences with homology to a dehydrine [GenBank: T11744], a catalase from Helianthus annuus [GenBank: AAF61733] and the most abundant sequence of the entire dataset (90 occurrences) which remains until now unidentified.
The datasets comprise occurrences of subtypes H5N1 or H3N2 but lack negative occurrences.
Our method can handle multiple data sources such as expression correlation datasets, co-occurrence of protein names in literature obtained via text-mining, or cross-species sequence comparisons (e.g. orthology networks [34], [35]).
The Ebola virus occurrence dataset was supplemented with a background record dataset generated by randomly sampling 10,000 locations across Africa, biased towards more populous areas as a proxy for reporting bias (Phillips et al., 2009).
Mauri, A., Strona, G. & San-Miguel-Ayanz, J. EU-Forest, a high-resolution tree occurrence dataset for Europe.
The Walter Reed Biosystematics Unit (WRBU) dataset contained 10,423 occurrence records, including two recent updates with 7 records.
Our steps to avoid spatial autocorrelation in the occurrence dataset resulted in the removal of different numbers of occurrence points with different distance filters: 11 of the 304 occurrences were randomly removed with the application of 20 km filter distance, 81 occurrences with 35 km filtering, and 52 occurrences with 50 km filtering.
Location We evaluate these hypotheses using a detailed dataset on the occurrence and abundance of terrestrial birds on nine islands off the coast of Britain and the Republic of Ireland.
