Application of a method for estimating effective population size and admixture using diagnostic single nucleotide polymorphisms (SNPs): implications for conservation of threatened Paiute cutthroat trout (Oncorhynchus clarkii seleniris) in Silver King Creek, California

2011 ◽  
Vol 68 (8) ◽  
pp. 1369-1386 ◽  
Author(s):  
Amanda J. Finger ◽  
Eric C. Anderson ◽  
Molly R. Stephens ◽  
Bernard P. May
Keyword(s):  
Oncorhynchus Mykiss ◽  
Population Size ◽  
Effective Population Size ◽  
Cutthroat Trout ◽  
Likelihood Method ◽  
Effective Population ◽  
Autosomal Snps ◽  
Single Nucleotide ◽  
Oncorhynchus Clarkii ◽  
Point Estimates

The threatened Paiute cutthroat trout ( Oncorhynchus clarkii seleniris , PCT) is endemic to Silver King Creek, California, USA, which was stocked with non-native trout beginning in 1930. Single nucleotide polymorphism (SNP) and microsatellite data reveal that the trout population in Silver King Creek is weakly structured and composed of introgressed California golden trout ( Oncorhynchus mykiss aguabonita , CAGT), hatchery rainbow trout ( Oncorhynchus mykiss , RT), and some native PCT. Two SNP groups were analyzed: (i) one mitochondrial and five autosomal SNPs, diagnostic between Lahontan cutthroat trout ( Oncorhynchus clarkii henshawi ) or PCT and CAGT or RT and (ii) one mitochondrial and five autosomal SNPs nearly diagnostic between CAGT and RT. The five autosomal cutthroat–rainbow SNPs were used to jointly estimate the cutthroat trout mixing proportion in Silver King Creek and effective population size (Ne) of the admixed population, using a coalescent-based maximum likelihood method. Given the stocking history of Silver King Creek, there are two different scenarios that bound the range of expected point estimates for Ne. We obtain point estimates of Ne = 150 and Ne = 750 for Silver King Creek under these two scenarios. This method will be useful in cases with differentiated taxa and in prioritizing conservation and restoration programs where the populations of concern are introgressed.

Evolutionary potential but not extinction risk of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) is associated with stream characteristics

2012 ◽  
Vol 69 (4) ◽  
pp. 615-626 ◽  
Author(s):  
Mary M. Peacock ◽  
Ned A. Dochtermann
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Extinction Risk ◽  
Spatial Scales ◽  
Cutthroat Trout ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Oncorhynchus Clarkii ◽  
Lahontan Cutthroat Trout ◽  
Habitat Variables

Habitat fragmentation represents a major extinction threat for species of all taxa. Isolated populations have a higher risk of local extinction because of environmental variability and demographic processes associated with small populations. Here we examine the relationships among isolation, habitat size, habitat characteristics and variability, and genetic effective population size with extinction risk for 10 isolated and three interconnected populations of Lahontan cutthroat trout ( Oncorhynchus clarkii henshawi ) sampled from throughout their range. Contrary to expectations, we did not find a relationship between most habitat variables and extinction risk. However, we did find strong relationships between habitat variables and genetic effective population size, including a significant negative correlation between pool density and effective population size. Small effective population sizes can result in reduced genetic variation and losses of evolutionary potential and adaptability to changing environments. The absence of strong habitat correlates with extinction risk — despite an observed relationship with effective population size — highlights the need to consider habitat diversity at multiple spatial scales when considering management scenarios to both promote population persistence and maintain evolutionary relevance.

scholarly journals An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9939
Author(s):  
Jessica F. McLaughlin ◽  
Kevin Winker
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Sample Size ◽  
Population Size ◽  
Effective Population Size ◽  
Population Level ◽  
Sample Sizes ◽  
Nucleotide Polymorphism ◽  
Effective Population ◽  
Single Nucleotide ◽  
Population Demographic

Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. We used datasets from eight diverging bird lineages to make pairwise comparisons at different levels of taxonomic divergence (populations, subspecies, and species). Our data are from loci linked to ultraconserved elements and our analyses used one single nucleotide polymorphism per locus. All individuals were genotyped at all loci, effectively doubling sample size for coalescent analyses. We estimated population demographic parameters (effective population size, migration rate, and time since divergence) in a coalescent framework using Diffusion Approximation for Demographic Inference, an allele frequency spectrum method. Using divergence-with-gene-flow models optimized with full datasets, we subsampled at sequentially smaller sample sizes from full datasets of 6–8 diploid individuals per population (with both alleles called) down to 1:1, and then we compared estimates and their changes in accuracy. Accuracy was strongly affected by sample size, with considerable differences among estimated parameters and among lineages. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than three diploid individuals per population, or 6:6 haplotypes in coalescent terms). Migration (m) was fairly consistently estimated until <2 individuals per population, and no consistent trend of over-or underestimation was found in either time since divergence (T) or theta (Θ = 4Nrefμ). Lineages that were taxonomically recognized above the population level (subspecies and species pairs; that is, deeper divergences) tended to have lower variation in scaled root mean square error of parameter estimation at smaller sample sizes than population-level divergences, and many parameters were estimated accurately down to three diploid individuals per population. Shallower divergence levels (i.e., populations) often required at least five individuals per population for reliable demographic inferences using this approach. Although divergence levels might be unknown at the outset of study design, our results provide a framework for planning appropriate sampling and for interpreting results if smaller sample sizes must be used.

The effect of a supplementation program on the genetic and life history characteristics of an Oncorhynchus mykiss population

2010 ◽  
Vol 67 (9) ◽  
pp. 1449-1458 ◽  
Author(s):  
Donald M. Van Doornik ◽  
Barry A. Berejikian ◽  
Lance A. Campbell ◽  
Eric C. Volk
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Oncorhynchus Mykiss ◽  
Population Size ◽  
Effective Population Size ◽  
Natural Environment ◽  
Natural Populations ◽  
Life History Trait ◽  
Effective Population ◽  
Important Life History Trait

Conservation hatcheries, which supplement natural populations by removing adults or embryos from the natural environment and rearing and releasing parr, smolts, or adults back into their natal or ancestral streams, are increasingly being used to avoid extinction of localized populations of Pacific salmonids. We collected data before and during a steelhead ( Oncorhynchus mykiss ) supplementation program to investigate the effect that the program has had on the population’s genetic diversity and effective population size and any changes to an important life history trait (residency or anadromy). We found that supplementation did not cause substantial changes in the genetic diversity or effective size of the population, most likely because a large proportion of all of the steelhead redds in the river each year were sampled to create the supplementation broodstock. Our data also showed that the captively reared fish released as adults successfully produced parr. Furthermore, we found that during supplementation, there was an increase in the proportion of O. mykiss with anadromous ancestry vs. resident ancestry.

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