Evaluating methods for estimating local effective population size with and without migration

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 N_e from genetic data have been developed that take advantage of various approaches for inferring N_e. The ability of these methods to accurately estimate N_e, however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating N_e 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 N_e 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 N_e estimates.     

Isolation-by-distance in landscapes: considerations for landscape genetics

In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, F_ST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern). We investigated if landscape configuration influenced the rate at which a case-IV pattern changed to a case-I pattern. We also determined at what interdeme distance the highest correlation was measured between genetic differentiation and geographic distance and whether this distance corresponded to the maximum migration distance. We set up a population genetic simulation study and assessed the development of IBD patterns for several habitat configurations and maximum migration distances. We show that the rate and likelihood of the transition of case-IV to case-I F_ST–distance relationships was strongly influenced by habitat configuration and maximum migration distance. We also found that the maximum correlation between genetic differentiation and geographic distance was not related to the maximum migration distance and was measured across all deme pairs in a case-I pattern and, for a case-IV pattern, at the distance where the F_ST–distance curve flattens out. We argue that in landscape genetics, separate analyses should be performed to either assess IBD or the landscape effects on gene flow.     

Methods for Fitting the Right-Truncated Weibull Distribution to Life-Test and Survival Data

This paper develops mathematical and computational methods for fitting, by the method of maximum likelihood (ML), the two-parameter, right-truncated Weibull distribution (RTWD) to life-test or survival data. Some important statistical properties of the RTWD are derived and ML estimating equations for the scale and shape parameters of the RTWD are developed. The ML equations are used to express the scale parameter as an analytic function of the shape parameter and to establish a computationally useful lower bound on the ML estimate of the shape parameter. This bound is a function only of the sample observations and the (known) truncation point T. The ML equations are reducible to a single nonlinear, transcendental equation in the shape parameter, and a computationally efficient algorithm is described for solving this equation. The practical use of the methods is illustrated in two numerical examples.     

Estimation of parameters in large offspring number models and ratios of coalescence times

The ratio of singletons to the total number of segregating sites is used to estimate a reproduction parameter in a population model of large offspring numbers without having to jointly estimate the mutation rate. For neutral genetic variation, the ratio of singletons to the total number of segregating sites is equivalent to the ratio of total length of external branches to the total length of the gene genealogy. A multinomial maximum likelihood method that takes into account more frequency classes than just the singletons is developed to estimate the parameter of another large offspring number model. The performance of these methods with regard to sample size, mutation rate, and bias, is investigated by simulation. The expected value of the ratio of the total length of external branches to the total length of the whole tree is, using simulation, shown to decrease for the Kingman coalescent as sample size increases, but can increase or decrease, depending on parameter values, for Λ coalescents. Considering ratios of tree statistics, as opposed to considering lengths of various subtrees separately, can yield better insight into the dynamics of gene genealogies.     

Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision

Unbiased estimates of θ = 4Nµ in a random mating population can be based on either the number of alleles or the average number of nucleotide differences in a sample. However, if there is population structure and the sample is drawn from a single subpopulation, these two estimates of θ behave differently. The expected number of alleles in a sample is an increasing function of the migration rates, whereas the expected average number of nucleotide differences is shown to be independent of the migration rates and equal to 4N_Tµ for a general model of population structure which includes both the island model and the circular stepping-stone model. This contrast in the behavior of these two estimates of θ is used as the basis of a test for population subdivision. Using a Monte-Carlo simulation developed so that independent samples from a single subpopulation could be obtained quickly, this test is shown to be a useful method to determine if there is population subdivision.     

Equilibrium between Genetic Drift and Migration at Various Mutation Rates: Simulation Analysis

Rates of approach to equilibrium values of F _ST /R _ST at various mutation rates and using different mutation models (K-allele model KAM and stepwise model SMM) were analyzed numerically for the finite island model and the one-dimensional stepping stone models of migration, using simulation. In the island model of migration and the KAM mutation model, the rate of approach to the equilibrium F _ST value was appreciably higher and the equilibrium value was almost twofold lower at μ (mutation rate) = m (migration rate) than at μ ≪ m. In the one-dimensional stepping stone model of migration and the KAM model of mutation, the mutation rate significantly affected both the rate of approaching F _ST equilibrium and the equilibrium value. In both island and one-dimensional stepping stone models and SMM, R _ST was not influenced by various mutation rates. The rate of approach to the equilibrium values of both F _ST and R _ST was lower for the stepping stone model than to the island model. R _ST was rather resistant to deviations from the SMM mutation model. __________ Translated from Genetika, Vol. 41, No. 9, 2005, pp. 1283–1288. Original Russian Text Copyright ? 2005 by Efremov.     

Temporal genetic samples indicate small effective population size of the endangered yellow-eyed penguin

There is an increasing awareness that the long-term viability of endemic island populations is negatively affected by genetic factors associated with population bottlenecks and/or persistence at small population size. Here we use contemporary samples and historic museum specimens (collected 1888–1938) to estimate the effective population size (N _e) for the endangered yellow-eyed penguin (Megadyptes antipodes) in South Island, New Zealand, and evaluate the genetic concern for this iconic species. The South Island population of M. antipodes—constituting almost half of the species’ census size—is thought to be descended from a small number of founders that reached New Zealand just a few hundred years ago. Despite intensive conservation measures, this population has shown dramatic fluctuations in size over recent decades. We compare estimates of the harmonic mean N _e for this population, obtained using one moment and three likelihood based-temporal methods, including one method that simultaneously estimates migration rate. Evaluation of the N _e estimates reveals a harmonic mean N _e in the low hundreds. Additionally, the inferred low immigration rates (m = 0.003) agree well with contemporary migration rate estimates between the South Island and subantarctic populations of M. antipodes. The low N _e of South Island M. antipodes is likely affected by strong fluctuations in population size, and high variance in reproductive success. These results show that genetic concerns for this population are valid and that the long-term viability of this species may be compromised by reduced adaptive potential.     

The Rate of Approach to the Equilibrium Value of F ST in Island and One-Dimensional Stepping-Stone Models of Migration

The rate of approach to the equilibrium value of F _ST was analyzed numerically for the finite island and one-dimensional stepping-stone models using computer simulation. For both models, this rate was shown to decrease with decreasing migration rate among subpopulations but in the case of the stepping-stone model, it takes thousands rather than tens of generations to reach the equilibrium. Unlike the island structure of migration, in the stepping-stone model an increase in the subpopulation number reduces the rate of reaching the equilibrium state.     

Bootstrap and Second‐Order Tests of Risk Difference

Summary Clinical trials data often come in the form of low‐dimensional tables of small counts. Standard approximate tests such as score and likelihood ratio tests are imperfect in several respects. First, they can give quite different answers from the same data. Second, the actual type‐1 error can differ significantly from nominal, even for quite large sample sizes. Third, exact inferences based on these can be strongly nonmonotonic functions of the null parameter and lead to confidence sets that are discontiguous. There are two modern approaches to small sample inference. One is to use so‐called higher order asymptotics ( Reid, 2003 , Annal of Statistics 31 , 1695–1731) to provide an explicit adjustment to the likelihood ratio statistic. The theory for this is complex but the statistic is quick to compute. The second approach is to perform an exact calculation of significance assuming the nuisance parameters equal their null estimate ( Lee and Young, 2005 , Statistic and Probability Letters 71 , 143–153), which is a kind of parametric bootstrap. The purpose of this article is to explain and evaluate these two methods, for testing whether a difference in probabilities p₂? p₁ exceeds a prechosen noninferiority margin δ₀ . On the basis of an extensive numerical study, we recommend bootstrap P‐values as superior to all other alternatives. First, they produce practically identical answers regardless of the basic test statistic chosen. Second, they have excellent size accuracy and higher power. Third, they vary much less erratically with the null parameter value δ₀ .     

QUANTIFYING THE PLEISTOCENE HISTORY OF THE OAK GALL PARASITOID CECIDOSTIBA FUNGOSA USING TWENTY INTRON LOCI

The longitudinal spread of temperate organisms into refugial populations in Southern Europe is generally assumed to predate the last interglacial. However, few studies have attempted to quantify this process in nonmodel organisms using explicit models and multilocus data. We used sequence data for 20 intron‐spanning loci (12 kb per individual) to resolve the history of refugial populations of a widespread western Palaearctic oak gall parasitoid Cecidostiba fungosa (Pteromalidae). Using maximum likelihood and Bayesian methods we assess alternative population tree topologies and estimate divergence times and ancestral population sizes under a model of divergence between three refugia (Middle East, Balkans and Iberia). Both methods support an “Out of the East” history for C. fungosa, matching the pattern previously inferred for their gallwasp hosts. However, coalescent‐based estimates of the ages of population divides are much more recent (coinciding with the Eemian interglacial) than nodal ages of single gene trees for C. fungosa and other species. We also find that increasing the sample size from one haploid sequence per refugial population to three only marginally improves parameter estimates. Our results suggest that there is significant information in the minimal samples currently analyzable with maximum likelihood methods, and that similar methods could be applied to multiple species to test alternative models of assemblage evolution.     

Comparison and Evaluation of Three Methods of Estimation of the Johnson Sb Distribution

Thre methods of estimating the parameters of the Johnson S₆ distribution were tested by simulation. The maximum likelihood method, the method based on percentiles of a sample and the method based on moments of a transformed random variable were taken into consideration. Many sets of samples were generated differing in sizes and in the actual values of parameters, whereupon the parameters were estimated by the three methods. It was proved that if the sample is small or the skewness of the distribution is considerable, the maximum likelihood estimates can assume preposterous values. The method based on moments is recommended due to its simplicity and to the fact that the estimates, though usually biased, never assume absurd values.     

A new trajectory analysis method for migratory planthoppers, Sogatella furcifera (Horváth) (Homoptera: Delphacidae) and Nilaparvata lugens (Stål), using an advanced weather forecast model

Abstract 1 A new method of backward trajectory analysis for planthopper migration is presented. The method consists of two components: an advanced weather forecast model, MM5, for weather simulation, and a migration model for trajectory calculation. The weather forecast model simulates wind fields in which trajectories are calculated by the migration model. 2 It is assumed that planthoppers, Sogatella furcifera and Nilaparvata lugens, are transported at wind speeds and in wind directions. The method is evaluated using a migration event observed at Chikugo in Japan on 25 June 1969, which was recorded in hourly catch data. 3 The results indicate that the takeoff responsible for the migration occurred at 21 UTC (Coordinated Universal Time) on 23 June along the coastal region of Fujian province in China. This is the first time that the source region of this event has been accurately identified. Determinations of the migrating duration and height are also consistent with observations. 4 Although the landing process is not considered in the model, it is shown that the method is able to simulate the migration and accurately estimate various parameters. This study also shows the importance of high‐quality weather simulation.     

Estimation of the neutral mutation rate in a finite population from DNA sequence data

The sampling theory for the infinite site model taking into account the phylogenetic relationship between the alleles is developed for those cases in which two or three alleles are observed in the sample. From this theory a maximum likelihood estimate of θ = 4Nμ can be obtained. Unlike the maximum likelihood estimate of θ based on the infinite allele model or the number of segregating sites, this estimate of θ is a function of the frequencies of the alleles. This method is used to estimate θ for mitochondrial DNA in Drosophila melanogaster and D. virilis from data obtained by Shah and Langley (1979. Nature (London)281, 696–699) using restriction endonucleases.     

Molecular Dynamics Studies of Diffusion in Model Cylindrical Pores at Very Low Densities

Abstract

Molecular dynamics simulation has been used to study diffusion of methane at ambient temperature in cylindrical pores at very low densities. The cylinders were modelled as a continuum solid which interacts with the methane in the radial direction only. At the lowest densities, the VACF method does not yield reliable values of the self diffusion coefficient, D_s , but a suitable choice of time step and run length enables values of D_s to be found from MSD plots that are below the classical Knudsen diffusion coefficients. When density is increased, D_s passes through a maximum although the adsorption isotherm remains inside the Henry law region. Maxima are found for two cylinder radii and for two adsorbent field strengths. The existence of a maximum is attributed to transient intermolecular interactions. Analysis of a molecular trajectory demonstrates that long diffusion paths can be triggered by the rare event of an intermolecular encounter which forces a molecule into the repulsive part of the wall potential. At sufficiently high density, subsequent collisions quench the tendency towards long paths, and D_s decreases again. The issue of simulation artefact as a source of these observations is discussed.     

创伤弧菌TF3全基因组包含的CRISPR-Cas系统及MGIVvuTF3基因岛分析

【目的】分析创伤弧菌(Vibrio vulnificus)全基因组框架序列,挖掘感兴趣的遗传位点,探索其是否具有CRISPR系统及其特征。【方法】在病虾体内分离获得了一株创伤弧菌TF3,通过Illumina Miseq测序得到基因组框架序列。经注释分析发现其基因组中存在一个CRISPR-Cas系统,命名为CRISPR-CasTF3,进一步分析发现CRISPR-CasTF3位于一个基因岛上,将该基因岛命名为MGIVvu TF3。对CRISPR-CasTF3及MGIVvu TF3的特征和来源进行了分析。【结果】CRISPR-CasTF3属于与大肠杆菌类似的Ι-E型CRISPR-Cas系统,CRISPR-CasTF3包括8个cas基因,其排列为cas3-cas8e-cse2-cas6-cas7-cas5-cas1-cas2;具有50个重复序列,每二个重复序列间为一个Spacer序列。MGIVvu TF3具有att L和att R序列,含有位点特异性整合、剪切、转移相关的基因。MGIVvu TF3与霍乱弧菌O395基因组中的一个基因岛MGIVch0395具较高相似性,二者最显著的差别在于Spacer序列完全不同,以及各有几个非保守的预测基因。【结论】MGIVvu TF3及CRISPR-CasTF3极有可能通过基因水平转移获得,并且CRISPR-CasTF3系统可以借助MGIVvu TF3实现水平转移。     

Calcium-stimulated myofibrillar ATPase activity correlates with shortening velocity of muscle fibres in Xenopus laevis

Summary The iliofibularis muscle ofXenopus laevis is reported to contain five types of fibres which have different force—velocity relationships. Ten fibres of each type were selected on the basis of succinate dehydrogenase activity, cross-sectional area and location in the muscle, in order to assess the validity of the fibre type classification.Maximum calcium-stimulated myofibrillar ATPase activity (V _max) and apparent Michaelis constant (K _m) for ATP were determined for these 50 fibres from serial sections. The values obtained varied according to the type of fibre. Type 1 had the highest and type 5 the lowest values forK _m andV _max.In a separate experiment, single freeze-dried fibres were used to determine the relationship between their ATP content and apparentK _m for ATP. There was a tendency for high ATP concentrations in fibres with highK _m values.When myofibrillar ATPase activity was related to the maximum velocity of shortening of the five fibre types, a significant correlation was found. It is concluded that calcium-stimulated myofibrillar ATPase histochemistry allows an estimate of the maximum shortening velocity of muscle fibres fromXenopus laevis.     

A phylogenetic study of Echidnopsis Hook. f. (Apocynaceae-Asclepiadoideae) - taxonomic implications and the colonization of the Socotran archipelago

We investigated the phylogeny, taxonomy and biogeography of the Eritreo-Arabian genus Echidnopsis Hook. f. (Apocynaceae-Asclepiadoideae). Phylogenetic reconstructions based on nrITS sequence data were obtained using maximum likelihood and parsimony analyses. The results reveal two weakly supported clades, each with a mix of African and Arabian taxa, including the genus Rhytidocaulon, and with four Socotran species forming a subclade of their own. Rather than a vicariance origin of these island elements, our data suggest a single dispersal event from eastern Africa. Echidnopsis thus parallels biogeographic patterns found for other Socotran endemic plants. Our revised taxonomy recognizes 28 species and 4 subspecies in the genus. Two new combinations, E. planiflora subsp. chrysantha and E. sharpei subsp. bavazzani are proposed.     

Interval Estimation of the Effective Population Size from Heterozygote‐Excess in SNP Markers

The effective population size N_e is an important parameter in population genetics and conservation biology. In recent years, there has been great interest in the use of molecular markers to estimate N_e. Although the point estimates from molecular markers in general suffer from a low reliability, the use of single nucleotide polymorphism (SNP) markers over a wide range of genome is expected to remarkably improve the reliability. In this study, expressions were derived for interval estimates of N_e from one published method, the heterozygote‐excess method, when it is applied to SNP markers. The conditional variance theory is applied to the derivation of a confidence interval for N_e under random union of gametes, monogamy and polygyny. Stochastic simulation shows that the obtained confidence interval is slightly conservative, but fairly useful for practical applications. The result is illustrated with real data on SNP markers in a pig strain.     

Long-distance migration timing of Tringa sandpipers adjusted to recent climate change

Capsule Evidence for earlier spring migration of Tringa sandpipers after warmer winters, but no clear pattern concerning autumn migration timing.

Aim To analyse the timing of migration of three Tringa sandpipers between 1966 and 2002 with respect to recent global warming on a local and a hemispheric scale.

Methods I analysed long-term migration timing variation in Greenshank Tringa nebularia, Spotted Redshank T. erythropus and Wood Sandpiper T. glareola at four Central European staging sites. Variation in passage onset, median and end per migration period was analysed using stepwise regression with respect to variation in (i) local abundance, residence time and age-dependent abundance as an estimate of breeding success and (ii) climate at the staging sites, snowmelt at the presumed central breeding area and the North Atlantic Oscillation (NAO).

Results All three species consistently showed an overall spring migration advance and autumn migration delay. Autumn passage timing varied with both climatic conditions at the breeding area and breeding success, while in 43% of all cases spring passage correlated with local and hemispheric climate variation.

Conclusion The distinction between population dynamic and climatic effects on timing of autumn migration requires separate data for local adult and juvenile passage or a larger sample of sites. In spring, the data strongly suggest a flexible response of migration timing to local weather conditions and the hemispheric variation of the North Atlantic Oscillation. This indicates that even long-distance migrants are able to adjust their overall migration pattern to fluctuating environmental conditions on a phenotypic basis.     

Report of the Alpine Section, 1958

Background: Over 10,000 island endemic angiosperms are highly threatened by extinction. Yet, few of these species have the temporal change in their range documented and quantified, particularly within a potentially informative context of a long period of botanical study.

Aim: Here, we used Roussea simplex a mono-specific genus endemic to Mauritius, itself an island with long botanical history and advanced habitat destruction extent, to investigate how the distribution and population of this model oceanic island plant changed through time.

Methods: All known localities and population size estimates were compiled from published literature, herbarium specimens, surveys and personal communications to estimate changes in population size, extent of occurrence and area of occupancy and investigate main distribution patterns.

Results: Roussea simplex survives in nine high elevation sites. Since the 1930s, its range halved relative to its maximum known distribution and its population size decreased much faster than direct habitat loss would predict. It now qualifies as Endangered according to the IUCN Red List categories.

Conclusions: Even in an extremely deforested island, endemic plant population decline may be driven more by diminishing habitat quality than diminishing habitat extent. This renders habitat protection alone insufficient, therefore addressing ecological interactions is vital to stem population decline.