Number Of Pairwise Nucleotide Differences Research Articles

Genetic similarity and diversity among three camel populations reared in Egypt

BackgroundMolecular genetics has been extremely useful in determining the relation between animal populations and documenting the degrees of genetic variation found within them. The present study was undertaken to evaluate genetic diversity and the relationships between the three camel populations reared in Egypt: Maghrabi, Sudani, and Baladi using mitochondrial 16S sequences and other breeds of camels in the world. MethodsBlood samples were collected from camels belonging to these three populations. Genomic DNA was extracted from the collected blood samples and subjected to PCR using specific primers for mitochondrial 16S region. The amplified products were purified using DNA purification kit to remove residual primers and dNTPs. Sequencing was performed in the Macrogen Incorporation. The amplified products were submitted to GenBank/NCBI under accession numbers OM 278349 and OM 278350 ResultsSequencing was done on the partial mitochondrial 16S amplified fragments at 530 bp. This amplified area had two haplotypes. There was one substitution (G/A) at nucleotide 309 of the amplified segment. The nucleotide (π) and Hd stand for haplotype diversity, respectively, at 0.00008 and 0.042, and the average number of pairwise nucleotide differences, k, is 0.042, according to Fu’s Fs statistic and Tajima’s D, which is −1.10686. Genetic distance percentages between the three populations under study range from 0.000 to 0.0312. A phylogenetic analysis of Egyptian camel populations and other Camelus dromedarius populations revealed a strong relationship between them. ConclusionsThis study suggests that the 16S rRNA sequencing in mitochondria plays a critical role in genetic variation studies and analysis of phylogeny between camel populations and breeds.

A comprehensive global perspective on phylogenomics and evolutionary dynamics of Small ruminant morbillivirus

A string of complete genome sequences of Small ruminant morbillivirus (SRMV) have been reported from different parts of the globe including Asia, Africa and the Middle East. Despite individual genome sequence-based analysis, there is a paucity of comparative genomic and evolutionary analysis to provide overarching and comprehensive evolutionary insights. Therefore, we first enriched the existing database of complete genome sequences of SRMVs with Pakistan-originated strains and then explored overall nucleotide diversity, genomic and residue characteristics, and deduced an evolutionary relationship among strains representing a diverse geographical region worldwide. The average number of pairwise nucleotide differences among the whole genomes was found to be 788.690 with a diversity in nucleotide sequences (0.04889 ± S.D. 0.00468) and haplotype variance (0.00001). The RNA-dependent-RNA polymerase (L) gene revealed phylogenetic relationship among SRMVs in a pattern similar to those of complete genome and the nucleoprotein (N) gene. Therefore, we propose another useful molecular marker that may be employed for future epidemiological investigations. Based on evolutionary analysis, the mean evolution rate for the complete genome, N, P, M, F, H and L genes of SRMV was estimated to be 9.953 × 10–4, 1.1 × 10–3, 1.23 × 10–3, 2.56 × 10–3, 2.01 × 10–3, 1.47 × 10–3 and 9.75 × 10–4 substitutions per site per year, respectively. A recombinant event was observed in a Pakistan-originated strain (KY967608) revealing Indian strains as major (98.1%, KR140086) and minor parents (99.8%, KT860064). Taken together, outcomes of the study augment our knowledge and current understanding towards ongoing phylogenomic and evolutionary dynamics for better comprehensions of SRMVs and effective disease control interventions.

Population structure inferred from COI data analyses for Bactrocera dorsalis (Diptera: Tephritidae) in the Karnataka region of India

ABSTRACTThe Oriental fruit fly, Bactrocera dorsalis (Hendel) causes tremendous losses in mango (Mangifera indica L.), its high level of polyphagy coupled with the ability to complete overlapping generations and mobility made this insect pest a unique example to study its population genetic diversity at both spatial and temporal levels. However, the genetic diversity and phylogeographic structure of B. dorsalis at regional level remain to be unexplored. We analysed the genetic diversity and population structure of B. dorsalis throughout the Karnataka region. Results revealed the existence of abundant haplotypes as well as nucleotide diversity in Tumkur and Kolar populations that showed high similarity to the neighbouring states viz., Vellore of Tamil Nadu and Chittoor of Andhra Pradesh. Genetic diversity indices [number of Haplotypes, haplotype diversity (Hd), nucleotide diversity (π), polymorphic sites (S) and the average number of pairwise nucleotide differences (k)] across Karnataka maintain high levels of genetic diversity at different geographic locations. All haplotypes were monophyletic and have a significant phylogeographic structure (Nst>Gst; P < 0.05). The star-like median-joining network of haplotypes distribution implied that most of the fruit flies derived from relicts and subsequently fragmented. Further, the neutrality tests and mismatch distribution analysis confirmed that B. dorsalis underwent a recent demographic expansion.

Extensive genetic divergence among Diptychus maculatus populations in northwest China

D. maculates is a kind of specialized Schizothoracinae fish has been locally listed as a protected animal in Xinjiang Province, China. Ili River located in north of Tianshan Mountain and Tarim River located in north of Qinghai-Tibetan Plateau were two main distribution areas of this fish. To investigate the genetic diversity and genetic structure of D. maculates, four populations from Tarim River system and two populations from Ili River system were collected in this study. A 570-bp sequence of the control region was obtained for 105 specimens. Twenty-four haplotypes were detected from six populations, only Kunes River population and Kashi River population shared haplotypes with each other. For all the populations examined, the haplotype diversity (h) was 0.904 8±0.012 6, nucleotide diversity (π) was 0.027 9±0.013 9, and the average number of pairwise nucleotide differences (k) was 15.878 3±7.139 1. The analysis of molecular variance (AMOVA) showed that 86.31% of the total genetic variation was apportioned among populations, and the variation within sampled populations was 13.69%. Genetic differences among sampled populations were highly significant. Fst statistical test indicated that all populations were significantly divergent from each other (P<0.01). The largest Fst value was between Yurungkash River population and Muzat River population, while the smallest Fst value was between Kunes River population and Kashi River population. NJ phylogenetic tree of D-loop haplotypes revealed two main clades. The neutrality test and mismatch distribution analysis suggested that the fish had went through a recent population expansion. The uplift of Tianshan Mountain and movement of Qinghai-Tibetan Plateau might contribute to the wide genetic divergence of D. maculates in northwest China.

Remarkable genetic divergence of Gymnodiptychus dybowskii between south and north of Tianshan Mountain in northwest China

Gymnodiptychus dybowskii is endemic to Xinjiang, China and has been locally listed as protected animals. To investigate its genetic diversity and structure, specimens were collected from six localities in Yili River system and Kaidu River. Fragments of 1092bp Cyt b gene were sequenced for 116 individuals. A total of 21 haplotypes were found in all samples, and no haplotype was shared between Yili River system and Kaidu River population. Sequence comparisons revealed 123 variable sites, with eight singleton sites and 115 parsimony informative sites. For all the populations examined, the haplotype diversity (h) was 0.8298 ± 0.0226, nucleotide diversity (π) was 0.2521 ± 0.1202, and average number of pairwise nucleotide differences (k) was 275.3369 ± 118.5660. AMOVA analysis showed that the differences were significant for total populations except for Yili River system populations. The pairwise Fst values revealed same conclusion with AMOVA analysis: Kaidu River population was divergent from Yili River system populations. The genetic distance between two groups was 0.108 and the divergence time was estimated at 5.4–6.6 Ma, the uplift of Tianshan Mountain might have separated them and resulted in the genetic differentiation. The neutrality test and mismatch analysis indicated that both two groups of G. dybowskii had went through population expansion, the expansion time of Yili River system and Kaidu River population was estimated at 0.5859–0.7146 Ma and 0.5151–0.6282 Ma, respectively. The climate changes of Qinghai-Tibetan Plateau might have influenced the demographic history of G. dybowskii.

Mitochondrial DNA variation in Tajiks living in Tajikistan.

This study aimed to characterize mtDNA control region (positions 16,024-576) of unrelated Tajiks living in Tajikistan. DNA was isolated from saliva specimens stored on FTA cards. The mtDNA fragments were amplified and directly sequenced in forward and reverse directions. Haplogroups were determined using HaploGrep and the diagnostic polymorphisms in the coding region of mtDNA. The Tajik mtDNA pool was characterized by substantial admixture of western and eastern Eurasian haplogroups, 62.6% and 26.4% sequences, respectively. It also contained 9.9% of South Asian and 1.1% of African haplotypes. The Tajik mtDNA sequences belonged to 90 different haplotypes defined by 148 transitions and 13 transversions in 156 of 1122 nucleotide sites. The Tajik mtDNA pool demonstrated the high genetic variation with genetic diversity of 0.999±0.002, nucleotide diversity of 0.014±0.007, and the mean number of pairwise nucleotide differences of 15.38±6.93. The random match probability and the power of discrimination were 0.0112 and 0.9888, respectively. Ethno-territorial groups of Tajiks demonstrated significant genetic differentiation with 2.67% of the genetic variance explained by differences between subpopulations. This study provides the insight into the mtDNA pool of Tajiks living in Tajikistan. The data should be taken into account in forensic identifications based on mtDNA.

Humans and Great Apes Cohabiting the Forest Ecosystem in Central African Republic Harbour the Same Hookworms

BackgroundHookworms are important pathogens of humans. To date, Necator americanus is the sole, known species of the genus Necator infecting humans. In contrast, several Necator species have been described in African great apes and other primates. It has not yet been determined whether primate-originating Necator species are also parasitic in humans.Methodology/Principal FindingsThe infective larvae of Necator spp. were developed using modified Harada-Mori filter-paper cultures from faeces of humans and great apes inhabiting Dzanga-Sangha Protected Areas, Central African Republic. The first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA and partial cytochrome c oxidase subunit 1 (cox1) gene of mtDNA obtained from the hookworm larvae were sequenced and compared. Three sequence types (I–III) were recognized in the ITS region, and 34 cox1 haplotypes represented three phylogenetic groups (A–C). The combinations determined were I-A, II-B, II-C, III-B and III-C. Combination I-A, corresponding to N. americanus, was demonstrated in humans and western lowland gorillas; II-B and II-C were observed in humans, western lowland gorillas and chimpanzees; III-B and III-C were found only in humans. Pairwise nucleotide difference in the cox1 haplotypes between the groups was more than 8%, while the difference within each group was less than 2.1%.Conclusions/SignificanceThe distinctness of ITS sequence variants and high number of pairwise nucleotide differences among cox1 variants indicate the possible presence of several species of Necator in both humans and great apes. We conclude that Necator hookworms are shared by humans and great apes co-habiting the same tropical forest ecosystems.

基于mtCOII基因对山东省越冬代亚洲玉米螟不同种群的遗传结构分析

PDF HTML阅读 XML下载 导出引用 引用提醒 基于mtCOII基因对山东省越冬代亚洲玉米螟不同种群的遗传结构分析 DOI: 10.5846/stxb201204120521 作者: 作者单位: 山东省农业科学院植保所,山东省农业科学院植保所,青岛农业大学农学与植物保护学院,青岛农业大学农学与植物保护学院,青岛农业大学农学与植物保护学院 作者简介: 通讯作者: 中图分类号: 基金项目: 现代农业产业技术体系专项资金CARS-02;"泰山学者"建设工程专项 Genetic structure of the overwintering Asian corn borer,Ostrinia furnacalis (Guenée)collections in Shandong of China based on mtCOII gene sequences Author: Affiliation: SAAS,,,,QINGDAO AGRICULTURAL UNIVERSITY Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:亚洲玉米螟Ostrinia furnacalis(Guenée)是我国重要农业害虫。为了全面揭示亚洲玉米螟遗传分化以及山东省亚洲玉米螟不同种群的遗传结构,对山东省越冬代亚洲玉米螟不同种群mtCOII基因序列与来自GenBank的相关序列进行了遗传结构分析,并建立了鉴别不同遗传支系的PCR-RFLP方法。基于对340条mtCOII序列的分析结果表明:所有样本共获得62个单倍型,其中单倍型17(H17)广泛分布于各种群之间,有6个单倍体型为山东种群所特有;亚洲玉米螟分化为2个遗传支系(支系Ⅰ与支系Ⅱ);2个遗传支系均在山东省发现,但以支系I为主;亚洲玉米螟各单倍体型散布于山东省各地理种群中,缺乏明显的地理分布格局。山东亚洲玉米螟总体的单倍体型多样性指数Hd为0.695,种群内单倍型多样性指数在0.333-0.889之间;总体的核酸多样性指数π为0.00424,种群内核酸多样性指数在0.00061-0.00809之间。总群体的固定系数 Fst 为0.79421。AMOVA分析结果表明山东亚洲玉米螟的遗传分化主要来自于2个支系之间(79.42%)。构建的亚洲玉米螟2个支系鉴别方法为其生物学与生态学的进一步研究奠定了基础。 Abstract:Ostrinia furnacalis(Guenée), the Asian corn borer, is one of the most important agricultural pests in China. It can damage crops during different crop growth stages, and can affect the yield and quality of maize. In addition, the pest has a wide geographic distribution and host range. With global warming and the expansion of corn acreage in recent years, the occurrence of the pest and associated damages have been increasing. Studying the genetic structure of the Asian corn borer is necessary for understanding the pest's evolution and migration in Shandong, a critical corn production region in China. In order to reveal the genetic diversity and structure of O. furnacalis in Shandong, China, and throughout the world, we analyzed 340 mtCOII sequences of O. furnacalis obtained both from the present study and GenBank (updated to October 1st, 2011). Of the mtCOII sequences analyzed, 214 sequences were obtained from GenBank while 126 sequences were obtained during the present study. The mtCOII sequences were aligned using MEGA5.05 and were then checked for indels and numts. Using DnaSP 5.0, a set of genetic parameters for mtCOII were estimated including: the number of polymorphic (segregating) sites (S); the total number of mutations (η); the average number of nucleotide differences (K); the number of haplotypes (H); the haplotype diversity (Hd);the nucleotide diversity (π), defined as the average number of pairwise nucleotide differences per site; and the nucleotide diversity with Jukes and Cantor correction for different host collections from Shandong Province. The results revealed that there were a total of 62 haplotypes, among which the haplotype H17 was the most widely distributed. Using the 62 haplotypes, a phylogenetic tree was constructed with the maximum likehood (ML) method; two clades (Clade Ⅰ and Clade Ⅱ) were revealed. The populations from Shandong Province consisted of two clades, although Clade I was the dominant clade. The haplotypes from Shandong were distributed randomly among 17 populations with no obvious geographical pattern. The haplotype diversity (Hd) of the populations from Shandong ranged from 0.333 to 0.889, and the Hd of the entire populations in Shandong was 0.695. The nucleotide diversity (π) of the populations from Shandong ranged from 0.00061 to 0.00809 and the π of total populations was 0.00424. Analysis of molecular variance (AMOVA) showed that 79.42% of the total genetic variance was contributed by the inter-clade variation and only 20.58% contributed by the intra-clade variation. Finally, to rapidly differentiate the two clades, a PCR-RFLP (polymerase chain reaction restriction fragment length polymorphism) method was developed. The PCR-RFLP method of differentiating the two clades within O. furnacalis will be helpful for future research on the biological and ecological differences between the two clades. Our work revealed that the incidence of Clade Ⅱ was less than Clade Ⅰ. This might suggest that they are different in biology, ecology and physiology. Such differences could affect the clade's geographic distributions and population diffusions. These studies' results serve as a guide for the sustainable control of the pest, however these issues need to be further studied. 参考文献 相似文献 引证文献

The distribution of the coalescence time and the number of pairwise nucleotide differences in a model of population divergence or speciation with an initial period of gene flow

This paper is concerned with a model of “isolation with an initial period of migration”, where a panmictic ancestral population split into n descendant populations which exchanged migrants symmetrically at a constant rate for a period of time and subsequently became completely isolated. In the limit as the population split occurred an infinitely long time ago, the model becomes an “isolation after migration” model, describing completely isolated descendant populations which arose from a subdivided ancestral population. The probability density function of the coalescence time of a pair of genes and the probability distribution of the number of pairwise nucleotide differences are derived for both models. Whilst these are theoretical results of interest in their own right, they also give an exact analytical expression for the likelihood, for data consisting of the numbers of nucleotide differences between pairs of DNA sequences where each pair is at a different, independent locus. The behaviour of the distribution of the number of pairwise nucleotide differences under these models is illustrated and compared to the corresponding distributions under the “isolation with migration” and “complete isolation” models. It is shown that the distribution of the number of nucleotide differences between a pair of DNA sequences from different descendant populations in the model of “isolation with an initial period of migration” can be quite different from that under the “isolation with migration model”, even if the average migration rate over time (and hence the total number of migrants) is the same in both scenarios. It is also illustrated how the results can be extended to other demographic scenarios that can be described by a combination of isolated panmictic populations and “symmetric island” models.

Population genetic structure of Guizhou snub‐nosed monkeys (Rhinopithecus brelichi) as inferred from mitochondrial control region sequences, and comparison with R. roxellana and R. bieti

The Guizhou snub-nosed monkey (Rhinopithecus brelichi) is a primate species endemic to the Wuling Mountains in southern China. With a maximum of 800 wild animals, the species is endangered and one of the rarest Chinese primates. To assess the genetic diversity within R. brelichi and to analyze its genetic population structure, we collected fecal samples from the wild R. brelichi population and sequenced the hypervariable region I of the mitochondrial control region from 141 individuals. We compared our data with those from the two other Chinese snub-nosed species (R. roxellana, R. bieti) and reconstructed their phylogenetic relationships and divergence times. With only five haplotypes and a maximum of 25 polymorphic sites, R. brelichi shows the lowest genetic diversity in terms of haplotype diversity (h), nucleotide diversity (π), and average number of pairwise nucleotide differences (Π). The most recent common ancestor of R. brelichi lived ∼0.36 million years ago (Ma), thus more recently than those of R. roxellana (∼0.91 Ma) and R. bieti (∼1.33 Ma). Phylogenetic analysis and analysis of molecular variance revealed a clear and significant differentiation among the three Chinese snub-nosed monkey species. Population genetic analyses (Tajima's D, Fu's F(s) , and mismatch distribution) suggest a stable population size for R. brelichi. For the other two species, results point in the same direction, but population substructure possibly introduces some ambiguity. Because of the lower genetic variation, the smaller population size and the more restricted distribution, R. brelichi might be more vulnerable to environmental changes or climate oscillations than the other two Chinese snub-nosed monkey species. Am J Phys Anthropol, 2012. © 2011 Wiley Periodicals, Inc.

The distribution of the coalescence time and the number of pairwise nucleotide differences in the “isolation with migration” model

This paper is concerned with the “isolation with migration” model, where a panmictic ancestral population gave rise to a symmetric n -island model, time τ ago. Explicit analytical expressions are derived for the probability density function of the coalescence time of a pair of genes sampled at random from the same subpopulation or from different subpopulations, and for the probability distribution of the number of pairwise nucleotide differences.

Variability of mitochondrial DNA in a population sample from Iceland

Over the past decade investigations of human mitochondrial DNA (mtDNA) have considerably contributed to our knowledge about human evolution and migration. The genome of the Icelandic population is of special interest since Iceland has been genetically isolated for centuries. The sequence of the hypervariable regions HVS-I and HVS-II of the mtDNA control region was generated for 100 Icelandic individuals. A total of 75 different mtDNA sequences were observed, of which 19 sequences were shared by more than one individual, 16 sequences were shared by two individuals and two sequences were shared by three individuals; the most frequent haplotype (16129 A, 16239 T, 00263 G and 00315.1 C) was found six times. Both the genetic diversity (0.9925±0.0031) and the average number of pairwise nucleotide differences (7.371) were comparable with most of the other European populations. However, we found a smaller number of distinct mitochondrial lineages, suggesting that founder effects and genetic drift may have exerted a visible influence on the Icelandic genetic diversity. We compared these data with 1400 other European sequences from the D-Loop-BASE database. The paper discusses the evolutionary relationship between Icelandic and Central European mtDNA under due consideration of the historical context. Finally, our study has been aimed at increasing the number of mtDNA sequences available throughout the world and contributing to human genome investigations.

Mitochondrial DNA sequence analysis in Sicily

This study reports data on the sequences of the first hypervariable segment of a sample of the Sicilian population from Alia (Palermo, Italy). The results show the presence of 32 different haplotypes in the 49 individuals examined. The average number of pairwise nucleotide differences was 4.04, i.e., 1.17% per nucleotide. The distribution of the nucleotide differences matches the theoretical distribution and indicates only one major episode of expansion that occurred between 20,732 and 59,691 years ago, between the Middle Paleolithic and Upper Paleolithic. Compared with the other populations, parameters of the Sicilian sample lie in an intermediate position between the eastern and western Mediterranean populations. This is due to numerous contacts that Sicily has had with the Mediterranean area since prehistoric times. At the same time, the singularity of some of the haplotypes present in the sample studied indicates the persistence of some characteristics caused by genetic drift and isolation that the population has endured in the course of its history. Am. J. Hum. Biol. 13:576–589, 2001. © 2001 Wiley-Liss, Inc.

Population paths implied by the mean number of pairwise nucleotide differences among mitochondrial DNA sequences.

Scenarios, such as populations experiencing a bottleneck or an exponential growth, have been suggested as candidates for explaining the observed differences among mitochondrial DNA sequences in a sample of a given population closed to migrations. Here, population size is considered as capable of varying, and the set of the at least 95% most probable population paths capable of producing the observed mean number of pairwise nucleotide differences is delineated. To do this, the mean and the variance of coalescence times of two genes taken in an n-genes sample with varying population size are expressed. The observed mean coalescence time already echoed a set of population paths due to the variance associated to the coalescent process, but only specific scenarios have been studied, such as the bottleneck or the exponential function. However, mitochondrial DNA data does not reflect a single scenario, after the effect of the variance. These scenarios implied by pairwise nucleotide differences are described through a set-valued function, the 'regulation map', a convenient way to represent temporal population paths.

Optimal sequencing strategies for surveying molecular genetic diversity.

Two commonly used measures of genetic diversity for intraspecies DNA sequence data are based, respectively, on the number of segregating sites, and on the average number of pairwise nucleotide differences. Expressions are derived for their variance in the presence of intragenic recombination for a panmictic population of fixed size that is at neutral equilibrium at the region sequenced. We show that, in contrast to the slow decrease in variance with increasing sample size, if the recombination rate is nonzero, the asymptotic rate of decrease of variance with increasing sequence length, for fixed sample size, is quite rapid. In particular, it is close to that which would be obtained by sequencing independent chromosome regions. The correlation between measures of diversity from linked regions is also examined. For a given total number of bases sequenced in a particular region, optimal sequencing strategies are derived. These typically involve sequencing relatively few (three to 10) long copies of the region. Under optimal strategies, the variances of the two measures are very similar for most parameter values considered. Results concerning optimal sequencing strategies will be sensitive to gross departures from the underlying assumptions, such as population bottlenecks, selective sweeps, and substantial population substructure.

The Amount of Genetic Variation at the DNA Level Maintained in a Finite Population

Abstract The amount of DNA polymorphism can be estimated either from the average number of pairwise nucleotide differences per site (π) or from the proportion of segregating (polymorphic) site (s) among a sample of DNA sequences. Under a number of assumptions, including panmictic population and neutrality, it is known that the expectations of π and s are given by E(π) =θ and E(s) = a1(n)θ, where θ= 4Nv, a1(n) = 1 + 1/2 +…+ 1/(n‐1), N is the effective population size, v is the mutation rate per site per generation, and n is the sample size. Therefore, θ can be estimated by π or s/a1(n). These assumptions, however, are not always correct. In this paper, using a simple non‐random sampling model, I have examined the effect of non‐random sampling on the estimates of the amount of DNA polymorphism. The results indicate that the effect of non‐random sampling on the proportion of segregating site is substantially large whereas the effect of non‐random sampling on the average number of nucleotide differences per site is negligibly small unless non‐randomness is extremely large. Using a finite site model with and without rate variation, I have also examined the effect of rate variation among sites on the estimates of the amount of DNA polymorphism. The results indicate that if the neutral mutation rate varies among sites substantially, the estimates of θ based on the infinite site model are substantially underestimated. New methods for estimating θ are also presented.

Statistical analysis of DNA polymorphism.

A large amount of genetic variation can be maintained in natural populations. In order to understand the mechanism maintaining genetic variation, we must first estimate the amount of genetic variation. There are two measures for estimating the amount of DNA polymorphism, i.e., the average number of pairwise nucleotide differences and the number of segregating sites among a sample of DNA sequences. Using these two measures, we can test the neutral mutation-random drift hypothesis (the neutral theory). The expectation of the amount of DNA polymorphism has been studied under several models, including population subdivision, change in population size, and natural selection. When a population is subdivided, a large amount of DNA polymorphism can be maintained in the population if the migration rates among subpopulations are small. In this case the amount of DNA polymorphism in the subpopulation with lower migration rate is expected to be smaller than that of higher migration rate. When the population size changes, the number of segregating sites changes more rapidly than does the average number of nucleotide differences. When purifying selection is operating, the number of segregating sites is more strongly affected by the existence of deleterious mutants than is the average number of nucleotide differences. On the other hand, when balancing selection is operating, the effect of the selection on the average number of nucleotide differences is larger than that on the number of segregating sites. A mutant under natural selection affects the amount of DNA polymorphism at linked sites (hitchhiking effect). DNA sequences are not random sequences and there may be conservative and variable regions in them. A statistical method for determining the window size and for finding nonrandom regions in the sequence is also presented.