Variation in Genetic Diversity across the Range of North American Brown Bears

Paetkau, David; Waits, Lisette P.; Clarkson, Peter L.; Craighead, Lance; Vyse, E. R.; Ward, Ryk; Strobeck, Curtis

doi:10.1046/j.1523-1739.1998.96457.x

Cited by 243 publications

(177 citation statements)

References 39 publications

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“…The brown bear case study The dramatic range of genetic diversity in brown bears that was observed by Paetkau et al (1998b) in North America is also evident at the global scale ( Table 2). Most of the observed patterns are expected-high genetic diversity in large populations (Alaska, Canada, Carpathians, Dinaric Mountains) and very low levels of genetic diversity in populations that have been isolated for a long time or have passed through severe demographic bottlenecks.…”

Section: Discussionmentioning

confidence: 93%

“…This latter population is relatively large (42500) and healthy, with low genetic diversity attributed to a long period of isolation from the bears on the continent (Paetkau et al, 1998a(Paetkau et al, , 1998b. On the other hand, the demographic history of the other populations with low genetic diversity is presumed to be one of a recent contraction and isolation.…”

Section: Discussionmentioning

confidence: 98%

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Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear

et al. 2012

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In species with large geographic ranges, genetic diversity of different populations may be well studied, but differences in loci and sample sizes can make the results of different studies difficult to compare. Yet, such comparisons are important for assessing the status of populations of conservation concern. We propose a simple approach of using a single well-studied reference population as a 'yardstick' to calibrate results of different studies to the same scale, enabling comparisons. We use a well-studied large carnivore, the brown bear (Ursus arctos), as a case study to demonstrate the approach. As a reference population, we genotyped 513 brown bears from Slovenia using 20 polymorphic microsatellite loci. We used this data set to calibrate and compare heterozygosity and allelic richness for 30 brown bear populations from 10 different studies across the global distribution of the species. The simplicity of the reference population approach makes it useful for other species, enabling comparisons of genetic diversity estimates between previously incompatible studies and improving our understanding of how genetic diversity is distributed throughout a species range.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 98%

Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear

et al. 2012

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“…Genetic differentiation of populations on the basis of microsatellites is often measured by using one of four standard parameters, D, F ST , R ST , and (␦ ) 2 . It is difficult to select a single adequate measure of differentiation (8,9) because of uncertainly concerning the underlying mutation processes (IAM and SMM). Furthermore, it can be argued a priori as well as empirically from the literature that different parameters have different drawbacks.…”

Section: Resultsmentioning

confidence: 99%

“…It was originally defined as an average value over all loci examined, but it can also be defined at each locus separately. Several variations of D have been used, for example, D C (20), D A , D m (14), D SW (17), and D LR (9). In a bear study (9), D and D LR were comparably satisfactory but failed to resolve the most distantly related pairs of species: when loci have no alleles shared between two populations, D and D LR are not defined or, as has been proposed by Nei (14), take an infinite value that is problematical for any quantitative comparison.…”

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confidence: 99%

When genetic distance matters: Measuring genetic differentiation at microsatellite loci in whole-genome scans of recent and incipient mosquito species

Wang

Zheng

Touré

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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Genetic distance measurements are an important tool to differentiate field populations of disease vectors such as the mosquito vectors of malaria. Here, we have measured the genetic differentiation between Anopheles arabiensis and Anopheles gambiae, as well as between proposed emerging species of the latter taxon, in whole genome scans by using 23-25 microsatellite loci. In doing so, we have reviewed and evaluated the advantages and disadvantages of standard parameters of genetic distance, F ST, RST, (␦ ) 2 , and D. Further, we have introduced new parameters, D and D K, which have well defined statistical significance tests and complement the standard parameters to advantage. D is a modification of D, whereas D K is a measure of covariance based on Pearson's correlation coefficient. We find that A. gambiae and A. arabiensis are closely related at most autosomal loci but appear to be distantly related on the basis of X-linked chromosomal loci within the chromosomal Xag inversion. The M and S molecular forms of A. gambiae are practically indistinguishable but differ significantly at two microsatellite loci from the proximal region of the X, outside the Xag inversion. At one of these loci, both M and S molecular forms differ significantly from A. arabiensis, but remarkably, at the other locus, A. arabiensis is indistinguishable from the M molecular form of A. gambiae. These data support the recent proposal of genetically differentiated M and S molecular forms of A. gambiae.M any major infectious diseases, such as malaria, leishmaniasis, and sleeping sickness, are transmitted by insect vectors. Molecular genetic markers have become powerful tools for elucidating the population biology and evolution of such vectors, topics that are highly relevant to disease transmission in the field (1-4). Genetic variation in vector populations contributes to their susceptibility to infection by the pathogen, their degree of anthropophily, their daily survival and reproductive rates, and the epidemiology of the disease in the human host (5). A case in point is the African mosquito of the Anopheles gambiae (sensu latu) complex (5). These include the most important vector of human malaria, A. gambiae (sensu strictu), as well as closely related species that are significant vectors in specific areas (e.g., Anopheles arabiensis) or are altogether unable to serve as vectors (Anopheles quadriannulatus). Furthermore, even within A. gambiae s.s., cytologically defined chromosomal forms (e.g., Mopti, Savanna, and Bamako) are reproductively isolated in the northern dry areas of West Africa, including Mali and Burkina Faso, and may represent emerging species with different disease transmission characteristics (5, 6). Although many DNA regions have been recently analyzed to examine genetic differentiation within A. gambiae s.s, the only fixed molecular differences found so far that consistently discriminate chromosomal forms are in the X-linked ribosomal (r)DNA region (1-4, 7). In Mali and Burkina Faso, these markers distinguish Mopti from Sava...

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“…For each locus, average ranking values were determined. Moreover, the probability of identity was estimated with a correction for small sample size (P ID unbiased; Paetkau et al, 1998) and the equivalent probability for a pair of siblings (P ID sib; Waits et al, 2001) with GenAlEx 6.41 (Peakall and Smouse, 2006). These values were used to estimate the minimum number of loci required for describing unique individual genotypes.…”

Section: Discussionmentioning

confidence: 99%

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

et al. 2015

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Endemic gene pools have been severely endangered by human-mediated hybridization, which is posing new challenges in the conservation of several vertebrate species. The endangered European wildcat is an example of this problem, as several natural populations are suffering introgression of genes from the domestic cat. The implementation of molecular methods for detecting hybridization is crucial for supporting appropriate conservation programs on the wildcat. In this study, genetic variation at 158 single-nucleotide polymorphisms (SNPs) was analyzed in 139 domestic cats, 130 putative European wildcats and 5 captive-bred hybrids (N = 274). These SNPs were variable both in wild (H E = 0.107) and domestic cats (H E = 0.340). Although we did not find any SNP that was private in any population, 22 SNPs were monomorphic in wildcats and pairwise F CT values revealed marked differences between domestic and wildcats, with the most divergent 35 loci providing an average F CT 40.74. The power of all the loci to accurately identify admixture events and discriminate the different hybrid categories was evaluated. Results from simulated and real genotypes show that the 158 SNPs provide successful estimates of admixture, with 100% hybrid individuals (two to three generations in the past) being correctly identified in STRUCTURE and over 92% using the NEWHYBRIDS' algorithm. None of the unclassified cats were wrongly allocated to another hybrid class. Thirty-five SNPs, showing the highest F CT values, provided the most parsimonious panel for robust inferences of parental and first generations of admixed ancestries. This approach may be used to further reconstruct the evolution of wildcat populations and, hopefully, to develop sound conservation guidelines for its legal protection in Europe.

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Variation in Genetic Diversity across the Range of North American Brown Bears

Cited by 243 publications

References 39 publications

Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear

Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear

When genetic distance matters: Measuring genetic differentiation at microsatellite loci in whole-genome scans of recent and incipient mosquito species

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

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