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AIS specifications


Unique identifier OMICS_29892
Name AIS
Alternative name Alleles in Space
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A file with sets of spatial coordinates for each observation in the dataset and a file including genetic data for each individual.
Operating system Windows
Computer skills Advanced
Stability Stable
Registration required Yes
Maintained Yes


No version available


  • person_outline Mark Miller
  • person_outline Mark Miller

Publication for Alleles in Space

AIS citations


Parapatric genetic divergence among deep evolutionary lineages in the Mediterranean green crab, Carcinus aestuarii (Brachyura, Portunoidea, Carcinidae), accounts for a sharp phylogeographic break in the Eastern Mediterranean

BMC Evol Biol
PMCID: 5896055
PMID: 29642852
DOI: 10.1186/s12862-018-1167-4

[…] erentiation are caused by isolation by distance (IBD), we ran the Mantel test [] for pairwise matrices between geographical and genetic distances. The Mantel test was performed with the software AIS (Alleles in Space) version 1.0 []. The statistical significance of the test was assessed by running 10,000 random permutations. Population genetic structure of C. aestuarii was also examined (by means […]


Spatial genetic diversity in the Cape mole rat, Georychus capensis: Extreme isolation of populations in a subterranean environment

PLoS One
PMCID: 5854370
PMID: 29543917
DOI: 10.1371/journal.pone.0194165

[…] or these tests were determined through 9 999 permutations of the data (Arlequin version 3.5; []). Isolation-by-distance was evaluated for the Western Cape region using a Mantel test as implemented in Alleles In Space version 1.0 []. Geographic distances were taken as straight-line distances between localities.A haplotype network was built using TCS 1.21 []; this network also provides an overall vi […]


Genetic Variation of the Endangered Neotropical Catfish Steindachneridion scriptum (Siluriformes: Pimelodidae)

Front Genet
PMCID: 5827538
PMID: 29520295
DOI: 10.3389/fgene.2018.00048

[…] replicates for every level of k (1–6) without origin information (“clustering of individuals”) and subsequently using “clustering of groups of individuals.” We used Mantel tests as implemented in the Alleles In Space (AIS) 1.0 () to test for a correlation of geographic stream distance and genetic distance (isolation-by-distance; IBD) expressed as FST, with 10,000 permutations to assess significanc […]


Geographical isolation and environmental heterogeneity contribute to the spatial genetic patterns of Quercus kerrii (Fagaceae)

PMCID: 5836588
PMID: 29279604
DOI: 10.1038/s41437-017-0012-7

[…] lected based on a backward elimination procedure. The genetic significant difference level among the Q. kerrii groups were tested using the Gp1 and C A (Cluster A from the Bayesian clustering) values.Alleles in Space (Miller ) was used to explore the possible genetic discontinuities and barriers among populations according to cpDNA and nSSR polymorphism. To avoid the effects of genetic distances a […]


Explaining large mitochondrial sequence differences within a population sample

R Soc Open Sci
PMCID: 5717637
PMID: 29291063
DOI: 10.1098/rsos.170730

[…] tion to both latitude and elevation. We visualized genetic distance patterns across the complete range of H. crassidens using three-dimensional surface plots known as ‘genetic landscape shapes' using Alleles In Space (AIS,, []). To do this, a connectivity network of sampled individuals was constructed and genetic distances (Zi, calculated as the average proport […]


Phylogeography of Nasutitermes corniger (Isoptera: Termitidae) in the Neotropical Region

BMC Evol Biol
PMCID: 5701342
PMID: 29169320
DOI: 10.1186/s12862-017-1079-8
call_split See protocol

[…] haplotypic network. The parameters calculated and their significance were tested in the phylogeographic inferences key of Templeton []. For verification of results, we conducted the Mantel test using Alleles in Space v.1.0 []. Significant r values nearest to 1 indicate strong positive correlation between the two variables. Significant values nearest to −1 indicate strong negative correlation betwe […]


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AIS institution(s)
Department of Biology, Utah State University, Logan, UT, USA

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