Alleles In Space (AIS): Computer Software for the Joint Analysis of Interindividual Spatial and Genetic Information

Miller, Mark P.

doi:10.1093/jhered/esi119

Cited by 521 publications

(453 citation statements)

References 22 publications

(18 reference statements)

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“…Spatial patterns of genetic differentiation were inferred and visualized by genetic landscape shape interpolation analysis as implemented in Alleles in Space 1.0 (AIS: Miller, 2005). The genetic landscape analysis was based on a Delauny triangulation connectivity network and residual genetic distances derived from the linear regression of genetic versus geographic distances (as recommended for data sets with substantial variation in geographic distances between sampling sites; Manni et al, 2004).…”

Section: Phylogeographic and Phylogenetic Analysis Within Altolamprolmentioning

confidence: 99%

Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

et al. 2016

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Stenotopic specialization to a fragmented habitat promotes the evolution of genetic structure. It is not yet clear whether small-scale population structure generally translates into large-scale intraspecific divergence. In the present survey of mitochondrial genetic structure in the Lake Tanganyika endemic Altolamprologus (Teleostei, Cichlidae), a rock-dwelling cichlid genus comprising A. compressiceps and A. calvus, habitat-induced population fragmentation contrasts with weak phylogeographic structure and recent divergence among genetic clades. Low rates of dispersal, perhaps along gastropod shell beds that connect patches of rocky habitat, and periodic secondary contact during lake level fluctuations are apparently sufficient to maintain genetic connectivity within each of the two Altolamprologus species. The picture of genetic cohesion was interrupted by a single highly divergent haplotype clade in A. compressiceps restricted to the northern part of the lake. Comparisons between mitochondrial and nuclear phylogenetic reconstructions suggested that the divergent mitochondrial clade originated from ancient interspecific introgression. Finally, 'isolation-with-migration' models indicated that divergence between the two Altolamprologus species was recent (67-142 KYA) and proceeded with little if any gene flow. As in other rock-dwelling cichlids, recent population expansions were inferred in both Altolamprologus species, which may be connected with drastic lake level fluctuations.

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Section: Phylogeographic and Phylogenetic Analysis Within Altolamprolmentioning

confidence: 99%

Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

et al. 2016

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“…The population structure determined using microsatellite data was initially analysed adopting three statistical approaches: the Bayesian methods implemented in the programme BAPS 4.14 (Corander et al, 2003(Corander et al, , 2004 and STRUCTURE 2.2 (Pritchard et al, 2000;Falush et al, 2003Falush et al, , 2007, and Genetic Landscape Shape analysis (Miller, 2005). The population structure based on mt data has been presented by Tollefsrud et al (2008b); here, we only performed Genetic Landscape Shape analysis of the mtDNA data to facilitate direct comparison between the geographical patterns of differentiation observed between the two marker types.…”

Section: Population Genetic Structurementioning

confidence: 99%

“…The Genetic Landscape Shapes analyses were produced using the programme, Alleles In Space (AIS; Miller, 2005). The procedure was initiated by constructing a Delaunay triangulation network among all the sampling coordinates.…”

Section: Population Genetic Structurementioning

confidence: 99%

Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies

et al. 2009

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Norway spruce of northern Europe expanded at the end of the last glacial out of one refugium in Russia. To provide a detailed insight into how the genetic structure in the northern European lineage of this species has been shaped by postglacial migration, recurrent pollen flow and marginality, we here compare variation at seven highly variable nuclear microsatellite loci in 37 populations (1715 trees) with mitochondrial DNA variation. Microsatellite diversity was high (H E ¼ 0.640) and genetic differentiation was low (F ST ¼ 0.029). The microsatellite structure supported a mitochondrial DNA (mtDNA)-based hypothesis of two migration routes out of a single Russian refugium; one northwestern over Finland to northern Scandinavia, and one southwestern across the Baltic Sea into southern Scandinavia. Microsatellite diversity was maintained along the southwestern migration routes, whereas a significant decrease was observed towards the north. In contrast, the mtDNA diversity suggested higher amounts of historical gene flow towards the north than along the southwestern migration route. This suggests that the loss of nuclear diversity after postglacial colonization has been efficiently replenished by pollen-mediated gene flow in the south. Towards the north, smaller effective population size because of more limited seed and pollen production may have caused decreased nuclear diversity and increased inbreeding, reflecting the ecological marginality of the species in the north.

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“…We visualized detailed patterns of spatial genetic structure among populations by genetic landscape shape interpolation using the AIS (Alleles in Space) software (Miller, 2005). This procedure is initiated by constructing a Delauney triangulation-based connectivity network of sampling areas, and it creates three-dimensional genetic landscapes by interpolation of measured genetic distances between sampled individuals.…”

Section: Spatial Genetic Analysesmentioning

confidence: 99%

Range shifts of Potentilla fruticosa on the Qinghai-Tibetan Plateau during glacial and interglacial periods revealed by chloroplast DNA sequence variation

Shimono

Ueno

et al. 2009

Heredity

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The Qinghai-Tibetan Plateau is one of the most extensive habitats for alpine plants in the world. Therefore, the patterns of genetic variation in populations on the Plateau can reveal the detailed demographic history of alpine plants. We analysed the geographical structure of chloroplast matK sequence variation in Potentilla fruticosa L. (Rosaceae), a shrub currently found across the entire Plateau. We obtained sequence data from 508 individuals from 23 populations at sites ranging from the high-altitude interior to the relatively low-altitude northeastern Plateau. In the interior region, genetic diversity was high and included ancestral haplotypes. In contrast, northeastern populations were characterized by relatively low genetic diversity and recently derived haplotypes. The estimated expansion time in the interior population was 17 times that in the northeastern population. These data suggest that P. fruticosa expanded its range on the Plateau during periods of climatic cooling and contracted to the interior region during warmer periods. Thus, the interior region acted as a refugium and greatly contributed to the diversification of P. fruticosa.

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Alleles In Space (AIS): Computer Software for the Joint Analysis of Interindividual Spatial and Genetic Information

Cited by 521 publications

References 22 publications

Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies

Range shifts of Potentilla fruticosa on the Qinghai-Tibetan Plateau during glacial and interglacial periods revealed by chloroplast DNA sequence variation

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