Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR

Holleley, Clare E.; Geerts, Paul

doi:10.2144/000113156

Cited by 337 publications

(218 citation statements)

References 16 publications

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“…Forward primers were labeled with a 5 0 fluorescent tag (6-FAM, NED, PET or VIC) for visualization. We performed six sets of multiplex PCR (Plex1: CMA1-CMD9-CMH12; Plex2: CMB3-CMD1; Plex3: CMB6-CMC109-CMC126; Plex4: CMC115-CMD102-CMH7; Plex5: CMA2-CMC5-CMD101-CMH9; and Plex6: CMC11-CMH8) designed by MULTIPLEXMANAGER v1.2 (Holleley and Geerts, 2009). We performed fragment analyses on an ABI Genetic Analyzer with LIZ600 size standard (Applied Biosystems).…”

Section: Methodsmentioning

confidence: 99%

Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide ranging, but endangered, freshwater mussel

et al. 2013

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Freshwater organisms of North America have had their contemporary genetic structure shaped by vicariant events, especially Pleistocene glaciations. Life history traits promoting dispersal and gene flow continue to shape population genetic structure. Cumberlandia monodonta, a widespread but imperiled (IUCN listed as endangered) freshwater mussel, was examined to determine genetic diversity and population genetic structure throughout its range. Mitochondrial DNA sequences and microsatellite loci were used to measure genetic diversity and simulate demographic events during the Pleistocene using approximate Bayesian computation (ABC) to test explicit hypotheses explaining the evolutionary history of current populations. A phylogeny and molecular clock suggested past isolation created two mtDNA lineages during the Pleistocene that are now widespread. Two distinct groups were also detected with microsatellites. ABC simulations indicated the presence of two glacial refugia and post-glacial admixture of them followed by simultaneous dispersal throughout the current range of the species. The Ouachita population is distinct from others and has the lowest genetic diversity, indicating that this is a peripheral population of the species. Gene flow within this species has maintained high levels of genetic diversity in most populations; however, all populations have experienced fragmentation. Extirpation from the center of its range likely has isolated remaining populations due to the geographic distances among them.

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Section: Methodsmentioning

confidence: 99%

Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide ranging, but endangered, freshwater mussel

et al. 2013

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“…Four loci (Calex‐1, Calex‐13, Calex‐17, Calex‐34) were excluded from further analyses because of their low variability. We selected 14 polymorphic loci for which at least two different alleles were detected and designed two multiplexes using multiplex manager v1.2 (Holleley & Geerts 2009). …”

Section: Methodsmentioning

confidence: 99%

Genetic isolation in an endemic African habitat specialist

Remedios

Küpper

Székely

et al. 2017

Ibis

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The Chestnut‐banded Plover Charadrius pallidus is a Near‐Threatened shorebird species endemic to mainland Africa. We examined levels of genetic differentiation between its two morphologically and geographically distinct subspecies, C. p. pallidus in southern Africa (population size 11 000–16 000) and C. p. venustus in eastern Africa (population size 6500). In contrast to other plover species that maintain genetic connectivity over thousands of kilometres across continental Africa, we found profound genetic differences between remote sampling sites. Phylogenetic network analysis based on four nuclear and two mitochondrial gene regions, and population genetic structure analyses based on 11 microsatellite loci, indicated strong genetic divergence, with 2.36% mitochondrial sequence divergence between individuals sampled in Namibia (southern Africa) and those of Kenya and Tanzania (eastern Africa). This distinction between southern and eastern African populations was also supported by highly distinct genetic clusters based on microsatellite markers (global FST = 0.309, GST′ = 0.510, D = 0.182). Behavioural factors that may promote genetic differentiation in this species include habitat specialization, monogamous mating behaviour and sedentariness. Reliance on an extremely small number of saline lakes for breeding and limited dispersal between populations are likely to promote reproductive and genetic isolation between eastern and southern Africa. We suggest that the two Chestnut‐banded Plover subspecies may warrant elevation to full species status. To assess this distinction fully, additional sample collection will be needed, with analysis of genetic and phenotypic traits from across the species’ entire breeding range.

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“…Twenty-four of the loci provided high quality amplifi cations with unambiguous allelic patterns and apparent polymorphism scored by agarose gel electrophoresis, and were retained for multiplex PCRs with fl uorescently labelled primers. Using the Multiplex Manager v1.1 software (Holleley & Geerts, 2009), they were arranged in three multiplex PCRs that minimised the formation of duplexes and maximised the range of amplifi cation product sizes (Table 1).…”

Section: Introductionmentioning

confidence: 99%

A new suite of twenty-two polymorphic microsatellite loci in the parasitic wasp, Habrobracon hebetor (Hymenoptera: Braconidae): Promising molecular tools for studying the population genetics of several beneficial braconid species

Garba¹,

Loiseau²,

Benoit³

et al. 2016

Eur. J. Entomol.

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Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR

Cited by 337 publications

References 16 publications

Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide ranging, but endangered, freshwater mussel

Phylogeographic and population genetic analyses reveal Pleistocene isolation followed by high gene flow in a wide ranging, but endangered, freshwater mussel

Genetic isolation in an endemic African habitat specialist

A new suite of twenty-two polymorphic microsatellite loci in the parasitic wasp, Habrobracon hebetor (Hymenoptera: Braconidae): Promising molecular tools for studying the population genetics of several beneficial braconid species

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