Steep,coincident, and concordant clines in mitochondrial and nuclear‐encoded genes in a hybrid zone between subspecies of Atlantic killifish,Fundulus heteroclitus

Steep genetic clines resulting from recent secondary contact between previously isolated taxa can either gradually erode over time or be stabilized by factors such as ecological selection or selection against hybrids. We used patterns of variation in 30 nuclear and two mitochondrial SNPs to examine the factors that could be involved in stabilizing clines across a hybrid zone between two subspecies of the Atlantic killifish, Fundulus heteroclitus. Increased heterozygote deficit and cytonuclear disequilibrium in populations near the center of the mtDNA cline suggest that some form of reproductive isolation such as assortative mating or selection against hybrids may be acting in this hybrid zone. However, only a small number of loci exhibited these signatures, suggesting locus‐specific, rather than genomewide, factors. Fourteen of the 32 loci surveyed had cline widths inconsistent with neutral expectations, with two SNPs in the mitochondrial genome exhibiting the steepest clines. Seven of the 12 putatively non‐neutral nuclear clines were for SNPs in genes related to oxidative metabolism. Among these putatively non‐neutral nuclear clines, SNPs in two nuclear‐encoded mitochondrial genes (SLC25A3 and HDDC2), as well as SNPs in the myoglobin, 40S ribosomal protein S17, and actin‐binding LIM protein genes, had clines that were coincident and concordant with the mitochondrial clines. When hybrid index was calculated using this subset of loci, the frequency distribution of hybrid indices for a population located at the mtDNA cline center was non‐unimodal, suggesting selection against advanced‐generation hybrids, possibly due to effects on processes involved in oxidative metabolism.     

Müllerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection

Hybrid zones, where distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Studying clines in genetic loci and adaptive traits across hybrid zones is a powerful method for understanding how selection drives differentiation within a single species, but can also be used to compare parallel divergence in different species responding to a common selective pressure. Here, we study parallel divergence of wing colouration in the butterflies Heliconius erato and H. melpomene, which are distantly related Müllerian mimics which show parallel geographic variation in both discrete variation in pigmentation, and quantitative variation in structural colour. Using geographic cline analysis, we show that clines in these traits are positioned in roughly the same geographic region for both species, which is consistent with direct selection for mimicry. However, the width of the clines varies markedly between species. This difference is explained in part by variation in the strength of selection acting on colour traits within each species, but may also be influenced by differences in the dispersal rate and total strength of selection against hybrids between the species. Genotyping‐by‐sequencing also revealed weaker population structure in H. melpomene, suggesting the hybrid zones may have evolved differently in each species, which may also contribute to the patterns of phenotypic divergence in this system. Overall, we conclude that multiple factors are needed to explain patterns of clinal variation within and between these species, although mimicry has probably played a central role.     

Genetic population structure of the large blue butterfly Maculinea alcon in Denmark

We have investigated the genetic population structure within and the genetic differentiation between local populations of the large blue butterfly Maculinea alcon throughout the Jutland peninsula. Samples were collected as eggs on foodplants (Gentiana pneumonanthe), and reared to 4th instar caterpillars in the laboratory. A significant excess of homozygotes was found for all the investigated allozyme loci in most of the populations. A North-South cline was observed for the allele frequencies at some of the loci and for several linkage groups. Because some of the allele frequency clines were parallel to clines in adult morphological variation, we interpret our results as evidence for the co-existence of at least two gene pools within the Danish Maculinea alcon populations. Multilocus electrophoretic data revealed highly positive but variable FST values, which under this scenario would reflect varying frequencies of the Maculinea gene pools across the local populations. The significantly positive FIS values indicate that these gene pools are at least partly reproductively isolated (Wahlund effect). The co-occurrence of several Maculinea alcon gene pools on many local sites in Jutland is of great importance for conservation of the fragmented Maculinea populations. Our results show that there is probably more Maculinea biodiversity to conserve than was previously thought, and suggests that extant populations are more fragmented and vulnerable than counts of flying adults or eggs on foodplants indicate.     

Isolation by Distance in a Quantitative Trait

Random genetic drift in a quantitative character is modeled for a population with a continuous spatial distribution in an infinite habitat of one or two dimensions. The analysis extends Wright's concept of neighborhood size to spatially autocorrelated sampling variation in the expected phenotype at different locations. Weak stabilizing selection is assumed to operate toward the same optimum phenotype in every locality, and the distribution of dispersal distances from parent to offspring is a (radially) symmetric function. The equilibrium pattern of geographic variation in the expected local phenotype depends on the neighborhood size, the genetic variance within neighborhoods, and the strength of selection, but is nearly independent of the form of the dispersal function. With all else equal, geographic variance is smaller in a two-dimensional habitat than in one dimension, and the covariance between expected local phenotypes decreases more rapidly with the distance separating them in two dimensions than in one. The equilibrium geographic variance is less than the phenotypic variance within localities, unless the neighborhood size is small and selection is extremely weak, especially in two dimensions. Nevertheless, dispersal of geographic variance created by random genetic drift is an important mechanism maintaining genetic variance within local populations. For a Gaussian dispersal function it is shown that, even with a small neighborhood size, a population in a two-dimensional habitat can maintain within neighborhoods most of the genetic variance that would occur in an infinite panmictic population.     

A Comprehensive Study of Genic Variation in Natural Populations of Drosophila melanogaster. II. Estimates of Heterozygosity and Patterns of Geographic Differentiation

A study of genic variation in natural population of D. melanogaster was undertaken (1) to obtain a better estimate of heterozygosity by sampling a relatively large number of gene loci and (2) to identify different groups of polymorphic loci whose variation patterns might suggest different kinds of selection forces. A total of 117 gene loci (coding for 79 enzymes and 38 abundant proteins) were studied in 15 geographically distant populations originating from different continents. The findings of this study are as follows: (1) of the 117 gene loci studied, 61 are polymorphic and 56 are uniformly monomorphic everywhere. (2) An average population is polymorphic for 43% of its gene loci and an average individual is heterozygous for 10% of its gene loci. These estimates are remarkably similar among populations. (3) The average within-locality heterozygosity (H(S)) for polymorphic loci is uniformly distributed over the range of heterozygosity observed; i.e. , given that a locus has any local variation, it is nearly as likely to have a lot as a little. (4) The distribution of F(ST) (fixation index) is strongly skewed, with a prominent mode at 8-10% and a long tail of high values reaching a maximum of 58%. Two-thirds of all loci fall within the bell-shaped distribution centered on an F(ST) of 8-10%, a result compatible with the notion that they are experiencing a common tendency toward small interlocality differences owing to extensive gene flow among populations. (5) The distribution of total heterozygosity (H(T)) has a prominent bimodal distribution. The lower mode consists of loci with single prominent allele and a few uncommon ones and the upper mode consists of clinally varying loci with a high F(ST ) (e.g., Adh and G6-pd), loci with many alleles in high frequency (e.g., Ao and Xdh) and loci with two alleles in high frequency in all populations but, with little interpopulational differentiation (e.g., Est-6 and alpha-Fuc). The loci in the lower mode are probably under purifying selection; a large proportion of those in the latter mode may be under balancing selection. (6) Comparison of genic variation for loci located inside vs. outside inversions, comparison of F(ST) for inversions and their associated genes, and comparison of F(ST) and map position for pairs of loci all suggest that, while linkage has some influence, it does not seem to constrain the pattern of variation that a locus may develop. (7) Eighteen polymorphic loci show latitudinal variation in allele frequencies which are consistent in populations from different continents. (8) Estimates of Nei genetic distance between population pairs are generally low between populations on the same continent and high between populations on different continents. There are two important exceptions: population pairs for which both localities are in the temperate zone show no relationship to distance, and in cases where both populations are tropical or subtropical, the genetic distance is higher than for the temperate-tropical comparisons and seem even higher than one would expect from the geographic distance separating them. The latter observation suggests that either geographic separation outweighs differences in environment in determining the genetic composition of a population or that all tropical populations are not experiencing the same environment.-The results are discussed in relation to the neutralist-selectionist controversy of genic variation and two important conclusions are drawn: First, there is a negative correlation between the number of loci sampled and the resulting heterozygosity. This means that available estimates of heterozygosity, 85% of which are based on 30 or fewer loci, are high and hence not appropriate for making between-taxa comparisons. Secondly, there is a group of loci, comprising one-third of polymorphic loci (or about 15% of all loci studied), that is distinguishable by different patterns of variation within and among populations. Most of these loci have clinal variation which is consistent with the hypothesis that their genetic variation is maintained by balancing selection.     

Quantitative Genetic Variation of Odor-Guided Behavior in a Natural Population of Drosophila Melanogaster

Quantitative genetic variation in behavioral response to the odorant, benzaldehyde, was assessed among a sample of 43 X and 35 third chromosomes extracted from a natural population and substituted into a common inbred background. Significant genetic variation among chromosome lines was detected. Heritability estimates for olfactory response, however, were low, as is typical for traits under natural selection. Furthermore, the loci affecting naturally occurring variation in olfactory response to benzaldehyde were not the same in males and females, since the genetic correlation between the sexes was low and not significantly different from zero for the chromosome 3 lines. Competitive fitness, viability and fertility of the chromosome 3 lines were estimated using the balancer equilibrium technique. Genetic correlations between fitness and odor-guided behavior were not significantly different from zero, suggesting the number of loci causing variation in olfactory response is small relative to the number of loci causing variation in fitness. Since different genes affect variation in olfactory response in males and females, genetic variation for olfactory response could be maintained by genotype X sex environment interaction. This unusual genetic architecture implies that divergent evolutionary trajectories for olfactory behavior may occur in males and females.     

Levels of variation in stress resistance in drosophila among strains, local populations, and geographic regions: patterns for desiccation, starvation, cold resistance, and associated traits

Stress resistance traits in Drosophila often show clinal variation. Although these patterns suggest selection, there is generally no attempt to test how large differences at the geographical level are relative to levels of variation within and between local populations. Here we compare these levels in D. melanogaster from temperate Tasmania versus tropical northern Queensland by focusing on adult resistance to desiccation, cold and starvation stress, as well as associated traits (size, lipid content). For starvation and desiccation resistance, levels of variation were highest among strains from the same population. whereas there was little differentiation among local populations and a low level of differentiation at the geographic level. For adult cold resistance, there was local differentiation and strain variation but no geographic variation. For size (thorax length), geographic differentiation was higher despite some overlap among strains from the tropical and temperate locations. Finally, for lipid levels there was only evidence for variation among strains. The low level of differentiation among geographic locations for stress resistance was further verified with the characterization of isofemale strains from 18 locations along a coastal transect extending from Tasmania to northern Queensland. Crosses among some of the isofemale strains showed that results were not confounded by inbreeding effects. Strains derived from a cross between a tropical and temperate strain differed for all traits, and variation among strains for body size was higher than strain variation within the geographic regions. Unlike in previous studies, lipid content and starvation resistance were not correlated in any set of strains, but there was a correlation between cold resistance and lipid content. There was also a correlation between desiccation resistance and size but only in the geographic cross strains. These findings suggest a large amount of variation in stress resistance at the population level and inconsistent correlation patterns across experimental approaches.     

Influence of voltine ecotype and geographic distance on genetic and haplotype variation in the Asian corn borer

Diapause is an adaptive dormancy strategy by which arthropods endure extended periods of adverse climatic conditions. Seasonal variation in larval diapause initiation and duration in Ostrinia furnacalis may influence adult mating generation number (voltinism) across different local environments. The degree to which voltine ecotype, geographic distance, or other ecological factors influence O. furnacalis population genetic structure remains uncertain. Genetic differentiation was estimated between voltine ecotypes collected from 8 locations. Mitochondrial haplotypes were significantly different between historically allopatric univoltine and bivoltine locations, but confounded by a strong correlation with geographic distance. In contrast, single nucleotide polymorphism (SNP) genotypes show low but significant levels of variation and a lack of influence of geographic distance between allopatric voltine locations. Regardless, 11 of 257 SNP loci were predicted to be under selection, suggesting population genetic homogenization except at loci proximal to factors putatively under selection. These findings provide evidence of haplotype divergent voltine ecotypes that may be maintained in allopatric and sympatric areas despite relatively high rates of nuclear gene flow, yet influence of voltinism on maintenance of observed haplotype divergence remains unresolved.     

Patterns of genetic diversity in population complexes of pacific chum salmon <Emphasis Type="Italic">Oncorhynchus keta</Emphasis> Walbaum,from Asia and America,inferred from allozyme polymorphism data

Based on the data of Russian and foreign researchers, a database, consisting of 100 allozyme-coding loci examined in 288 chum salmon populations from Asia and Northern America, was constructed. Using G-test, genetic heterogeneity of Asian population samples of chum salmon was evaluated. Correlations between the frequencies of major alleles and geographic latitude of the mouths of native rivers were estimated. Using the methods of Nei and Cavalli-Sforza and Edwards, for different local chum salmon stock groups the genetic distances at the number of polymorphic enzyme loci were determined. Analysis of these distances made it possible to evaluate the patterns of genetic diversity in regional population groups from the Russian Far East, Japan, and North America. The proportions of genetic variation at each hierarchical level, identified in accordance with the geographical positions of the populations, were estimated through partitioning of variation in Asian populations into within and between-population components. It was demonstrated that intraspecific genetic structure of chum salmon corresponded geographic subdivision into regional population groups.     

Inversions fail to account for allozyme clines

Allozyme and inversion data from natural populations of Drosophila melanogaster from the eastern United States were analyzed to determine whether the clines at allozyme loci are due to nonrandom associations with common cosmopolitan inversions. All inversions show strong clines. Clines were large and significant for half of the eight allozyme loci. An analysis of the contribution of inversions to clines of allozyme genes revealed three outcomes: the inversion cline (1) enhanced the allozyme cline, but was only partly responsible, (2) reduced the allozyme cline, and (3) had no effect. The allozyme clines were mainly determined by the pattern of allele frequencies within the chromosomal arrangements. Consequently, it was concluded that allozyme clines would exist in the absence of inversion clines.     

Chromosomal and allelic variation in Drosophila americana: selective maintenance of a chromosomal cline.

Geographically structured genetic variation, as represented by clines and hybrid zones, offers unique opportunities to study adaptation and speciation in natural populations. A hybrid zone has been reported between Drosophila americana americana and Drosophila americana texana, two taxa that are distinguished solely by the arrangement of their X and 4th chromosomes. In this study, samples of D. americana were collected along a latitudinal transect across the inferred hybrid zone, and the frequency of the alternative chromosomal arrangements is reported. These data illustrate that the alternative chromosomal arrangements are distributed along a shallow cline over a broad geographic region, and that the frequency of the arrangements is tightly correlated with latitude. Allelic variants at 13 RFLP loci in three genes on chromosome 4 exhibit no evidence of association with the cline. Presence of a cline for the chromosomal arrangements, as well as a general absence of geographic structure for variation at these genes, is interpreted as evidence that natural selection is responsible for the maintenance of this chromosomal cline. Furthermore, these results demonstrate that taxonomic subdivision of D. americana is unwarranted, because it exists as a cohesive species that is segregating a chromosomal fusion.     

Sequence variation patterns along a latitudinal cline in Scots pine (Pinus sylvestris): signs of clinal adaptation?

Adaptive clinal variation is abundant in nature, and its genetic basis is of great interest. The polygenic nature of this variation poses a challenge for identifying the causative loci underlying these adaptations. Here, we have examined the patterns of sequence variation in ten candidate genes for timing of bud set and cold tolerance, traits that form strong latitudinal clines in Scots pine (Pinus sylvestris). A set of reference genes was used for comparison and to infer a simplified demographic background model with approximate Bayesian computation methods. Against the resulting bottleneck model, the neutrality tests show little signs for local adaptation, but species-wide selection is suggested in some of the studied genes. In line with the theoretical expectations, we see little evidence for adaptive differentiation with F _ST methods. Instead, allele frequency clines were found in three genes (dhn1, ftl2, and prr1). Our results add to the discussion on which molecular signals best characterize a gene subject to clinally varying selection. This will be especially relevant when these kinds of observations can be examined in parallel with association study results.     

Genomics,environment and balancing selection in behaviourally bimodal populations: The caribou case

Selection forces that favour different phenotypes in different environments can change frequencies of genes between populations along environmental clines. Clines are also compatible with balancing forces, such as negative frequency‐dependent selection (NFDS), which maintains phenotypic polymorphisms within populations. For example, NFDS is hypothesized to maintain partial migration, a dimorphic behavioural trait prominent in species where only a fraction of the population seasonally migrates. Overall, NFDS is believed to be a common phenomenon in nature, yet a scarcity of studies were published linking naturally occurring allelic variation with bimodal or multimodal phenotypes and balancing selection. We applied a Pool‐seq approach and detected selection on alleles associated with environmental variables along a North–South gradient in western North American caribou, a species displaying partially migratory behaviour. On 51 loci, we found a signature of balancing selection, which could be related to NFDS and ultimately the maintenance of the phenotypic polymorphisms known within these populations. Yet, remarkably, we detected directional selection on a locus when our sample was divided into two behaviourally distinctive groups regardless of geographic provenance (a subset of GPS‐collared migratory or sedentary individuals), indicating that, within populations, phenotypically homogeneous groups were genetically distinctive. Loci under selection were linked to functional genes involved in oxidative stress response, body development and taste perception. Overall, results indicated genetic differentiation along an environmental gradient of caribou populations, which we found characterized by genes potentially undergoing balancing selection. We suggest that the underlining balancing force, NFDS, plays a strong role within populations harbouring multiple haplotypes and phenotypes, as it is the norm in animals, plants and humans too.     

A statistical analysis of nucleotide sequences of introns and exons in human genes

DNA sequences of 56 human genes for which information on both exons and introns was available were examined. The variance in G+C content among genes is estimated and shown to be substantial. There is a high correlation in G+C content between exons and introns within the same gene. The dinucleotide frequencies of introns are similar to those of intergenic spacer regions and are in reasonable agreement with predictions from substitution rates estimated from pseudogenes, except that the observed deficiency of TA doublets is not predicted. Duplicated bases also show a frequency greater than the expectation under independence. There is marked variability among genes in the frequency of the doublet CG relative to its expectation under independence. This variation is evolutionarily conserved and is correlated with the G+C content. Pseudogenes behave as if they are in a low -G+C, CG-deficient part of the genome, although the genes from which they arose are variable in these respects.      

Within-island microgeographic variation in the colour pattern of the skink,Chalcides sexlineatus: Pattern and cause

The colour pattern of the Gran Canarian skink is described with eight independent colour pattern characters. Significant geographic variation occurs in each character. There are generally high levels of congruence between the patterns of geographic variation in each character although some differences exist. In canonical variate analyses, the first canonical variate expresses most of the among-locality variation in colour pattern, indicating a largely unidimensional pattern. Patterns of geographic variation in the colour pattern are portrayed by contouring. This reveals north-east/south-west clines for seven of the individual characters and the generalized pattern (CV1). Four causal hypotheses were erected which predicted four different unidimensional patterns of geographic variation. Mantel tests and partial correlation analyses were used to compare the observed patterns of microgeographic variation with the four hypothesized patterns. This method suggests differential selection occurring between ecotones as the cause of the microgeographic variation. Microgeographic variation in some aspects of the colour pattern can be explained by selection for different anti-predator strategies in the hot, arid southern areas vs the cooler, lusher northern areas.     

野古草种群克隆的遗传变异和遗传结构

用酶电泳法和同工酶分析对东北松嫩草原西北部野古草种群克隆遗传变异性和种群遗传结构做了探讨。讨论了遗传多样性、地理距离和遗传距离之间的关系、大种群和小种群的遗传变异性和种群间的基因流 ;种群间 ,包括大种群和小种群间基因流、遗传和地理距离对遗传多样性的影响、昆虫和风传粉、种群籽苗的补充、遗传多样性的发生和保持 ,自交不亲和性和无性繁殖及体细胞突变     

Inferred Paternity and Male Reproductive Success in a Killer Whale (Orcinus orca) Population

We used data from 78 individuals at 26 microsatellite loci to infer parental and sibling relationships within a community of fish-eating ("resident") eastern North Pacific killer whales (Orcinus orca). Paternity analysis involving 15 mother/calf pairs and 8 potential fathers and whole-pedigree analysis of the entire sample produced consistent results. The variance in male reproductive success was greater than expected by chance and similar to that of other aquatic mammals. Although the number of confirmed paternities was small, reproductive success appeared to increase with male age and size. We found no evidence that males from outside this small population sired any of the sampled individuals. In contrast to previous results in a different population, many offspring were the result of matings within the same "pod" (long-term social group). Despite this pattern of breeding within social groups, we found no evidence of offspring produced by matings between close relatives, and the average internal relatedness of individuals was significantly less than expected if mating were random. The population's estimated effective size was <30 or about 1/3 of the current census size. Patterns of allele frequency variation were consistent with a population bottleneck.