Distribution,habitat and conservation status of desert pupfish (Cyprinodon macularius) in the Lower Colorado River Basin,Mexico

In order to better determine the currentstatus of desert pupfish populations (Cyprinodon macularius macularius) in the LowerColorado River Basin of Mexico, bimonthly fishsampling and habitat evaluations were carriedout from September 1996 to August 1997 in sixlocalities of Baja California and Sonora.Desert pupfish were collected using minnowseines and traps. Four sampling sites are inSonora, in shallow marginal habitats of theCiénega Santa Clara (Hunters' Camp, Outletof the Welton-Mohawk channel, El Doctor andFlor del Desierto) and two are in BajaCalifornia (Cerro Prieto and streams south ofCerro Prieto). The most abundant fish speciessampled was native desert pupfish (C.macularius, 59%) followed by sailfin molly(Poecilia latipinna, 19%), redbellytilapia (Tilapia cf. zilli, 10%) and western mosquito fish (Gambusiaaffinis, 7%). Significant temporalfluctuations in distribution and abundance ofdesert pupfish populations, as previouslyreported for these populations, was againdocumented. The main anthropogenic factorsaffecting distribution and abundance of desertpupfish populations in the Mexican portion ofthe Lower Colorado River Basin are progressivealteration of aquatic and riparian habitats, aswell as presence of exotic fishes that havecaused the displacement or elimination ofnative fish populations. Both habitat andpresence of the desert pupfish populations inthe study area are controlled by theperiodicity, quality and volume of dischargesinto the Mexican portion of the basin from theUnited States.     

Rapid genetic and morphologic divergence between captive and wild populations of the endangered Leon Springs pupfish,Cyprinodon bovinus

The Leon Springs pupfish (Cyprinodon bovinus) is an endangered species currently restricted to a single desert spring and a separate captive habitat in southwestern North America. Following establishment of the captive population from wild stock in 1976, the wild population has undergone natural population size fluctuations, intentional culling to purge genetic contamination from an invasive congener (Cyprinodon variegatus) and augmentation/replacement of wild fish from the captive stock. A severe population decline following the most recent introduction of captive fish prompted us to examine whether the captive and wild populations have differentiated during the short time they have been isolated from one another. If so, the development of divergent genetic and/or morphologic traits between populations could contribute to a diminished ability of fish from one location to thrive in the other. Examination of genomewide single nucleotide polymorphisms and morphologic variation revealed no evidence of residual C. variegatus characteristics in contemporary C. bovinus samples. However, significant genetic and morphologic differentiation was detected between the wild and captive populations, some of which might reflect local adaptation. Our results indicate that genetic and physical characteristics can diverge rapidly between isolated subdivisions of managed populations, potentially compromising the value of captive stock for future supplementation efforts. In the case of C. bovinus, our findings underscore the need to periodically inoculate the captive population with wild genetic material to help mitigate genetic, and potentially morphologic, divergence between them and also highlight the utility of parallel morphologic and genomic evaluation to inform conservation management planning.     

Preservation of behavior after fifteen years of isolation: comparisons of wild and captive endangered pupfish in their natural habitat

Endangered species are often maintained in captivity to serve as a safeguard in the event of an extirpation of natural populations. However, wild and captive populations can rapidly diverge in genetic and phenotypic characteristics, including behavior, when maintained in isolation and under different environmental conditions. Here, we compare two populations of the endangered Leon Springs pupfish (Cyprinodon bovinus): a captive population maintained at the Southwestern Native Aquatic Resources and Recovery Center (SNARRC) and the only remaining wild population. Wild fish in the natural Texan Diamond Y desert spring are remnants of a past reintroduction of captive SNARRC fish, which occurred in 1998. The fifteen years of isolation have led to genetic and morphologic differences between the two populations. To assess the behavioral implications of such divergence, we released previously captive C. bovinus into natural habitat and quantified behaviors under natural conditions and in semi-controlled mesocosms and then replicated these conditions with the established natural population. Both populations exhibited similar levels of reproduction, foraging, and agonistic behavior. Despite divergence in genetic and morphometric characteristics, overall behavioral patterns of C. bovinus remained consistent in similar environments. This stability suggests that captive C. bovinus could again be successful establishing in their natural habitat. It is our hope that this investigation will help focus future conservation efforts towards monitoring the persistence of reintroduced C. bovinus in addition to providing a framework for other recovery plans reintroducing captive stock into ancestral habitats.     

Contemporary evolutionary divergence for a protected species following assisted colonization

Background

Contemporary evolution following assisted colonization may increase the probability of persistence for refuge populations established as a bet-hedge for protected species. Such refuge populations are considered “genetic replicates” that might be used for future re-colonization in the event of a catastrophe in the native site. Although maladaptive evolutionary divergence of captive populations is well recognized, evolutionary divergence of wild refuge populations may also occur on contemporary time scales. Thus, refuge populations may lose their “value” as true genetic replicates of the native population. Here, we show contemporary evolutionary divergence in body shape in an approximately 30-year old refuge population of the protected White Sands pupfish (Cyprinodon tularosa) resulting in a body-shape mismatch with its native environment.

Methodology/Principal Findings

Geometric morphometic data were collected from C. tularosa cultures raised in experimental mesocosms. Cultures were initiated with fish from the two native populations, plus hybrids, in high or low salinity treatments representing the salinities of the two native habitats. We found that body shape was heritable and that shape variation due to phenotypic plasticity was small compared to shape variation due to population source. C. tularosa from the high salinity population retained slender body shapes and fish from the low salinity population retained deep body shapes, irrespective of mesocosm salinity. These data suggest that the observed divergence of a recently established pupfish population was not explained by plasticity. An analysis of microsatellite variation indicated that no significant genetic drift occurred in the refuge population, further supporting the adaptive nature of changes in body shape. These lines of evidence suggest that body shape divergence of the refuge population reflects a case of contemporary evolution (over a 30-year period).

Conclusions/Significance

These results suggest assisted colonization can introduce novel, and/or relaxed selection, and lead to unintended evolutionary divergence.     

The conservation genetics of Ash Meadows pupfish populations. I. The Warm Springs pupfish <Emphasis Type="Italic">Cyprinodon nevadensis pectoralis</Emphasis>

The Warm Springs pupfish (Cyprinodon nevadensis pectoralis) inhabits several low flow (<0.15 cfs) springs in an otherwise dry Mojave Desert landscape. Increasing demands on groundwater coupled with predictions of decreased precipitation from global warming make this species a sentinel for biodiversity dependent on springs. Here we examine mitochondrial DNA haplotypes and nuclear microsatellite genotypes for individuals sampled in 1998 and 2007 as a means of inferring the historical demography of the subspecies. Estimates of genetic effective population size from comparison of allele frequencies over time underscores that all spring populations support small populations, typically <100 individuals. Such small population sizes suggest spring populations may have heightened probabilities of extirpation. Despite small population sizes, all springs harbor relatively high levels of genetic variation for both nuclear and mitochondrial DNA. Unexpectedly high levels of variation may be explained by recent declines in population size coupled with rare episodes of gene flow between springs suspected of occurring during flooding events. The inferences gained from the genetic data provide the basis for evaluating current and future restoration plans. The genetic data suggest there is a need to balance the predicted positive effects of restoring hydrological connectivity with the potential negative impacts of providing avenues for the spread of exotic species detrimental to pupfish populations.     

Patterns of polyploid evolution in Greek marsh orchids (Dactylorhiza; Orchidaceae) as revealed by allozymes, AFLPs, and plastid DNA data

Polyploidy is common in higher plants, and speciation in polyploid complexes is usually the result of reticulate evolution. We examined variation in nuclear AFLP fingerprints, nuclear isozymes, and hypervariable plastid DNA loci to describe speciation patterns and species relationships in the Dactylorhiza incarnata/maculata polyploid complex (marsh orchids; Orchidaceae) in Greece. Several endemic taxa with restricted distribution have been described from this area, and to propose meaningful conservation priorities, detailed relationships need to be known. We identified four independently derived allopolyploid lineages, which is a pattern poorly correlated with prevailing taxonomy. Three lineages were composed of populations restricted to small areas and may be of recent origins from extant parental lineages. One lineage with wide distribution in northern Greece was characterized by several unique plastid haplotypes that were phylogenetically related and evidently older. The D. incarnata/maculata polyploid complex in Greece has high levels of genetic diversity at the polyploid level. This diversity has accumulated over a long time and may include genetic variants originating from now extinct parental populations. Our data also indicate that the Balkans may have constituted an important refuge from which northern European Dactylorhiza were recruited after the Weichselian ice age.     

Population divergence in plasticity of the AVT system and its association with aggressive behaviors in a Death Valley pupfish

Behavioral differences can evolve rapidly in allopatry, but little is known about the neural bases of such changes. Allopatric populations of Amargosa pupfish (Cyprinodon nevadensis) vary in aggression and courtship behaviors in the wild. Two of these wild populations were recently found to differ in brain expression of arginine vasotocin (AVT)--a peptide hormone shown previously to modulate aggression in pupfish. These populations have been isolated for less than 4000 years, so it remained unclear whether the differences in behavior and neural AVT phenotype were evolved changes or plastic responses to ecologically dissimilar habitats. Here, I tested whether these population differences have a genetic basis by examining how aggressive behavior and neural AVT phenotype responded to ecologically relevant variation in salinity (0.4 ppt or 3 ppt) and temperature (stable or daily fluctuating). Pupfish from Big Spring were more aggressive than pupfish from the Amargosa River when bred and reared under common laboratory conditions. Morphometric analysis of preoptic AVT immunoreactivity showed that the populations differed in how the AVT system responded to salinity and temperature conditions, and revealed that this plasticity differed between parvocellular and magnocellular AVT neuron groups. Both populations also showed relationships between neural AVT phenotype and aggression in the rearing environment, although populations differed in how aggression related to variation in magnocellular AVT neuron size. Together, these results demonstrate that the pupfish populations have diverged in how physical and social conditions affect the AVT system, and provide evidence that the AVT system can evolve quickly to ecologically dissimilar environments.     

Phylogeographic patterns in populations of the black-chinned tilapia complex (Teleostei,Cichlidae) from coastal areas in West Africa: support for the refuge zone theory

Within the tilapiines, a major African cichlid lineage, quite limited genetic informations are available on phylogenetic interrelationships and phylogeographical patterns at both macro- and micro-evolutionary scales. The present study examines the genetic diversity of the black-chinned tilapia complex from coastal areas in West Africa (Senegal to Congo-Brazzaville) based on mtDNA control region sequences. Phylogenetic inferences provide support for the monophyly of both taxa involved. It is suggested that Sarotherodon melanotheron and Sarotherodon nigripinnis have diverged probably since the early Pleistocene. The occurrence of the main intraspecific lineages could be dated back to about 500,000-900,000 years. Our data suggest that West African Pleistocene refuge zones may have strongly influenced the degree and level of genetic differentiation among populations and thus the observed phylogeographic patterns. The spatial distribution of mtDNA lineages and the centres of intrapopulational genetic diversity clearly correspond to proposed lowland refuge zones and core areas of Central Africa. Moreover, this study genetically supports the existence of Sarotherodon melanotheron leonensis for the first time and further confirms the validity of the most recently introduced subspecies, e.g., Sarotherodon nigripinnis dolloi.     

Genetic variation of the major histocompatibility complex (MHC class II β gene) in the threatened Gila trout, <Emphasis Type="Italic">Oncorhynchus gilae gilae</Emphasis>

Gila trout (Oncorhynchus gilae gilae) was federally protected in 1973 because of severe declines in abundance and geographic range size. At present, four relict genetic lineages of the species remain in mountain streams of New Mexico and Arizona, USA. Management actions aimed at species recovery, including hatchery production and restocking of formerly occupied streams, have been guided by information from non-functional genetic markers. In this study, we investigated genetic variation at exon 2 of the major histocompatibility complex (MHC) class II β gene that is involved in pathogen resistance and thus presumably under natural selection. Phylogenetic analysis revealed trans-species polymorphism and a significantly high ratio of non-synonymous to synonymous amino acid changes consistent with the action of historical balancing selection that maintained diversity at this locus in the past. However, Gila trout exhibited low allelic diversity (five alleles from 142 individuals assayed) compared to some other salmonid fishes, and populations that originated exclusively from hatcheries possessed three or fewer MHC alleles. Comparative analysis of genetic variation at MHC and six presumably neutrally evolving microsatellite loci revealed that genetic drift cannot be rejected as a primary force governing evolution of MHC in contemporary populations of Gila trout. Maintenance of diversity at MHC will require careful implementation of hatchery breeding protocols and continued protection of wild populations to prevent loss of allelic diversity due to drift.     

Fish habitat associations in a spatially variable desert stream

White sands pupfish Cyprinodon tularosa were sampled with minnow traps along the length of Lost River, a highly variable desert stream in New Mexico, to evaluate if their abundance, median standard length ( L _S) and sex ratio values differed by microhabitat variables. Habitat measurements were made in a 4 m² area around the minnow trap. White Sands pupfish populations were primarily structured by L _S. As specific conductance and surface area increased, median size of fish decreased. Shallow areas with higher specific conductance were correlated with an increased number of fish.     

Population structure and genetic diversity distribution in wild and cultivated populations of the traditional Chinese medicinal plant Magnolia officinalis subsp. biloba (Magnoliaceae)

Magnolia officinalis subsp. biloba, a traditional Chinese medicinal plant, experienced severe declines in the number of populations and the number of individuals in the late 20th century due to the widespread harvest of the subspecies. A large-scale cultivation program was initiated and cultivated populations rapidly recovered the loss in individual plant numbers, but wild populations remained small as a consequence of cutting. In this study, the levels of genetic variation and genetic structure of seven wild populations and five domestic populations of M. officinalis subsp. biloba were estimated employing an AFLP methodology. The plant exhibited a relatively high level of intra-population genetic diversity (h = 0.208 and H _j = 0.268). The cultivated populations maintained approximately 95% of the variation exhibited in wild populations, indicating a slight genetic bottleneck in the cultivated populations. The analysis of genetic differentiation revealed that most of the AFLP diversity resided within populations both for the wild group (78.22%) and the cultivated group (85.92%). Genetic differentiation among populations in the wild group was significant (F _ST = 0.1092, P < 0.005), suggesting wild population level genetic structure. Principal coordinates analysis (PCO) did not discern among wild and cultivated populations, indicating that alleles from the wild population were maintained in the cultivated gene pool. Results from the present study provide important baseline data for effectively conserving the genetic resources of this medicinal subspecies.     

Molecular systematics of Hispaniolan pupfishes (Cyprinodontidae: Cyprinodon): implications for the biogeography of insular Caribbean fishes

We used sequence variation in the mtDNA control-region and ND2 and cyt b genes to assess the systematics and biogeography of the five species of pupfish (Cyprinodon) on Hispaniola. These include four endemics, the relatively large-bodied Cyprinodon bondi, Cyprinodon nichollsi, and Cyprinodon sp., each from a separate lake in southwestern Hispaniola, and Cyprinodon higuey from a coastal lake in eastern Hispaniola. The fifth species consists of coastal populations referable to Cyprinodon variegatus riverendi. The results indicate that Hispaniola has been invaded by at least two forms, first by a late Pliocene progenitor of Cyprinodon variegatus ovinus and the large-bodied Hispaniolan species, and, more recently, by one or more ancestral forms allied with Cyprinodon variegatus variegatus and C. v. riverendi. Levels of divergence indicate that large expanses of open sea have not acted as long-term barriers to inter-island dispersal of cyprinodontiform fishes. This study, together with the molecular systematics of other insular Caribbean fishes, indicates that most insular groups originated from late Neogene dispersal from the mainland. The patterns of mtDNA variation in Cyprinodon showed little congruence with the species/subspecies taxonomy.     

Exogenous vasotocin alters aggression during agonistic exchanges in male Amargosa River pupfish (Cyprinodon nevadensis amargosae)

Pupfishes in the Death Valley region have rapidly differentiated in social behaviors since their isolation in a series of desert streams, springs, and marshes less than 20,000 years ago. These habitats can show dramatic fluctuations in ecological conditions, and pupfish must cope with the changes by plastic physiological and behavioral responses. Recently, we showed differences among some Death Valley populations in brain expression of arginine vasotocin (AVT). As AVT regulates both hydromineral balance and social behaviors in other taxa, these population differences may indicate adaptive changes in osmoregulatory and/or behavioral processes. To test whether AVT is relevant for behavioral shifts in these fish, here we examined how manipulations to the AVT system affect agonistic and reproductive behaviors in Amargosa River pupfish (Cyprinodon nevadensis amargosae). We administered exogenous AVT (0.1, 1, and 10 microg/g body weight) and an AVP V1 receptor antagonist (Manning compound, 2.5 microg/g body weight) intraperitoneally to males in mixed-sex groups in the laboratory. We found that AVT reduced the initiation of aggressive social interactions with other pupfish but had no effect on courtship. The effects of AVT were confirmed in males in the wild where AVT (1 microg/g body weight) reduced the aggressive initiation of social interactions and decreased aggressive responses to the behavior of other males. Combined, these results show that AVT can modulate agonistic behaviors in male pupfish and support the idea that variation in AVT activity may underlie differences in aggression among Death Valley populations.     

Barriers,rather than refugia,underlie the origin of diversity in toads endemic to the Brazilian Atlantic Forest

In this study, we investigated the relative contribution of geographic barriers and Pleistocene refuges in the diversification of the Rhinella crucifer species complex, a group of endemic toads with a widespread distribution in the Brazilian Atlantic Forest (AF). We used intensive sampling and multilocus DNA sequence data to compare nucleotide diversity between refuge and nonrefuge areas, investigate regional demographic patterns, estimate demographic parameters related to genetic breaks and test refuge versus barrier scenarios of diversification using approximate Bayesian computation. We did not find higher levels of genetic diversity in putative refuge areas, either at regional or biome scale. Rather, the demographic history of the species complex supports regional differences with moderate population growth in the north and central regions and stability in southern AF. Genetic breaks were dated to the Plio–Pleistocene; however, our analyses rejected the role of refuges in creating a northern and central divergence, supporting a recent colonization scenario at a smaller scale within the central AF. Overall, our data rule out massive climatically driven fragmentation and large‐scale recolonization events for populations across the biome. We confirmed the importance of geographic barriers in creating main divergences and underscored the importance of searching for cryptic discontinuities in the landscape. Comparison of our results with those of other AF taxa indicates organismal specific responses to moderate shifts in habitat and that multiple refuges may constitute a more realistic model for diversification of Atlantic Forest biota.     

Condition status of the endangered desert pupfish,Cyprinodon macularius Baird and Girard, 1853, in the Lower Colorado River Basin (Mexico)

The length‐weight relationship (LWR) was used to test differences in the fish somatic condition factor among four populations of the endangered desert pupfish, Cyprinodon macularius, from the Lower Colorado River Basin, Mexico. Bimonthly fish sampling and habitat assessments were carried out from September 1996 to August 1997 for four sites in Baja California and Sonora. Slope b of the WLR varied from 3.238 (Cerro Prieto population) to 3.613 (Welton‐Mohawk population), showing in all populations a positive allometric growth. Male b values were higher than those of females for Cerro Prieto (3.303 vs 3.071), Welton‐Mohawk (3.866 vs 3.579), and Flor del Desierto (3.357 vs 3.169) populations. The Cerro Prieto population showed the highest somatic condition (y‐intercept, a = ?11.759). Water depth and salinity were the ecological variables that better accounted for most of the variation in the somatic condition of this pupfish, with a negative and a positive effect, respectively.     

Divergence and hybridization in the desert plant Reaumuria soongarica

Speciation is widely accepted to be a complex and continuous process. Due to complicated evolutionary histories, desert plants are ideal model systems to understand the process of speciation along a continuum. Here, we elucidate the evolutionary history of Reaumuria soongarica (Pall.) Maxim., a typical desert plant that is wildly distributed across arid central Asia. Based on variation patterns present at nine nuclear loci in 325 individuals (representing 41 populations), we examined the demographic history, patterns of gene flow, and degree of ecological differentiation among wild R. soongarica. Our findings indicate that genetic divergence between the ancient western and eastern lineages of R. soongarica occurred approximately 0.714 Mya, probably due to the Kunlun–Yellow River tectonic movement and the Naynayxungla glaciation. Later, multiple hybridization events between the western and eastern lineages that took place between 0.287 and 0.543 Mya, and which might have been triggered by the asynchronous historical expansion of the western and eastern deserts, contributed to the formation of a hybrid northern lineage. Moreover, despite continuing gene flow into this population from its progenitors, the northern lineage maintained its genetic boundary by ecological differentiation. The northern lineage could be an incipient species, and provides an opportunity to study the continuous process of speciation. This study suggests that two opposite evolutionary forces, divergence and hybridization, coexisting in the continuous speciation of the desert plant R. soongarica in a short time. Moreover, we provide evidence that this continuous speciation process is affected by geological events, climatic change, and ecological differentiation.     

荒漠沙蜥遗传多样性的地理变异

荒漠沙蜥(Phrynocephalus przewalskii)是一种进化地位至今存在争议的沙漠蜥蜴,该文基于12个不同地理种群119号荒漠沙蜥样本线粒体基因组ND2序列,在分析其系统进化历史的同时,研究了不同环境因素对其遗传多样性的影响。结果发现,12个地理种群聚类成3个明显的分枝,变色沙蜥(P.versicolor)和A枝处于与B、C两枝并列的位置。所调查种群的遗传多样性存在显著的地理变异,分析显示纬度、降雨和降雨变异对种群的遗传多样性都存在影响:随纬度升高、降雨增加,或降雨变异增加,种群遗传多样性均有下降趋势。推测纬度可能通过影响降雨和降雨变异对遗传多样性产生作用。     

Population structure of and mycotoxin production by Fusarium graminearum from maize in South Korea

Fusarium graminearum (Gibberella zeae) is an important pathogen of wheat, maize, barley, and rice in South Korea, and harvested grain often is contaminated with trichothecenes such as deoxynivalenol and nivalenol. In this study, we examined 568 isolates of F. graminearum collected from maize at eight locations in South Korea. We used amplified fragment length polymorphisms (AFLPs) to identify four lineages (2, 3, 6, and 7); lineage 7 was the most common (75%), followed by lineage 6 (12%), lineage 3 (12%), and lineage 2 (1%). The genetic identity among populations was high (>0.98), and the effective migration rate between locations was higher than that between lineages. Female fertility varied by lineage: all lineage 7 isolates were fertile, while 70%, 26%, and 14% of the isolates in lineages 6, 3, and 2, respectively, were fertile. All lineage 3 and lineage 7 isolates produced deoxynivalenol, whereas most lineage 2 and 6 isolates produced nivalenol. Genotypic diversity in lineage 3 and lineage 6 populations is similar to that found in previously described Korean rice populations, but genotypic diversity in lineage 7 is much lower, even though similar levels of gene flow occur between lineage 7 populations. We conclude that lineage 7 was relatively recently introduced into South Korea, perhaps accompanying imported maize seeds.     

Summer movements of desert pupfish among habitats at the Salton Sea

Summer movement behavior of native desert pupfish (Cyprinodon macularius Baird and Girard) was evaluated among various habitats around the Salton Sea, located in southern California. Agricultural drains, shoreline pools, and Salt Creek were sampled six times between June 28 and September 16, 1999. Collected pupfish were marked using fluorescent elastomer implants. Unique marks were used at each site. Movements were detected from locations of recaptured pupfish. Desert pupfish were found in 10 of 12 sites sampled. Of 3239 pupfish captured during the study, 278 were recaptures, including 27 recaptures at areas different from where they were initially marked. The best evidence of pupfish movements was in the southwestern area of the Salton Sea between a drain and a connected shoreline pool. Movements were also observed from lower Salt Creek into a shoreline pool at the mouth of the creek as the water level dropped. The use of the Salton Sea as a migration corridor between habitats was not documented during this short study. The marking technique was successful and showed promise for future mark and recapture studies of desert pupfish.     

Large‐ and small‐scale geographic structures affecting genetic patterns across populations of an Alpine butterfly

Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio‐temporal genetic patterns have focused on patterns across wide geographic areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here, we consider these issues in the Sooty Copper butterfly (Lycaena tityrus) from the European Alps, using genome‐wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the west may result from (a) admixture of different western refuges, (b) more recent demographic changes, or (c) introgression of lowland L. tityrus populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine L. tityrus should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP‐based approaches for understanding patterns of genetic diversity, gene flow, and selection in a region that is expected to be particularly vulnerable to climate change.