Fast, Cost-Effective Development of Species-Specific Microsatellite Markers by Genomic Sequencing

Abdelkrim, Jawad; Robertson, Bruce C.; Stanton, Jo‐Ann L.; Gemmell, Neil J.

doi:10.2144/000113084

Cited by 309 publications

(285 citation statements)

References 11 publications

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“…Of the 13 microsatellite markers previously developed for blue duck (Abdelkrim et al 2009), Hmal12 was monomorphic in the present study and Hmal20 proved hard to score; both markers were subsequently removed from analyses. Touchdown PCR amplifications were performed independently for each marker.…”

Section: Microsatellite Genotypingmentioning

confidence: 81%

Strong isolation by distance argues for separate population management of endangered blue duck (Hymenolaimus malacorhynchos)

et al. 2016

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Knowledge of genetic diversity and population structuring represents a key component for the conservation of endangered species, especially where translocations and re-introduction operations are integral tools for population management. The blue duck (Hymenolaimus malacorhynchos) is a threatened riverine specialist that is endemic to New Zealand. Populations from the North and South Island form two distinct mitochondrial lineages, which currently necessitate separate conservation management. Here we examine the patterns of variability at 11 microsatellite loci and mitochondrial control region data to assess the range-wide genetic diversity and population structure of blue duck. Our data suggest that North and South Island blue duck populations likely diverged in the late Pleistocene with very limited gene flow, strongly reinforcing the current management strategy to avoid translocation between islands. Genetic diversity within both islands follows a pattern of isolation by distance with relatively high levels of gene flow among populations, likely driven by male-juvenile dispersal. The overall genetic diversity in blue duck is low and effective population size is small. These data will provide important information for conservation management of this species.

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Section: Microsatellite Genotypingmentioning

confidence: 81%

Strong isolation by distance argues for separate population management of endangered blue duck (Hymenolaimus malacorhynchos)

et al. 2016

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“…More microsatellite loci (preferably loci which have no overlapping alleles between parent species; Senn and Pemberton 2009) are needed to find a set of microsatellites which could be used for hybrid detection (Vaha and Primmer 2006). The development and characterization of large number of polymorphic microsatellites is possible and efficient via next-generation sequencing techniques (Abdelkrim et al 2009;Gardner et al 2011;Kajtoch et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Tests of multiple molecular markers for the identification of Great Spotted and Syrian Woodpeckers and their hybrids

et al. 2014

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Great Spotted and Syrian Woodpeckers (Dendrocopos major and D. syriacus) are known to hybridize in nature; however, the extent of this phenomenon is not known due to difficulties in hybrid detection based on plumage analyses. Here, we tested five markers (one mitochondrial and four nuclear) and a set of six microsatellite loci for the identification of these two Woodpeckers and their hybrids. Sequencing of DNA from 26 individuals of both Woodpeckers from different parts of their ranges: one allopatric (D. major; Norway) and two sympatric (Poland and Bulgaria) showed that both species can be clearly separated based on all sequence markers. The highest number of fixed nucleotide sites were found in the mtDNA control region and intron 5 of the transforming growth factor. Analyses of microsatellite data distinguished the two species, but all loci showed a large number of common alleles and their utility in identifying hybrids is therefore doubtful. According to the DNA sequence analyses, 2 out of 18 specimens within the sympatric range in Poland were identified as possible hybrids, most probably paternal backcrosses. Moreover, both hybrids are from synantropic populations (settled in cities), whereas none of the D. major sampled in forests and in its allopatric range (Norway) showed signs of an intermixed genotype. Further research on hybridization and introgression in woodpeckers is undoubtedly needed and could be useful for understanding ecological and ethological interactions among these species, particularly for D. syriacus, which is relatively rare in Europe.

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“…Both problems were largely removed with incremental advances and efficiencies but have recently been addressed decisively by nextgeneration sequencing and genomics (Vernesi and Bruford 2009). Microsatellite development can now be achieved rapidly for very little work and $US1000-2000 using next-generation sequencing, and costs will continue to fall (Abdelkrim et al 2009). It is also tractable to apply the same or equivalent markers among species and obtain quantitatively comparable estimates of population demography, for example using resources based on comparing the Chicken genome with genomes of other birds including the Zebra Finch (Hillier et al 2004;Backström et al 2008;Karaiskou et al 2008;Kimball et al 2009).…”

Section: The Genomics Revolution and Associated Technical Advancementioning

confidence: 99%

Towards modelling persistence of woodland birds: the role of genetics

Sunnucks

2011

Emu - Austral Ornithology

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Abstract. Assessing how environmental change affects the probability of persistence of organisms requires an understanding of dispersal through, and occupation of, landscapes, and the associated demographic outcomes. Projections of differences in persistence probability can then be made under different scenarios of land-use and global environmental change. Rates and distances of dispersal, and demographic change and trajectories, are difficult to measure accurately, but genetic approaches can make major contributions. For two decades the field of molecular ecology has been providing useful life-history information relevant to population management, including key ecological attributes such as disease-resistance and thermal biology, mobility, dispersal and gene flow, habitat connectivity, the spatial and temporal scales of population processes, and demography. Genetic estimators of these factors could be employed to a much greater extent than they are currently. To facilitate this increased use, genetic estimates of functional connectivity (mobility and gene flow of organisms) and demography need to be integrated directly into decision-making processes. Population genetics is well suited to Bayesian approaches, with associated benefits including the ability to consider many factors, and estimation of error and parameter sensitivities. Genetic estimators based on the mobility and reproductive success of individual organisms and their key ecological traits can make unique contributions alongside other types of data into agent-based, spatially explicit modelling approaches of real landscape scenarios at the range of scales needed by managers. Virtually all the tools to do this exist. It is imperative that genetic samples be collected for contemporary and future analyses.

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Fast, Cost-Effective Development of Species-Specific Microsatellite Markers by Genomic Sequencing

Cited by 309 publications

References 11 publications

Strong isolation by distance argues for separate population management of endangered blue duck (Hymenolaimus malacorhynchos)

Strong isolation by distance argues for separate population management of endangered blue duck (Hymenolaimus malacorhynchos)

Tests of multiple molecular markers for the identification of Great Spotted and Syrian Woodpeckers and their hybrids

Towards modelling persistence of woodland birds: the role of genetics

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