Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers

Abstract.— We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon ( Oncorhynchus nerka ) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus ( sAH ), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.     

Variation at 4 short tandem repeat loci in 8 population groups of India.

We have determined the nature and extent of variation at 4 STR loci (CSF1P0, TPOX, TH01, VWA) in 8 caste and tribal population groups of eastern and northern India. Large differences in allele frequencies among the groups were found. Average heterozygosities in all populations were high (approximately 80%). The overall extent of gene differentiation among the 8 groups was high (GST = 0.04). The nature of genomic affinities based on these 4 STR loci does not completely agree with our earlier finding based on classical genetic markers that geographic proximity of habitat has a greater influence on genetic similarity between populations than sociocultural proximity does.     

Comparative analysis of introgression at three marker classes: a case study in a stocked population of brown trout

Comparative analysis of protein loci, microsatellite and mtDNA markers revealed generally comparable estimates for introgression and apparent admixture rates in stocked brown trout populations at two sites in the River Doubs (Rhône dainage, Switzerland), which are 10 km apart and which belong to the same management unit. At one site, a significant deviation between mtDNA and nuclear markers could be explained by stocking of F1 hybrids originating from crosses between hatchery females and males from the local population. Substantial differences between diagnostic protein loci and protein loci having non-fixed private alleles indicated that caution must be exercised when using genetic markers not strictly diagnostic for the distinction of the populations under investigation. Congruent estimates of introgression and apparent admixture rates between diagnostic protein loci and presumed diagnostic microsatellite loci suggest that the latter can be regarded as reliable genetic markers for the estimation of introgression in Mediterranean brown trout populations stocked with trout of Atlantic origin. Significant differences in introgression and apparent admixture rates between the two sites and between age-classes of one study site were observed. Introgression is suggested to depend on environmental factors. Significantly lower introgression rates in age-class 2+ years as compared to juvenile trout might further indicate that introduced Atlantic brown trout and hybrids decrease in proportion between age-classes 1+ and 2+ years.     

Assessing genetic structure with multiple classes of molecular markers: a case study involving the introduced fire ant Solenopsis invicta.

We used 30 genetic markers of 6 different classes to describe hierarchical genetic structure in introduced populations of the fire ant Solenopsis invicta. These included four classes of presumably neutral nuclear loci (allozymes, codominant random amplified polymorphic DNAs (RAPDs), microsatellites, and dominant RAPDs), a class comprising two linked protein-coding nuclear loci under selection, and a marker of the mitochondrial DNA (mtDNA). Patterns of structure revealed by F statistics and exact tests of differentiation were highly concordant among the four classes of neutral nuclear markers, although the microsatellites were the most effective markers for detecting structure. The results from the mtDNA complemented those from the neutral nuclear markers by revealing that strong limitations to female-mediated gene flow were the cause of the local structure registered by the nuclear markers. The pattern of structure inferred from the selected nuclear loci was markedly different from the patterns derived from the other sets of markers but was predictable on the basis of the presumed mode of selection acting on these loci. In general, the results for all six classes of markers can be explained by known features of the social and reproductive biology of fire ants. Thus, the results from these diverse sets of markers, combined with detailed natural history data, provide an unusually complete picture of how the fundamental evolutionary forces of gene flow, drift, and selection govern the distribution of genetic variation within and between fire ant populations.     

Successful genotyping of microsatellites in the woolly mammoth

Genetic analyses using ancient DNA from Pleistocene and early Holocene fossils have largely relied on mitochondrial DNA (mtDNA) sequences. Among woolly mammoths, Mammuthus primigenius, mtDNA analyses have identified 2 distinct clades (I and II) that diverged 1-2 Ma. Here, we establish that microsatellite markers can be effective on Pleistocene samples, successfully genotyping woolly mammoth specimens at 2 loci. Although significant differentiation at the 2 microsatellite loci was not detected between 16 clade I and 4 clade II woolly mammoths, our results demonstrate that the nuclear population structure of Pleistocene species can be examined using fast-evolving nuclear microsatellite markers.     

Patterns of population subdivision and gene flow in the ant Nothomyrmecia macrops reflected in microsatellite and mitochondrial DNA markers

The Australian endemic ant Nothomyrmecia macrops is renowned for having retained a large proportion of 'primitive' morphological and behavioural characters. Another less studied peculiarity of this species is the production of short-winged (brachypterous) female sexuals, which presumably are poor dispersers. The males, in contrast, bear a full set of normally developed wings and thus may disperse widely. We investigated patterns of genetic differentiation within and among three distantly separated populations in South Australia using nine polymorphic microsatellite loci and four regions of mitochondrial DNA (COI, COII, Cytb, lrRNA). We sampled eight subpopulations, one in the Lake Gilles CP, two near Penong and five around Poochera where distances ranged from 360 km to sites separated by 2-10 km. Only little differentiation was found at the local scale (within the assumed dispersal distance of males) using nuclear markers, whereas the three distant locations were moderately differentiated (FST = 0.06). Mitochondrial DNA genetic structure was much more pronounced on all scales (phiST = 0.98), with regular differences in both haplotype composition and frequency even occurring among closely located sites. This lack of congruence between nuclear and mitochondrial markers strongly suggests limited female dispersal and male-biased gene flow among populations. As to the conservation status of the species there is no evidence for severe population reductions in the recent past, which would have left populations genetically depauperate.     

Genetic population structure of the paper wasp Polistes olivaceus (Hymenoptera: Vespidae) in Bangladesh

Dispersal triggers gene flow, which in turn strongly affects the ensuing genetic population structure of a species. Using nuclear microsatellite loci and mitochondrial DNA (mtDNA), we estimated the genetic population structure of the wasp Polistes olivaceus throughout Bangladesh. The level of population differentiation using nuclear markers (F _ST) appeared to be much lower than that estimated using mtDNA haplotype sequences (Ф_ST), even after correcting for effective population size differences between the two markers. These results suggest a philopatric tendency, in which gynes disperse less than males. We observed no isolation by distance among the study populations at either the nuclear or mtDNA level, suggesting nonequilibrium between gene flow and drift as a result of very frequent interpopulation movement. For the nuclear markers, an individual assignment test showed no genetically and geographically distinct groups. Instead, phylogenetic analyses as well as a minimum spanning network using mtDNA haplotypes consistently revealed two distinct lineages. The distribution of haplotypes indicated western populations with a single lineage and offered clear evidence for restricted gene flow across the Jamuna–Padma–Upper Meghna river system. Mismatch distributions exhibited a unimodal distribution, which along with a starlike haplotype network, suggested a population expansion in lineage I but not in lineage II. Overall, these results suggest that gene flow among populations of P. olivaceus was affected by both female philopatry and a major river system across Bangladesh.     

种间转移扩增法筛选长爪沙鼠微卫星位点

目的筛选长爪沙鼠新的微卫星位点,为长爪沙鼠遗传分析提供遗传标记物。方法从GenBank中随机选取小鼠微卫星位点引物536对,用这些引物对长爪沙鼠基因组DNA扩增,将阳性目的条带进行序列分析,找出符合微卫星序列特征的短串联重复序列。结果 536对小鼠微卫星引物在长爪沙鼠基因组中扩增出了313个阳性条带,经序列分析,确定130个长爪沙鼠微卫星位点;其中完美型位点占80.77%(105/130),不完美型位点占19.23%(25/130),与小鼠同源性为24.3%(130/536)。将筛选出的微卫星位点在GenBank中注册,注册号从GU562694到GU562823。结论小鼠和沙鼠的微卫星位点具有较高的同源性,用小鼠的微卫星位点引物直接扩增长爪沙鼠基因组DNA可有效地筛选出长爪沙鼠微卫星位点。     

Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test whether the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of postglacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian computation approach, but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonization abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.     

RAPD variation and population genetic structure in Prunus mahaleb (Rosaceae), an animal-dispersed tree

We examined the patterns of random amplified polymorphic DNA (RAPD) variation among seven Prunus mahaleb (Rosaceae) populations extending over approximately 100 km2 to examine local differentiation in relation to spatial isolation due to both geographical distance and differences in elevation. No less than 51. 4% of the RAPD loci were polymorphic, but very few were fixed and among-population variation accounted for 16.46% of variation in RAPD patterns. Mean gene diversity was 0.1441, with mean Nei's genetic diversity for individual populations ranging between 0.089 and 0.149. Mean GST value across loci was 0.1935 (range, 0.0162-0.4685), giving an average estimate for Nm of 1.191. These results suggest extensive gene flow among populations, but higher GST and lower Nm values relative to other outcrossing, woody species with endozoochorous dispersal, also suggest a process of isolation by distance. The combined effect of both geographical and elevation distances and nonoverlapping flowering and fruiting phenophases on the GST matrix was partially significant, revealing only marginal isolation of the P. mahaleb populations. The matrix correlation between estimated Nm values among populations and the geographical + elevation distance matrices (r = -0.4623, P = 0.07), suggests a marginal trend for more isolated populations to exchange less immigrants. Long-distance seed dispersal by efficient medium-sized frugivorous birds and mammals is most likely associated to the high levels of within-population genetic diversity. However, vicariance factors and demographic bottlenecks (high postdispersal seed and seedling mortality) explain comparatively high levels of local differentiation.     

Forensic and population genetic analyses of the GlobalFiler STR loci in the Mongolian population

We have analyzed 24 loci including autosomal and Y-chromosomal short tandem repeats (STRs), Y-indel, and sex-determining marker in a sample of 267 unrelated individuals from the Mongolian population using the GlobalFiler? PCR Amplification Kit to provide an expanded and more reliable forensic database. Khalkh among 15 Mongolian minor-groups accounts for about 80% of the entire Mongolian population. A total of 267 different DNA profiles were found in this work. The highest gene diversity was observed in the SE33 (0.9376) locus, and the lowest value was found in the TPOX (0.6142) locus. Although individual power of discrimination estimates varied at the studied loci, combined probability of match from the 21 STR loci was estimated to be 1.139?×?10^?24, which is highly informative. Based on the results of pairwise F _ST genetic distances and multi-dimensional scaling plot showed that Mongolians were clustered into Europeans and Asians, although Mongolia is geographically located in Northeastern Asia. Thus, the present survey of the Mongolian population may help establish a comprehensive reference database for forensic and population genetic analyses.     

Geographic Structure of Mitochondrial and Nuclear Gene Polymorphisms in Australian Green Turtle Populations and Male-Biased Gene Flow

The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.     

Nuclear DNA restriction site polymorphisms and the phylogeny and population structure of an intertidal snail species complex (Littorina)

Primers for amplification of four novel, unlinked nuclear DNA loci, the first reported for the rough periwinkles of the genus Littorina, are described. Patterns of restriction site polymorphism for these loci are detailed within the rough periwinkles. RFLPs are not found to be diagnostic for any of the currently accepted species within this group, nor for any of the contentious subspecies, or forms, whose taxonomic status is uncertain. However, there are important differences in allele frequencies between these taxa and certain of these mirror differences detected in a previous study of the mitochondrial DNA. These allele frequency data are used to construct a phylogeny in which groupings of the three recognised species are obvious when either Nei's genetic distances or Reynold's distances are clustered. Contentious forms (L. neglecta, L. saxatilis 'b' and L. tenebrosa) do not cluster as distinct taxa, although populations of L. neglecta have important allele frequency differences from L. saxatilis. These four loci have confirmed the consensus view of Littorina phylogeny and provided important information on population structure-however four loci is insufficient for reaching definitive conclusions. Since analysis of nuclear DNA polymorphisms such as these is invaluable for analysis of phylogeny, population structure and phylogeography, identification of additional loci is considered imperative.     

Molecular mapping of the Oregon Wolfe Barleys: a phenotypically polymorphic doubled-haploid population

A phenotypically polymorphic barley (Hordeum vulgare L.) mapping population was developed using morphological marker stocks as parents. Ninety-four doubled-haploid lines were derived for genetic mapping from an F₁ using the Hordeum bulbosum system. A linkage map was constructed using 12 morphological markers, 87 restriction fragment length polymorphism (RFLP), five random amplified polymorphic DNA (RAPD), one sequence-tagged site (STS), one intron fragment length polymorphism (IFLP), 33 simple sequence repeat (SSR), and 586 amplified fragment length polymorphism (AFLP) markers. The genetic map spanned 1,387 cM with an average density of one marker every 1.9 cM. AFLP markers tended to cluster on centromeric regions and were more abundant on chromosome 1 (7H). RAPD markers showed a high level of segregation distortion, 54% compared with the 26% observed for AFLP markers, 27% for SSR markers, and 18% for RFLP markers. Three major regions of segregation distortion, based on RFLP and morphological markers, were located on chromosomes 2 (2H), 3 (3H), and 7 (5H). Segregation distortion may indicate that preferential gametic selection occurred during the development of the doubled-haploid lines. This may be due to the extreme phenotypes determined by alleles at morphological trait loci of the dominant and recessive parental stocks. Several molecular markers were found to be closely linked to morphological loci. The linkage map reported herein will be useful in integrating data on quantitative traits with morphological variants and should aid in map-based cloning of genes controlling morphological traits. Received: 23 August 2000 / Accepted: 15 December 2000     

长筒石蒜居群遗传多样性RAPD分析

利用RAPD标记对长筒石蒜3个居群的遗传多样性及分化程度进行了研究。12条随机引物扩增出94个可分析位点,多态位点比率(PPB)为65.96%,表明长筒石蒜具有比较高的遗传多样性。经POP-GENE32分析表明:Nei’s基因多样性指数(h)为0.1897,香农多样性指数(Ⅰ)为0.2945,基因分化系数(GST)为0.1191,基因流(Nm)为3.6980。经WINAMOVA分析表明:居群内遗传变异占71.75%,而居群间只占28.25%。遗传多样性分析表明,各居群的遗传多样性水平由高到低为琅琊山居群>宝华山居群>盱眙居群。遗传分化表明:长筒石蒜各居群间遗传分化程度较低;大部分遗传变异存在于居群内部,表明其具有较强的进化潜力,自然情况下不会处于濒危状态,野生种质资源的破坏,主要来自于人为干扰。     

Comparison of the physical and recombination maps of the mouse X chromosome

The locations of five random mouse genomic DNA markers and five cloned genes, including the genes for clotting factors VIII and IX (Cf-8 and Cf-9), Duchenne muscular dystrophy (Dmd), phosphoglycerate kinase-1 (Pgk-1), and alpha-galactosidase (Ags), on the mouse X chromosome were determined by in situ hybridization. The five random DNA markers provide new genetic loci with useful restriction fragment length polymorphisms between mouse strains and species, including one locus close to the centromeric region of the mouse X chromosome. The physical map and the recombination map of these loci on the X chromosome were compared. There was good agreement in the order of loci. Relative distances between loci were consistent along the X chromosome, with the exception of the telomeric end of the long arm, where the recombination fraction observed between loci closely associated on the physical map was higher than that between similarly spaced markers located in the proximal region of the X chromosome. These results are discussed in comparison to the human X-chromosome map.     

Multilocus population genetic analysis of the Southwest Pacific malaria vector Anopheles punctulatus

The population structure and history of the cryptic malaria vector species, Anopheles punctulatus (Doenitz), was investigated throughout Papua New Guinea and the Solomon Islands with the aim of detailing genetic subdivisions and the potential for movement through this biogeographically complex region. We obtained larval collections from over 80 sites and utilised a diverse array of molecular markers that evolve through different processes. Individuals were initially identified to species and genotyped using the ribosomal DNA second internal transcribed spacer. DNA sequencing of a single copy nuclear ribosomal protein S9 and the mitochondrial cytochrome oxidase I loci were then investigated and 12 nuclear microsatellite markers were developed and analysed. Our data revealed three genetically distinct populations – one in Papua New Guinea, the second on Buka Island (Bougainville Province, Papua New Guinea), and the third on Guadalcanal Island (Solomon Islands). Genetic differentiation within Papua New Guinea was much lower than that found in studies of other closely related species in the region. The data does suggest that A. punctulatus has undergone a population bottleneck followed by a recent population and range expansion in Papua New Guinea. Humans and regional economic growth may be facilitating this population expansion, as A. punctulatus is able to rapidly occupy human modified landscapes and traverse unsealed roads. We therefore anticipate extensive movement of this species through New Guinea – particularly into the highlands, with a potential increase in malaria frequency in a warming climate – as well as relatively unrestricted gene flow of advantageous alleles that may confound vector control efforts.     

Polymorphic NumtS trace human population relationships

The human genome is constantly subjected to evolutionary forces which shape its architecture. Insertions of mitochondrial DNA sequences into nuclear genome (NumtS) have been described in several eukaryotic species, including Homo sapiens and other primates. The ongoing process of the generation of NumtS has made them valuable markers in primate phylogenetic studies, as well as potentially informative loci for reconstructing the genetic history of modern humans. Here, we report the identification of 53 human-specific NumtS by inspection of the UCSC genome browser, showing that they may be direct insertions of mitochondrial DNA into the human nuclear DNA after the human-chimpanzee split. In silico analyses allowed us to identify 14 NumtS which are polymorphic in terms of their presence/absence within the human genome in individuals of different ancestry. The allele frequencies of these polymorphic NumtS were calculated for 1000 Genomes Project sequence data from 13 populations worldwide, and principal components analysis and hierarchical clustering methods allowed the detection of strong signals of geographical structure related to the genetic diversity of these loci. All identified polymorphic human-specific NumtS together with a tandemly duplicated NumtS have also been validated by PCR amplification on a panel of 60 samples belonging to five native populations worldwide, confirming the expected NumtS variability. On the basis of these findings, we have succeeded in depicting the landscape of variation of a series of NumtS in several ethnic groups, making an advance in their identification as useful markers in the study on human population genetics.     

Genetic differentiation of pedunculate oak Quercus robur L. in the European part of Russia based on RAPD markers

Using randomly amplified polymorphic DNA markers (RAPD), genetic variation and differentiation in four populations of pedunculate oak Quercus robur L. were examined. The populations occupy a large part of the Quercus robur range in the European Russia (Voronezh and Novgorod oblasts; Republics of Mordovia and Bashkortostan). With each of six random primers (A02, A09, A17, B01, B08, B11), 96 DNA samples were analyzed by PCR. In all, 48 putative polymorphic RAPD loci were detected. We failed to reveal population-specific DNA fragments for any primer although the frequencies of 14 fragments were significantly different among populations. The oak populations studied exhibited high variability: 73-90% of genes were polymorphic and the effective allele number was about 1.4. The total genetic variation varied from 0.202 (Vor) to 0.245 (Nov), which corresponded to the estimates for populations of this species from Central and Western Europe. The populations examined showed low among-population differentiation (GST = 0.098); gene flow Nem was 4.61. The proportion of among-population variation of the RAPD loci studied accounted for 7% of the total variability; more than 93% of the total variability was explained by individual and within--population variation.     

Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer

Range-wide genetic variation of black spruce (Picea mariana) was studied using polymerase chain reaction-random fragment length polymorphism markers of the mitochondrial genome. Four polymorphic mitochondrial DNA (mtDNA) loci were surveyed and two or three alleles were detected at each locus, resulting in 10 multilocus mtDNA types or mitotypes. A significant subdivision of population genetic diversity was detected (GST = 0.671; NST = 0.726), suggesting low levels of gene flow among populations. The distribution of mitotypes was not random (NST > GST; P < 0.05) and revealed four partially overlapping zones, presumably representative of different glacial populations. Comparison of the genetic structure derived from mtDNA markers and the colonization paths previously deduced from the fossil and pollen records allow us to infer at least three southern and one northeastern glacial populations for black spruce. The patterns revealed in this study suggest that black spruce shares its biogeographical history with other forest-associated North American species.