Isolation and characterisation via 454 sequencing of microsatellites from the tawny frogmouth, Podargus strigoides (Class Aves, Family Podargidae)

2012 ◽  
Vol 60 (2) ◽  
pp. 133
Author(s):  
Fiona E. Hogan ◽  
Marian Weaving ◽  
Gregory R. Johnston
Keyword(s):  
Population Genetics ◽  
Gene Flow ◽  
Microsatellite Markers ◽  
Reproductive Ecology ◽  
454 Sequencing ◽  
Urban Environments ◽  
Shotgun Sequencing ◽  
Target Species ◽  
Single Population ◽  
Polymorphic Microsatellite

We isolated 24 novel polymorphic microsatellite markers from the tawny frogmouth, a nocturnal bird endemic to Australia, which has successfully adapted to urban environments. Initially, 454 shotgun sequencing was used to identify 733 loci with primers designed. Of these, we trialled 30 in the target species of which all amplified a product of expected size. Subsequently, all 30 of these loci were screened for variation in 25 individuals, from a single population in Melbourne, Victoria, Australia. Twenty-eight loci were polymorphic with observed heterozygosity ranging from 0.03 to 0.96 (mean 0.58) and the number of alleles per locus ranged from 2 to 18 (average of 6.5); we confirmed that 24 loci conformed to Hardy–Weinberg expectations. The 24 loci identified here will be sufficient to unequivocally identify individuals and will be useful in understanding the reproductive ecology, population genetics and the gene flow amongst localities in urban environments where this bird thrives.

scholarly journals Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

2018 ◽  
Author(s):  
Bruce F Murray ◽  
Michael A Reid ◽  
Shu-Biao Wu
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Extreme Variability ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

scholarly journals Population Genetics of the Red Rock Lobster,  Jasus edwardsii

2021 ◽  
Author(s):  
◽  
Luke Thomas
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Rocky Reef ◽  
Rock Lobster ◽  
Wide Range ◽  
Jasus Edwardsii ◽  
Polymorphic Microsatellite

<p>Understanding patterns of gene flow across a species range is a vital component of an effective fisheries management strategy. The advent of highly polymorphic microsatellite markers has facilitated the detection of fine-scale patterns of genetic differentiation at levels below the resolving power of earlier techniques. This has triggered the wide-spread re-examination of population structure for a number of commercially targeted species. The aims of thesis were to re-investigate patterns of gene flow of the red rock lobster Jasus edwardsii throughout New Zealand and across the Tasman Sea using novel microsatellite markers. Jasus edwardsii is a keystone species of subtidal rocky reef system and supports lucrative export markets in both Australia and New Zealand. Eight highly polymorphic microsatellite markers were developed from 454 sequence data and screened across a Wellington south coast population to obtain basic diversity indices. All loci were polymorphic with the number of alleles per locus ranging from 6-39. Observed and expected heterozygosity ranged from 0.563-0.937 and 0.583-0.961, respectively. There were no significant deviations from Hardy-Weinberg equilibrium following standard Bonferroni corrections. The loci were used in a population analysis of J. edwardsii that spanned 10 degrees of latitude and stretched 3,500 km across the South Pacific. The analysis rejected the null-hypothesis of panmixia based on earlier mDNA analysis and revealed significant population structure (FST=0.011, RST=0.028) at a wide range of scales. Stewart Island was determined to have the highest levels of genetic differentiation of all populations sampled suggesting a high degree of reproductive isolation and self-recruitment. This study also identified high levels of asymmetric gene flow from Australia to New Zealand indicating a historical source-sink relationship between the two countries. Results from the genetic analysis were consistent with results from oceanographic dispersal models and it is likely that the genetic results reflect historical and contemporary patterns of Jasus edwardsii dispersal and recruitment throughout its range.</p>

Twenty-five new polymorphic microsatellites for the eastern mosquitofish, Gambusia holbrooki (Actinopterygii : Poeciliidae), an invasive species in Australia

2012 ◽  
Vol 60 (4) ◽  
pp. 235 ◽  
Author(s):  
Kate D. L. Umbers ◽  
Michael D. Jennions ◽  
J. Scott Keogh
Keyword(s):  
Invasive Species ◽  
Paternity Analysis ◽  
Gambusia Holbrooki ◽  
Target Species ◽  
Single Population ◽  
Invasive Range ◽  
Polymorphic Microsatellites ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Eastern Mosquitofish

We isolated 25 new polymorphic microsatellite markers from the eastern mosquitofish, Gambusia holbrooki. Initially, 454 shotgun sequencing was used to identify 1187 loci for which primers could be designed. Of these 1187, we trialled 48 in the target species, 40 of which amplified a product of expected size. Subsequently, those 40 loci were screened for variation in 48 individuals from a single population in Canberra, Australia. Twenty loci were in Hardy–Weinberg equilibrium and polymorphic, with observed heterozygosity ranging from 0.04 to 0.72 (mean: 0.45 ± 0.18) and the number of alleles per locus ranged from 2 to 5 (mean: 3.20 ± 1.05). These loci will be useful in understanding genetic variation, paternity analysis and in managing this species across both its native and invasive range.

Novel polymorphic microsatellite markers for population genetics of the endangered Caribbean star coral, Montastraea faveolata

2012 ◽  
Vol 43 (2) ◽  
pp. 167-172 ◽  
Author(s):  
Sarah W. Davies ◽  
Muneeb Rahman ◽  
Eli Meyer ◽  
Elizabeth A. Green ◽  
Emmanual Buschiazzo ◽  
...  
Keyword(s):  
Population Genetics ◽  
Microsatellite Markers ◽  
Montastraea Faveolata ◽  
Polymorphic Microsatellite

Development and characterization of 15 polymorphic microsatellite markers for North Pacific albatrosses using paired-end Illumina shotgun sequencing

2014 ◽  
Vol 6 (2) ◽  
pp. 491-493
Author(s):  
Luis D. Hernandez ◽  
Zachary T. Lounsberry ◽  
Paul W. Collins ◽  
Robert W. Henry ◽  
Seth D. Newsome ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
North Pacific ◽  
Shotgun Sequencing ◽  
Polymorphic Microsatellite

Isolation and characterisation of eighteen microsatellite markers from the sea cucumber Holothuria scabra (Echinodermata : Holothuriidae)

2012 ◽  
Vol 60 (6) ◽  
pp. 368 ◽  
Author(s):  
Alison J. Fitch ◽  
Grant Leeworthy ◽  
Xiaoxu Li ◽  
Will Bowman ◽  
Luke Turner ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Sea Cucumber ◽  
Asia Pacific ◽  
Asia Pacific Region ◽  
Single Population ◽  
Important Species ◽  
Holothuria Scabra ◽  
Commercially Important ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

We isolated 18 new, polymorphic, microsatellite markers from Holothuria scabra, a commercially important species of sea cucumber found throughout the Asia-Pacific region. Next-generation sequencing was used to identify 206 unique loci for which primers were designed. Of these unique loci, we trialled 65 primer pairs in the target species, and 48 (74%) amplified a product of the expected size. Eighteen loci were found to be polymorphic and reliable, and were screened for variation in 50 individuals, from a single population from Croker Island, Northern Territory, Australia. Observed heterozygosity ranged from 0.00 to 0.96 (mean = 0.46) and the number of alleles per locus from 2 to 28 (mean = 9.61). These loci will be useful for the investigation of population structure and mating systems in H. scabra and may also be of use in other holothurian species.

scholarly journals Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

2018 ◽  
Author(s):  
Bruce F Murray ◽  
Michael A Reid ◽  
Shu-Biao Wu
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Extreme Variability ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

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