Nationwide abundance and distribution of African forest elephants across Gabon using non-invasive SNP genotyping

Single nucleotide polymorphisms (SNPs) which represent the most widespread source of sequence variation in genomes, are becoming a routine application in several fields such as forensics, ecology and conservation genetics. Their use, requiring short amplifications, may allow a more efficient genotyping of degraded DNA. We provide the first application of SNP genotyping in an Italian non-invasive genetic monitoring project of the wolf. We compared three different techniques for genotyping SNPs: pyrosequencing, SNaPshot? and TaqMan? Probe Assay in Real-Time PCR. We successively genotyped nine SNPs using the TaqMan Probe Assay in 51 Italian wolves, 57 domestic dogs, 15 wolf x dog hybrids and 313 wolf scats collected in the northern Apennines. The obtained results were used to estimate genetic variability and PCR error rates in SNP genotyping protocols compared to standard microsatellite analysis. We evaluated the cost, laboratory effort and reliability of these different markers and discuss the possible future use of VeraCode, SNPlex and Fluidigm EP1 system in wild population monitoring.

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Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples

Conservation Genetics Resources ◽

10.1007/s12686-021-01208-5 ◽

2021 ◽

Author(s):

Robert Ekblom ◽

Malin Aronsson ◽

Franziska Elsner-Gearing ◽

Malin Johansson ◽

Toby Fountain ◽

...

Keyword(s):

Snp Array ◽

Snp Genotyping ◽

Individual Identification ◽

Nucleotide Polymorphisms ◽

Genetic Management ◽

Gulo Gulo ◽

Non Invasive ◽

Species Of Conservation Concern ◽

Different Types ◽

Improved Performance

AbstractFor 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.

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First Hydroacoustic Assessment Of Fish Abundance And Distribution In The Shallow Sub-Basin Of Lake Titicaca

Aquaculture & Fisheries ◽

10.24966/aaf-5523/100034 ◽

2020 ◽

Vol 4 (2) ◽

pp. 1-7

Author(s):

Erick Loayza ◽

Keyword(s):

Climate Change ◽

South America ◽

Great Lake ◽

Lake Titicaca ◽

Non Invasive ◽

Untreated Wastewater ◽

El Alto ◽

Invasive Techniques ◽

Abundance And Distribution ◽

Tropical Freshwater

For the last two decades, a rapid eutrophication process impacts Lake Titicaca, the largest tropical freshwater lake in South America and the main highest Great Lake. This is especially notorious in the Bolivian sector of its shallow Lago Menor sub-basin. Lago Menor is deteriorated by the combination of multiple contaminations (domestic, industrial and mining) from untreated wastewater discharged from the urban area of El Alto, indiscriminate overfishing, and climate change. These threats particularly affect the native Andean killifish genus Orestias, the ecology and dynamics of which require in-depth studies with non-invasive techniques.

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An accurate molecular method to sex savannah elephants using PCR amplification of Amelogenin gene

10.1101/856419 ◽

2019 ◽

Author(s):

George G Lohay

Keyword(s):

Pcr Amplification ◽

Sex Identification ◽

Molecular Method ◽

Genetic Studies ◽

Non Invasive ◽

Y Chromosomes ◽

Forest Elephants ◽

Observational Errors ◽

A New Technique ◽

Forward Primer

AbstractThe use of molecular methods to identify the sex of elephants from non-invasive samples is essential for studies of population dynamics and population genetics. We designed a new technique for sex identification in savannah elephants using Amelogenin (AMEL) genes. The X-Y homologs of AMEL genes is known to be suitable for sex determination in pigs and some bovids. In this study on savannah elephants, the use of AMEL genes was more successful than previous methods that relied on genes found exclusively on Y-chromosomes, such as SRY, to distinguish males from females. We designed a common forward primer and two reverse primers for X- and Y-specific AMEL genes to obtain 262 bp and 196 bp PCR amplicons from X and Y genes, respectively. We tested the primers for the identification of the sex of 132 savannah elephants from fecal samples. The sex of 126 individuals (95.45%) matched observational data, while 6 (4.54%) did not match. This discrepancy observed was likely due to observational errors in the field, where high grass reduces the ability to accurately sex young individuals. Through our stool sample results, we have shown that the use of only three primers for AMELX/Y provides a highly accurate PCR-based method for sex identification in savannah elephants. The method is fast and shows more success than the SRY system by avoiding the inherent ambiguities of the previous PCR-based methods that made it difficult to distinguish between female samples and failed amplification reactions. Our sex identification method is non-invasive and can potentially be applied in population genetic studies and forensics tests on both savannah as well as forest elephants.

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Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs

10.21203/rs.3.rs-870405/v1 ◽

2021 ◽

Author(s):

Stefan Gavriliuc ◽

Salman Reza ◽

Chanwoori Jeong ◽

Fitsum Getachew ◽

Philip Dunstan McLoughlin ◽

...

Keyword(s):

High Throughput Sequencing ◽

Snp Genotyping ◽

Nucleotide Polymorphisms ◽

Feral Horses ◽

Non Invasive ◽

Genetics Research ◽

Snp Data ◽

Genome Wide ◽

Snp Microarrays ◽

Template Dna

Abstract The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of Single Nucleotide Polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics’ Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10ng of host DNA (ATG’s recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 86.7% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.

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X-ray microtomography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100107058 ◽

1988 ◽

Vol 46 ◽

pp. 998-999

Author(s):

H.W. Deckman ◽

B.F. Flannery ◽

J.H. Dunsmuir ◽

K.D' Amico

Keyword(s):

Computed Tomography ◽

Internal Structure ◽

Imaging Technique ◽

Three Dimensional ◽

Tissue Structure ◽

Individual Element ◽

X Ray ◽

Non Invasive ◽

Panoramic Imaging ◽

Three Dimensional Images

We have developed a new X-ray microscope which produces complete three dimensional images of samples. The microscope operates by performing X-ray tomography with unprecedented resolution. Tomography is a non-invasive imaging technique that creates maps of the internal structure of samples from measurement of the attenuation of penetrating radiation. As conventionally practiced in medical Computed Tomography (CT), radiologists produce maps of bone and tissue structure in several planar sections that reveal features with 1mm resolution and 1% contrast. Microtomography extends the capability of CT in several ways. First, the resolution which approaches one micron, is one thousand times higher than that of the medical CT. Second, our approach acquires and analyses the data in a panoramic imaging format that directly produces three-dimensional maps in a series of contiguous stacked planes. Typical maps available today consist of three hundred planar sections each containing 512x512 pixels. Finally, and perhaps of most import scientifically, microtomography using a synchrotron X-ray source, allows us to generate maps of individual element.

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