A Unique Genetic Distance

The problem of measuring distances between discrete frequency distributions is considered. Three conditions are stated, which are believed to reflect basic, intuitive requirements to be met by a distance measure of the above kind with particular reference to genetic frequency distributions. These conditions chiefly concern aspects of maximum distance and linearity. It is shown that exactly one function meets the conditions, and this function, having all properties of a metric, is explicitly given.     

The Statistical Properties of Genetic Absolute Distance

The statistical properties of one estimator of absolute genetic distance (1/2) ^K∑_i=1 |pxi-yr|, tween two populations X and Y, are presented. It is shown that using this distance in small samples can be misleading particularly when populations are close to each other.     

Species delimitation and geography

Despite the importance of the geographical arrangement of populations for the inference of species boundaries, only a few approaches that integrate spatial information into species delimitation have thus far been developed. Persistent differentiation of sympatric groups of individuals is the best criterion for species status. Species delimitation becomes more prone to error if allopatric metapopulations are considered because it is often difficult to assess whether observed differences between allopatric metapopulations would be sufficient to prevent the fusion of these metapopulations upon contact. We propose a novel approach for testing the hypothesis that the multilocus genetic distances between individuals or populations belonging to two different candidate species are not larger than expected based on their geographical distances and the relationship of genetic and geographical distances within the candidate species. A rejection of this null hypothesis is an argument for classifying the two studied candidate species as distinct species. Case studies show that the proposed tests are suitable to distinguish between intra‐ and interspecific differentiation. The regression approach proposed here is more appropriate for testing species hypotheses with regard to isolation by distance than (partial) Mantel tests. Our tests assume a linear relationship between genetic and (transformed) geographical distances. This assumption can be compromised by a high genetic variability within populations as found in a case study with microsatellite markers.     

杀虫灯诱杀昆虫的有效距离及生态学参数

采用人工标记释放回收技术,探讨了杀虫灯诱杀斜纹夜蛾Spodoptera litura Fabricius和甜菜夜蛾Spodoptera exigua Hübner的有效距离及不同安装高度的诱杀效果。诱杀结果表明,标记释放虫源离灯越远,其灯下回收率越低;灯高0.8m的灯下回收率显著高于灯高1.3m。提出了用"可控距离CID"、"诱杀中距离MTD50"、"诱杀黄金距离GTD61.8"3个生态学参数量化与规范杀虫灯对昆虫的诱杀距离。拟合结果表明,高0.8m杀虫灯诱杀斜纹夜蛾和甜菜夜蛾的可控距离分别为115.1m、110.9m,诱杀中距离分别为71.8m、67.4m,诱杀黄金距离分别为61.5m、57.1m,可控面积分别是4.2hm2、3.9hm2;高1.3m杀虫灯诱杀斜纹夜蛾和甜菜夜蛾的可控距离分别为108.1m、107.8m,诱杀中距离分别为66.6m、64.7m,诱杀黄金距离分别为56.7m、54.5m,可控面积分别是3.7hm2、3.6hm2。     

Determination of Taxonomic Status of Pathogenic and Nonpathogenic Entamoeba histolytica Zymodemes Using Isoenzyme Analysis

ABSTRACT Entamoeba histolytica infection results in either asymptomatic colonization or invasion of host tissues leading generally to clinical symptoms. Zymodeme studies have demonstrated a correlation between isoenzyme profiles and clinical presentation. Thus, strains have been attributed to pathogenic or nonpathogenic groups according to their zymodeme. To determine the taxonomic relationship of these two groups, the isoenzyme profiles of 14 loci of 38 E. histolytica strains (pathogenic and nonpathogenic) and seven strains of other species of the same genus were analyzed. Genetic distance analysis clearly demonstrates the existence of two separate groups within the species E. histolytica .     

Cranial metric and discrete trait variation and biological differentiation in the terminal Late Archaic of Ohio: the Duff site cemetery

Cranial metric and discrete traits were collected from adult individuals of the terminal Late Archaic Duff site cemetery (33 LO 111). Comparisons of cranial metric traits among eight terminal Late Archaic samples including the Duff site sample showed that all samples shared the same generalized variance and by inference the same pattern of shape variation. Some significant size differences were found but these were interpreted as reflecting only minor differences in the underlying polygenic system or differences in environmental interactions. The overall similarity in cranial metrics among the terminal Late Archaic samples strongly suggests that they represent populations that, at least, shared a recent common ancestor. Analysis of discrete trait variation in all the terminal Late Archaic samples showed that the biological distances between samples are associated significantly with the between-sample geographical distances. This association accounts for approximately 25% of the variation in discrete trait frequencies. These results along with the results of the analysis of cranial metrics indicate that all of the terminal Late Archaic samples considered here are related, but geographically nearer samples are more closely related than distant ones.     

Consequences of population topology for studying gene flow using link‐based landscape genetic methods

Many landscape genetic studies aim to determine the effect of landscape on gene flow between populations. These studies frequently employ link‐based methods that relate pairwise measures of historical gene flow to measures of the landscape and the geographical distance between populations. However, apart from landscape and distance, there is a third important factor that can influence historical gene flow, that is, population topology (i.e., the arrangement of populations throughout a landscape). As the population topology is determined in part by the landscape configuration, I argue that it should play a more prominent role in landscape genetics. Making use of existing literature and theoretical examples, I discuss how population topology can influence results in landscape genetic studies and how it can be taken into account to improve the accuracy of these results. In support of my arguments, I have performed a literature review of landscape genetic studies published during the first half of 2015 as well as several computer simulations of gene flow between populations. First, I argue why one should carefully consider which population pairs should be included in link‐based analyses. Second, I discuss several ways in which the population topology can be incorporated in response and explanatory variables. Third, I outline why it is important to sample populations in such a way that a good representation of the population topology is obtained. Fourth, I discuss how statistical testing for link‐based approaches could be influenced by the population topology. I conclude the article with six recommendations geared toward better incorporating population topology in link‐based landscape genetic studies.     

Managing human disturbance: factors influencing flight-initiation distance of birds in a West African nature reserve

Escape behaviour in response to perceived predators can be employed as a guide when designating protected areas around sensitive bird species to minimise the impact of human disturbance. A key measure of escape response is flight-initiation distance (FID), the distance at which a prey animal initiates its escape when approached by a potential predator. We tested the predictions of optimal escape theory by determining the factors that influence FID of bird species in a Nigerian reserved area and its surrounding habitats, and so the potential utility of FID in managing human disturbance on birds, for the first time within a West African context. We tested how FID varied with group size, proximity to vegetation acting as protective cover, levels of human use, and survival rate, and whether these relationships varied by species. We collected 504 FIDs for seven bird species in Amurum Forest Reserve and its surrounding habitats (Jos, Nigeria). The FID was lower in larger groups and when species were closer to protective cover. The FID was lower outside of the protected area because animals in sites with higher levels of human presence and use may become habituated. The FID was higher for species with higher survival, being consistent with predictions from life history theory. Overall, birds perceived humans as a potential threat and responded in accordance to the predictions of optimal escape theory, with FID increasing with increased cost of staying. Reserve managers in Africa could use species- and context-specific FIDs to designate buffer distances for the protection of wildlife from human disturbance.     

中国金色果蝇复合种的染色体研究——Ⅱ.中国及日本金色果蝇复合种的体细胞同源染色体联会

对采自北京、上海等7个地区及来自日本的金色果蝇Ⅰ(Drosophila auraria)和金色果蝇Ⅲ(Orosophila triauraria)的三龄幼虫的脑神经节进行核型分析。发现在其有丝分裂的晚前期、中期阶段,4对同源染色体都在进行联会。联会发生的频率约为34％。XY染色体往往无联会的表现。常染色体联会时,各对染色体的常染色质区紧密靠拢,而着丝粒区则彼此稍有分开。 本文并提出了以每对同源染色体着丝粒距离的“R_d”值作为判断同源染色体联会的数量指标,通过随机取得的119个细胞的476个R_d值的分析,发现同源染色体联会频率与在显微镜下所观察的结果相吻合。 体细胞同源染色体联会,在双翅目昆虫的特殊现象和在真核生物及其他高等动、植物中作为一般现象的遗传进化意义,本文亦作了初步探讨。     

环境和扩散对草地群落构建的影响

植物群落构建机制是生态学研究的热点之一.长久以来这个难题并没有得到很好的解释,且争议较多.生态位理论或中性理论,或是二者的共同作用,这样的结论在不同的研究中都有印证.以黄土高原子午岭地区的草地群落为例,对3种不同的草地群落(5a的弃耕地、阴坡和阳坡的草地)进行了野外群落学调查,采用Mantel test和主轴邻距法(PCNM)分析方法,研究了空间地理距离和环境资源差异对于草本植物群落分布的影响,结果表明:地理距离和环境差异共同解释了群落组成相似性的79.3％,剔除环境因子的影响,地理距离解释了群落组成相似性的33.8％;而剔除地理距离的影响,环境因子解释了群落组成相似性的14.2％.无论是生态位理论还是中性理论,其在黄土高原草本群落构建过程中都有作用,但中性理论扮演了更为重要的角色.     

Regional and Ecotype Traits in Lotus corniculatus L., with Reference to Restoration Ecology

To assess the relative importance of distance (geographical or ecological) as a consideration when collecting seeds for restoration projects, there is a need for more research on regional and ecotypic variation in a range of species. We used Lotus corniculatus L., a legume frequently included in grassland seed mixes, to investigate phenotypic variation between British accessions in a common garden experiment. The aim of this study was to investigate the effect of seed origin on plant phenotype and fecundity and to determine whether there was any evidence of correlation with distance (geographical or ecological) in populations grown from seed collected from different locations. Regional differences were detected in plant size, growth habit, pubescence, leaf shape, and fecundity. Geographical distance between sites was shown to be positively correlated with an increased difference in seed yield. Differences in size, growth habit, and leaf shape between paired habitats of origin within region and also between "ecotypes" were evident. However, there was no correlation between ecological distance and any of the measured traits. These findings suggest that:

• (1)  

  Differences in phenotype and fecundity between geographically separated populations of L. corniculatus may be sufficient to lead to differences in survival and fitness when seeds are sown in a restoration environment.
• (2)  

  Although it is important to consider geographical location, the choice of habitat within region is also important because phenotypic variation between ecotypes may have long-term consequences for plant persistence.

     

A phylogenetic study of the free-living amoeba

Immunological distances were determined for four strains of the free-living amoeba classified as Amoeba proteus, two strains classified as Polychaos dubia and a single strain classified as Chaos carolinensis. The data show that the _ShP strain does not belong to the proteus group; that A. proteus is more closely related to C. carolinensis and is derived from Chaos as is the _ShP strain; that P. dubia and C. carolinensis are the more distantly related species and appear to be the first of the above to have diverged from a common ancestor; and that the amoebae have a long evolutionary history. The accuracy of the phylogenetic tree and the distance Wagner network was discussed. Since the amoebae may be polyphyletic in origin, the latter was assumed to be a more accurate representation of the immunological distance data.     

Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites

A general model for estimating the number of amino acid substitutions per site (d) from the fraction of identical residues between two sequences (q) is proposed. The well-known Poisson-correction formula q = e ^–d corresponds to a site-independent and amino-acid-independent substitution rate. Equation q = (1 – e ^–2d )/2d, derived for the case of substitution rates that are site-independent, but vary among amino acids, approximates closely the empirical method, suggested by Dayhoff et al. (1978). Equation q = 1/(1 + d) describes the case of substitution rates that are amino acid-independent but vary among sites. Lastly, equation q = [ln(1 + 2d)]/2d accounts for the general case where substitution rates can differ for both amino acids and sites.     

A Comparative Statistical Analysis of Genetic Distances. I - Estimation of Distances and of their Variances: Distribution of the Estimators

We present a Monte-Carlo simulation analysis of the statistical properties of absolute genetic distance and of Nei's minimum and standard genetic distances. The estimation of distances (bias) and of their variances is analysed as well as the distributions of distance and variance estimators, taking into account both gamete and locus samplings. Both of Nei's statistics are non-linear when distances are small and consequently the distributions of their estimators are extremely asymmetrical. It is difficult to find theoretical laws that fit such asymmetrical distributions. Absolute genetic distance is linear and its distributions are better fit by a normal distribution. When distances are medium or large, minimum distance and absolute distance distributions are close to a normal distribution, but those of the standard distance can never be considered as normal. For large distances the jack-knife estimator of the standard distance variance is bad; another standard distance estimator is suggested. Absolute distance, which has the best mathematical properties, is particularly interesting for small distances if the gamete sample size is large, even when the number of loci is small. When both distance and gamete sample size are small, this statistic is biased.     

Effects of brown and turbid water on piscivore–prey fish interactions along a visibility gradient

1. Environmental changes such as eutrophication and increasing inputs of humic matter (brownification) may have strong effects on predator–prey interactions in lakes through a reduction in the visual conditions affecting foraging behaviour of visually oriented predators. 2. In this experiment, we studied the effects of visual range (25–200 cm) in combination with optically deteriorating treatments (algae, clay or brown humic water) on predator–prey interactions between pike (Esox lucius) and roach (Rutilus rutilus). We measured effects on reaction distance and strike distance for pike and escape distance for roach, when pike individuals were exposed to free‐swimming roach as well as to roach held in a glass cylinder. 3. We found that reaction distance decreased with decreasing visual range caused by increasing levels of algae, clay or humic matter. The effect of reaction distance was stronger in turbid water (clay, algae) than in the brown water treatment. 4. Strike distance was neither affected by visual range nor by optical treatment, but we found shorter strike distances when pike attacked roach using visual cues only (roach held in a cylinder) compared to when pike could use multiple senses (free‐swimming roach). Escape distance for roach was longer in turbid than in brown water treatments. 5. Changes in environmental drivers, such as eutrophication and brownification, affecting the optical climate should thus have consequences for the strength of predator–prey interactions through changes in piscivore foraging efficiency and prey escape behaviour. This in turn may affect lake ecosystems through higher‐order interactions.     

Statistical aspects of Mahalanobis distance based methodology

After a methodological introduction (section 1) it is indicated why Cherry et al. (1982) were not fair in suggesting that Mahalanobis distance is less reliable than other simple characteristics of morphological distance. The argument is that these authors used the type of Mahalanobis distance where the covariance matrix is based on the scores of the pair of samples to be compared. They should also have considered the much less unreliable type, where the same covariance matrix is used for all pairwise comparisons. This, at least, would not have displayed violations of the triangle inequality (section 2). The methodological discussions in the rest of the paper give a sense of the various uncertainties the statistician and the physical anthropologist are confronted with when trying to find solutions for outstanding anthropological problems. As a whole, the discussion is more philosophical than solution-oriented. The physical anthropologist and the statistician need to cut their way through the forest of uncertainties when a concrete problem is tackled. To do this it may be useful if various arguments have been listed, even if they are somewhat contradictory.     

pathmatrix: a geographical information system tool to compute effective distances among samples

pathmatrix is a tool used to compute matrices of effective geographical distances among samples using a least‐cost path algorithm. This program is dedicated to the study of the role of the environment on the spatial genetic structure of populations. Punctual locations (e.g. individuals) or zones encompassing sample data points (e.g. demes) are used in conjunction with a species‐specific friction map representing the cost of movement through the landscape. Matrices of effective distances can then be exported to population genetic software to test, for example, for isolation by distance. pathmatrix is an extension to the geographical information system (GIS) software arcview 3.x.     

Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites

Correspondence to: M. Nei 0871