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.     

Geography is more important than host plant use for the population genetic structure of a generalist insect herbivore

Population divergence can occur due to mechanisms associated with geographic isolation and/or due to selection associated with different ecological niches. Much of the evidence for selection‐driven speciation has come from studies of specialist insect herbivores that use different host plant species; however, the influence of host plant use on population divergence of generalist herbivores remains poorly understood. We tested how diet breadth, host plant species and geographic distance influence population divergence of the fall webworm (Hyphantria cunea; FW). FW is a broadly distributed, extreme generalist herbivore consisting of two morphotypes that have been argued to represent two different species: black‐headed and red‐headed. We characterized the differentiation of FW populations at two geographic scales. We first analysed the influence of host plant and geographic distance on genetic divergence across a broad continental scale for both colour types. We further analysed the influence of host plant, diet breadth and geographic distance on divergence at a finer geographic scale focusing on red‐headed FW in Colorado. We found clear genetic and morphological distinction between red‐ and black‐headed FW, and Colorado FW formed a genetic cluster distinct from other locations. Although both geographic distance and host plant use were correlated with genetic distance, geographic distance accounted for up to 3× more variation in genetic distance than did host plant use. As a rare study investigating the genetic structure of a widespread generalist herbivore over a broad geographic range (up to 3,000 km), our study supports a strong role for geographic isolation in divergence in this system.     

Natural selection at genomic regions associated with obesity and type-2 diabetes: East Asians and sub-Saharan Africans exhibit high levels of differentiation at type-2 diabetes regions

Different populations suffer from different rates of obesity and type-2 diabetes (T2D). Little is known about the genetic or adaptive component, if any, that underlies these differences. Given the cultural, geographic, and dietary variation that accumulated among humans over the last 60,000 years, we examined whether loci identified by genome-wide association studies for these traits have been subject to recent selection pressures. Using genome-wide SNP data on 938 individuals in 53 populations from the Human Genome Diversity Panel, we compare population differentiation and haplotype patterns at these loci to the rest of the genome. Using an “expanding window” approach (100–1,600 kb) for the individual loci as well as the loci as ensembles, we find a high degree of differentiation for the ensemble of T2D loci. This differentiation is most pronounced for East Asians and sub-Saharan Africans, suggesting that these groups experienced natural selection at loci associated with T2D. Haplotype analysis suggests an excess of obesity loci with evidence of recent positive selection among South Asians and Europeans, compared to sub-Saharan Africans and Native Americans. We also identify individual loci that may have been subjected to natural selection, such as the T2D locus, HHEX, which displays both elevated differentiation and extended haplotype homozygosity in comparisons of East Asians with other groups. Our findings suggest that there is an evolutionary genetic basis for population differences in these traits, and we have identified potential group-specific genetic risk factors.     

Congruence between environmental parameters, morphology and genetic structure in Australia’s most widely distributed eucalypt, Eucalyptus camaldulensis

Eucalyptus camaldulensis is one of the most widely utilised eucalypts. It is also the only eucalypt that occurs across the Australian continent, playing a key ecological role as fauna habitat and in riverbank stabilisation. Despite its ecological and economic importance, uncertainty remains regarding the delineation of genetic and morphological variants. Nine hundred and ninety trees from 97 populations, representing the species’ geographic range were genotyped using 15 microsatellite loci and patterns of diversity compared with restriction fragment length polymorphisms in 29 of these populations. Both markers showed that despite having a riverine distribution, downstream seed dispersal has had less influence than geographic distance on dispersal patterns. Spatial patterns in the distribution of microsatellite genotypes were compared with environmental parameters and boundaries defined by river systems, drainage basins and proposed subspecies. Significant genetic differences among populations within river systems indicated that rivers should not be treated as a single genetic entity in conservation or breeding programmes. Strong geographic trends were evident with 40% of variation in genetic diversity explained by latitude and moisture index. Isolation by distance and significant correlations between genetic distance and environmental parameters for most loci suggest historical factors have had more influence than selection on current patterns of distribution of genetic diversity. Geographic structuring of molecular variation, together with congruence between genetic and morphological variation indicate that E. camaldulensis should be treated as a number of subspecies rather than a single variable taxon. High levels of genetic diversity and geographic trends in the distribution of variation provide a firm basis for further exploration of the species’ genetic resources.     

Integrating QTL mapping and genome scans towards the characterization of candidate loci under parallel selection in the lake whitefish (Coregonus clupeaformis)

As natural selection must act on underlying genetic variation, discovering the number and location of loci under the influence of selection is imperative towards understanding adaptive divergence in evolving populations. Studies employing genome scans have hypothesized that the action of divergent selection should reduce gene flow at the genomic locations implicated in adaptation and speciation among natural populations, yet once 'outlier' patterns of variation have been identified the function and role of such loci needs to be confirmed. We integrated adaptive QTL mapping and genomic scans among diverging sympatric pairs of the lake whitefish (Coregonus clupeaformis) species complex in order to test the hypothesis that differentiation between dwarf and normal ecotypes at growth-associated QTL was maintained by directional selection. We found evidence of significantly high levels of molecular divergence among eight growth QTL where two of the strongest candidate loci under the influence of directional selection exhibited parallel reductions of gene flow over multiple populations.     

Character displacement in sailfin mollies, <Emphasis Type="Italic">Poecilia latipinna</Emphasis>: allozymes and behavior

Synopsis We analyzed variation in allozymes and mating preferences in 12 populations across much of the range of the sailfin molly, Poecilia latipinna. Sailfin mollies can be sympatric with its sexual parasite Amazon mollies, P. formosa. Amazon mollies must co-exist and mate with bisexual males of closely related species (including sailfin mollies) to induce embryogenesis but inheritance is strictly maternal. Where sailfin and Amazon mollies are sympatric there is evidence of reproductive character displacement as males show a significantly stronger mating preference for sailfin molly females over Amazon mollies compared to preferences of males from allopatric populations. From the allozyme data we found a moderate amount of genetic variation across all populations but this variation did not reveal significant partitioning between sympatric and allopatric populations. Additionally, we found no evidence for isolation by distance as genetic distance was not significantly correlated with geographic distance. While allozyme variation also did not significantly correlate with male mating preferences, there was a significant correlation between male mating preferences and geographic distance. This correlation between mating preferences and geographic distance may have arisen from coevolution with Amazon mollies resulting in reproductive character displacement. Taken together, the distribution of genetic and behavioral variation among sympatric and allopatric populations suggests that behavioral evolution has outpaced evolution at the allozyme loci we examined in P. latipinna.     

Isolation by environment in White‐breasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach

Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long‐standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms or identification of genes potentially under selection. Using landscape genomics, the simultaneous study of genomic and ecological landscapes, we investigated the processes driving population genetic patterns of White‐breasted Nuthatches (Sitta carolinensis) in sky islands (montane forest habitat islands) of the Madrean Archipelago. Using more than 4000 single nucleotide polymorphisms and multiple tests to investigate the relationship between genetic differentiation and geographic or ecological distance, we identified IBE, and a lack of IBD, among sky island populations of S. carolinensis. Using three tests to identify selection, we found 79 loci putatively under selection; of these, seven matched CDS regions in the Zebra Finch. The loci under selection were highly associated with climate extremes (maximum temperature of warmest month and minimum precipitation of driest month). These results provide evidence for IBE – disentangled from IBD – in sky island vertebrates and identify potential adaptive genetic variation.     

Genetic divergence and isolation by thermal environment in geothermal populations of an aquatic invertebrate

Temperature is one of the most influential forces of natural selection impacting all biological levels. In the face of increasing global temperatures, studies over small geographic scales allowing investigations on the effects of gene flow are of great value for understanding thermal adaptation. Here, we investigated genetic population structure in the freshwater gastropod Radix balthica originating from contrasting thermal habitats in three areas of geothermal activity in Iceland. Snails from 32 sites were genotyped at 208 AFLP loci. Five AFLPs were identified as putatively under divergent selection in Lake Mývatn, a geothermal lake with an almost 20 °C difference in mean temperature across a distance of a few kilometres. In four of these loci, variation across all study populations was correlated with temperature. We found significant population structure in neutral markers both within and between the areas. Cluster analysis using neutral markers classified the sites mainly by geography, whereas analyses using markers under selection differentiated the sites based on temperature. Isolation by distance was stronger in the neutral than in the outlier loci. Pairwise differences based on outlier F_ST were significantly correlated with temperature at different spatial scales, even after correcting for geographic distance or neutral pairwise F_ST differences. In general, genetic variation decreased with increasing environmental temperature, possibly suggesting that natural selection had reduced the genetic diversity in the warm origin sites. Our results emphasize the influence of environmental temperature on the genetic structure of populations and suggest local thermal adaptation in these geothermal habitats.     

Environmental Heterogeneity Explains the Genetic Structure of Continental and Mediterranean Populations of Fraxinus angustifolia Vahl

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.     

Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands' environmental gradient

Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation by distance (IBD) vs. isolation by environment (IBE) on ecotype divergence, (iii) identify outlier loci under selection and (iv) assess the association between outlier loci and climate. Using two primer sets, we genotyped 378 plants at 384 polymorphic AFLP loci across regional ecotypes from central and eastern Kansas and Illinois. Neighbour‐joining tree and PCoA revealed strong genetic differentiation between Kansas and Illinois ecotypes, which was better explained by IBE than IBD. We found high genetic variability within prairies (80%) and even fragmented Illinois prairies, surprisingly, contained high within‐prairie genetic diversity (92%). Using Bayenv 2, 14 top‐ranked outlier loci among ecotypes were associated with temperature and precipitation variables. Six of seven BayeScan F_ST outliers were in common with Bayenv 2 outliers. High genetic diversity may enable big bluestem populations to better withstand changing climates; however, population divergence supports the use of local ecotypes in grassland restoration. Knowledge of genetic variation in this ecological dominant and other grassland species will be critical to understanding grassland response and restoration challenges in the face of a changing climate.     

Molecular signatures of divergence and selection in closely related pine taxa

Efforts to detect loci under selection in plants have mostly focussed on single species. However, assuming that intraspecific divergence may lead to speciation, comparisons of genetic variation within and among recently diverged taxa can help to locate such genes. In this study, coalescent and outlier detection methods were used to assess nucleotide polymorphism and divergence at 79 nuclear gene fragments (1212 SNPs) in 16 populations (153 individuals) of the closely related, but phenotypically and ecologically distinct, pine taxa Pinus mugo, P. uliginosa and P. uncinata across their European distributions. Simultaneously, mitochondrial DNA markers, which are maternally inherited in pines and distributed by seeds at short geographic distance, were used to assess genetic relationships of the focal populations and taxa. The majority of nuclear loci showed homogenous patterns of variation between the taxa due to a high number of shared SNPs and haplotypes, similar levels of polymorphism, and low net divergence. However, against this common genetic background and an overall low population structure within taxa at mitochondrial markers, we identified several genes showing signatures of selection, accompanied by significant intra- and interspecific divergence. Our results indicate that loci involved in species divergence may be involved in intraspecific local adaptation.     

Association between the PRNP 1368 polymorphism and the occurrence of sporadic Creutzfeldt-Jakob disease

Creutzfeldt-Jakob disease (CJD) is a rare transmissible neurodegenerative disorder. The etiology of sporadic form of CJD remains unsolved. In addition to the codon 129 polymorphism, polymorphisms in the non-coding region of PRNP are considered as important factors in sCJD development. To assess a possible association between PRNP 1368 SNP and sCJD, we compared the genotype, allele and haplotype frequencies of the 1368 SNP among 46 sCJD patients of Dutch origin with the respective frequencies in healthy controls. We detected a significant association between sCJD and 1368T/T genotype. A significant difference was also observed in 1368 alleles’ distribution. In the haplotype analysis, haplotype 1368C-129G was associated with decreased risk of sCJD in Dutch population. Our findings support the hypothesis that genetic variations in the regulatory region of the PRNP gene may influence the pathogenesis of sCJD.     

Geographic influences on fine-scale,hierarchical population structure in northern Canadian populations of anadromous Arctic Char (Salvelinus alpinus)

Assessments of fine-scale population structure in natural populations are important for understanding aspects of ecology, life history variation and evolutionary history and can provide novel insights into resource management. Although Arctic char, Salvelinus alpinus, represent one of the most culturally and commercially important salmonids in the Canadian Arctic, fine-scale assessments of genetic structure in northern populations of this species are rare. In this study, we assessed population structure in anadromous Arctic char from Cumberland Sound in Canada’s Nunavut territory using 18 microsatellite loci. Specifically, we aimed at identifying potential habitat and landscape/geographic features influencing genetic variation and population structure and resolving potential barriers to gene flow. Overall population structure was moderate (global F_ST and Jost’s D of 0.042 and 0.236 respectively) and significant among all sampling locations. Habitat and landscape/geographic features, with the exception of fluvial (shoreline) distance, appeared to have little influence on genetic variation and population structure. Bayesian clustering revealed a hierarchical model of population structure, in which the 14 sampling locations were nested within two distinct clusters corresponding to the north and south shores of Cumberland Sound. Both isolation-by-distance analysis and calculations of mean dispersal distance suggest dispersal and gene flow is highest among proximate locations. Finally, several putative barriers to gene flow were identified and one, a putative barrier separating north and south Cumberland Sound, was consistent with the hierarchical STRUCTURE results. Our results suggest that the current river-specific management of commercially harvested Arctic char is appropriate. Overall, we provide further insights into the evolution of genetic variation and population structure in iteroparous, Arctic salmonids.     

Distribution of the genetic diversity of the Siberian stone pine,Pinus sibirica Du Tour,along the latitudinal and longitudinal profiles

The Siberian stone pine (Pinus sibirica Du Tour) is one of the main forest-forming coniferous species of the boreal ecosystems of Western Siberia. We used the isozyme method to analyze 11 ecotypes representing the latitudinal and longitudinal profiles within the species range, including samples from the geographic boundaries of the distribution. The genetic structure of the ecotypes is described on the basis of the variability for 26 isozyme loci encoding for 16 enzyme systems. The greatest genetic diversity was observed in the taiga ecotypes in the central part of the studied area, while the ecotypes along the species range boundaries were shown to be genetically depauperized. Approximately 8.1 % of the observed genetic diversity is attributed to differences between the studied ecotypes. We detected high levels of genetic diversity for the Fest-2, Pgm-1, Sod-4, and a few other loci, as well as a correlation between allele frequencies and geographical locations of the populations. The results of multivariate analysis of allelic frequencies as well as cluster analysis allowed us to discriminate three major groups of ecotypes: north-eastern, central and south-western. In view of our results, we compare two hypotheses: one which attributes the spatial distribution of genetic variations to the selectivity for some of the polymorphic allozyme loci, and the other based in the history of the formation of the range of the Siberian stone pine.     

Genetic variation within and among populations of Arabidopsis thaliana.

We investigated levels of nucleotide polymorphism within and among populations of the highly self-fertilizing Brassicaceous species, Arabidopsis thaliana. Four-cutter RFLP data were collected at one mitochondrial and three nuclear loci from 115 isolines representing 11 worldwide population collections, as well as from seven commonly used ecotypes. The collections include multiple populations from North America and Eurasia, as well as two pairs of collections from locally proximate sites, and thus allow a hierarchical geographic analysis of polymorphism. We found no variation at the mitochondrial locus Nad5 and very low levels of intrapopulation nucleotide diversity at Adh, Dhs1, and Gpa1. Interpopulation nucleotide diversity was also consistently low among the loci, averaging 0.0014. gst, a measure of population differentiation, was estimated to be 0.643. Interestingly, we found no association between geographical distance between populations and genetic distance. Most haplotypes have a worldwide distribution, suggesting a recent expansion of the species or long-distance gene flow. The low level of polymorphism found in this study is consistent with theoretical models of neutral mutations and background selection in highly self-fertilizing species.     

Intron sequences of arginine kinase in an intertidal snail suggest an ecotype-specific selective sweep and a gene duplication

Many species with restricted gene flow repeatedly respond similarly to local selection pressures. To fully understand the genetic mechanisms behind this process, the phylogeographic history of the species (inferred from neutral markers) as well as the loci under selection need to be known. Here we sequenced an intron in the arginine kinase gene (Ark), which shows strong clinal variation between two locally adapted ecotypes of the flat periwinkle, Littorina fabalis. The ‘small-sheltered'' ecotype was almost fixed for one haplotype, H1, in populations on both sides of the North Sea, unlike the ‘large-moderately exposed ecotype'', which segregated for ten different haplotypes. This contrasts with neutral markers, where the two ecotypes are equally variable. H1 could have been driven to high frequency in an ancestral population and then repeatedly spread to sheltered habitats due to local selection pressures with the colonization of both sides of the North Sea, after the last glacial maximum (∼18 000 years ago). An alternative explanation is that a positively selected mutation, in or linked to Ark, arose after the range expansion and secondarily spread through sheltered populations throughout the distribution range, causing this ecotype to evolve in a concerted fashion. Also, we were able to sequence up to four haplotypes consistently from some individuals, suggesting a gene duplication in Ark.     

Genetic differentiation among cottontails from isolated playa basins

Protein variation in 182 Sylvilagus floridanus from 19 playa basins in Castro Co., Texas was examined using starch-gel electrophoresis. Heterozygote deficiencies were noted for all populations. This heterozygote deficiency may be due to differential selection against heterozygous individuals over the winter months. Results of F-statistics indicated a significant degree of population differentiation at six loci. Nei's genetic distance between populations ranged from 0.20 to 0.388 and a significant association between genetic distance and linear geographic distance among playas was found. These results suggest that genetic exchange and long-distance dispersal may be hindered by expanses of unsuitable habitat.     

Arctic fox Vulpes lagopus population structure: circumpolar patterns and processes

Movement is a prominent process shaping genetic population structure. In many northern mammal species, population structure is formed by geographic distance, geographical barriers and various ecological factors that influence movement over the landscape. The Arctic fox Vulpes lagopus is a highly mobile, opportunistic carnivore of the Arctic that occurs in two main ecotypes with different ecological adaptations. We assembled microsatellite data in 7 loci for 1834 Arctic foxes sampled across their entire distribution to describe the circumpolar population structure and test the impact of (1) geographic distance, (2) geographical barriers and (3) ecotype designation on the population structure. Both Structure and Geneland demonstrated distinctiveness of Iceland and Scandinavia whereas low differentiation was observed between North America–northern Greenland, Svalbard and Siberia. Genetic differentiation was significantly correlated to presence of sea ice on a global scale, but not to geographical distance or ecotype designation. However, among areas connected by sea ice, we recorded a pattern of isolation by distance. The maximum likelihood approach in Migrate suggested that connectivity across North America–northern Greenland and Svalbard was particularly high. Our results demonstrate the importance of sea ice for maintaining connectivity between Arctic fox populations and we therefore predict that climate change will increase genetic divergence among populations in the future.     

Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison‐dart frog

Phenotypic and genetic divergence can be influenced by a variety of factors, including sexual and natural selection, genetic drift and geographic isolation. Investigating the roles of these factors in natural systems can provide insight into the relative influences of allopatric and ecological modes of biological diversification in nature. The strawberry poison frog, Dendrobates pumilio, presents an excellent opportunity for this kind of research, displaying a diverse array of colour morphs and inhabiting a heterogeneous landscape that includes oceanic islands, fragmented rainforest patches and wide expanses of suitable habitat. In this study, we use 15 highly polymorphic microsatellite loci to estimate population structure and gene flow among populations from across the range of D. pumilio and a causal modelling framework to statistically test 12 hypotheses regarding the geographic and phenotypic variables that explain genetic differentiation within this system. Our results demonstrate that the genetic distance between populations is most strongly associated with differences in dorsal coloration. Previous experimental studies have shown that phenotypic differences can result in sexual and natural selection against non‐native phenotypes, and our results now show that these forces lead to genetic isolation between different colour morphs in the wild, presenting a potential case of incipient speciation through selection.