QTL analysis of the photoperiodic response and clinal distribution of period alleles in Nasonia vitripennis

In seasonal environments, organisms synchronize their life cycle with the annual cycle of environmental factors. In many insect species, this includes a diapause response: a timed dormant stage that allows to survive harsh winter conditions. Previously, we have shown that larval diapause in the parasitic wasp Nasonia vitripennis is induced by the mother upon exposure to a threshold number of short photoperiods (named switch point) and diapause response follows a latitudinal cline in natural populations. Here, we present a QTL analysis using two lines derived from the extremes of this clinal distribution: a northern line from Oulu, Finland and a southern line from Corsica, France. A genomic region on chromosome 1 and one on chromosome 5 were found to be associated with photoperiodic diapause induction. Interestingly, these regions contain the putative clock genes period, cycle (chromosome 1) and cryptochrome (chromosome 5). An analysis of period polymorphisms in seven European populations showed a clinal distribution of two main haplotypes that correlate with the latitudinal cline for diapause induction.     

Footprints of selection in wild populations of Bicyclus anynana along a latitudinal cline

One of the major questions in ecology and evolutionary biology is how variation in the genome enables species to adapt to divergent environments. Here, we study footprints of thermal selection in candidate genes in six wild populations of the afrotropical butterfly Bicyclus anynana sampled along a c. 3000 km latitudinal cline. We sequenced coding regions of 31 selected genes with known functions in metabolism, pigment production, development and heat shock responses. These include genes for which we expect a priori a role in thermal adaptation and, thus, varying selection pressures along a latitudinal cline, and genes we do not expect to vary clinally and can be used as controls. We identified amino acid substitution polymorphisms in 13 genes and tested these for clinal variation by correlation analysis of allele frequencies with latitude. In addition, we used two F_ST‐based outlier methods to identify loci with higher population differentiation than expected under neutral evolution, while accounting for potentially confounding effects of population structure and demographic history. Two metabolic enzymes of the glycolytic pathway, UGP and Treh, showed clinal variation. The same loci showed elevated population differentiation and were identified as significant outliers. We found no evidence of clines in the pigmentation genes, heat shock proteins and developmental genes. However, we identified outlier loci in more localized parts of the range in the pigmentation genes yellow and black. We discuss that the observed clinal variation and elevated population divergence in UGP and Treh may reflect adaptation to a geographic thermal gradient.     

Genome‐wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America

Understanding the genetic underpinnings of adaptive change is a fundamental but largely unresolved problem in evolutionary biology. Drosophila melanogaster, an ancestrally tropical insect that has spread to temperate regions and become cosmopolitan, offers a powerful opportunity for identifying the molecular polymorphisms underlying clinal adaptation. Here, we use genome‐wide next‐generation sequencing of DNA pools (‘pool‐seq’) from three populations collected along the North American east coast to examine patterns of latitudinal differentiation. Comparing the genomes of these populations is particularly interesting since they exhibit clinal variation in a number of important life history traits. We find extensive latitudinal differentiation, with many of the most strongly differentiated genes involved in major functional pathways such as the insulin/TOR, ecdysone, torso, EGFR, TGFβ/BMP, JAK/STAT, immunity and circadian rhythm pathways. We observe particularly strong differentiation on chromosome 3R, especially within the cosmopolitan inversion In(3R)Payne, which contains a large number of clinally varying genes. While much of the differentiation might be driven by clinal differences in the frequency of In(3R)P, we also identify genes that are likely independent of this inversion. Our results provide genome‐wide evidence consistent with pervasive spatially variable selection acting on numerous loci and pathways along the well‐known North American cline, with many candidates implicated in life history regulation and exhibiting parallel differentiation along the previously investigated Australian cline.     

Adaptive latitudinal cline of photoperiodic diapause induction in the parasitoid Nasonia vitripennis in Europe

Living in seasonally changing environments requires adaptation to seasonal cycles. Many insects use the change in day length as a reliable cue for upcoming winter and respond to shortened photoperiod through diapause. In this study, we report the clinal variation in photoperiodic diapause induction in populations of the parasitoid wasp Nasonia vitripennis collected along a latitudinal gradient in Europe. In this species, diapause occurs in the larval stage and is maternally induced. Adult Nasonia females were exposed to different photoperiodic cycles and lifetime production of diapausing offspring was scored. Females switched to the production of diapausing offspring after exposure to a threshold number of photoperiodic cycles. A latitudinal cline was found in the proportion of diapausing offspring, the switch point for diapause induction measured as the maternal age at which the female starts to produce diapausing larvae, and the critical photoperiod for diapause induction. Populations at northern latitudes show an earlier switch point, higher proportions of diapausing individuals and longer critical photoperiods. Since the photoperiodic response was measured under the same laboratory conditions, the observed differences between populations most likely reflect genetic differences in sensitivity to photoperiodic cues, resulting from local adaptation to environmental cycles. The observed variability in diapause response combined with the availability of genomic tools for N. vitripennis represent a good opportunity to further investigate the genetic basis of this adaptive trait.     

Clinal variation in post‐winter male fertility retention; an adaptive overwintering strategy in Drosophila melanogaster

In insects including Drosophila melanogaster, females can overwinter at the adult stage by adopting a shallow reproductive diapause, but almost nothing is known about male reproductive diapause. In this study, we test for the maintenance of fertility in overwintering males from the eastern Australian D. melanogaster cline. Males from southern temperate populations maintained in field cages in temperate Melbourne had a higher fertility in spring compared with males from tropical locations. Temperate males successfully inseminated more females, and there were also more offspring produced per inseminated female. The resulting linear post‐winter fertility clines were unrelated to male body size. In contrast, there was no clinal variation for fertility in nonoverwintering males held in the laboratory. The cline in overwintering male fertility is likely to have evolved as an adaptive response to latitudinal climatic variation over the last 100 years.     

Explaining the sawtooth: latitudinal periodicity in a circadian gene correlates with shifts in generation number

Many temperate insects take advantage of longer growing seasons at lower latitudes by increasing their generation number or voltinism. In some insects, development time abruptly decreases when additional generations are fit into the season. Consequently, latitudinal ‘sawtooth’ clines associated with shifts in voltinism are seen for phenotypes correlated with development time, like body size. However, latitudinal variation in voltinism has not been linked to genetic variation at specific loci. Here, we show a pattern in allele frequency among voltinism ecotypes of the European corn borer moth (Ostrinia nubilalis) that is reminiscent of a sawtooth cline. We characterized 145 autosomal and sex‐linked SNPs and found that period, a circadian gene that is genetically linked to a major QTL determining variation in post‐diapause development time, shows cyclical variation between voltinism ecotypes. Allele frequencies at an unlinked circadian clock gene cryptochrome1 were correlated with period. These results suggest that selection on development time to ‘fit’ complete life cycles into a latitudinally varying growing season produces oscillations in alleles associated with voltinism, primarily through changes at loci underlying the duration of transitions between diapause and other life history phases. Correlations among clock loci suggest possible coupling between the circadian clock and the circannual rhythms for synchronizing seasonal life history. We anticipate that latitudinal oscillations in allele frequency will represent signatures of adaptation to seasonal environments in other insects and may be critical to understanding the ecological and evolutionary consequences of variable environments, including response to global climate change.     

Rapid seasonal adaptation of an alien bruchid after introduction: geographic variation in life cycle synchronization and critical photoperiod for diapause induction

Whether alien insects that are introduced into temperate regions adapt to seasonally changing environmental conditions is an important question in evolutionary biology. If rapid evolution has occurred in a non‐native environment, a latitudinal cline in critical photoperiod for diapause induction (i.e., the photoperiod at which half of the individuals enter diapause) and in life cycle synchronization with host plant phenology should be evident among locations. The alien bruchid Acanthoscelides pallidipennis (Motschulsky) (Coleoptera: Bruchidae) is native to North America and introduced into Japan with the host plant Amorpha fruticosa L. (Fabaceae) in the late 1940s. To examine whether seasonal adaptation has occurred in A. pallidipennis, we conducted a laboratory experiment and phenological observations using three latitudinally different populations. We bred F1 eggs at 22 °C and five photoperiodic regimens – L:D = 10:14, 13:11, 14:10, 15:9, or 16:8 hours – and examined whether diapause was induced. The estimated critical photoperiod for diapause induction was longest in the most northern population and shortest in the most southern population. Life cycle was found to be synchronized with host phenology in each location. Also voltinism varied geographically, from univoltine in the northern population to bivoltine in the southern populations. These results showed that A. pallidipennis rapidly adapted to seasonal environmental conditions in Japan after its introduction.     

Finding needles in a genomic haystack: targeted capture identifies clear signatures of selection in a nonmodel plant species

Teasing apart neutral and adaptive genomic processes and identifying loci that are targets of selection can be difficult, particularly for nonmodel species that lack a reference genome. However, identifying such loci and the factors driving selection have the potential to greatly assist conservation and restoration practices, especially for the management of species in the face of contemporary and future climate change. Here, we focus on assessing adaptive genomic variation within a nonmodel plant species, the narrow‐leaf hopbush (Dodonaea viscosa ssp. angustissima), commonly used for restoration in Australia. We used a hybrid‐capture target enrichment approach to selectively sequence 970 genes across 17 populations along a latitudinal gradient from 30°S to 36°S. We analysed 8462 single‐nucleotide polymorphisms (SNPs) for F_ST outliers as well as associations with environmental variables. Using three different methods, we found 55 SNPs with significant correlations to temperature and water availability, and 38 SNPs to elevation. Genes containing SNPs identified as under environmental selection were diverse, including aquaporin and abscisic acid genes, as well as genes with ontologies relating to responses to environmental stressors such as water deprivation and salt stress. Redundancy analysis demonstrated that only a small proportion of the total genetic variance was explained by environmental variables. We demonstrate that selection has led to clines in allele frequencies in a number of functional genes, including those linked to leaf shape and stomatal variation, which have been previously observed to vary along the sampled environmental cline. Using our approach, gene regions subject to environmental selection can be readily identified for nonmodel organisms.     

Bayesian estimation of genomic clines

We developed a Bayesian genomic cline model to study the genetic architecture of adaptive divergence and reproductive isolation between hybridizing lineages. This model quantifies locus‐specific patterns of introgression with two cline parameters that describe the probability of locus‐specific ancestry as a function of genome‐wide admixture. ‘Outlier’ loci with extreme patterns of introgression relative to most of the genome can be identified. These loci are potentially associated with adaptive divergence or reproductive isolation. We simulated genetic data for admixed populations that included neutral introgression, as well as loci that were subject to directional, epistatic or underdominant selection, and analysed these data using the Bayesian genomic cline model. Under many demographic conditions, underdominance or directional selection had detectable and predictable effects on cline parameters, and ‘outlier’ loci were greatly enriched for genetic regions affected by selection. We also analysed previously published genetic data from two transects through a hybrid zone between Mus domesticus and M. musculus. We found considerable variation in rates of introgression across the genome and particularly low rates of introgression for two X‐linked markers. There were similarities and differences in patterns of introgression between the two transects, which likely reflects a combination of stochastic variability because of genetic drift and geographic variation in the genetic architecture of reproductive isolation. By providing a robust framework to quantify and compare patterns of introgression among genetic regions and populations, the Bayesian genomic cline model will advance our understanding of the genetics of reproductive isolation and the speciation process.     

Photoperiod-dependent adult diapause within a geographical cline in the multivoltine bruchid Bruchidius dorsalis

Abstract The bruchid beetle Bruchidius dorsalis Fahraeus (Coleoptera: Bruchidae) has been known to undergo larval diapause during the final instar under short photoperiods ( Kurota & Shimada, 2001 ). This species has a multivoltine life cycle and the overwintering stages show a geographical variation across Japan ( Kurota & Shimada, 2002 ). In cooler areas, overwintering occurs during the final instar, whereas in warmer climates overwintering can occur during several developmental stages: non‐diapausing young instars, diapausing instars, and adults. In this study, we investigated the adult reproductive diapause in three populations from different geographical regions to clarify the role of geographical variation on overwintering strategies. We found that: (1) B. dorsalis entered reproductive diapause in addition to larval diapause under short photoperiods, (2) diapause propensity was higher and the critical photoperiod was longer in populations from cooler regions, and (3) the sensitive photoperiod range was the first 5 days after emergence. Predictions of the overwintering stage, derived from critical photoperiods, were consistent with actual overwintering stages observed in each population. The geographical variation in diapause induction is likely to reflect the adaptive overwintering strategy in each local environment.     

Latitudinal clines in alternative life histories in a geometrid moth

The relative roles of genetic differentiation and developmental plasticity in generating latitudinal gradients in life histories remain insufficiently understood. In particular, this applies to determination of voltinism (annual number of generations) in short‐lived ectotherms, and the associated trait values. We studied different components of variation in development of Chiasmia clathrata (Lepidoptera: Geometridae) larvae that originated from populations expressing univoltine, partially bivoltine or bivoltine phenology along a latitudinal gradient of season length. Indicative of population‐level genetic differentiation, larval period became longer while growth rate decreased with increasing season length within a particular phenology, but saw‐tooth clines emerged across the phenologies. Indicative of phenotypic plasticity, individuals that developed directly into reproductive adults had shorter development times and higher growth rates than those entering diapause. The most marked differences between the alternative developmental pathways were found in the bivoltine region suggesting that the adaptive correlates of the direct development evolve if exposed to selection. Pupal mass followed a complex cline without clear reference to the shift in voltinism or developmental pathway probably due to varying interplay between the responses in development time and growth rate. The results highlight the multidimensionality of evolutionary trajectories of life‐history traits, which either facilitate or constrain the evolution of integrated traits in alternative phenotypes.     

Natural hybridization in eastern-Mediterranean firs: The case of Abies borisii-regis

The genus Abies is represented in southern Balkans by A. alba, A. cephalonica, and A. borisii-regis. To infer the status of southern-Balkans firs, as well as the extent and patterns of introgression within this taxonomical complex, we analyzed genetic variation patterns of 29 indigenous fir populations in Bulgaria, Macedonia, Greece, and Calabria using a combination of maternally and biparentally inherited markers. Three mitochondrial lineages were observed, one comprising Calabrian populations and two distributed in the Balkans, coinciding with A. alba and A. cephalonica. The boundary between lineages is sharp; only two populations containing a mixture of haplotypes were found. Bayesian analysis of population structure based on seven nuclear microsatellite (nSSR) loci revealed the existence of two clusters whose proportions exhibited a latitudinal cline with a width of 2.3° ( ≈ 255 km). Populations in the center of the latitudinal cline exhibit the most symmetrical, the flattest, and the broadest distributions of cluster proportions within individual tree genomes. A neighbor-net network reflects the cline resulting from the Bayesian analysis. The observed variation patterns are not consistent with the hypothesis of A. borisii-regis as a monophyletic taxon or a stabilized hybridogenous species resulted from ancient hybridization; the taxon rather is a product of recent introgression.     

Life‐history traits related to diapause in univoltine and bivoltine populations of Ypthima multistriata (Lepidoptera: Satyridae) inhabiting similar latitudes

In most temperate insects, diapause strategies and voltinism generally exhibit latitudinal clines, supporting the concept that they represent adaptations to climate. In contrast, in the satyrine butterfly Ypthima multistriata Butler, local populations with different voltinism patterns are geographically intermingled, suggesting that life‐history traits related to diapause may differ even between geographically and phylogenetically close populations. In this study, we experimentally examined the critical photoperiod for diapause induction and the larval developmental period in two univoltine and two bivoltine populations of Y. multistriata, all of which inhabit virtually the same latitude (34.652–34.750°N). We found that the critical photoperiod for diapause induction was longer in the univoltine populations than in the bivoltine populations. Moreover, the larval period under the long day length treatment was different among populations in both sexes, although significant differences were also detected between populations with the same voltinism. These results indicate that in Y. multistriata, life‐history traits related to diapause can not be attributed merely to climatic conditions such as temperature or day length, which depend largely on latitude. Therefore, we suggest that biotic elements, such as leaf toughness, as well as abiotic elements should be taken into account in attempts to explain the enigmatic pattern of geographic variation in the diapause strategies of Y. multistriata.     

Genomic variation in cline shape across a hybrid zone

Hybrid zones are unique biological interfaces that reveal both population level and species level evolutionary processes. A genome‐scale approach to assess gene flow across hybrid zones is vital, and now possible. In Mexican towhees (genus Pipilo), several morphological hybrid gradients exist. We completed a genome survey across one such gradient (9 populations, 140 birds) using mitochondrial DNA, 28 isozyme, and 377 AFLP markers. To assess variation in introgression among loci, cline parameters (i.e., width, center) for the 61 clinally varying loci were estimated and compiled into genomic distributions for tests against three empirical models spanning the range of observed cline shape. No single model accounts for observed variation in cline shape among loci. Numerous backcross individuals near the gradient center confirm a hybrid origin for these populations, contrary to a previous hypothesis based on social mimicry and character displacement. In addition, the observed variation does not bin into well‐defined categories of locus types (e.g., neutral vs. highly selected). Our multi‐locus analysis reveals cross‐genomic variation in selective constraints on gene flow and locus‐specific flexibility in the permeability of the interspecies membrane.     

Geographic structure of genetic and phenotypic variation in the hybrid zone between Quercus affinis and Q. laurina in Mexico

Analyzing the structure of hybrid zones is important for inferring their origin, dynamics and evolutionary significance. We examined the geographic structure of phenotypic and genetic variation in the contact zone between two Mexican red oaks, Quercus affinis and Q. laurina. A total of 105 individuals from seven populations were sampled along a 600‐km latitudinal gradient representing the distribution area of the two species and their contact zone. Individuals were genotyped for nine nuclear and four chloroplast DNA microsatellite loci (ncSSR and cpSSR, respectively), and characterized for several leaf and acorn traits. The cpSSR data revealed extensive haplotype sharing among populations of the two species, while a Bayesian assignment analysis based on ncSSRs identified two main genetic groups, each corresponding to one of the species, and two populations in the contact zone showing evidence of admixture. The proportion of genetic ancestry in the populations was strongly associated with latitude and showed a pattern of variation with the shape of a narrow sigmoidal cline. The variation in three of the seven phenotypic traits was partially congruent with molecular variation, while the other traits did not conform to a geographic cline but instead were correlated with environmental variables. In conclusion, the hybrid zone between the two oak species has some of the characteristics of a tension zone, but heterogeneous variation across traits suggests differential introgression and the action of extrinsic selection.     

THREE SELECTIONS ARE BETTER THAN ONE: CLINAL VARIATION OF THERMAL QTL FROM INDEPENDENT SELECTION EXPERIMENTS IN DROSOPHILA

We report the results of two independent selection experiments that have exposed distinct populations of Drosophila melanogaster to different forms of thermal selection. A recombinant population derived from Arvin California and Zimbabwe isofemale lines was exposed to laboratory natural selection at two temperatures (T_AZ: 18°C and 28°C). Microsatellite mapping identified quantitative trait loci (QTL) on the X‐chromosome between the replicate “Hot” and “Cold” populations. In a separate experiment, disruptive selection was imposed on an outbred California population for the “knockdown” temperature (T_KD) in a thermal column. Microsatellite mapping of the “High” and “Low” populations also uncovered primarily X‐linked QTL. Notably, a marker in the shaggy locus at band 3A was significantly differentiated in both experiments. Finer scale mapping of the 3A region has narrowed the QTL to the shaggy gene region, which contains several candidate genes that function in circadian rhythms. The same allele that was increased in frequency in the High T_KD populations is significantly clinal in North America and is more common at the warm end of the cline (Florida vs. Maine; however, the cline was not apparent in Australia). Together, these studies show that independent selection experiments can uncover the same target of selection and that evolution in the laboratory can recapitulate putatively adaptive clinal variation in nature.     

Genetic differentiation in diapause response along a latitudinal cline in European yellow dung fly populations

Abstract.  1. Seasonality is a prime selective factor expected to result in local adaptation of life cycles and dormancy. Genetic differentiation in diapause response was investigated along a European latitudinal cline in the dung fly Scathophaga stercoraria (Diptera: Scathophagidae). Such differentiation may be mediated by additive or dominance genetic and/or maternal effects, which need to be distinguished.
2. Replicate sibships from five European populations (Lugano, Switzerland: 46.00°N; Zurich, Switzerland: 47.37°N; Oxford, U.K.: 51.75°N; Lund, Sweden: 55.70°N; Reykjavik, Iceland: 64.15°N) were raised in a common laboratory environment known to induce pupal winter diapause (12 °C and 12 h light), revealing a genetic latitudinal cline in both the proportion of individuals entering diapause and diapause duration in response to winter length estimated from weather data.
3. Populations from the extremes of the cline (Lugano and Reykjavik) were further reciprocally crossed to investigate the underlying genetics. This experiment revealed evidence for diapause induction at 12 °C being dominant (i.e. not merely additive) and clearly rejected maternal effects as the primary source of this between-population variation.     

Latitudinal clines in body size,but not in thermal tolerance or heat‐shock cognate 70 (HSC70), in the highly‐dispersing intertidal gastropod Littorina keenae (Gastropoda: Littorinidae)

Natural populations of widely‐distributed animals often exhibit clinal variation in phenotypic traits or in allele frequencies of a particular gene over their geographical range. A planktotrophic intertidal snail, Littorina keenae is broadly distributed along the north‐eastern Pacific coast through a large latitudinal range (24°50′N–43°18′N). We tested for latitudinal clines in two complex phenotypic traits – thermal tolerance and body size – and one single locus trait – heat shock cognate 70 (HSC70) – in L. keenae along almost its entire geographical range. We found only weak evidence for a latitudinal cline in the thermal tolerance and no evidence for a cline in allele frequencies at HSC70. However, as predicted by Bergmann's rule, we detected a strong latitudinal cline that accounted for 60% of the variance in body size (R² = 0.598; P < 0.001). In contrast, body size did not significantly affect thermal tolerance. HSC70 showed no genetic differentiation among the populations, supporting our previous mitochondrial gene‐based estimate of high gene flow during this snail's free‐swimming larval stage. Given that L. keenae experiences panmixia along its species range, the observed size cline may be partially or entirely caused by a phenotypically plastic response to local thermal environments rather than by genetic divergence in body size among populations in response to locally optimizing natural selection. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 494–505.     

Countergradient vs. cogradient variation in growth and diapause in a lichen‐feeding moth,Eilema depressum (Lepidoptera: Arctiidae)

Separating genetic and environmental causes of the latitudinal differences among populations is crucial when evaluating the potential for microevolutionary responses to the changing environment. We studied among‐population and environmental components of variation in several life‐history traits of a lichen‐feeding moth Eilema depressum when offspring of replicate Swiss and Finnish females were reared in a common‐garden factorial experiment. A partial second generation was produced only among Swiss larvae, more likely so at higher temperature regime and higher host quality, and more frequently among the offspring of particular females. Growth rates of larvae that chose the diapause development were higher in northern individuals. Our results thus reveal adaptive differences between latitudinal populations in studied life‐history traits, allowing to expect rapid adaptation of the species to further environmental changes. In contrast, invariable responses of the growth rates of the larvae to temperature and host quality support the idea that some basic parameters of insect growth show a high degree of evolutionary conservatism.     

Parapatric diversification after post-glacial range expansion in the gall fly Urophora cardui (Tephritidae)

Aim Primary and secondary genetic clines in post-glacial colonized regions have different implications for biogeographic distributions and the origin of species. Primary clines arise in situ after colonization as adaptive responses to environmental gradients, while secondary clines are caused by contact between vicariant lineages. Here we analyse primary versus secondary origin of a genetic cline in the tephritid fly Urophora cardui in Jutland, Denmark, in a post-glacial landscape. Location Western Palaearctic. Methods Phylogeographic and demographic analyses of U. cardui based on mitochondrial DNA (mtDNA) genealogies, hierarchical genetic variance tests based on allozymes and distribution analysis of a rare allele from the Jutland cline. Results There was no phylogeographic divergence between the Jutland population of U. cardui north of the cline and neighbouring western European regional populations, which all shared the common western European mtDNA haplotype H1. At nuclear loci, by contrast, the North Jutland population was diverged above the mean level of divergence among regional populations and had no loss of genetic variation. A rare allozyme allele that was frequent in the cline area (up to 45%) and was missing north of the cline also occurred at low frequency (0–14%) elsewhere in the sampling range. Shallow phylogeographic divergence was observed between Russian and western European populations and between English and continental populations. Main conclusions The genetic variation patterns support primary cline evolution and parapatric divergence in Jutland following a demographic expansion of a western European ancestral source population of U. cardui, and suggest cryptic refugia and/or selection in other European population assemblages. The patterns of intra-specific regional divergence are discussed with respect to the interpretation of cryptic refugia in Europe after the most recent ice age.