Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster.

The recognition that evolution can happen on ecological timescales (Hairston et al. 2005; Pelletier et al. 2009; Ellner et al. 2011; Becks et al. 2012) has prompted the integration of ecology and evolution, while easier access to high-throughput sequencing technologies has increased the number of genetic nonmodel species entering the ‘omics’ era (e.g. Turner et al. 2010; Colbourne et al. 2011; Jones et al. 2012). We are now in a position to identify the genetic basis of adaptation and the mechanisms of adaptive responses in the wild. It nonetheless remains a challenge to go beyond descriptive measures of patterns of genetic variation and to identify the evolutionary processes driving species adaptation and evolution. This special issue represents a broad cross-section of research into evolutionary adaptation at the genetic level. The approaches used vary from classic QTL studies to RAD sequencing and RNAseq. Given the rapid advance of sequencing technology, we fully expect that ‘genomic’ as defined here will be merely ‘genetic’ in a few years, but we nonetheless hope that the results and methods described in this special issue will serve as a blueprint for future work in this field.

Allometric equations on wing dimensions versus body mass are given for eight species of megabats and 76 species of microbats, on forearm length versus mass for 14 species of mega bats and 90 species of microbats, and on lower leg length versus mass for 11 species of megabats and 45 species of microbats. Megabats have, on average, shorter wing span, small wing area, higher wing loading and lower aspect ratio than have frugivorous microbats and the insectivorous vespertilionids of similar mass. Vespertilionids have the longest span, largest wing area and lowest wing loading in relation to body mass of the bat groups for which regression lines were calculated (megabats, frugivorous microbats, vespertilionids, molossids), characteristics that are important for slow flight and manoeuvrability for insect capture. Molossids have the highest wing loading of the groups. There is a weak tendency towards higher aspect ratio for larger bats than for smaller ones (positive slope). The slopes for most characters fit geometric similarity or have confidence intervals including the value for geometric similarity. Only in three cases does the slope lie nearer that for elastic similarity: for the forearm in nycterids and emballonurids and the lower leg length in molossids. Also in these cases the confidence intervals are wide and include the value for elastic similarity and that for geometric similarity as well. In megabats the slope for the lower leg length is much steeper than for geometric similarity. The slope for the forearm length is rather similar to that for wing span in the various groups. Megabats and frugivorous microbats have rather similar slopes for all the characters measured, but differ from the other groups only in wing area, wing loading and aspect ratio. The two frugivorous bat groups also have about the same elevation of the regression lines for aspect ratio and forearm length. Megabats and frugivorous microbats thus show a close convergence in wing area, wing loading, aspect ratio and forearm length. The regression equations provide ‘norms’ for the respective bat groups. Those species that deviate 10% or more from the mean trends for wing measurements are divided into different groups, based on the wing’s aspect ratio and loading. Bats with low aspect ratio wings usually have large pinnae, which improve the ability to discover small objects such as insects on leaves. Families or species of bats with wings of low aspect ratio are, for instance, Megadermatidae, Nycteridae, Rhinolophus ferrumequinum (Rhinolophidae), Chrotopterus auritus (Phyllostomidae) and Plecotus (Vespertilionidae). The group with average aspect ratio wings contains bats with different kinds of flight style and foraging behaviour, for instance many pteropodids, phyllostomids and vespertilionids. Bats with high aspect ratio wings are, for instance, Molossidae, Rhynchonycteris naso (Emballonuridae) and Nyctalus leisleri (Vespertilionidae). The regression lines for wing span, area and loading in megabats lie almost in the region of the lines for Greenewalt’s (1975) passeriform group, whereas the span and area for vespertilionid bats are larger and the wing loading much smaller than for most birds of similar mass. Molossid bats have a larger relative wing span and aspect ratio than have most birds, and a wing area and loading similar to those of small birds of the passeriform group. Vespertilionid bats have about the same aspect ratio as birds of the passeriform group, whereas megabats have somewhat lower ratios. Molossid bats show strong convergence with swifts and swallows in foraging behaviour and in wing form. Similar convergences can be found between various vespertilionid bats, flycatchers and swallows.

• Key message Understanding the adaptive mechanisms of forest species is vital to ensure their survival in a climate change scenario. This study aimed at uncovering the relationship between genetic variability and environmental variables in natural Castanea sativa populations, unveiling how different climate scenarios drove local adaption processes using a landscape genomics approach. Our findings provide useful data for future management of this species. • Context Temperate forest species, such as chestnut (Castanea sativa Mill.), are currently threatened by increasing temperature together with disruption and reduction of precipitation due to climate change. In this context, understanding the adaptation processes of species will help to manage and ensure the conservation of forests.• Aims We studied the relationship between genetic variability and climate variables in natural populations of C. sativa using a landscape genomics approach aimed to identify local adaption processes.• Methods Using five genomic SSRs and eight functional EST-SSRs markers, 268 individuals belonging to ten different natural European chestnut populations distributed in contrasting climatic sites were genotyped. In addition, associations between allelic variation and climatic variables (environmental association analyses approach) were performed using Samβada and LFMM.• Results Results highlighted a strong inter-relationship between climate variables and evolutionary processes resulting in adaptive variation. STRUCTURE analysis based on functional markers split the populations in three separate gene pools (K = 3), mostly in agreement with the different climatic conditions existing in the studied areas. Divergent spatial patterns of genetic variation between rainy and arid areas were found. We detected a total of 202 associations with climate among 22 different alleles, 9% of which related with the outlier locus FIR059, known to be implicated in regulatory mechanisms during water stress adaptation processes.• Conclusion Landscape genomics analyses revealed a pattern of adaptive variation, where specific climatic variables influenced the frequencies distribution and fixation of several alleles, resulting in local adaptation processes of the populations in the investigated areas. Our findings underline the close inter-relationship existing between climate and genetic variability and indicate how this approach could provide valuable information for the management of forest species in a rapidly changing environment.

Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST-based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.

We examined 20 Drosophila melanogaster populations collected from a 2600-km north-south transect in Australia. In laboratory culture at constant temperature and standard larval density, a genetic cline in thorax length and wing area was found, with both traits increasing with latitude. The cline in wing area was based on clines in both cell size and cell number, but was primarily determined by changes in cell number. Body size and larval development time were not associated among populations. We discuss our results in the context of selection processes operating in natural and experimental populations.

In Drosophila melanogaster, ovariole number and thorax length are morphological characters thought to be associated with fitness. Maximum daily egg production in females is positively correlated with ovariole number, while thorax length is correlated with male reproductive success and female fecundity. Though both traits are related to fitness, ovariole number is likely to be under stabilizing selection, while thorax length appears to be under directional selection. Current research has focused on examining the sources of variation for ovariole number in relation to fitness, with a view towards elucidating how segregating variation is maintained in natural populations. Here, we utilize a diallel design to explore the genetic architecture of ovariole number and thorax length in nine isogenic lines derived from a natural population. The full diallel design allows the estimation of general combining ability (GCA), specific combining ability (SCA), and also describes variation due to reciprocal effects (RGCA and RSCA). Ovariole number and thorax length differed with respect to their genetic architecture, reflective of the independent selective forces acting on the traits. For ovariole number, GCA accounted for the majority (67.3%) of variation segregating between the lines, with no evidence of reciprocal effects or inbreeding depression; SCA accounted for a small percentage (3.9%) of the variance, suggesting dominance variation; no reciprocal effects were observed. In contrast, for thorax length, the majority of the non-error variance was accounted for by SCA (17.9%), with only one third as much variance (6.2%) due to GCA. Interestingly, RSCA (nuclear-extranuclear interactions) accounted for slightly more variation (7.5%) than GCA in these data. Thus, genetic variation for thorax length is largely in accord with predictions for a fitness trait under directional selection: little additive genetic variation and substantial dominance variation (including a suggestion of inbreeding depression); while the mechanisms underlying the maintenance of variation for ovariole number are more complex.

Microbiomes affect many aspects of host biology, but the eco-evolutionary forces that shape their diversity in natural populations remain poorly understood. Geographical gradients, such as latitudinal clines, generate predictable patterns in biodiversity at macroecological scales, but whether these macroscale processes apply to host-microbiome interactions is an open question. To address this question, we sampled the microbiomes of 13 natural populations of Drosophila melanogaster along a latitudinal cline in the eastern United States. The microbiomes were surprisingly consistent across the cline, as latitude did not predict either alpha or beta diversity. Only a narrow taxonomic range of bacteria were present in all microbiomes, indicating that strict taxonomic filtering by the host and neutral ecological dynamics are the primary factors shaping the fly microbiome. Our findings reveal the complexity of eco-evolutionary interactions shaping microbial variation in D. melanogaster and highlight the need for additional sampling of the microbiomes in natural populations along environmental gradients.

The budding yeast Saccharomyces cerevisiae is the best studied eukaryote in molecular and cell biology, but its utility for understanding the genetic basis of phenotypic variation in natural populations is limited by inefficient association mapping due to strong and complex population structure. To overcome this challenge, we generated genome sequences for 85 strains and performed a comprehensive population genomic survey of a total of 190 diverse strains. We identified considerable variation in population structure among chromosomes and identified 181 genes that are absent from the reference genome. Many of these nonreference genes are expressed and we functionally confirmed that two of these genes confer increased resistance to antifungals. Next, we simultaneously measured the growth rates of over 4,500 laboratory strains, each of which lacks a nonessential gene, and 81 natural strains across multiple environments using unique DNA barcode present in each strain. By combining the genome-wide reverse genetic information gained from the gene deletion strains with a genome-wide association analysis from the natural strains, we identified genomic regions associated with fitness variation in natural populations. To experimentally validate a subset of these associations, we used reciprocal hemizygosity tests, finding that while the combined forward and reverse genetic approaches can identify a single causal gene, the phenotypic consequences of natural genetic variation often follow a complicated pattern. The resources and approach provided outline an efficient and reliable route to association mapping in yeast and significantly enhance its value as a model for understanding the genetic mechanisms underlying phenotypic variation and evolution in natural populations.

Deleterious genetic variation is abundant in wild populations, and understanding the ecological and conservation implications of such variation is an area of active research. Genomic methods are increasingly used to quantify the impacts of deleterious variation in natural populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of mutations. Computational simulations of deleterious variation offer a complementary tool that can help overcome these limitations, although such approaches have yet to be widely employed. In this perspective article, we aim to encourage ecological and conservation genomics researchers to adopt greater use of computational simulations to aid in deepening our understanding of deleterious variation in natural populations. We first provide an overview of the components of a simulation of deleterious variation, describing the key parameters involved in such models. Next, we discuss several approaches for validating simulation models. Finally, we compare and validate several recently proposed deleterious mutation models, demonstrating that models based on estimates of selection parameters from experimental systems are biased toward highly deleterious mutations. We describe a new model that is supported by multiple orthogonal lines of evidence and provide example scripts for implementing this model (https://github.com/ckyriazis/simulations_review).

Phenotypic Variation and Natural Selection at Catsup, a Pleiotropic Quantitative Trait Gene in Drosophila

Patterns of variation within and between Carex gynodynama and C. mendocinensis were investigated by studying allozyme and chromosome variation in natural populations and structural variation using herbarium specimens. Multivariate analyses of structural data demonstrated that C. gynodynama is clearly distinct from C. mendocinensis, and that sterile specimens similar to C. mendocinensis are intermediate between that species and C. gynodynama. The mean genetic distance between the two species, based on allozyme phenotypes at 17 enzyme‐coding loci, was 0.22 ± 0.12. The sterile putative hybrids had the expected heterozygous pattern at three enzyme‐coding loci at which the parental species were fixed for different alleles. Chromosome numbers are reported for the first time for both species and their putative hybrid. Carex mendocinensis had a different number in each of the three populations examined with n = 28, n = 29, or n = 30. Chromosome counts from one population of C. gynodynama revealed five plants with n = 25 and one with n = 26. Putative hybrids from this population exhibited irregular pairing at meiosis with 2n = ca. 55–57. Patterns of allozyme variation also suggest that C. mendocinensis has an outcrossing or mixed mating system but that C. gynodynama is an inbreeding species. Carex gynodynama exhibited very little variation in structure, habitat, or at the enzyme‐coding loci examined, suggesting that it may have experienced a genetic bottleneck relatively recently. Carex mendocinensis had higher levels of variation both within and between populations at enzyme‐coding loci and in structural features. This pattern of variation and a geographic distribution centered in serpentine areas of the Klamath–Siskiyou region, with disjunct smaller populations in serpentine areas farther south, suggest that C. mendocinensis once may have been a more widespread species.

SUMMARYThe often remarkable similarity in structural gene products among related species has led to the hypothesis that species differences may reside largely in changes at regulatory gene loci. This hypothesis assumes that groups capable of speciating have allelic variation at regulatory loci in their natural populations. We have undertaken an analysis of the mode of regulation of theesterase 6(Est 6) locus inDrosophila melanogasterto determine the nature and extent of regulatory gene variation in natural populations. Analyses of esterase 6 (EST 6) activity among strains carrying the same thermostability variants reveal that significant, specific-activity differences are present. Reciprocal crosses between lines having high and low EST 6 activity show that loci other than theEst 6structural gene influence EST 6 activity. Analyses of male hybrids from crosses betweenD. melanogasterandsimulansindicate that theXchromosome of these flies affects the expression of theEst 6locus, resulting in unequal levels of enzyme activity from the two alleles. The effect is sex and tissue specific. Female hybrids carrying theXchromosomes of both species exhibit equal expression of the twoEst 6alleles. We have determined whether natural populations are polymorphic forXchromosomes which affect EST 6 activity by extracting singleXchromosomes from wild-collected males and placing these chromosomes in identical genetic backgrounds. Stocks which are otherwise genetically identical but carry independently derivedXchromosomes show significant differences in the activity of EST 6. These data suggest that regulatory loci may be commonly polymorphic in natural populations.

Contributors. Part 1: Verification of Response to Stress. Stress responses in Scots pine (Pinus sylvestris L.). Cloning and characterisation of an ozone-inducible pinysylvin methyltransferase H. Chiron, et al. Screening of Sitka spruce genotypes for resistances to the White Pine Weevil in British Columbia J.N. King, R.I. Alfaro. Genetic variation in two heavily polluted stands of Norway spruce (Picea abies [L Karst.) as indicated by nuclear and organelle DNA markers R. Riegel, et al. Effects of extreme SO2-air pollution in winter 1995/96 on vitality and growth of SO2-tolerant Norway spruce (Picea abies [L. Karst.) clones in the Ore mountains H. Wolf. Variation in adaptation and growth as indicated by provenance trial Platycladus orientalis (L.) Franco X. Shen, X. Chen. Influence of nursery environment and pollution on alders L. Mejnartowicz. Part 2: Genetic Variation under Diverse Environmental Conditions. Small scale spatial genetic structure of six tropical tree species in French Guiana B. Degen, et al. Genetic variation in natural populations of Araucaria angustifolia (Bert.) O. Kuntze in Brazil V.A. Sousa, H.H. Hattemer. Microsatellite DNA markers and their usefulness in poplars, and conservation of microsatellite DNA loci in Salicaceae O.P. Rajora, M.H. Rahman. PCR-RFLP analysis of introns of nuclear genes in Populus and Prunus B. Heinze. Genetic types in white oak populations north of the Alps and in the Danube valley U.M. Csaikl, A.O. Konig. Highly polymorphic uniparentally inherited DNA markers for spatial genetic analysis of silver fir (Abies alba Mill.) populations B. Ziegenhagen, et al. Levels of genetic differentiation inPinus halepensis Mill. in Spain using quantitative traits, isozymes, RAPDs and cp-microsatellites R. Alia, et al. Geographical variation of gene diversity of Pinus pinaster Ait. in the Iberian Peninsula S.C. Gonzalez-Martinez, et al. Is autochthony an operational concept? F.N. Schoppa, H.-R. Gregorius. Part 3: Genetic Resources, Reproduction, Management. Molecular markers in sustainable management, conservation, and restoration of forest genetic resources O.P. Rajora, A. Mosseler. Sustainable treatment of resources: The genetic basis H.-R. Gregorius. Genetic diversity and differentiation of individual effective pollen clouds in trees H.H. Hattemer, et al. Microsatellite analysis of small anonymous seedlot samples from pedunculate oak (Quercus robur): a promising approach to monitor the number of different seed parents and pollen donors C. Lexer, et al. Fructification and genetic structures of Fagus sylvatica mixed stands in upper regions of the Harz mountains D. Krabel, et al. Dispersal of seed and effective pollen in small stands of European beech (Fagus sylvatica L.) K. Wang, H.H. Hattemer. Patterns of seed dispersal in a scattered forest tree species (Sorbus torminalis) based on multi-scale investigation of population genetic structure for chloroplast DNA S. Oddou-Muratorio, et al. Gene flow and mating system in a seedling seed orchard and a natural stand of Pinus merkusii Jungh. et de Vriese in Indonesia I.Z. Siregar, H.H. Hattemer. The pattern of genetic variation in Pinus nigra subspecies pallasiana natural populations from the Kazdag and Bolkar mountains, Turkey: Implications for in situ gene conservation Z. Kaya, et al. Genetic

For many molecular ecologists, the mantra and mission of the field of ecological genomics could be encapsulated by the phrase 'to find the genes that matter' (Mitchell-Olds ; Rockman ). This phrase of course refers to the early hope and current increasing success in the search for genes whose variation underlies phenotypic variation and fitness in natural populations. In the years since the modern incarnation of the field of ecological genomics, many would agree that the low-hanging fruit has, at least in principle, been plucked: we now have several elegant examples of genes whose variation influences key adaptive traits in natural populations, and these examples have revealed important insights into the architecture of adaptive variation (Hoekstra et al. ; Shapiro et al. ; Chan et al. ). But how well will these early examples, often involving single genes of large effect on discrete or near-discrete phenotypes, represent the dynamics of adaptive change for the totality of phenotypes in nature? Will traits exhibiting continuous rather than discrete variation in natural populations have as simple a genetic basis as these early examples suggest (Prasad et al. ; Rockman )? Two papers in this issue (Robinson et al. ; Santure et al. ) not only suggest answers to these questions but also provide useful extensions of statistical approaches for ecological geneticists to study the genetics of continuous variation in nature. Together these papers, by the same research groups studying evolution in a natural population of Great Tits (Parus major), provide a glimpse of what we should expect as the field begins to dissect the genetic basis of what is arguably the most common type of variation in nature, and how genome-wide surveys of variation can be applied to natural populations without pedigrees.

INTRODUCTION Understanding the genetic basis of complex adaptive traits is key to understanding how natural and anthropomorphic factors have influenced and will influence the shape of genetic diversity and trajectory of evolution in natural populations. Complex adaptive traits are quantitative traits – those that vary on a continuous scale, and even more generally, are sometimes defined as traits that are expressed as a function of products from multiple genes (Falconer & MacKay 1996; Roff 1997; Lynch & Walsh 1998). Although classical quantitative genetics has revealed the genetic basis to numerous morphological, physiological, and life history traits in plants and animals, the actual genes (loci) and allelic variation with loci underlying key functional differences among organisms remain unknown. Understanding the genes involved in species- and population-level diversity can provide important tools (i.e., genetic markers) for resource managers that are charged with conservation, management, and restoration of natural populations. In this chapter, our examples and review are focused on non-model, non-domesticated organisms as it is the diversity in natural populations, shaped by the natural processes of evolution, with which natural resource managers are most concerned. Population genetics has undoubtedly been one of the most important fields in the conservation, management, and restoration of native plant and animal species. Together with ecological and life history information, “neutral” genetic markers, or those mirroring the neutral demographic processes of natural populations, are important tools for the delineation of management units or evolutionary significant units for conservation and management. Loci that have been shaped by natural selection, in the process of adaptive population divergence, can however exhibit levels of differentiation markedly different than neutral loci (Leinonen et al. 2008; Vali et al. 2008; Nosil et al. 2009).