Molecular systematics of the western rattlesnake, Crotalus viridis (Viperidae), with comments on the utility of the D-loop in phylogenetic studies of snakes.

Crotalus viridis, the western rattlesnake, ranges throughout western North America and has been divided into at least eight subspecies. However, the validity of and relationships among these subspecies and the monophyly of C. viridis as a whole are questionable. We used mitochondrial DNA sequence data from the D-loop region and ND2 gene to examine the relationships among 26 populations of C. viridis and to test the monophyly of this species. These data were analyzed separately and combined using maximum-likelihood and maximum-parsimony. The C. viridis group was monophyletic in all combined analyses, consisting of two strongly divergent clades. We recommend that these clades be recognized as two distinct evolutionary species: C. viridis and C. oreganus. Crotalus viridis should be restricted to the subspecies viridis and nuntius and the remaining subspecies be assigned to the species C. oreganus. Our data do not allow strong evaluation of the validity of the subspecies. We found that the ND2 gene had greater sequence divergences among closely related individuals than the D-loop region, but this relationship reversed at higher levels of divergence. This pattern is apparently due to: (1) ND2 third positions evolving faster than the D-loop but becoming saturated at higher levels of divergence, and (2) the D-loop evolving faster than ND2 second (and possibly first) positions. Our results suggest that the ND2 gene is preferable for examining intraspecific relationships and the D-loop may better resolve relationships between species of snakes. The latter result is contrary to the common perception of the phylogenetic utility of the D-loop. Another unusual result is that the 145 bp spacer region, adjacent to the 5' end of the light strand of the D-loop, provides greater phylogenetic resolution than the 1030 bp D-loop.     

Body size variation among mainland populations of the western rattlesnake (Crotalus viridis)

In general, squamate reptiles follow the converse to Bergmann's rule, attaining smaller sizes in cooler environments, whereas other vertebrate groups follow Bergmann's rule, attaining larger sizes in cooler areas. Intensive studies of body size evolution for species of squamates are necessary to understand the processes responsible for this trend. Here I present data on body size variation among mainland populations of the western rattlesnake, Crotalus viridis. This species consists of two well-differentiated phylogenetic clades, therefore all analyses were performed for the C. viridis group as a whole and separately for each of the two clades within the C. viridis group. Although both phylogenetic and nonphylogenetic analyses were performed, the data did not show phylogenetic conservatism, and therefore the nonphylogenetic results are preferred. I found no significant relationships between mean adult female snout-vent length and any of the physical and climatic variables that were examined for the C. viridis group using simple linear regression analysis. Examined separately, I found that individuals of the western clade, C. oreganus, were smaller in cooler and more seasonal environments, whereas individuals of the eastern clade. C. viridis sensu stricto, were larger in cooler and more seasonal areas. Thus, the observed size trends were in opposite directions for the two clades. Multiple regression analysis revealed that seasonality was a stronger predictor of body size variation than was temperature for both clades. The differences in body size trends between these clades may be due to differences in mortality rates among populations.     

Lack of genetic differentiation between monarch butterflies with divergent migration destinations

Monarch butterflies are best known for their spectacular annual migration from eastern North America to Mexico. Monarchs also occur in the North American states west of the Rocky Mountains, from where they fly shorter distances to the California Coast. Whether eastern and western North American monarchs form one genetic population or are genetically differentiated remains hotly debated, and resolution of this debate is essential to understand monarch migration patterns and to protect this iconic insect species. We studied the genetic structure of North American migratory monarch populations, as well as nonmigratory populations in Hawaii and New Zealand. Our results show that eastern and western migratory monarchs form one admixed population and that monarchs from Hawaii and New Zealand have genetically diverged from North American butterflies. These findings suggest that eastern and western monarch butterflies maintain their divergent migrations despite genetic mixing. The finding that eastern and western monarchs form one genetic population also suggests that the conservation of overwintering sites in Mexico is crucial for the protection of monarchs in both eastern and western North America.     

Phylogeography of the red-tailed chipmunk (Tamias ruficaudus), a northern Rocky Mountain endemic

The northern Rocky Mountains have experienced a complex history of geological events and environmental fluctuation, including Pleistocene glaciation. To provide an initial assessment of the genetic impact of this history on the regional biota we estimated phylogenetic relationships within Tamias ruficaudus, a regional endemic, from cytochrome b sequence variation using parsimony, maximum likelihood, and nested clade analysis. Analyses of sequence variation in 187 individuals from 43 localities across the distribution of T. ruficaudus indicate a history of vicariance events and range fluctuation consistent with successive periods of extensive Pleistocene glaciation in the northern Rocky Mountains. Intraspecific divergence levels (c. 4.7% uncorrected) and phylogenetic structure are consistent with a genealogical vicariance initiated prior to the Late Pleistocene, whereas nested clade analyses indicate more recent population history structured by both fragmentation and range expansion. A comparison of sequence variation with bacular morphology indicates that the two genetically and morphologically differentiated entities exhibit a zone of differential character introgression. Sequence data support a multiple refugia hypothesis and provide a phylogeographical case study for the ongoing synthesis of regional biogeography for northern Rocky Mountain endemics.     

Population structure and migration pattern of a conifer pathogen, Grosmannia clavigera, as influenced by its symbiont, the mountain pine beetle

We investigated the population structure of Grosmannia clavigera (Gc), a fungal symbiont of the mountain pine beetle (MPB) that plays a crucial role in the establishment and reproductive success of this pathogen. This insect-fungal complex has destroyed over 16 million ha of lodgepole pine forests in Canada, the largest MPB epidemic in recorded history. During this current epidemic, MPB has expanded its range beyond historically recorded boundaries, both northward and eastward, and has now reached the jack pine of Alberta, potentially threatening the Canadian boreal forest. To better understand the dynamics between the beetle and its fungal symbiont, we sampled 19 populations in western North America and genotyped individuals from these populations with eight microsatellite markers. The fungus displayed high haplotype diversity, with over 250 unique haplotypes observed in 335 single spore isolates. Linkage equilibria in 13 of the 19 populations suggested that the fungus reproduces sexually. Bayesian clustering and distance analyses identified four genetic clusters that corresponded to four major geographical regions, which suggested that the epidemic arose from multiple geographical sources. A genetic cluster north of the Rocky Mountains, where the MPB has recently become established, experienced a population bottleneck, probably as a result of the recent range expansion. The two genetic clusters located north and west of the Rocky Mountains contained many fungal isolates admixed from all populations, possibly due to the massive movement of MPB during the epidemic. The general agreement in north-south differentiation of MPB and G. clavigera populations points to the fungal pathogen's dependence on the movement of its insect vector. In addition, the patterns of diversity and the individual assignment tests of the fungal associate suggest that migration across the Rocky Mountains occurred via a northeastern corridor, in accordance with meteorological patterns and observation of MPB movement data. Our results highlight the potential of this pathogen for both expansion and sexual reproduction, and also identify some possible barriers to gene flow. Understanding the ecological and evolutionary dynamics of this fungus-beetle association is important for the modelling and prediction of MPB epidemics.     

Regional differences in content of small basic peptide toxins in the venoms of Crotalus adamanteus and Crotalus horridus.

1. Reverse-phase HPLC and organic solvents were used to isolate small basic peptide (SBP) toxins from the venoms of Crotalus adamanteus, C. durissus terrificus, C. horridus, C. scutulatus scutulatus, C. viridis concolor, C. viridis helleri and C. viridis viridis. 2. Acid-DEP analyses indicated a high degree of toxin purity which was obtained with a single HPLC run. 3. The combined results of HPLC, immunodiffusion and electrophoresis analyses of venoms from different geographical regions indicate that the SBP toxin content in the venoms of Crotalus adamanteus, Crotalus horridus, Crotalus scutulatus and Crotalus viridis viridis may vary regionally.     

Combining phylogenetic and ecological niche modeling approaches to determine distribution and historical biogeography of Black Hills mountain snails (Oreohelicidae)

We aim to show how a combination of molecular systematics and ecological niche modelling approaches can be used to test historical biogeographical hypotheses for species of conservation concern. We focus on the land snail genus Oreohelix (Oreohelicidae), a group found throughout the Rocky Mountains. In addition to its larger distribution, a group of Oreohelix is also found in the Black Hills of Wyoming and South Dakota, an isolated, easternmost extension of the Rocky Mountains. We determine the number, distribution, and relationships of Black Hills Oreohelicids, which are a current conservation concern due to their fragmented distribution. We compared Black Hills groups to those in the main part of the Rockies to test historical biogeographical patterns that explain current diversity. We collected mtDNA data (COI and 12S sequences) from multiple populations of Oreohelix throughout the Black Hills and in adjacent populations in the Rocky Mountains to construct phylogenetic hypotheses. To determine whether favourable environmental conditions currently exist between the Black Hills and the north-eastern Rocky Mountains, we used DesktopGARP to generate an ecological niche model for distinct lineages discovered in the molecular phylogenetic analysis. Results show that all Black Hills populations are likely Oreohelix cooperi and that little genetic differentiation exists within this clade. In addition, Black Hills groups are genetically similar or identical to populations found in the Judith Mountains and Bighorn Mountains (north-eastern Rockies). Ecological niche models show that suitable environmental conditions may exist between eastern Rockies and Black Hills O. cooperi samples. Taken together, the phylogenetic and niche model data, along with the low vagility of the snails, support passive long-distance dispersal as a likely explanation for current arrangement of biodiversity.     

Snake venom dipeptidyl peptidase IV: taxonomic distribution and quantitative variation

The present study examined the taxonomic distribution of dipeptidyl peptidase IV (DPP IV) activity in venoms of 59 ophidian taxa, representing seven subfamilies of the Families Elapidae and Viperidae. DPP IV activity is extremely variable at all taxonomic levels. It ranged from essentially none in laticaudine, hydrophiine, and some bungarine and elapine venoms, to 10.72 μmol 4-methoxy-β-naphthylamine liberated per min per 200 μg venom, for Ophiophagus hannah. Intra- and interpopulational variation were examined among eight populations of prairie rattlesnakes (Crotalus viridis viridis), Great Basin rattlesnakes (Crotalus viridis lutosus) and southern Pacific rattlesnakes (Crotalus viridis helleri). Among these populations, the mean weighted range of variation was 4.9-fold, and even among litter mates of C. v. lutosus, DPP IV activity varied as much as 5.6-fold. The two most salient findings, the near ubiquity of DPP IV in snake venoms and its great quantitative variability, even among full siblings, are paradoxical. The widespread distribution of the enzyme suggests an important role in envenomation, while the variable activity levels suggest that DPP IV and by extension, other individual enzymatic constituents, may not be under much individual selective pressure.     

Molecular evolution of PIII-SVMP and RGD disintegrin genes from the genus Crotalus

Several types of disintegrins have been isolated from Crotalus spp rattlesnakes, including RGD disintegrins, and PIII-SVMPs. We isolated six cDNAs from snake venom glands using RT-PCR. Three RGD disintegrins (atroxatin, mojastin, and viridistatin) and three PIII-SVMPs (catroriarin, scutiarin, and viristiarin) cDNAs were isolated from the rattlesnakes Crotalus atrox, Crotalus scutulatus scutulatus, and Crotalus viridis viridis, respectively. Atroxatin and Viridistatin shared 90% amino acid identity to each other, and 87% identity to Mojastin. Scutiarin and Viristiarin were identical. All PIII-SVMPs isolated in this study shared the highest amino acid identity with Catrocollastatin. cDNA and protein sequences for RGD disintegrins, one MVD disintegrin, and PIII-SVMPs of the genus Crotalus (present in the NCBI database), were used in phylogenetic analysis. Neighbor-joining analysis of PIII-SVMP and RGD/MVD disintegrin-coding DNA sequences showed that these groups of genes separate into separate clades. A Phi(ST) pairwise comparison and Analysis of Molecular Variance (AMOVA) between PIII-SVMPs and RGD/MVD disintegrins showed significant genetic differences. Mutations observed in ten of the cDNAs analyzed did not affect Cys-coding sequences. Our K(A)/K(S) data suggest that rapid evolution occurred between the genes coding for PIII-SVMPs resulting, in the production of RGD disintegrin-coding genes. However, once these genes diverged, mutations in the PIII-SVMP-coding genes were accumulated less frequently.     

Molecular evidence for Pleistocene glacial cycles driving diversification of a North American desert spider, Agelenopsis aperta

The influence of historical climatic vs. geological changes on species diversification patterns was investigated in a widely distributed North American desert spider, Agelenopsis aperta (Araneae: Agelenidae), with particular reference to Pleistocene glacial cycles and earlier patterns of mountain building. Levels of sequence divergence obtained from the mitochondrial gene, cytochrome oxidase I, dated to the Pleistocene, eliminating Rocky Mountain orogeny as a cause of diversification, as orogeny ended 4 million years ago. The results of phylogenetic and network analyses showed the presence of three geographically defined clades, which were consistent with the presence of at least three glacial refugia: (i) east of the Rocky Mountains; (ii) between the Rocky Mountains and Sierra Nevadas; and (iii) west of the Sierra Nevadas. In addition, populations within the Rocky Mountains exhibited significantly lower genetic diversity than populations east of the Rocky Mountains and the haplotypes found within the Rockies were a subset of eastern haplotypes. These patterns suggest that a post-Pleistocene range expansion occurred out of an eastern glacial refugium into the Rocky Mountains. Examination of phylogeographical studies of other North American desert taxa indicated that mountain building explained diversification patterns more effectively for some taxa but Pleistocene climate change was more important for others, including A. aperta.     

A new small myotoxin from the venom of the prairie rattlesnake (Crotalus viridis viridis)

Fast atom bombardment (FAB) mass spectrometry was used to identify a new small myotoxin from the venom of the prairie rattlesnake (Crotalus viridis viridis). FAB mass spectrometry and Edman degradation were used to characterize its structure. This toxin is similar to myotoxin I from C. v. concolor, except that it possesses an additional. C-terminal asparaginyl-alanine. At 45 residues it is the longest known myotoxin a homolog. A myotoxin of 43 residues, identical to myotoxin I from C. v. concolor, was also found. To date no other species has been shown to produce more than one length of myotoxin. The present paper documents 42-, 43-, and 45-residue myotoxins from the venom of a single animal.     

A biosystematic analysis of the Caltha leptosepala (Ranunculaceae) complex in the Rocky Mountains I. Chromatography and cytotaxonomy

Part one of a biosystematic study of theCaltha leptosepala complex in the Rocky Mountains involves a brief history of the taxonomic problem in addition to analyses of phenolic chromatography and cytotaxonomy. Data obtained from the natural populations sampled support the premise that only one species,Caltha leptosepala, can be taxonomically justified for the Rocky Mountains.     

Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North American desert biogeography

The western diamondback rattlesnake (Crotalus atrox) is a prominent member of North American desert and semi-arid ecosystems, and its importance extends from its impact on the region's ecology and imagery, to its medical relevance as a large deadly venomous snake. We used mtDNA sequences to identify population genetic structure and historical demographic patterns across the range of this species, and relate these to broader patterns of historical biogeography of desert and semi-arid regions of the southwestern USA and adjacent Mexico. We inferred a Late Pliocene divergence between peninsular and continental lineages of Crotalus, followed by an Early Mid Pleistocene divergence across the continental divide within C. atrox. Within desert regions (Sonoran and Chihuahuan Deserts, Southern Plains, and Tamaulipan Plain) we observed population structure indicating isolation of populations in multiple Pleistocene refugia on either side of the continental divide, which we attempt to identify. Evidence of post-glacial population growth and range expansion was inferred, particularly in populations east of the continental divide. We observed clear evidence of (probably recent) gene flow across the continental divide and secondary contact of haplotype lineages. This recent gene flow appears to be particularly strong in the West-to-East direction. Our results also suggest that Crotalus tortugensis (Tortuga Island rattlesnake) and a population of 'C. atrox' inhabiting Santa Cruz Island (in the Gulf of California) previously suggested to be an unnamed species, are in fact deeply phylogenetically nested within continental lineages of C. atrox. Accordingly, we suggest C. tortugensis and 'C. atrox' from Santa Cruz Island be placed in the synonymy of C. atrox.     

Regional patterns of genetic diversity in Pinus flexilis (Pinaceae) reveal complex species history

Pinus flexilis (limber pine) is patchily distributed within its large geographic range; it is mainly restricted to high elevations in the Rocky Mountains and the Basin and Range region of western North America. We examined patterns of allozyme diversity in 30 populations from throughout the species' range. Overall genetic diversity (H(e) = 0.186) was high compared with that of most other pine species but was similar to that of other pines widespread in western North America. The proportion of genetic diversity occurring among populations (G(ST) = 0.101) was also high relative to that for other pines. Observed heterozygosity was less than expected in 28 of the 30 populations. When populations were grouped by region, there were notable differences. Those in the Basin and Range region had more genetic diversity within populations, a higher proportion of genetic diversity among populations, and higher levels of inbreeding within populations than populations from either the Northern or Utah Rocky Mountain regions. Patterns of genetic diversity in P. flexilis have likely resulted from a complex distribution of Pleistocene populations and subsequent gene flow via pollen and seed dispersal.     

Latitudinal clines in the timing and temperature-sensitivity of photoperiodic reproductive diapause in Drosophila montana

Reproductive diapause is a primary mechanism used by arthropods to synchronize their life cycle with seasonal changes in temperate regions. Our study species, Drosophila montana, represents the northern insect species where flies enter reproductive diapause under short day conditions and where the precise timing of diapause is crucial for both survival and offspring production. We have studied clinal variation in the critical day length for female diapause induction (CDL) and their overall susceptibility to enter diapause (diapause incidence), as well as the temperature sensitivity of these traits. The study was performed using multiple strains from four latitudinal clines of the species – short clines in Finland and Alaska and long clines in the Rocky Mountains and the western coast of North America – and from one population in Kamchatka, Russia. CDL showed strong latitudinal clines on both continents, decreasing by one hour per five degrees decline in latitude, on average. CDL also decreased in all populations along with an increase in fly rearing temperature postponing the diapause to later calendar time, the effects of temperature being stronger in southern than in northern population. Female diapause incidence was close to 100% under short day/low temperature conditions in all populations, but decreased below 50% even under short days in 19°C in the southern North American western coast populations and in 22°C in most populations. Comparing a diversity of climatic data for the studied populations showed that while CDL is under a tight photoperiodic regulation linked with latitude, its length depends also on climatic factors determining the growing season length. Overall, the study deepens our understanding of how spatial and environmental parameters affect the seasonal timing of an important biological event, reproductive diapause and helps to estimate the evolutionary potential of insect populations to survive in changing climatic conditions.     

IMPLICATIONS OF MORPHOLOGICAL AND ANATOMICAL VARIATION IN ABIES BALSAMEA AND A. LASIOCARPA (PINACEAE) FROM WESTERN CANADA

Abies balsamea and A. lasiocarpa are closely related North American balsam firs that are generally thought to hybridize and intergrade where their ranges overlap in west-central Alberta. To test this hypothesis, a series of collections was made from ten populations along an east-west transect between western Saskatchewan and central British Columbia. Each tree was scored for various vegetative and cone characters. The resulting data were analyzed by Principal Components Analysis and Canonical Variates Analysis. Analyses based on vegetative data produced somewhat different results from analyses based on cone data, indicating that vegetative and sexual features of the trees respond to different selection pressures at the ecologically diverse sample sites. The combined results of analyses of vegetative and sexual data indicate that the ten populations do not represent elements of two morphologically distinct taxa. Instead, the results apparently reflect population differentation within a single, regionally variable complex in response to local selection pressures following east-west gene flow. It is recommended that the separate species designations, A. balsamea and A. lasiocarpa, be retained since: 1) present day elements of the complex are evidently derived from separate refugia isolated by the Rocky Mountains during past glacial periods, and 2) gradual morphological differences exist between populations on each side of the Rocky Mountain crest.     

Molecular genetic evidence for the post-Pleistocene divergence of populations of the arctic-alpine ground beetle Amara alpina (Paykull) (Coleoptera: Carabidae)

Aim This study examines the hypothesis that the biogeographic history of a species is reflected in the distribution of molecular genetic diversity and the phylogenies of extant populations. Location Populations of arctic-alpine ground beetle Amara alpina were analysed from Beringia (Alaska and northernmost British Columbia), the Hudson Bay region, the northern Appalachian Mountains, and the central Rocky Mountains of North America. Methods Mitochondrial restriction site variation of specimens from twenty-two populations were assayed by using radioactively labelled mtDNA to probe Southern membranes containing restriction enzyme digested total DNA. Restriction sites were mapped and genetic distances were calculated by pairwise comparison of presence and absence of restriction sites. Genetic distances were used in a molecular analysis of variance and to construct a minimal spanning tree. Parsimony methods were used to investigate the phylogenetic relationships between the haplotypes. These results were compared to an existing model for postglacial dispersal based on fossil and modern occurrences of arctic-alpine beetles. Results Among the twenty-two populations, fifteen haplotypes were detected. Genetic variation within each of the four regions corresponded to that expected from the palaeontologically based model. Beringian populations were the most genetically diverse. In contrast, no restriction site variation was observed in populations from the Hudson Bay region. Intermediate amounts of variation were observed in alpine populations of the Rocky and Appalachian Mountains. Maximum parsimony and cluster analysis provide evidence that at least two ancestral haplotypes existed in the Southern refugium from which the Rocky and the Appalachian Mountains populations were founded. Main conclusions The genetic results are generally consistent with the palaeontologically based model. The diversity of Beringian populations is consistent with this region having been continuously inhabited by Amara alpina throughout the Pleistocene. The Hudson Bay region was not deglaciated until about 6000 years, and its populations have no restriction site variation. The molecular genetic data support the interpretation that the Hudson Bay region was colonized from Beringia based on the occurrence of the same haplotype in both regions.     

Characterization of microsatellite loci isolated in midget faded rattlesnake (Crotalus viridis concolor)

Primers for five polymorphic microsatellite loci were developed for the midget faded rattlesnake (Crotalus viridis concolor), a rare subspecies of western rattlesnake (Crotalus viridus) found only in parts of Wyoming, Colorado, and Utah. Five polymorphic microsatellites were isolated, four of which had relatively high levels of diversity (eight to nine alleles). We found only two departures from Hardy–Weinberg equilibrium and they occurred in different loci, so null alleles are likely not a problem. Moreover, we found that no two loci were linked. These loci will be applicable for population genetic analysis and perhaps analysis of paternity and mating systems.     

Finding fishers: determining fisher occupancy in the Northern Rocky Mountains

Monitoring rare and elusive carnivores is inherently challenging because they often occur at low densities and require more resources to effectively assess status and trend. The fisher (Pekania pennanti) is an elusive mesocarnivore endemic to North America; in its western populations it is classified as a species of greatest conservation need. During winter of 2018–2019, we deployed remotely triggered cameras in randomly selected, spatially balanced 7.5-km × 7.5-km grid cells across a broad study area in western Montana, Idaho, and eastern Washington, USA. As part of this large-scale, multi-state monitoring effort, we conducted an occupancy assessment of the Northern Rocky Mountain fisher population at a range-wide scale. We used non-spatial occupancy models to determine the current extent of fisher occurrence in the Northern Rocky Mountains and to provide baseline occupancy estimates across a broad study area and a refined sampling frame for future monitoring. We used a spatial occupancy model to determine patterns in fisher occurrence across their Northern Rocky Mountain range while explicitly correcting for spatially induced overdispersion. Additionally, we assessed factors that influenced fisher occurrence through covariate occupancy modeling that considered predicted fisher habitat, site-level environmental characteristics, and the influence of available harvest records (incidental and regulated). We detected fishers in 32 out of 318 (10%) of our surveyed cells, and estimated that overall, 160 (14%; 95% CI = 115–218) of 1,143 grid cells were occupied by fishers. Fisher occupancy was positively associated with our stratum that contained cells with a greater proportion of predicted fisher habitat and with proximity to nearest 2000–2015 harvest location. Fisher occupancy was weakly and positively associated with increased canopy cover. Our spatial model identified 2 areas with higher predicted occupancy: a large area across the Idaho Nez Perce-Clearwater National Forest, and a smaller area in the Cabinet Mountain Range crossing the northern border of Idaho and Montana. We used spatial occupancy results from our original sampling frame to create a biologically derived refined sampling frame for future monitoring. Within the bounds of our refined sampling frame, we estimated that 155 (22%; 95% CI = 110–209) of 700 grid cells were occupied by fishers. By incorporating our increasing understanding of fisher habitat with contemporary analytical techniques, we defined current range-wide occupancy of the Northern Rocky Mountain fisher population, identified core areas of fisher occurrence for future conservation efforts, and used our model results to create a refined sampling frame for future fisher monitoring in the Northern Rocky Mountains.     

Historic cycles of fragmentation and expansion in Parnassius smintheus (papilionidae) inferred using mitochondrial DNA

Climate oscillations of the Quaternary drove the repeated expansion and contraction of ecosystems. Alpine organisms were probably isolated in sky island refugia during warm interglacials, such as now, and expanded their range by migrating down-slope during glacial periods. We used population genetic and phylogenetic approaches to infer how paleoclimatic events influenced the distribution of genetic variation in the predominantly alpine butterfly Parnassius smintheus. We sequenced a 789 bp region of cytochrome oxidase I for 385 individuals from 20 locations throughout the Rocky Mountains, ranging from southern Colorado to northern Montana. Analyses revealed at lease two centers of diversity in the northern and southern Rocky Mountains and strong population structure. Nested clade analysis suggested that the species experienced repeated cycles of population expansion and fragmentation. The estimated ages of these events, assuming a molecular clock, corresponded with paleoclimatic data on habitat expansion and contraction over the past 400,000 years. We propose that alpine butterflies persisted in an archipelago of isolated sky islands during interglacials and that populations expanded and became more connected during cold glacial periods. An archipelago model implies that the effects of genetic drift and selection varied among populations, depending on their latitude, area, and local environment. Alpine organisms are sensitive indicators of climate change and their history can be used to predict how high-elevation ecosystems might respond to further climate warming.