Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass, Zostera marina.

Ecological studies often assume that genetically similar individuals will be more similar in phenotypic traits, such that genetic diversity can serve as a proxy for trait diversity. Here, we explicitly test the relationship between genetic relatedness and trait distance using 40 eelgrass (Zostera marina) genotypes from five sites within Bodega Harbor, CA. We measured traits related to nutrient uptake, morphology, biomass and growth, photosynthesis, and chemical deterrents for all genotypes. We used these trait measurements to calculate a multivariate pairwise trait distance for all possible genotype combinations. We then estimated pairwise relatedness from 11 microsatellite markers. We found significant trait variation among genotypes for nearly every measured trait; however, there was no evidence of a significant correlation between pairwise genetic relatedness and multivariate trait distance among individuals. However, at the subpopulation level (sites within a harbor), genetic (FST) and trait differentiation were positively correlated. Our work suggests that pairwise relatedness estimated from neutral marker loci is a poor proxy for trait differentiation between individual genotypes. It remains to be seen whether genomewide measures of genetic differentiation or easily measured "master" traits (like body size) might provide good predictions of overall trait differentiation

Optimizing passive acoustic sampling of bats in forests

Passive acoustic methods are increasingly used in biodiversity research and monitoring programs because they are cost-effective and permit the collection of large datasets. However, the accuracy of the results depends on the bioacoustic characteristics of the focal taxa and their habitat use. In particular, this applies to bats which exhibit distinct activity patterns in three-dimensionally structured habitats such as forests. We assessed the performance of 21 acoustic sampling schemes with three temporal sampling patterns and seven sampling designs. Acoustic sampling was performed in 32 forest plots, each containing three microhabitats: forest ground, canopy, and forest gap. We compared bat activity, species richness, and sampling effort using species accumulation curves fitted with the clench equation. In addition, we estimated the sampling costs to undertake the best sampling schemes. We recorded a total of 145,433 echolocation call sequences of 16 bat species. Our results indicated that to generate the best outcome, it was necessary to sample all three microhabitats of a given forest location simultaneously throughout the entire night. Sampling only the forest gaps and the forest ground simultaneously was the second best choice and proved to be a viable alternative when the number of available detectors is limited. When assessing bat species richness at the 1-km(2) scale, the implementation of these sampling schemes at three to four forest locations yielded highest labor cost-benefit ratios but increasing equipment costs. Our study illustrates that multiple passive acoustic sampling schemes require testing based on the target taxa and habitat complexity and should be performed with reference to cost-benefit ratios. Choosing a standardized and replicated sampling scheme is particularly important to optimize the level of precision in inventories, especially when rare or elusive species are expected

Quantifying the efficiency and biases of forest Saccharomyces sampling strategies

Saccharomyces yeasts are emerging as model organisms for ecology and evolution, and researchers need environmental Saccharomyces isolates to test ecological and evolutionary hypotheses. However, methods for isolating Saccharomyces from nature have not been standardized and isolation methods may influence the genotypes and phenotypes of studied strains. We compared the effectiveness and potential biases of an established enrichment culturing method against a newly developed direct plating method for isolating forest floor Saccharomyces spp. In a European forest, enrichment culturing was both less successful at isolating S. paradoxus per sample collected and less labor intensive per isolated S. paradoxus colony than direct isolation. The two methods sampled similar S. paradoxus diversity: the number of unique genotypes sampled (i.e., genotypic diversity) per S. paradoxus isolate and average growth rates of S. paradoxus isolates did not differ between the two methods, and growth rate variances (i.e., phenotypic diversity) only differed in one of three tested environments. However, enrichment culturing did detect rare S. cerevisiae in the forest habitat, and also found two S. paradoxus isolates with outlier phenotypes. Our results validate the historically common method of using enrichment culturing to isolate representative collections of environmental Saccharomyces. We recommend that researchers choose a Saccharomyces sampling method based on resources available for sampling and isolate screening. Researchers interested in discovering new Saccharomyces phenotypes or rare Saccharomyces species from natural environments may also have more success using enrichment culturing. We include step-by-step sampling protocols in the supplemental materials

Intraspecific variation in thermal acclimation and tolerance between populations of the winter ant, Prenolepis imparis.

Thermal phenotypic plasticity, otherwise known as acclimation, plays an essential role in how organisms respond to short-term temperature changes. Plasticity buffers the impact of harmful temperature changes; therefore, understanding variation in plasticity in natural populations is crucial for understanding how species will respond to the changing climate. However, very few studies have examined patterns of phenotypic plasticity among populations, especially among ant populations. Considering that this intraspecies variation can provide insight into adaptive variation in populations, the goal of this study was to quantify the short-term acclimation ability and thermal tolerance of several populations of the winter ant, Prenolepis imparis. We tested for correlations between thermal plasticity and thermal tolerance, elevation, and body size. We characterized the thermal environment both above and below ground for several populations distributed across different elevations within California, USA. In addition, we measured the short-term acclimation ability and thermal tolerance of those populations. To measure thermal tolerance, we used chill-coma recovery time (CCRT) and knockdown time as indicators of cold and heat tolerance, respectively. Short-term phenotypic plasticity was assessed by calculating acclimation capacity using CCRT and knockdown time after exposure to both high and low temperatures. We found that several populations displayed different chill-coma recovery times and a few displayed different heat knockdown times, and that the acclimation capacities of cold and heat tolerance differed among most populations. The high-elevation populations displayed increased tolerance to the cold (faster CCRT) and greater plasticity. For high-temperature tolerance, we found heat tolerance was not associated with altitude; instead, greater tolerance to the heat was correlated with increased plasticity at higher temperatures. These current findings provide insight into thermal adaptation and factors that contribute to phenotypic diversity by revealing physiological variance among populations

Root endophytes and invasiveness: no difference between native and non‐native Phragmites in the Great Lakes Region

Microbial interactions could play an important role in plant invasions. If invasive plants associate with relatively more mutualists or fewer pathogens than their native counterparts, then microbial communities could foster plant invasiveness. Studies examining the effects of microbes on invasive plants commonly focus on a single microbial group (e.g., bacteria) or measure only plant response to microbes, not documenting the specific taxa associating with invaders. We surveyed root microbial communities associated with co‐occurring native and non‐native lineages of Phragmites australis, across Michigan, USA. Our aim was to determine whether (1) plant lineage was a stronger predictor of root microbial community composition than environmental variables and (2) the non‐native lineage associated with more mutualistic and/or fewer pathogenic microbes than the native lineage. We used microscopy and culture‐independent molecular methods to examine fungal colonization rate and community composition in three major microbial groups (bacteria, fungi, and oomycetes) within roots. We also used microbial functional databases to assess putative functions of the observed microbial taxa. While fungal colonization of roots was significantly higher in non‐native Phragmites than the native lineage, we found no differences in root microbial community composition or potential function between the two Phragmites lineages. Community composition did differ significantly by site, with soil saturation playing a significant role in structuring communities in all three microbial groups. The relative abundance of some specific bacterial taxa did differ between Phragmites lineages at the phylum and genus level (e.g., Proteobacteria, Firmicutes). Purported function of root fungi and respiratory mode of root bacteria also did not differ between native and non‐native Phragmites. We found no evidence that native and non‐native Phragmites harbored distinct root microbial communities; nor did those communities differ functionally. Therefore, if the trends revealed at our sites are widespread, it is unlikely that total root microbial communities are driving invasion by non‐native Phragmites plants.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146836/1/ecs22526-sup-0001-AppendixS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146836/2/ecs22526.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146836/3/ecs22526_am.pd

Control of seminal fluid protein expression via regulatory hubs in Drosophila melanogaster

Highly precise, yet flexible and responsive coordination of expression across groups of genes underpins the integrity of many vital functions. However, our understanding of gene regulatory networks (GRNs) is often hampered by the lack of experimentally tractable systems, by significant computational challenges derived from the large number of genes involved or from difficulties in the accurate identification and characterization of gene interactions. Here we used a tractable experimental system in which to study GRNs: the genes encoding the seminal fluid proteins that are transferred along with sperm (the ‘transferome’) in Drosophila melanogaster fruit flies. The products of transferome genes are core determinants of reproductive success and, to date, only transcription factors have been implicated in the modulation of their expression. Hence, as yet, we know nothing about the post-transcriptional mechanisms underlying the tight, responsive and precise regulation of this important gene set. We investigated this omission in the current study. We first used bioinformatics to identify potential regulatory motifs that linked the transferome genes in a putative interaction network. This predicted the presence of putative microRNA (miRNA) ‘hubs’. We then tested this prediction, that post-transcriptional regulation is important for the control of transferome genes, by knocking down miRNA expression in adult males. This abolished the ability of males to respond adaptively to the threat of sexual competition, indicating a regulatory role for miRNAs in the regulation of transferome function. Further bioinformatics analysis then identified candidate miRNAs as putative regulatory hubs and evidence for variation in the strength of miRNA regulation across the transferome gene set. The results revealed regulatory mechanisms that can underpin robust, precise and flexible regulation of multiple fitness-related genes. They also help to explain how males can adaptively modulate ejaculate composition

Ark or park: the need to predict relative effectiveness of ex situ and in situ conservation before attempting captive breeding

1. When species face extinction, captive breeding may be appropriate. However, captive breeding may be unsuccessful, while reducing motivation and resources for in situ conservation and impacting wild source populations. Despite such risks, decisions are generally taken without rigorous evaluation. We develop an individual-based, stochastic population model to evaluate the potential effectiveness of captive-breeding and release programmes, illustrated by the Critically Endangered Ardeotis nigriceps Vigors great Indian bustard. 2. The model was parameterized from a comprehensive review of captive breeding and wild demography of large bustards. To handle uncertainty in the standards of captive-breeding performance that may be achieved we explored four scenarios of programme quality: ‘full-range’ (parameters sampled across the observed range), ‘below-average’, ‘above-average’ and ‘best possible’ (performance observed in exemplary breeding programmes). Results are evaluated examining i) the probability of captive population extirpation within 50 years and ii) numbers of adult females subsequently established in the wild following release, compared to an alternative strategy of in situ conservation without attempting captive breeding. 3. Successful implementation of captive breeding, involving permanent retention of 20 breeding females and release of surplus juveniles, required collection of many wild eggs and consistent ‘best possible’ performance across all aspects of the programme. Under ‘full-range’ and ‘above-average’ scenarios captive population extirpation probabilities were 73–88% % and 23‒51%% respectively, depending on egg collection rates. 4. Although most (73‒92%) ‘best possible’ programmes supported releases, re-establishment of free-living adults also required effective in situ conservation. Incremental implementation of effective conservation measures over the initial 10 years resulted in more free-living adults within 35 years if eggs were left in the wild without attempting captive breeding. 5. Synthesis and applications. For the great Indian bustard Ardeotis nigriceps, rapid implementation of in situ conservation offers a better chance to avoid extinction than captive breeding. Demographic modelling should be used to examine whether captive breeding is likely to bring net benefits to conservation programmes

Not all surveillance data are created equal—A multi‐method dynamic occupancy approach to determine rabies elimination from wildlife

1. A necessary component of elimination programmes for wildlife disease is effective surveillance. The ability to distinguish between disease freedom and non‐detection can mean the difference between a successful elimination campaign and new epizootics. Understanding the contribution of different surveillance methods helps to optimize and better allocate effort and develop more effective surveillance programmes. 2. We evaluated the probability of rabies virus elimination (disease freedom) in an enzootic area with active management using dynamic occupancy modelling of 10 years of raccoon rabies virus (RABV) surveillance data (2006–2015) collected from three states in the eastern United States. We estimated detection probability of RABV cases for each surveillance method (e.g. strange acting reports, roadkill, surveillance‐trapped animals, nuisance animals and public health samples) used by the USDA National Rabies Management Program. 3. Strange acting, found dead and public health animals were the most likely to detect RABV when it was present, and generally detectability was higher in fall– winter compared to spring–summer. Found dead animals in fall–winter had the highest detection at 0.33 (95% CI: 0.20, 0.48). Nuisance animals had the lowest detection probabilities (~0.02). 4. Areas with oral rabies vaccination (ORV) management had reduced occurrence probability compared to enzootic areas without ORV management. RABV occurrence was positively associated with deciduous and mixed forests and medium to high developed areas, which are also areas with higher raccoon (Procyon lotor) densities. By combining occupancy and detection estimates we can create a probability of elimination surface that can be updated seasonally to provide guidance on areas managed for wildlife disease. 5. Synthesis and applications. Wildlife disease surveillance is often comprised of a combination of targeted and convenience‐based methods. Using a multi‐method analytical approach allows us to compare the relative strengths of these methods, providing guidance on resource allocation for surveillance actions. Applying this multi‐method approach in conjunction with dynamic occupancy analyses better informs management decisions by understanding ecological drivers of disease occurrence

Things turned upside down

Aim: Soils and their biological communities face increasing pressure from multiple global drivers, including land management and climate change. In soils, earthworms play key roles in ecosystem functioning, but the environmental controls on their global communities are not fully understood. Here, an earthworm dataset was compiled to investigate the effects of environmental controls and land management on global earthworm communities. Location: 40 ° S – 65 ° N. Time period: 1962 to 2016. Major taxa studied: Earthworms Methods: A dataset of 899 earthworm community observations, together with environmental variables, was compiled across 169 globally distributed sites. Sites included natural forests and grasslands or managed arable, pasture or plantation ecosystems. Total, anecic, endogeic and epigeic abundances were compared in natural and managed ecosystems to quantify the effects of land management across climates. A hierarchical model was used to test interactions between earthworm communities with environmental controls and management across eighteen ecosystem types. Results: Land management prompted little change in total earthworm abundance at the global scale, but reduced species richness and shifted community composition. Endogeic earthworms were more abundant in managed ecosystems, while anecic and epigeic earthworms show variable responses across ecosystem types. Global relationships between total earthworm species richness and abundance were explained by climate, soil pH and land management. Main conclusions: Land management modulates the effects of environmental controls on global earthworm communities, through direct disturbance and indirect changes in edaphic conditions

Photosynthesis, growth, and decay traits in Sphagnum - a multispecies comparison

Peat mosses (Sphagnum) largely govern carbon sequestration in Northern Hemisphere peatlands. We investigated functional traits related to growth and decomposition in Sphagnum species. We tested the importance of environment and phylogeny in driving species traits and investigated trade-offs among them. We selected 15 globally important Sphagnum species, representing four sections (subgenera) and a range of peatland habitats. We measured rates of photosynthesis and decomposition in standard laboratory conditions as measures of innate growth and decay potential, and related this to realized growth, production, and decomposition in their natural habitats. In general, we found support for a trade-off between measures of growth and decomposition. However, the relationships are not strong, with r ranging between 0.24 and 0.45 for different measures of growth versus decomposition. Using photosynthetic rate to predict decomposition in standard conditions yielded R-2 = 0.20. Habitat and section (phylogeny) affected the traits and the trade-offs. In a wet year, species from sections Cuspidata and Sphagnum had the highest production, but in a dry year, differences among species, sections, and habitats evened out. Cuspidata species in general produced easily decomposable litter, but their decay in the field was hampered, probably due to near-surface anoxia in their wet habitats. In a principal components analysis, PCA, photosynthetic capacity, production, and laboratory decomposition acted in the same direction. The species were imperfectly clustered according to vegetation type and phylogeny, so that some species clustered with others in the same section, whereas others clustered more clearly with others from similar vegetation types. Our study includes a wider range of species and habitats than previous trait analyses in Sphagnum and shows that while the previously described growth-decay trade-off exists, it is far from perfect. We therefore suggest that our species-specific trait measures offer opportunities for improvements of peatland ecosystem models. Innate qualities measured in laboratory conditions translate differently to field responses. Most dramatically, fast-growing species could only realize their potential in a wet year. The same species decompose fast in laboratory, but their decomposition was more retarded in the field than that of other species. These relationships are crucial for understanding the long-term dynamics of peatland communities