| 1. |
- Charrier, Grégory, 1978, et al.
(författare)
-
Development of new microsatellite markers derived from expressed sequence tags for the great scallop (Pecten maximus)
- 2012
-
Ingår i: Conservation Genetics Resources. - : Springer Science and Business Media LLC. - 1877-7252 .- 1877-7260. ; 4:4, s. 931-934
-
Tidskriftsartikel (refereegranskat)abstract
- Nine microsatellites were developed from expressed sequence tags sequences for the great scallop (Pecten maximus), and were tested in three natural populations. These markers displayed low to moderate levels of variability. On average across all populations, the number of alleles per locus ranged from 1.333 to 8.667, and the observed and expected heterozygosities ranged from 0.029 to 0.703 and 0.028 to 0.711, respectively. All loci conformed to Hardy-Weinberg equilibrium, except PmGC20 in one single population. These new loci might be very useful for the genetic monitoring of the possible impact of aquaculture on the genetic diversity of native scallop populations.
|
|
| 2. |
- De Wit, Pierre, 1978, et al.
(författare)
-
Single nucleotide polymorphisms are suitable for assessing the success of restocking efforts of the European lobster (Homarus gammarus, L.)
- 2022
-
Ingår i: Conservation Genetics Resources. - : Springer Science and Business Media LLC. - 1877-7252 .- 1877-7260. ; 14:1, s. 47-52
-
Tidskriftsartikel (refereegranskat)abstract
- The European lobster (Homarus gammarus) forms the base of an important fishery along the coasts of Europe. However, stocks have been in decline for many years, prompting new regulations in the fishery and also restocking efforts. An important feature of any restocking effort is the assessment of success in the number of released juveniles that stay and become adult over time. Here, we tested the power of a single nucleotide polymorphism (SNP) DNA marker panel developed for population assignment to correctly infer parentage on the maternal side of lobster larvae, in the absence of known fathers, using lobsters included in a current restocking effort on the Swedish west coast. We also examined the power to reconstruct the unknown paternal genotypes, and examined the number of fathers for each larval clutch. We found that the 96-SNP panel, despite only containing 78 informative markers, allowed us to assign all larvae to the correct mother. Furthermore, with ten genotyped larvae or more, confident paternal genotypes could be reconstructed. We also found that 15 out of 17 clutches were full siblings, whereas two clutches had two fathers. To our knowledge, this is the first time a SNP panel of this size has been used to assess parentage in a crustacean restocking effort. Our conclusion is that the panel works well, and that it could be an important tool for the assessment of restocking success of H. gammarus in the future.
|
|
| 3. |
- Dumilag, Richard V., et al.
(författare)
-
Genotype introduction affects population composition of native Philippine Kappaphycus (Gigartinales, Rhodophyta)
- 2016
-
Ingår i: Conservation Genetics Resources. - : Springer Science and Business Media LLC. - 1877-7252 .- 1877-7260. ; 8:4, s. 439-441
-
Tidskriftsartikel (refereegranskat)abstract
- We present evidence on the presence of introduced red seaweed Kappaphycus cultivar in native Kappapphycus populations in Hoyanjog Island, Surigao del Norte, Philippines. This is the first actual report that native populations of Kappaphycus in the Philippines may possibly face genotype shifting from native to introduced. Our findings call for a challenge in conservation laws to design resource management strategies and to regulate Kappaphycus farming in sites where there are known native Kappaphycus genotypes.
|
|
| 4. |
- Ekblom, Robert, Docent, 1976-, et al.
(författare)
-
Development of transcriptome genetic markers for the great snipe (Gallinago media)
- 2017
-
Ingår i: Conservation Genetics Resources. - : SPRINGER. - 1877-7252 .- 1877-7260. ; 9:4, s. 643-645
-
Tidskriftsartikel (refereegranskat)abstract
- We sequenced the transcriptomes of 14 great snipe (Gallinago media) males from the Gavalia study population (central Norway) using Roche 454 technology. The assembled transcriptome sequences (RNA-Seq) was used to identify 140 microsatellite repeat sequences with sufficient flanking sequence information for primer design. In addition several 1000 single nucleotide polymorphisms in the transcriptome were identified, and a small subset of these were verified by independent genotyping.
|
|
| 5. |
- Ekblom, Robert, Docent, 1976-, et al.
(författare)
-
Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples
- 2021
-
Ingår i: Conservation Genetics Resources. - : Springer Nature. - 1877-7252 .- 1877-7260. ; 13:3, s. 261-274
-
Tidskriftsartikel (refereegranskat)abstract
- For conservation genetic studies using non-invasively collected samples, genome-wide data may be hard to acquire. Until now, such studies have instead mostly relied on analyses of traditional genetic markers such as microsatellites (SSRs). Recently, high throughput genotyping of single nucleotide polymorphisms (SNPs) has become available, expanding the use of genomic methods to include non-model species of conservation concern. We have developed a 96-marker SNP array for use in applied conservation monitoring of the Scandinavian wolverine (Gulo gulo) population. By genotyping more than a thousand non-invasively collected samples, we were able to obtain precise estimates of different types of genotyping errors and sample dropout rates. The SNP panel significantly outperforms the SSR markers (and DBY intron markers for sexing) both in terms of precision in genotyping, sex assignment and individual identification, as well as in the proportion of samples successfully genotyped. Furthermore, SNP genotyping offers a simplified laboratory and analysis pipeline with fewer samples needed to be repeatedly genotyped in order to obtain reliable consensus data. In addition, we utilised a unique opportunity to successfully demonstrate the application of SNP genotype data for reconstructing pedigrees in wild populations, by validating the method with samples from wild individuals with known relatedness. By offering a simplified workflow with improved performance, we anticipate this methodology will facilitate the use of non-invasive samples to improve genetic management of many different types of populations that have previously been challenging to survey.
|
|
| 6. |
- Hemmilä, Sofia, 1984-, et al.
(författare)
-
Development of eleven microsatellite markers in the red-listed tree species Myristica malabarica
- 2010
-
Ingår i: Conservation Genetics Resources. - : Springer Science and Business Media LLC. - 1877-7252 .- 1877-7260. ; 2:Suppl. 1, s. 305-307
-
Tidskriftsartikel (refereegranskat)abstract
- The Myristicaceae family is a primitive angiosperm family and is characterized by species that are highly endemic to the Western Ghats area of India. Myristica malabarica is confined to the evergreen forests of Western Ghats and Sri Lanka. In this paper we describe for the first time the development of eleven polymorhpic microsatellite markers for Myristica malabarica, which had 2–14 alleles per locus. These microsatellite markers could be used to study the population genetic structure of the species.
|
|
| 7. |
- Hoyos, Manuel, et al.
(författare)
-
A simple and cost-effective method for obtaining DNA from a wide range of animal wildlife samples
- 2017
-
Ingår i: Conservation Genetics Resources. - : Springer Science and Business Media LLC. - 1877-7252 .- 1877-7260. ; 9:4, s. 513-521
-
Tidskriftsartikel (refereegranskat)abstract
- Genetic analyses have become increasingly important in animal wildlife research where they have provided information of direct relevance to species and population management. An integral part of genetic analysis is the isolation of PCR-amplifiable DNA. However, addressing the issue of DNA isolation in animal wildlife research can be challenging due to the wide range of potential biological sources used to obtain DNA. Here, we present a modified silica-based DNA isolation method for obtaining PCR-amplifiable DNA from a wide range of biological sources typically encountered in animal wildlife research. We compared the present method with commonly used non-commercial and commercially available DNA extraction methods. Our results show that DNA yield, quality and purity (as assessed by PCR amplification) are qualitatively comparable, and in many cases even better, than commonly used non-commercial and commercially available DNA extraction methods. We describe the main factors that can affect DNA yield and provide variants of the basic protocol that can be performed according to the DNA source. The simplicity, versatility and cost-effectiveness of this method, as well as the absence of hazardous reagents, makes it a valuable addition to the molecular toolbox of any wildlife genetics laboratory.
|
|
| 8. |
- Hughes, Morgan, et al.
(författare)
-
Successful DNA amplification of DNA from non-destructive buccal swabbing in Vespertilionid and Rhinolophid bats
- 2024
-
Ingår i: Conservation Genetics Resources. - : Springer Nature. - 1877-7252 .- 1877-7260. ; 16:2, s. 199-202
-
Tidskriftsartikel (refereegranskat)abstract
- Acquiring DNA from wild bats (Mammalia: Chiroptera) is typically undertaken utilizing highly invasive (but non-lethal) sampling techniques comprising wing biopsies and occasional blood samples. While non-invasive sampling is possible through the extraction of DNA from faecal samples, it is not always possible to acquire samples from individual bats whilst conducting fieldwork, and as such, this method is primarily applicable to roost occupancy identification. Similarly, wing swabbing is liable to cross-contamination from roost mates. Here we present the first use of oral (buccal) swabbing for successful, species-resolution DNA sequencing of Vespertilionidae and Rhinolophidae in 10 bat species (nine Vespertilionidae and one Rhinolophidae) from the UK.
|
|
| 9. |
- Jackson, Jennifer A., et al.
(författare)
-
Guidelines for collecting and maintaining archives for genetic monitoring
- 2012
-
Ingår i: Conservation Genetics Resources. - : Springer Science and Business Media LLC. - 1877-7252 .- 1877-7260. ; 4:2, s. 527-536
-
Forskningsöversikt (refereegranskat)abstract
- Rapid advances in molecular genetic techniques and the statistical analysis of genetic data have revolutionized the way that populations of animals, plants and microorganisms can be monitored. Genetic monitoring is the practice of using molecular genetic markers to track changes in the abundance, diversity or distribution of populations, species or ecosystems over time, and to follow adaptive and non-adaptive genetic responses to changing external conditions. In recent years, genetic monitoring has become a valuable tool in conservation management of biological diversity and ecological analysis, helping to illuminate and define cryptic and poorly understood species and populations. Many of the detected biodiversity declines, changes in distribution and hybridization events have helped to drive changes in policy and management. Because a time series of samples is necessary to detect trends of change in genetic diversity and species composition, archiving is a critical component of genetic monitoring. Here we discuss the collection, development, maintenance, and use of archives for genetic monitoring. This includes an overview of the genetic markers that facilitate effective monitoring, describes how tissue and DNA can be stored, and provides guidelines for proper practice.
|
|
| 10. |
- Jansson, Mija, 1979-, et al.
(författare)
-
mPed : a computer program for converting pedigree data to a format used by the PMx-software for conservation genetic analysis
- 2013
-
Ingår i: Conservation Genetics Resources. - : Springer Science and Business Media LLC. - 1877-7252 .- 1877-7260. ; 5:3, s. 651-653
-
Tidskriftsartikel (refereegranskat)abstract
- There is a growing need for conservation genetic management of animal populations when individual relatedness data (pedigrees) are available. Such data can be used to monitor rates of inbreeding and loss of genetic diversity. Traditionally, pedigree analysis for conservationmanagement has focused on zoo populations of threatened wild animals; available software has been developed in that context. Population Management x (PMx) is a free software for estimating genetic parameters including inbreeding, kinship, founder allele contribution and survival. PMx is an accessory program to the zoo studbook platform Single Population Analysis and Records Keeping System (SPARKS) and is not easily applied outside this platform, but such use is of interest for various domestic breeds or wild populations. We developed a converter program (mPed) for making pedigrees of any studbook format fitting the input requirements of PMx. mPed can be downloaded free at www.popgen.su.se/mped.php
|
|
