Spatial asynchrony and cross-scale climate interactions in populations of a coldwater stream fish.

Climate change affects populations over broad geographic ranges due to spatially autocorrelated abiotic conditions known as the Moran effect. However, populations do not always respond to broad-scale environmental changes synchronously across a landscape. We combined multiple datasets for a retrospective analysis of time-series count data (5-28 annual samples per segment) at 144 stream segments dispersed over nearly 1,000 linear kilometers of range to characterize the population structure and scale of spatial synchrony across the southern native range of a coldwater stream fish (brook trout, Salvelinus fontinalis), which is sensitive to stream temperature and flow variations. Spatial synchrony differed by life stage and geographic region: it was stronger in the juvenile life stage than in the adult life stage and in the northern sub-region than in the southern sub-region. Spatial synchrony of trout populations extended to 100-200 km but was much weaker than that of climate variables such as temperature, precipitation, and stream flow. Early life stage abundance changed over time due to annual variation in summer temperature and winter and spring stream flow conditions. Climate effects on abundance differed between sub-regions and among local populations within sub-regions, indicating multiple cross-scale interactions where climate interacted with local habitat to generate only a modest pattern of population synchrony over space. Overall, our analysis showed higher degrees of response heterogeneity of local populations to climate variation and consequently population asynchrony than previously shown based on analysis of individual, geographically restricted datasets. This response heterogeneity indicates that certain local segments characterized by population asynchrony and resistance to climate variation could represent unique populations of this iconic native coldwater fish that warrant targeted conservation. Advancing the conservation of this species can include actions that identify such priority populations and incorporate them into landscape-level conservation planning. Our approach is applicable to other widespread aquatic species sensitive to climate change.

Temperature variation generates interspecific synchrony but spatial asynchrony in survival for freshwater fish communities.

Identifying environmental drivers of demographic variation is key to predicting community-level impacts in response to global change. Climate conditions can synchronize population trends and can occur both spatially for populations of the same species, and across multiple species within the same local community. The aim of this study was to investigate patterns of temporal variation in survival for freshwater fish communities in two geographically close but isolated sites and to understand the amount of variation accounted for by abiotic covariates including metrics of water temperature and stream flow. Using mark-recapture data, we estimated bi-monthly apparent survival in a Bayesian Cormack-Jolly-Seber framework. The model included random effects to quantify temporal variance to understand species synchrony with the rest of the fish community and between sites. Study species included bluehead chub (Nocomis leptocephalus), creek chub (Semotilus atromaculatus), and striped jumprock (Moxostoma rupiscartes) in the southeastern USA. Results showed that survival varied over time and periods of low survival were associated with higher mean water temperature. However, temporal patterns of survival differed among species and between sites, where survival was synchronous among species within a site but asynchronous between sites for the same species despite their spatial proximity. Study streams differed in summer thermal regimes, which resulted in contrasting summer survival patterns, suggesting sensitivity of these fishes to warming. We found that interspecific synchrony was greater than spatial synchrony, where regional drivers such as temperature may interact with local habitat leading to differences in survival patterns at fine spatial scales. Finally, these findings show that changes in the timing and magnitude of environmental conditions can be critical in limiting vital rates and that some populations may be more resilient to climate variation than others.

Simple statistical models can be sufficient for testing hypotheses with population time-series data.

Time-series data offer wide-ranging opportunities to test hypotheses about the physical and biological factors that influence species abundances. Although sophisticated models have been developed and applied to analyze abundance time series, they require information about species detectability that is often unavailable. We propose that in many cases, simpler models are adequate for testing hypotheses. We consider three relatively simple regression models for time series, using simulated and empirical (fish and mammal) datasets. Model A is a conventional generalized linear model of abundance, model B adds a temporal autoregressive term, and model C uses an estimate of population growth rate as a response variable, with the option of including a term for density dependence. All models can be fit using Bayesian and non-Bayesian methods. Simulation results demonstrated that model C tended to have greater support for long-lived, lower-fecundity organisms (K life-history strategists), while model A, the simplest, tended to be supported for shorter-lived, high-fecundity organisms (r life-history strategists). Analysis of real-world fish and mammal datasets found that models A, B, and C each enjoyed support for at least some species, but sometimes yielded different insights. In particular, model C indicated effects of predictor variables that were not evident in analyses with models A and B. Bayesian and frequentist models yielded similar parameter estimates and performance. We conclude that relatively simple models are useful for testing hypotheses about the factors that influence abundance in time-series data, and can be appropriate choices for datasets that lack the information needed to fit more complicated models. When feasible, we advise fitting datasets with multiple models because they can provide complementary information.

Size-dependent growth tactics of a partially migratory fish before migration.

In many migratory species, smaller migrants suffer higher mortality rates during the risky migration. To minimize the size-selective mortality, migrants with smaller body sizes would need to accelerate growth rates or delay migration timing to attain a large enough body size prior to migration. To test these predictions, we investigated size-dependent patterns of growth rates and migration timing of juvenile masu salmon (Oncorhynchus masou) before their oceanic migration. We tracked uniquely marked individuals in a study population consisted of oceanic migrants and river-dwelling residents using mark-recapture surveys and PIT-tag antenna-reader system. Data supported our predictions about size-dependent growth rates and migration timing. For approximately 6 months before outmigration (i.e., between the decision of migration and the start of migration), eventual migrants grew more than residents if their initial size was smaller, but such a difference in growth rate diminished for fish with larger initial sizes. In addition, smaller eventual migrants delayed the timing of outmigration compared to larger individuals, to attain a larger body size in the river prior to migration. These results suggest that size-selective mortality during migration has shaped size-dependent patterns of the pre-migration growth in migratory masu salmon. Size-conditional changes in growth rate and duration of pre-migration period may be an adaptive tactic for the migratory animals.

Interspecific social dominance networks reveal mechanisms promoting coexistence in sympatric charr in Hokkaido, Japan.

Coexistence of species requires equalizing mechanisms that minimize fitness differences, which are balanced by stabilizing mechanisms that enhance negative intraspecific interactions versus interspecific ones. Here, we develop a simple theoretical framework that allows measuring the relative strength of intraspecific versus interspecific competition in dominance hierarchies. We use it to evaluate mechanisms promoting coexistence between two congeneric charr that compete for foraging positions, which strongly influence density-dependent growth and survival. Agonistic interactions (n = 761) among 71 Dolly Varden Salvelinus malma and whitespotted charr Salvelinus leucomaenis were measured by snorkelling in two pools in the sympatric zone of a Hokkaido stream during two summers. Interspecific dominance hierarchies, analysed using three methods, were closely correlated with fish length but the species treated each other equally. Ranks for the most dominant fish in each pool, determined directly by knockout experiments, were also virtually identical to ranks by length. Similarly, exponential random graph modelling of the social networks provided no evidence that either species was dominant over the other. Instead, larger fish were more likely to win contests, especially over fish of the next lower ranks. These results demonstrated that the two species were nearly ecological equivalents in accessing key resources in this sympatric zone. Nearly identical growth and stable densities over 4 years further supported this inference, although Dolly Varden were a minority (29% of the assemblage), a sign of some fitness difference. Detailed foraging observations coupled with two concurrent studies revealed an effective stabilizing mechanism. Dolly Varden shifted to feeding directly from the benthos when drifting invertebrates declined, a behaviour enhanced by morphological character displacement, thereby partitioning food resources and enhancing intraspecific competition while avoiding agonistic encounters with whitespotted charr. The plurality of evidence indicates that fitness differences between these ecologically equivalent species are small in this local assemblage, and balanced by resource partitioning, a modest stabilizing mechanism that promotes coexistence. The theoretical framework presented here is a useful tool to evaluate the strength of interspecific versus intraspecific competition, which combined with information on trade-offs in ecological performance can contribute to a mechanistic understanding of species coexistence.

Phenotypic Diagnosis of Lineage and Differentiation During Sake Yeast Breeding.

Sake yeast was developed exclusively in Japan. Its diversification during breeding remains largely uncharacterized. To evaluate the breeding processes of the sake lineage, we thoroughly investigated the phenotypes and differentiation of 27 sake yeast strains using high-dimensional, single-cell, morphological phenotyping. Although the genetic diversity of the sake yeast lineage is relatively low, its morphological diversity has expanded substantially compared to that of the Saccharomycescerevisiae species as a whole. Evaluation of the different types of breeding processes showed that the generation of hybrids (crossbreeding) has more profound effects on cell morphology than the isolation of mutants (mutation breeding). Analysis of phenotypic robustness revealed that some sake yeast strains are more morphologically heterogeneous, possibly due to impairment of cellular network hubs. This study provides a new perspective for studying yeast breeding genetics and micro-organism breeding strategies.

Seasonal weather patterns drive population vital rates and persistence in a stream fish.

Climate change affects seasonal weather patterns, but little is known about the relative importance of seasonal weather patterns on animal population vital rates. Even when such information exists, data are typically only available from intensive fieldwork (e.g., mark-recapture studies) at a limited spatial extent. Here, we investigated effects of seasonal air temperature and precipitation (fall, winter, and spring) on survival and recruitment of brook trout (Salvelinus fontinalis) at a broad spatial scale using a novel stage-structured population model. The data were a 15-year record of brook trout abundance from 72 sites distributed across a 170-km-long mountain range in Shenandoah National Park, Virginia, USA. Population vital rates responded differently to weather and site-specific conditions. Specifically, young-of-year survival was most strongly affected by spring temperature, adult survival by elevation and per-capita recruitment by winter precipitation. Low fall precipitation and high winter precipitation, the latter of which is predicted to increase under climate change for the study region, had the strongest negative effects on trout populations. Simulations show that trout abundance could be greatly reduced under constant high winter precipitation, consistent with the expected effects of gravel-scouring flows on eggs and newly hatched individuals. However, high-elevation sites would be less vulnerable to local extinction because they supported higher adult survival. Furthermore, the majority of brook trout populations are projected to persist if high winter precipitation occurs only intermittently (≤3 of 5 years) due to density-dependent recruitment. Variable drivers of vital rates should be commonly found in animal populations characterized by ontogenetic changes in habitat, and such stage-structured effects may increase population persistence to changing climate by not affecting all life stages simultaneously. Yet, our results also demonstrate that weather patterns during seemingly less consequential seasons (e.g., winter precipitation) can have major impacts on animal population dynamics.

Modeling structured population dynamics using data from unmarked individuals.

The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark-recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark-recapture) and extensive (e.g., counts) data sources.

Ethanol fermentation driven by elevated expression of the G1 cyclin gene CLN3 in sake yeast.

Cellular and subcellular morphology reflects the physiological state of a cell. To determine the physiological nature of sake yeast with superior fermentation properties, we quantitatively analyzed the morphology of sake yeast cells by using the CalMorph system. All the sake strains examined here exhibited common morphological traits that are typically observed in the well-characterized whiskey (whi) mutants that show accelerated G(1)/S transition. In agreement with this finding, the sake strain showed less efficient G(0)/G(1) arrest and elevated expression of the G(1) cyclin gene CLN3 throughout the fermentation period. Furthermore, deletion of CLN3 remarkably impaired the fermentation rate in both sake and laboratory strains. Disruption of the SWI6 gene, a transcriptional coactivator responsible for Cln3p-mediated G(1)/S transition, also resulted in a decreased fermentation rate, whereas whi mutants exhibited significant improvement in the fermentation rate, demonstrating positive roles of Cln3p and its downstream signalling pathway in facilitating ethanol fermentation. The combined results indicate that enhanced induction of CLN3 contributes to the high fermentation rate of sake yeast, which are natural whi mutants.

Fine-scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks.

Linear and heterogeneous habitat makes headwater stream networks an ideal ecosystem in which to test the influence of environmental factors on spatial genetic patterns of obligatory aquatic species. We investigated fine-scale population structure and influence of stream habitat on individual-level genetic differentiation in brook trout (Salvelinus fontinalis) by genotyping eight microsatellite loci in 740 individuals in two headwater channel networks (7.7 and 4.4 km) in Connecticut, USA. A weak but statistically significant isolation-by-distance pattern was common in both sites. In the field, many tagged individuals were recaptured in the same 50-m reaches within a single field season (summer to fall). One study site was characterized with a hierarchical population structure, where seasonal barriers (natural falls of 1.5-2.5 m in height during summer base-flow condition) greatly reduced gene flow and perceptible spatial patterns emerged because of the presence of tributaries, each with a group of genetically distinguishable individuals. Genetic differentiation increased when pairs of individuals were separated by high stream gradient (steep channel slope) or warm stream temperature in this site, although the evidence of their influence was equivocal. In a second site, evidence for genetic clusters was weak at best, but genetic differentiation between individuals was positively correlated with number of tributary confluences. We concluded that the population-level movement of brook trout was limited in the study headwater stream networks, resulting in the fine-scale population structure (genetic clusters and clines) even at distances of a few kilometres, and gene flow was mitigated by 'riverscape' variables, particularly by physical barriers, waterway distance (i.e. isolation-by-distance) and the presence of tributaries.