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opencc-zeroJan 2020View details →

Geography, seasonality, and host-associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal

The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture and daylight. Muskoxen (Ovibos moschatus) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season (spring/summer/winter), year (2007-2016), and host genetic structure on population-level microbiome variation in muskoxen from the Canadian Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal microbial communities of 78 male muskoxen encompassing two population genetic clusters.<a name="_Hlk534564036"> These clusters are defined by Arctic Mainland and Island populations, including; 1) two mainland sampling locations of the Northwest Territories and Nunavut; and 2) four locations of Victoria Island. </a>Between these geographic populations, we found that differences in the microbiome reflected host-associated genetic cluster with evidence of migration. Within populations, seasonality influenced bacterial diversity with no significant differences between years of sampling. We found evidence of pathogenic bacteria, with significantly higher presence in mainland samples. Our findings demonstrate the effects of seasonality and the role of host population-level structure in driving fecal microbiome differences in a large Arctic mammal.

opencc-zeroDec 2020View details →

Transcriptomic regulation of seasonal coat color change in hares

Color molts from summer brown to winter white coats have evolved in several species to maintain camouflage year-round in environments with seasonal snow. Despite the eco-evolutionary relevance of this key phenological adaptation, its molecular regulation has only recently begun to be addressed. Here, we analyze skin transcription changes during the autumn molt of the mountain hare (Lepus timidus) and integrate the results with an established model of gene regulation across the spring molt of the closely related snowshoe hare (L. americanus). We quantified differences in gene expression among three stages of molt progression – "brown" (early molt), "intermediate" and "white" (late molt). We found 632 differentially expressed genes, with a major pulse of expression early in the molt, followed by a milder one in late molt. The functional makeup of differentially expressed genes anchored the sampled molt stages to the developmental timeline of the hair growth cycle, associating anagen to early molt and the transition to catagen to late molt. The progression of color change was characterized by differential expression of genes involved in pigmentation, circadian and behavioral regulation. We found significant overlap between differentially expressed genes across the seasonal molts of mountain and snowshoe hares, particularly at molt onset, suggesting conservatism of gene regulation across species and seasons. However, some discrepancies suggest seasonal differences in melanocyte differentiation and the integration of nutritional cues. Our established regulatory model of seasonal coat color molt provides an important mechanistic context to study the functional architecture and evolution of this crucial seasonal adaptation.

opencc-by-4.0Jan 2021View details →

Mitigating the impact of bad rainy seasons in poor agricultural regions to tackle deforestation

I provide the stata files that allow to reproduce the results presented in the paper  "Mitigating the impact of bad rainy seasons in poor agricultural regions to tackle deforestation" by Antoine Leblois. The replication folder contains two files: 1- *.dta file: database 2- *.do file: do-file containing the codes to replicate the results Stata 14 was used for this work.

opencc-zeroDec 2020View details →

Seasonal isotopic niche of a rodent: High between-individual variation but no changes in individual niche width during the rich-resource period

The dynamics of trophic niche width in animals at both population- and individual-level is potentially influenced by temporal variation of food resources, by between-individual differences in food-resource rank preferences, and also by competition. Using stable isotope of carbon and nitrogen (δ13C and δ15N) of fecal samples, we investigated the trophic niche dynamics and individual variation in food-resource use by the arboreal rat Rhipidomys macrurus, in the highly seasonal Brazilian savanna (Cerrado). We tested the hypothesis that dietary niche expansion during the rich-resource period (wet season) occurs via individual specialization and consequently lower individual niche overlap in contrast with niche retraction during the low-resource period (dry season) via increase in niche overlap and expansion of individual niches. The results indicated that R. macrurus is primarily frugivorous and presents a wider isotopic niche in the rich-resource period in comparison to the low-resource period. The increase in niche width was achieved by individual specialization (decrease in niche overlap), as expected. During the low-resource period, however, individual niche widths were not wider than during the rich-resource period. Additionally, individual body condition was lower in the wet season than in the dry season, suggesting higher competition in this period. We conclude that an increase in the population niche may involve only between-individual variation and not necessarily requiring changes in individual niche width. We propose that the combination of ecological opportunity (high resource diversity) in addition to a greater competition in the warm-wet season leads to expansion of the population trophic niche width via individual specialization.

opencc-zeroDec 2020View details →

Seasonal niche tracking of climate emerges at the population level in a migratory bird

Seasonal animal migration is a widespread phenomenon. At the species level, it has been shown that many migratory animal species track similar climatic conditions throughout the year. However, it remains unclear whether such niche tracking pattern is a direct consequence of individual behaviour or emerges at the population or species level through behavioural variability. Here, we estimated seasonal niche overlap and seasonal niche tracking at the individual and population level of Central European White Storks (Ciconia ciconia). We quantified niche tracking for both weather and climate conditions to control for the different spatio-temporal scales over which ecological processes may operate. Our results indicate that niche tracking is a bottom-up process. Individuals mainly track weather conditions while climatic niche tracking mainly emerges at the population level. This result may be partially explained by a high degree of intra- and inter-individual variation in niche overlap between seasons. Understanding how migratory individuals, populations and species respond to seasonal environments is key for anticipating the impacts of global environmental changes.

opencc-zeroJan 2021View details →

Synchronization of seasonal acclimatization and short-term heat hardening improves physiological resilience in a changing climate

Summary 1. Animal survival and species distribution in the face of global warming and increasing occurrences of heatwave largely depend on how heat tolerance shifts with plastic responses at different spatiotemporal scales, including long-term acclimation/acclimatization and short-term heat hardening. However, knowledge about the interaction of these plastic responses is still unclear. 2. To understand how plastic responses at different timescales work together to adjust heat tolerance of organisms, we examined the effect of heat hardening on the upper thermal limits of an intertidal mudflat bivalve, the razor clam Sinonovacula constricta, for different seasons by using heart rate as a proxy. 3. We observed a stronger heat hardening response of S. constricta in warm seasons, implying that heat hardening worked synchronously with seasonal acclimatization to increase resistance of the clams to high temperatures in warm seasons. In warm seasons, heat hardening increased heat tolerance by 2-4°C and showed a 24-h temporal dependence, suggesting an adaptation to the diel fluctuation of thermal regimes in summer. 4. Furthermore, thermal stress resembling seasonal maximum environmental temperature induced stronger heat hardening effects, indicating that heat hardening is an essential plastic response to extreme hot weather, complementing seasonal acclimatization. 5. Our results suggest that high temperature risk can be alleviated jointly by seasonal acclimatization and heat hardening, and emphasize the importance of considering physiological plasticity on both long-term and short-term temporal scales in evaluating and forecasting vulnerability of organisms to climate change.

opencc-zeroJul 2019View details →

Data from: Effects of dry-season irrigation on leaf physiology and biomass allocation in tropical lianas and trees

Lianas are more abundant in seasonal forests than in wetter forests and are thought to perform better than trees when light is abundant and water is limited. We tested the hypothesis that lianas perform better than trees during seasonal drought using a common garden experiment with 12 taxonomically diverse species (6 liana and 6 tree species) in 12 replicated plots. We irrigated six of the plots during the dry season for four years, while the remaining 6 control plots received only ambient rainfall. In year 5, we measured stem diameters for all individuals and harvested above- and belowground biomass for a subset of individuals to quantify absolute growth and biomass allocation to roots, stems, and leaves, as well as total root length and maximum rooting depth. We also measured photosynthesis, intrinsic water use efficiency (iWUE), pre-dawn and midday water potential, and a set of functional and hydraulic traits. During the peak of the dry season, lianas in control plots had 54% higher predawn leaf water potentials (ΨPD), and 45% higher photosynthetic rates than trees in control plots. By contrast, during the peak of the wet season, these physiological differences between lianas and trees become less pronounced and, in some cases, even disappeared. Trees had higher SLA than lianas; however, no other functional trait differed between growth forms. Trees responded to the irrigation treatment with 15% larger diameters and 119% greater biomass than trees in control plots. Liana growth, however, did not respond to irrigation; liana diameter and biomass were similar in control and irrigation plots, suggesting that lianas were far less limited by soil moisture than were trees. Contrary to previous hypotheses, lianas did not have deeper roots than trees; however, lianas had longer roots per stem diameter than did trees. Our results support the hypothesis that lianas perform better and experience less physiological stress than trees during seasonal drought, suggesting clear differences between growth forms in response to altered rainfall regimes. Ultimately, better dry-season performance may explain why liana abundance peaks in seasonal forests compared to trees, which peak in abundance in less seasonal, wetter forests.

opencc-zeroJun 2021View details →

Predictability of temporal variation in climate and the evolution of seasonal polyphenism in tropical butterflies

Phenotypic plasticity in heterogeneous environments can provide tight environment-phenotype matching. However, the pre-requisite is a reliable environmental cue(s) that enables organisms to use current environmental information to induce the development of a phenotype with high fitness in a forthcoming environment. Here we quantify predictability in the timing of precipitation and temperature change to examine how this is associated with seasonal polyphenism in tropical Mycalesina butterflies. Seasonal precipitation in the tropics typically results in distinct selective environments, the wet- and dry seasons, and changes in temperature can be a major environmental cue. We sampled communities of Mycalesina butterflies from two seasonal and one aseasonal location. Quantifying environmental predictability using wavelet analysis and Colwell's indices confirmed a strong periodicity of precipitation over a 12-month period at both seasonal locations compared to the aseasonal one. However, temperature seasonality and periodicity differed between the two seasonal locations. We further show that: (1) most females from both seasonal locations synchronise their reproduction with the seasons by breeding in the wet season but arresting reproduction in the dry season. In contrast, all species breed throughout the year in the aseasonal location, and (2) species from the seasonal locations, but not those from the aseasonal location, exhibited polyphenism in wing pattern traits (eyespot size). We conclude that seasonal precipitation and its predictability are primary factors shaping the evolution of polyphenism in Mycalesina butterflies, and populations or species secondarily evolve local adaptations for cue use that depend on the local variation in the environment.

Data from: Two-year bee, or not two-year bee? How voltinism is affected by temperature and season length in a high-elevation solitary bee

Organisms must often make developmental decisions without complete information about future conditions. This uncertainty—for example, about the duration of conditions favorable for growth—can favor bet-hedging strategies. Here, we investigated the causes of life-cycle variation in Osmia iridis, a bee exhibiting a possible bet-hedging strategy with co-occurring one- and two-year life cycles. One-year bees reach adulthood quickly but die if they fail to complete pupation before winter; two-year bees adopt a low-risk, low-reward strategy of postponing pupation until the second summer. We reared larval bees in incubators in various experimental conditions and found that warmer—but not longer—summers, and early birth dates, increased the frequency of one-year life cycles. Using in situ temperature measurements and developmental trajectories of laboratory- and field-reared bees, we estimated degree-days required to reach adulthood in a single year. Local long-term (1950–2015) climate records reveal that this heat requirement is met in only ~7% of summers, suggesting that the observed distribution of life cycles is adaptive. Warming summers will likely decrease average generation times in these populations. Nevertheless, survival of bees attempting one-year life cycles—particularly those developing from late-laid eggs—will be <100%; consequently, we expect the life-cycle polymorphism to persist.

Figure 5 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems

Figure 5. Occlusal view of the lower molars of the Sigmodontine rodents from Tyto furcata pellets from the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Brazil. (A) = Akodon azarae, UFSC-CF 43-2-2, right m1-m2. (B) = Akodon sp., UFSC-CF 32-4-2, right m1-m3; (C) = Bibimys sp., UFSC-CF 32-5-2, right m1-m3. (D) = Calomys sp., UFSC-CF 32-6-2, right m1-m3. (E) = Holochilus sp., UFSC-CF 43-4-2, left m1-m3. (F) = Lundomys molitor, UFSC-CF 32-9-1, left m1-m3. (G) = Nectomys squamipes, UFSC-CF 32-10-1, right m1-m3. (H) = Oligoryzomys sp., UFSC-CF 32-11-2, right m1-m3. (I) = Oxymycterus sp., UFSC-CF 32-12-2, right m1-m3. (J) = Sooretamys angouya, UFSC-CF 32-13-2, left m1-m2. (K) = Wilfredomys oenax, UFSC-CF 32-14-2, left m1-m3. Scale bars: H = 200 µm; A, B, C, D, G, I, J, K = 500 µm; E, F = 1 mm.

Figure 4 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems

Figure 4. Occlusal view of the upper molars of the Sigmodontine rodents from the Tyto furcata pellets from the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Brazil. (A) = Akodon azarae, UFSC-CF 43-2-1, left M1-M3. (B) = Akodon sp., UFSC-CF 32-4-1, left M1-M3. (C) = Bibimys sp., UFSC-CF 32-5-1, left M1-M3. (D) = Calomys sp., UFSC-CF 32-6-1, left M1-M3. (E) = Juliomys sp., UFSC-CF 32-7-1, left M1-M3. (F) = Holochilus sp., UFSC-CF 43-4-1, left M1-M3. (G) = Oligoryzomys sp., UFSC-CF 32-11-1, left M1-M3. (H) = Oxymycterus sp., UFSC-CF 32-12-1, left M1-M3. (I) = Sooretamys angouya, UFSC-CF 32-13-1, right M1-M3. (J) = Wilfredomys oenax, UFSC-CF 32-14-1, left M1-M3. Scale bars: C = 200 µm; A, B, D, E, F, G, H, I, J = 500 µm.

Figure 1 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems

Figure 1. Location of the sampling sites of the Tyto furcata pellets at the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Southern Brazil. BV1 = Boa Vista I; BV2 = Boa Vista II; BOQ = Boqueirão; CGA = Canta Galo; EV1 = Evaristo I; EV2 = Evaristo II; ANT = Picada das Antas; PF1 = Picada Feliz I; PF2 = Picada Feliz II; QV1 = Quevedos I; QV2 = Quevedos II; RES = Reserva. Map modified from MMA (1992).

Figure 3 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems

Figure 3. Chiroptera specimens from the Tyto furcata pellets from the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Brazil. (A) = ventral view of the skull of Sturnira lilium, UFSC-CF 40-5-1. (B) = labial view of the right dentary of Tadarida brasiliensis, UFSC-CF 42-11-1. Scale bars: 1 mm.

Figure 2 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems

Figure 2. Didelphimorphia specimens from the Tyto furcata pellets from the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Brazil. (A) = labial view of the left dentary of Cryptonanus guahybae, UFSC-CF 32-2-1. (B) = labial view of the right dentary of Gracilinanus microtarsus, UFSC-CF 42-10-1. Scale bars: 1 mm.

Figure 6 in Small mammal diversity in Semi-deciduous Seasonal Forest of the southernmost Brazilian Pampa: the importance of owl pellets for rapid inventories in human-changing ecosystems

Figure 6. Occlusal view of the upper and lower molars of the Muridae and Caviidae rodents fromTytofurcata pellets from the Municipality of São Lourenço do Sul, State of Rio Grande do Sul, Brazil.(A) = Mus musculus, UFSC-CF 32-15-1, left M1-M3. (B) = Rattus rattus, UFSC-CF 35-9-1, right M1-M3. (C) = Cavia aperea, UFSC-CF 43-8-1, left P4-M3. (D) = M. musculus, UFSC-CF 32-15-2, right m1-m3. (E) = R. rattus, UFSC-CF 35-9-2, right m1-m3. (F) = C. aperea, UFSC-CF 43-8-2, right p4-m3. Scale bars A, D = 200 µm; B, C, E, F = 1 mm.

opencc-zeroApr 2020View details →

Metabolic rate in common shrews is unaffected by seasonal temperature, leading to reduction of energetic costs through size reduction

Small endothermic mammals have high metabolisms, particularly at cold temperatures. In light of this, some species have evolved a seemingly illogical strategy: they reduce the size of the brain and several organs to become even smaller in winter. To test how this morphological strategy affects energy consumption across seasonally shifting ambient temperatures, we measured oxygen consumption and behaviour in the three seasonal phenotypes of the common shrew (Sorex araneus), which differ in size by about 20%. Body mass was the main driver of oxygen consumption, not the reduction of metabolically expensive brain mass. Against our expectations, we found no change in relative oxygen consumption with low ambient temperature. Thus, smaller body size in winter resulted in significant absolute energy savings. This could only partly be explained by a change in activity budgets. Our findings highlight that these shrews manage to avoid one of the most fundamental and intuitive rules of ecology allowing them to subsist with lower resource availability and successfully survive the harsh conditions of winter.

Data from: Female investment in offspring size and number shifts seasonally in a lizard with single-egg clutches

The timing of reproduction strongly influences reproductive success in many organisms. For species with extended reproductive seasons, the quality of the environment may change throughout the season in ways that impact offspring survival, and, accordingly, aspects of reproductive strategies may shift to maximize fitness. Life-history theory predicts that if offspring environments deteriorate through the season, females should shift from producing more, smaller offspring early in the season to fewer, higher quality offspring later in the season. We leverage multiple iterations of anole breeding colonies, which control for temperature, moisture, and food availability, to identify seasonal changes in reproduction. These breeding colonies varied only by the capture date of the adult animals from the field. We show that seasonal cohorts exhibit variation in key reproductive traits such as inter-clutch interval, egg size and hatchling size consistent with seasonal shifts in reproductive effort. Overall, reproductive effort was highest early in the season due to a relatively high rate of egg production. Later season cohorts produced fewer, but larger offspring We infer that these results indicate a strategy for differential allocation of resources through the season. Females maximize offspring quantity when environments are favorable, and maximize offspring quality when environments are poor for those offspring. Our study also highlights that subtle differences in methodology (such as capture date of study animals) may influence the interpretation of results. Researchers interested in reproduction must be conscious of how their organism's reproductive patterns may shift through the season when designing experiments or comparing results across studies.

Data from: Causes of seasonal decline in reproduction of the cooperatively-breeding acorn woodpecker

Clutch size and reproductive success decline seasonally in a wide range of temperate avian taxa. Two competing hypotheses have been proposed to explain such declines: the "timing" hypothesis, which states that conditions affecting reproduction decline intrinsically with date, and the "quality" hypothesis, which proposes that high-quality individuals or individuals in high-quality situations breed earlier. We contrasted the relative importance of these two hypotheses using a long-term dataset of the cooperatively-breeding acorn woodpecker (Melanerpes formicivorus) in central coastal California (USA). This population exhibits an 11% seasonal decline in clutch size, a 60% seasonal decline in fledging success, and a 77% seasonal decline in fledgling overwinter survival. Clutch size tracks seasonal availability of flying insects, which are a likely ecological driver of the seasonal decline in reproduction and, because of the nonlinear relationship of flying insects with date, constitute a likely factor constraining even earlier nesting. By parsing lay date data into within-female and between-female components, we found that only the within-female component had a statistically significant direct effect on clutch size, supporting the timing hypothesis. For both fledging success and overwinter survival, however, both within- and between-female effects were highly significant, with between-female effects (differences in female quality) being stronger than within-female effects. These results suggest that timing per se is a key factor affecting the seasonal decline in clutch size, but that both differences in female quality and an intrinsic seasonal decline in conditions drive the even more dramatic seasonal declines in fledging success and overwinter survivorship of fledglings.

Data from: Breeding season length and nest mortality drive cryptic life history variation in Dark-eyed Juncos (Junco hyemalis) breeding across a montane elevation gradient

The manner in which individual life history traits respond to the environment and to each other, and how these traits combine to form overall patterns of life history variation, remains poorly characterized in wild populations. We monitored breeding Dark-eyed Juncos (Junco hyemalis) across a 700-m elevational range. We compared breeding season length, temporal patterns of breeding activity, adult body size, clutch size, brood size, nestling quality, and nest mortality among elevations. We also compared environmental measures across the studied elevations to determine whether abiotic factors explained life history trait variation. We used 12 microsatellite loci to test for genetic differentiation in populations at different elevations. Finally, we constructed a computer simulation to evaluate the combined effects of observed variation in life history traits. We found differences among elevations in breeding season length and in patterns of reproductive timing, which did not match each other and which were not explained solely by abiotic factors. We found no differences among elevations in adult body size, clutch size, brood size, or nestling quality. Nest mortality increased significantly with elevation. Genetic differentiation was too low to define distinct subpopulations. The simulation suggested that differences in mortality, in combination with differences in breeding season length, contributed to substantial differences in reproductive success among elevations. Thus, although individual life history traits showed little evidence of variation in response to the environment or to each other and little genetic differentiation, variation in breeding season length and in nest mortality were potential drivers of substantial elevational variation in overall life history in this system. These results demonstrate that individual life history traits may vary substantially in their patterns of variation, and that some life history traits may have disproportionate effects on overall life history.

Data from: Seasonally sympatric but allochronic: differential expression of hypothalamic genes in a songbird during gonadal development

Allochrony, the mismatch of reproductive schedules, is one mechanism that can mediate sympatric speciation and diversification. In songbirds, the transition into breeding condition and gonadal growth is regulated by the hypothalamic-pituitary-gonadal (HPG) axis at multiple levels. We investigated whether the difference in reproductive timing between two, seasonally sympatric subspecies of dark-eyed juncos (Junco hyemalis) was related to gene expression along the HPG axis. During the sympatric pre-breeding stage, we measured hypothalamic and testicular mRNA expression of candidate genes via qPCR in captive male juncos. For hypothalamic mRNA, we found our earlier breeding subspecies had increased expression of gonadotropin-releasing hormone (GnRH) and decreased expression of androgen receptor, estrogen receptor alpha, and mineralocorticoid receptor (MR). Subspecies did not differ in expression of hypothalamic gonadotropin-inhibitory hormone (GnIH) and glucocorticoid receptor (GR). While our earlier breeding subspecies had higher mRNA expression of testicular GR, subspecies did not differ in testicular luteinizing hormone receptor, follicle-stimulating hormone receptor, or MR mRNA expression levels. Our findings indicate increased GnRH production and decreased hypothalamic sensitivity to sex steroid negative feedback as factors promoting differences in the timing of gonadal recrudescence between recently diverged populations. Differential gene expression along the HPG axis may facilitate species diversification under seasonal sympatry.