Counting Alleles with Rarefaction: Private Alleles and Hierarchical Sampling Designs

Kalinowski, Steven T.

doi:10.1023/b:coge.0000041021.91777.1a

Cited by 612 publications

(492 citation statements)

References 14 publications

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“…Allelic richness of populations of an endangered tree species was compared to identify genetically diverse populations so that these populations could be protected (Petit et al 1998). The number of rare alleles in a population (private allelic richness) is a simple measure of genetic distinctiveness (Kalinowski 2004). A total of 20 rare alleles were identified from the eight polymorphic loci.…”

Section: Discussionmentioning

confidence: 99%

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Ganie

Borgohain

Kritika

et al. 2016

Physiol Mol Biol Plants

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Eight Saltol quantitative trait locus (QTL) linked simple sequence repeat (SSR) markers of rice (Oryza sativa L.) were used to study the polymorphism of this QTL in 142 diverse rice genotypes that comprised salt tolerant as well as sensitive genotypes. The SSR profiles of the eight markers generated 99 alleles including 20rare alleles and 16 null alleles. RM8094 showed the highest number (13) of alleles followed by RM3412 (12), RM562 (11), RM493 (9) and RM1287 (8) while as, RM10764 and RM10745 showed the lowest number (6) of alleles. Based on the highest number of alleles and PIC value (0.991), we identified RM8094 as suitable marker for discerning salt tolerant genotypes from the sensitive ones. Based upon the haplotype analysis using FL478 as a reference (salt tolerant genotypes containing Saltol QTL), we short listed 68 rice genotypes that may have at least one allele of FL478 haplotype. Further study may confirm that some of these genotypes might have Saltol QTL and can be used as alternative donors in salt tolerant rice breeding programmes.

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Section: Discussionmentioning

confidence: 99%

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Ganie

Borgohain

Kritika

et al. 2016

Physiol Mol Biol Plants

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“…The program HP-RARE version June 2006 (Kalinowski, 2004;2005) was used to estimate allelic richness and private allelic richness with a rarefaction method to account for uneven sample sizes. The program GenePop 4.2.2.…”

Section: Methodsmentioning

confidence: 99%

Does connectivity exist for remnant boreal caribou (Rangifer tarandus caribou) along the Lake Superior Coastal Range? Options for landscape restoration

Drake

Manseau²,

Klütsch³

et al. 2018

Ran

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Genetic analysis can provide important information on the dynamic and spatial structure of groups of animals or populations. Little is known of the genetic population structure of caribou that inhabit the Lake Superior Coastal Range (LSCR) and the level of gene flow between individuals within the range and beyond. From a landscape perspective, this range is spatially isolated and genetic connectivity within the range is presumed limited due to large water crossings on Lake Superior. This study aims to answer if animal movement can be discerned, using genetic population and relatedness analyses, within and beyond the LSCR. Faecal and hair samples collected between 2005 and 2015 in Pukaskwa National Park were analyzed for genetic markers and compared to 131 unique genotypes previously obtained from both within the LSCR and in the two next closest ranges. Animals from one nearshore island (i.e. Otter) were more closely associated with offshore islands than other mainland caribou, likely a result of past movement and translocation rather than ongoing movement. Conversely, on another nearshore island (i.e. Pic), individuals assigned to a different genetic cluster and were related to animals further north outside the range, demonstrating some connectivity through the discontinuous distribution to the coast. Long-term population declines have been observed in the LSCR despite genetic connectivity within the range and relatively low total habitat disturbance. Restoring connectivity of the LSCR so that it is not isolated from populations to the north is required for the recovery of the mainland portion of the coastal range. These genetic analyses provide some insights on where movements may occur and where landscape restoration efforts may best be directed to enhance connectivity.

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“…Thus, genetic diversity within populations is fundamental for conservation biology; better adaptation potential is expected in populations with high levels of genetic diversity (Kalinowski, 2004). The main parameters that are used to evaluate the intrapopulational genetic diversity include allelic diversity, H o , H e , and the inbreeding coefficient (Berg & Hamrick, 1997).…”

Section: Discussionmentioning

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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Counting Alleles with Rarefaction: Private Alleles and Hierarchical Sampling Designs

Cited by 612 publications

References 14 publications

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Does connectivity exist for remnant boreal caribou (Rangifer tarandus caribou) along the Lake Superior Coastal Range? Options for landscape restoration

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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