Clinal Variation Research Articles

A revision of recent taxonomic changes to the eyelash palm pitviper, Bothriechis schlegelii (Serpentes, Viperidae)

The taxonomy of the Bothriechis schlegelii species group has recently been expanded, nearly doubling the number of recognized species within this genus. However, the validity of these new species, defined primarily by mitochondrial DNA and without a robust evaluation of nuclear DNA and morphological data, warrants critical reassessment. This study re-examines the integrative data used in the initial analysis and employs additional visualizations of the genetic and morphological datasets. The results suggest that the genetic differences previously interpreted as species boundaries may instead reflect clinal variation, not independent lineages. Furthermore, DELINEATE species delimitation analysis and morphological assessments challenge the distinction of the proposed taxa. The findings indicate that only three species in the B. schlegelii group should be maintained as valid (B. nigroadspersus, B. schlegelii, and B. supraciliaris), while most taxa proposed by Arteaga et al. (2024) should be considered junior synonyms, or at most, as subspecies. This has significant implications for conservation priorities and resource allocation. In highlighting the need for a cautious and thorough approach to species delimitation, this study contributes to the broader discussion of taxonomic practices, the issue of taxonomic inflation, and their impact on biodiversity conservation.

Clinal Variation in Short Tandem Repeats Linked to Gene Expression in Sunflower (Helianthus annuus L.).

Short tandem repeat (STR) variation is rarely explored as a contributor to adaptive evolution. An intriguing mechanism involving STRs suggests that STRs function as "tuning knobs" of adaptation whereby stepwise changes in STR allele length have stepwise effects on phenotypes. Previously, we tested the predictions of the "tuning knob" model at the gene expression level by conducting an RNA-Seq experiment on natural populations of common sunflower (Helianthus annuus L.) transecting a well-defined cline from Kansas to Oklahoma. We identified 479 STRs with significant allele length effects on gene expression (eSTRs). In this study, we expanded the range to populations further north and south of the focal populations and used a targeted approach to study the relationship between STR allele length and gene expression in five selected eSTRs. Seeds from 96 individuals from six natural populations of sunflower from Nebraska and Texas were grown in a common garden. The individuals were genotyped at the five eSTRs, and gene expression was quantified with qRT-PCR. Linear regression models identified that eSTR length in comp26672 was significantly correlated with gene expression. Further, the length of comp26672 eSTR was significantly correlated with latitude across the range from Nebraska to Texas. The eSTR locus comp26672 was located in the CHUP1 gene, a gene associated with chloroplast movement in response to light intensity, which suggests a potential adaptive role for the eSTR locus. Collectively, our results from this targeted study show a consistent relationship between allele length and gene expression in some eSTRs across a broad geographical range in sunflower and suggest that some eSTRs may contribute to adaptive traits in common sunflower.

Expression-environment associations in transcriptomic heat stress responses for a global plant lineage.

The increasing frequency and severity of heatwaves will intensify stress on plants. Given regional variation in heatwave exposure and expected differences in thermal tolerance between species it is unlikely that all plant species will be affected equally by climate change. However, little is currently known about variation in the responses of plants to heat stress, or how those responses differ among closely related species adapted to different environments. Here we quantify the response of 17 Acacia species (175 RNA-seq libraries), from across Australia's diverse biomes, to a multi-day experimental heatwave treatment to identify variation in transcriptomic and physiological responses to heat stress. Genes with known heat response functions showed consistent responses across Acacia species. Up to 10% of all genes and over 100 gene families showed significant clinal variation in the magnitude of their expression plasticity across species. Specifically, gene families linked to the temperature stress response were overrepresented among significant relationships with home range temperature conditions. Gene expression responses seen on the first day of the heatwave were more frequently associated with home range climates, while expression responses by day four were more commonly related to photosystem II acclimation. Comparative transcriptomics on non-model species has the potential to provide key information on stress response plasticity, especially when linked with our understanding of model species. Our study indicates that the pressing challenge to identifying potentially vulnerable species to climate change could be benefited by the further exploration of clinal variation in transcriptome plasticity.

GENETIC DETERMINANTS OF CARBOHYDRATE METABOLISM: INTRA- AND INTERETHNIC VARIABILITY OF THE LACTASE LCT, TREHALASE TREH AND SUCRASE-ISOMALTASE SI GENES IN THE EVENKI AND OTHER INDIGENOUS PEOPLES OF SIBERIA

Introduction. The authors consider the features of genetic determinants of disaccharide assimilation as the corollary of adaptation to the environment. The aim of the study was to assess the polymorphism of the genes that determine activity of disaccharidase enzymes lactase (LCT, rs4988235), trehalase (TREH, rs2276064) and sucrase-isomaltase (SI, rs781470490) in different territorial groups of Evenks. Materials and methods. Biomaterial samples from 1365 unrelated individuals representing 15 ethno-territorial population groups in European Russia, Siberia, and the Far East of the Russian Federation were genotyped. "Focus" groups include "Western" (N=65), "Transbaikal" (N=50), and "Okhotsk" (N=81) Evenks (Krasnoyarsk Krai, Northern Transbaikalia, Okhotsk-Aldan region). The other study groups allow us to assess the specificity of the distribution of genetic determinants of disaccharide assimilation in populations that differ from racial, ecological, and subsistence perspectives. Results. The Evenki territory subgroups do not differ from each other in terms of allele frequencies and genotype distribution of LCT (p>0.2) and TREH (p>0.8) and are similar to Yakuts, Buryats, Mongols, and populations of the Far East and Chukotka. The SI delAG deletion was not found in the Western Evenki subgroup. Discussion. A question of similarity between taiga hunters Evenks to cattle breeders Buryats, Mongols, and Yakuts in terms of C*LCT frequencies requires further elaboration. Possible explanations may include a weakening of selection for the T*LCT allele due to the shift in traditional diet toward replacement of fresh milk with fermented dairy products, high activity of specific intestinal microflora, or the existence of other lactase synthesis genetic determinants, besides LCT*C/T-13910. The evolutionary origins of the clinal variation in the TREH gene allele frequencies, which appears to be associated with the expression of the Mongoloid ancestral component in the gene pool of populations in Northern Eurasia, remain unclear. It seems appropriate to conduct genetic screening in the indigenous populations of the Russian Far East in order to assess the prevalence of SI delAG deletion as an inducer of the sucrase-isomaltase deficiency.

Evolution of species recognition when ecology and sexual selection favor signal stasis.

The process of reproductive character displacement involves divergence and/or the narrowing of variance in traits involved in species recognition, driven by interactions between taxa. However, stabilizing sexual selection may favor stasis and species similarity in these same traits if signals are optimized for transmission through the prevailing environment. Further, sexual selection may promote increased variability within species to facilitate individual recognition. Here we ask how the conflicting selection pressures of species recognition and sexual selection are resolved in a genus of Himalayan birds that sing exceptionally similar songs. We experimentally show that small differences in two traits (note shape and peak frequency) are both necessary and sufficient for species recognition. Song frequency shows remarkable clinal variation along the Himalayan elevational gradient, being most divergent where species co-occur, the classic signature of reproductive character displacement. Note shape shows no such clinal variation but varies more between individuals of an allopatric species than it does among individuals within species that co-occur. We argue that the different note shapes experience similar transmission constraints, and differences produced through species interactions spread back through the entire species range. Our results imply that reproductive character displacement is likely to be common.

Clinal variation in quantitative traits but not in evolutionary potential along elevational and latitudinal gradients in the widespread Anthyllis vulneraria.

Strong elevational and latitudinal gradients allow the study of genetic differentiation in response to similar environmental changes. However, it is uncertain whether the environmental changes along the two types of gradients result in similar genetically based changes in quantitative traits. Peripheral arctic and alpine populations are thought to have less evolutionary potential than more central populations do. We studied quantitative traits of the widespread Anthyllis vulneraria in a common garden. Plants originated from 20 populations along a 2000-m elevational gradient from the lowlands to the elevational limit of the species in the Alps, and from 20 populations along a 2400-km latitudinal gradient from the center of the distribution of the species in Central Europe to its northern distributional margin. Most traits showed similar clinal variations with elevation and latitude of origin, and the magnitude of all measured traits in relation to mean annual temperature was similar. Higher QST values than FST values in several traits indicated diversifying selection, but for others QST was smaller than FST. Genetic diversity of quantitative traits and neutral molecular markers was not correlated. Plasticity in response to favorable conditions declined with elevation and less strongly with latitude of origin, but the evolvability of traits did not. The clinal variation suggests adaptive differentiation of quantitative traits along the two gradients. The evolutionary potential of peripheral populations is not necessarily reduced, but lower plasticity may threaten their survival under rapidly changing climatic conditions.

Range‐wide intraspecific variation reflects past adaptation to climate in a gypsophile Mediterranean shrub

Abstract Phenotypic differences among populations stem from the interaction between neutral and adaptive processes, and phenotypic plasticity. Although clinal trait variation along climatic gradients often evolves in widely distributed species, it is unknown whether substrate specialization, such as that of Mediterranean gypsum plants, has constrained adaptation to climate. Using a common garden experiment with two contrasting watering treatments, we quantified phenotypic plasticity, assessed evidence for footprints of selection using FST – QST comparisons, and evaluated the ecological factors driving genetically based phenotypic differentiation of 11 populations encompassing the full environmental range of the gypsum shrub Lepidium subulatum. We found evidence for genetic differentiation among populations related to climatic differences, with populations from warmer and drier sites showing lower specific leaf area and leaf N, earlier phenology, greater water use efficiency and greater fitness. Multiple lines of evidence suggest that this differentiation was driven by past divergent selection rather than neutral processes. All populations showed high phenotypic plasticity, indicating that plasticity has not been selected against, even in populations from sites with harsher climatic conditions. Synthesis. Our results indicate that despite strong substrate specialization, adaptive differentiation related to climatic gradients occurs in this species. However, we also found that populations from mesic sites may be particularly vulnerable to future climate change given their relatively lower fitness under both wet and dry conditions.

Does climate shape geographical morphological variation of spines in Neotropical spiny rats (Rodentia, Echimyidae, Trinomys)?

Abstract Flattened and flexible spiny hairs, the aristiforms, evolved independently in some lineages of rodents, but unlikely capable of causing severe damage to predators. Their biological roles are not yet clearly known and some different thermoregulatory functions have been proposed, often associated with severe climatic conditions but not yet tested. In this study we investigated whether climate may be a major factor shaping geographic variation of length and width of aristiform hairs of 2 species of Neotropical spiny rats of the genus Trinomys (Echimyidae) occurring in eastern Brazil: T. albispinus and T. setosus. Results revealed clinal variation in these hairs. While bioclimatic factors and geographic distance together accounted for up to a third of the morphometric variation, the exclusive impact of climate was limited, explaining only up to 3% of the observed variation. However, considering the close association between climate and geographic distance, the role of climate in shaping aristiform hair cannot be discounted. While our results did not fully support the hypothesis that well-developed, wide spiny hairs are selected for greater protection against rain for underhairs, they marginally supported their role in facilitating heat loss in warm environments by facilitating water condensation. More consistently, results show that narrow spiny hairs tended to evolve in cold environments, likely enhancing thermal insulation. The length of aristiform hair in T. albispinus also appeared to respond to this function, becoming longer in cold and high-altitude regions. However, we cannot rule out the possibility of an evolutionary response correlated with selection on underhairs. Future experimental studies should test the thermoregulatory function of flexible spiny hairs and investigate the geographic variation of these structures in other rodent species.

Ecogeographic rules in a common Neotropical treefrog: No clinal variation along a mountain range

AbstractBody and limb size are associated with many aspects of the biology of animals. Geographic variation in morphological traits has often been investigated through ecogeographical rules. Bergmann's rule posits an inverse relationship between body size and temperature in homeotherms, while Allen's rule posits that endothermic animals inhabiting colder climates have relatively shorter protruding parts (e.g., limbs) in comparison to populations from warmer climates. However, the applicability and validity of these rules in poikilotherms are currently contentious. In this study, we aimed to test predictions of Bergmann's and Allen's rules in populations of the Neotropical frog Boana platanera. We analysed 142 adult male museum specimens from 17 localities along a mountain range in western Venezuela. We obtained six external morphological measurements and assessed the correlation of body size and limb size with temperature data for each locality. Our results were contrary to the expectations but consistent with previous studies. All this together indicates that exceptions to the Bergmann's and Allen's rules are frequent and idiosyncratic in anurans. We discuss alternative hypotheses that could explain geographic variation of body and limb size in future studies.

Trans-Atlantic genomic differentiation and parallel environmental and allelic variation in Lumpfish (Cyclopterus lumpus)

Abstract In marine species with large populations and high dispersal potential, large-scale genetic differences and clinal trends in allele frequency can provide insight into the evolutionary processes that shape diversity. Lumpfish, Cyclopterus lumpus, is found throughout the North Atlantic and has traditionally been harvested for roe and more recently used as a cleaner fish in salmon aquaculture. We used a 70 K SNP array to evaluate trans-Atlantic differentiation, genetic structuring, and clinal variation across the North Atlantic. Basin-scale structuring between the Northeast and Northwest Atlantic was significant, with enrichment for loci associated with developmental/mitochondrial function. We identified a putative structural variant on chromosome 2, likely contributing to differentiation between Northeast and Northwest Atlantic Lumpfish, and consistent with post-glacial trans-Atlantic secondary contact. Redundancy analysis identified climate associations both in the Northeast (N = 1269 loci) and Northwest (N = 1637 loci), with 103 shared loci between them. Clinal patterns in allele frequencies were observed in some loci (15%—Northwest and 5%—Northeast) of which 708 loci were shared and involved with growth, developmental processes, and locomotion. The combined evidence of trans-Atlantic differentiation, environmental associations, and clinal loci, suggests that both regional and large-scale potentially-adaptive population structuring is present across the North Atlantic.

Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data.

Studying range expansions is central for understanding genetic variation through space and time as well as for identifying refugia and biological invasions. Range expansions are characterized by serial founder events causing clines of decreasing genetic diversity away from the center of origin and asymmetries in the two-dimensional allele frequency spectra. These asymmetries, summarized by the directionality index (ψ), are sensitive to range expansions and persist for longer than clines in genetic diversity. In continuous and finite meta-populations, genetic drift tends to be stronger at the edges of the species distribution in equilibrium populations and populations undergoing range expansions alike. Such boundary effects are expected to affect geographic patterns in genetic diversity and ψ. Here we demonstrate that boundary effects cause high false positive rates in equilibrium meta-populations when testing for range expansions. In the simulations, the absolute value of ψ (|ψ|) in equilibrium data sets was proportional to the fixation index (FST). By fitting signatures of range expansions as a function of ɛ |ψ|/FST and geographic clines in ψ, strong evidence for range expansions could be detected in data from a recent rapid invasion of the cane toad, Rhinella marina, in Australia, but not in 28 previously published empirical data sets from Australian scincid lizards that were significant for the standard range expansion tests. Thus, while clinal variation in ψ is still the most sensitive statistic to range expansions, to detect true signatures of range expansions in natural populations, its magnitude needs to be considered in relation to the overall levels of genetic structuring in the data.

Geographical variation in the forewing shape of the red dwarf honeybees revealed by landmark-based geometric morphometrics

Accurate intraspecific variation assessment is the prerequisite for determining subspecies, evolutionarily significant units, or management units across a species' range. However, intraspecific variation assessment is often hindered by inaccurate morphological results from traditional methods or high-cost genetic analyses. Geometric morphometrics is a promising technique for quantifying and visualising intraspecific diversity. We used landmark-based geometric morphometrics to investigate forewing shape variation and microtaxonomy of populations of Apis florea Fabricius 1787 (Apidae: Apini), which originated from some parts of Asia and Africa based on the 19 landmarks plotted at the venation intersections of forewings. We collected samples of 162 colonies from 36 different localities. On average, 13 workers per colony were analysed (1851 bees in total). Distinct spatial structures and significant differences in wing shape between the studied populations were revealed using canonical variate analysis, and no considerable overlap was detected between the colonies belonging to the western and eastern populations. The populations at higher latitudes showed significantly larger centroid sizes than those at lower latitudes, and a clinal variation in forewing size was confirmed. Significant distance-decay relationships between the studied populations were observed so that the populations located at the maximum geographical distance showed the most significant distance from each other and vice versa. Wing geometric morphometrics was an accurate tool for the reliable estimation of the population structure of the red dwarf honeybees. It is essential to increase the reliability of these variations by combining the results with further molecular data.

Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations

Abstract The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species’ demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.

Phylogenomics of Tetraopes longhorn beetles unravels their evolutionary history and biogeographic origins

Tetraopes longhorn beetles are known for their resistance to milkweed plant toxins and their coevolutionary dynamics with milkweed plants (Asclepias). This association is considered a textbook example of coevolution, in which each species of Tetraopes is specialized to feed on one or a few species of Asclepias. A major challenge to investigating coevolutionary hypotheses and conducting molecular ecology studies lies in the limited understanding of the evolutionary history and biogeographical patterns of Tetraopes. By integrating genomic, morphological, paleontological, and geographical data, we present a robust phylogeny of Tetraopes and their relatives, using three inference methods with varying subsets of data, encompassing 2–12 thousand UCE loci. We elucidate the diversification patterns of Tetraopes species across major biogeographical regions and their colonization of the American continent. Our findings suggest that the genus originated in Central America approximately 21 million years ago during the Miocene and diversified from the Mid-Miocene to the Pleistocene. These events coincided with intense geological activity in Central America. Additionally, independent colonization events in North America occurred from the Late Miocene to the early Pleistocene, potentially contributing to the early diversification of the group. Our data suggest that a common ancestor of Tetraopini migrated into North America, likely facilitated by North Atlantic land bridges, while closely related tribes diverged in Asia and Europe during the Paleocene. Establishing a robust and densely sampled phylogeny of Tetraopes beetles provides a foundation for investigating micro- and macroevolutionary phenomena, including clinal variation, coevolution, and detoxification mechanisms in this ecologically important group.

Integrative taxonomy of Cercomacroides serva (Sclater, 1858) demonstrates the validity of C. hypomelaena (Sclater, 1890) comb. nov. (Aves: Thamnophilidae)

Abstract Cercomacroides serva is widely distributed in northern South America. However, this species has never been thoroughly evaluated taxonomically. We conducted a taxonomic study of three taxa currently classified under Cercomacroides serva, based on a study of 307 skins and 145 recordings of male loudsongs. Females from the northwest Amazonian population differ qualitatively from populations from the southwest Amazon in the coloration of the upperparts, primary, and tail. Male loudsongs are superficially similar between these two populations, but the shape of the notes differs significantly. There is no evidence of intergradation or clinal variation in female plumage or male loudsongs. Based on differences in plumage coloration, loudsongs, and lack of evidence of intergradation, we suggest that two species are best recognized. The name Cercomacroides serva is here restricted to populations north of the Marañon River in Peru, to the north in Ecuador, and in southwestern Colombia. The name Cercomacroides hypomelaenacomb. nov. is revived. This species is found south of the Marañon River, and on both banks of the Ucayali River in Peru, to the eastern left bank of the Madeira River in Brazil, and in northern Bolivia.

Taxonomic revision of the Scaled Antbird Drymophila squamata (Aves: Thamnophilidae) reveals a new and critically endangered taxon from northeastern Brazil.

The Scaled Antbird Drymophila squamata is a suboscine passerine endemic to the Atlantic Forest of eastern Brazil. Two subspecies, putatively diagnosed by the presence/absence of white spots on the crown, have traditionally been recognized: the nominate, ranging from Pernambuco to Bahia in northeastern Brazil, and D. squamata stictocorypha, from Minas Gerais to Santa Catarina in southeastern and southern Brazil. Here we combine morphological, acoustic, and genetic data to examine geographic variation in and revise the taxonomy of D. squamata. We show that there are two separately evolving population lineages in D. squamata, one south and the other north of the So Francisco River. The latter is unnamed and is thus described herein. We found that crown variation is not as geographically structured as previously thought, and thus we suggest that D. squamata stictocorypha is not a valid taxon. Finally, we also provide evidence of clinal variation in the species vocalizations and underscore the importance of broad geographic sampling when assessing species limits using vocalizations.

Weak local adaptation to drought in seedlings of a widespread conifer.

Tree seedlings from populations native to drier regions are often assumed to be more drought tolerant than those from wetter provenances. However, intraspecific variation in drought tolerance has not been well-characterized despite being critical for developing climate change mitigation and adaptation strategies, and for predicting the effects of drought on forests. We used a large-scale common garden drought-to-death experiment to assess range-wide variation in drought tolerance, measured by decline of photosynthetic efficiency, growth, and plastic responses to extreme summer drought in seedlings of 73 natural populations of the two main varieties of Douglas-fir (Pseudotsuga menziesii var. menziesii and var. glauca). Local adaptation to drought was weak in var. glauca and nearly absent in menziesii. Var. glauca showed higher tolerance to drought but slower growth than var. menziesii. Clinal variation in drought tolerance and growth species-wide was mainly associated with temperature rather than precipitation. A higher degree of plasticity for growth was observed in var. menziesii in response to extreme drought. Genetic variation for drought tolerance in seedlings within varieties is maintained primarily within populations. Selective breeding within populations may facilitate adaptation to drought more than assisted gene flow.

The incredible shrinking puffin: Decreasing size and increasing proportional bill size of Atlantic puffins nesting at Machias Seal Island.

Climate change imposes physiological constraints on organisms particularly through changing thermoregulatory requirements. Bergmann's and Allen's rules suggest that body size and the size of thermoregulatory structures differ between warm and cold locations, where body size decreases with temperature and thermoregulatory structures increase. However, phenotypic plastic responses to malnutrition during development can result in the same patterns while lacking fitness benefits. The Gulf of Maine (GOM), located at the southern end of the Labrador current, is warming faster than most of the world's oceans, and many of the marine species that occupy these waters exist at the southern edge of their distributions including Atlantic puffins (Fratercula arctica; hereafter "puffin"). Monitoring of puffins in the GOM, at Machias Seal Island (MSI), has continued annually since 1995. We asked whether changes in adult puffin body size and the proportional size of bill to body have changed with observed rapid ocean warming. We found that the size of fledgling puffins is negatively related to sea surface temperature anomalies (warm conditions = small fledgers), adult puffin size is related to fledgling size (small fledgers = small adults), and adult puffins have decreased in size in recent years in response to malnutrition during development. We found an increase in the proportional size of bill to wing chord, likely in response to some mix of malnutrition during development and increasing air temperatures. Although studies have assessed clinal variation in seabird morphology with temperature, this is the first study addressing changes in seabird morphology in relation to ocean warming. Our results suggest that puffins nesting in the GOM have morphological plasticity that may help them acclimate to ocean warming.

Clinal variation in natural populations of Drosophila melanogaster: An old debate about natural selection and neutral processes.

Distinguishing between environmental adaptations and neutral processes poses a challenge in population genetics and evolutionary studies, particularly when phenomena can be explained by both processes. Clines are genotypic or phenotypic characters correlated with environmental variables, because of that correlation, they are used as examples of spatially varying selection. At the same time, many genotypic clines can be explained by demographic history, like isolation by distance or secondary contact zones. Clines have been extensively studied in Drosophila melanogaster, especially in North America and Australia, where they are attributed to both differential selection and various demographic processes. This review explores existing literature supporting this conclusion and suggests new approaches to better understand the influence of these processes on clines. These innovative approaches aim to shed light on the longstanding debate regarding the importance of natural selection versus neutral processes in maintaining variation in natural populations.

Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints.

The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.