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.

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.

scholarly journals Being abundant is not enough: a decrease in effective population size over eight generations in a Norwegian population of the seaweed, Fucus serratus

2008 ◽  
Vol 4 (6) ◽  
pp. 755-757 ◽  
Author(s):  
James A Coyer ◽  
Galice Hoarau ◽  
Kjersti Sjøtun ◽  
Jeanine L Olsen
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allelic Richness ◽  
Environmental Changes ◽  
Extinction Risk ◽  
Rocky Intertidal ◽  
Effective Population ◽  
Norwegian Population ◽  
Fucus Serratus ◽  
Southern Norway

The brown alga Fucus serratus is a key foundation species on rocky intertidal shores of northern Europe. We sampled the same population off the coast of southern Norway in 2000 and 2008, and using 26 microsatellite loci, we estimated the changes in genetic diversity and effective population size ( N e ). The unexpectedly low N e (73–386) and N e / N ratio (10 −3 –10 −4 ), in combination with a significant decrease (14%) in allelic richness over the 8-year period, suggests an increased local extinction risk. If small N e proves to be a common feature of F. serratus , then being abundant may not be enough for the species to weather future environmental changes.

scholarly journals The paradox of retained genetic diversity of Hippocampus guttulatus in the face of demographic decline

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rupert Stacy ◽  
Jorge Palma ◽  
Miguel Correia ◽  
Anthony B. Wilson ◽  
José Pedro Andrade ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Population Decline ◽  
Genetic Bottleneck ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Hippocampus Guttulatus ◽  
Ria Formosa

AbstractGenetic diversity is the raw foundation for evolutionary potential. When genetic diversity is significantly reduced, the risk of extinction is heightened considerably. The long-snouted seahorse (Hippocampus guttulatus) is one of two seahorse species occurring in the North-East Atlantic. The population living in the Ria Formosa (South Portugal) declined dramatically between 2001 and 2008, prompting fears of greatly reduced genetic diversity and reduced effective population size, hallmarks of a genetic bottleneck. This study tests these hypotheses using samples from eight microsatellite loci taken from 2001 and 2013, on either side of the 2008 decline. The data suggest that the population has not lost its genetic diversity, and a genetic bottleneck was not detectable. However, overall relatedness increased between 2001 to 2013, leading to questions of future inbreeding. The effective population size has seemingly increased close to the threshold necessary for the population to retain its evolutionary potential, but whether these results have been affected by sample size is not clear. Several explanations are discussed for these unexpected results, such as gene flow, local decline due to dispersal to other areas of the Ria Formosa, and the potential that the duration of the demographic decline too short to record changes in the genetic diversity. Given the results presented here and recent evidence of a second population decline, the precise estimation of both gene flow and effective population size via more extensive genetic screening will be critical to effective population management.

Genetic variation and effective population size in isolated populations of coastal cutthroat trout

2010 ◽  
Vol 11 (5) ◽  
pp. 1929-1943 ◽  
Author(s):  
Andrew R. Whiteley ◽  
Kim Hastings ◽  
John K. Wenburg ◽  
Chris A. Frissell ◽  
Jamie C. Martin ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Cutthroat Trout ◽  
Effective Population ◽  
Isolated Populations ◽  
Coastal Cutthroat Trout

Likelihood-Based Estimation of the Effective Population Size Using Temporal Changes in Allele Frequencies: A Genealogical Approach

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 741-751 ◽  
Author(s):  
Pierre Berthier ◽  
Mark A Beaumont ◽  
Jean-Marie Cornuet ◽  
Gordon Luikart
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Classical Method ◽  
Extinction Risk ◽  
Effective Population ◽  
Upper Limit ◽  
Credible Intervals ◽  
Using Data ◽  
Statistic Approach

AbstractA new genetic estimator of the effective population size (Ne) is introduced. This likelihood-based (LB) estimator uses two temporally spaced genetic samples of individuals from a population. We compared its performance to that of the classical F-statistic-based Ne estimator () by using data from simulated populations with known Ne and real populations. The new likelihood-based estimator () showed narrower credible intervals and greater accuracy than () when genetic drift was strong, but performed only slightly better when genetic drift was relatively weak. When drift was strong (e.g., Ne = 20 for five generations), as few as ~10 loci (heterozygosity of 0.6; samples of 30 individuals) are sufficient to consistently achieve credible intervals with an upper limit <50 using the LB method. In contrast, ~20 loci are required for the same precision when using the classical F-statistic approach. The estimator is much improved over the classical method when there are many rare alleles. It will be especially useful in conservation biology because it less often overestimates Ne than does and thus is less likely to erroneously suggest that a population is large and has a low extinction risk.

scholarly journals Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkleMelarhaphe neritoides(Mollusca: Gastropoda)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2549 ◽  
Author(s):  
Séverine Fourdrilis ◽  
Patrick Mardulyn ◽  
Olivier J. Hardy ◽  
Kurt Jordaens ◽  
António Manuel de Frias Martins ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Nucleotide Diversity ◽  
Spatial Scales ◽  
Haplotype Diversity ◽  
Mtdna Mutation ◽  
Effective Population ◽  
Marine Gastropods

We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkleMelarhaphe neritoides(Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytbgene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity inM. neritoidesis characterized by extremely high haplotype diversity (Hd= 0.999 ± 0.001), high nucleotide diversity (π= 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (πsyn= 0.0677). Haplotype richness is very high even at spatial scales as small as 100m2. Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identifyM. neritoides. The mtDNA hyperdiversity inM. neritoidesis best explained by the remarkably high mutation rate at the COI locus (μ= 5.82 × 10−5per site per yearorμ= 1.99 × 10−4mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (Ne= 5, 256; CI = 1,312–3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to highμvalues and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated.

scholarly journals Initial approach to the Conservation Genetics of the Guatemalan Beaded Lizard (Heloderma charlesbogerti): A route to genetic rescue

2021 ◽  
Author(s):  
Sergio A Gonzalez-Mollinedo ◽  
Thomas Schrei ◽  
Brad Locke
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Extinction Risk ◽  
Genetic Erosion ◽  
Unknown Origin ◽  
Single Individual ◽  
Effective Population ◽  
Genetic Management ◽  
Low Genetic Diversity

In this study, samples from 33 Guatemalan Beaded Lizard (Heloderma charlesbogerti) were analyzed for genetic diversity. Twenty-three samples were obtained from wild individuals from two separate population areas, and 10 samples were obtained from captive individuals. Because the seasonally dry tropical forest habitat sampled for this study, is degraded and fragmented, it was hypothesized that beaded lizard populations were small and isolated and would be subject to genetic erosion and an elevated extinction risk. To test this hypothesis, eight microsatellite markers were employed to analyze 22 individual samples from the population of Cabanas, Zacapa, a single individual from the eastern-most population and 10 captive individuals of unknown origin. An average of three alleles per maker was reported for the Cabanas population, evidencing a low genetic diversity. In addition, a recent bottleneck event was detected and an effective population size of 19.6 was estimated. Demographic reconstruction using a Bayesian approach was inconclusive possibly due to a small dataset and shallow coalescence trees obtained with the generated data. No clear structuring pattern was detected for the Cabanas population and most samples from individuals in captivity were found to have similar alleles to the ones from Cabanas. Population designation is challenging without the genotyping of every wild population, but unique alleles were found in captive individuals of unknown origin that could suggest that different genotypes might exist within other, less studied, wild populations. Low genetic diversity, and a small effective population size represent a risk for the Cabanas population facing the threats of isolation, habitat loss and climate change. These findings suggest that genetic management of the Cabanas population might be utilized to avoid high rates of inbreeding and subsequent inbreeding depression.

Predicting cutthroat trout (Oncorhynchus clarkii) abundance in high-elevation streams: revisiting a model of translocation success

2005 ◽  
Vol 62 (10) ◽  
pp. 2399-2408 ◽  
Author(s):  
Michael K Young ◽  
Paula M Guenther-Gloss ◽  
Ashley D Ficke
Keyword(s):  
Population Size ◽  
Habitat Complexity ◽  
Cutthroat Trout ◽  
High Elevation ◽  
Stream Length ◽  
Oncorhynchus Clarkii ◽  
Abundance Estimates ◽  
Population Sizes ◽  
Bankfull Width ◽  
Habitat Variables

Assessing viability of stream populations of cutthroat trout (Oncorhynchus clarkii) and identifying streams suitable for establishing populations are priorities in the western United States, and a model was recently developed to predict translocation success (as defined by an index of population size) of two subspecies based on mean July water temperature, pool bankfull width, and deep pools counts. To determine whether the translocation model applied to streams elsewhere with more precise abundance estimates, we examined the relation between electrofishing-based estimates of cutthroat trout abundance and these habitat variables plus occupied stream length. The preferred model was (population size)1/2 = 0.00508(stream length (m)) + 5.148 (N = 31). In contrast, a model based on data from the original translocation model included stream temperature and deep pool counts as variables. Differences in models appear to largely have a methodological rather than biological basis. Additional habitat coupled with increased habitat complexity may account for the form of the abundance – stream length relation in the electrofishing-based model. Model-derived estimates imply that many cutthroat trout populations are below thresholds associated with reduced risk of extinction. We believe that this model can reduce uncertainty about projected population sizes when selecting streams for reintroductions or evaluating unsampled streams.

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