A novel primer set for mammal species identification from feces samples

Grattarola, Florencia; González, Susana; Cosse, Mariana

doi:10.1007/s12686-014-0359-5

Cited by 9 publications

(5 citation statements)

References 13 publications

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“…In the small number of cases where a clear sequence was not obtained from a scat, we found that the sequences obtained were mixed, probably arising from the amplification of 2 or more species in the same sample. This could arise from cross-contamination among samples but is more likely the result of the amplification of prey DNA present in the scat [ 14 , 55 ]. We have previously observed this phenomenon when using a single species test to detect fox DNA, where rabbit or hare DNA were sometimes erroneously amplified [ 37 ].…”

Section: Discussionmentioning

confidence: 99%

A single mini-barcode test to screen for Australian mammalian predators from environmental samples

2017

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Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover. Instead, targeted short diagnostic markers are required to serve as diagnostic mini-barcodes. The mitochondrial genome is a useful source of such trace DNA markers because it provides good resolution at the species level and occurs in high copy numbers per cell. We developed a mini-barcode based on a short (178 bp) fragment of the conserved 12S ribosomal ribonucleic acid mitochondrial gene sequence, with the goal of discriminating amongst the scats of large mammalian predators of Australia. We tested the sensitivity and specificity of our primers and can accurately detect and discriminate amongst quolls, cats, dogs, foxes, and devils from trace DNA samples. Our approach provides a cost-effective, time-efficient, and non-invasive tool that enables identification of all 8 medium-large mammal predators in Australia, including native and introduced species, using a single test. With modification, this approach is likely to be of broad applicability elsewhere.

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Section: Discussionmentioning

confidence: 99%

A single mini-barcode test to screen for Australian mammalian predators from environmental samples

2017

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“…Las técnicas no invasivas de muestreo genético se utilizan para realizar diversos estudios en distintas especies de mamíferos neotropicales (González and Barbanti Duarte 2007;RuizGarcía et al 2007;Trinca et al 2013;Rodgers and Janečka 2013;Grattarola et al 2015;Byrne et al 2015;Trigila et al 2016). Particularmente, para los mamíferos se han realizado distintos esfuerzos por optimizar la obtención de ADN a partir de pelos y heces.…”

Section: Nardelli and Ji Túnezunclassified

Aportes de la genética de la conservación al estudio de los mamíferos neotropicales: revisión y análisis crítico

Nardelli

Túnez

2017

Ecol. Austral

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R��.Si bien todos los seres vivos modifican su entorno, nuestra especie ha adquirido la capacidad de hacerlo a una escala espacio-temporal superlativa. Como resultado de la industrialización y del uso de nuevas tecnologías, el impacto antrópico ha ido en aumento en los últimos siglos, lo que causó la disminución de los tamaños poblacionales o la extinción de numerosas poblaciones silvestres. En este sentido, desde el campo de la genética de la conservación, en las últimas décadas se realizaron diversos esfuerzos para aportar conocimientos nuevos que contribuyan a la conservación de poblaciones, especies y hábitats. Las propiedades de los distintos marcadores moleculares han permitido estudiar la variabilidad genética de las especies y cómo esa variabilidad se estructura en las poblaciones y define las llamadas Unidades de Manejo, que son unidades genéticas cuyo nombre deriva de actividades extractivistas. En este artículo revisamos y analizamos críticamente los esfuerzos científicos en el área de la genética de la conservación realizados entre 2006 y 2015 en pos de la conservación de los mamíferos del Neotrópico. También criticamos el concepto de Unidad de Manejo y analizamos las perspectivas a futuro en el campo de la genética de la conservación de los mamíferos neotropicales.[Palabras clave: biología de la conservación, fauna neotropical, especies amenazadas, marcadores moleculares] A��. Contributions of conservation genetics to the study of neotropical mammals: review and critical analysis.Although all living beings modify their environment, our species has acquired the ability to do so on a superlative space-time scale. As a result of industrialization and the use of new technologies, the anthropic impact has been increasing in the last centuries, causing the decrease in population sizes or the extinction of numerous wild populations. In this sense, from the field of conservation genetics, diverse efforts have been made in the last decades in order to provide new knowledge that contributes to the conservation of populations, species and habitats. The properties of the different molecular markers have allowed studying the genetic variability of the species and how it is structured in the populations, defining the so-called Management Units, genetic units whose name derives from extractivist activities. In this article we perform a review and critical analysis of the scientific efforts in the area of conservation genetics carried out between the years 2006 and 2015 for the conservation of mammals of the Neotropics, criticize the concept of Management Unit and analyze future perspectives in the field of conservation genetics of neotropical mammals.

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“…eDNA has proved useful in situations in which invasive sampling of elusive species is logistically difficult and/or ethically fraught [ 8 , 9 ], including the estimation of their abundance, genetic diversity, and population structure [ 10 , 11 ]. Most recently, eDNA extracted from scats, in particular, has been employed successfully for bioprospecting and biomonitoring [ 12 , 13 , 14 ]. Still, the difficulty of isolating high quality (i.e., high molecular weight) genomic DNA from scats has, until recently, constrained the sequencing and assembly of relatively long sequences such as bacterial or mitochondrial genomes directly from scats.…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals

Baeza

Barata

Rajapakse

et al. 2023

Genes

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The abundance of many large-bodied vertebrates, both in marine and terrestrial environments, has declined substantially due to global and regional climate stressors that define the Anthropocene. The development of genetic tools that can serve to monitor population’s health non-intrusively and inform strategies for the recovery of these species is crucial. In this study, we formally evaluate whether whole mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples. Mitogenomes of four different large vertebrates, the panda bear (Ailuropoda melanoleuca), the moon bear (Ursus thibetanus), the Java pangolin (Manis javanica), and the the North Atlantic right whale (Eubalaena glacialis) were assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 12x to 480x in 14 out of 18 different eDNA samples. Partial mitochondrial genomes were retrieved from three other eDNA samples. The complete mitochondrial genomes of the studied species were AT-rich and comprised 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative D-loop/control region. Synteny observed in all assembled mitogenomes was identical to that reported for specimens of the same and other closely related species. This study demonstrates that it is possible to assemble accurate whole mitochondrial chromosomes from eDNA samples (scats) using forthright bench and bioinformatics workflows. The retrieval of mitochondrial genomes from eDNA samples represents a tool to support bioprospecting, bio-monitoring, and other non-intrusive conservation strategies in species considered ‘vulnerable’, ‘endangered’, and/or ‘critically endangered’ by the IUCN Red List of Threatened Species.

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A novel primer set for mammal species identification from feces samples

Cited by 9 publications

References 13 publications

A single mini-barcode test to screen for Australian mammalian predators from environmental samples

A single mini-barcode test to screen for Australian mammalian predators from environmental samples

Aportes de la genética de la conservación al estudio de los mamíferos neotropicales: revisión y análisis crítico

Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals

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