Non-invasive genetic sampling for molecular sexing and microsatellite genotyping of hyacinth macaw (Anodorhynchus hyacinthinus)

Abstract

Molted feather sampling is a useful tool for genetic analyses of endangered species, but it is often very laborious due to the low quality and quantity of the DNA obtained. In the present study we show the parts of feathers that resulted in better yield of DNA. In descending order these were: blood clot outside the umbilicus, umbilicus (without blood clot), tip, inner membrane, and small calamus. Compared to DNA extracted from blood samples, DNA extracted from feathers produced microsatellite alleles of poorer quality and had to be processed immediately after extraction. As expected due to the level of DNA degradation, molecular sexing protocols that result in shorter PCR products were more efficient.

Tracking pan-continental trends in environmental contamination using sentinel raptors—what types of samples should we use?

“…All types of feathers can be used for contaminant analysis and as a tool for other studies, such as genetic studies (Speller et al 2011 ; Presti et al 2013 ). Choice of feather type can depend on the moulting pattern of the species, preening behaviour and the end point of the study.…”

DNA sampling from eggshells and microsatellite genotyping in rare tropical birds: Case study on Brazilian Merganser

“…Some studies have used microsatellites for accessing genetic diversity from noninvasive samples ( Presti et al , 2013 ; Moodley et al , 2015 ), due to the fact that these markers are widely distributed in the genome, have high levels of polymorphism, and are easy to detect using PCR ( Hoshino et al , 2012 ). Thus, microsatellites have been frequently used to monitor biodiversity, evaluate paternity and to attribute individuals to populations ( Beebee and Rowe, 2008 ).…”

“…Furthermore, primers developed in one species may be used in related taxa ( Barbará et al , 2007 ; Santos et al , 2012 ). Nonetheless the success of cross-species amplification of microsatellites depends on conservation of flanking regions, the polymorphism level, the phylogenetic relatedness among the species involved, with success being higher in closely related species ( Barbará et al , 2007 ; Presti et al , 2013 ; Moodley et al , 2015 ). In this context, the use of noninvasive samples and polymorphic markers, such as microsatellites, can help to monitor the genetics of rare and endangered species.…”

“…DNA was successfully extracted from eggshells exposed to environmental conditions before sampling, in spite of the DNA concentration of noninvasive samples being lower (~30 ng/μl) than that of invasive samples (> 300 ng/μl). Most avian genetics studies that employ noninvasive sampling use feathers ( Segelbacher, 2002 ; Presti et al , 2013 ), although a few have used eggshell membranes ( Trimbos et al , 2009 ), eggshell powder by surface abrasion ( Egloff et al , 2009 ), or eggshell swabbing ( Martin-Galvez et al. , 2011 ).…”

Use of mucus as a non‐invasive sampling method for DNA barcoding of stingrays and skates (batoid elasmobranchs)

“…However, the use of this tool is still very dependent on tissue sampling (e.g., muscle, scale and blood), usually obtained from dead animals in fish markets and fishing vessels or from live animals, with many challenges involving the angling and handling processes, such as physical injuries and pathology due to hook removal or retention, and post-release survivorship (Danylchuck et al, 2014). On the other hand, less invasive procedures for DNA extraction has been tested in a wide variety of vertebrates (including large species of elasmobranchs) to assess information on genetic population, forensic identification, sex determination and genetic diversity (Alvarado Bremer et al, 2014;Hilsdorf et al, 1999;Kashiwagi et al, 2015;Lieber et al, 2013;Presti et al, 2013). Such outcomes demonstrated the feasibility of non-destructive approaches to DNA extraction and its use in different analyses, at a low cost and with a high degree of sensitivity and confidence.…”