Analysis of F ST outliers at allozyme loci in Pacific salmon: implications for natural selection

Natural selection has been invoked to explain the observed geographic distribution of allozyme allele frequencies for a number of teleost species. The effects of selection on allozyme loci in three species of Pacific salmon were tested. A simulation-based approach to estimate the null distribution of population differentiation (F _ST) and test for F _ST outliers was used. This approach showed that a majority of allozyme loci conform to neutral expectations predicted by the simulation model, with relatively few F _ST outliers found. No consistent F _ST outlier loci were found across species. Analysis of population sub-groups based on geography and genetic identity reduced the number of outlier loci for some species, indicating that large geographic groups may include genetically divergent populations and/or that there is geographic heterogeneity in selection pressure upon allozyme loci. Two outlier allozyme loci found in this analysis, lactate dehydrogenase-B and malic enzyme, have been shown to be influenced by selection in other teleost species. This approach is also useful in identifying allozyme loci (or other genetic markers) that meet assumptions for population genetic study.     

Measures of gene flow in the Columbian ground squirrel

From analyses of published data and a review of the literature, I studied indirect and direct measures of gene flow among populations of Columbian ground squirrels, Spermophilus columbianus. New analyses were used to examine an allozyme data set (seven polymorphic loci) that had been collected by Zammuto and Millar (1985a) from six populations of ground squirrels that were spread over 183 km. G-tests indicated significant variation in allele frequencies among populations, but F-statistics revealed relatively little population differentiation (average F _ST=0.026). F _ST values were used to estimate rates of gene flow indirectly and indicated fairly high rates of gene flow (average N _e m=13.5). Recorded dispersal distances of individual ground squirrels were fairly short (most<4 km, maximum recorded distance was 8.5 km), and the minimum distance between populations used to create the allozyme data set was about 25 km. Thus, direct dispersal among the populations in the allozyme data set was highly unlikely. Small genetically effective populations may have experienced high rates of migration over short distances (about 43% of adults in local populations were immigrants), however, resulting in homogeneous allele frequencies over the geographic range. This explanation provides an alternative to invoking gene flow in the recent past to explain discrepancies between dispersal distances in the field and homogenization of allele frequencies over large ranges, Mammalian species that have virtually complete dispersal of subadult males from the natal area might be expected to exhibit relatively high rates of gene flow, regardless of actual dispersal distances. Genetically effective populations may be much smaller than more extensive ecological populations and experience higher rates of gene flow.     

Low levels of quantitative and molecular genetic differentiation among natural populations of Medicago ciliaris Kroch. (Fabaceae) of different Tunisian eco-geographical origin

In this paper, we analyze the genetic variability in four Tunisian natural populations of Medicago ciliaris using 19 quantitative traits and six polymorphic microsatellite loci. We investigated the amplification transferability of 30 microsatellites developed in the model legume M. truncatula to M. ciliaris. Results revealed that about 56.66% of analyzed markers are valuable genetic markers for M. ciliaris. The most genetic diversity at quantitative traits and microsatellite loci was found to occur within populations (>80%). Low differentiations among populations at quantitative traits Q _ST  = 0.146 and molecular markers F _ST  = 0.18 were found. The majority of measured traits exhibited no significant difference in the level of Q _ST and F _ST . Furthermore, significant correlations established between these traits and eco-geographical factors suggested that natural selection should be invoked to explain the level of phenotypic divergence among populations rather than drift. There was no significant correlation between population differentiation at quantitative traits and molecular markers. Significant spatial genetic structure consistent with models of isolation by distance was detected within all studied populations. The site-of-origin environmental factors explain about 9.07% of total phenotypic genetic variation among populations. The eco-geographical factors that influence more the variation of measured traits among populations are the soil texture and altitude. Nevertheless, there were no consistent pattern of associations between gene diversity (He) and environmental factors.     

Genetic variation in island populations of tuatara (<Emphasis Type="Italic">Sphenodon</Emphasis> spp) inferred from microsatellite markers

Tuatara (Sphenodon spp) populations are restricted to 35 offshore islands in the Hauraki Gulf, Bay of Plenty and Cook Strait of New Zealand. Low levels of genetic variation have previously been revealed by allozyme and mtDNA analyses. In this new study, we show that six polymorphic microsatellite loci display high levels of genetic variation in 14 populations across the geographic range of tuatara. These populations are characterised by disjunct allele frequency spectra with high numbers of private alleles. High F _ST (0.26) values indicate marked population structure and assignment tests allocate 96% of all individuals to their source populations. These genetic data confirm that islands support genetically distinct populations. Principal component analysis and allelic sequence data supplied information about genetic relationships between populations. Low numbers of rare alleles and low allelic richness identified populations with reduced genetic diversity. Little Barrier Island has very low numbers of old tuatara which have retained some relictual diversity. North Brother Island’s tuatara population is inbred with fixed alleles at 5 of the 6 loci.     

Relative performance of Bayesian clustering software for inferring population substructure and individual assignment at low levels of population differentiation

Traditional methods for characterizing genetic differentiation among populations rely on a priori grouping of individuals. Bayesian clustering methods avoid this limitation by using linkage and Hardy–Weinberg disequilibrium to decompose a sample of individuals into genetically distinct groups. There are several software programs available for Bayesian clustering analyses, all of which describe a decrease in the ability to detect distinct clusters as levels of genetic differentiation among populations decrease. However, no study has yet compared the performance of such methods at low levels of population differentiation, which may be common in species where populations have experienced recent separation or high levels of gene flow. We used simulated data to evaluate the performance of three Bayesian clustering software programs, PARTITION, STRUCTURE, and BAPS, at levels of population differentiation below F _ST=0.1. PARTITION was unable to correctly identify the number of subpopulations until levels of F _ST reached around 0.09. Both STRUCTURE and BAPS performed very well at low levels of population differentiation, and were able to correctly identify the number of subpopulations at F _ST around 0.03. The average proportion of an individual’s genome assigned to its true population of origin increased with increasing F _ST for both programs, reaching over 92% at an F _ST of 0.05. The average number of misassignments (assignments to the incorrect subpopulation) continued to decrease as F _ST increased, and when F _ST was 0.05, fewer than 3% of individuals were misassigned using either program. Both STRUCTURE and BAPS worked extremely well for inferring the number of clusters when clusters were not well-differentiated (F _ST=0.02–0.03), but our results suggest that F _ST must be at least 0.05 to reach an assignment accuracy of greater than 97%.     

Latitudinal allozymic variability in natural populations ofZaprionus indianus from India

Twelve natural populations ofZ. indianus from India, collected along lines of latitude, were analyzed electrophoretically and the geographical pattern of variation was compared at 15 allozyme loci. Except forMdh-2, all the loci revealed extensive polymorphism. The allele frequency variation revealed a statistically significant correlation as well as regression coefficients with the latitude. The populations revealed extensive clinal variation at all the polymorphic loci, which depicted moderate to higherF _ST values. Thus, the observed genetic divergence in colonizing populations ofZ. indianus shows the role of natural selection that varies spatially along the north-south axis of the Indian subcontinent.Financial assistance from UGC, New Delhi, is gratefully acknowledged.     

Is F ST obsolete?

Since the introduction of allozyme methods inthe mid 1960s it has been a standard practiceto report Wright's measure of populationsubdivision, F _ST, for surveys ofgenetic variation. Its widespread use hasprovided us with a sense of what values can beexpected in particular situations and how theycan be interpreted. With some theoreticaljustification, F _ST has also beenused to estimate rates of gene flow. Howeverthere are conditions under which F _STis inappropriate for gene flow estimation andcan lead to incorrect or even absurdconclusions. These pitfalls have promptedcritics to suggest that F _ST hasfailed to deliver what its proponents havepromised and should be abandoned. A furtherchallenge has been the development of newmethods that offer even greater promise. Thusit is reasonable to ask if perhaps it is timeto retire F _ST and turn to new andmore powerful methods for the inference of geneflow from genetic markers. Here I will arguethat although gene flow should be estimated bymore powerful approaches whenever practical,F _ST remains a useful measure of theaverage effects of gene flow and will continueto be used for comparative purposes.     

Morphological and microsatellite diversity associated with ecological factors in natural populations of Medicago laciniata Mill. (Fabaceae)

Genetic variability in 10 natural Tunisian populations of Medicago laciniata were analysed using 19 quantitative traits and 12 polymorphic microsatellite loci. A large degree of genetic variability within-populations and among-populations was detected for both quantitative characters and molecular markers. High genetic differentiation among populations for quantitative traits was seen, with Q _ST = 0.47, and F _ST = 0.47 for microsatellite markers. Several quantitative traits displayed no statistical difference in the levels of Q _ST and F _ST . Further, significant correlations between quantitative traits and eco-geographical factors suggest that divergence in the traits among populations may track environmental differences. There was no significant correlation between genetic variability at quantitative traits and microsatellite markers within populations. The site-of-origin of eco-geographical factors explain between 18.13% and 23.40% of genetic variance among populations at quantitative traits and microsatellite markers, respectively. The environmental factors that most influence variation in measured traits among populations are assimilated phosphorus (P₂0₅) and mean annual rainfall, followed by climate and soil texture, altitude and organic matter. Significant associations between eco-geographical factors and gene diversity, H _e , were established in five-microsatellite loci suggesting that these simple sequence repeats (SSRs) are not necessarily biologically neutral.     

An exploratory analysis of geographic genetic variation in southern African nyala (Tragelaphus angasii)

We report patterns of genetic variation based on microsatellite, allozyme and mitochondrial control region markers in nyala from geographic locations sampled in South Africa, Mozambique, Malawi and Zimbabwe. Highly significant differences were observed among allele frequencies at three microsatellite loci between populations from KwaZulu-Natal, Limpopo and Malawi, with the Malawi and KwaZulu-Natal groupings showing the highest differentiation (R_ST=0.377). Allozyme frequencies showed minor, non-statistically significant regional differences among the South African populations, with maximum F_ST values of 0.048–0.067. Mitochondrial DNA analyses indicated a unique haplotype in each location sampled. Since none of these indices of population differentiation showed significant correlation to absolute geographic distance, we conclude that geographic variation in this species is probably a function of a distribution pattern stemming from habitat specificity. It is suggested that translocations among geographically distant regional populations be discouraged at present, pending a more elaborate investigation. Transfer of native individuals among local populations may, however, be required for minimizing the likelihood of inbreeding depression developing in small captive populations.     

Population Structure of the Giant Garter Snake, Thamnophis gigas

The giant garter snake, Thamnophis gigas, is a threatened species endemic to California’s Central Valley. We tested the hypothesis that current watershed boundaries have caused genetic differentiation among populations of T. gigas. We sampled 14 populations throughout the current geographic range of T. gigas and amplified 859 bp from the mitochondrial gene ND4 and one nuclear microsatellite locus. DNA sequence variation from the mitochondrial gene indicates there is some genetic structuring of the populations, with high F_ST values and unique haplotypes occurring at high frequency in several populations. We found that clustering populations by watershed boundary results in significant between-region genetic variance for mtDNA. However, analysis of allele frequencies at the microsatellite locus NSU3 reveals very low F_ST values and little between-region variation in allele frequencies. The discordance found between mitochondrial and microsatellite data may be explained by aspects of molecular evolution and/or T. gigas life history characteristics. Differences in effective population size between mitochondrial and nuclear DNA, or male-biased gene flow, result in a lower migration rate of mitochondrial haplotypes relative to nuclear alleles. However, we cannot exclude homoplasy as one explanation for homogeneity found for the single microsatellite locus. The mitochondrial nucleotide sequence data supports conservation practices that identify separate management units for T. gigas.     

Host races and sympatric speciation in small ermine moths, Yponomeutidae

The amount of genetic differentiation at various levels of evolutionary divergence (conspecific populations, sibling species and non-sibling species) in Yponomeuta was determined. Genetic distances between siblings or non-siblings were found to cover a wide range. It is concluded that such estimates do not give much information on the speciation process itself. Inbreeding coefficients were calculated for populations of Y. padellus from a total of six host plants. The grand mean F _ST value is 0.030±0.012. F _ST values for populations sampled from Crataegus, the common food plant of Y. padellus, are 2–3.5 times smaller than those for populations from the other food plants taken together. Host race formation, as measured by significant differences in allozyme frequencies between sympatric populations on two or more food plants, was investigated in four areas. Host race formation seems to occur in Y. padellus and sympatric speciation is a likely event.

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Résumé Le degré de différenciation génétique en allozymes à des niveaux divers de divergence évolutive (populations conspécifiques, sibling species et non-sibling species) d'Yponomeuta a été déterminé. Les distances génétiques entre des sibling species ou des non-sibling species sont très larges. Il en est conclu que de telles estimations ne fournissent pas beaucoup d'informations sur le phénomène de spéciation même. Des coéfficients de reproduction consanguine (F _ST) ont été calculés pour des populations d'Y. padellus provenant de six plantes-hôtes. La valeur moyenne F _STest .030±.012. Les valuers de F _ST des populations recueillies sur Crataegus, (plante-hôte habituelle d'Y. padellus), sont inférieures 2–3.5 fois à celles des populations de l'ensemble des autres plantes-hôtes. L'apparition de races en fonction de l'hôte, mesurée par les différences importantes dans de fréquences des allozymes entre populations sympatriques sur plusieurs plantes-hôtes, a été examinée dans quatre régions. Il apparaît ainsi que la formation de races en fonction de l'hôte se produit chez Y. padellus et que la spéciation sympatrique est un évènement très vraisemblable.

     

Demography, and genetic and morphological variability of the endangered Sophronitis sincorana (Orchidaceae) in the Chapada Diamantina, Brazil

We carried out a demographic study and evaluated the genetic and morphological variability in five populations of the endangered Sophronitis sincorana (Orchidaceae) endemic to Northeastern Brazil, based on allozyme and morphometric analyses. Plant density was approximately 0.5 plants/m², and the projected total number of plants was approximately 50,000 individuals. However, fruit set and recruitment of individuals are rare. The genetic variability was very high in all populations (P = 100, A = 3.0−3.5, H _e = 0.33−0.48), and all populations presented similar values of morphological variability. Low genetic and morphological structuring were found in the species (F _ST = 0.053, A_MRPP = 0.018). The elevated coefficient of endogamy encountered in populations of S. sincorana indicates the occurrence of structuring within the populations. The lack of correlation between morphological and genetic variation in this species indicates that none of the markers examined should be used separately for either conservation purposes.     

Inter and intra‐population phenotypic and genotypic structuring in the European whitefish Coregonus lavaretus,a rare freshwater fish in Scotland

This study revealed between‐lake genetic structuring between Coregonus lavaretus collected from the only two native populations of this species in Scotland, U.K. (Lochs Eck and Lomond) evidenced by the existence of private alleles (12 in Lomond and four in Eck) and significant genetic differentiation (F_ST = 0·056) across 10 microsatellite markers. Juvenile C. lavaretus originating from eggs collected from the two lakes and reared in a common‐garden experiment showed clear phenotypic differences in trophic morphology (i.e. head and body shape) between these populations indicating that these characteristics were, at least partly, inherited. Microsatellite analysis of adults collected from different geographic regions within Loch Lomond revealed detectable and statistically significant but relatively weak genetic structuring (F_ST = 0·001–0·024) and evidence of private alleles related to the basin structure of the lake. Within‐lake genetic divergence patterns suggest three possibilities for this observed pattern: (1) differential selection pressures causing divergence into separate gene pools, (2) a collapse of two formerly divergent gene pools and (3) a stable state maintained by balancing selection forces resulting from spatial variation in selection and lake heterogeneity. Small estimates of effective population sizes for the populations in both lakes suggest that the capacity of both populations to adapt to future environmental change may be limited.     

Population cytogenetics of <Emphasis Type="Italic">Chironomus circumdatus</Emphasis> Kieffer, 1921 (Diptera,Chironomidae) from Thailand

The objectives of this study were to explore cytogenetic variation and the role of chromosomal change on local adaptation and genetic differentiation of Chironomus circumdatus Kieffer from Thailand. A total of 1,505 larvae from 24 populations were examined cytologically. Twelve chromosomal inversions were found and most of these (9 of 12) were rare inversions. All populations were in Hardy–Weinberg equilibrium. Significant association (P < 0.001) between the A2 and B5 inversions was detected in one population. Population genetic structure analysis indicated significant genetic differentiation between populations (F _ST = 0.037, P < 0.001). Geographic distance was the principal factor limiting gene flow between populations. Nei’s modified genetic distance (D _A) between populations ranged from 0.001 to 0.011 with an average of 0.003. An UPGMA population phenogram depicting relationship between populations based on D _A values revealed three groups of populations, group I, II and III each characterized by different inversions/inversion frequencies. Significant correlation of inversion C3 and water temperature suggested that this inversion might have a role to play on adaptation to high temperature habitat. However, if detection of significant population subdivision and relationship between genetic and geographic distance are taken into account, relationship between C3 and water temperature will also be due to the effect of migration/drift alone without the effect of selection.     

Microsatellite markers reveal spatial genetic structure of Tetranychus urticae (Acari: Tetranychidae) populations along a latitudinal gradient in Europe

The genetic structure of populations of the two-spotted spider mite Tetranychus urticae was investigated along a south–north European transect spanning from southern France to The Netherlands. Mites were collected on Urtica dioica in 6 sampling zones. Microsatellite variation at 5 loci revealed considerable genetic variation with an average heterozygozity of 0.49. Significant heterozygote deficiency was found in 7 populations out of the 18 samples analyzed and one of them was completely monomorphic. Tetranychus urticae populations show some level of genetic structuring. First, genetic differentiation between localities (F _ST estimates) was significant for all comparisons. Second, the analysis of molecular variance, AMOVA, indicates that there is an effect, albeit low (9%), of the locality in accounting for allele frequency variance. Geographic distance emerges as a factor responsible for this genetic structure. The results are discussed in relation to the biological features of the species and the known patterns of migration. Related agronomical issues are addressed.     

Comparative population structure of Chinese sumac aphid <Emphasis Type="Italic">Schlechtendalia chinensis</Emphasis> and its primary host-plant <Emphasis Type="Italic">Rhus chinensis</Emphasis>

Most of our current understanding of comparative population structure has been come from studies of parasite–host systems, whereas the genetic comparison of gallnut-aphids and their host-plants remain poorly documented. Here, we examined the population genetic structure of the Chinese sumac aphid Schlechtendalia chinensis and its unique primary host-plant Rhus chinensis in a mountainous province in western China using inter-simple sequence repeat (ISSR) markers. Despite being sampled from a mountainous geographic range, analysis of molecular variance (AMOVA) showed that the majority of genetic variation occurred among individuals within populations of both the aphid and its host. The aphid populations were found to be structured similarly to their primary host populations (F _ST values were 0.239 for the aphid and 0.209 for its host), suggesting that there are similar patterns of gene flow between the populations of the aphid and between populations of its host-plant. The genetic distances (F _ST/1 − F _ST) between the aphid populations and between its host-plant populations were uncorrelated, indicating that sites with genetically similar host-plant populations may not always have genetically similar aphid populations. The lack of relationships between genetic and geographical distance matrices suggested that isolation by distance (IBD) played a negligible role at this level. This may be mainly attributed to the founder effect, genetic drift and the relative small spatial scale between populations. Zhumei Ren and Bin Zhu contributed equally to this work.     

Genetic variation amongst viviparid snails in the genus Mekongia (Prosobranchia: Viviparidae) in Thailand

Allozyme variation in viviparid snails from the genus Mekongia in Thailand were examined across the different species, subspecies and geographical locations (river drainage systems). Using horizontal starch gel electrophoresis, 11 presumed allozyme loci (eight polymorphic) from eight enzyme systems were screened. Heterozygosity was moderately low (Hexp = 0.000–0.109, mean = 0.037). One population of Mekongia pongensis (Nong Khai) was monomorphic at all 11 examined loci in contrast to the other two populations, suggesting bottleneck within this population. Populations were more differentiated in the Mekongia sphaericula complex (F_ST = 0.587) than in either the Mekongia swainsoni complex (F_ST = 0.161) or M. pongensis species (F_ST = 0.073). Mekongia sphaericula sphaericula and Mekongia sphaericula extensa exhibited fixed allele differences at two loci, a high genetic distance (D = 0.265–0.300) and a potential polyphyletic relationship, suggesting two distinct lineages (species).     

Allozyme variation in the diploid (A genome) populations ofScilla scilloides (Hyacinthaceae)

Allozyme variation at eleven loci encoding seven enzyme systems were examined in 20 populations of diploid (genome AA, 2n = 16)Scilla scilloides in China. In comparison with the average species of seed plants studied, populations of this species display a high amount of genetic variation (A = 2.0, P = 58.6%, H_o = 0.172, and H_e = 0.185). Allozyme variation pattern revealed predominant outcrossing within populations and considerable differentiation (F_ST = 0.314) among populations as well as between the subtropic and temperate regions. The wide distribution, long existence and outcrossing are presumably the main factors responsible for the high genetic diversity within populations. But the gravity dispersal of seeds and pollination by small insects set limits to the increase of genetic variation within populations and promote differentiation between populations and regions. In addition, allozyme variation does not distinguishS. scilloides var.albo-viridis and suggests that subtropic populations may be considered as a genetic entity.     

Allozyme variation of the pygmy wood mouse <Emphasis Type="Italic">Apodemus uralensis</Emphasis> (Rodenita,Muridae) in the ural region

Variation of 17 allozyme loci was examined in 530 Apodemus uralensis individuals caught in the Ural region from 2005 to 2007. In the populations examined, the mean value of the genetic differentiation index F _ST constituted 0.169. It was demonstrated that F _ST values for the samples obtained from the 1-km2 plot in different years, as well as for the samples trapped at a distance from 0.3 to 5 km during one year, could be remarkably higher than the mean value, pointing to their high, statistically significant differentiation. It seems likely that this differentiation was caused by spatial population subdivision, associated with the mice migrations, temporal change of the population structure, and the gene drift. Population of A. uralensis from radioactively contaminated zone displayed no specificities in the allozyme set and frequencies, which could basically distinguish these animals from the other Ural populations.     

Population Genetic structure ofPotentilla fragariodes var.major (Rosaceae) in Korea

The genetic diversity and population structure of eighteenPotentilla fragariodes var.major (Rosaceae) populations in Korea were determined using genetic variations at 22 allozyme loci. The percent of polymorphic loci within the enzymes was 66.7%. Genetic diversity at the species level and at the population level was high (Hes = 0.203; Hep = 0.185, respectively), whereas the extent of the population divergence was relatively low (G_ST = 0.069). F_IS, a measure of the deviation from random mating within the 18 populations, was 0.075. An indirect estimate of the number of migrants per generation (Nm = 3.36) indicated that gene flow was high among Korean populations of the species. In addition, analysis of fixation indices revealed a slight heterozygote deficiency in some populations and at some loci. Wide geographic ranges, perennial herbaceous nature and the persistence of multiple generations are associated with the high level of genetic variation. AlthoughP. fragariodes var.major usually propagated by asexually-produced ramets, we could not rule out the possibility that sexual reproduction occurred at a low rate because each ramet may produce terminal flowers. Mean genetic identity between populations was 0.983. It is highly probable that directional movement toward genetic uniformity in a relatively homogeneous habitat operates among Korean populations ofP. fragariodes var.major.