High-elevation Populations Research Articles

Genome-wide DNA methylation and their transgenerational pattern differ in Arabidopsis thaliana populations originated along the elevation of West Himalaya

Methylation at 5' cytosine of DNA molecule is an important epigenetic mark. It is known to play critical role in adaptation of organisms under different biotic and abiotic stressors via modulating gene expression and/or chromatin architecture. Plant populations evolved under variable climatic conditions may have evolved different epigenetic marks including DNA methylation. Here we, describe the genome-wide DNA methylation pattern under native field, F1 and F6 generation followed by their association with phenotypes, climate and global gene expression in the three Arabidopsis thaliana populations originated at different elevation ranges of Indian West Himalaya. We show that the global methyl cytosine (mC) content is more or less similar in the three populations but differ in their distribution across genome. There was an increase in differential methylation between the populations as elevation increased. The methylation divergence was the highest between the low and the high elevation populations. The high elevation populations were hypo-methylated than the low elevation population. The methylation in the genes was associated with population specific phenotypes and climate of the region. The genes which were differentially methylated as well as differentially expressed between the low and high elevation populations were mostly related to abiotic stresses. When grown under controlled condition, there was gain of differential methylation over native condition and the maximum percent changes was observed in CHH-sequence context. Further ~ 99.8% methylated cytosines were stably passed on from F1 to F6 generation. Overall, our data suggest that high elevation population is epigenetically more plastic under changing environmental condition.BackgroundArabidopsis thaliana is the model plant species and has been extensively studied to understand plants life processes. There are numerous reports on its origin, demography, evolution, epigenomes and adaptation etc. however, Indian populations of Arabidopsis thaliana evolved along wide elevation ranging from ~ 700 m amsl to ~ 3400 m amsl not explored yet. Here we, describe the genome-wide DNA methylation pattern under native field, F1 and F6 generation followed by their association with phenotypes, climate and global gene expression in the three Arabidopsis thaliana populations originated at different elevation ranges of Indian West Himalaya.Results In our study we found that total mCs percent was more or less similar in the three populations but differ in their distribution across genome. The proportion of CG-mCs was the highest, followed by CHH-mCs and CHG-mCs in all the three populations. Under native field condition the methylation divergence was more prominent between low and high elevation populations and the high elevation populations were hypo-methylated than the low elevation population. The methylation in the genes was linked to population-specific phenotypes and the regional climate. The genes that showed differential methylation and expression between low and high elevation populations were primarily associated with abiotic stress responses. When grown under controlled condition, there was gain of differential methylation compared to the native condition and the maximum percent changes was observed in CHH-sequence context. Further 99.8% methylated cytosines were stably passed on from F1 to F6 generation.Conclusions The populations of A. thaliana adapted at different climatic conditions were significantly differentially methylated both under native and controlled condition. However, the magnitude and extent of gain or loss of methylation were most significant between the low and the high elevation populations. Overall, our data suggest that high elevation population is epigenetically more plastic under changing environmental condition.

Early Life History Divergence Mediates Elevational Adaptation in a Perennial Alpine Plant

ABSTRACTSpatially divergent natural selection can drive adaptation to contrasting environments and thus the evolution of ecotypes. In perennial plants, selection shapes life history traits by acting on subsequent life stages, each contributing to fitness. While evidence of adaptation in perennial plants is common, the expression of life history traits is rarely characterized, limiting our understanding of their role in adaptive evolution. We conducted a multi‐year reciprocal transplant experiment with seedlings from low and high elevation populations of the alpine carnation Dianthus carthusianorum to test for adaptation linked to contrasting climates and inferred specific contributions of early life stages to fitness. We assessed genotype by environment interactions in single fitness components, applied matrix population models to achieve an integrated estimate of fitness through population growth rates, and performed trade‐off analyses to investigate the advantage of alternate life history traits across environments. We found evidence of genotype by environment interactions consistent with elevational adaptation at multiple stages of the early life cycle. Estimates of population growth rates corroborated a strong advantage of the local genotype. Early reproduction and survival are alternate major contributors to adaptation at low and high elevation, respectively, and are linked by trade‐offs that underlie the evolution of divergent life history traits across environments. While these traits have a strong genetic basis, foreign populations express co‐gradient plasticity, reflecting the adaptive strategy of the local populations. Our study reveals that selection associated to climate has driven the evolution of divergent life histories and the formation of elevational ecotypes. While the high energy environment and strong competition favor investment in early reproduction at low elevation, limiting resources favor a more conservative strategy relying on self‐maintenance at high elevation. The co‐gradient plasticity expressed by high‐elevation populations may facilitate their persistence under warming climatic conditions.

Behavioural Thermoregulation of Flowers via Petal Movement.

Widely documented in animals, behavioural thermoregulation mitigates negative impacts of climate change. Plants experience especially strong thermal variability but evidence for plant behavioural thermoregulation is limited. Along a montane elevation gradient, Argentina anserina flowers warm more in alpine populations than at lower elevation. We linked floral temperature with phenotypes to identify warming mechanisms and documented petal movement and pollinator visitation using time-lapse cameras. High elevation flowers were more cupped, focused light deeper within flowers and were more responsive to air temperature than low; cupping when cold and flattening when warm. At high elevation, a 20° increase in petal angle resulted in a 0.46°C increase in warming. Warming increased pollinator visitation, especially under cooler high elevation temperatures. A plasticity study revealed constitutive elevational differences in petal cupping and stronger temperature-induced floral plasticity in high elevation populations. Thus, plant populations have evolved different behavioural responses to temperature driving differences in thermoregulatory capacity.

The impact of elevation and prediction of climate change on an ultra high-elevation ectotherm.

Climate change may affect the survival and reproduction of ectotherms. The toad-headed lizard Phrynocephalus theobaldi, which holds the distinction of occupying the highest elevation among all reptile species on Earth, with an elevational range from 3600 to 5000 m, represents an ideal model for studying the adaptations to climatic changes across elevational gradients. Here, we used mechanistic and hybrid species distribution models (HSDM) together with characteristic measurements of thermal biology (CTmax, CTmin, and Tsel) to simulate and compare the distribution and activity periods of the lizard across elevations in response to climate change. NicheMapR simulations using only climate factors predicted that all populations will be negatively impacted by climate change (+3°C) by suffering a reduced distribution. However, the impact was clearly reduced in simulations that accounted for thermal physiological traits. Longer activity periods were predicted for all populations during climate change. The suitable distribution is predicted to change slightly, with an increase anticipated for both high and low elevation populations. However, the forecast indicates a more pronounced increase in suitable habitats for populations at higher elevations (>4200 m) compared to those at lower elevations (<4200 m). This study underscores the key influence of climate change on population establishment and stresses the importance of physiological traits in distribution simulation for future studies to understand the potential constraints in animal adaptation to extreme high environments.

Elevated [CO2] and temperature augment gas exchange and shift the fitness landscape in a montane forb.

Climate change is simultaneously increasing carbon dioxide concentrations ([CO2]) and temperature. These factors could interact to influence plant physiology and performance. Alternatively, increased [CO2] may offset costs associated with elevated temperatures. Furthermore, the interaction between elevated temperature and [CO2] may differentially affect populations from along an elevational gradient and disrupt local adaptation. We conducted a multifactorial growth chamber experiment to examine the interactive effects of temperature and [CO2] on fitness and ecophysiology of diverse accessions of Boechera stricta (Brassicaceae) sourced from a broad elevational gradient in Colorado. We tested whether increased [CO2] would enhance photosynthesis across accessions, andwhether warmer conditions would depress the fitness of high-elevation accessions owing to steep reductions in temperature with increasing elevation in this system. Elevational clines in [CO2] are not as evident, making it challenging to predict how locally adapted ecotypes will respond to elevated [CO2]. This experiment revealed that elevated [CO2] increased photosynthesis and intrinsic water use efficiency across all accessions. However, these instantaneous responses to treatments did not translate to changes in fitness. Instead, increased temperatures reduced the probability of reproduction for all accessions. Elevated [CO2] and increased temperatures interacted to shift the adaptive landscape, favoring lower elevation accessions for the probability of survival and fecundity. Our results suggest that elevated temperatures and [CO2] associated with climate change could have severe negative consequences, especially for high-elevation populations.

Variation in amphibian maturation rates influences population vulnerability to disease‐induced declines

AbstractUnderstanding factors that influence population‐level responses to emerging threats in declining species is crucial for informed conservation action. In amphibian species impacted by the chytrid fungus (Batrachochytrium dendrobatidis), a pathogen that has caused amphibian declines globally, a commonly reported pattern is that more severe population declines tend to occur at higher elevations. Previous research has suggested that this pattern could be driven by reduced environmental suitability for chytrid fungus at lower elevations. However, delayed amphibian maturation, which is common in cold, high elevation populations, could also increase vulnerability to population decline. Here, we tackle this key knowledge gap, focusing on the critically endangered corroboree frogs (Pseudophryne corroboree and P. pengilleyi), which have experienced a pattern of extirpation at higher elevations, with remnant populations persisting at lower elevations. First, we quantify the age structure of two extant low elevation P. pengilleyi populations and museum specimens (both species) collected before the emergence of chytrid fungus in Australia. Male age to maturation varied from 1 to 3 years, with the extant population with higher chytrid prevalence displaying severe age structure truncation. Second, we use population simulations to calculate elasticity values under a range of scenarios with varying ages to maturation and chytrid‐associated mortality. When the population growth rate was fixed at 1, adult survival became increasingly important as age to maturation increases, particularly under a scenario of high chytrid‐associated mortality. Our simulation results indicate that delayed maturation could be a previously underappreciated factor associated with an increased risk of amphibian population decline and that earlier maturation could contribute to population persistence. Our study highlights the importance of examining variation in life history traits to better understand population‐level responses to novel threats and guide the development of appropriate conservation actions.

Being an annual plant in a water-limited Mediterranean-alpine mountain; the case of rare-endemic and threatened Arenaria nevadensis

Mountain ecosystems are proving to be particularly vulnerable to the effects of global change, with Mediterranean high mountains standing out as among the most susceptible regions worldwide. The impact of climate change on biota operates across key levels: metabolism, phenology, evolution, and spatial distribution. Monitoring species within these ecosystems is crucial to establish early warning indicators for effective mitigation and adaptation strategies. Within this context, annual plants, like the critically endangered species Arenaria nevadensis endemic to Sierra Nevada, could offer advantages as indicators due to their rapid life cycles and dependence on water sources.This study aims to investigate the impact of climatic change on this specific annual, endemic, and threatened species while assessing its potential as an indicator for shifting snow patterns affecting alpine biota. Analyzing data collected between 2005 and 2021 from four populations of Arenaria nevadensis alongside hydro-meteorological data revealed notable variations in population parameters linked to climatic fluctuations. Factors such as precipitation and snowpack significantly influenced plant size, reproductive potential, and population size, with neighboring populations showing distinct responses to climatic variations.The observed unpredictability in population trends across consecutive years underscores the climatic stochasticity inherent in Mediterranean mountains, particularly Sierra Nevada. Forecasts of decreased precipitation and increased temperatures are expected to diminish snowpack depth and duration, posing a severe threat to this critically endangered species. Conservation efforts should prioritize managing higher elevation populations and exploring new suitable habitats for restoration or assisted migration.While Arenaria nevadensis demonstrates promise as a climate change indicator owing to its short life cycle, restricted distribution, and sensitivity to climatic shifts, comprehensive understanding of its germination ecology, seed bank role, and reproductive biology remains lacking. Addressing these knowledge gaps is crucial to enhance its effectiveness as an indicator species.

Elevation-driven modifications in tissue architecture and physiobiochemical traits of Panicum antidotale Retz. in the Pothohar Plateau, Pakistan

Mountainous ecosystems are experiencing rapid shifts in distribution patterns and community structure due to the impacts of climate change and vegetation dynamics. This study offers a comprehensive insight into the adaptive mechanisms of Panicum antidotale to varying elevations within the Pothohar Plateau, shedding light on its survival strategies in climate-affected regions. The findings reveal that populations at lower elevations exhibit maximum height, leaf area, shoot length, and fresh weight, whereas those at higher elevations display significant decrease in these parameters. Moreover, a significant decline in species density, frequency and cover is evident at high elevation. High-elevation populations demonstrate decreased photosynthetic traits, including chlorophyll, carotenoid, and Na and Ca content. Furthermore, there are notable variations in the antioxidant enzyme activity across elevation gradients. Populations at lower elevations exhibit higher activities of superoxide dismutase and peroxidase. Across the gradient, there were significant reductions in root and stem radius, sclerenchyma thickness, bulliform cell size, metaxylem vessels, and phloem area. Populations at moderate elevations displayed thicker lamina and epidermis, larger cortical cells, wider xylem vessels, and increased phloem area; however, these traits declined at higher elevations. High-elevation populations showed thicker lamina and epidermis, extensive sclerenchyma, greater cortical cell area, and higher stomatal density. Photosynthetic traits and enzymatic activity were major contributors at moderate elevations while stem and leaf traits were significantly changed at high elevations. Overall, this research contributes significantly to the broader knowledge of plant adaptation in mountainous ecosystems and stresses the importance of considering elevation as a critical factor in ecological studies.

Thermal limits along tropical elevational gradients: Poison frog tadpoles show plasticity but maintain divergence across elevation

Temperature is arguably one of the most critical environmental factors impacting organisms at molecular, organismal, and ecological levels. Temperature variation across elevation may cause divergent selection in physiological critical thermal limits (CTMAX and CTMIN). Generally, high elevation populations are predicted to withstand lower environmental temperatures than low elevation populations. Organisms can also exhibit phenotypic plasticity when temperature varies, although theory and empirical evidence suggest that tropical ectotherms have relatively limited ability to acclimate. To study the effect of temperature variation along elevational transects on thermal limits, we measured CTMAX and CTMIN of 934 tadpoles of a poison frog species, Epipedobates anthonyi, along two elevational gradients (200–1700 m asl) in southwestern Ecuador to investigate their thermal tolerance across elevation. We also tested if tadpoles could plastically shift their critical thermal limits in response to exposure to different temperatures representing the range of temperatures they experience in nature (20 °C, 24 °C, and 28 °C). Overall, we found that CTMAX did not change across elevation. In contrast, CTMIN was lower at higher elevations, suggesting that elevational variation in temperature influences this thermal trait. Moreover, all populations shifted their CTMAX and CTMIN according to treatment temperatures, demonstrating an acclimation response. Overall, trends in CTMIN among high, mid, and low elevation populations were maintained despite plastic responses to treatment temperature. These results demonstrate that, for tadpoles of E. anthonyi across tropical elevational gradients, temperature acts as a selective force for CTMIN, even when populations show acclimation abilities in both, CTMAX and CTMIN. Our findings advance our understanding on how environmental variation affects organisms’ evolutionary trajectories and their abilities to persist in a changing climate in a tropical biodiversity hotspot.

Causes and consequences of pre-hibernation body mass in golden-mantled ground squirrels (Callospermophilus lateralis)

Abstract Mammals that cope with harsh environmental conditions by hibernating show seasonal variation in body mass, as fat reserves are accumulated during summer and depleted during winter. In hibernating species, pre-hibernation mass is often considered a key phenotypic trait that can influence future survival and reproductive success—yet we know little about how variation in environmental conditions and seasonality affect pre-hibernation mass. We used 30 years of demographic data from a high-elevation population of golden-mantled ground squirrels (Callospermophilus lateralis) to identify life history and environmental variables that influenced pre-hibernation mass in females. Additionally, we determined if pre-hibernation mass influenced overwinter survival or subsequent reproduction. Growth curves revealed female-biased size dimorphism in body mass; adult mass was not attained until age 2 years, so we considered 3 age classes of females: juveniles, yearlings, and adults (≥2 years). We found that earlier snow melt during spring is associated with higher subsequent pre-hibernation body mass for yearlings and adults, and that juveniles emerging earlier from their natal burrows had higher pre-hibernation masses than later-emerging juveniles. Estimates of food quantity or quality did not affect pre-hibernation mass for any age class, nor was there an effect of reproductive status. Juvenile females with greater pre-hibernation mass were more likely to survive overwinter and reproduce as yearlings, but we found no such effect for yearlings or adult females. We did not find an effect of snow depth or winter duration on either survival or reproduction. Our results indicate that time appears to be the key variable for golden-mantled ground squirrels to acquire sufficient body mass to survive and reproduce, but the effects vary by age class.

Gamete sex and elevation affect genetically based variation for unreduced gamete production in a mixed-ploidy plant.

Unreduced gametes are the primary mechanism of neopolyploid formation. Their production in diploid populations is arguably maladaptive, but the magnitude and patterns of genetically based variation maintained in natural populations are poorly understood. We examined variation in male and female unreduced gamete production among plants from different elevations in fireweed, Chamerion angustifolium, grown in a common environment. Using seeds from three high-elevation and three low-elevation diploid populations in one study, and a single diploid population in another, we estimated realized rates of unreduced male (sperm) and female (egg) gamete production by reciprocally pollinating diploid and tetraploid plants and estimating the incidence of tetraploid seeds using flow cytometry. Unreduced gamete frequencies per plant were similar in the two studies (0.12% vs. 0.08%). High-elevation populations had a greater percentage of fruit with seeds from unreduced gametes, but a lower percentage of seeds per fruit than low-elevation populations. Female unreduced gamete frequencies differed among elevations, but male frequencies did not, and the gamete sexes were not correlated at the plant level. We conclude that genetically based variation for unreduced gametes is maintained within and among natural populations, despite their fitness disadvantages, suggesting that local selection may be ineffective at purging them under some conditions.

Divergent gametic thermal performance and floral warming across an elevation gradient.

Thermal environments vary widely across species ranges, establishing the potential for local adaptation of thermal performance optima and tolerance. In the absence of local adaptation, selection should favor mechanisms to meet thermal optima. Floral temperature is a major determinant of reproductive success in angiosperms, yet whether gametic thermal performance shows signatures of local adaptation across temperature gradients, and how variation in gametic thermal performance influences floral evolution, is unknown. We characterized flowering season temperatures for the forb, Argentina anserina, at extremes of a 1000 m elevation gradient and generated thermal performance curves for pollen and ovule performance in populations at each extreme. Thermal optima fell between mean and maximum intrafloral temperatures. However, cooler high-elevation populations had ~4 °C greater pollen thermal optima than warmer low-elevation populations, while tolerance breadths did not differ. We then tested whether plants at elevational extremes differentially warmed the floral microenvironment. High-elevation flowers warmed significantly more than low, bringing intrafloral temperatures nearer the pollen optima. A manipulative experiment demonstrated that stronger warming in high elevation was conferred by floral tissues. Elevational divergence in floral warming may be driven, in part, by selection on flowers to meet different thermal demands of the gametophytes.

Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes

Unraveling molecular mechanisms of adaptation to complex environments is crucial to understanding tolerance of abiotic pressures and responses to climatic change. Epigenetic variation is increasingly recognized as a mechanism that can facilitate rapid responses to changing environmental cues. To investigate variation in genetic and epigenetic diversity at spatial and thermal extremes, we use whole genome and methylome sequencing to generate a high-resolution map of DNA methylation in the bumble bee Bombus vosnesenskii. We sample two populations representing spatial and environmental range extremes (a warm southern low-elevation site and a cold northern high-elevation site) previously shown to exhibit differences in thermal tolerance and determine positions in the genome that are consistently and variably methylated across samples. Bisulfite sequencing reveals methylation characteristics similar to other arthropods, with low global CpG methylation but high methylation concentrated in gene bodies and in genome regions with low nucleotide diversity. Differentially methylated sites (n = 2066) were largely hypomethylated in the northern high-elevation population but not related to local sequence differentiation. The concentration of methylated and differentially methylated sites in exons and putative promoter regions suggests a possible role in gene regulation, and this high-resolution analysis of intraspecific epigenetic variation in wild Bombus suggests that the function of methylation in niche adaptation would be worth further investigation.

The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees.

A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.

Counter-gradient variation and the expensive tissue hypothesis explain parallel brain size reductions at high elevation in cricetid and murid rodents

To better understand functional morphological adaptations to high elevation (> 3000 m above sea level) life in both North American and African mountain-associated rodents, we used microCT scanning to acquire 3D images and a 3D morphometric approach to calculate endocranial volumes and skull lengths. This was done on 113 crania of low-elevation and high-elevation populations in species of North American cricetid mice (two Peromyscus species, n = 53), and African murid rodents of two tribes, Otomyini (five species, n = 49) and Praomyini (four species, n = 11). We tested two distinct hypotheses for how endocranial volume might vary in high-elevation populations: the expensive tissue hypothesis, which predicts that brain and endocranial volumes will be reduced to lessen the costs of growing and maintaining a large brain; and the brain-swelling hypothesis, which predicts that endocranial volumes will be increased either as a direct phenotypic effect or as an adaptation to accommodate brain swelling and thus minimize pathological symptoms of altitude sickness. After correcting for general allometric variation in cranial size, we found that in both North American Peromyscus mice and African laminate-toothed (Otomys) rats, highland rodents had smaller endocranial volumes than lower-elevation rodents, consistent with the expensive tissue hypothesis. In the former group, Peromyscus mice, crania were obtained not just from wild-caught mice from high and low elevations but also from those bred in common-garden laboratory conditions from parents caught from either high or low elevations. Our results in these mice showed that brain size responses to elevation might have a strong genetic basis, which counters an opposite but weaker environmental effect on brain volume. These results potentially suggest that selection may act to reduce brain volume across small mammals at high elevations but further experiments are needed to assess the generality of this conclusion and the nature of underlying mechanisms.

Drivers of strong isolation and small effective population size at a leading range edge of a widespread plant

Climate change has influenced species distributions worldwide with upward elevational shifts observed in many systems. Leading range edge populations, like those at upper elevation limits, are crucial for climate change responses but can exhibit low genetic diversity due to founder effects, isolation, or limited outbreeding. These factors can hamper local adaptation at range limits. Using the widespread herb, Argentina anserina, we measured ecological attributes (population density on the landscape, area of population occupancy, and plant and flower density) spanning a 1000 m elevation gradient, with high elevation populations at the range limit. We measured vegetative clonal potential in the greenhouse for populations spanning the gradient. We combined these data with a ddRAD-seq dataset to test the hypotheses that high elevation populations would exhibit ecological and genomic signatures of leading range edge populations. We found that population density on the landscape declined towards the high elevation limit, as is expected towards range edges. However, plant density was elevated within edge populations. In the greenhouse, high elevation plants exhibited stronger clonal potential than low elevation plants, likely explaining increased plant density in the field. Phylogeographic analysis supported more recent colonization of high elevation populations which were also more genetically isolated, had more extreme heterozygote excess and had smaller effective population size than low. Results support that colonization of high elevations was likely accompanied by increased asexuality, contributing to a decline in effective population size. Despite high plant density in leading edge populations, their small effective size, isolation and clonality could constrain adaptive potential.

Larval Life History of Coastal Tailed Frogs (Ascaphus truei) Across an Elevational Gradient in Northern California: Implications for a Changing Climate

Coastal Tailed Frogs (Ascaphus truei) range across the Pacific Northwest from northern California, USA, into British Columbia, Canada, and from sea level to >2,131 m. Previous work has shown a variable larval period but has not clearly separated elevational from latitudinal effects. Therefore, we examined size at beginning of metamorphosis, larval period, individual growth rates, and timing of metamorphosis of A. truei populations along an elevational gradient from 152 to 2,131 m across a small latitudinal range (29 km) to reduce potential latitudinal effects, all within the Klamath Mountains of northern California. We sampled larvae at 15 study sites, of which we used 6 sites as intensive capture–mark–recapture (CMR) locations, and the other 9 for supplemental data on larval period and size at metamorphosis. In CMR sites, we individually marked tadpoles to determine within-season growth rates. We found that the A. truei larval period in these populations ranges from 2 yr in low and middle elevations to ‡3 yr in high-elevation populations. We also found decreased size at beginning of metamorphosis and increased growth rates of tadpoles with increasing elevation. Our high-elevation populations had the longest larval period documented in California. The associations of growth and timing of metamorphosis to elevation in A. truei populations suggest that responses to changing climate may differ across elevations.

Gene abundance linked to climate zone: Parallel evolution of gene content along elevation gradients in lichenized fungi.

Intraspecific genomic variability affects a species' adaptive potential toward climatic conditions. Variation in gene content across populations and environments may point at genomic adaptations to specific environments. The lichen symbiosis, a stable association of fungal and photobiont partners, offers an excellent system to study environmentally driven gene content variation. Many of these species have remarkable environmental tolerances, and often form populations across different climate zones. Here, we combine comparative and population genomics to assess the presence and absence of genes in high and low elevation genomes of two lichenized fungi of the genus Umbilicaria. The two species have non-overlapping ranges, but occupy similar climatic niches in North America (U. phaea) and Europe (U. pustulata): high elevation populations are located in the cold temperate zone and low elevation populations in the Mediterranean zone. We assessed gene content variation along replicated elevation gradients in each of the two species, based on a total of 2050 individuals across 26 populations. Specifically, we assessed shared orthologs across species within the same climate zone, and tracked, which genes increase or decrease in abundance within populations along elevation. In total, we found 16 orthogroups with shared orthologous genes in genomes at low elevation and 13 at high elevation. Coverage analysis revealed one ortholog that is exclusive to genomes at low elevation. Conserved domain search revealed domains common to the protein kinase superfamily. We traced the discovered ortholog in populations along five replicated elevation gradients on both continents and found that the number of this protein kinase gene linearly declined in abundance with increasing elevation, and was absent in the highest populations. We consider the parallel loss of an ortholog in two species and in two geographic settings a rare find, and a step forward in understanding the genomic underpinnings of climatic tolerances in lichenized fungi. In addition, the tracking of gene content variation provides a widely applicable framework for retrieving biogeographical determinants of gene presence/absence patterns. Our work provides insights into gene content variation of lichenized fungi in relation to climatic gradients, suggesting a new research direction with implications for understanding evolutionary trajectories of complex symbioses in relation to climatic change.

Gene expression reveals immune response strategies of naïve Hawaiian honeycreepers experimentally infected with introduced avian malaria.

The unprecedented rise in the number of new and emerging infectious diseases in the last quarter century poses direct threats to human and wildlife health. The introduction to the Hawaiian archipelago of Plasmodium relictum and the mosquito vector that transmits the parasite has led to dramatic losses in endemic Hawaiian forest bird species. Understanding how mechanisms of disease immunity to avian malaria may evolve is critical as climate change facilitates increased disease transmission to high elevation habitats where malaria transmission has historically been low and the majority of the remaining extant Hawaiian forest bird species now reside. Here, we compare the transcriptomic profiles of highly susceptible Hawai'i 'amakihi (Chlorodrepanis virens) experimentally infected with P. relictum to those of uninfected control birds from a naïve high elevation population. We examined changes in gene expression profiles at different stages of infection to provide an in-depth characterization of the molecular pathways contributing to survival or mortality in these birds. We show that the timing and magnitude of the innate and adaptive immune response differed substantially between individuals that survived and those that succumbed to infection, and likely contributed to the observed variation in survival. These results lay the foundation for developing gene-based conservation strategies for Hawaiian honeycreepers by identifying candidate genes and cellular pathways involved in the pathogen response that correlate with a bird's ability to recover from malaria infection.

Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee.

Understanding historical range shifts and population size variation provides an important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (N e) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate N e variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee Bombus vancouverensis Cresson (Hymenoptera: Apidae: Bombus Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of N e through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in N e. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. N e fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater N e over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period, which matched the loss of range area near these sites; however, bottlenecks were not sufficient to erode diversity maintained during periods of large N e. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent postglacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in N e dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.