Effective Sizes and Dynamics of Uniparentally and Diparentally Inherited Genes

Models to determine the temporal dynamics and spatial heterogeneity for maternally and paternally inherited genes were derived for populations that may or may not exhibit spatial subdivision. Results were compared to those for diparentally inherited genes. The models permit definition of parameters for mean and variance of litter sizes, breeding group (subpopulation) sizes, and numbers of female mates per male, dispersal rates, and multiple paternity. Exact solutions for asymptotic effective size and spatial divergence (F(LS)) for maternal and paternal genes are derived. It is shown that solutions for effective size and F(LS) are transformations of the same quadratic equation. When compared to values for diparentally inherited genes, it is shown that effective sizes for maternal genes may be considerably higher when female dispersal is low as in many mammalian taxa. Likewise, effective sizes for paternal genes may be higher than for diparentally inherited traits when male dispersal is relatively low, as in many species of birds. The traditional assumption that the effective size for maternal genes is approximately equal to the number of females is seldom realized. Spatial heterogeneity and temporal dynamics of genes are inextricably linked as is shown by the interdependency of effective size and spatial heterogeneity.     

Genetic polymorphisms in autochthonous Basques from northern Navarre

This survey reports primary results of classical allele frequencies on ten protein loci in a Basque population sample from northern Navarre, the less known from an anthropological and genetic point of view than the populations of the other Basque territories of Spain. Since ancient times this has been a zone of Basque population settlement, and the Basque language (Euskera) still remains deeply rooted among its autochthonous population. A total of 122 blood samples from unrelated northern Navarrese with autochthonous ascendants to the third generation were typed for GC, HP, PI, TF, ACP1, AK1, CA2, ESD, PGD and PGM1 genetic systems. Basque surnames and birthplaces were the criteria used to define family origins. Genetic structure was analyzed on different population hierarchical levels. Northern Navarre seems to be the most genetically deviated area in comparison with other Basque groups. The highest level of differentiation is observed between Navarrese and Alava Basques whereas Guipúzcoa province, the territory adjacent to northern Navarre, presents the lowest genetic distance from the study area. Northern Navarrese show some distinguishing genetic characteristics in relation to other Basque relative samples, which include high frequencies for PI*M1 and TF*C1 and low levels of PGD*C and PGM1*2 alleles. When the genetic data reported here are analyzed jointly with GM allotypes frequencies, the results significantly reinforce the relative position of Navarrese Basques as well as the topology of the Basque cluster on genetic maps. The analysis of relationships among the genetic structures of Basque population samples leads us to ask ourselves which of them fits in best with the ancient Basque population. Classical geographers placed the tribe of the Vascones in the geographical region currently known as Navarre, so extant Navarrese Basques might be considered firm candidates to denote the anthropological and genomic distinctiveness of the ancient Basques.     

Uniparental Markers of Contemporary Italian Population Reveals Details on Its Pre-Roman Heritage

Background

According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country.

Methods/Principal Findings

A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers.

Conclusions/Significance

Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.     

Genetic Structure of Iranian-Speaking Populations from Azerbaijan Inferred from the Frequencies of Immunological and Biochemical Gene Markers

The data on the genetic studies of Iranian-speaking populations from Azerbaijan (Talyshs and Tats) are presented. In these populations gene frequency distributions for the immunological (AB0, MN, Rhesus-D, -C, -E, P, Lewis, and Kell-Chellano) and biochemical (HP, GC, C3, TF, 6PGD, GLO1, ESD, ACP1, and PGM1) gene markers were determined. Comparison of the genetic structure of the populations examined with the other Iranian-speaking populations (Persians and Kurds from Iran, Ossetins, and Tajiks) and Azerbaijanis showed that Iranian-speaking populations from Azerbaijan were more close to Azerbaijanis, than to Iranian-speaking populations inhabiting other world regions.     

The Redbird Focus: Cranial Evidence in Tribal Identification

Abstract

The Redbird Focus was defined in 1956, and was initially (Wood 1956) related to both Lower Loup and historic Pawnee Focus materials. Wood (1965) later took the position that Redbird was a more probable antecedent to the historic Ponca. These opposing hypotheses are tested using human crania representing the relevant populations. Samples of the following were available: Arikara from 39ST216, Pawnee from 25BU1 and 25WT1, Omaha from 25DK10 and 25DK2A, Ponca from 25KX1, and Redbird from 25KX9. Cranial measurements in a multivariate context were employed to test Wood’s suggestions regarding: (1) Ponca identification of remains from the Ponca Fort site, 25KX1, and (2) the tribal identity of the Redbird Focus crania. The Ponca Fort site is identified as historic Ponca, but with the probable presence of some Arikara females. The hypothesis that Redbird is antecedent to Ponca is found tenable on the basis of available cranial evidence.     

Microsatellite Markers Reveal Strong Genetic Structure in the Endemic Chilean Dolphin

Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02′S) to Chiloé (42°00′S), and a southern habitat with highly fragmented inshore coastline, channels and fjords between Chiloé and Navarino Island (55°14′S). With the aim of evaluating the potential existence of conservation units for this species, we analyzed the genetic diversity and population structure of the Chilean dolphin along its entire range. We genotyped 21 dinucleotide microsatellites for 53 skin samples collected between 1998 and 2012 (swab: n = 8, biopsy: n = 38, entanglement n = 7). Bayesian clustering and spatial model analyses identified two genetically distinct populations corresponding to the northern and southern habitats. Genetic diversity levels were similar in the two populations (He: 0.42 v/s 0.45 for southern and northern populations, respectively), while effective size population was higher in the southern area (Ne: 101 v/s 39). Genetic differentiation between these two populations was high and significant (F_ST = 0.15 and R_ST = 0.19), indicating little or no current gene flow. Because of the absence of evident geographical barriers between the northern and southern populations, we propose that genetic differentiation may reflect ecological adaptation to the different habitat conditions and resource uses. Therefore, the two genetic populations of this endemic and Near Threatened species should be considered as different conservation units with independent management strategies.     

用SSR研究栲树群体遗传结构

利用微卫星（SSR）分子标记对福建省内4个栲树（Castanopsis fargesii Franch.）群体遗传结构进行了研究。SSR标记揭示了栲树群体丰富的遗传变异：平均等位基因数A＝9.0,平均有效等位基因数Ne=4.8,平均期望杂合度He=0.65,而群 具有较低的Fst值（Fst=0.031）。SSR每个位点的等位基因频率分布在栲树群体间都存在显或极显差异,表明根据SSR等位基因频率分布亦能了解各体的分化。SSR标记使栲树群体中一些稀有等位基因得以表现,54个SSR等位基因中有15个等位基因仅出现在1个或2个群体中,且频率较低,在遗传多样性保护中更应注重保护这些稀有的等位变异。     

中国新疆野苹果[Malus sieversii(Lebed.)Roem.]群体遗传结构的SSR分析

以中国新疆伊犁地区的巩留县莫合镇库尔德宁、新源县交吾托海、霍城县大西沟和塔城地区的裕民县巴尔鲁克山4个种下居群的109个新疆野苹果实生株系为材料,利用8对苹果SSR引物进行群体遗传结构的研究。结果表明:8对SSR引物在4个居群中可平均扩增出16条带,其中巩留县居群多态性带数百分比最高为89.06%,各位点平均Nei基因多样度为0.257;4个群体共扩增出128个位点,在种级水平及巩留县、新源县、霍城县和裕民县4个居群水平多态性位点百分比分别为100%、88.28%、84.38%、87.50%、78.12%,种级水平Nei基因多样度(H=0.2619)和香农信息指数(I=0.4082)大于种下居群,4个种下居群Nei基因多样度和香农信息指数比较巩留县>霍城县>新源县>裕民县;巩留县居群和新源县居群遗传一致度最大,遗传距离最近;根据基因分化系数(GST=0.064)值,测得的基因流Nm为7.265。UPGMA聚类分析结果表明,巩留县和新源县居群遗传关系最近,霍城县居群次之,裕民县居群远离其他3个居群,巩留县、新源县、霍城县和裕民县4个居群是相对独立的群体,但同时存在部分基因交流。所有参数分析表明,巩留县遗传多样性最丰富,故在制定原位种质保护计划时应优先考虑巩留县居群。     

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers

Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (F _st = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei’s genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These data provide comprehensive information for the development of conservation strategies of these valuable hazelnut resources.     

Hierarchical Analysis of Genetic Structure in Native Fire Ant Populations: Results from Three Classes of Molecular Markers

We describe genetic structure at various scales in native populations of the fire ant Solenopsis invicta using two classes of nuclear markers, allozymes and microsatellites, and markers of the mitochondrial genome. Strong structure was found at the nest level in both the monogyne (single queen) and polygyne (multiple queen) social forms using allozymes. Weak but significant microgeographic structure was detected above the nest level in polygyne populations but not in monogyne populations using both classes of nuclear markers. Pronounced mitochondrial DNA (mtDNA) differentiation was evident also at this level in the polygyne form only. These microgeographic patterns are expected because polygyny in ants is associated with restricted local gene flow due mainly to limited vagility of queens. Weak but significant nuclear differentiation was detected between sympatric social forms, and strong mtDNA differentiation also was found at this level. Thus, queens of each form seem unable to establish themselves in nests of the alternate type, and some degree of assortative mating by form may exist as well. Strong differentiation was found between the two study regions using all three sets of markers. Phylogeographic analyses of the mtDNA suggest that recent limitations on gene flow rather than longstanding barriers to dispersal are responsible for this large-scale structure.     

Genetic Diversity of Protein Markers in Sheep Populations from Ukraine

Based on polymorphism of genes for antigen factors of six blood-group systems and four blood protein loci, genetic structure and the main variation parameters were studied in three sheep breeds and three sheep breed types constituting the basis of purebred sheep resources in Ukraine. Specific features of the distribution of genotypes and alleles of polymorphic loci were determined in each of the studied sheep groups depending on their origin and production type. The molecular–genetic markers used in the analysis of the genetic relationships between the sheep breeds and breed types were shown to objectively reflect their breeding history and evolution. Integrally, each of the studied gene pools had a specific profile of gene frequencies reflecting breeding specificity, breed history, and genetic differentiation of breeds.     

Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (F_ST = 0.049) as evidenced by high level of gene flow estimate (N_m = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia.     

Analysis of Genetic Diversity and Structure of Guanzhong Horse Using Microsatellite Markers

To determine the genetic diversity and validate the pedigree record of Chinese Guanzhong horse, 67 individuals were genotyped with eight microsatellite markers. In our study, the mean observed and expected heterozygosities were 0.51 and 0.66, respectively. The mean observed number of alleles for the Guanzhong horse was 3.88. Nonetheless, the total value of F_ST multiloci clearly indicates that about 0.5% of overall genetic variation is due to line founder differences, while differences among individuals are responsible for the remaining 99.5%. In addition, the polymorphic information content (PIC) result showed that five loci (HTG7, HMS7, HMS2, AHT4, and HMS6) were highly polymorphic (PIC?>?0.5) and three loci (HMS3, HTG6, and COR071) were moderate polymorphic (PIC?>?0.25). Genetic distances and cluster analysis showed that the genetic relationship among 67 Guanzhong horse was generally consistent with pedigree recorded. Our results not only evaluated the genetic diversity of Chinese Guanzhong horse, but also suggested that the eight microsatellite markers might be used as subservient markers for parentage verification and individual identification in the Guanzhong horse.     

广东高州7个普通野生稻居群遗传结构的SSR分析

利用32对SSR引物对来自全部7个自然居群的217份广东高州普通野生稻（简称＂高野＂）材料进行遗传结构、多样性和遗传聚类分析。结果表明,高野各居群因遗传结构存在差异而相对独立,但各居群之间由于存在基因渗透又具有一定的相似性。高野总体多样性指数（Ht）为0.65,居群内的多样性（HS=0.431）略大于居群间的多样性（DS=0.392）,二者差异并不显著。居群间的遗传分化系数（GST）为0.611,说明高野群体的遗传差异是由居群内和居群间的遗传分化共同作用的结果。其中A、B、E居群间,D、F、G居群间遗传相似性较高,C居群与其它居群之间存在较大差异。根据7个居群的遗传结构,结合其地理分布状况,认为遗传多样性最大的B和E居群以及遗传分化最小的C居群应作为重点对象进行保护。     

Analysis of the Genetic Structure of Endangered Bovine Breeds from the Western Pyrenees Using Dna Microsatellite Markers

In the Western Pyrenees, three out of four native cattle breeds are in grave danger of extinction. Genetic variation of all four breeds was assessed by analyzing 478 animals using 11 microsatellite markers. A moderate/high within-breed variability was found, a favorable factor to consider when planning conservation and improvement programs. Interestingly, the only selected commercial breed, the Pirenaica, showed depressed heterozygosity levels and a low average number of alleles, perhaps explainable by intensive human selection exacerbated by a bottleneck effect. The Pirenaica also exhibited pronounced genetic differences and was the largest contributor of diversity among the breeds from the Western Pyrenees. Among endangered cattle breeds from this region, our results highlight the singularity of the Betizu. Geographic isolation among herds may be responsible for the large F(IS) value found in the Betizu breed. Lastly, our study suggests that the use of highly selected breeds may be one of the causes of distortion in phylogenetic analyses.     

Genetic Structure and Diversity of Glycyrrhiza Populations Based on Transcriptome SSR Markers

Plant Molecular Biology Reporter - Glycyrrhiza is a widely used traditional Chinese herb with medicinal value. Recently, however, Glycyrrhiza biodiversity has faced an unprecedented threat due to...     

The Genetic Structure of a Tribal Population, the Yanomama Indians. Xiv. Clines and Their Interpretation

The Yanomama Indians are a South American tribe distributed over an irregular area approximately 200 x 300 miles. The gene frequencies observed at 12 loci in 47 villages within this area have been analyzed for the occurrence of clines. Apparently significant clines are observed for alleles of the Rh, MNSs, Kidd, Gm, Inv and serum albumin system. Available data concerning recent tribal expansion and admixture permit a tentative analysis of the causes of these clines. Although the action of selection cannot be rigorously excluded, it seems unlikely to be the major cause. Admixture with surrounding tribes plays a role which can be quantified because of the fortuitous circumstance of two genetic markers for admixture. It is suggested that an important factor in the origin of these clines is the manner in which the tribe has recently expanded through successive village fissionings and a predominantly centrifugal pattern of village migration.     

利用微卫星标记分析马氏珠母贝4个养殖群体遗传结构

2007年4月,从马氏珠母贝基础群体选取2、4、32和158个亲本分别繁殖4个子代群体,分别命名为P1、P2、P3和P4。2009年7月,从这4个子代群体随机取样30个个体,利用7对微卫星引物分析其遗传结构。结果表明,7对微卫星引物共检测到22个等位基因,每个座位的等位基因数目为2~4个,平均等位基因数为3个,平均有效等位基因数为2.3193。P1、P2、P3和P4群体平均观测杂合度分别为0.4737、0.5489、0.6767和0.7143;P1、P2、P3和P4群体平均期望杂合度分别为0.4737、0.5489、0.6767和0.7143;P1、P2、P3和P4群体的多态信息含量分别为0.4472、0.4224、0.4726和0.4930。本结果表明4个养殖群体均具有较高的遗传多样性,而且有效亲本数目对子代遗传结构有较大的影响,这为马氏珠母贝的遗传育种提供依据。     

Microsatellite Markers to Determine Population Genetic Structure in the Golden Anchovy,Coilia dussumieri

Coilia dussumieri (Valenciennes, 1848) commonly called as golden anchovy, constitutes a considerable fishery in the northern part of both the west and east coasts of India. Despite its clear-cut geographic isolation, the species is treated as a unit stock for fishery management purposes. We evaluated 32 microsatellite primer pairs from three closely related species (resource species) belonging to the family Engraulidae through cross-species amplification in C. dussumieri. Successful cross-priming was obtained with 10 loci, which were sequenced for confirmation of repeats. Loci were tested for delineating the genetic stock structure of four populations of C. dussumieri from both the coasts of India. The number of alleles per locus ranged from 8 to 18, with a mean of 12.3. Results of pairwise F _ST indicated genetic stock structuring between the east and west coast populations of India and also validated the utilization of identified microsatellite markers in population genetic structure analysis.