Characterisation of 14 microsatellite markers for the Australian fig psylloid, Mycopsylla fici

2015 ◽  
Vol 63 (4) ◽  
pp. 233 ◽  
Author(s):  
Caroline Fromont ◽  
Markus Riegler ◽  
James M. Cook
Keyword(s):  
Illumina Miseq ◽  
Insect Herbivore ◽  
Vertebrate Species ◽  
Moreton Bay ◽  
Lord Howe Island ◽  
Hardy Weinberg Equilibrium ◽  
Sap Feeding ◽  
Polymorphic Microsatellite ◽  
Individual Trees ◽  
Two Populations

The Australian fig psylloid, Mycopsylla fici, is a sap-feeding insect herbivore that is host-specific to the Moreton Bay fig, Ficus macrophylla. It has periodic major outbreaks that can cause complete defoliation of individual trees and massive decrease in local leaf and fruit availability, with significant effects for many insect and vertebrate species that utilise the tree’s resources. We used ⅛ of an Illumina MiSeq run to sequence genomic DNA from two pools of five psylloids from two different field sites. We identified 14 polymorphic microsatellite loci and characterised them in 43 individuals from two populations (Sydney and Lord Howe Island, Australia). Within populations, the number of alleles ranged from 4 to 15 per locus with observed heterozygosity of 0–0.9. Four loci deviated from Hardy–Weinberg equilibrium. The microsatellite primers will be useful for the study of population genetics and gene flow within and between psylloid populations.

Isolation and characterisation of 16 novel polymorphic microsatellite loci for the Eurasian coot (Fulica atra)

2016 ◽  
Vol 64 (6) ◽  
pp. 430
Author(s):  
Tianshu Lv ◽  
Wanchao Zhu ◽  
Shuyu Xue ◽  
Huanxin Zhang ◽  
Xiaodong Gao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Genomic Library ◽  
Enriched Genomic Library ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Fulica Atra ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Two Populations

To study the genetic diversity of the Eurasian coot (Fulica atra), 16 novel microsatellites were isolated and characterised using a (AC)12-enriched genomic library. Polymorphism of each locus was detected in 19 individuals from Weishan Lake and Zhaoyang Lake, both located in Shandong Province, China. These microsatellite loci revealed 3–12 alleles in two populations. One locus (Fa6) showed significant deviations from Hardy–Weinberg equilibrium in the Zhaoyang Lake population. By means of Principal Coordinates Analysis, 19 individuals were divided into two groups, which verified they were from two populations. These novel microsatellites will be useful for further studies and genetic analyses of the Eurasian coot.

scholarly journals Population Genetic Structure of Rhizoctonia oryzae-sativae from Rice in Latin America and Its Adaptive Potential to Emerge as a Pathogen on Urochloa Pastures

2017 ◽  
Vol 107 (1) ◽  
pp. 121-131 ◽  
Author(s):  
Danilo A. dos Santos Pereira ◽  
Paulo C. Ceresini ◽  
Vanina L. Castroagudín ◽  
Lina M. Ramos-Molina ◽  
Edisson Chavarro-Mesa ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Reproductive System ◽  
Population Genetic ◽  
Upland Rice ◽  
Adaptive Potential ◽  
Rhizoctonia Oryzae ◽  
Hardy Weinberg Equilibrium ◽  
Two Populations ◽  
Brazilian Populations

The fungus Rhizoctonia oryzae-sativae is an important pathogen that causes the aggregated sheath spot disease on rice. In this study, we investigated the genetic structure of rice-adapted populations of R. oryzae-sativae sampled from traditional rice-cropping areas from the Paraíba Valley, São Paulo, Brazil, and from Meta, in the Colombian Llanos, in South America. We used five microsatellite loci to measure population differentiation and infer the pathogen’s reproductive system. Gene flow was detected among the three populations of R. oryzae-sativae from lowland rice in Brazil and Colombia. In contrast, a lack of gene flow was observed between the lowland and the upland rice populations of the pathogen. Evidence of sexual reproduction including low clonality, Hardy-Weinberg equilibrium within loci and gametic equilibrium between loci, indicated the predominance of a mixed reproductive system in all populations. In addition, we assessed the adaptive potential of the Brazilian populations of R. oryzae-sativae to emerge as a pathogen to Urochloa spp. (signalgrass) based on greenhouse aggressiveness assays. The Brazilian populations of R. oryzae-sativae were probably only incipiently adapted as a pathogen to Urochloa spp. Comparison between RST and QST showed the predominance of diversifying selection in the divergence between the two populations of R. oryzae-sativae from Brazil.

Woodhen

2013 ◽  
Author(s):  
Clifford Frith
Keyword(s):  
Captive Breeding ◽  
Wild Population ◽  
Breeding Biology ◽  
Vertebrate Species ◽  
Success Story ◽  
Potential Threat ◽  
Lord Howe Island ◽  
Captive Breeding Programme ◽  
History Of ◽  
Constant Potential

This book tells the fascinating success story of saving the flightless Woodhen of Lord Howe Island. This unique large rail, an iconic and highly endangered Australian bird, was at the very brink of extinction with just 15 individuals found in 1980, when bold and risky actions were taken to save it. The book begins with the discovery and ecology of Lord Howe Island. It then details the history of the Woodhen, its place among the rails and their evolution of flightlessness, the planning, implementation and trials, tribulations and successes of the captive breeding programme and the way in which the wild population recovered. The ecology, behaviour and breeding biology of this unique flightless island rail are also discussed. The text is accompanied by numerous photographs and drawings. This is a story of survival, yet the bird remains highly endangered as it is under constant potential threat, which could tip it over the brink and to extinction. The Woodhen provides gripping insights into the potential for both losing and saving vertebrate species. Winner of a 2014 Whitley Awards Certificate of Commendation for Historical Zoology.

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.

Characterization of 17 novel microsatellite loci in the Nile monitor (Varanus niloticus) via 454 pyrosequencing

2016 ◽  
Vol 37 (1) ◽  
pp. 121-125 ◽  
Author(s):  
Jared P. Wood ◽  
Todd S. Campbell ◽  
Robert B. Page
Keyword(s):  
Microsatellite Loci ◽  
454 Pyrosequencing ◽  
Sequence Similarity ◽  
Null Alleles ◽  
The Us ◽  
Hardy Weinberg Equilibrium ◽  
The City ◽  
Two Populations ◽  
Genotypic Disequilibrium

We used 454 pyrosequencing to characterize 17 novel microsatellite loci from the Nile monitor (Varanus niloticus), using samples from an invasive population in the US state of Florida. These markers were screened for variation in 40 individuals from the City of Cape Coral. Observed heterozygosity ranged from 0.18 to 0.73 (mean ± SE = 0.46 ± 0.06) and the number of alleles per locus ranged from 1 to 4 (mean ± SE = 2.5 ± 0.2). Preliminary genotyping of samples from populations in West Palm Beach and Homestead revealed two loci (Mon6andMon15) that are monomorphic in Cape Coral, but polymorphic in these other two populations. We found no statistical departures from Hardy-Weinberg equilibrium or evidence of null alleles. However, there was statistical evidence for genotypic disequilibrium betweenMon1-Mon14andMon3-Mon8. BLASTn searches of NCBI’s nr/nt database identified four microsatellites containing 454 fragments that exhibit substantial sequence similarity to loci in other reptilian genomes, suggesting these markers should be prioritized by researchers interested in cross-amplification in other varanids. The resources we have developed will enable investigations of the population genetic dynamics of invasive Nile monitors in Florida and may facilitate studies within this species native range.

scholarly journals Characterisation of nine new polymorphic microsatellite loci in the reticulated glass frog Hyalinobatrachium valerioi (Centrolenidae)

2014 ◽  
Vol 35 (2) ◽  
pp. 243-246 ◽  
Author(s):  
Eva Ringler ◽  
Alexandra Mangold ◽  
Katharina Trenkwalder ◽  
Max Ringler ◽  
Walter Hödl
Keyword(s):  
Evolutionary Biology ◽  
Behavioural Ecology ◽  
Field Site ◽  
Local Populations ◽  
Wide Range ◽  
Hardy Weinberg Equilibrium ◽  
Individual Mating ◽  
Genetic Mating System ◽  
Polymorphic Microsatellite ◽  
Scientific Questions

Here we document the development of thirteen novel microsatellite markers for the reticulated glass frog Hyalinobatrachium valerioi (Centrolenidae). Nine of those markers were polymorphic and contained between 4 and 34 alleles per locus (mean = 20.3) in 138 individuals (91 males, 47 females) from the field site ‘La Gamba’, Costa Rica. Average observed heterozygosity was 0.76. Two loci (Hyval19 and Hyval21) significantly deviated from Hardy-Weinberg equilibrium. We did not find evidence for linkage disequilibrium among any of the loci. These markers will serve to identify the genetic mating system in H. valerioi, investigate gene flow between local populations, and reconstruct parent-offspring relationships for studies on individual mating and reproductive success. Therefore, these markers will serve to answer a wide range of scientific questions in conservation, behavioural ecology, and also evolutionary biology.

scholarly journals Validation and characterization of thirteen microsatellite markers for queen conch, Lobatus gigas

2016 ◽  
Author(s):  
Nathan K Truelove ◽  
Loong Fai Ho ◽  
Richard F Preziosi ◽  
Stephen J. Box
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Null Allele ◽  
Florida Keys ◽  
Illumina Miseq ◽  
Allele Frequencies ◽  
Null Alleles ◽  
Queen Conch ◽  
Hardy Weinberg Equilibrium

We report the development and characterization of 13 novel microsatellite loci for the Caribbean queen conch, Lobatus gigas, an ecologically and commercially important marine gastropod. Paired-end sequencing was carried out on genomic DNA from a single queen conch using half a flow cell lane of an Illumina MiSeq. A total of 48 potentially amplifiable loci containing microsatellites were tested on 45 individuals from the Florida Keys and Bahamas. In total, 13 consistently amplifying and polymorphic microsatellite loci were identified. The number of alleles ranged from 4 to 26 and observed heterozygosities ranged from 0.340 to 1.00. There was no evidence of scoring error, large allele dropout, or evidence of linkage disequilibrium at any locus. Four loci deviated from Hardy-Weinberg equilibrium due to moderate levels of null alleles (null allele frequencies ranged from 0.081 to 0.230). Although null alleles were detected at four microsatellite loci, the high levels of polymorphism and moderate null allele frequencies suggest that these 13 novel microsatellite markers will be useful for researchers carrying out conservation genetic studies of L. gigas.

scholarly journals Isolation and Characterization of Polymorphic Microsatellite loci from the Invasive Worm Branchiomma luctuosum (Grube, 1870) (Annelida: Sabellidae)

2018 ◽  
Author(s):  
Flávia Ariany Belato ◽  
Elisa Maria Costa-Paiva ◽  
Paulo Cesar Paiva ◽  
Anderson Vilasboa
Keyword(s):  
Null Alleles ◽  
Anthropogenic Activity ◽  
Brazilian Coast ◽  
Isolation And Characterization ◽  
History Of ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
High Level ◽  
Activity Areas

Introduction of exotic species in new areas through anthropic action is one of the major problems that can affect biodiversity. Branchiomma luctuosum is known for its highly invasive potential and the actual occurrence of species commonly associated with port activity areas is an extra evidence that this anthropogenic activity should not be underestimated. In order to develop suitable molecular markers for future studies on colonization routes and population dynamics of the invading individuals of B. luctuosum, nine highly polymorphic microsatellite loci were isolated and their polymorphism levels were evaluated. These loci showed a range of number of alleles per locus from five to ten and all loci had a high level of genetic diversity, and exhibited significant heterozygote deficiencies probably due to the presence of null alleles. Significant deviations from the Hardy-Weinberg equilibrium were detected at several loci and most of them were related to a heterozygous deficit. Heterozygous deficiency can be expected in this case due to the biology and history of this invasive species, in relation to its recent introduction in Brazilian coast and possible action of multiple introductory events.

Development and characterization of 20 polymorphic microsatellite markers for the white-bellied pangolin Phataginus tricuspis (Mammalia, Pholidota)

2020 ◽  
Author(s):  
Samantha Aguillon ◽  
Alain Din Dipita ◽  
Emilie Lecompte ◽  
Alain Didier Missoup ◽  
Maurice Tindo ◽  
...  
Keyword(s):  
Microsatellite Loci ◽  
Unknown Origin ◽  
Conservation Strategies ◽  
Multilocus Genotype ◽  
Intermediate Hosts ◽  
North East ◽  
Discriminating Power ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Source Populations

Abstract Pangolins, or scaly anteaters, have recently been flagshiped as one of the most illegally traded mammals, and as a corollary, as potential intermediate hosts at the origin of the COVID-19 pandemic. In order to improve the traceability of their trade, we developed 20 polymorphic microsatellite loci for the white-bellied pangolin (Phataginus tricuspis), the species most frequently found on African bushmeat markets. We genotyped 24 white-bellied pangolins from the Douala market, Cameroon, originating from the Ebo forest c. 75 km north-east of Douala. The number of alleles per locus ranged from 4 to 12 (mean=6.95), and mean observed and expected heterozygosities were 0.592 (0.208-0.875) and 0.671 (0.469-0.836), respectively. Genetic diversity was higher than that cross-estimated from microsatellite loci developed for other species of pangolins. Two loci deviated from Hardy-Weinberg equilibrium and two loci showed linkage disequilibrium. Genetic variance (PCoA) was increased with the addition of 13 pangolins of unknown origin, possibly suggesting that the Douala market is fed from differentiated source populations of white-bellied pangolins. Each of the 37 individuals had a unique multilocus genotype. The unbiased probability of identity (uPI) and the probability of identity among siblings (PIsibs) were both very low (uPI=8.443 e-21; PIsibs=1.011 e-07). Only five microsatellite loci were needed to reach the conservative value of PIsibs < 0.01, overall indicating a powerful discriminating power of our combined loci. These 20 newly developed microsatellite loci might prove useful in tracing the local-to-global trade of the white-bellied pangolin, and will hopefully contribute to the DNA-assisted implementation of future conservation strategies at reasonable costs.

Sign in / Sign up

Export Citation Format

Share Document