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Hybridization can serve as an evolutionary stimulus, but we have little understanding of introgression at early stages of hybrid zone formation. We analyze reproductive isolation and introgression between a range-limited and a widespread species. Reproductive barriers are estimated based on differences in flowering time, ecogeographic distributions, and seed set from crosses. We find an asymmetrical mating barrier due to cytonuclear incompatibility that is consistent with observed clusters of coincident and concordant tension zone clines (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of concordant clines are spread across the hybrid zone, resulting in weak coupling among barrier loci and extensive introgression. Neutral clines had nearly equal introgression into both species' ranges, while putative cases of adaptive introgression had exceptionally wide clines with centers shifted towards one species. Analyses of cline shape indicate that secondary contact was initiated within the last 800 generations with the per-generation dispersal between 200 and 400 meters, and provide some of the first estimates of the strength of selection required to account for observed levels of adaptive introgression. The weak species boundary between these species appears to be in early stages of dissolution, and ultimately will precipitate genetic swamping of the range-limited species. This article is protected by copyright. All rights reserved.

Background Patterns of multi-locus differentiation (i.e., genomic clines) often extend broadly across hybrid zones and their quantification can help diagnose how species boundaries are shaped by adaptive processes, both intrinsic and extrinsic. In this sense, the transitioning of loci across admixed individuals can be contrasted as a function of the genome-wide trend, in turn allowing an expansion of clinal theory across a much wider array of biodiversity. However, computational tools that serve to interpret and consequently visualize ‘genomic clines’ are limited, and users must often write custom, relatively complex code to do so. Results Here, we introduce the ClineHelpR R-package for visualizing genomic clines and detecting outlier loci using output generated by two popular software packages, bgc and Introgress. ClineHelpR bundles both input generation (i.e., filtering datasets and creating specialized file formats) and output processing (e.g., MCMC thinning and burn-in) with functions that directly facilitate interpretation and hypothesis testing. Tools are also provided for post-hoc analyses that interface with external packages such as ENMeval and RIdeogram. Conclusions Our package increases the reproducibility and accessibility of genomic cline methods, thus allowing an expanded user base and promoting these methods as mechanisms to address diverse evolutionary questions in both model and non-model organisms. Furthermore, the ClineHelpR extended functionality can evaluate genomic clines in the context of spatial and environmental features, allowing users to explore underlying processes potentially contributing to the observed patterns and helping facilitate effective conservation management strategies.

The name Rhodanthidium caturigense (s.l.) combines several similar taxa which have been described on the level of form, subspecies or species and which occur in an area which extends from Iran in the south-east, across the Alps in the north and to the Iberian Peninsula in the west. A detailed quantitative assessment of 17 parameters describing the colour pattern reveals that it follows a smooth geographical cline, with rich yellow coloration in the south being gradually replaced by more melanic colorations in the north. The correlation between geographic latitude and colour scores follows a linear pattern and is highly significant in both sexes (p 0.05), the males are on average 9.7% larger than the females in the northernmost populations (p

Adaptation across environmental gradients has been demonstrated in numerous systems with extensive dispersal, despite high gene flow and consequently low genetic structure. The speed and mechanisms by which such adaptation occurs remain poorly resolved, but are critical to understanding species spread and persistence in a changing world. Here, we investigate these mechanisms in the European green crab Carcinus maenas, a globally distributed invader. We focus on a northwestern Pacific population that spread across12 degrees of latitude in 10 years from a single source, following its introduction35 years ago. Using six locations spanning1500 km, we examine genetic structure using 9376 single nucleotide polymorphisms (SNPs). We find high connectivity among five locations, with significant structure between these locations and an enclosed lagoon with limited connectivity to the coast. Among the five highly connected locations, the only structure observed was a cline driven by a handful of SNPs strongly associated with latitude and winter temperature. These SNPs are almost exclusively found in a large cluster of genes in strong linkage disequilibrium that was previously identified as a candidate for cold tolerance adaptation in this species. This region may represent a balanced polymorphism that evolved to promote rapid adaptation in variable environments despite high gene flow, and which now contributes to successful invasion and spread in a novel environment. This research suggests an answer to the paradox of genetically depauperate yet successful invaders: populations may be able to adapt via a few variants of large effect despite low overall diversity.

Genetic stock identification (GSI) is a major management tool of Pacific salmon (Oncorhynchus Spp.) that has provided rich genetic baseline data of allozymes, microsatellites, and single‐nucleotide polymorphisms (SNPs) across the Pacific Rim. Here, we analyzed published data sets for adult chum salmon (Oncorhynchus keta), namely 10 microsatellites, 53 SNPs, and a mitochondrial DNA locus (mtDNA3, control region, and NADH‐3 combined) in samples from 495 locations in the same distribution range (n = 61,813). TreeMix analysis of the microsatellite loci identified the greatest convergence toward Japanese/Korean populations and suggested two admixture events from Japan/Korea to Russia and the Alaskan Peninsula. The SNPs had been purposively collected from rapidly evolving genes to increase the power of GSI. The largest expected heterozygosity was observed in Japanese/Korean populations for microsatellites, whereas it was largest in Western Alaskan populations for SNPs, reflecting the SNP discovery process. A regression of SNP population structures on those of microsatellites indicated the selection of the SNP loci according to deviations from the predicted structures. Specifically, we matched the sampling locations of the SNPs with those of the microsatellites and performed regression analyses of SNP allele frequencies on a 2‐dimensional scaling (MDS) of matched locations obtained from microsatellite pairwise F ST values. The MDS first axis indicated a latitudinal cline in American and Russian populations, whereas the second axis showed differentiation of Japanese/Korean populations. The top five outlier SNPs included mtDNA3, U502241 (unknown), GnRH373, ras1362, and TCP178, which were identified by principal component analysis. We summarized the functions of 53 nuclear genes surrounding SNPs and the mtDNA3 locus by referring to a gene database system and propose how they may influence the fitness of chum salmon., By regressing the SNP population structures on those of the microsatellites, we estimated the selection on the SNP loci according to deviations from the predicted structures. The top five outlier SNPs were mtDNA3 (control region and NADH‐3 combined), U502241 (unknown), GnRH373, ras1362, and TCP178, which significantly differentiated in Japanese/Korean populations. The functions of the outlier SNPs related to fitness, namely endurance exercise training, oxygen consumption, reproduction, and growth.

Geographically connected species pairs with weakly differentiated genomes could either represent cases of genomic homogenization in progress or of incipient parapatric speciation. Discriminating between these processes is difficult because intermediate stages of either may produce weakly differentiated genomes that diverge at few locations. We used coalescent modelling applied to a genome-wide sample of SNPs to discriminate between speciation with gene flow and genomic homogenization in two phenotypically distinct but genomically weakly diverged species of elevationally replacing Ramphocelus tanagers, forming a hybrid zone in the Andean foothills. We found overwhelming support for a model of genomic homogenization following secondary contact. Simulating under this model suggested that our species pair was differentiated (FST = 0.30) at secondary contact but that most of the genome has rapidly homogenized during 254 Ky of high gene flow towards the present (FST = 0.02). Despite extensive genome-wide homogenization, plumage remains distinctive with a narrower than expected geographic cline width, indicating divergent selection on colour. We found two SNPs significantly associated with plumage colour, which retain moderately high FST . We conclude that the majority of the genome has fused, but that divergent selection on select loci probably maintains the geographically structured colour differences between these incipient species.

Summary Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance.We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance.Our findings indicate that the chloroplast genome had substantially deeper divergence (branch‐length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation‐by‐distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome.Altogether, this study highlights a critical role of sex‐biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance.

Wing, tail and bill lengths of Hooded Vultures were measured on 36 wild-caught birds and 75 in museum collections. A further 60 measurements were taken from literature, and 40 measurements were received from the Musée royal de l’Afrique centrale (Tervuren, Belgium). By grouping them into regions of Africa it was shown that the smallest birds were in West Africa and the largest in southern Africa (which is well known), with a gradation in between. Sizes varied according to a cline, and were correlated with average altitude. Given that the species has the same colouration (head, caruncles, plumage) from one end of the range to the other, indeed that populations are contiguous from Senegal to South Africa, then this goes against recognising any subspecies, but rather an intraspecific trend in sizes

The courtship song of male Drosophila melanogaster is generated by wing vibration and contains an interpulse interval (IPI) which is species-specific and usually falls in the mean range of 30–40 ms. The IPI is extremely temperature-sensitive, so we wondered whether flies collected along the eastern coast of Australia between latitudes 16.9°S and 42.9°S might have adapted to the different thermal conditions and show differences in mean IPI. We observe a significant correlation between IPI and latitude in addition to the well-known association between latitude and body size (Bergmannn’s Rule). However, somewhat surprisingly we could not detect a significant association between body size and IPI. We also examined flies collected from the North and South-facing slopes of ‘Evolution Canyon’ in Israel and observed differences in IPI that support the view that thermal adaptation can shape this important song character. We also examined the songs of flies from Kenya and observed no correlation between altitude of collection and IPI. In all three experiments, body size did not correlate with IPI. A global analysis of all three sets of populations on three continents revealed a strong association between IPI and latitude. We speculate that IPI is shaped by thermal and sexual selection whereas body size is also shaped by natural selection.

The use of genomic and phenotypic data to scan for outliers is a mainstay for studies of hybridization and speciation. Geographic cline analysis of natural hybrid zones is widely used to identify putative signatures of selection by detecting deviations from baseline patterns of introgression. As with other outlier-based approaches, demographic histories can make neutral regions appear to be under selection and vice versa. In this study, we use a forward-time individual-based simulation approach to evaluate the robustness of geographic cline analysis under different evolutionary scenarios. We modelled multiple stepping-stone hybrid zones with distinct age, deme sizes, and migration rates, and evolving under different types of selection. We found that drift distorts cline shapes and increases false positive rates for signatures of selection. This effect increases with hybrid zone age, particularly if migration between demes is low. Drift can also distort the signature of deleterious effects of hybridization, with genetic incompatibilities and particularly underdominance prone to spurious typing as adaptive introgression. Our results suggest that geographic clines are most useful for outlier analysis in young hybrid zones with large populations of hybrid individuals. Current approaches may overestimate adaptive introgression and underestimate selection against maladaptive genotypes.

Body pigmentation is an evolutionarily diversified and ecologically relevant trait with substantial variation within and between species, and important roles in animal survival and reproduction. Insect pigmentation, in particular, provides some of the most compelling examples of adaptive evolution, including its ecological significance and genetic bases. Pigmentation includes multiple aspects of color and color pattern that may vary more or less independently, and can be under different selective pressures. We decompose Drosophila thorax and abdominal pigmentation, a valuable eco‐evo‐devo model, into distinct measurable traits related to color and color pattern. We investigate intra‐ and interspecific variation for those traits and assess its different sources. For each body part, we measured overall darkness, as well as four other pigmentation properties distinguishing between background color and color of the darker pattern elements that decorate each body part. By focusing on two standard D. melanogaster laboratory populations, we show that pigmentation components vary and covary in distinct manners depending on sex, genetic background, and temperature during development. Studying three natural populations of D. melanogaster along a latitudinal cline and five other Drosophila species, we then show that evolution of lighter or darker bodies can be achieved by changing distinct component traits. Our results paint a much more complex picture of body pigmentation variation than previous studies could uncover, including patterns of sexual dimorphism, thermal plasticity, and interspecific diversity. These findings underscore the value of detailed quantitative phenotyping and analysis of different sources of variation for a better understanding of phenotypic variation and diversification, and the ecological pressures and genetic mechanisms underlying them., We characterize genetic and environmental sources of intra‐ and interspecies variation in distinct quantitative properties of Drosophila body pigmentation, of interest in eco‐evo‐devo studies.

The insulin insulin-like growth factor signaling pathway has been hypothesized as a major determinant of life history profiles that vary adaptively in natural populations. InDrosophila melanogaster, multiple components of this pathway vary predictably with latitude; this includesfoxo, a conserved gene that regulates insulin signaling and has pleiotropic effects on a variety of fitness-associated traits. We hypothesized that allelic variation atfoxounderlies genetic variance for traits that vary with latitude and reflect local adaptation. To evaluate this, we generated recombinant outbred populations in which the focalfoxoallele was homozygous and fixed for either the allele common at high latitude or low latitude and the genomic background was randomized across 20 inbred lines. After eight generations of recombination, experimental populations were phenotyped for a series of traits related to gene function. Our results demonstrate that natural allelic variation atfoxohas major and predictable effects on body size and starvation tolerance, but not on development time. These patterns mirror those observed in natural populations collected across the latitudinal gradient in the eastern U.S.: clines were observed for starvation tolerance and body size, but development time exhibited no association with latitude. Furthermore, differences in size betweenfoxogenotypes were equivalent to those observed between populations sampled from the latitudinal extremes, although contribution to the genetic variance for starvation tolerance was less pronounced. These results suggest that allelic variation atfoxois a major contributor to adaptive patterns of life history variation in natural populations of this genetic model.

During secondary contact between two species when hybrids are less fit than parents, mating signals are expected to diverge, while aggressive signals are expected to converge. If a single signal trait is used in both mating and aggression, then the dynamics between these two forces could influence the evolutionary trajectory of that trait. We studied such a situation in an avian hybrid zone between two Setophaga species, where birdsong is used in both mate attraction and territory defense. We hypothesized that song modules of the two species will show separate and distinct geographic patterns due to the influence of selective pressures for effective territorial aggression and for effective mate attraction. We conducted geographic cline analyses and playback experiments across this hybrid zone. We found an unexpected geographic pattern of asymmetric introgression of song rhythm, which may be explained by results of the playback experiments that suggest that differences in song rhythm serve a greater role in mate attraction than in territory defense. In contrast, differences in syllable morphology show little evidence of importance in mate attraction or territorial defense. Song features converge in the hybrid zone, yet patterns of trait change suggest that the song production modules may vary in their modes of development and inheritance. Syringeal motor gesturing, which gives rise to syllable morphology, shows a nonclinal mosaic pattern, suggesting that this trait may be predominantly learned. In contrast, respiratory patterning, which forms song rhythm, shows a clinal geographic transition, suggesting that this trait could be more innate. The results indicate that opposing forces act independently on song via distinct modules of the song production mechanism, driving complex patterns of song trait evolution., In a hybrid zone between two songbird species, we find complex patterns of behavioral trait evolution. We interpret results from geographic cline analyses and playback studies to suggest that opposing forces act independently on song via distinct modules of the song production mechanism.

When species are continuously distributed across environmental gradients, the relative strength of selection and gene flow shape spatial patterns of genetic variation, potentially leading to variable levels of differentiation across loci. Determining whether adaptive genetic variation tends to be structured differently than neutral variation along environmental gradients is an open and important question in evolutionary genetics. We performed exome-wide population genomic analysis on deer mice sampled along an elevational gradient of nearly 4,000 m of vertical relief. Using a combination of selection scans, genotype−environment associations, and geographic cline analyses, we found that a large proportion of the exome has experienced a history of altitude-related selection. Elevational clines for nearly 30% of these putatively adaptive loci were shifted significantly up- or downslope of clines for loci that did not bear similar signatures of selection. Many of these selection targets can be plausibly linked to known phenotypic differences between highland and lowland deer mice, although the vast majority of these candidates have not been reported in other studies of highland taxa. Together, these results suggest new hypotheses about the genetic basis of physiological adaptation to high altitude, and the spatial distribution of adaptive genetic variation along environmental gradients.

Distinguishing between secondary versus primary hybrid zone formation remains a challenging task as, for instance, the time window in which these historical (vicariant) versus contemporary (environmental‐selective) processes are distinguishable may be relatively narrow. Here, we examine the origin and structure of a transition zone between two subspecies of Tephroseris helenitis along the central Northern Alps, using molecular (AFLP) and morphological (achene type) data in combination with ecological niche models (ENMs) to hindcast ranges at the Last Glacial Maximum (LGM) and mid‐Holocene. Samples were collected over a c. 350 km long transect, largely covered by ice during the LGM. Genetically nonadmixed individuals of subspp. helenitis versus salisburgensis dominated the westernmost versus eastern transect areas, with admixed individuals occurring in between. Clines for achene morphology and outlier loci potentially under climate‐driven selection were steep, largely noncoincidental, and displaced to the east of the cline centre for neutral AFLPs. During the LGM, ssp. helenitis should have been able to persist in a refugium southwest of the transect, while suitable habitat for ssp. salisburgensis was apparently absent at this time. Together with patterns of genetic and clinal variation, our ENM data are suggestive of a primary hybrid zone that originated after the species’ postglacial, eastward expansion. The observed clinal changes may thus reflect random/nonadaptive processes during expansion and selection on particular loci, and possibly achene type, in response to a long‐term, west‐to‐east climate gradient in the direction of more stressful (e.g., wetter/cooler) conditions. Overall, this study adds to the vast hybrid zone literature a rare example of a hybrid zone caused by primary differentiation within a plant species, underlaid by historical range expansion.

Invasive species are one of the main causes of biodiversity loss worldwide. As introduced, populations increase in abundance and geographical range, so does the potential for negative impacts on native communities. As such, there is a need to better understand the processes driving range expansion as species become established in recipient landscapes. Through an investigation into capacity for population growth and range expansion of introduced populations of a non‐native lizard (Podarcis muralis), we aimed to demonstrate how multi‐scale factors influence spatial spread, population growth, and invasion potential in introduced species. We collated location records of P. muralis presence in England, UK through data collected from field surveys and a citizen science campaign. We used these data as input for presence‐background models to predict areas of climate suitability at a national‐scale (5 km resolution), and fine‐scale habitat suitability at the local scale (2 m resolution). We then integrated local models into an individual‐based modeling platform to simulate population dynamics and forecast range expansion for 10 populations in heterogeneous landscapes. National‐scale models indicated climate suitability has restricted the species to the southern parts of the UK, primarily by a latitudinal cline in overwintering conditions. Patterns of population growth and range expansion were related to differences in local landscape configuration and heterogeneity. Growth curves suggest populations could be in the early stages of exponential growth. However, annual rates of range expansion are predicted to be low (5–16 m). We conclude that extensive nationwide range expansion through secondary introduction is likely to be restricted by currently unsuitable climate beyond southern regions of the UK. However, exponential growth of local populations in habitats providing transport pathways is likely to increase opportunities for regional expansion. The broad habitat niche of P. muralis, coupled with configuration of habitat patches in the landscape, allows populations to increase locally with minimal dispersal., We investigated the potential for population growth and range expansion of introduced populations of a non‐native lizard (Podarcis muralis), considering multi‐scale factors influencing growth, and spatial spread. National‐scale models indicated climate suitability restricted to the southern parts of the UK, limited by a latitudinal cline in overwintering conditions. Patterns of local population growth and range expansion were related to differences in local landscape configuration and heterogeneity. The broad habitat niche of P. muralis, coupled with configuration of habitat patches in the landscape, allows populations to increase locally with minimal dispersal

Diaphanosoma s.l., with 40+ described species, is the largest genus of the Sididae and the Ctenopoda, similar in many ways to the anomopod genus Daphnia. Here, we offer a c morphological evaluation of 33 species and contrast it with an analysis of the bar coding fragment of the cytochrome c oxidase subunit (COI) gene in order to gain insight into the taxonomy and phylogeny of the group. A search for structure in the genus based on micromorphological characters identified (1) the number of setae on the endopodite of P6 and (2) the relative length of the three apical setae of the exopodite of P6 as consistent markers, recovering two clades, the hexa-clade (with six endital setae) and the hepta-group (with seven setae). A third character is the armament of the posterior zone of the ventral margin of the valves, denticulated in the hexa-group, with fine filaments between the denticles in the hepta-group. Taxonomically, the two clades are assigned the rank of genera. Valid names for both are available in the published literature (Diaphanosoma Fischer s.s. and Neodiaphanosoma Paggi and Da Rocha, amended). A COI-based phylogenetic estimate leads to the same conclusion as morphology, but reveals cryptic speciation as well. COI reveals relatively small genetic distances within and between temperate climate species (e.g., in the D. birgei group) and large differences that form a cline from Australia (the terra typica) across southeast Asia in the tropical Neodiaphanosoma species D. excisum. African populations need more study, but probably represent a separate species. The entire group shows (macro)morphological stasis in the presence of molecular evolution but Neodiaphanosoma is evolving at a much faster rate than Diaphanosoma s.s. that is either a younger group. This hypothesis needs more testing, however. A biogeographic map recovers Neodiaphanosoma (containing slightly over 10 species) as restricted to the tropics, with limited penetration of the subtropics in the southern hemisphere. The more speciose Diaphanosoma group (up to 30 species) lives in the temperate and continental climate zone, with limited extension into subpolar zones, but considerable penetration of the subtropics and tropics. The subtropics, where both groups broadly overlap, is the zone with the highest species richness.

We studied the population genetic structure underlying the geographic variation in the structural colour of the geotrupid dung beetle, Phelotrupes auratus, which exhibits metallic body colours of different reflectance wavelengths perceived as red, green and indigo. These forms occur parapatrically in an area of Japan. The colour variation was not related to variation in climatic factors. Using single nucleotide polymorphisms (SNPs) from restriction-site-associated DNA sequences, we discriminated five groups of populations (west/red, south/green, south/indigo, south/red and east/red) by a combination of genetic clusters (west, south and east) and three colour forms. There were three transition zones for the colour forms: two between the red and green forms were hybrid zones with steep genetic clines, which implies the existence of barriers to gene flow between regions with different colours. The remaining transition zone between the green and indigo forms lacked genetic differentiation, despite the evident colour changes, which implies regionally specific selection on the different colours. In a genomewide association study, we identified four SNPs that were associated with the red/green or indigo colour and were not linked with one another, which implies that the coloration was controlled by multiple loci, each affecting the expression of a different colour range. These loci may have controlled the transitions between different combinations of colours. Our study demonstrates that geographic colour variation within a species can be maintained by nonuniform interactions among barriers to gene flow, locally specific selection on different colours, and the effects of different colour loci.

Local adaptation can occur at small spatial scales relative to the dispersal capacity of species. Alpine ecosystems have sharp environmental clines that offer an opportunity to investigate the effects of fine-scale shifts in species' niche breadth on adaptive genetic processes. Here we examine two grasshopper species endemic to the Australian Alps (Kosciuscola spp.) that differ in elevational niche breadth: one broader, K. usitatus (1400-2200 m), and one narrower, K. tristis (1600-2000 m). We examine signatures of selection with respect to environmental and morphological variables in two mountain regions using FST outlier tests and environmental association analyses (EAAs) applied to single nucleotide polymorphism (SNP) data (K. usitatus: 9017 SNPs, n = 130; K. tristis: 7363 SNPs, n = 135). Stronger genetic structure was found in the more narrowly distributed K. tristis, which showed almost twice the number of SNPs under putative selection (10.8%) compared with K. usitatus (5.3%). When examining SNPs in common across species (n = 3058), 260 SNPs (8.5%) were outliers shared across species, and these were mostly associated with elevation, a proxy for temperature, suggesting parallel adaptive processes in response to climatic drivers. Additive polygenic scores (an estimate of the cumulative signal of selection across all candidate loci) were nonlinearly and positively correlated with elevation in both species. However, a steeper correlation in K. tristis indicated a stronger signal of spatially varying selection towards higher elevations. Our study illustrates that the niche breadth of co-occurring and related species distributed along the same environmental cline is associated with differences in patterns of microgeographical adaptation.

Speciation mechanisms remain controversial. Two speciation models occur in Israeli subterranean mole rats, genus Spalax: a regional speciation cline southward of four peripatric climatic chromosomal species and a local, geologic-edaphic, genic, and sympatric speciation. Here we highlight their genome evolution. The five species were separated into five genetic clusters by single nucleotide polymorphisms, copy number variations (CNVs), repeatome, and methylome in sympatry. The regional interspecific divergence correspond to Pleistocene climatic cycles. Climate warmings caused chromosomal speciation. Triple effective population size, N(e), declines match glacial cold cycles. Adaptive genes evolved under positive selection to underground stresses and to divergent climates, involving interspecies reproductive isolation. Genomic islands evolved mainly due to adaptive evolution involving ancient polymorphisms. Repeatome, including both CNV and LINE1 repetitive elements, separated the five species. Methylation in sympatry identified geologically chalk-basalt species that differentially affect thermoregulation, hypoxia, DNA repair, P53, and other pathways. Genome adaptive evolution highlights climatic and geologic-edaphic stress evolution and the two speciation models, peripatric and sympatric.

Parallel evolution is one of the striking patterns in nature. The presence of repeated evolution of the same phenotypes, suites of traits, and adaptations suggests a strong role for natural selection in shaping biological diversity. The reasoning is straightforward: each instance of repeated evolution makes it less likely that these features evolved neutrally or due to stochastic forces in each population or species. With the growing sequencing capability, we are now poised to examine the genetic basis of parallel evolution in model and nonmodel systems. On pages 4102-4117 of this issue of Molecular Ecology, van Boheemen and Hodgins (2020) provide an exemplar study of this kind, using common ragweed (Ambrosia artemisiifolia; Figure 1a). Their study is noteworthy and ambitious in many respects, and we think will serve as a model for studying parallel adaptation, even in nonmodel species.

Hybrid zones act as natural laboratories where divergent genomes interact, providing powerful systems for examining the evolutionary processes underlying biological diversity. In this study, we characterized patterns of genomic and phenotypic variation resulting from hybridization between divergent intraspecific lineages of the Neotropical red-eyed treefrog (Agalychnis callidryas). We found genetic evidence of a newly discovered contact zone and phenotypic novelty in leg colour-a trait suspected to play a role in mediating assortative mating in this species. Analysis of hybrid ancestry revealed an abundance of later-generation Fn individuals, suggesting persistence of hybrids in the contact zone. Hybrids are predominantly of southern ancestry but are phenotypically more similar to northern populations. Genome-wide association mapping revealed QTL with measurable effects on leg-colour variation, but further work is required to dissect the architecture of this trait and establish causal links. Further, genomic cline analyses indicated substantial variation in patterns of introgression across the genome. Directional introgression of loci associated with different aspects of leg colour are inherited from each parental lineage, creating a distinct hybrid colour pattern. We show that hybridization can generate new phenotypes, revealing the evolutionary processes that potentially underlie patterns of phenotypic diversity in this iconic polytypic frog. Our study is consistent with a role of hybridization and sexual selection in lineage diversification, evolutionary processes that have been implicated in accelerating divergence in the most phenotypically diverse species.

Cerebral lateralization involves information being processed differently by the brain’s two hemispheres and is often associated with behavioural laterality such as preferential use of right or left limbs. Despite having evolved widely in animals, laterality of limb use has been mostly studied in humans and other primates (e.g. handedness) and is relatively poorly understood in other taxa. Perhaps accordingly, the possibility of geographic variation in laterality has been largely overlooked. Foot preferences in parrots have been established as a tractable model for behavioural laterality investigations. Here we tested for geographic and temporal variation in lateralization of foot use in an Australian parrot complex, the crimson rosella (Platycercus elegans). We observed lateralization of foot use during foraging in N = 458 wild individuals over nine years, from 42 locations and four subspecies. We show, for the first time to our knowledge in any animal, a cline in laterality. In the morphologically highly variable P. e. adelaidae subspecies, which occupies a marked latitudinal habitat cline, we show that right side lateralization increased at higher (more southerly) latitudes. We also found ambidexterity varied between subspecies, and was present almost exclusively in the morphologically intermediate populations which occupy intermediate habitats, reaching 11% of individuals in one such population. Across all populations, strong lateralization at individual and population levels existed, with 93% of birds consistently lateralized, and 64% using the right foot preferentially. Age, year, season, or whether the bird was perched or on the ground, had no effects on foot preference. Using captive birds, we show that foot preferences were largely stable within individuals over time. Our findings provide rare examples of an intraspecific cline in behavioural lateralization and population differences in ambidexterity, and provide novel support for the hypothesis that ecological factors such as habitat and/or diet influences behavioural laterality within free-living animals.

The alien cynipid waspDryocosmus kuriphilusYasumatsu, 1951 is a serious pest of chestnuts(Castaneaspp.) in Japan, North America and Europe, causing fruit losses while inducing gallsin buds. WhileD. kuriphilusgalls have a recognizable and roughly invariable globular shape,their size varies, reaching up to 4 cm in diameter. Among other factors, such variation maydepend on different climatic conditions in different attacked areas. Here, we sampled andmeasured 375D. kuriphilusgalls from 25 localities throughout the Iberian Peninsula, includ-ing both cold and rainy northern (Eurosiberian) areas and warm and dry central-southern(Mediterranean) areas, to test the effects of climate and geographical location on gall morph-ology. The analyses indicate that gall mass and volume follow a pattern that can be associatedwith a climatic cline. In particular, the Eurosiberian galls were smaller than the Mediterraneangalls according to differences in climatic conditions. In the southern areas, the greaterinsolation regime does not allow the chestnut trees to be distributed at lower altitudes, butthe high rainfall and humidity regime of the mountain enclaves allow their presence. Theseconditions of insolation and precipitation seem to influence the morphological characteristicsof the galls ofD. kuriphilus., This study was financed by an Encomienda de Gestión from MAPAMA to Agencia Estatal CSIC, 16MNES003, awarded to JLNA,DGT, JF Gómez and CP, and by project AGL2016-76262-R (AEI/FEDER,UE), awarded to JLNA.

Thermal and nutritional stress are commonly experienced by animals. This will become increasingly so with climate change. Whether populations can plastically respond to such changes will determine their survival. Plasticity can vary among populations depending on the extent of environmental heterogeneity. However, theory conflicts as to whether environmental heterogeneity should increase or decrease plasticity. Using three locally adapted populations of Drosophila melanogaster sampled from a latitudinal gradient, we investigated whether plastic responses to combinations of nutrition and temperature increase or decrease with latitude for four traits: egg-adult viability, egg-adult development time, and two body size traits. Employing nutritional geometry, we reared larvae on 25 diets varying in protein and carbohydrate content at two temperatures: 18 and 25°C. Plasticity varied among traits and across the three populations. Viability was highly canalized in all three populations. The tropical population showed the least plasticity for development time, the sub-tropical showed the highest plasticity for wing area, and the temperate population showed the highest plasticity for femur length. We found no evidence of latitudinal plasticity gradients in either direction. Our data highlight that differences in thermal variation and resource predictability experienced by populations along a latitudinal cline are not sufficient to predict their plasticity.

Describing the structure and dynamics of hybrid zones has important consequences for our understanding of lineage diversification. Herbarium collections constitute an extensive, though often underutilized, morphological resource that can potentially be leveraged to identify and describe hybrid zones. We demonstrate the use of herbarium collections to describe the structure of a hybrid zone between two North American columbines, Aquilegia flavescens S. Watson and A. formosa Fisch. ex DC. Hybrid indices were calculated from floral morphology measurements and mapped using geolocation data, revealing an extensive and consistent pattern of floral intermediacy in several contact zones. Population phenotype samples from contact zones corroborate these findings and strongly suggest introgression. At one locality with a confirmed hybrid population, floral phenotypes show clinal variation in parental-type morphology along an elevational gradient, in the direction predicted by the divergent elevational distributions of these taxa. We argue that these patterns together reflect a habitat-associated mosaic hybrid zone, consistent with divergent ecological selection maintaining the structure of the hybrid zone.

Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700–2000 BP that affected primarily marine-based groups, and a later one impacting all, How Indigenous populations in the southern tip of South America have changed over time has been unclear. Here the authors generate genome-wide data for 20 ancient individuals and examine how past migrations and admixture events correlate to geography and shifts in the archaeological record.

Two subspecies of ayu, Plecoglossus altivelis altivelis (nominotypical subspecies) and P. a. ryukyuensis (Ryukyu-ayu), differ morphologically, behaviorally, and genetically. Specimens from nine populations comprising both subspecies were investigated to examine whether their meristic characteristics follow a widely observed geographical tendency known as Jordan’s rule. Seven out of the eleven characteristics increased in frequency with latitude, following Jordan’s rule. Contrarily to the expectation from Jordan’s rule, however, Ryukyu-ayu had more anal fin rays than nominotypical subspecies in the temperate zone, suggesting genetic divergence underlying this characteristic between these two subspecies. The two subtropical populations showed a reversal of the geographic cline in the number of scales and dorsal fin rays, indicating these do not share a gene pool. The present study, without using genetic indicator, remains disputable to consider genetic status within Ryukyu-ayu further.

Reproductive isolation is a fundamental step in speciation. While sex chromosomes have been linked to reproductive isolation in many model systems, including hominids, genetic studies of the contribution of sex chromosome loci to speciation for natural populations are relatively sparse. Natural hybrid zones can help identify genomic regions contributing to reproductive isolation, like hybrid incompatibility loci, since these regions exhibit reduced introgression between parental species. Here, we use a primate hybrid zone (Alouatta palliata × Alouatta pigra) to test for reduced introgression of X-linked SNPs compared to autosomal SNPs. To identify X-linked sequence in A. palliata, we used a sex-biased mapping approach with whole-genome re-sequencing data. We then used genomic cline analysis with reduced-representation sequence data for parental A. palliata and A. pigra individuals and hybrids (n = 88) to identify regions with non-neutral introgression. We identified ~26 Mb of non-repetitive, putatively X-linked genomic sequence in A. palliata, most of which mapped collinearly to the marmoset and human X chromosomes. We found that X-linked SNPs had reduced introgression and an excess of ancestry from A. palliata as compared to autosomal SNPs. One outlier region with reduced introgression overlaps a previously described “desert” of archaic hominin ancestry on the human X chromosome. These results are consistent with a large role for the X chromosome in speciation across animal taxa and further, suggest shared features in the genomic basis of the evolution of reproductive isolation in primates.

Global change is shifting both temperature patterns and the geographic distribution of pathogens, and infection has already been shown to substantially reduce host thermal performance, potentially placing populations at greater risk that previously thought. But what about individuals that are able to successfully clear an infection? Whilst the direct damage a pathogen causes will likely lead to reductions in host's thermal tolerance, the response to infection often shares many underlying pathways with the general stress response, potentially acting as a buffer against subsequent thermal stress. Here, by exposing Drosophila melanogaster to heat-killed bacterial pathogens, we investigate how activation of a host's immune system can modify any response to both heat and cold temperature stress. In a single focal population, we find that immune activation can improve a host's knockdown times during heat shock, potentially offsetting some of the damage that would subsequently arise as an infection progresses. Conversely, immune activation had a detrimental effect on CTmax and did not influence lower thermal tolerance as measured by chill-coma recovery time. However, we also find that the influence of immune activation on heat knockdown times is not generalizable across an entire cline of locally adapted populations. Instead, immune activation led to signals of local adaptation to temperature being lost, erasing the previous advantage that populations in warmer regions had when challenged with heat stress. Our results suggest that activation of the immune system may help buffer individuals against the detrimental impact of infection on thermal tolerance; however, any response will be population specific and potentially not easily predicted across larger geographic scales, and dependent on the form of thermal stress faced by a host.

The variation in size along elevations has been investigated in various insect species, with contradictory results regarding Bergmann’s or James’ rules. Positive, negative, or hump-shaped patterns have been commonly found, but the sources of variation are generally unknown, because the contribution of genetic and environmental factors is not usually estimated. Social insects offer the opportunity to study the intraspecific variation and heritability of morphological traits due to the ease of finding family groups in the wild. Thus, we aimed to assess the variation in morphological characters of Atta cephalotes and to estimate their heritability as an attempt to understand the sources of variation. We sampled 30 soldiers from five nests at six different elevations in Colombia; soldiers were dissected, and ten morphometric characters were measured. Variation was analysed through nested MANOVA and REML analyses, and heritabilities and co-heritabilities were estimated using a full-sib model. We found significant differences between elevations and nests, with larger soldiers occurring at localities in intermediate elevations. Heritabilities varied when they were estimated with all data together or separated by locality, showing low-to-intermediate values, while co-heritabilities were intermediate to high. The nonlinear cline found in this study could be a result of the interactions among the factors generating Bergmann’s patterns, such as temperature, the ecology of leaf-cutting ants (management of temperature inside nests) and resource availability. The heritability results imply a genotype-environment interaction, with an overall greater effect of the environment on body size variation in A. cephalotes soldiers.

Populus tremuloides is the widest‐ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome‐wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of P. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal–Cascades (cluster 1), east‐slope Cascades–Sierra Nevadas–Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the P. tremuloides range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the “stable‐edge hypothesis” that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited “trailing‐edge” dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the “inland dispersal hypothesis” predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific‐coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable‐edge, refugial locations, and postglacial expansion within P. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific‐coastal genetic lineage of quaking aspen.

Wild plants with a wide distribution, including those exposed to a wide variety of environmental conditions, may have variations in key functional traits relevant for agricultural applications. The East Asian wild radish (Raphanus sativus var. raphanistroides) is an appropriate model plant because it is widely distributed and has outstanding sink capacity as well as two cultivars within the species. Multiple common garden trials with 14 populations and three testing sites were conducted across the Japanese archipelago to quantify variations in yield and allocation. Significant inter-population variations and interaction effects with testing sites were detected for the root and shoot mass and the root mass fraction (RMF). While the rank order of the population changed drastically among sites and the variance components of genetic effects were small in yield traits (2.4%-4.7%), RMF displayed a large genetic variance (23.2%) and was consistently higher in the northern populations at all sites. Analyses revealed that the mean temperature of growing season of the seed origin was the most prominent factor explaining variation in RMF, irrespective of the sites. We concluded that the trait of resource allocation had a temperature-related cline and plants in cooler climates could invest more resources into their roots.

Background The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors of present-day Italians may thus improve the understanding of demographic and biological processes that contributed to shape the gene pool of European populations. However, previous SNP array-based studies failed to investigate the full spectrum of Italian variation, generally neglecting low-frequency genetic variants and examining a limited set of small effect size alleles, which may represent important determinants of population structure and complex adaptive traits. To overcome these issues, we analyzed 38 high-coverage whole-genome sequences representative of population clusters at the opposite ends of the cline of Italian variation, along with a large panel of modern and ancient Euro-Mediterranean genomes. Results We provided evidence for the early divergence of Italian groups dating back to the Late Glacial and for Neolithic and distinct Bronze Age migrations having further differentiated their gene pools. We inferred adaptive evolution at insulin-related loci in people from Italian regions with a temperate climate, while possible adaptations to pathogens and ultraviolet radiation were observed in Mediterranean Italians. Some of these adaptive events may also have secondarily modulated population disease or longevity predisposition. Conclusions We disentangled the contribution of multiple migratory and adaptive events in shaping the heterogeneous Italian genomic background, which exemplify population dynamics and gene-environment interactions that played significant roles also in the formation of the Continental and Southern European genomic landscapes.

Across latitudinal clines, the juvenile developmental rates of ectotherms often covary with the length of the growing season, due to life-history trade-offs imposed by the time-constrained environments. However, as the start of the growing season often varies substantially across years, adaptive parental effects on juvenile developmental rates may mediate the costs of a delayed season. By employing a meta-analysis, we tested whether larval developmental rates across a latitudinal cline of the common frog (Rana temporaria) are affected by fluctuating onsets of breeding, across years. We predicted that larval developmental rate will be inversely related to the onset of breeding, and that northern populations will be more prone to shorten their developmental rate in response to late breeding, as the costs of delayed metamorphosis should be highest in areas with a shorter growing season. We found that the larval period of both northern and southern populations responded to parental environmental conditions to a similar degree in absolute terms, but in different directions. In northern populations, a late season start correlated with decreased development time, suggesting that the evolution of parental effects aids population persistence in time-constrained environments. In southern populations, late season start correlated with increased development time, which could potentially be explained as a predator avoidance strategy. Our findings suggest that local ecological variables can induce adaptive parental effects, but responses are complex, and likely trade-off with other ecological factors. Electronic supplementary material The online version of this article (10.1007/s00442-020-04642-8) contains supplementary material, which is available to authorized users.

Daylength is a major environmental condition that varies seasonally and predictably along a latitudinal cline, where higher latitudes exhibit greater ranges in total daylengths. Generally, ...

AIM: Introduced species may display or foster novel latitudinal clines because they are not well adapted to their new habitats. We tested the hypothesis that the latitudinal cline in nematode diversity in salt marshes would differ between the native (United States) and introduced (China) ranges of Spartina alterniflora. LOCATION: East Coasts of the United States (30.32–43.33°N) and China (30.36–39.14°N). METHODS: We extracted nematodes from soil samples collected at 32 sites along the United States East Coast and 41 sites along the Chinese coast. We compared latitudinal patterns in nematode diversity and composition between the native and introduced ranges. RESULTS: In the native range of S. alterniflora, nematode richness at lower latitudes was almost twice as high as that at higher latitudes. In contrast, we found no latitudinal pattern in nematode richness or diversity in the introduced range of S. alterniflora. Nematode genus richness at all sites in China was about half that at lower latitudes in the United States. Beta diversity of nematodes increased with geographic distance in the United States, but not China. MAIN CONCLUSIONS: Nematode diversity did not show latitudinal clines in salt marshes dominated by introduced S. alterniflora in China. A likely explanation is that the recently introduced populations are still relatively genetically homogenous, whereas in the native range, genetic variation in plant populations across latitude drives different nematode communities. We suggest that future studies of introduced species will gain additional insights by taking an explicitly geographic perspective.

Biological invasions offer model systems of contemporary evolution. We examined trait differences and evolution across geographic clines among continents of the intertidal grass Spartina alterniflora within its invasive and native ranges. We sampled vegetative and reproductive traits in the field at 20 sites over 20° latitude in China (invasive range) and 28 sites over 17° in the US (native range). We grew both Chinese and US plants in a glasshouse common garden for 3yr. Chinese plants were c.15% taller, c. 10% denser, and set up to four times more seed than US plants in both the field and common garden. The common garden experiments showed a striking genetic cline of seven-fold greater seed set at higher latitudes in the introduced but not the native range. By contrast, there was a slight genetic cline in some vegetative traits in the native but not the introduced range. Our results are consistent with others showing that introduced plants can evolve rapidly in the new range. S.alterniflora has evolved different trait clines in the native and introduced ranges, showing the importance of phenotypic plasticity and genetic control of change during the invasion process.

Author(s): Liu, W; Chen, X; Strong, DR; Pennings, SC; Kirwan, ML; Chen, X; Zhang, Y | Abstract: Introduced plants provide a unique opportunity to examine how plants respond through plasticity and adaptation to changing climates. We compared plants of Spartina alterniflora from the native (United States, 27–43°N) and introduced (China, 19–40°N) ranges. In the field and greenhouse, aboveground productivity of Chinese plants was greater than that of North American plants. Aboveground biomass in the field declined with increasing latitude in the native range, a pattern that persisted in the greenhouse, indicating a genetic basis. Aboveground biomass in the field displayed hump-shaped relationships with latitude in China, but this pattern disappeared in field and greenhouse common gardens, indicating phenotypic plasticity. Relationships in both geographic regions were explained by temperature, which is probably the underlying environmental factor affecting aboveground biomass. S. alterniflora has evolved greater biomass in China, but in the four decades since it was introduced, it has not yet evolved the genetic cline in biomass seen in its native range. By working at lower latitudes in the introduced range than have been sampled in the native range, we identified an optimum temperature in the introduced range above which aboveground productivity decreases.

A lack of optimal gene combinations, as well as low levels of genetic diversity, is often associated with the formation of species range margins. Conservation efforts rely on predictive modelling using abiotic variables and assessments of genetic diversity to determine target species and populations for controlled breeding, germplasm conservation and assisted migration. Biotic factors such as interspecific competition and hybridization, however, are largely ignored, despite their prevalence across diverse taxa and their role as key evolutionary forces. Hybridization between species with well‐developed barriers to reproductive isolation often results in the production of offspring with lower fitness. Generation of novel allelic combinations through hybridization, however, can also generate positive fitness consequences. Despite this possibility, hybridization‐mediated introgression is often considered a threat to biodiversity as it can blur species boundaries. The contribution of hybridization towards increasing genetic diversity of populations at range margins has only recently gathered attention in conservation studies. We assessed the extent to which hybridization contributes towards range dynamics by tracking spatio‐temporal changes in the central location of a hybrid zone between two recently diverged species of pines: Pinus strobiformis and P. flexilis. By comparing geographic cline centre estimates for global admixture coefficient with morphological traits associated with reproductive output, we demonstrate a northward shift in the hybrid zone. Using a combination of spatially explicit, individual‐based simulations and linkage disequilibrium variance partitioning, we note a significant contribution of adaptive introgression towards this northward movement, despite the potential for differences in regional population size to aid hybrid zone movement. Overall, our study demonstrates that hybridization between recently diverged species can increase genetic diversity and generate novel allelic combinations. These novel combinations may allow range margin populations to track favourable climatic conditions or facilitate adaptive evolution to ongoing and future climate change.

Patterns of body size variation along geographical gradients have long been searched for and generalized into eco-geographical rules. However, no rodent species has yet been analyzed in relation to the 3 dimensions of latitude, longitude and altitude. We analyzed geographical clines and dimorphism of body and skull size in the herb field mouse (Apodemus uralensis) across the species range, based on field data and on data from the literature. Sexual dimorphism in adult A. uralensis was not expressed at a large scale, while local patterns were inconsistent. Age-dependent size changes were most expressed in adult individuals: most characters of adults exceeded in size those of subadults, while subadult-juvenile size differences were only significant in body weight and length, zygomatic skull width, length of cranial diastema and breadth of braincase. Despite central morphological niches along the clines being separated, A. uralensis populations showed a high degree of size overlap in morphological space. We found the species to be characterized by high size variability, with the largest individuals inhabiting the eastern and southern edges of the distribution range. Tail, hind foot and ear lengths were largest in the southern part of the range, in agreement with Allen's rule. The main measurements that we analyzed, namely body mass, zygomatic skull width and condylobasal skull length, show the presence of 3 clines in the size of adult A. uralensis: (i) a decreasing south-north cline, opposing Bergmann's rule; (ii) an increasing west-east cline, in accordance with Murphy's rule; and (iii) an increasing altitudinal cline.

The number of clines (i.e., nonconstant equilibria) maintained by viability selection, migration, and partial global panmixia in a step-environment with a geographical barrier is investigated. Our results extend the results of T. Nagylaki (2016, Clines with partial panmixia across a geographical barrier, Theor. Popul. Biol. 109) from the no dominance case to arbitrary dominance and to various other selection functions. Unexpectedly, besides the usual monotone clines, we discover nonmonotone clines with both equal and unequal limits at \begin{document}$ \pm\infty $\end{document} .

For regulatory purposes, the name ‘Asian gypsy moth’ refers to a group of closely related Asian Lymantria species and subspecies whose female moths display flight capability, a trait believed to confer enhanced invasiveness relative to the European gypsy moth, Lymantria dispar dispar, whose females are flightless. Lymantria albescens and Lymantria postalba are Asian gypsy moths occurring in the southern Ryukyu Islands and in the northern Ryukyu and adjacent Kyushu and Shikoku Islands of Japan, respectively. Although once considered subspecies of L. dispar, their status as distinct species, relative to the latter, is now well established. While postalba was subsequently considered a subspecies of L. albescens, largely on the basis of differences in forewing ground colour in males, both taxa were later given distinct species status by Pogue & Schaefer (2007) following their revision of the genus Lymantria. Here, we re‐examined the validity of this revised status through the sequencing of a large portion of the mitochondrial genome (c. 60%) and multiple nuclear marker genes [elongation factor 1‐alpha (Ef‐1α), wingless (Wgl), internal transcribed spacer 2 (ITS‐2), ribosomal protein S5 (RpS5)] in representative specimens of both taxa and other Lymantria species, including L. monacha, L. xylina, L. mathura and members of the L. dispar + L. umbrosa clade. A comparison of the number of substitutions in these genomic regions among the taxa we considered showed lower or equivalent variation between L. albescens and L. postalba compared with subspecies of L. dispar, for mitochondrial and nuclear sequences, respectively. This finding was reflected in the maximum likelihood trees generated independently for mitochondrial and nuclear data, where L. albescens and L. postalba formed, in both analyses, a short‐branch sister clade basal to the L. dispar + L. umbrosa clade. We further sequenced three markers [cytochrome c oxydase 1 (COI), EF‐1α, Wgl] in multiple L. albescens–L. postalba specimens collected along a south‐to‐north transect across the Ryukyu Arc and observed no clear distinction among the sampled specimens as a function of taxonomic designation. We conclude that L. albescens and L. postalba form a single species, with postalba representing a darker‐winged morph along an apparent south‐to‐north wing colour cline. Accordingly, L. postalba is relegated to synonymy under L. albescens (syn.n.).

This study assesses whether the distinct altitudinal cline in leaf morphology (decreased leaf width and length with increased altitude) in Tasmanian mountain pepper (Tasmannia lanceolata) is associated with changes in the leaf chemistry of wild populations from different ecological landscapes and altitudes. The presence of distinct pungent drimane sesquiterpenoid chemotypes was identified: subalpine woodland and wet sclerophyll forest chemotypes. Isolation studies and analysis of extracts revealed that wet sclerophyll forest T. lanceolata populations featured polygodial as the principal terpenoid, with profiles similar to the commercial cultivars sampled. In contrast, the subalpine woodland populations contained the drimane sesquiterpenoids 1β-acetoxy-9-deoxyisomuzigadial and 3β-acetoxydrimenin and the conspicuous absence of the pungent principle polygodial.

The Asian corn borer, Ostrinia furnacalis, is a serious pest and is widely distributed in corn-producing regions throughout China. This insect enters facultative diapause as fully grown larvae in response to short day lengths. Here, we evaluate the changes in diapause incidence and critical day length (CDL) by crossing a tropical strain with five subtropical and temperate strains from a 2897-km latitudinal gradient to investigate the latitudinal variations in diapause induction and CDL and their heredity. Photoperiodic responses of diapause induction in the different geographical strains at different temperatures showed that diapause incidence and CDL increased with increasing latitude and decreased with increasing temperature. Similarly, diapause incidence and CDL for the hybrid strains also showed an increase with increasing latitude or decreasing temperature. Conversely, the diapause incidences were significantly lower and the CDLs were significantly shorter in hybrid strains than their parents with high diapause incidence. Furthermore, the males had significantly more influence than the females on the incidence of diapause in subsequent progeny. Diapause incidence and CDL in O. furnacalis are strikingly different among pure strains and hybrid strains. The photoperiodic response controlling diapause is strongly heritable, with diapause being a partial dominant character over nondiapause, with the incidence of diapause mainly determined by the male parent. These results can help us to predict the time course of diapause induction in nature and may provide a genetic means for pest management by providing information on the overwintering capabilities of the hybrids.

Background: Hmong-Mien speaking Miao, also called Hmong, is the sixth largest ethnic group in mainland China. However, the fine-scale genetic profiles and population history of Miao populations in southwest China, especially in Guizhou province, remain uncharacterised due to a scarcity of samples of genome-wide data from different tribes. Aim: To further investigate the population substructure and admixture history of the Guizhou Miao minority. Subjects and methods: We collected 29 samples from three Miao tribes of Guizhou province in southwest China and genotyped about 700,000 genome-wide SNPs of each sample. We analysed newly generated data in together with published modern/ancient East Asian populations datasets via a series of population genetic methods, including principal component analysis (PCA), ADMIXTURE, Fst, TreeMix, f-statistics, qpWave, and qpAdm. Results: PCA and ADMIXTURE results showed that the three studied Guizhou Miao groups consistently fell on the Hmong-Mien-related genetic cline and were relatively genetically homogeneous, displaying a genetic affinity with neighbouring Tai-Kadai speaking populations such as Dong. These results were further confirmed by the observed genetic clade in Fst, TreeMix, outgroup-f3-statistics, and f4-statistics. Furthermore, f4-based allele sharing patterns illustrated that compared with Hunan Miao in central China, Guizhou Miao shared more alleles with Hmong-Mien-speaking Vietnam Hmong and Tai-Kadai-speaking CoLao, Dong, while exhibiting less northeast Asian-related ancestry. Admixture-f3 and f4-statistics revealed the North-South admixture pattern for the studied Guizhou Miao. A qpAdm-based two-way admixture model further revealed that the studied Guizhou Miao harboured 44%-55.4% indigenous Austronesian-speaking Atayal-related ancestry and 44.6%-56% Late Neolithic Yellow River farmer-related ancestry. Conclusions: The population structure within Hmong-Mien-related populations showed a geographic correlation. Hmong-Mien speaking Hunan Miao, Guizhou Miao, and Vietnam Hmong presented close genetic relationships although they dwelt in different regions, suggesting the preservation of the original Hmong-related genetic diversity. The results based on genome-wide SNPs data generally matched the migration history for the Miao population. Our study contributes to a better knowledge of Miao populations and the population structure in southwest China.

Plumage pigmentation is fundamental to a bird's phenotype, with pigment deposition causing relative crypsis or conspicuousness, depending on the environmental context. Geographic variation in plumage melanin tends to be predictable, suggesting that aspects of climate cause local matching of plumage to environment via genetic adaptation. Ecogeographic rules describe this predictability: Gloger's rule predicts that populations in wetter and warmer environments will be more pigmented; Bogert's Rule predicts more pigmentation in cold environments. The Great Horned Owl (Bubo virginianus) exhibits extensive geographic variation in the degree of melanin-based pigmentation. We examined fine-scale spatial variation in owl plumage melanism along environmental gradients in southwestern North America. We tested whether variation is explained by either of two non-mutually exclusive hypotheses: (1) a history of allopatric divergence between subspecies or (2) in situ local adaptation consistent with ecogeographic rules. The allopatric divergence hypothesis predicts a bimodal distribution of plumage melanism, with a geographic cline across a zone of secondary contact, whereas the local adaptation hypothesis predicts that climate explains variation independently of geography. Using a colorimeter, we measured coloration in 101 museum specimens of breeding-season Great Horned Owls that had been obtained from variable environments and elevations. Specimens previously identified as separate subspecies were distinguishable by colorimetry. Plumage lightness, however, was continuously distributed, rather than bimodal. While accounting for males having reduced pigmentation relative to females, linear models revealed that lighter plumage was associated with low latitude, low elevation, high temperature, and low precipitation. These findings suggest that variation in Great Horned Owl plumage pigmentation is best understood as continuous ecogeographic variation, consistent with ecogeographic predictions, and currently maintained in situ along multiple environmental gradients that characterize the “sky island” topography of the southwestern USA.

The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of S. marinoi grown in a common garden. Our experiment included eight genotypes from source populations spanning the Baltic Sea salinity cline. Changes in gene expression revealed a shared response to salinity across genotypes, where low salinities induced profound changes in cellular metabolism, including upregulation of carbon fixation and storage compound biosynthesis, and increased nutrient demand and oxidative stress. Nevertheless, the genotype effect overshadowed the salinity effect, as genotypes differed significantly in their response, both in the magnitude and direction of gene expression. Intraspecific differences included regulation of transcription and translation, nitrogen metabolism, cell signaling, and aerobic respiration. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond and adapt to environmental change.

While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays) and its wild teosinte relative, mexicana (Zea mays ssp. mexicana). Introgression from ecologically diverse teosinte may have facilitated maize’s global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low FST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations., Author summary When species expand their ranges, new encounters with diverse wild relatives can introduce deleterious genetic variation, but may also accelerate the colonization of novel environments by providing ‘ready-made’ genetic adaptations. Maize today is a global staple, far exceeding the original ecological niche of its wild progenitor. We show that gene flow from highland-endemic wild mexicana facilitated maize’s range expansion from the valleys where it was domesticated to sites over 1500m in the mountains of Mexico. We find loci where mexicana ancestry has been repeatedly favored in highland maize populations. We also find loci (including a newly identified inversion) where mexicana ancestry increases steeply with elevation, providing evidence for adaptive trade-offs. We additionally demonstrate selection against mexicana ancestry, especially near domestication genes. We sampled mexicana growing alongside maize fields, yet find little evidence that introgression is recent or locally-sourced genomewide or at adaptive loci. Rather, the majority of mexicana ancestry was introduced into maize over 1000 generations ago, and subsequently diverged and was sorted by selection in individual populations. These results add to our understanding of the effects of introgression on range expansions and adaptation.