<scp>hp‐rare</scp> 1.0: a computer program for performing rarefaction on measures of allelic richness

Kalinowski, Steven T.

doi:10.1111/j.1471-8286.2004.00845.x

Cited by 2,022 publications

(1,521 citation statements)

References 6 publications

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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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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

View full text Add to dashboard Cite

show abstract

“…1) defined a priori according to Stewart (2008), we quantified genetic diversity as expected (H E ;Nei 1987) and observed heterozygosity (HO) using the microsatellite toolkit (Park 2001). Allelic richness was estimated using the rarefaction method implemented in HP-RARE 1.0 (Kalinowski 2005). Duplicate genotypes were identified and removed (but see detection of migrants below).…”

Section: Statistical Analysesmentioning

confidence: 99%

Microsatellite assessment of walrus (<i>Odobenus rosmarus rosmarus</i>) stocks in Canada

et al. 2014

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Walruses (Odobenus rosmarus rosmarus) occur in Canada from James Bay to Smith Sound and from the Canada-Greenland international boundary in Davis Strait to the longitudinal center of Canada (Fig. 1). Within this range, walruses are subdivided into seven stocks based on summering areas for the purpose of making management decisions that affect walrus and walrus habitat (Stewart 2008). Stock assessments (e.g. Breiwik and York 2009, Lugten 2010) rely on identifying units that can be managed without impact on other units. In the absence of definitive information, it is more precautionary to assume greater subdivision than exists in nature rather than to assume less (Taylor 1997, Taylor andDizon 1999). However, overly conservative subdivision can lead stock managers to overestimate the risk of stock extirpation, potentially leading to negative effects on resource users. NAMMCO Scientific Publications PS-LS), North Foxe Basin (N-FB), Central Foxe Basin (C-FB), Hudson Bay Davis Strait (HB-DS) and Southern and EasternHudson Bay (SE-HB). In this study, walrus were sampled from six of the seven stocks (SE-HB samples were not available) and genotyped at 10 microsatellite loci. All stocks were genetically diverse (average heterozygosity of 0.58) with no evidence of inbreeding (average F IS of 0.03). We detected significant genetic differentiation among the stocks and a pattern of genetic spatial autocorrelation that suggests a moderate effect of geographic distance on gene flow among stocks. Bayesian clustering suggested the six recognized stocks were elements of two larger genetic clusters-a northern Arctic population (containing BB, WJS, and PS-LS stocks) and a central Arctic population (containing C-FB, N-FB, and HB-DS stocks). These populations are moderately differentiated (F ST = 0.07), but based on evidence of contemporary movement from assignment tests, are not completely isolated. There was support for maintaining the WJS stock and a combined BB+PS-LS stock, although the latter conclusion is based on a small sample size. Similarly, there was some evidence suggesting separation of the Foxe Basin stocks from the HB-DS but not the N-FB from the C-FB stock. However, given that there are morphological and chemical differences between N-FB and C-FB stocks, there is currently insufficient evidence to support a revision of the current stock designations.

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“…Allelic richness (A), corrected for sample size was calculated using HP-Rare v. 1.1 (Kalinowski, 2005). Nei's gene diversity (H exp ) (Nei, 1978), as well as estimators of F ST and F IS (Wright, 1969) as h and f (Weir and Cockerham, 1984) were calculated with Genetix v.4.03 (Belkhir et al, 2001).…”

Section: Single-strand Conformation Polymorphism (Sscp)mentioning

confidence: 99%

Evolution and diversification within the intertidal brown macroalgae Fucus spiralis/F. vesiculosus species complex in the North Atlantic

Coyer¹,

Hoarau²,

Costa³

et al. 2011

Molecular Phylogenetics and Evolution

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hp‐rare 1.0: a computer program for performing rarefaction on measures of allelic richness

Cited by 2,022 publications

References 6 publications

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

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

Microsatellite assessment of walrus (<i>Odobenus rosmarus rosmarus</i>) stocks in Canada

Evolution and diversification within the intertidal brown macroalgae Fucus spiralis/F. vesiculosus species complex in the North Atlantic

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