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The Atacama Desert in Chile—hyperarid and with high–ultraviolet irradiance levels—is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre–Lejia transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil–microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growth-promoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codon-based methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a “genetic goldmine” to engineer crop resilience to face climate change.

Research conductedWith the ongoing global warming, there are serious concerns about the persistence of locally adapted populations. Indeed, with the raising of temperature, the phenological cycle of tree species may be strongly affected since higher winter temperatures may have a negative impact on endodormancy release if chilling requirements are not fulfilled during winter and late frost in spring may expose trees if buds flush too early. Thus, Environmental gradients (showing continuous variations of environmental conditions) constitute a design of choice to analyze the effect of winter dormancy in locally adapted population.MethodsIn the present study, we used an elevation gradient in the Pyrenees to explore the gene expression network involved in dormancy regulation in natural populations of sessile oak locally adapted to temperature. Terminal buds were harvested during dormancy induction and release at different elevations. Then, gene expression was quantified using RNAseq and we used a likelihood ratio test to identify genes displaying significant dormancy, elevation or dormancy-by-elevation interaction effects.Key resultsOur results highlight molecular processes in locally adapted populations along this elevation cline, and made it possible to identify key dormancy-by-elevation responsive genes revealing that locally adapted populations have evolved distinct molecular strategies to adapt their bud phenology in response to environmental variation (i.e. temperature).

Background The causes of geographic variation of body size in ectotherms have generally been attributed to environmental variables. Research in amphibians has favored mechanisms that involve water availability as an explanation for the geographic variation of body size. However, there are few studies at intraspecific level on amphibians that inhabit desert or semi-desert environments, where hydric restrictions are stronger. Here, we describe and inquire as to the causes of the geographic variation of body size in the semi-desert toad Rhinella atacamensis, a terrestrial anuran that is distributed over 750 km along a latitudinal aridity gradient from the southern extreme of the Atacama Desert to the Mediterranean region of central Chile. We measured the snout-vent length of 315 adults from 11 representative localities of the entire distribution of the species. Then, using an information-theoretic approach, we evaluate whether the data support eight ecogeographic hypotheses proposed in literature. Results Rhinella atacamensis exhibits a gradual pattern of decrease in adult body size towards the north of its distribution, where the climate is more arid, which conforms to a Bergmann’s cline. The best model showed that the data support the mean annual precipitation as predictor of body size, favoring the converse water availability hypothesis. Conclusions Most studies in amphibians show that adult size increases in arid environments, but we found a converse pattern to expected according to the hydric constraints imposed by this type of environment. The evidence in R. atacamensis favors the converse water availability hypothesis, whose mechanism proposes that the foraging activity determined by the precipitation gradient has produced the clinal pattern of body size variation. The variation of this trait could also be affected by the decreasing productivity that exists towards the north of the species distribution. In addition, we found evidence that both pattern and mechanism are independent of sex. Lastly, we suggest that behavioral traits, such as nocturnal habits, might also play an important role determining this differential response to aridity. Therefore, the support for the converse water availability hypothesis found in this study shows that amphibians can respond in different ways to water restrictions imposed by arid environments.

Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range, and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed flyCoelopa frigidaalong a bioclimatic gradient stretching across 10° of latitude, a salinity gradient and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyse 1,446 low-coverage whole genomes collected along those gradients. We found several large non-recombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.

Leaf shape exhibits tremendous diversity in angiosperms. It has long been argued that leaf shape can affect major physiological and ecological properties of plants and thus is likely to be adaptive, but the evolutionary evidence is still scarce. Oxytropis diversifolia (Fabaceae) is polymorphic for leaf shape (1 leaflet, 1–3 leaflets, and 3 leaflets) and exhibits clinal variation in steppes of Nei Mongol, China. With two close relatives predominantly fixed for one phenotype as comparison (Oxytropis neimonggolica with 1 leaflet and Oxytropis leptophylla with 5–13 leaflets), we used a comprehensive cline-fitting approach to assess the role of natural selection in shaping the spatial pattern of leaf-shape variation in this system. For 551 individuals sampled from 22 populations, we quantified leaf-morphological differentiation, evaluated patterns of neutral genetic variation using five chloroplast DNA intergenic regions and 11 nuclear microsatellite loci, and performed microhabitat and macroclimatic-association analyses. We found that 1-leaflet proportions in O. diversifolia populations significantly increased from west to east, and three phenotypes also differed in leaflet-blade size. However, compared with the other two species, populations of O. diversifolia showed little neutral genetic differentiation, and no population structure was detected at either marker. We further revealed that the leaf-shape cline could largely be explained by three macroclimatic variables, with leaflet number decreasing and leaflet-blade size increasing with annual precipitation and showing the reverse trends with temperature seasonality and isothermality. Our results suggest that spatially varying abiotic environmental factors contribute to shape the leaf-shape cline in O. diversifolia, while the interspecific pattern may be due to both local adaptation and historical events.

Baltic blue mussels can colonise and dominate habitats with far lower salinity (Mytilus congeners. Pervasive gene flow was observed between Western Baltic Mytilus edulis living at high salinity conditions and Eastern Baltic M. trossulus living at lower salinites, with highest admixture proportions within a genetic transition zone located at intermediate salinities (Darss Sill area). Yet, we do not understand the impacts of low salinity on larval performance, and how salinity may act as an early selective pressure during passive larval drift across salinity gradients. This study tested whether larvae originating from two different populations along the natural salinity cline in the Baltic Sea have highest fitness at their native salinities. Our results suggest that Eastern Baltic M. trossulus (Usedom, 7 psu) and Western Baltic M. edulis (Kiel, 16 psu) larvae display better performance (fitness components: growth, mortality, settlement success) when reared at their respective native salinities. This suggests that these populations are adapted to their local environment. Additionally, species diagnostic markers were used for genetic analyses of transition zone (Ahrenshoop, 11 psu) mussel larvae exposed to low salinity. This revealed that low salinity selection resulted in a shift towards allele frequencies more typical for Eastern Baltic M. trossulus. Thus, salinity acts as a selective pressure during the pre-settlement phase and can shape the genetic composition of Baltic mussel populations driving local adaptation to low salinity. Future climate change driven desalination, therefore, has the potential to shift the Baltic Sea hybrid gradient westward with consequences for benthic ecosystem structure.

Microsatellites have long been considered non-functional, neutrally evolving regions of the genome. Recent findings suggest that they can function as drivers of rapid adaptive evolution. Previous work on common sunflower identified 479 transcribed microsatellites where allele length significantly correlates with gene expression (eSTRs) in a stepwise manner. Here, a population genetic approach is used to test whether eSTR allele length variation is under selection. Genotypic variation among and within populations at 13 eSTRs was compared with that at 19 anonymous microsatellites in 672 individuals from 17 natural populations of sunflower from across a cline running from Saskatchewan to Oklahoma. Expected heterozygosity, allelic richness, and allelic diversity were significantly lower at eSTRs, a pattern consistent with higher relative rates of purifying selection. Further, an analysis of variation in microsatellite allele lengths (lnRV), and heterozygosities (lnRH), indicate recent selective sweeps at the eSTRs. Mean microsatellite allele lengths at four eSTRs within populations are significantly correlated with latitude consistent with the predictions of the tuning knob model which predicts stepwise relationships between microsatellite allele length and phenotypes. This finding suggests that shorter or longer alleles at eSTRs may be favored in climatic extremes. Collectively, our results imply that eSTRs are likely under selection and that they may be playing a role in facilitating local adaptation across a well-defined cline in the common sunflower.

Populations of short-lived organisms can respond to spatial and temporal environmental heterogeneity through local adaptation. Local adaptation can be reflected on both phenotypic and genetic levels, and it has been documented in many organisms. Although some complex fitness-related phenotypes have been shown to vary across latitudinal clines and seasons in similar ways in Drosophila melanogaster populations, we lack a general understanding of the genetic architecture of local adaptation across space and time. To address this problem, we examined patterns of allele frequency change across latitudinal clines and between seasons at previously reported expression quantitative trait loci (eQTLs). We divided eQTLs into groups by utilizing differential expression profiles of fly populations collected across a latitudinal cline or exposed to different environmental conditions. We also examined clinal and seasonal patterns of allele frequency change at eQTLs grouped by tissues. In general, we find that clinally varying polymorphisms are enriched for eQTLs, and that these eQTLs change in frequency in predictable ways across the cline and in response to starvation tolerance. The enrichment of eQTL among seasonally varying polymorphisms is more subtle, and the direction of allele frequency change at eQTL appears to be somewhat idiosyncratic. Taken together, we suggest that clinal adaptation at eQTLs is distinct than that of seasonal adaptation.

Significance A defining goal in genetics is linking variation in DNA sequence to trait evolution between populations and, ultimately, species. Genome sequencing efficiently captures such variation but typically in millions of tiny fragments that omit haplotype or linkage information. We present “haplotagging,” a simple, rapid linked-read sequencing technique that allows high-throughput sequencing without sacrificing haplotype information. We validated this affordable approach for whole-genome haplotyping in large populations. We used haplotagging to investigate the rise of a novel hybrid morph in parallel hybrid zones of two comimetic Heliconius butterfly species in Ecuador. Our results reveal that strikingly parallel divergences in their genomes produced coordinated shifts in haplotype frequencies across the hybrid zone, giving rise to comimetic hybrid morphs in each species., Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. Yet, genomic data often omit haplotype information due to constraints in sequencing technologies. Here, we present “haplotagging,” a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species, the geographic clines for the major wing-pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the center of the hybrid zone. We propose that shared warning signaling (Müllerian mimicry) may couple the cline shifts seen in both species and facilitate the parallel coemergence of a novel hybrid morph in both comimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.

Background Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate). Results Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations. Conclusions Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.

Studies of the current Chilean population performed using classical genetic markers have established that the Chilean population originated primarily from the admixture of European people, particularly Spaniards, and Amerindians. A socioeconomic-ethno-genetic cline was established soon after the conquest. Spaniards born in Spain or Chile occupied the highest Socioeconomic Strata, while Amerindians belonged to the lowest. The intermediate strata consisted of people with different degrees of ethnic admixture; the larger the European admixture, the higher the Socioeconomic Level. The present study of molecular genomic markers sought to calculate the percentage of Amerindian admixture and revealed a finer distribution of this cline, as well as differences between two Amerindian groups: Aymara and Mapuche. The use of two socioeconomic classifications - Class and Socioeconomic Level - reveals important differences. Furthermore, Self-reported Ethnicity (self-assignment to an ethnic group) and Self-reported Ancestry (self-recognition of Amerindian ancestors) show variations and differing relationships between socioeconomic classifications and genomic Amerindian Admixture. These data constitute a valuable input for the formulation of public healthcare policy and show that the notions of Ethnicity, Socioeconomic Strata and Class should always be a consideration in policy development.

Genetic differentiation among different natural populations of a species depends upon the environmental factors and the evolutionary forces that operate on them. In this study, seven Indian natural populations of D. bipectinata, two from north and five from south India, have been studied for their chromosomal inversion polymorphism. A total of nine paracentric autosomal inversions were recorded from these seven places but only three of them, present on the 2L, 2R and 3L were found to be cosmopolitan in distribution. In all the populations, the frequency of standard gene arrangement was found to be high than their respective cosmopolitan inversion gene arrangement. The average heterozygosity (Ho) of cosmopolitan inversions increases from north to south. There is a latitudinal cline in the distribution of three cosmopolitan inversion arrangements because their frequency increases with the decreasing latitude, i.e. from north to south India. A comparison of the genetic profile of two north Indian and five south Indian natural populations of D. bipectinata reveals the role of natural selection as well as bottleneck effect in the genetic structuring of these populations which may be due to their varying ecological conditions to which they are constantly encountered. Further, the presence of all kinds of paracentric inversions in individual populations was analysed following Poisson distribution to see whether these inversions occur randomly in natural populations or not and the results indicate that north Indian populations show the random occurrence of these inversions than the populations derived from the south.

We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the United States. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the United States, but identified a deep east-west split (∼0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.

Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.

Do genetic covariances promote or impede rapid adaptation to changing environments? Hangartner et al. found that genetic covariances among traits and between sexes aligned with the inferred direction of selection along a latitudinal cline, suggesting that genetic covariances can augment the evolutionary response to climatic selection.

Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of a widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or sibling) lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

BackgroundSecondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes.ResultsWe observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat.ConclusionsOur data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa.

The live-bearing genus Sebastes is renowned for its outstanding species richness and color diversity, and its speciation has been a point of interest. This study investigated the age, growth, reproductive biology, color pattern and ontogenetic divergence of a pair of closely related rockfishes from the coasts of the Shandong Peninsula, namely, Sebastes koreanus (n=879) and S. nudus (n=257). Marginal increment analysis of sectioned otoliths showed that annulus formation occurred once a year between June and July in both species. The sex-pooled growth curves of S. nudus and 3 populations of S. koreanus differed significantly from each other. No apparent latitudinal cline in growth parameters was found in S. koreanus. For both species, the peak parturition periods were from April to May, and the peak copulation periods were from November to December. S. nudus has a highly variable and conspicuous color pattern while S. koreanus has a stable and dull color pattern. This difference, together with the overlapping distribution and the close relationship, make S. koreanus and S. nudus an ideal model to investigate the color-driven speciation of the Sebastes. We confirmed that S. nudus changes its body color with age and season and fully expresses the carotenoid-based nuptial coloration when the fish reaches first maturity. Moreover, our comparisons of morphological traits that are likely related to survival and quality of these fishes suggested that S. nudus may suffer higher predation risk and foraging difficulty beginning at age 3. In light of the ontogenetic development of the color pattern in S. nudus, we suggested that the full expression of nuptial coloration most likely triggers the strong selective pressure to enhance swimming performance, anti-predator defense and foraging capacity of S. nudus through predator-prey interactions. By understanding all these details, we further inferred a hypothesis that both color pattern and bathymetric segregation play key roles in facilitating the speciation of demersal rockfishes.

Hybrid zones are particularly valuable for understanding the evolution of partial reproductive isolation between differentiated populations. An increasing number of hybrid zones have been inferred to move over time, but in most such cases zone movement has not been tested with long-term genomic data. The hybrid zone between Townsend's Warblers (Setophaga townsendi) and Hermit Warblers (S. occidentalis) in the Washington Cascades was previously inferred to be moving from northern S. townsendi southwards towards S. occidentalis, based on plumage and behavioural patterns as well as a 2000-km genetic wake of hermit mitochondrial DNA (mtDNA) in coastal Townsend's Warblers. We directly tested whether hybrid zone position has changed over 2-3 decades by tracking plumage, mtDNA and nuclear genomic variation across the hybrid zone over two sampling periods (1987-94 and 2015-16). Surprisingly, there was no significant movement in genomic or plumage cline centres between the two time periods. Plumage cline widths were narrower than expected by neutral diffusion, consistent with a 'tension zone' model, in which selection against hybrids is balanced by movement of parental forms into the zone. Our results indicate that this hybrid zone is either stable in its location or moving at a rate that is not detectable over 2-3 decades. Despite considerable gene flow, the stable clines in multiple phenotypic and genotypic characters over decades suggest evolutionary stability of this young pair of sister species, allowing divergence to continue. We propose a novel biogeographic scenario to explain these patterns: rather than the hybrid zone having moved thousands of kilometres to its current position, inland Townsend's met coastal Hermit Warbler populations along a broad front of the British Columbia and Alaska coast and hybridization led to replacement of the Hermit Warbler plumage with Townsend's Warbler plumage patterns along this coastline. Hence, hybrid zones along British Columbia and Alaska moved only a short distance from the inland to the coast, whereas the Hermit Warbler phenotype appears stable in Washington and further south. This case provides an example of the complex biogeographic processes that have led to the distribution of current phenotypes within and among closely related species.

AIM: To understand the population structure and its potential drivers at different spatial scales in a migratory bird, the black‐fronted tern (Chlidonias albostriatus), a specialist of the spatially and temporally dynamic environments of braided rivers. LOCATION: New Zealand. METHODS: We used a three‐pronged approach based on 17 microsatellites, two mitochondrial loci (cytochrome b/control region) and phenotypic data (head‐bill length, bill depth, wing length, weight). We determined large‐scale genetic structure throughout the whole breeding range (approx. 150,000 km²), calculated genetic divergence of breeding colonies and tested for isolation‐by‐distance between colonies. We investigated the level of fine‐scale genetic structure based on spatial autocorrelation analyses and assessed the presence of a body size cline based on phenotypic data. Lastly, we compared phenotypic divergence (PST) and the level of divergence by genetic drift (FST) among breeding colonies to test for underlying mechanisms of population differentiation. RESULTS: Nuclear and mitochondrial DNA showed that across their range black‐fronted terns were effectively panmictic, with low genetic divergence between breeding colonies overall and no isolation‐by‐distance. However, at fine geographical scales black‐fronted terns accrued significant genetic structure for distances up to 75 km, primarily driven by males, indicating more frequent female dispersal. Furthermore, a phenotypic cline in accordance with Bergmann's rule was evident. PST exceeded FST in three traits, suggestive of local adaptation. MAIN CONCLUSIONS: Significant fine‐scale structure can be present in highly mobile, specialist species while not affecting spatial structures at larger scales. Hence, methodologies applied to both whole landscapes and local scales are important to appropriately estimate connectivity in dynamic metapopulations and investigate the processes behind connectivity. Conservation management will need to include protecting currently uninhabited patches to facilitate natural colonization of suitable habitat. For black‐fronted terns, managing whole catchments throughout the entire breeding range would be preferable to managing single patches.

Silphium spp. have garnered interest in Europe as a bioenergy crop and in North America as a perennial oilseed crop. However, very little has been done at this early stage of domestication to characterize wild collections for many key characteristics, including important oilseed traits. The objective of this work was to develop a basic understanding of how biogeography and associated population genetic forces have shaped seed phenotypes in plant collections across the native range of Silphium integrifolium Michx. (Asteraceae: Heliantheae), the primary domestication candidate for oilseed use. A collection of 53 accessions was grown in a common environment in Salina, KS, which is a location well within the native range of the species in central North America. Plants from each collection site were randomly mated by hand to produce seed representative of each accession, and the seeds subjected to seed dimensional trait, oil content and oil composition analyses. Kernel width varied along a latitudinal cline of collection site, while kernel length varied across a longitudinal cline. Palmitic and linoleic acids were inversely correlated with each other and varied along a longitudinal cline of the collection site. The results indicate that accessions collected from more southwesterly sites tended to have larger seed and those from more westerly sites had higher linoleic acid content and lower palmitic and myristic acids, which are all desirable phenotypes for an oilseed Silphium.

The modern distribution of the Western Eurasian subboreal butterfly Coenonympha leander (Esper, 1784) was studied in the Urals region, with its northeastern range limits specified at 56°N and 65°E. There are isolated local C. leander populations in the forest-steppe, while in the steppe zone the species is distributed fairly uniformly. In the Ural steppes the species is tolerant to moderate anthropogenic transformation of natural communities; the species is not rare and cannot serve as an indicator of intact communities, as opposed to other parts of its range. The geographic variations in the wing length and also the diameters and frequency of eyespots in the wing pattern are analyzed. The highest morphological specificity was detected in the marginal outpost populations, especially the northernmost population of Nizhnee Tukbaevo in Bashkortostan, which lives under the unique conditions of the azonal Mesyagutovo forest-steppe and tends to form a cline, with the wing size decreasing and the eyespot diameters and frequency increasing from north to south.

Rapid adaptation in response to novel environments can facilitate species invasions and range expansions. Understanding how invasive disease vectors rapidly evolve to novel conditions—particularly at the edge of its non‐native range—has important implications for mitigating the prevalence and spread of disease. Here, we evaluate the role of local adaptation in overwintering capability of the Asian tiger mosquito, Aedes albopictus. This species invaded the Southern United States in the 1980s and rapidly spread northward into novel climate compared to its native range. Photoperiodically induced egg diapause is a key trait contributing to the establishment and spread of Ae. albopictus in temperate latitudes, and diapause incidence rapidly developed a cline along a latitudinal gradient in the United States shortly after its initial invasion. However, variation in overwintering survival of diapause‐induced eggs along this gradient is not known, but is critical to the fitness‐related role of diapause evolution in the establishment of Ae. albopictus in its northern US range. Using reciprocal transplants, we detected local adaptation in overwinter survival of diapausing Aedes albopictus eggs. In northern range‐edge winters, eggs produced by range‐edge individuals survived better than those produced by range‐core individuals. Diapause eggs from range‐edge and range‐core locations survived equally well in range‐core winters, and no eggs survived a winter beyond the current northern range limit in the United States. Synthesis and applications. These results demonstrate rapid (~3 decades) local adaptation of egg diapause, a key trait facilitating overwinter survival and range expansion for the invasive Asian tiger mosquito. In light of these results, control efforts could shift from targeting satellite populations to a focus on preventing dispersal into locally adapted, range‐edge locations and to aim removal efforts towards areas surrounding locally adapted populations. Adopting new approaches to target rapidly adapting populations will require large‐scale collaboration among control agencies and research institutions, and should begin in the northern US range to better control Aedes albopictus mosquito populations in the face of rapid adaptation.

Dry forests characterize many of the biomes of southern South America and the Andes, such as the Chaco and the inter-Andean valley forests, which form a continuous belt (Chaco–Andes dry forest belt). Some of the taxa that inhabit this forest belt present genetic and phenotypic differentiation between edges of the region, which suggests the action of divergent evolutionary processes between forests (i.e., parapatric divergence). In order to test this hypothesis, we studied the morphological and phylogeographic variation of the White-tipped Plantcutter Phytotoma rutila (Cotingidae) and evaluated predictions of genetic and morphological evolutionary processes (e.g., local adaptation). The results supported that the environmental gradient along the Chaco–Andes dry forests might be promoting diversification because we found that body size of the White-tipped Plantcutter varied according to a step cline related to altitude, and thus parapatric processes might be responsible for this pattern. There are other taxa co-distributed across the study region presenting similar patterns of geographic variation, which suggests the action of concerted evolutionary phenomena in the Chaco–Andes dry forest. Fil: Rodríguez Cajarville, María José. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina Fil: Calderón, Pablo Luciano Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; Argentina Fil: Tubaro, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina Fil: Cabanne, Gustavo Sebastián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina

Spatial sorting on invasion fronts drives the evolution of dispersive phenotypes, and in doing so can push phenotypes in the opposite direction to natural selection. The invasion of cane toads (Rhinella marina) through tropical Australia has accelerated over recent decades because of the accumulation of dispersal-enhancing traits at the invasion front, driven by spatial sorting. One such trait is the length of the forelimbs: invasion-front toads have longer arms (relative to body length) in comparison with populations 10-20 years after invasion. Such a shift likely has fitness consequences: an increase of forearm length would decrease the strength with which a male could cling to a female during amplexus and so render such a male less competitive in competition for mates, compared to short-armed conspecifics. Our laboratory trials of attachment strength confirmed that males with relatively longer arms were easier to displace, and competition trials show higher duration of amplexus for males with shorter arms. Together with the sharp cline in limb length observed behind the invasion front, these results imply an opposition of selective forces: spatial sorting optimizes dispersal, but as this force wanes behind the invasion front, we see the primacy of natural selection reassert itself.

The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.

Recent climate warming is expected to have changed the phenology of organisms. The cricket Dianemobius nigrofasciatus (Matsumura) (Orthoptera: Trigonidiidae) has univoltine and bivoltine life cycles in northern and southern regions of Japan, respectively, because of latitudinal variation in the growing season length. Its adult body size increases with decreasing latitude, and decreases at a latitude where the number of annual generations increases. The present study aims to examine whether the range of the bivoltine life cycle has expanded northward due to climate warming. We compared a latitudinal saw-tooth body size cline between the 1960s and the 2010s. The body size showed a latitudinal saw-tooth cline in adults collected in recent years, as it did in adults collected five decades ago. However, no significant difference was observed between these two clines, suggesting that the bivoltine life cycle has not expanded in the last five decades. These results contrast to those recently reported in a closely related species, Polionemobius mikado (Shiraki) (Orthoptera: Trigonidiidae), in which the turning points of the saw-tooth cline had shifted northward in the last four decades. The stable latitudinal distribution of life cycles in D. nigrofasciatus might result from the different photoperiodic regulation of growth rate involved in the different responses to climate warming.

Summary The present paper studies grammaticalisation of verbs in Coptic. Various (classes of) expressions found in this language can be shown to occupy different sections or ‘points’ on the continuum/cline of evolution of verbs posited in linguistics that extends from lexical items to auxiliaries, affixes, parts of other lexemes, and finally zero (nothing). The mechanisms that ‘push’ verbs along this continuum turn out to be those seen also in other languages, and the same holds for the semantic and morpho-syntactic signals thereof. Besides being of typological interest, this again emphasises the importance and necessity of studying Coptic from a more diachronic perspective.

The rough periwinkle Littorina saxatilis is characterised for showing shell phenotypic variation associated to environmental clines and this is found in parallel across shores. In order to disentangle the additive genetic effects and the environmental factors involved in this variation, we analysed natural populations subjected to a gradient in wave exposure and crab predation in 3 different Rias (primary estuaries) from Galicia (NW Spain). In addition to previously described “Crab” and “Wave” ecotypes , we studied a new phenotype (“Crab+”) associated to the most sheltered habitats of the gradient. We obtained estimates of heritability and Q st (between population genetic differentiation) in embryos and Pst (between population phenotypic differentiation) in adults for shell morphology traits. Heritability estimates were close to one for shell size and relative shell aperture, suggesting a low impact of environmental factors in embryos. Estimates of Qst between ecotypes were significant and typically much higher than published Fst estimates from neutral markers, indicating a role for selection on shaping additive genetic variation. Estimates of Pst between ecotypes for adults were substantially larger than embryos´ Qst , suggesting also a role of phenotypic plasticity in ecotype differentiation. Our results suggest that P st vs Fst comparisons should be taken with caution because they might not reflect real additive genetic effects, but Pst vs Qst comparisons could shed light into the role of phenotypic plasticity.

Geographic range shifts can cause secondary contact and hybridization between closely related species, revealing mechanisms of species formation and integrity. These dynamics typically play out in restricted geographic regions, but highly vagile species may experience major distributional changes resulting in broad areas of contact. The Glossy Ibis (Plegadis falcinellus) is a dispersive waterbird of the Old World and Australia that colonized eastern North America in the early 19th century and came into contact with the native White-faced Ibis (P. chihi). Putative hybrids between the two species have been observed across North America. To examine the population genomic consequences of this natural invasion, we sequenced 4,616 ultraconserved elements from 66 individuals sampled across the distributions of falcinellus, chihi, and the Puna Ibis (P. ridgwayi) of South America. We found genomic differentiation among the three species. Loci with high sequence divergence were often shared across all pairwise species comparisons, were associated with regions of high nucleotide diversity, and were concentrated on the Z chromosome. We detected signals of genetic admixture between chihi and falcinellus in individuals both near and far from their core area of sympatry. Genomic cline analyses revealed evidence of greater introgression into falcinellus from chihi, but we found little evidence for selection against hybrids. We also found signals of admixture between ridgwayi and South American populations of chihi. Our results indicate vagile species can experience pervasive introgression upon secondary contact, although we suggest these dynamics may be more ephemeral than the stable hybrid zones often observed in less dispersive organisms.

The existence of a temperature gradient across latitudes is crucial to explain the patterns presented in the early life-history characteristics of marine fish species over large geographical areas. Hence, the aim of the present work was to analyse the temperature-related pattern in the early life-history events and characteristics of the common sole, Solea solea, along most of its geographical distribution area, focusing on key nursery areas for this species: Venice lagoon (Italy), Mondego estuary (Portugal), Vilaine estuary (France) and Balgzand (Netherlands). Otolith microstructure from metamorphosed age 0 juveniles was used to estimate age, the pelagic larval and metamorphosis stages duration, and the spawning period. A latitudinal cline was found for the main processes of the early life cycle: spawning started in December in the southernmost areas (Mondego estuary and Venice Lagoon) and in February in the Balgzand population. Hatching started earlier in the Venice lagoon, where warmer water temperatures in the winter led to an earlier development. The longest pelagic stage was observed in the French coast populations, which differed significantly from those of the Mediterranean, while metamorphosis lasted longer in the North Sea (Balgzand), when compared with the Portuguese Atlantic coast (Mondego). Populations further north were characterized by higher growth rates, suggesting an adaptation to local conditions. Despite that several abiotic factors play an important role in flatfish early life history, the observed temperature gradient seems to be one of the most important drivers.

Determining the mechanisms that create and maintain biodiversity is a central question in ecology and evolution. Speciation is the process that creates biodiversity. Speciation is mediated by incompatibilities that lead to reproductive isolation between divergent populations and these incompatibilities can be observed in hybrid zones. Gecko lizards are a speciose clade possessing an impressive diversity of behavioral and morphological traits. In geckos, however, our understanding of the speciation process is negligible. To address this gap, we used genetic sequence data (both mitochondrial and nuclear markers) to revisit a putative hybrid zone between Sphaerodactylus nicholsi and Sphaerodactylus townsendi in Puerto Rico, initially described in 1984. First, we addressed discrepancies in the literature on the validity of both species. Second, we sampled a 10-km-wide transect across the putative hybrid zone and tested explicit predictions about its dynamics using cline models. Third, we investigated potential causes for the hybrid zone using species distribution modeling and simulations; namely, whether unique climatic variables within the hybrid zone might elicit selection for intermediate phenotypes. We find strong support for the species-level status of each species and no evidence of movement, or unique climatic variables near the hybrid zone. We suggest that this narrow hybrid zone is geographically stable and is maintained by a combination of dispersal and selection. Thus, this work has identified an extant model system within geckos that that can be used for future investigations detailing genetic mechanisms of reproductive isolation in an understudied vertebrate group.

Adaptation to climate is expected to increase the performance of invasive species and their community-level impacts. However, while the fitness gains from adaptation should, in general, promote invader competitive ability, empirical demonstrations of this prediction are scarce. Furthermore, climate adaptation, in the form of altered timing of life cycle transitions, should affect the phenological overlap between nonnative and native competitors, with potentially large, but poorly tested, impacts on native species persistence. We evaluated these predictions by growing native California grassland plants in competition with nonnative Lactuca serriola, a species that flowers earlier in parts of its nonnative range that are drier than its putative European source region. In common garden experiments in southern California with L. serriola populations differing in phenology, plants originating from arid climates bolted up to 48 d earlier than plants from more mesic climates, and selection favored early flowering, supporting an adaptive basis for the phenology cline. The per capita competitive effects of L. serriola from early flowering populations on five early flowering native species were greater than the effects of L. serriola from later flowering populations. Consequently, the ability of the native species to increase when rare in competition with L. serriola, as inferred from field-parameterized competition models, declined with earlier L. serriola phenology. Indeed, changes to L. serriola phenology affected whether or not one native species was predicted to persist in competition with L. serriola. Our results suggest that evolution in response to new climatic conditions can have important consequences for species interactions, and enhance the impacts of biological invasions on natural communities.

This study describes autosomal STR profiles of the populations of South and North Afghanistan. A total of 188 unrelated individuals residing north (n = 42) and south (n = 146) of the Hindu Kush Range within the territory of Afghanistan were examined against the background of 54 geographically targeted reference populations from Eurasia and North East Africa. The main objective of this study was to investigate longitudinal gene flow across the Hindu Kush Range and Eurasia. Genetic differentiation tests between North and South Afghanistan generated insignificant genetic differences for all loci. Multidimensional scaling (MDS) plots based on Fst distances and Neighbor-Joining (N-J) analysis indicated genetic affinities between the Afghani groups and Indian/Near East/West Asian populations. Admixture and Structure analyses demonstrate a gradient of genetic continuity within a major east to west cline that includes North and South Afghanistan as intermediate populations. Overall, although Afghanistan is surrounded by a number of natural barriers, instead of an isolated territory, it has been a genetically porous region providing a migrational nexus to the rest of Eurasia.

Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in a hybrid zone between common (Bufo bufo) and spined toads (B. spinosus), using 31 nuclear and one mtDNA SNPs along a transect in the northwest of France. Average effective selection in Bufo hybrids is low and clines vary in shape and centre. A weak pattern of asymmetric introgression is inferred from cline discordance of seven nuclear markers. The dominant direction of gene flow is from B. spinosus to B. bufo and is in support of southward movement of the hybrid zone. Conversely, a peak of admixture linkage disequilibrium north of the hybrid zone suggests northward movement. These contrasting results can be explained by reproductive isolation of the B. spinosus and B. bufo gene pools at the southern (B. spinosus) side of the hybrid zone. The joint occurrence of asymmetric introgression and admixture linkage disequilibrium can also be explained by the combination of low dispersal and random genetic drift due to low effective population sizes.

Speciation is the result of an accumulation of reproductive barriers between populations, but pinpointing the factors involved is often difficult. However, hybrid zones can form when these barriers are not complete, especially when lineages come into contact in intermediate or modified habitats. We examine a hybrid zone between two closely related riverine turtle species, Sternotherus depressus and S. peltifer, and use dual-digest RAD sequencing to understand how this hybrid zone formed and elucidate genomic patterns of reproductive isolation. First, the geographical extent and timing of formation of the hybrid zone is established to provide context for understanding the role of extrinsic and intrinsic reproductive isolating mechanisms in this system. The strength of selection on taxon-specific contributions to maintenance of the hybrid zone is then inferred using a Bayesian genomic cline model. These analyses identify a role for selection inhibiting introgression in some genomic regions at one end of the hybrid zone and promoting introgression in many loci at the other. When selective pressures necessary to generate outliers to the genomic cline are considered with the geographical and temporal context of this hybrid zone, we conclude that habitat-specific selection probably limits introgression from S. depressus to S. peltifer in the direction of river flow. However, selection is mediating rapid, unidirectional introgression from S. peltifer to S. depressus, which is probably facilitated by anthropogenic habitat alteration. These findings indicate a potentially imminent threat of population-level genomic extinction for an already imperiled species due to ongoing human-caused habitat alteration.

The introgression from genetically modified soybean (Glycine max (L)) to wild soybean (Glycine soja Sieb. et Zucc.) could be threat the genetic diversity of wild soybean. Flowering synchrony is essential to the occurrence of outcrossing, but the flowering phenology of wild soybean is less well researched than that of cultivated soybean. We developed models to predict flowering initiation of wild soybean, based on the flowering initiation dates of wild soybean five accessions from different latitudes (31.4°N to 42.6°N) in growth chambers in which temperature and day length varied. Our proposed models predicted the flowering initiation date of wild soybean in the natural habitat well; the averaged difference from observed date in 5 areas was -1.8 days (-8 to +5). In the long day condition, there was a clear latitudinal cline of photoperiodic sensitivity throughout Japan. Accessions in southern part of Japan archipelago required higher temperature even under the short-day conditions and northern accessions were less-sensitive to long-day conditions. Our result showed the possibility of predicting the flowering initiation of wild soybean, corresponding to latitudes.

Endangerment and extinction of threatened populations can often be accelerated by genomic contamination through infiltration with alien alleles. With a growing anthropogenic footprint, many such hybridization events are human-mediated. The Milky Stork (Mycteria cinerea) is one such species whose genomic composition is threatened by human-mediated hybridization with its sister taxon, the Painted Stork (Mycteria leucocephala). A comprehensive investigation of the stork population in Singapore using three complementary population-genomic approaches revealed a large proportion of hybrids that have undergone several generations of genomic leakage from Painted Storks and fall along a genetic cline that closely mirrors a phenotypic cline from pure Milky to pure Painted. Although originating from a limited number of introduced Painted Storks, these hybrids are now an integral part of both the wild and captive Singaporean and southern peninsular Malaysian stork population. Genetically informed conservation management including the isolation of hybrids in captivity and a strict removal of hybrids from the wild along with a release of genetically pure Milky Storks is imperative for continued survival. Similar approaches must become routine in endangered species conservation as human-mediated hybridization increases in volume.

Monarch butterfly wing morphology varies substantially throughout their global range, both between resident and migratory populations and also within the migratory North American population. Here, we use a dataset comprising more than 1800 North American individuals collected between 1878-2017 to characterize the factors shaping continent-wide patterns of wing morphological variation. North American overwintering butterflies have forewings that are approximately 4.4% larger than those collected in summer breeding areas. Monarchs overwintering in Mexico have forewings that are approximately 1.8% larger than monarchs overwintering in California, conducive to the idea that migration distance is positively correlated with wing area. We find evidence for a latitudinal cline within North America, such that butterflies collected at higher latitudes have significantly larger and more elongated forewings. We also find a significant increase of approximately 4.9% in forewing area between 1878-2017, but no difference through time in wing elongation. This result is corroborated by a reanalysis of a recently published dataset of more than 600 butterflies from Mexican overwintering sites. We discuss possible reasons for this increase in wing size through time, including northward shifts in the monarch’s breeding range and changes in relative abundance of milkweed hosts, and present experimental data addressing the influence of larval host plant on adult wing morphology. Our analysis suggests that (1) migration is indeed an important selective force for monarch wing morphology; (2) wing size has increased through time in North America; (3) factors such as host plant identity must be considered to fully understand monarch wing morphological variation.

The Indus Valley has been the backdrop for several historic and prehistoric population movements between South Asia and West Eurasia. However, the genetic structure of present-day populations from Northwest India is poorly characterized. Here we report new genome-wide genotype data for 45 modern individuals from four Northwest Indian populations, including the Ror, whose long-term occupation of the region can be traced back to the early Vedic scriptures. Our results suggest that although the genetic architecture of most Northwest Indian populations fits well on the broader North-South Indian genetic cline, culturally distinct groups such as the Ror stand out by being genetically more akin to populations living west of India; such populations include prehistorical and early historical ancient individuals from the Swat Valley near the Indus Valley. We argue that this affinity is more likely a result of genetic continuity since the Bronze Age migrations from the Steppe Belt than a result of recent admixture. The observed patterns of genetic relationships both with modern and ancient West Eurasians suggest that the Ror can be used as a proxy for a population descended from the Ancestral North Indian (ANI) population. Collectively, our results show that the Indus Valley populations are characterized by considerable genetic heterogeneity that has persisted over thousands of years. ispartof: AMERICAN JOURNAL OF HUMAN GENETICS vol:103 issue:6 pages:918-929 ispartof: location:United States status: published

To establish and spread in a new location, an invasive species must be able to carry out its life cycle in novel environmental conditions. A key trait underlying fitness is the shift from vegetative to reproductive growth through floral development. In this study, we used a common garden experiment and genotyping-by-sequencing to test whether the latitudinal flowering cline of the North American invasive plant Medicago polymorpha was translocated from its European native range through multiple introductions, or whether the cline rapidly established due to evolution following a genetic bottleneck. Analysis of flowering time in 736 common garden plants showed a latitudinal flowering time cline in both the native and invaded ranges where genotypes from lower latitudes flowered earlier. Genotyping-by-sequencing of 9,658 SNPs in 446 individuals revealed two major subpopulations of M. polymorpha in the native range, only one of which is present in the invaded range. Additionally, native range populations have higher genetic diversity than invaded range populations, suggesting that a genetic bottleneck occurred during invasion. All invaded range individuals are closely related to plants collected from native range populations in Portugal and southern Spain, and population assignment tests assigned invaded range individuals to this same narrow source region. Taken together, our results suggest that latitudinal clinal variation in flowering time has rapidly evolved across the invaded range despite a genetic bottleneck following introduction.

Hybridization is an evolutionary process that can generate diverse outcomes, such as reinforcing species boundaries, generating new species, or facilitating the introgression of locally-adapted alleles into new genomic backgrounds. Liolaemus is a highly diverse clade of South American lizards with ∼260 species and as many as ten new species are described each year. Previous Liolaemus studies have detected gene flow and introgression among species using phylogenetic network methods and/or through comparisons of nuclear and mitochondrial DNA patterns, yet no study has systematically studied hybrid zones between Liolaemus species. Here, we compared three hybrid zones between four species in the Liolaemus fitzingerii group of lizards in Central Argentina where two species, L. melanops and L. xanthoviridis, each hybridize withtwo other species (L. shehuen and L. fitzingerii). We sampled three transects that were each ∼120 km in length and sequenced both mitochondrial and genome-wide SNP data for 267 individuals. In our analyses of nuclear DNA, we also compared bi-allelic SNPs to phased alleles (50 bp RAD loci). Population structure analyses confirmed that boundaries separating species are sharp, and all clines are

López, Aldana Soledad. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro Regional Patagonia Norte. Estación Experimental Agropecuaria Bariloche (EEA Bariloche). Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB). Bariloche, Río Negro, Argentina. López, Aldana Soledad. CONICET - Instituto Nacional de Tecnología Agropecuaria (INTA). Centro Regional Patagonia Norte. Estación Experimental Agropecuaria Bariloche (EEA Bariloche). Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB). Bariloche, Río Negro, Argentina. López, Dardo Rubén. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro Regional Córdoba. Estación Experimental Agropecuaria Manfredi (EEA Manfredi). Agencia De Extensión Rural Villa Dolores. Córdoba, Argentina. Arana, María Verónica. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro Regional Patagonia Norte. Estación Experimental Agropecuaria Bariloche (EEA Bariloche). Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB). Bariloche, Río Negro, Argentina. Arana, María Verónica. CONICET - Instituto Nacional de Tecnología Agropecuaria (INTA). Centro Regional Patagonia Norte. Estación Experimental Agropecuaria Bariloche (EEA Bariloche). Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB). Bariloche, Río Negro, Argentina. Batlla, Diego. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Vegetal. Cátedra de Cerealicultura. Buenos Aires, Argentina. Marchelli, Paula. Instituto Nacional de Tecnología Agropecuaria (INTA). Centro Regional Patagonia Norte. Estación Experimental Agropecuaria Bariloche (EEA Bariloche). Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB). Bariloche, Río Negro, Argentina. Marchelli, Paula. CONICET - Instituto Nacional de Tecnología Agropecuaria (INTA). Centro Regional Patagonia Norte. Estación Experimental Agropecuaria Bariloche (EEA Bariloche). Instituto de Investigaciones Forestales y Agropecuarias Bariloche (IFAB). Bariloche, Río Negro, Argentina. Sensitivity to water availability is a key physiological trait for grassland species located in arid and semiarid environments, where successful germination is closely related to rainfall dynamics. Festuca pallescens inhabits diverse environments along a steep precipitation gradient in North Patagonia, thus ofering a suitable model for the study of germination behavior in response to water availability. \nBy analyzing germination in nine populations using a hydrotime model approach, we aimed to fnd within-species variation. Seed population behavior was analyzed under diferent hydric conditions using hydrotime model parameters (hydrotime, mean base water potential and its standard deviation). We estimated the mean base water potential for F. pallescens (micro b(50) = − 2.79 ± 0.45 MPa), which did not difer signifcantly between populations. However, the hydrotime parameter (θH) varied markedly, suggesting physiological adaptation to local environments. Higher values of H were found in populations located at the extremes of the distribution gradient, indicating that germination may be prevented or delayed in conditions that are suboptimal for the species. Since the variation in hydrotime model parameters did not follow a cline, micro-environmental cues may have the greatest infuence on the physiological behavior of the species, rather than the macroscale rainfall gradient. grafs., tbls.

Intertidal organisms must tolerate a wide range of environmental parameters each day which may result in tolerance to multiple stressors correlating. The intertidal copepod Tigriopus californicus experiences diurnal variation in dissolved oxygen levels and pH as the opposing processes of photosynthesis and cellular respiration lead to coordinated highs during the day and lows at night. While environmental parameters with overlapping spatial gradients frequently result in correlated traits, less attention has been given to exploring temporally correlated stressors. We investigated whether hypoxia tolerance correlated with acid tolerance by testing the hypoxia and low pH stress tolerance of 6 genetically differentiated populations of T. californicus. We checked for similarities in tolerance for the two stressors by latitude, sex, size, and time since collection as predictors. We found that although hypoxia tolerance correlated with latitude, acid tolerance did not, and no predictor was significant for both stressors. We concluded that temporally coordinated exposure to low pH and low oxygen did not result in populations developing equivalent tolerance for both.

A period of isolation in allopatry typically precedes local adaptation and subsequent divergence among lineages. Alternatively, locally adapted phenotypes may arise and persist in the face of gene flow, resulting in strong correlations between ecologically-relevant phenotypic variation and corresponding environmental gradients. Quantifying genetic, ecological, and phenotypic divergence in such lineages can provide insights into the abiotic and biotic mechanisms that structure populations and drive the accumulation of phenotypic and taxonomic diversity. Low-vagility organisms whose distributions span ephemeral geographic barriers present the ideal evolutionary context within which to address these questions. Here, we combine genetic (mtDNA and genome-wide SNPs) and phenotypic data to investigate the divergence history of caecilians (Amphibia: Gymnophiona) endemic to the oceanic island of São Tomé in the Gulf of Guinea archipelago. Consistent with a previous mtDNA study, we find two phenotypically and genetically distinct lineages that occur along a north-to-south axis with extensive admixture in the centre of the island. Demographic modelling supports divergence in allopatry (~300 kya) followed by secondary contact (~95 kya). Consequently, in contrast to a morphological study that interpreted latitudinal phenotypic variation in these caecilians as a cline within a single widespread species, our analyses suggest a history of allopatric lineage divergence and subsequent hybridization that may have blurred species boundaries. We propose that late Pleistocene volcanic activity favoured allopatric divergence between these lineages with local adaptation to climate maintaining a stable hybrid zone in the centre of São Tomé Island. Our study joins a growing number of systems demonstrating lineage divergence on volcanic islands with stark environmental transitions across small geographic distances.Um período de isolamento em alopatria geralmente precede adaptação local e divergência subsequente entre linhagens evolutivas. Alternativamente, fenótipos adaptados localmente podem surgir e persistir apesar de fluxo gênico, resultando em fortes correlações entre variação fenotípica ecologicamente relevante e os gradientes ambientais correspondentes. Quantificar divergência genética, ecológica e fenotípica em tais linhagens pode ajudar a clarificar os mecanismos abióticos e bióticos que estruturam as populações e levam ao acúmulo de diversidade fenotípica e taxonômica. Organismos de baixa vagilidade, cujas áreas de distribuição incluem barreiras geográficas efêmeras, representam um contexto evolutivo ideal para abordar essas questões. Neste estudo, combinamos dados genéticos (mtDNA e SNPs genômicos) e fenotípicos para investigar a história de divergência de cecílias endêmicas da ilha oceânica de São Tomé, no arquipélago do Golfo da Guiné. Consistentemente com um estudo anterior de mtDNA, encontramos duas linhagens fenotipicamente e geneticamente distintas que ocorrem ao longo de um eixo norte-sul, com extensa mistura genética no centro da ilha. Modelagem demográfica suportou um cenário de divergência em alopatria (~ 300 mil anos atrás) seguida de contato secundário (~ 95 mil anos atrás). Ao contrário de um estudo morfológico que interpretou a variação fenotípica latitudinal nessas cecílias como uma clina dentro de uma única espécie amplamente difundida, nossas análises sugerem uma história de divergência de linhagens em alopatria e subsequente hibridização que pode ter confundido os limites das espécies. Propomos que atividade vulcânica durante o Pleistoceno tardio favoreceu divergência alopátrica entre essas linhagens, com adaptação local ao clima mantendo uma zona híbrida estável no centro da Ilha de São Tomé. Nosso estudo se une a um número crescente de sistemas que demonstram divergência entre linhagens em ilhas vulcânicas com transições ambientais marcantes ao longo de distâncias geográficas curtas.

An overview of previously described fossil nitidulids is given with details on deposits with confirmed nitidulid representation. Notes on estimated ages and potential placement of fossils described to the species level is also given. A new genus and species of cillaeine sap beetle, Palaeopeplus cascus Powell & Cline is described from Dominican amber. A diagnosis and images are provided to distinguish this genus from all other New World Cillaeinae.

The Green Odorous Frog (Odorrana margaretae) around the Sichuan Basin of western China displays a ring-shaped distributional pattern and possesses multiple replicate contact zones between lineages at various levels of differentiation. To understand its unique speciation history and mechanisms, we obtained 1,540 SNPs from 29 populations and 227 individuals using ddRAD sequencing. Population structure analysis revealed three groups within the species: The West, the North & South, and the East groups. These groups were initially isolated at ~2.03 million years ago, and subsequent post-glacial expansion produced the current ring-shaped distribution around Sichuan Basin with three contact zones. Hybridization in those zones involved lineages with different levels of divergence and produced greatly different outcomes. Both the hybrid zones at southwest (S-W) and southeast (E-NS) of the Basin have extensive admixture and less barrier effect. Consequently, the southern region has the highest genetic diversity and becomes an ‘evolutionary melting pot’. In contrast, the hybrid zone at northwestern corner (N-W), which resembles the overlap zone between two expansion terminals of a ring species, has limited admixture with a narrow geographic cline, suggesting partial reproductive isolation between the northern and western populations. The three hybrid zones likely resemble three time points along a speciation continuum; while both E-NS and S-W hybrid zones are merging, the N-W zone may have passed the ‘tipping point’ and is destined for a complete reproductive isolation over time.

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 FSTbetween 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 SummaryWhen 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.

When the ranges of closely-related lineages are large, and overlapping, we can often study introgression at many “replicated” contacts, with different locations and spatial scales. Here we analysed multiple contact zones of the M. edulis complex of marine mussel species, which represent a mosaic distribution of heterogeneously differentiated, semi-isolated genomes. Our aim was to contrast ongoing introgression at the heart of hybrid zones, with past introgression between similar parental populations, at increasing distance from the contact. Using a panel of ancestry-informative SNPs derived from a previous genomic study, we first confirm, with a broader sampling, that local introgression, affecting one but not all of the populations compared, is both widespread and heterogeneous across the genome. Some outlier loci show patterns of complete introgression in certain populations, and an absence of introgression in others. Genomic cline analyses reveal a globally high concordance among loci at a local scale, albeit with signals of asymmetric introgression at a few loci. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants, or less loaded alleles. Given the mosaic structure of the M. edulis complex, with a succession of genetic barriers to gene flow, variants with enhanced introgression through one barrier can be trapped, maybe transiently, at the next barrier, confining introgression locally. This makes the Mytilus complex an ideal model of the heterogeneous porosity of species barriers.