A new PCR assay for reliable molecular sexing of endangered Tasmanian devils (Sarcophilus harrisii) from non-invasive genetic samples

SummaryThe Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations.PaperClip

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“… (A) Y chromosome gene SRY is not detectable in DFTD using PCR. Primer sequences are available ( Lachish et al., 2011; Murchison et al., 2010 ). …”

Section: Figurementioning

confidence: 99%

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

Murchison

Schulz-Trieglaff

Ning

et al. 2012

Cell

310

425

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“…Camera traps can be used to obtain information on population abundance, behaviour, habitat occupancy, and population structure (Silveira et al 2003;Claridge et al 2010). Non-invasive genetic monitoring, including the use of faecal samples, can provide information on population abundance, population structure, sex, diet, habitat occupancy, and population genetic diversity (Piggott et al 2006a;Lachish et al 2011;Tende et al 2014;Moßbrucker et al 2015;Morales-Contreras et al 2016;Camp et al 2020;Bannister et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Non-invasive monitoring and reintroduction biology of the brush-tailed rock-wallaby (

Kleemann

Sandow²,

Stevens³

et al. 2022

Aust. J. Zool.

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Thirty-nine endangered brush-tailed rock-wallabies (Petrogale penicillata) were reintroduced to Grampians National Park, western Victoria, between 2008 and 2012. Subsequent high mortality, low breeding, and no recruitment were linked to fox predation and physical disturbance during monitoring. From 2014 to 2017, the colony was left undisturbed and monitored only by remote camera. Five adult animals were identified across this period (1 ♂ and 3 ♀s – all tagged; and one untagged female), and an average of 0.7 pouch young were birthed per tagged female per year. In 2019, camera-monitoring and non-invasive genetic monitoring (faecal) were used to identify colony members, genetic diversity, and breeding. Camera monitoring in 2019 identified the same five individuals, whereas genetic monitoring using 12 microsatellites identified eight individuals (two male and six female genotypes). Genetic diversity within the colony was moderate (expected heterozygosity (He) = 0.655, observed heterozygosity (Ho) = 0.854). Leaving the colony undisturbed after 2013 correlated with improved adult survival, increased breeding, and successful recruitment of young to the population. Recommendations for the Grampians colony include continuation of regular camera- and scat monitoring to improve our understanding of the reintroduction biology of P. penicillata and other marsupials in open, unfenced landscapes.

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“…Likewise, sexing juveniles can be particularly difficult even in sexually dimorphic species, as dimorphism in size and secondary sexual traits is often not expressed until adulthood. Recently, due to practical and ethical concerns, there has been an increasing interest in non-invasive techniques to study natural populations [8], in particular when species status is uncertain and presents special conservation concern [9] [10]. Moreover, research in areas like conservation genetics and wildlife forensic is increasingly based on non-invasive samples, whose origins are completely unknown [11].…”

Section: Introductionmentioning

confidence: 99%

Sex Determination in the Near Threatened Guadalupe Fur Seal: Molecular Markers and Their Potential Applications

Sanvito¹,

Fabiani²,

Galimberti³

2014

OJAS

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The determination of sex by simple observation is often difficult in marine mammals, even in sexually dimorphic species. Moreover, there is often the practical necessity to determine sex in samples that have been collected without handling or observing the subjects. In these cases, a molecular assay for sex determination is required. We adapted an assay that targets the zinc-finger region and is based on a single primer pair, to the Guadalupe fur seal, a near threatened species that has a very limited breeding range. First, we validated the assay with a sample of pups in which we determined the sex by direct observation during handling; second, we compared it to a more recent assay, based on two different primer pairs and, finally, we evaluated the effect of DNA quantity on its reliability. The assay that we tested produced excellent results and was more reliable than the other one based on two primers. Reliable results were also obtained when only remarkably small quantities of DNA were amplified. These results show the potential use of this molecular assay in case of non-invasive sampling, an overly common situation when dealing with species of problematic conservation status.

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A new PCR assay for reliable molecular sexing of endangered Tasmanian devils (Sarcophilus harrisii) from non-invasive genetic samples

Cited by 5 publications

References 17 publications

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

Non-invasive monitoring and reintroduction biology of the brush-tailed rock-wallaby (

Sex Determination in the Near Threatened Guadalupe Fur Seal: Molecular Markers and Their Potential Applications

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