gimlet: a computer program for analysing genetic individual identification data

Valière, Nathaniel

doi:10.1046/j.1471-8286.2002.00228.x

Cited by 281 publications

(265 citation statements)

References 8 publications

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“…Polymerase chain reactions (PCRs) for blood and faecal samples were carried out in 10 ml reactions containing 5 ml of Qiagen Multiplex PCR Master Mix, 1 ml Q-Solution and 0.06 mM of FH2054, 0.08 mM of AHT125, 0. (c) Probability of identity and heterozygosity PID values were calculated for these loci from 126 individuals who were born into the population between 1984 (this is the estimated year of birth for the first wolf radio-collared on ISRO) and 2009 using program Gimlet [24]. Observed and expected heterozygosities and number of alleles were also calculated for each locus using Gimlet [24].…”

Section: (A) Field Methodsmentioning

confidence: 99%

“…(c) Probability of identity and heterozygosity PID values were calculated for these loci from 126 individuals who were born into the population between 1984 (this is the estimated year of birth for the first wolf radio-collared on ISRO) and 2009 using program Gimlet [24]. Observed and expected heterozygosities and number of alleles were also calculated for each locus using Gimlet [24]. To assess what impact the male immigrant had on the heterozygosity of the ISRO population, observed heterozygosities were calculated for 18 wolves present on the island prior to the immigration event and 81 wolves present on the island after the immigration event.…”

Section: (A) Field Methodsmentioning

confidence: 99%

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Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population

et al. 2011

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Genetic rescue, in which the introduction of one or more unrelated individuals into an inbred population results in the reduction of detrimental genetic effects and an increase in one or more vital rates, is a potentially important management tool for mitigating adverse effects of inbreeding. We used molecular techniques to document the consequences of a male wolf ( Canis lupus ) that immigrated, on its own, across Lake Superior ice to the small, inbred wolf population in Isle Royale National Park. The immigrant's fitness so exceeded that of native wolves that within 2.5 generations, he was related to every individual in the population and his ancestry constituted 56 per cent of the population, resulting in a selective sweep of the total genome. In other words, all the male ancestry (50% of the total ancestry) descended from this immigrant, plus 6 per cent owing to the success of some of his inbred offspring. The immigration event occurred in an environment where space was limiting (i.e. packs occupied all available territories) and during a time when environmental conditions had deteriorated (i.e. wolves' prey declined). These conditions probably explain why the immigration event did not obviously improve the population's demography (e.g. increased population numbers or growth rate). Our results show that the beneficial effects of gene flow may be substantial and quickly manifest, short-lived under some circumstances, and how the demographic benefits of genetic rescue might be masked by environmental conditions.

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Section: (A) Field Methodsmentioning

confidence: 99%

Section: (A) Field Methodsmentioning

confidence: 99%

Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population

et al. 2011

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“…The probability of identity or the probability that two individuals drawn from a population will by chance have the same genotype at multiple loci was calculated using GIMLET (Valiè re, 2002). The expected probability of identity among full sibs was estimated to give a theoretical upper limit to the probability that pairs of individuals will share genotypes, as suggested by Waits et al (2001).…”

Section: Methodsmentioning

confidence: 99%

The Parasites of Giant Pandas: Individual-Based Measurement in Wild Animals

Zhang

Yang

et al. 2011

Journal of Wildlife Diseases

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ABSTRACT:There is a growing recognition of parasites as a significant factor in the successful conservation of endangered species. Determining parasite infection and load in free-ranging populations traditionally is done via necropsy or coproscopy. For studies of wild animals, fecal sample collection can result in bias because the individual identity of animals is unknown and multiple samples may be collected from the same individual, yet treated as unrelated samples. We studied parasite load in wild giant pandas (Ailuropoda melanoleuca) across six mountain ranges in China. Genetic identification was used to determine the exact number of individuals sampled. The parasite fauna consisted of five species, dominated by Baylisascaris shroederi. The pattern of statistical difference between mountains was artificially inflated when animal identity was not included in the model. Our results suggest that caution should be exercised in inferring patterns from comparative parasitologic studies when samples cannot be attributed to specific individuals. Using noninvasive genetic sampling to avoid such bias should form a standard tool in the management of endangered species and their parasites.

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“…83 genotypes obtained by NGS or from carcasses recovered from 2005 to 2016). The occurrence of matches with genotypes already recorded in the area was tested using Gimlet ver 1.3.3 (Valière 2002). The probability of identity (i.e.…”

Section: Genetic Analysismentioning

confidence: 99%

Efficient, Noninvasive Genetic Sampling for Monitoring Reintroduced Wolves

et al. 2010

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Traditional methods of monitoring gray wolves (Canis lupus) are expensive and invasive and require extensive efforts to capture individual animals. Noninvasive genetic sampling (NGS) is an alternative method that can provide data to answer management questions and complement already‐existing methods. In a 2‐year study, we tested this approach for Idaho gray wolves in areas of known high and low wolf density. To focus sampling efforts across a large study area and increase our chances of detecting reproductive packs, we visited 964 areas with landscape characteristics similar to known wolf rendezvous sites. We collected scat or hair samples from 20% of sites and identified 122 wolves, using 8–9 microsatellite loci. We used the minimum count of wolves to accurately detect known differences in wolf density. Maximum likelihood and Bayesian single‐session population estimators performed similarly and accurately estimated the population size, compared with a radiotelemetry population estimate, in both years, and an average of 1.7 captures per individual were necessary for achieving accurate population estimates. Subsampling scenarios revealed that both scat and hair samples were important for achieving accurate population estimates, but visiting 75% and 50% of the sites still gave reasonable estimates and reduced costs. Our research provides managers with an efficient and accurate method for monitoring high‐density and low‐density wolf populations in remote areas.

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gimlet: a computer program for analysing genetic individual identification data

Cited by 281 publications

References 8 publications

Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population

Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population

The Parasites of Giant Pandas: Individual-Based Measurement in Wild Animals

Efficient, Noninvasive Genetic Sampling for Monitoring Reintroduced Wolves

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