Spatial and temporal non-stationarity in long-term population dynamics of over-wintering birds of North America

Stephen Murphy, Marta Jarzyna. Authorea. July 27, 2022. DOI: 10.22541/au.165890198.84826153/v1

Abstract

Understanding population change across long time scales and at fine spatiotemporal resolutions is important for confronting a broad suite of conservation challenges. However, this task is hampered by a lack of quality long-term census data for multiple species collected across large geographic regions. Here, we used century-long (1919-2018) data from the Audubon Christmas Bird Count (CBC) survey to assess population changes in over 300 avian species in North America and evaluate their temporal non-stationarity. To estimate population sizes across the entire century, we employed a Bayesian hierarchical model that accounts for species detection probabilities, variable sampling effort, and missing data. We evaluated population trends using generalized additive models (GAMs) and assessed temporal non-stationarity in the rate of population change by extracting the first derivatives from the fitted GAM functions. We then summarized the population dynamics across species, space, and time using a non-parametric clustering algorithm that categorized individual population trends into four distinct trend clusters. We found that species varied widely in their population trajectories, with over 90% of species showing a considerable degree of spatial and/or temporal non-stationarity, and many showing strong shifts in the direction and magnitude of population trends throughout the past century. Species were roughly equally distributed across the four clusters of population trajectories, though grassland, forest, and desert specialists more commonly showed declining trends. Interestingly, for many species, region-wide population trends often differed from those observed at individual sites, suggesting that conservation decisions need to be tailored to fine spatial scales. Together, our results highlight the importance of considering spatial and temporal non-stationarity when assessing long-term population changes. More generally, we demonstrate the promise of novel statistical techniques for improving the utility and extending the temporal scope of existing citizen science datasets.

Assessing model adequacy for Bayesian Skyline plots using posterior predictive simulation

Emanuel M. Fonseca, Drew J. Duckett, Filipe G. Almeida, Megan L. Smith, Maria Tereza C. Thomé, Bryan C. Carstens. 2022. PLoS ONE 17(7): e0269438. https://doi.org/10.1371/journal.pone.0269438

Abstract

Bayesian skyline plots (BSPs) are a useful tool for making inferences about demographic history. For example, researchers typically apply BSPs to test hypotheses regarding how climate changes have influenced intraspecific genetic diversity over time. Like any method, BSP has assumptions that may be violated in some empirical systems (e.g., the absence of population genetic structure), and the naïve analysis of data collected from these systems may lead to spurious results. To address these issues, we introduce P2C2M.Skyline, an R package designed to assess model adequacy for BSPs using posterior predictive simulation. P2C2M.Skyline uses a phylogenetic tree and the log file output from Bayesian Skyline analyses to simulate posterior predictive datasets and then compares this null distribution to statistics calculated from the empirical data to check for model violations. P2C2M.Skyline was able to correctly identify model violations when simulated datasets were generated assuming genetic structure, which is a clear violation of BSP model assumptions. Conversely, P2C2M.Skyline showed low rates of false positives when models were simulated under the BSP model. We also evaluate the P2C2M.Skyline performance in empirical systems, where we detected model violations when DNA sequences from multiple populations were lumped together. P2C2M.Skyline represents a user-friendly and computationally efficient resource for researchers aiming to make inferences from BSP.

The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest

Megan L. Smith, Jessica Wallace, David C. Tank, Jack Sullivan, Bryan C. Carstens. 03 July 2022. https://doi.org/10.1111/mec.16595

Abstract

Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated species distribution models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine-learning approach to compare models with and without gene flow between populations upon secondary contact after the last glacial maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and increased habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa, and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support a role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages.

Molecular identification and phylogenetic analysis of free-living amoeba in the water resources of Arak, Iran

Malihe Fani, Paul A Fuerst, Mahdi Mosayebi, Amir Javadi, Majid Fasihi Harandi, Mehrzad Saraei, Milad Badri, Elham Hajialilo. J Water Health. 2022 Jul;20(7):1051-1063.  doi: 10.2166/wh.2022.030.

Abstract

The aim of the present study was to detect free-living amoeba (FLA) in the water resources of Arak, Iran using molecular tools. A total of 154 samples were collected from different water supplies. Molecular analyses, sequencing, and phylogenetic study were conducted to confirm the species and genotypes of FLA. Fisher exact test was used to determine the significance. Of 154 water samples, 19 (12.3%) samples were tested positive for FLA. Three genotypes of Acanthamoeba including T4, subtype D, and T5 were identified among the isolates. The pathogenicity assay showed that the isolate of Acanthamoeba in drinking water was highly pathogenic. Three species of Naegleria, including N. australiensis, N. pagei, and N. gruberi were found among the samples. Six isolates of Vermamoeba were identified as V. vermiformis. Meanwhile, three other species including Vannella sp., Vahlkampfia avara, and Stenamoeba polymorpha were also recovered from the water samples. Statistical analysis showed a significant difference between the various water resources contaminated with FLA. This is the first study to reveal the presence of S. polymorpha in water sources in Iran. According to the findings of the present study, health officials should be beware of potential public health impacts of FLA in water resources.

Disturbance has variable effects on the structural complexity of a temperate forest landscape

Christopher M.Gough, Jeff W.Atkins, Robert T.Fahey, Peter S.Curtis, Gil Bohrer, Brady S.Hardiman, Laura J.Hickey, Lucas E. Nave, Kerstin M. Niedermaier, Cameron Clay, Jason M. Tallant, Ben Bond-Lamberty. Ecological Indicators Volume 140, July 2022, 109004. https://doi.org/10.1016/j.ecolind.2022.109004

Abstract

The temporal dynamics of forest canopy structure are influenced by disturbances that alter vegetation quantity and distribution. While canopy structural indicators such as leaf area index (LAI), canopy cover, and canopy height have been widely studied in the context of disturbance, the post-disturbance temporal dynamics of structural complexity, which summarizes the heterogeneity of vegetation arrangement, are poorly understood. With the goal of advancing conceptual and empirical understanding of the temporal dynamics of structural complexity following disturbance, we synthesized results from three large-scale disturbance manipulation experiments at the University of Michigan Biological Station (UMBS): the 4-year Forest Resilience Threshold Experiment (FoRTE) manipulating levels of disturbance severity; the decade-long Forest Accelerated Succession Experiment (FASET), in which all early successional tree species were stem-girdled within 39 ha in the same landscape; and forest chronosequences established following clear-cut harvesting. We found that the temporal dynamics of canopy structure following disturbance were dependent upon three factors: (1) the source and severity of disturbance; (2) the spatial and temporal scales of analysis; and (3) the measure of structure assessed. Unlike vegetation area index and canopy cover, which initially decreased in response to disturbance, structural complexity measures such as canopy and top rugosity did not consistently respond to moderate levels of disturbance severity. Over multi-decadal timescales, structural complexity increased to a maximum, regardless of whether fire occurred at the time of stand establishment, but intervening low-to-moderate severity disturbance in regrown century-old forests altered trajectories of canopy rugosity. We conclude that structural complexity indicators display a more nuanced temporal and directional response to disturbance than conventional leaf area and cover indexes. Predicting what disturbance conditions modify trajectories of structural complexity remains critical to disturbance characterization and the inference of ecosystem functioning.

Elevational diversity patterns of rodents differ between wet and arid mountains

Brooks A. Kohli, Reymond J. Miyajima, Marta A. Jarzyna. 2022. Global Ecology and Biogeography. https://doi.org/10.1111/geb.13552

Abstract

Aim

Patterns of species richness along elevation gradients vary with geographic and environmental factors but evidence for similar variation in functional and phylogenetic diversity remains scarce. Here, we provide the most comprehensive evaluation to date of elevational gradients in taxonomic, functional, and phylogenetic diversity of rodents – one of the most ecologically diverse groups of mammals – and test the effects of latitude and aridity on their variation for the first time.

Location

Forty-nine mountains on five continents.

Time period

Contemporary.

Major taxa studied

Rodents (Rodentia).

Methods

We compiled elevational distributions of 374 rodent species across 49 elevational gradients. For each gradient, we quantified – in 100-m elevational bins – rodent species richness and functional and phylogenetic richness, evenness, and dispersion, and their species richness-corrected equivalents. To assess how rodent diversity varies with elevation, we fitted a series of models that included elevation, average latitude, and aridity of each mountain system while accounting for variation in study design and sampling effort.

Results

A common mid-elevational peak in species richness among mountains contrasts with functional and phylogenetic diversity pattern variation (model shape and slope) explained by the aridity at a mountain's base. Specifically, we find that functional and phylogenetic richness and dispersion decline with elevation in wet mountain systems but increase with elevation in arid mountains.

Main conclusions

In this first comparative analysis of mammal functional and phylogenetic elevational gradients, we find that the decoupling of each from species richness is particularly pronounced in arid regions. Wet-mountain lowlands and arid-mountain highlands harbour the most functionally and phylogenetically diverse rodent communities, indicating that water availability is a strong environmental filter in structuring diversity of small mammals on mountain gradients. High regularity of species distances within assemblages supports a constant role for competition across all elevations and niche expansion in elevations with greater species richness.

Utility of carbon and nitrogen stable isotopes for inferring wild bee (Hymenoptera: Apoidea) use of adjacent foraging habitats

Jessie Lanterman Novotny, Karen Goodell. 2022. PLoS ONE 17(7): e0271095. https://doi.org/10.1371/journal.pone.0271095

Abstract

Isotope analysis has proven useful for understanding diets of animals that are difficult to track for extended periods. Bees are small yet highly mobile and often forage from multiple habitats. However, current methods of assessing diet are limited in scope. Efficient methods of tracking bee diets that integrate across life stages, distinguish habitat use, and are sensitive to taxonomic differences will inform conservation strategies. We evaluated the utility of stable isotope analysis for estimating contributions of adjacent habitats to bees’ diets. We also investigated taxonomic variation in bee and flower isotope composition. We measured natural abundance of carbon and nitrogen stable isotopes in two body regions from three wild bee genera, as well as in 25 species of flowers that likely comprised their diets. Bee ∂13C and ∂15N varied with habitat and taxonomic groups (conflated with month), but did not match spatial or seasonal trends in their food plants. Flower ∂13C was lowest in the forest and in April–June, as expected if driven by water availability. However, bee ∂13C was elevated in the spring, likely from overwintering nutritional stress or unpredictable food availability. Bumble bees (Bombus) were enriched in ∂15N compared to others, possibly reflecting differences in larval feeding. Bee diet mixing models had high variation and should be interpreted with caution. Models estimated similar habitat contributions to diets of spring Andrena and overwintered Bombus queens. Summer Bombus queens and workers were indistinguishable. Sweat bees (Halictus) were estimated to use comparatively more field flowers than others. Overall, taxon more strongly influenced isotope composition than either foraging habitat or month, likely because of associated differences in sociality and timing of annual activity. Future studies seeking to reveal bee diets by isotope analysis may gain better resolution in more isotopically distinct habitats, in conjunction with controlled feeding or isotope labeling experiments.