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opencc-zeroJan 2021View details →

Data from: Evidence for spatial clines and mixed geographic modes of speciation for North American cherry-infesting Rhagoletis (Diptera:Tephritidae) flies

An important criterion for understanding speciation is the geographic context of population divergence. Three major modes of allopatric, parapatric, and sympatric speciation define the extent of spatial overlap and gene flow between diverging populations. However, mixed modes of speciation are also possible, whereby populations experience periods of allopatry, parapatry, and/or sympatry at different times as they diverge. Here, we report clinal patterns of variation for 21 nuclear-encoded microsatellites and a wing spot phenotype for cherry-infesting Rhagoletis (Diptera: Tephritidae) across North America consistent with these flies having initially diverged in parapatry followed by a period of allopatric differentiation in the early Holocene. However, mitochondrial DNA (mtDNA) displays a different pattern; cherry flies at the ends of the clines in the eastern USA and Pacific Northwest share identical haplotypes, while centrally located populations in the southwestern USA and Mexico possess a different haplotype. We hypothesize that the mitochondrial difference could be due to lineage sorting but more likely reflects a selective sweep of a favorable mtDNA variant or the spread of an endosymbiont. The estimated divergence time for mtDNA suggests possible past allopatry, secondary contact, and subsequent isolation between USA and Mexican fly populations initiated before the Wisconsin glaciation. Thus, the current genetics of cherry flies may involve different mixed modes of divergence occurring in different portions of the fly's range. We discuss the need for additional DNA sequencing and quantification of prezygotic and postzygotic reproductive isolation to verify the multiple mixed mode hypothesis for cherry flies, and draw parallels from other systems to assess the generality that speciation may commonly involve complex biogeographies of varying combinations of allopatric, parapatric, and sympatric divergence.

opencc-zeroDec 2015View details →

Data from: Anatomy of a cline: dissecting anti-predatory adaptations in a marine gastropod along the U.S. Atlantic coast

The scope of anti-predatory adaptation is expected to be greater in warm than in cold environments. High temperatures lower the costs associated with the production and maintenance of energetically expensive traits and enable ecological interactions to intensify. We tested this hypothesis by characterizing the expression of anti-predatory morphology within a marine gastropod species (the knobbed whelk, Busycon carica) over a large (>1,400 km) geographic area that spans more than 10°C annual temperature variation. We also conducted experimental predation studies with a powerful durophagous predator, the stone crab (Menippe), to verify the anti-predatory advantages of a heavily ornamented shell morphology (e.g., increased thickness, pronounced spines), and we used repair scar data to assess clinal variation in selective pressure from predators. We predicted that repair scar rates would be greatest in warm southernmost latitudes, and that expression of energetically costly anti-predatory morphology would peak in concert with elevated predation pressures. Experiments confirmed that whelks with energetically costly, heavily ornamented shells had higher survivorship rates than those with weakly ornamented shells. As predicted, we also found that the expression of anti-predatory traits was greatest in the southern part of B. carica's range. After standardizing shells for size, shape, and exposure time to enemies, repair scar rates also peaked to the south. Taken together, these results suggest that the expression of anti-predatory traits along the geographic cline is governed by the interaction of two selective factors: temperature and predation, with the former acting as the ultimate control on the scope of adaptation both by escalating predation pressure in the southern part of B. carica's range and by physically limiting (to the north) and facilitating (to the south) the production of anti-predatory traits. Feedbacks between temperature and predation thus causally interact to enable and drive, respectively, the observed geographic cline in energy-intensive anti-predatory shell traits.

opencc-zeroJul 2019View details →

Data from: SNPs reveal a genetic cline across the northeast Atlantic and enable powerful population assignment in the European lobster

Resolving stock structure is crucial for fisheries conservation to ensure that the spatial implementation of management is commensurate with that of biological population units. To address this in the economically important European lobster (Homarus gammarus), genetic structure was explored across the species' range using a small panel of single nucleotide polymorphisms (SNPs) previously isolated from restriction-site associated DNA sequencing; these SNPs were selected to maximise differentiation at a range of both broad- and fine-scales. After quality control and filtering, 1,278 lobsters from 38 sampling sites were genotyped at 79 SNPs. The results revealed a pronounced phylogeographic break between the Atlantic and Mediterranean basins, while structure within the Mediterranean was also apparent, partitioned between lobsters from the central Mediterranean and the Aegean Sea. In addition, a genetic cline across the northeast Atlantic was revealed using both putatively neutral and outlier SNPs, but the precise driver(s) of this clinal pattern –isolation-by-distance, secondary contact, selection across an environmental gradient, or a combination of these factors– remains undetermined. Putatively neutral markers differentiated lobsters from Oosterschelde, an estuary on the Dutch coast, a finding likely explained by past bottlenecks and limited gene flow with adjacent North Sea populations. Building on the findings of our spatial genetic analysis, we were able to test the accuracy of assigning lobsters at various spatial scales, including to basin of origin (Atlantic or Mediterranean), region of origin and sampling location. The predictive model assembled using 79 SNPs correctly assigned 99.7 % of lobsters not used to build the model to their basin of origin, but accuracy decreased to region of origin and again to sampling location. These results are of direct relevance to managers of lobster fisheries and hatcheries, and provide the basis for a genetic tool for tracing the origin of European lobsters in the food supply chain.

opencc-zeroApr 2020View details →

Contribution of genetic versus plastic responses to adaptive patterns in a widespread butterfly along a latitudinal cline

Understanding how organisms adapt to complex environments is a central goal of evolutionary biology and ecology. This issue is of special interest in the current era of rapidly changing climatic conditions. Here, we investigate clinal variation and plastic responses in life history, morphology, and physiology in the butterfly Pieris napi along a pan-European gradient by exposing butterflies raised in captivity to different temperatures. We found clinal variation in body size, growth rates and concomitant development time, wing aspect ratio, wing melanisation, and heat tolerance. Individuals from warmer environments were more heat-tolerant, had less melanised wings and a shorter development but still they were larger than individuals from cooler environments. These findings suggest selection for rapid growth in the warmth and for wing melanisation in the cold, and thus fine-tuned genetic adaptation to local climates. Irrespective of the origin of butterflies, the effects of higher developmental temperature were largely as expected, speeding up development, reducing body size, potential metabolic activity, and wing melanisation, while increasing heat tolerance. At least in part, these patterns likely reflect adaptive phenotypic plasticity. In summary, our study revealed pronounced plastic and genetic responses, which may indicate high adaptive capacities in our study organism. Whether this may help such species though to deal with current climate change needs further investigation, as clinal patterns have typically evolved over long periods.

opencc-zeroDec 2015View details →

Data from: Persistence of a Wolbachia infection frequency cline in Drosophila melanogaster and the possible role of reproductive dormancy

Field populations of arthropods are often polymorphic for Wolbachia but the factors maintaining intermediate Wolbachia frequencies are generally not understood. In Drosophila melanogaster, Wolbachia frequencies are highly variable across the globe. We document the persistence of a Wolbachia infection frequency cline in D. melanogaster populations from eastern Australia across at least 20 years, with frequencies generally high in the tropics but lower in cool temperate regions. The results are interpreted using a model of frequency dynamics incorporating cytoplasmic incompatibility, imperfect maternal transmission and Wolbachia effects on fitness. Clinal variation is less pronounced in eastern North America which may reflect annual recolonization at higher latitudes. Limited samples from Africa from latitudes matching our tropical and subtropical samples from Australia and North America show comparably high infection frequencies, but some equatorial samples show lower frequencies. Adult dormancy across cold periods may contribute to the Australian Wolbachia cline. Infected flies exposed to cold conditions for an extended period had reduced fecundity and viability, an effect not evident in unexposed controls. These fitness costs may contribute to the relatively low Wolbachia frequencies in Australian temperate areas; whereas different processes, including cytoplasmic incompatibility induced by young males, may contribute to higher frequencies in tropical locations.

opencc-zeroDec 2013View details →

Data from: Speciation in Western Scrub-Jays, Haldane's rule, and genetic clines in secondary contact

Background: Haldane's Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior lineages of Western Scrub-Jays (Aphelocoma californica) to test for a signature of Haldane's Rule: a narrower cline of introgression in mtDNA compared to nuclear markers. Results: Our initial phylogeographic analysis revealed that there is only one major area of contact between coastal and interior lineages and identified five genetic clusters with strong spatial structuring: Pacific Slope, Interior US, Edwards Plateau (Texas), Northern Mexico, and Southern Mexico. Consistent with predictions from Haldane's Rule, mtDNA showed a narrower cline than nuclear markers across a transect through the hybrid zone. This result is not being driven by female-biased dispersal because neutral diffusion analysis, which included estimates of sex-specific dispersal rates, also showed less diffusion of mtDNA. Lineage-specific plumage traits were associated with nuclear genetic profiles for individuals in the hybrid zone, indicating that these differences are under genetic control. Conclusions: This study adds to a growing list of studies that support predictions of Haldane's Rule using cline analysis of multiple loci of differing inheritance modes, although alternate hypotheses like selection on different mtDNA types cannot be ruled out. That Haldane's Rule appears to be operating in this system suggests a measure of reproductive isolation between the Pacific Slope and interior lineages. Based on a variety of evidence from the phenotype, ecology, and genetics, we recommend elevating three lineages to species level: A. californica (Pacific Slope); A. woodhouseii (Interior US plus Edwards Plateau plus Northern Mexico); A. sumicrasti (Southern Mexico). The distinctive Edwards Plateau population in Texas, which was monophyletic in mtDNA except for one individual, should be studied in greater detail given habitat threat.

opencc-zeroDec 2013View details →

Data from: Evidence of genetic change in the flowering phenology of sea beets along a latitudinal cline within two decades

Sea beets grown from seeds collected in 1989 and 2009 along the coasts of France and adjacent regions were compared for flowering date under controlled conditions. Seeds from both collection years were sown simultaneously and cultivated under the same glasshouse conditions. Date of flowering onset and year of first flowering were recorded. There was an overall northward shift in flowering time of about 0.35° latitude (i.e. 39 km) over the 20 year period. The southern portion of the latitudinal gradient — i.e. from 44.7°N to 47.28°N — flowered significantly later by a mean of 1.78 days, equivalent to a 43.2 km northward shift of phenotypes. In the northern latitudes between 48.6°N and 52°N, flowering date was significantly earlier by a mean of 4.04 days, corresponding to a mean northward shift of 104.9 km, and this shift was apparently due to a diminished requirement of exposure to cold temperatures (i.e. vernalization), for which we found direct and indirect evidence. As all plants were grown from seed under identical conditions, we conclude that genetic changes occurred in the sensitivity to environmental cues that mediate the onset of flowering in both the northern and the southern latitudes of the gradient. Microevolution and gene flow may have contributed to this change. There was no significant change in the frequency of plants that flowered without vernalization. The lack of vernalization requirement may be associated with environmental instability rather than with climate conditions.

opencc-zeroDec 2013View details →

Data from: Morphological clines and weak drift along an urbanization gradient in the butterfly, Pieris rapae

Urban areas are increasing globally, providing opportunities for biodiversity researchers to study the process in which species become established in novel, highly disturbed habitats. This ecological process can be understood through analyses of morphological and genetic variation, which can shed light on patterns of neutral and adaptive evolution. Previous studies have shown that urban populations often diverge genetically from non-urban source populations. This could occur due to neutral genetic drift, but an alternative is that selection could lead to allele frequency changes in urban populations. The development of genome scan methods provides an opportunity to investigate these outcomes from samples of genetic variation taken along an urbanization gradient. Here we examine morphological variation in wing size and diversity at neutral amplified fragment length polymorphisms in the butterfly Pieris rapae L. (Lepidoptera, Pieridae) sampled from the center to the periphery of Marseille. We utilize established and novel environmental correlation approaches to scan genetic variation for evidence of selection. We find significant morphological differences in urban populations, as well as weak genetic structure and decreased genetic diversity in urban versus non-urban sites. However, environmental correlation tests provide little support for selection in our dataset. Our comparison of different methods and allele frequency clines suggests that loci identified as significant are false positives. Although there is some indication that selection may be acting on wing size in urban butterflies, genetic analyses suggest P. rapae are undergoing neutral drift.

Data from: Altitudinal clinal variation in wing form in African Drosophila melanogaster: one cline or many?

Geographical patterns of morphological variation have been useful in addressing hypotheses about environmental adaptation. In particular, latitudinal clines in phenotypes have been studied in a number of Drosophila species. Some environmental conditions along latitudinal clines—for example, temperature—also vary along altitudinal clines, but these have been studied infrequently and it remains unclear whether these environmental factors are similar enough for convergence or parallel evolution. Most clinal studies in Drosophila have dealt exclusively with univariate phenotypes, allowing for the detection of clinal relationships, but not for estimating the directions of covariation between them. We measured variation in wing shape and size in D. melanogaster derived from populations at varying altitudes and latitudes across sub-Saharan Africa. Geometric morphometrics allows us to compare shape changes associated with latitude and altitude, and manipulating rearing temperature allows us to quantify the extent to which thermal plasticity recapitulates clinal effects. Comparing effect vectors demonstrates that altitude, latitude, and temperature are only partly associated, and that the altitudinal shape effect may differ between Eastern and Western Africa. Our results suggest that selection responsible for these phenotypic clines may be more complex than just thermal adaptation.

Data from: Geographic clines in wing morphology relate to colonization history in New World but not Old World populations of yellow dung flies

Geographic clines offer insights about putative targets and agents of natural selection as well as tempo and mode of adaptation. However, demographic processes can lead to clines that are indistinguishable from adaptive divergence. Using the widespread yellow dung fly Scathophaga stercoraria (Diptera: Scathophagidae), we examine quantitative genetic differentiation (QST) of wing shape across North America, Europe and Japan, and compare this differentiation with that of ten microsatellites (FST). Morphometric analyses of 28 populations reared at three temperatures revealed significant thermal plasticity, sexual dimorphism and geographic differentiation in wing shape. In North America morphological differentiation followed the decline in microsatellite variability along the presumed route of recent colonization from the southeast to the northwest. Across Europe, where S. stercoraria presumably existed for much longer time and where no molecular pattern of isolation by distance was evident, clinal variation was less pronounced despite significant morphological differentiation (QST>FST). Shape vector comparisons further indicate that thermal plasticity (hot-to-cold) does not mirror patterns of latitudinal divergence (south-to-north), as might have been expected under a scenario with temperature as the major agent of selection. Our findings illustrate the importance of detailed phylogeographic information when interpreting geographic clines of dispersal traits in an adaptive evolutionary framework.

Data from: Modern spandrels: the roles of genetic drift, gene flow and natural selection in the formation of parallel clines

Urban environments offer the opportunity to study the role of adaptive and non-adaptive evolutionary processes on an unprecedented scale. While the presence of parallel clines in heritable phenotypic traits is often considered strong evidence for the role of natural selection, non-adaptive evolutionary processes can also generate clines, and this may be more likely when traits have a non-additive genetic basis due to epistasis. In this paper, we use spatially-explicit simulations modelled according to the cyanogenesis (HCN) polymorphism in white clover (Trifolium repens) to examine the formation of phenotypic clines along urbanization gradients under varying levels of drift, gene flow and selection. HCN results from an epistatic interaction between two Mendelian-inherited loci. Our results demonstrate that the genetic architecture of this trait makes natural populations susceptible to decreases in HCN frequencies via drift. Gradients in the strength of drift across a landscape resulted in phenotypic clines with lower frequencies of HCN in strongly drifting populations, giving the misleading appearance of deterministic adaptive changes in the phenotype. Studies of heritable phenotypic change in urban populations should generate null models of phenotypic evolution based on the genetic architecture underlying focal traits prior to invoking selection's role in generating adaptive differentiation.

opencc-zeroDec 2012View details →

Data from: Vanishing chromosomal inversion clines in Drosophila subobscura from Chile: is behavioral thermoregulation to blame?

Chromosomal inversion clines paralleling the long-standing ones in native Palearctic populations of Drosophila subobscura evolved swiftly after this species invaded the Americas in the late 1970s and early 1980s. However, the new clines did not consistently continue to converge on the Old World baseline. Our recent survey of Chilean populations of D. subobscura shows that inversion clines have faded or even changed sign with latitude. Here, we investigate the hypothesis that this fading of inversion clines might be due to the Bogert effect, namely, that flies' thermoregulatory behavior has eventually compensated for environmental variation in temperature, thus buffering selection on thermal-related traits. We show that latitudinal divergence in thermal preference (Tp) has evolved in Chile for females, with higher-latitude flies having a lower mean Tp. Plastic responses in Tp also lessen latitudinal thermal variation because flies developed at colder temperatures prefer warmer microclimates. Our results are consistent with the idea that active behavioral thermoregulation might buffer environmental variation and reduce the potential effect of thermal selection on other traits as chromosomal arrangements.

Data from: 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 ~3,000 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 FST-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.

opencc-zeroDec 2014View details →

Data from: Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa

Clines in life history traits, presumably driven by spatially varying selection, are widespread. Major latitudinal clines have been observed, for example, in Drosophila melanogaster, an ancestrally tropical insect from Africa that has colonized temperate habitats on multiple continents. Yet, how geographic factors other than latitude, such as altitude or longitude, affect life history in this species remains poorly understood. Moreover, most previous work has been performed on derived European, American and Australian populations, but whether life history also varies predictably with geography in the ancestral Afro-tropical range has not been investigated systematically. Here, we have examined life history variation among populations of D. melanogaster from sub-Saharan Africa. Viability and reproductive diapause did not vary with geography, but body size increased with altitude, latitude and longitude. Early fecundity covaried positively with altitude and latitude, whereas lifespan showed the opposite trend. Examination of genetic variance–covariance matrices revealed geographic differentiation also in trade-off structure, and QST-FST analysis showed that life history differentiation among populations is likely shaped by selection. Together, our results suggest that geographic and/or climatic factors drive adaptive phenotypic differentiation among ancestral African populations and confirm the widely held notion that latitude and altitude represent parallel gradients.

opencc-zeroDec 2016View details →

Data from: Breakdown of a geographic cline explains high performance of introduced populations of a weedy invader

1. What drives the evolution of increased growth and fecundity in plants introduced to a novel range is not well understood. 2. We investigate between-range differences in performance for Verbascum thapsus, a weedy invader known to grow larger in its introduced than native range. Specifically, we question whether adaptation to herbivory or climate best explains increased performance of introduced populations. 3. We grew 14 native and 22 introduced populations of V. thapsus in two common garden locations: near Prague, Czech Republic (native range) and in Colorado, USA (introduced range). By removing herbivores from half of the plants within each garden we tested the prediction of the Evolution of Increased Competitive Ability (EICA) hypothesis: increased performance is driven by an evolutionary shift of resources away from defence against herbivory towards growth and reproduction. We then investigated whether genetically based clines in performance are expressed along climate gradients within both the native and introduced ranges. 4. On average, seeds produce larger rosettes when collected from the introduced versus native range. While this evolution of increased growth in introduced populations in part matches the prediction of EICA, climate, not herbivory, best explains this between-range difference. Specifically, seeds collected from the native range produce smaller rosettes as the climate of origin becomes cooler and drier, while there is no cline in performance in rosettes grown from seed collected from the introduced range, which are large regardless of climate of origin. Thus, a climate-based cline within the native range best explains lower average performance of native compared to introduced populations. SYNTHESIS: The breakdown in a potentially adaptive cline emphasizes the need to more closely investigate the evolutionary processes that shape geographic structuring (or its absence) within the introduced range. In addition, EICA is not universally applicable to all invasion scenarios, and our findings underscore the importance of testing underlying assumptions alongside the predictions of this hypothesis.

Data from: 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.

Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow

Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally-suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasises that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.

Data from: Genetic architecture in a marine hybrid zone: comparing outlier detection and genomic clines analysis in the bivalve Macoma balthica

The role of natural selection in speciation has received increasing attention and support in recent years. Different types of approaches have been developed that can detect genomic regions influenced by selection. Here we address the question whether two highly different methods - Fst outlier analysis and admixture analysis - detect largely the same set of non-neutral genomic elements or, instead, complementary sets. We study genetic architecture in a natural secondary contact zone where extensive admixture occurs. The marine bivalves Macoma balthica rubra and M. b. balthica descend from two independent trans-Arctic invasions of the north Atlantic and hybridize extensively where they meet, for example in the Kattegat - Danish Straits - Baltic Sea region. The Kattegat - Danish Straits region forms a steep salinity cline and is the only entrance to the recently (ca 8000 years ago) established brackish water basin the Baltic Sea. Salinity along the contact zone drops from 30‰ (Skagerrak, M.b.rubra) to 3‰ (Baltic, M.b.balthica). Both outlier analysis and genomic clines analysis suggest that large parts of the genome are influenced by non-neutral effects. Contrasting samples from well outside the hybrid zone, outlier analysis detects 16 of 84 amplified fragment length polymorphism (AFLP) markers as significant Fst outliers. Genomic clines analysis detects 31 out of 84 markers as non-neutral inside the hybrid zone. Remarkably, only three markers are detected by both methods. We conclude that the two methods together identify a suite of markers that are under the influence of non-neutral effects.

Data from: An inversion supergene in Drosophila underpins latitudinal clines in survival traits

Chromosomal inversions often contribute to local adaptation across latitudinal clines, but the underlying selective mechanisms remain poorly understood. We and others have previously shown that a clinal inversion polymorphism in Drosophila melanogaster, In(3R)Payne, underpins body size clines along the North American and Australian east coasts. Here we ask whether this polymorphism also contributes to clinal variation in other fitness-related traits, namely survival traits (lifespan, survival upon starvation, and survival upon cold shock). We generated homokaryon lines, either carrying the inverted or standard chromosomal arrangement, isolated from populations approximating the endpoints of the North American cline (Florida, Maine), and phenotyped the flies at two growth temperatures (18°C, 25°C). Across both temperatures, high-latitude flies from Maine lived longer and were more stress resistant than low-latitude flies from Florida, as previously observed. Interestingly, we find that this latitudinal pattern is partly explained by the clinal distribution of the In(3R)P polymorphism, which is at ~50% frequency in Florida but absent in Maine: inverted karyotypes tended to be shorter-lived and less stress resistant than uninverted karyotypes. We also detected an interaction between karyotype and temperature on survival traits. Since In(3R)P influences body size and multiple survival traits, it can be viewed as a 'supergene', a cluster of tightly linked loci affecting multiple complex phenotypes. We conjecture that the inversion cline is maintained by fitness trade-offs and balancing selection across geography; elucidating the mechanisms whereby this inversion affects alternative, locally adapted phenotypes across the cline is an important task for future work.