A comparison of pedigree‐ and <scp>DNA</scp>‐based measures for identifying inbreeding depression in the critically endangered <scp>A</scp>ttwater's <scp>P</scp>rairie‐chicken

Hammerly, Susan C.; Morrow, Michael E.; Johnson, Jeff

doi:10.1111/mec.12482

Cited by 44 publications

(64 citation statements)

References 124 publications

(134 reference statements)

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“…In some cases, the performance of the estimator was reported, but found to be low, and this was not discussed in terms of the validity of the conclusions formed (e.g., Hammerly et al. 2013). The fact that studies involving marker-based estimates of r xy and F are sometimes published without stating the estimator used is surprising as it reduces the repeatability of the study.…”

Section: Discussionmentioning

confidence: 99%

The use and abuse of genetic marker‐based estimates of relatedness and inbreeding

Taylor

2015

Ecology and Evolution

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Genetic marker-based estimators remain a popular tool for measuring relatedness (rxy) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of rxy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker-based estimators of rxy and F in a species with very low genetic diversity, New Zealand’s little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of rxy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated rxy or F is relatively high (Pearson’s r = 0.66–0.72 and 0.81–0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker-based estimates of rxy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator’s performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of rxy and F debatable.

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Section: Discussionmentioning

confidence: 99%

The use and abuse of genetic marker‐based estimates of relatedness and inbreeding

Taylor

2015

Ecology and Evolution

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“…Therefore, because Jackson Hole and Gros Ventre Greater Sage-Grouse populations possess small N b , they are expected to lose more genetic diversity due to drift compared with larger populations over the same time period. Reduction in genetic diversity in small, isolated populations has been shown to negatively influence fitness due to increased inbreeding (Keller 1998, Daniels and Walters 2000, Blomqvist et al 2010, Hammerly et al 2013. In contrast, however, if the population has been small for hundreds of generations, deleterious traits may have been purged, and management should focus more on maintaining adequate habitat for long-term sustainability (e.g., Johnson et al 2009) as opposed to introgression of genes that may result in outbreeding depression (Frankham et al 2011 Table 2), it is not known whether the differentiation is largely due to a recent reduction in population size and drift or represents a long-term pattern of isolation, with long-term isolation of more concern relative to outbreeding depression.…”

Section: Discussionmentioning

confidence: 99%

Low neutral genetic diversity in isolated Greater Sage-Grouse (Centrocercus urophasianus) populations in northwest Wyoming

Schulwitz¹,

Bedrosian²,

Johnson³

2014

The Condor

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Identifying small, isolated populations is a conservation priority, not only because isolation may result in negative fitness consequences, but these populations may also harbor unique genetic diversity. The Greater Sage-Grouse (Centrocercus urophasianus) is a widespread obligate species of the sagebrush biome in western North America that has experienced range-wide contraction over the past century. To prevent local extirpation, efforts have been made to identify isolated populations. Here, we analyzed 16 microsatellite loci from 300 Greater Sage-Grouse individuals to assess genetic structure among populations in Wyoming and southeast Montana, particularly with the Jackson Hole and Gros Ventre populations in northwest Wyoming. Four genetic clusters were observed with Pinedale (central-west) and Casper (central) populations forming a cluster, Powder River Basin (central-north) and southeast Montana forming a second cluster, and both Jackson Hole and Gros Ventre forming distinct population clusters. All but the Jackson Hole and Gros Ventre genetic differentiation correspond with designated ecoregions and possessed an isolation-bydistance pattern of differentiation. Both Jackson Hole and Gros Ventre were identified as separate populations with asymmetrical dispersal into Gros Ventre. Both populations also possessed significantly reduced genetic diversity and low effective number of breeders (N b ). Because both populations are surrounded by extensive forested mountain ranges nearly devoid of sagebrush habitat, the Jackson Hole and Gros Ventre populations may have long been isolated from other Greater Sage-Grouse populations; however, only a few alleles were unique to the Jackson Hole and Gros Ventre populations. The observed genetic differentiation was largely due to allele frequency differences rather than private alleles, suggesting some historical gene flow. More work is needed to determine the timing of isolation and whether managers should focus on maintaining and increasing adequate sagebrush habitat, allowing the population to increase in size, or population supplementation to increase genetic diversity.

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“…DNA techniques have enabled the degree of inbreeding to be inferred, even when pedigree information is not available, in a wide range of animal species including endangered species, so-called model species and commercial livestock. Examples include Attwater's prairie chicken (Hammerly et al 2013), the zebra finch (Santure et al 2010) and commercial Kenyan and Norwegian dairy cattle (Gorbach et al 2010;Hillestad et al 2014). The genetic architecture of inbreeding depression and of the purging of disadvantageous alleles has also been investigated using genetic markers, principally in livestock species and especially in modern commercial cattle breeds (e.g.…”

Section: Introductionmentioning

confidence: 99%

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non‐random SNP heterozygosity

et al. 2015

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SummaryLocal breeds of livestock are of conservation significance as components of global biodiversity and as reservoirs of genetic variation relevant to the future sustainability of agriculture. One such rare historic breed, the Chillingham cattle of northern England, has a 350-year history of isolation and inbreeding yet shows no diminution of viability or fertility. The Chillingham cattle have not been subjected to selective breeding. It has been suggested previously that the herd has minimal genetic variation. In this study, high-density SNP genotyping with the 777K SNP chip showed that 9.1% of loci on the chip are polymorphic in the herd, compared with 62-90% seen in commercial cattle breeds. Instead of being homogeneously distributed along the genome, these loci are clustered at specific chromosomal locations. A high proportion of the Chillingham individuals examined were heterozygous at many of these polymorphic loci, suggesting that some loci are under balancing selection. Some of these frequently heterozygous loci have been implicated as sites of recessive lethal mutations in cattle. Linkage disequilibrium equal or close to 100% was found to span up to 1350 kb, and LD was above r 2 = 0.25 up to more than 5000 kb. This strong LD is consistent with the lack of polymorphic loci in the herd. The heterozygous regions in the Chillingham cattle may be the locations of genes relevant to fitness or survival, which may help elucidate the biology of local adaptation in traditional breeds and facilitate selection for such traits in commercial cattle.

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A comparison of pedigree‐ and DNA‐based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie‐chicken

Cited by 44 publications

References 124 publications

The use and abuse of genetic marker‐based estimates of relatedness and inbreeding

The use and abuse of genetic marker‐based estimates of relatedness and inbreeding

Low neutral genetic diversity in isolated Greater Sage-Grouse (Centrocercus urophasianus) populations in northwest Wyoming

Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non‐random SNP heterozygosity

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