Distinguishing adaptive from nonadaptive genetic differentiation: comparison of Q(ST) and F(ST) at two spatial scales

Genetic differentiation in 20 hierarchically sampled populations of wild barley was analyzed with quantitative traits, allozymes and Random Amplified Polymorphic DNAs (RAPDs), and compared for three marker types at two hierarchical levels. Regional subdivision for both molecular markers was much lower than for quantitative traits. For both allozymes and RAPDs, most loci exhibited minor or no regional differentiation, and the relatively high overall estimates of the latter were due to several loci with exceptionally high regional differentiation. The allozyme- and RAPD-specific patterns of differentiation were concordant in general with one another, but not with quantitative trait differentiation. Divergent selection on quantitative traits inferred from very high regional Q(ST) was in full agreement with our previous results obtained from a test of local adaptation and multilevel selection analysis. In contrast, most variation in allozyme and RAPD variation was neutral, although several allozyme loci and RAPD markers were exceptional in their levels of regional differentiation. However, it is not possible to answer the question whether these exceptional loci are directly involved in the response to selection pressure or merely linked to the selected loci. The fact that Q(ST) and F(ST) did not differ at the population scale, that is, within regions, but differed at the regional scale, for which local adaptation has been previously shown, implies that comparison of the level of subdivision in quantitative traits, as compared with molecular markers, is indicative of adaptive population differentiation only when sampling is carried out at the appropriate scale.     

Q(ST) in a hierarchically structured population

Under some circumstances, selection and drift can be disentangled with comparisons of the Q(ST) of a quantitative trait and the F(ST) of putatively neutral loci. Most previous comparisons of F(ST) and Q(ST) are carried out at a single spatial scale. We derive a hierarchical Q(ST) appropriate for study across varying levels of spatial structure.     

Adaptive divergence in moor frog (Rana arvalis) populations along an acidification gradient: inferences from Q(st) -F(st) correlations

Microevolutionary responses to spatial variation in the environment seem ubiquitous, but the relative role of selection and neutral processes in driving phenotypic diversification remain often unknown. The moor frog (Rana arvalis) shows strong phenotypic divergence along an acidification gradient in Sweden. We here used correlations among population pairwise estimates of quantitative trait (P(ST) or Q(ST) from common garden estimates of embryonic acid tolerance and larval life-history traits) and neutral genetic divergence (F(ST) from neutral microsatellite markers), as well as environmental differences (pond pH, predator density, and latitude), to test whether this phenotypic divergence is more likely due to divergent selection or neutral processes. We found that trait divergence was more strongly correlated with environmental differences than the neutral marker divergence, suggesting that divergent natural selection has driven phenotypic divergence along the acidification gradient. Moreover, pairwise P(ST) s of embryonic acid tolerance and Q(ST) s of metamorphic size were strongly correlated with breeding pond pH, whereas pairwise Q(ST) s of larval period and growth rate were more strongly correlated with geographic distance/latitude and predator density, respectively. We suggest that incorporating measurements of environmental variation into Q(ST) -F(ST) studies can improve our inferential power about the agents of natural selection in natural populations.     

Patterns of genetic and taxonomic differentiation in three Melitaea (subg. Mellicta) species (Lepidoptera, Nymphalidae, Nymphalinae)

In conservation genetics the existence of Evolutionarily Significant Units (ESU) is a crucial question in threatened or vulnerable species. It is of particular concern to determine whether different subspecies or ecotypes of a species can be considered as separate ESUs. Some Melitaea subg. Mellicta species (e.g. Mellicta aurelia, Mellicta britomartis) are declining or scarce in Europe. Therefore, the level of genetic differentiation and pattern of genetic variation were surveyed in three Melitaea (subg. Mellicta) species. Their habitat requirements and food plants partly overlap; accordingly they often co-occur in the same habitat. M. britomartis and M. aurelia have one brood per year in Hungary, while Mellicta athalia has a monovoltine and a bivoltine ecotype. The purpose of the study was to estimate the number of genetically differentiated ESUs among these species in the Carpathian basin. Samples were taken from 5 Hungarian regions and a few samples were collected in Transylvania as well. Enzyme polymorphism was studied using polyacrylamide gel electrophoresis. The structure of genetic variation was analysed by F-statistics, AMOVA, PCA and Bayesian clustering method. UPGMA dendrogram was constructed on the basis of Cavalli-Sforza and Edwards chord distances. The three species are clearly differentiated from each other in all statistical analyses. They are evidently different Evolutionary Significant Units. The two ecotypes of M. athalia, however, do not show any genetic differentiation.     

A genetic polymorphism maintained by natural selection in a temporally varying environment

ABSTRACT Environments that are crowded with larvae of the fruit fly, Drosophila melanogaster, exhibit a temporal deterioration in quality as waste products accumulate and food is depleted. We show that natural selection in these environments can maintain a genetic polymorphism with one group of genotypes specializing on the early part of the environment and a second group specializing on the late part. These specializations involve trade-offs in fitness components. The early types emerge first from crowded cultures and have high larval feeding rates, which are positively correlated with competitive ability but exhibit lower absolute viability than the late phenotype, especially in food contaminated with the nitrogenous waste product, ammonia. The late emerging types have reduced feeding rates but higher absolute survival under conditions of severe crowding and high levels of ammonia. Organisms that experience temporal variation within a single generation are not uncommon, and this model system provides some of the first insights into the evolutionary forces at work in these environments.     

Low genetic diversity but local genetic differentiation in endemic Minasia (Asteraceae) species from Brazil

Espinhaço Range is a Brazilian chain of mountains, extremely rich in endemic species. Minasia has six species, all perennial herbs endemic to this range. Twenty-two populations were sampled from all Minasia species and assayed for allozyme variation. The species showed low genetic variation, compatible with the expectation for endemics. Genetic identities in Serra do Cipó and Diamantina were high, even between populations of different species. On the other hand M. cabralensis, from Serra do Cabral, was more differentiated from the other species. We also observed a marked genetic differentiation within M. cabralensis. Most strikingly, two close populations of this species showed very different allele frequencies. Our findings highlight the importance of local differentiation in campos rupestres. The observed genetic structure indicates that substantial portions of genetic diversity could be lost with the extinction of only one population, which is especially threatening considering the already low genetic diversity.     

Slow genital and genetic but rapid non-genital and ecological differentiation in a pair of spider species (Araneae,Pholcidae)

Like most animals with internal fertilization, spiders tend to have species-specific genitalia, allowing closely related species to be identified by their reproductive morphology more easily than by non-genital characters. This implies that genitalia evolve on average more rapidly than non-genital morphological traits. Here we describe two putative species of Pholcidae from Taiwan (Pholcus pingtung, n. sp.; Pholcus chengpoi, n. sp.) that differ conspicuously in their microhabitat (rocks vs. leaves), coloration, color pattern, and body proportions, but have almost indistinguishable genitalia and cytochrome oxidase I (co1) sequences. The two species have identical yet highly unusual male cheliceral modifications, strongly arguing for sister species. Despite the almost identical genitalia and co1 sequences, we treat the two ‘morphs’ as species for three reasons: (1) they are easily distinguished by several characters; no intermediate specimens were found; (2) subtle yet consistent differences in genital (uncus) shape support the idea of reproductively isolated entities beyond the more conspicuous non-genital differences; (3) each locality provided both types of microhabitat but only one of the two species, arguing against environmental plasticity or polymorphism. We conclude that probably a very recent expansion into a novel microhabitat has led to speciation and rapid ecological and non-genital differentiation, with insufficient time to accumulate significant genital and genetic differences.     

Herbivory and local genetic differentiation in natural populations of Arabidopsis thaliana (Brassicaceae)

To explore genetic variation in defence against the natural herbivores of Arabidopsis thaliana, we transplanted genotypes between a dune habitat and inland habitat in both of which A. thaliana occurred naturally. In previous years we had observed that the specialist weevils Ceutorhynchus atomus and C. contractus (Curculionidae) fed conspicuously on flowers and fruits of A. thaliana in the dunes, while these weevils were always rare in inland habitats. Taking all plants together, total fruit damage was indeed much higher in our experimental plots in the dune habitat (59.7%) relative to the inland garden habitat (18.9%). Within a habitat, additional differences existed between plants of different origins, pointing to genetic differences in ecologically relevant characters; plants of inland origin flowered a week earlier, grew better and produced more fruits than plants of dune origin. However, plants of inland origin experienced more total fruit damage by the specialist weevils (75.4%) than plants of dune origin (44.0%) when the two types grew side by side in the dune habitat. Escape from herbivory gives dune genotypes an advantage in their native habitat, whereas stronger growth and higher survival gives inland genotypes an edge under garden conditions.     

Pattern of genetic differentiation in the Maculinea alcon species group (Lepidoptera, Lycaenidae) in Central Europe

The taxonomic status of Alcon Blues living in Central and Western Europe (conventionally: Maculinea alcon and Maculinea rebeli ) is quite confused. Some authors distinguish them as separate species of the M. alcon species group, while others consider them as subspecies or simply ecological forms. Our aim was to study the pattern of genetic differentiation among several populations of these taxa with reference to their taxonomic position. Imagoes were collected from 27 localities in Central Europe between 1999 and 2003. Samples originated from four regions: northern Hungary, central Hungary, Romania: Transylvania and Slovenia. Enzyme polymorphism was analysed using polyacrylamide gel electrophoresis. In all samples 16 enzyme loci were studied. In the analysis of the data, F -statistics was computed and the total genetic variation was partitioned into within and between population components. Nei's genetic distances were calculated and UPGMA dendrogram was constructed on the basis of the distance matrix. Hierarchical F -statistics and amova was computed to study the pattern of genetic differentiation among the samples. Principal component analysis (PCA) was also carried out using the allele frequencies of the samples. The results of all analyses indicated a high level of differentiation among the samples. The differences among the samples collected in different years from the same population accounted for a considerable amount of the between sample variation. The distribution of the between sample variation did not exhibit a species pattern. The results of amova and PCA indicated that the geographic pattern was slightly more expressed in the between sample variation compared with the species pattern of it. These results seem to contradict with the conventional taxonomical subdivision.     

Molecular, morphological, and ecological niche differentiation of sympatric sister oak species, Quercus virginiana and Q. geminata (Fagaceae)

The genus Quercus (the oaks) is notorious for interspecific hybrization, generating questions about the mechanisms that permit coexistence of closely related species. Two sister oak species, Quercus virginiana and Q. geminata, occur in sympatry in Florida and throughout the southeastern United States. In 11 sites from northern and southeastern regions of Florida, we used a leaf-based morphological index to identify individuals to species. Eleven nuclear microsatellite markers significantly differentiated between the species with a high correspondence between molecular and morphological typing of specimens. Nevertheless, Bayesian clustering analysis indicates interspecific gene flow, and six of 109 individuals had mixed ancestry. The identity of several individuals also was mismatched using molecular markers and morphological characters. In a common environment, the two species performed differently in terms of photosynthetic performance and growth, corresponding to their divergent ecological niches with respect to soil moisture and other edaphic properties. Our data support earlier hypotheses that divergence in flowering time causes assortative mating, allowing these ecologically distinct sister species to occur in sympatry. Limited gene flow that permits ecological differentiation helps to explain the overdispersion of oak species in local communities.     

Population differentiation in a purported ring species,Acacia karroo (Mimosoideae)

Acacia karroo Hayne (Mimosoideae; Fabaceae) is a highly polymorphic species, ranging in height from 1 m to more than 30 m, and with enormous variation in the architecture of adults. Some populations of A. karroo with different morphologies are situated less than 20 km apart. This species has been considered to be a ring species on the basis of allozyme variation. I wished to determine whether this was supported by sapling morphology, and by chemical and physical defences to herbivory. I raised four phenotypes from the restricted area of Zululand (South Africa) in a common garden with controls, and with water and nutrient supplementation. I found that each of the four phenotypes maintained their differences in spite of nutrient and water supplementation. There was no significant genotype by environment interaction. I also found that the coastal population was significantly larger than another phenotype that grows just 12 km inland from it, suggesting that there might be local adaptation of these genotypes to particular soil types. I confirm that A. karroo maintains morphological differentiation even when there is substantial alteration of water and nutrient availability. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 748–755.     

Biflavonoid differentiation in sixBartramia species (Bartramiaceae,Musci)

The occurrence of eight biflavones belonging to the biluteolin series, the apigenin-luteolin series and the 2,3-dihydro-biluteolin series, and one monomeric flavone with an acid group, was investigated in six taxa ofBartramia with emphasis on sect.Ithyphyllae. The variation of biflavone profiles contributes to the characterization of theBartramia species studied; substitution patterns signalize relevance also on the sectional level. Based upon the flavonoid composition,Bartramia afro-ithyphylla is suggested to be transferred from sect.Ithyphyllae to sect.Bartramia of the genusBartramia.     

Deep genetic differentiation between two morphologically similar species of wolf herrings (Teleostei,Clupeoidei, Chirocentridae)

Wolf herrings (Chirocentridae; Clupeoidei) are commonly found in local fish markets throughout the Indo‐West Pacific region where they constitute an auxiliary source of food and income for local communities. The validity of the two species of wolf herrings, Chirocentrus dorab Forsskål, 1775 and C. nudus Swainon, 1839, is only supported by slight morphological differences. The identification of either species is challenging, especially for juveniles, and precludes accurate assessments of these natural resources at a species level. As a step towards gaining better knowledge of the genetic structure of these fishes, we examined genetic differentiation between these two species by reconstructing their entire mitogenomic sequences using high‐throughput sequencing technology. We found that the mitogenome of each species shared the same gene content and order that were the same for those found in most other teleost fishes. Despite their high morphological similarity, these two species of Chirocentrus were genetically well differentiated (p‐distance = 16.3% at their cytochrome oxidase I). A mitogenomic time‐calibrated phylogenetic analysis showed that wolf herrings originated about 35 million years ago, and they represent a case of morphological stasis. Furthermore, comparison of published and newly determined mitochondrial COI barcode region sequences from 22 individuals revealed species‐level cryptic genetic diversity within C. dorab. Altogether, these mitochondrial data are effective in discriminating species within this genus and informing population genetic relationships within species of wolf herrings.     

A study of Y-chromosome microsatellite variation in sub-Saharan Africa: a comparison between F(ST) and R(ST) genetic distances

Seven Y-chromosome microsatellite loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393) were analyzed in three populations from sub-Saharan Africa: the Bamileke and Ewondo populations from Cameroon and the Hutu from Rwanda. Complete typing was obtained for 112 individuals, and a total of 53 different haplotypes was observed. The single-locus gene diversity, averaged across populations, ranges from 0.100 for the DYS392 locus to 0.610 for the DYS389I locus. The haplotype diversity ranges from 0.832 (Ewondo) to 0.965 (Hutu), with an intermediate value of 0.918 in the Bamileke. The diversity among Bamileke, Ewondo, Hutu, and other sub-Saharan populations selected from the literature was analyzed using both a classical (F(ST)) and a stepwise-based (R(ST)) genetic distance method. The pattern of interpopulational diversity based on F(ST) was congruent with anthropological knowledge, while that based on R(ST) revealed unexpected and unconvincing population affinities. From a practical point of view, our study indicates that Y-chromosome microsatellite data may provide useful information for analyses of interpopulational diversity among sub-Saharan populations if an adequate number of loci and individuals along with an appropriate genetic distance method are used. On a theoretical ground, we propose that the lesser performance of R(ST) compared to F(ST) could be explained by the important role played by genetic drift in shaping the relationships among examined populations.     

High genetic diversity vs. low genetic differentiation in Nouelia insignis (Asteraceae), a narrowly distributed and endemic species in China, revealed by ISSR fingerprinting

BACKGROUND AND AIMS: Nouelia insignis Franch., a monotypic genus of the Asteraceae, is an endangered species endemic in Yunnan and Sichuan Provinces of China. Most of the populations are seriously threatened. Some of them are even at the brink of extinction. In this study, the genetic diversity and differentiation between populations of this species were examined in two drainage areas. METHODS: DNA fingerprinting based on inter-simple sequence repeat polymorphisms was employed to detect the genetic variation and population structure in the species. KEY RESULTS: Genetic diversity at species level was high with P=65.05% (percentage of polymorphic loci) and Ht=0.2248 (total genetic diversity). The coefficient of genetic differentiation among populations, Gst, which was estimated by partitioning the total gene diversity, was 0.2529; whereas, the genetic differentiation between populations in the Jinsha and Nanpan drainage areas was unexpectedly low (Gst=0.0702). CONCLUSIONS: Based on the genetic analyses of the DNA fingerprinting, recent habitat fragmentation may not have led to genetic differentiation or the loss of genetic diversity in the rare species. Spatial apportionment of fingerprinting polymorphisms provides a footprint of historical migration across geographical barriers. The high diversity detected in this study holds promise for conservation and restoration efforts to save the endangered species from extinction.     

Adaptive radiation and genetic differentiation in the woodySonchus alliance (Asteraceae:Sonchinae) in the Canary Islands

The woodySonchus alliance consists of 19 species ofSonchus subg.Dendrosonchus, one species ofSonchus subg.Sonchus and species of five genera (i.e.Babcockia, Sventenia, Taeckholmia, Lactucosonchus, Prenanthes), and is restricted primarily to the archipelago of the Canaries in the Macaronesian phytogeographical region. An enzyme electrophoretic study, including 13 loci, was conducted to assess genetic diversity within and divergence among species of the alliance. Nei's genetic identities (distances) between genera and/or subgenera range from 0.490 (0.714) to 0.980 (0.013), and pairwise comparisons of all populations show relatively high genetic identities, with a mean of 0.804. The high identities further support the genetic cohesiveness of the alliance and its single origin on the Macaronesian islands. Species in the alliance also show about 50%; higher total genetic diversity (H_T) than the mean for other oceanic endemics. There is greater divergence between endemics or species on older islands compared to those on younger islands, which suggests that time is a factor for divergence at allozyme loci. Furthermore, populations on older islands have higher total genetic diversities and lower identities than conspecific populations on younger islands. These results imply early colonization, radiation, and divergence of the woodySonchus alliance on older islands followed by subsequent colonization to younger islands. The taxonomic distribution of alleles in the alliance indicates lineage sorting also played a role in divergence among species. Lineage sorting may also produce nonconcordance with either taxonomic designation or the pattern of variation obtained from other molecular markers such as ITS sequences of nrDNA. Timing for the origin and radiation of the alliance agrees with the estimate based on ITS sequences, and suggests that the early divergence and rapid radiation took place during the Late Tertiary on either Gran Canaria or Tenerife.     

Adaptive divergence within and between ecotypes of the terrestrial garter snake, Thamnophis elegans, assessed with F(ST)-Q(ST) comparisons

Populations of the terrestrial garter snake (Thamnophis elegans) around Eagle Lake in California exhibit dramatic ecotypic differentiation in life history, colouration and morphology across distances as small as a few kilometres. We assayed the role of selection in ecotypic differentiation in T. elegans using F(ST)-Q(ST) analysis and identified selective agents using direct and indirect observations. We extended the conventional implementation of the F(ST)-Q(ST) approach by using three-level analyses of genetic and phenotypic variance to assess the role of selection in differentiating populations both within and between ecotypes. These results suggest that selection has driven differentiation between as well as within ecotypes, and in the presence of moderate to high gene flow. Our findings are discussed in the context of previous correlational selection analyses which revealed stabilizing and correlational selection for some of the traits examined.     

Isozymes in macroalgae (seaweeds): genetic differentiation,genetic variability and applications in systematics

Use of isozymes (including allozymes) in studies of population genetics and systematics of seaweeds has increased sufficiently in the last decade to allow some generalization. Only a single locus has been observed for about half the enzymes analysed in seaweeds, compared with 29% in vascular plants. Compared with higher plants, macroalgal species generally have low amounts of electrophoretically detectable genetic variation; the lowest levels of genetic variation found in natural populations are those reported for seaweeds. Nonetheless, seaweeds show an association between levels of genetic diversity as revealed by isozymes and species-specific attributes, such as mating system and predominance of asexual versus sexual reproduction. In systematic studies, isozymes have revealed cryptic species and identified pairs of sibling taxa. The quaternary structure of enzymes appears to be conserved at the phylum level. With the current availability of improved techniques for enzyme electrophoresis and for data interpretation, we expect future studies utilizing isozyme electrophoresis to provide further insight into population and evolutionary processes in seaweeds.     

Extreme genetic depauperation and differentiation of both populations and species in Eurasian feather grasses (Stipa)

A highly selfing breeding system affects gene flow, which may have consequences for patterns of genetic variation and differentiation on both the population and species level. Feather grasses (Stipa spp.) are dominant elements of Eurasian steppes that persist in Central Europe in scattered isolated populations that are of great conservation interest. Cleistogamy is common in the Stipa pennata group, the phylogeny of which is largely unresolved. Intraspecific patterns of genetic variation can be characterised by lack of gene flow due to selfing, but also by large-scale historical migrations and long-term isolation. We analysed both 5 species within the S. pennata group and 33 populations of Stipa pulcherrima sampled across a large part of its range. Using AFLP markers we assessed phylogenetic relationships of the S. pennata group and patterns of genetic variation within and among populations. The S. pennata group formed a consistent clade separated from S. capillata. Stipa pulcherrima was sister to S. eriocaulis, but the relationships among S. pennata s. str., S. borysthenica., and S. tirsa remained unresolved. Within-population genetic variation was extremely low in all species of the S. pennata group (H _e = 0.0–0.013). In S. pulcherrima, genetic variation was consistently relatively high in the east (Romania, Russia) and declined toward western populations, with many populations at the western range edge lacking genetic variation entirely. Populations were strongly differentiated (F _ST = 0.762), and this differentiation did not follow a classical pattern of isolation by distance. Bayesian cluster analysis revealed nine gene pools in S. pulcherrima, which were mostly geographically clustered. Overall the results suggest that S. pulcherrima and species of the S. pennata group are characterised by a cleistogamous breeding system leading to extremely low levels of genetic variation and high levels of population differentiation at both the population and species level. Postglacial colonisation, current population isolation, and population bottlenecks at the western range periphery have further reduced genetic variation and obviated gene exchange. Thus, genetic variation can only be preserved by the conservation of multiple populations.