Repeated Habitat Disturbances by Fire Decrease Local Effective Population Size

Aim Describing the landscape variables that accurately reflect how environmental and topographic variations affect population connectivity and demography is a major goal of landscape genetics and conservation biology. However, few landscape genetics studies have quantified the relationships between landscape variables and effective population size (Ne), although Ne is a key conservation and population genetics parameter. In this study, I estimated genetic structure and effective population sizes in the Yosemite toad (Bufo canorus) and tested for associations with environmental and geographic variables.Location Yosemite National Park, California, USA.Methods I estimated FST, Dps and Ne using 10 microsatellite loci amplified from 781 individuals from 24 populations. I used three landscape variables (environmental variation, topography and slope) to generate geographic distance models and a series of regression analyses to identify the variables that contributed to genetic structure in this species. I also tested for correlations between Ne and a suite of variables, including geographic and genetic isolation, habitat suitability, elevation, temperature and precipitation.Results I found substantial variation in genetic distances between populations (FST = 0.004–0.396, Dps = 0.045–0.839) and in effective population sizes (Ne = 9–52). Environmental variation and slope played important roles in explaining variation in genetic distances, and precipitation variables were significantly correlated with Ne.Main conclusions These results show that environmental and topographic variables are both important for understanding population connectivity in B. canorus and provide some of the first evidence, in any species, for a link between environmental variables and effective population size.

Effective population size is a fundamental parameter in population genetics, evolutionary biology, and conservation biology, yet its estimation can be fraught with difficulties. Several methods to estimate Ne from genetic data have been developed that take advantage of various approaches for inferring Ne . The ability of these methods to accurately estimate Ne , however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating Ne from genetic data (Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP, and NeEstimator including LDNe) across simulated datasets with populations experiencing migration or no migration. The simulated population demographies are an isolated population with no immigration, an island model metapopulation with a sink population receiving immigrants, and an isolation by distance stepping stone model of populations. We find considerable variance in performance of these methods, both within and across demographic scenarios, with some methods performing very poorly. The most accurate estimates of Ne can be obtained by using LDNe, MLNe, or TMVP; however each of these approaches is outperformed by another in a differing demographic scenario. Knowledge of the approximate demography of population as well as the availability of temporal data largely improves Ne estimates.

Habitat disturbance in tropical forests has affected the viability of several tree species. In Mexico, populations of Guaiacum sanctum have disappeared in some regions due to a strong habitat reduction which could endanger the genetic diversity and connectivity of remnant populations. In this study, 17 populations from the Yucatán Peninsula were analyzed with seven nuclear microsatellites. Several parameters describing the genetic diversity were estimated. The genetic structure was evaluated using Bayesian cluster analysis. Population bottlenecks, effective population size, and genetic connectivity were estimated. Populations of G. sanctum showed high values of genetic diversity. Two genetic groups with contrasting distributions were detected, the first one located in northern Yucatán and Quintana Roo and the second, in southern Campeche. Evidence of population bottleneck was detected only for Campeche populations. Also, we found indications of significant levels of inbreeding and a low effective population size. The connectivity analysis revealed exchange among populations of G. sanctum but the habitat fragmentation may act to impede gene flow, contributing to the division observed between clusters. This genetic differentiation was possibly caused by environmental pressures, although effects of historical extensive logging practices occurred in southern Mexico during the last few decades cannot be discarded. Fragmentation has a negative effect on ecosystem services and on the availability of favorable sites for seedling establishment, which could disturb pollination and dispersion processes, modifying in the long term the effective population size.

The decrease in biodiversity due to increasing urbanization has been well documented, but the processes of colonization and maintenance of wildlife populations in urban areas remain poorly understood. We address this issue using 462 individuals from 10 urban populations of the ant Formica japonica in Kobe City, Japan. We sampled workers regardless of colony identity, genotyped them using 6 microsatellite loci, and estimated allele frequencies and genotypes of reproductive individuals, together with other population genetic parameters, by estimating kinship structure using a likelihood method. Estimated genetic diversity and effective size of populations were not associated with environmental parameters, suggesting that populations are unaffected by urbanization. However, effective population sizes were small, and frequent population bottlenecks were detected. These results suggest that urban F. japonica populations are unstable, and the possibility of frequent extinctions and recolonizations in urban habitats. Populations were moderately differentiated without isolation by distance, suggesting a strong dispersal ability that enables colonization of urban habitats. Dispersal was male biased. Collectively, F. japonica was regarded as an urban adapter, which can colonize urban habitats by virtue of its preference for open ground and high dispersal ability but can persist in urban populations for only a short time, showing a tendency as a temporary urban inhabitant.

Local Extinction and Recolonization, Species Effective Population Size, and Modern Human Origins

We previously estimated the predicted effective population size for the endangered winter-run chinook salmon, Oncorhynchus tshawytscha, based on a number of assumptions, including random survival and return of released fish. Here we present data from actual returning spawners, identified to family by microsatellite loci, and calculate the observed effective population size. In 1994 and 1995, the observed effective population sizes were 93.6 and 78.2% of predicted values, respectively, suggesting that the numbers of returning fish were very close to random expectations in 1994 and less close to random in 1995. The ratio of the effective population size to the adult number, Ne/N, was greater than unity for 1994 and approximately 0.5 in 1995. The high ratio in 1994 reflects the success of the breeding protocol to equalize individual contributions and near random returns, while the lower number in 1995 appears to be the result of both less successful equalization and less close to random returns in that year. These findings provide an optimistic outlook for the success of this supplementation program and suggest that the overall effective population size has not been greatly reduced, since returning spawners represent a broad sample of parents and not fish from only a few families.

Effective population size (Ne) is a key parameter in population genetics. It has important applications in evolutionary biology, conservation genetics and plant and animal breeding, because it measures the rates of genetic drift and inbreeding and affects the efficacy of systematic evolutionary forces, such as mutation, selection and migration. We review the developments in predictive equations and estimation methodologies of effective size. In the prediction part, we focus on the equations for populations with different modes of reproduction, for populations under selection for unlinked or linked loci and for the specific applications to conservation genetics. In the estimation part, we focus on methods developed for estimating the current or recent effective size from molecular marker or sequence data. We discuss some underdeveloped areas in predicting and estimating Ne for future research.

Over three consecutive years, we surveyed the temporal variability in genetic structure of sardine populations in the Bay of Biscay and effective population size. Based on individual age, the genetic structure of year classes of the fishes was also surveyed, showing that populations of sardines have weak but significant genetic differences between sampling years and between year classes. We used two different methods to assess effective population size. The methods resulted in different values but a similar range, indicating a low effective population for Sardina pilchardus. Effective population size decreased over the 3 years, probably resulting from an abundance of fish in the Bay. Based on these results, we conclude that temporal variability in the genetic structure of the sardine population and effective size are likely related to environmental conditions in the Bay. Finally, we propose to use effective population size to estimate biomass of sardines in the Bay.

North Greenland Polar Eskimos are the only hunter-gatherer population, to our knowledge, who can offer precise genealogical records spanning several generations. This is the first report from Eskimos on two key parameters in population genetics, namely, generation time (T) and effective population size (Ne). The average mother-daughter and father-son intervals were 27 and 32 years, respectively, roughly similar to the previously published generation times obtained from recent agricultural societies across the world. To gain an insight for the generation time in our distant ancestors, we calculated maternal generation time for two wild chimpanzee populations. We also provide the first comparison among three distinct approaches (genealogy, variance and life table methods) for calculating Ne, which resulted in slightly differing values for the Eskimos. The ratio of the effective to the census population size is estimated as 0.6-0.7 for autosomal and X-chromosomal DNA, 0.7-0.9 for mitochondrial DNA and 0.5 for Y-chromosomal DNA. A simulation of alleles along the genealogy suggested that Y-chromosomal DNA may drift a little faster than mitochondrial DNA in this population, in contrast to agricultural Icelanders. Our values will be useful not only in prehistoric population inference but also in understanding the shaping of our genome today.

Summary 1. Habitat fragmentation of stream ecosystems often results in decreased connectivity between populations and lower population sizes. Hence, understanding how habitat fragmentation affects genetic erosion is important for the preservation of freshwater biodiversity, in particular, as small populations suffer from loss of genetic diversity through genetic drift and loss of fitness because of inbreeding, increasing the risk of extinction. 2. Here, we assess the impact of demographic factors on population differentiation in the endangered freshwater crayfish Austropotamobius pallipes by analysing population genetic structure, estimating effective population sizes and comparing levels of polymorphism at five microsatellite loci with density estimates of 10 populations within a small French catchment that has become progressively confined to headwaters over the last six decades. 3. Levels of expected heterozygosity and allelic richness per population were relatively low (0.214–0.396 and 1.6–2.6, respectively). We found strong genetic differentiation between these geographically close populations (FST = 0.283), with weak statistical evidence for a pattern of isolation by distance. Estimates of effective population size were low (<150) in most populations, but potentially reached several thousands in three populations. 4. Population density and allelic richness were strongly positively correlated. A robust relationship between population density and heterozygosity values was also noted, but only after discarding two populations for which significant genetic signatures of a recent bottleneck were found; these two populations displayed high expected heterozygosity compared with a very low density. Populations with the highest densities of individuals had the highest effective population size estimates and vice versa. 5. Our results clearly show the importance of demographic factors and genetic drift on A. pallipes populations. Furthermore, analysis of genetic and population density data is a pragmatic and efficient approach to corroborate inferences from genetic data and can be particularly useful in the identification of populations experiencing a bottleneck and therefore in conservation genetics studies aiming at identifying priority populations for conservation.

The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, with high levels of adaptive evolution in Drosophila, bacteria, and viruses but very little evidence of widespread adaptive evolution in hominids. Although estimates in plants are more limited, some recent work has suggested that rates of adaptive evolution in a range of plant taxa are surprisingly low and that there is little association between adaptive evolution and effective population size in contrast to patterns seen in other taxa. Here, we analyze data from 35 loci for six sunflower species that vary dramatically in effective population size. We find that rates of adaptive evolution are positively correlated with effective population size in these species, with a significant fraction of amino acid substitutions driven by positive selection in the species with the largest effective population sizes but little or no evidence of adaptive evolution in species with smaller effective population sizes. Although other factors likely contribute as well, in sunflowers effective population size appears to be an important determinant of rates of adaptive evolution.

This study was conducted to estimate the extent of linkage disequilibrium (LD) and effective population size using whole genomic single nucleotide polymorphisms (SNP) genotyped by DNA chip in Hanwoo. Using the blood samples of 35 young bulls born from 2005 to 2008 and their progenies (N=253) in a Hanwoo nucleus population collected from Hanwoo Improvement Center, 51,582 SNPs were genotyped using Bovine SNP50 chips. A total of 40,851 SNPs were used in this study after elimination of SNPs with a missing genotyping rate of over 10 percent and monomorphic SNPs (10,730 SNPs). The total autosomal genome length, measured as the sum of the longest syntenic pairs of SNPs by chromosome, was 2,541.6 Mb (Mega base pairs). The average distances of all adjacent pairs by each BTA ranged from 0.55 to 0.74 cM. Decay of LD showed an exponential trend with physical distance. The means of LD (r2) among syntenic SNP pairs were 0.136 at a range of 0-0.1 Mb in physical distance and 0.06 at a range of 0.1-0.2 Mb. When these results were used for Luo’s formula, about 2,000 phenotypic records were found to be required to achieve power > 0.9 to detect 5% QTL in the population of Hanwoo. As a result of estimating effective population size by generation in Hanwoo, the estimated effective population size for the current status was 84 heads and the estimate of effective population size for 50 generations of ancestors was 1,150 heads. The average decreasing rates of effective population size by generation were 9.0% at about five generations and 17.3% at the current generation. The main cause of the rapid decrease in effective population size was considered to be the intensive use of a few prominent sires since the application of artificial insemination technology in Korea. To increase and/or sustain the effective population size, the selection of various proven bulls and mating systems that consider genetic diversity are needed.

Evaluation of genetic variability loss in a captive population of Pacific white shrimp Penaeus (Litopenaeus) vannamei using microsatellite and pedigree information

Monitoring temporal changes in population genetic diversity and effective population size can provide vital information on future viability. The dusky gopher frog, Lithobates sevosus, is a critically endangered species found only in coastal Mississippi, with low genetic variability as a consequence of isolation and population size reduction. Conservation management practices have been implemented, but their efficacy has not been addressed. We genotyped individuals collected 1997–2014 to determine temporal trends in population genetic variation, structure, and effective size. Observed and expected heterozygosity and allelic richness revealed temporally stable, but low, levels of genetic variation. Positive levels of inbreeding were found in each year. There was weak genetic structure among years, which can be attributed to increased effects of genetic drift and inbreeding in small populations. L. sevosus exhibited an increase in effective population size, and currently has an estimated effective size of 33.0–58.6 individuals, which is approximately half the census size. This large ratio could possibly be explained by genetic compensation. We found that management practices have been effective at maintaining and improving effective size and genetic diversity, but that additional strategies need to be implemented to enhance viability of the species.

For a Wright-Fisher model with mutation whose population size fluctuates stochastically from generation to generation, a heterozygosity effective population size is defined by means of the equilibrium average heterozygosity of the population. It is shown that this effective population size is equal to the harmonic mean of population size if and only if the stochastic changes of population size are uncorrelated. The effective population size is larger (resp. smaller) than the harmonic mean when the stochastic changes of population size are positively (resp. negatively) autocorrelated. These results and those obtained so far for other stochastic models with fluctuating population size suggest that the property that effective population sizes are always larger than the harmonic mean under the fluctuation of population size holds only for continuous time models such as diffusion and coalescent models, whereas effective population sizes can be equal to or smaller than the harmonic mean for discrete time models.