Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data

Piry, Sylvain; Luikart, Gordon; Cornuet, Jean‐Marie

doi:10.1093/jhered/90.4.502

Cited by 3,027 publications

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“…The occurrence of recent genetic bottlenecks was tested using BOTTLENECK [16]. In the testing, the ratio of allele numbers and expected heterozygosities was compared to the ratio expected under the mutation-drift equilibrium [9].…”

Section: Resultsmentioning

confidence: 99%

“…The equilibrium heterozygosities were obtained from 1000 iterations, assuming that the allelic states of microsatellites change according to the Stepwise Mutation Model (SMM) and Two-phased model of mutations (TPM) [4]. The default settings for the proportion of stepwise and larger mutations and variance of allele size change were used [16]. After simulation, the significances of deviations were tested with the Wilcoxon sign-rank test.…”

Section: Resultsmentioning

confidence: 99%

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Genetic differentiation between the Old and New types ofSerbianTsigaisheep

Ćinkulov¹,

Tapio²,

Ozerov³

et al. 2008

Genet. Sel. Evol.

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-Two Tsigai sheep populations exist in Serbia: the Old type, calledČokan, and the New type. It is assumed that the New type results from upgrading Tsigai sheep with exotic genetic material. We investigated genetic diversity and differentiation of these types by analysing 23 autosomal microsatellites. Tests for Hardy-Weinberg proportions, linkage equilibrium between genotypes across loci and the calculation of inbreeding coefficients were performed and the deficiency in the number of alleles within the Tsigai types was examined using a Wilcoxon sign-rank test. The New type displayed a higher level of genetic variability than theČokan in terms of allele numbers, but the New Tsigai showed a pattern of heterozygosity deficiency. The positive f value for theČokan suggests the occurrence of inbreeding in this type. The proportion of linkage disequilibrium was below that expected by chance. Exclusion of two loci in HardyWeinberg disequilibrium did not alter our conclusions based on the entire data set i.e. the two Tsigai types are clearly differentiated and the New Tsigai type has been influenced by crossbreeding. Therefore, theČokan Tsigai should be considered as a distinct endangered breed in the FAO classification.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Genetic differentiation between the Old and New types ofSerbianTsigaisheep

Ćinkulov¹,

Tapio²,

Ozerov³

et al. 2008

Genet. Sel. Evol.

View full text Add to dashboard Cite

show abstract

“…A jackknife approach with 1,000 bootstrap replicates was employed to assess statistical significance (Chapuis & Estoup, 2007). Next, BOTTLENECK 1.2.02 (Piry, Luikart, & Cornuet, 1999) was used to test the prediction that both contemporary populations (CI and CN) experienced a recent genetic bottleneck. Populations that have undergone a genetic bottleneck are often associated with a loss of (rare) alleles and display elevated levels of heterozygosity when compared to stable populations (Piry et al., 1999).…”

Section: Methodsmentioning

confidence: 99%

“…Next, BOTTLENECK 1.2.02 (Piry, Luikart, & Cornuet, 1999) was used to test the prediction that both contemporary populations (CI and CN) experienced a recent genetic bottleneck. Populations that have undergone a genetic bottleneck are often associated with a loss of (rare) alleles and display elevated levels of heterozygosity when compared to stable populations (Piry et al., 1999). Thus, significant heterozygote excess was evaluated for each of the three groups using a Wilcoxon rank test (10,000 iterations) for two mutational models often associated with microsatellite evolution: the two‐phase mutation model (TPM) and the infinite alleles model (IAM).…”

Section: Methodsmentioning

confidence: 99%

The ghost of introduction past: Spatial and temporal variability in the genetic diversity of invasive smallmouth bass

Diedericks

Henriques

Heyden

et al. 2018

Evolutionary Applications

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Understanding the demographic history of introduced populations is essential for unravelling their invasive potential and adaptability to a novel environment. To this end, levels of genetic diversity within the native and invasive range of a species are often compared. Most studies, however, focus solely on contemporary samples, relying heavily on the premise that the historic population structure within the native range has been maintained over time. Here, we assess this assumption by conducting a three‐way comparison of the genetic diversity of native (historic and contemporary) and invasive (contemporary) smallmouth bass (Micropterus dolomieu) populations. Analyses of a total of 572 M. dolomieu samples, representing the contemporary invasive South African range, contemporary and historical native USA range (dating back to the 1930s when these fish were first introduced into South Africa), revealed that the historical native range had higher genetic diversity levels when compared to both contemporary native and invasive ranges. These results suggest that both contemporary populations experienced a recent genetic bottleneck. Furthermore, the invasive range displayed significant population structure, whereas both historical and contemporary native US populations revealed higher levels of admixture. Comparison of contemporary and historical samples showed both a historic introduction of M. dolomieu and a more recent introduction, thereby demonstrating that undocumented introductions of this species have occurred. Although multiple introductions might have contributed to the high levels of genetic diversity in the invaded range, we discuss alternative factors that may have been responsible for the elevated levels of genetic diversity and highlight the importance of incorporating historic specimens into demographic analyses.

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“…The sign test utilizes parametric analysis in which the null hypothesis can be rejected based on excess heterozygosity by considering the difference H o and H e in a significant number of loci in the studied population (Cornuet & Luikart, 1996). The Wilcoxon test compares the observed excess heterozygosity over H e to a null hypothesis and is a more robust and sensitive method (Piry et al., 1999). …”

Section: Methodsmentioning

confidence: 99%

Genetic structure of twoProsopisspecies in Chaco areas: A lack of allelic diversity diagnosis and insights into the allelic conservation of the affected species

Alves

Sartori

Zucchi

et al. 2018

Ecology and Evolution

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The Gran Chaco is the largest continuous region of the South American dry forest, spanning Argentina, Paraguay, Bolivia, and Brazil. Prosopis rubriflora and Prosopis ruscifolia are typical tree species of chaquenian area forests, which have been subjected to continuous fragmentation caused by cattle raising. This study evaluated P. rubriflora and P. ruscifolia in areas with varying levels of disturbance. We investigated the contemporary genetic diversities of both species in areas with distinct anthropogenic disturbances. Even with a lower heterozygote frequency, disturbed areas can provide important storage for alleles, allowing the maintenance of diversity. The genetic diversity of P. rubriflora was surprisingly similar to that of P. ruscifolia (H e = 0.59 and H e = 0.60, respectively) even with very different distribution ranges of both species. However, P. ruscifolia exhibited a higher intrapopulation fixation index than P. rubriflora. P. rubriflora showed evidence of bottlenecking in 64% of the sampled areas, while P. ruscifolia showed such evidence in 36% of the sampled areas. Additionally, P. rubriflora had two distinct populations due to its disjunctive geographic distribution, whereas P. ruscifolia had a single population that exhibited few signs of population structure in some areas, possibly due to the main pollinators presenting a short range of dispersion. Our results suggest that 42 Chaco areas should be conserved to retain the minimum of 500 individuals necessary to maintain genetic diversity for 100–1,000 generations. This study improves our understanding of these two Prosopis species and provides information for the conservation of their genetic diversities.

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Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data

Cited by 3,027 publications

References 0 publications

Genetic differentiation between the Old and New types ofSerbianTsigaisheep

Genetic differentiation between the Old and New types ofSerbianTsigaisheep

The ghost of introduction past: Spatial and temporal variability in the genetic diversity of invasive smallmouth bass

Genetic structure of twoProsopisspecies in Chaco areas: A lack of allelic diversity diagnosis and insights into the allelic conservation of the affected species

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