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158 results for “effective population size”

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zenodo28/100

Figure 2. The effective population size through recent time for 3 in Comparative analyses of past population dynamics between two subterranean zokor species and the response to climate changes

Figure 2. The effective population size through recent time for 3 clades of plateau zokor (Eospalax baileyi).

opencc-by-4.0Feb 2013View details →

dryad28/100

Data from: Estimation of contemporary effective population size and population declines using RAD sequence data

Large genomic datasets generated with restriction-site associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of species. We used a simulation approach to examine the potential for RADseq datasets to accurately estimate effective population size (Ne) over the course of stable and declining population trends, and we compare the ability of two methods of analysis to accurately distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Using a linkage disequilibrium-based analysis, individual sampling (i.e., n ≥ 30) had the greatest effect on Ne estimation and the detection of population-size declines, with declines reliably detected across scenarios approximately 10 generations after they began. Coalescent-based inference required fewer sampled individuals (i.e., n = 15), and instead was most influenced by the size of the SNP dataset, with 25,000 to 50,000 SNPs required for accurate detection of population trends and at least 20 generations after decline began. The number of samples available and targeted number of RADseq loci are important criteria when choosing between these methods. Neither method suffered any apparent bias due to the effects of allele dropout typical of RAD data. With an understanding of the limitations and biases of these approaches, researchers can make more informed decisions when designing their sampling and analyses. Overall, our results reveal that demographic inference using RADseq data can be successfully applied to infer recent population size change and may be important tools for population monitoring and conservation biology.

opencc-zeroDec 2016View details →

dryad28/100

Data from: Effective number of breeders, effective population size and their relationship with census size in an iteroparous species, Salvelinus fontinalis

Effective number of breeders, Nb, effective population size, Ne, iteroparity, small population size, brook trout, age at maturation Abstract: The relationship between the effective number of breeders (Nb) and the generational effective size (Ne) has rarely been examined empirically in species with overlapping generations and iteroparity. Based on a suite of 11 microsatellite markers we examine the relationship between Nb, Ne, and census population size (Nc) in 14 brook trout (Salvelinus fontanels) populations inhabiting 12 small streams in Nova Scotia and sampled at least twice between 2009 and 2015. Unbiased estimates of Nb obtained with individuals of a single cohort, adjusted on the basis of age at first maturation (α) and adult life span (AL) were from 1.66 to 0.24 times the average estimates of Ne obtained with random samples of individuals of mixed ages [i.e., N ̂(b(adj2))/〖mean(N ̂ (e(mixed ages)))]. In turn, these differences led to adjusted Ne estimates that were from nearly 5 to 0.7 times the estimates derived from mixed aged individuals. These differences translate into the same range of variation in the ratio of effective to census population size (N ̂_(e(adj2))N ̂_c) within populations. Adopting N ̂(e(adj2)) as the more precise and unbiased estimates, we found that these brook trout populations differ markedly in their effective to census population sizes (range ~0.3 to ~0.001). Using AgeNe we then show that the variance in reproductive success or reproductive skew varied among populations by a factor of 40 from a Vk/k≈5 to 200. These results suggest wide differences in population dynamics likely resulting from differences in productivity affecting the intensity of competition for access to mates or redds and thus, reproductive skew. Understanding the relationship between Ne, Nb and Nc and how these relate to population dynamics and fluctuations in population size are important for the design of robust conservation strategies in small populations with overlapping generations and iteroparity.

opencc-zeroDec 2015View details →

dryad28/100

Data from: Genetic signatures of small effective population sizes and demographic declines in an endangered rattlesnake, Sistrurus catenatus

Endangered species that exist in small isolated populations are at elevated risk of losing adaptive variation due to genetic drift. Analyses that estimate short-term effective population sizes, characterize historical demographic processes, and project the trajectory of genetic variation into the future are useful for predicting how levels of genetic diversity may change. Here, we use data from two independent types of genetic markers (single nucleotide polymorphisms [SNPs] and microsatellites) to evaluate genetic diversity in 17 populations spanning the geographic range of the endangered eastern massasauga rattlesnake (Sistrurus catenatus). First, we use SNP data to confirm previous reports that these populations exhibit high levels of genetic structure (overall Fst = 0.25). Second, we show that most populations have contemporary Ne estimates less than 50. Heterozygosity-fitness correlations in these populations provided no evidence for a genetic cost to living in small populations, though these tests may lack power. Third, model-based demographic analyses of individual populations indicate that all have experienced declines, with the onset of many of these declines occurring over timescales consistent with anthropogenic impacts (<200 years). Finally, forward simulations of the expected loss of variation in relatively large (Ne = 50) and small (Ne = 10) populations indicate they will lose a substantial amount of their current standing neutral variation (63% and 99%, respectively) over the next 100 years. Our results argue that drift has a significant and increasing impact on levels of genetic variation in isolated populations of this snake, and efforts to assess and mitigate associated impacts on adaptive variation should be components of the management of this endangered reptile.

opencc-zeroDec 2017View details →

dryad28/100

Data from: Evolution of a dominant natural isolate of Escherichia coli in the human gut over the course of a year suggests a neutral evolution with reduced effective population size

In vitro and in vivo evolution experiments on Escherichia coli revealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior of E. coli in its natural environment. We attempted here to study the evolution in the human gut of a commensal dominant E. coli clone ED1a belonging to B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed amutation rate of 6.90x10-7 per base per year of the chromosome for E. coli ED1a in healthy human gut. We observed a very limited genomic diversity, and could not detect any evidence of selection contrary to what is observed in experimental evolution over similar length of time. We therefore suggest that ED1a being well adapted to the healthy human gut evolves mostly neutrally with a low effective population size (Ne ≈ 500 – 1700).

opencc-zeroDec 2017View details →

dryad28/100