Collection, storage and analysis of non-invasive genetic material in primate biology

Goossens, Benoît; Anthony, Nicola M.; Jeffery, Kathryn J.; Johnson-Bawe, Mireille; Bruford, Michael William

doi:10.1017/cbo9780511921643.023

Cited by 7 publications

(6 citation statements)

References 47 publications

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“…We collected dung samples at 61 and 82 points of the grid during the dry (June-August 2013) and wet (October 2013-March 2014) seasons, respectively ( Figure 1). Fresh dung piles estimated to be less than 24 hr old, that is, wet and shiny with surface covered with mucus, (Goossens, Anthony, Jeffery, Johnson-Bawe, & Bruford, 2003) were collected. A team of three people navigated toward the most accessible point and searched for fresh dung for 1 km (500 m each side of an elephant trail), walking at 1 km/hr with the aid of a compass and global positioning system, and with minimal opening of vegetation (recce transects, Walsh & White, 1999).…”

Section: Methodsmentioning

confidence: 99%

“…In addition, the team followed recent trails within a 500-m radius from the point for about 10 min. Fresh dung piles estimated to be less than 24 hr old, that is, wet and shiny with surface covered with mucus, (Goossens, Anthony, Jeffery, Johnson-Bawe, & Bruford, 2003) were collected. For each sample, we collected approximately 10 g of the external layer of dung and stored it in a 50-mL polypropylene tube.…”

Section: Methodsmentioning

confidence: 99%

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Patterns of genetic diversity in African forest elephants living in a human‐modified landscape in southwest Gabon

Johnson

Parker

Vanthomme

et al. 2019

Conservat Sci and Prac

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We investigated the patterns of genetic diversity and structure of African forest elephants in a human-modified landscape in the Gamba complex of protected areas (GCPA), a tropical wilderness area along the southwest coast of Gabon. We collected 298 elephant fecal samples from four sites (Sette Cama, Gamba area, Vera Plains, and Mayonami), along approximately 80 km of coastline from north to south. We used microsatellites and mitochondrial DNA (mtDNA) to successfully genotype 295 of the 298 fecal samples, and identified 213 individuals. Using sex markers, we identified 84 males and 118 females; we could not determine the sex of the remaining 11 individuals. We also characterized the sex, group size, and social status of crop-raiding elephants and did not find characteristics distinguishing them from nonraiders. Overall, our mtDNA and microsatellite markers revealed that elephants in the research area maintain high levels of genetic variation and low levels of subdivision. Gene flow appears to be mostly mediated by male dispersal away from natal herds. Our structure analysis revealed two highly admixed genetic clusters, attributable to high connectivity among the protected areas. However, forest areas within the GCPA have become increasingly fragmented by human-induced habitat modification. We detected a pattern of isolation by distance, accentuated by the presence of the town of Gamba between Sette-Cama and Mayonami. We found a high degree of connectivity among sampling locations within the GCPA. This supports the importance of establishing agricultural best practices to reduce habitat loss that may sever gene exchange and to maintain connectivity, as well as to avoid human-elephant conflict that can result in retaliatory killing of elephants in this area. This study emphasizes the importance of conducting baseline monitoring of demographic data, genetic diversity, and structure to enable future comparisons to assess the long-term impact of human-induced habitat fragmentation. K E Y W O R D Scrop raids, forest elephant, genetics, land cover change

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Patterns of genetic diversity in African forest elephants living in a human‐modified landscape in southwest Gabon

Johnson

Parker

Vanthomme

et al. 2019

Conservat Sci and Prac

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“…The technique involves the extraction of DNA from materials like faeces, shed hair, feathers, urine and sloughed skin (Höss et al 1992; Kohn and Wayne 1997;Goossens et al 1998;Segelbacher 2002;Fernando et al 2003). The methodology has been increasingly applied to a wide variety of species (Taberlet et al 1997;Reed et al 1997;Kohn et al 1999;Ernest et al 2000;Garnier et al 2001;Eggert et al 2003;Goossens et al 2003;Hedmark et al 2004;Vidya and Sukumar 2005;Smith et al 2006;Bhagavatula and Singh 2006). Studies on the genetic diversity of tigers have focused on mitochondrial DNA (Zhang et al 2006a), and microsatellites (Zhang et al 2006b;Xu et al 2005;Williamson et al 2002).…”

Section: Introductionmentioning

confidence: 99%

Noninvasive genetic monitoring of tiger (Panthera tigris tigris) population of Orang National Park in the Brahmaputra floodplain, Assam, India

Borthakur¹,

Barman²,

Das³

et al. 2010

Eur J Wildl Res

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“…For many years, genetic studies of wild primate populations were limited by the difficulty of obtaining biological material useful as DNA source [Goossens et al, 2003]. However, recent advances in molecular biology permit DNA to be extracted from samples collected using noninvasive sampling techniques, which are being increasingly used in studies of genetic structure, social structure, parentage analysis and population censuses of primates [Constable et al, 1995;Di Fiore & Fleischer, 2005;Gagneux et al, 1999;Hapke et al, 2001;Nsubuga et al, 2008;Vigilant et al, 2001].…”

Section: Introductionmentioning

confidence: 99%

“…Noninvasive genetic samples include saliva, urine, feces and hairs (shed or fresh plucked) [Goossens et al, 2003]. DNA extraction from saliva, urine and fecal samples can be complicated, and the genetic material obtained is frequently found in low concentration, is highly fragmented or contains polymerase chain reaction (PCR) inhibitory compounds [Goossens et al, 2000;Hashimoto et al, 1996;Taberlet & Luikart, 1999;Valiere & Taberlet, 2000].…”

Section: Introductionmentioning

confidence: 99%

Noninvasive collection of fresh hairs from free‐ranging howler monkeys for DNA extraction

Améndola-Pimenta

Serio-Silva

Rico-Gray

2009

American J Primatol

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The use of noninvasive collected samples as source of DNA in studies of wild primate populations has increased in recent years. Fresh-plucked hairs represent an important source of DNA, with relatively high quality and concentration. In this study, we describe a low-cost noninvasive technique for collecting fresh-plucked hairs used to obtain DNA samples from free-ranging black howler monkey populations (Alouatta pigra). We designed and manufactured darts made of wooden dowels, with the anterior part smeared with glue, which were projected with blowpipes to trap howler monkey hairs. All of the materials to make the darts are inexpensive and are available locally. We collected 89 samples from 76 individuals residing in 15 troops, and the total number of hairs obtained was 754. We found no differences in the number of hairs collected among sex-age classes or among localities but the percentage of darts recovered with sample varied among localities. Preliminary results indicate that over 96% of samples yielded DNA suitable for polymerase chain reaction-based microsatellite marker analysis. The technique proved successful for collecting fresh-plucked hairs of free-ranging black howler monkeys without any trauma to the animals and can be easily adapted to obtain samples from other wild primate and mammal species.

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Collection, storage and analysis of non-invasive genetic material in primate biology

Cited by 7 publications

References 47 publications

Patterns of genetic diversity in African forest elephants living in a human‐modified landscape in southwest Gabon

Patterns of genetic diversity in African forest elephants living in a human‐modified landscape in southwest Gabon

Noninvasive genetic monitoring of tiger (Panthera tigris tigris) population of Orang National Park in the Brahmaputra floodplain, Assam, India

Noninvasive collection of fresh hairs from free‐ranging howler monkeys for DNA extraction

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