cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/2jrhbg
title: Soil biogeochemistry across Central and South American tropical dry forests

description: AbstractThe availability of nitrogen (N) and phosphorus (P) controls the flow of carbon (C) among plants, soils, and the atmosphere, thereby shaping terrestrial ecosystem responses to global change. Soil C, N, and P cycles are linked by drivers operating at multiple spatial and temporal scales: landscape-level variation in macroclimate, seasonality, and soil geochemistry; stand-scale heterogeneity in forest composition and structure; and microbial community dynamics at the soil pore scale. Yet in many biomes, we do not know at which scales most of the biogeochemical variation emerges, nor which processes drive cross-scale feedbacks. Here, we examined the drivers and spatial/temporal scales of variation in soil biogeochemistry across four tropical dry forests spanning steep gradients of climate, soil parent material, and plant community structure. To do so, we quantified soil C, N, and P pools, extracellular enzyme activities, and microbial community structure across wet and dry seasons in sixteen plots located in Colombia, Costa Rica, Mexico, and Puerto Rico. Soil biogeochemistry exhibited marked heterogeneity across the sixteen plots, with total organic C, N, and P pools varying four-fold, and inorganic nutrient pools by an order of magnitude. Most soil characteristics changed more across space (i.e., among sites and plots) than over time (between dry and wet season samplings). We observed stoichiometric decoupling among C, N, and P cycles, which may reflect their divergent biogeochemical drivers. Organic C and N pool sizes were positively correlated with the relative abundance of ectomycorrhizal trees and legumes. By contrast, the distribution of soil P pools was driven by soil geochemistry, with larger inorganic P pools in soils with P-rich parent material. Most earth system models assume that soils within a texture class operate similarly, and ignore sub-grid cell variation in soil properties. Here we reveal that soil nutrient pools and fluxes exhibit as much variation among four Neotropical dry forests as is observed across terrestrial ecosystems at the global scale. Thus, the biogeochemical patterns we observed across the Neotropical dry forest biome challenge representation of soil processes in ecosystem models.
DOI: 10.5683/sp2/ipdkyb
title: Speciation and gene flow across an elevational gradient in New Guinea kingfishers

description: AbstractClosely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks, and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high elevation and low elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modeling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that while in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.
DOI: 10.5683/sp2/b7jelz
title: Species differences in phenology shape coexistence

description: AbstractEcological theory produces opposing predictions about whether differences in the timing of life history transitions, or ‘phenology’, promote or limit coexistence. Phenological separation is predicted to create temporal niche differences, increasing coexistence, yet phenological separation could also competitively favour one species, increasing fitness differences and hindering coexistence. We experimentally manipulated relative germination timing, a critical phenological event, of two annual grass species, Vulpia microstachys and V. octoflora, to test these contrasting predictions. We parameterized a competition model to estimate within-season niche differences, fitness differences, and coexistence, and to estimate coexistence when year-to-year fluctuations of germination timing occur. Increasing germination separation caused parallel changes in niche and fitness differences, with the net effect of weakening within-year coexistence. Both species experienced a competitive advantage by germinating earlier and a four-day head start allowed the generally inferior competitor to exclude the otherwise superior competitor. The overall consequence of germination separation was to limit coexistence within a given year, although year-to-year variation in relative timing of germination was sufficient to support long-term coexistence. Our results clarify how phenological differences structure competitive interactions and highlight the need to quantify year-to-year variation in these differences to better understand species coexistence.
DOI: 10.5683/sp2/xn3fy7
title: Supplemental material for: The dynamics of bird diversity in the new world

description: AbstractThree prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (1) time for speciation, (2) diversification rates, and (3) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and GIS, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are differentially important (with ecological limits playing the dominant role), each contributes uniquely to the formation of richness gradients. Further, my results reveal the likely interplay between the explanations. They indicate that ecological limits hinder the diversification process, such that the accumulation of species within a region gradually slows down over time. Yet, it does not seem to converge toward a hard ceiling on regional richness. Instead, species-rich regions show suppressed, but continued, diversification, coupled with signatures of possible competition (esp. Neotropical lowlands). Conversely, species-poor, newly-colonized regions show fast diversification and weak to no signs of competition (esp. Nearctic highlands). These results held across five families of birds, across grid cells, biomes, and elevations. Together, my findings begin to illuminate the rich, yet highly consistent, interplay of the mechanisms that together shape richness gradients in the New World, including the most species-rich biodiversity hotspots on the planet, the Andes and the Amazon.
DOI: 10.5683/sp2/rrcprj
title: Supplementary material: How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature

description: AbstractPhylogenetic comparative methods are often used to test functional relationships between traits. However, million-year macroevolutionary observational datasets cannot definitively prove causal links between traits --- correlation does not equal causation and experimental manipulation over such timescales is impossible. While this caveat is widely understood, it is far less appreciated that different phylogenetic approaches make different causal assumptions about the functional relationships of traits. In order to make meaningful inferences, it is critical that our statistical methods make biologically reasonable assumptions. Here we illustrate the importance of causal reasoning in comparative biology by examining a recent study by Avaria-Llautureo et al. (2019) that tested for the evolutionary coupling of metabolic rate and body temperature across endotherms and made the notable discoveries that these traits were unlinked through evolutionary time and that body temperatures were, on average, higher in the early Cenozoic than they are today. We argue that the causal assumptions embedded into their models made it impossible for them to actually test the relevant functional and evolutionary hypothesis. We then re-analyze their data using more biologically appropriate models and find support for the exact opposite conclusions, corroborating previous evidence from physiology and paleontology. We highlight the vital need for causal thinking, even when experiments are impossible.
DOI: 10.5683/sp2/u09a3s
title: Supplementary materials: Monitoring recovery of overgrazed lichen communities on Hagemeister Island, southwestern Alaska

description: AbstractUnderstanding the recovery rate of overgrazed lichen communities has value to mangers of lands in northern regions. We describe lichen community composition and present recovery rate measurements for a 12-year period following overgrazing by reindeer (Rangifer tarandus) on Hagemeister Island, Alaska. Reindeer were removed from the island in 1993 following overgrazing and average total lichen biomass increased from 504.2 kg/ha (SD 205.4) in 2003 to 795.3 (SD 489.6) in 2015. We estimate time to recovery with three competing growth curves which estimate grazeable biomass may be reached in 34-41 years. However, estimates of full recovery to climax biomass varied among the models, ranging from 71 to 400 years. In 2015, lichen communities were composed of various mixtures of at least 78 lichen taxa, and were dominated by Cladina stygia and other important reindeer forage species. While reindeer overgrazing diminished forage quantity, it did not extirpate preferred forage taxa.
DOI: 10.5683/sp2/roqgys
title: Temporal instability of lake charr phenotypes: Synchronicity of growth rates and morphology linked to environmental variables?

description: AbstractPathways through which phenotypic variation among individuals arise can be complex. One assumption often made in relation to intraspecific diversity is that the stability or predictability of the environment will interact with expression of the underlying phenotypic variation. To address biological complexity below the species level, we investigated variability across years in morphology and annual growth increments between and within two sympatric lake charr Salvelinus namaycush ecotypes in Rush Lake, USA. A rapid phenotypic shift in body and head shape was found within a decade. The magnitude and direction of the observed phenotypic change was consistent in both ecotypes, which suggests similar pathways caused the variation over time. Over the same time period, annual growth increments declined for both lake charr ecotypes and corresponded with a consistent phenotypic shift of each ecotype. Despite ecotype-specific annual growth changes in response to winter conditions, the observed annual growth shift for both ecotypes was linked, to some degree, with variation in the environment. Particularly, a declining trend in regional cloud cover was associated with an increase of early stage (ages 1-3) annual growth for lake charr of Rush Lake. Underlying mechanisms causing changes in growth rates and constrained morphological modulation are not fully understood. An improved knowledge of the biology hidden within the expression of phenotypic variation promises to clarify our understanding of temporal morphological diversity and instability.
DOI: 10.5683/sp2/lbneen
title: The effectiveness of flower strips and hedgerows on pest control, pollination services and crop yield: a quantitative synthesis

description: AbstractFloral plantings are promoted to foster ecological intensification of agriculture through provisioning of ecosystem services. However, a comprehensive assessment of the effectiveness of different floral plantings, their characteristics and consequences for crop yield is lacking. Here we quantified the impacts of flower strips and hedgerows on pest control (18 studies) and pollination services (17 studies) in adjacent crops in North America, Europe and New Zealand. Flower strips, but not hedgerows, enhanced pest control services in adjacent fields by 16% on average. However, effects on crop pollination and yield were more variable. Our synthesis identifies several important drivers of variability in effectiveness of plantings: pollination services declined exponentially with distance from plantings, and perennial and older flower strips with higher flowering plant diversity enhanced pollination more effectively. These findings provide promising pathways to optimize floral plantings to more effectively contribute to ecosystem service delivery and ecological intensification of agriculture in the future.
DOI: 10.5683/sp2/oeoex3
title: The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic

description: AbstractThe Arctic is one of the most extreme terrestrial environments on the planet. Here we present the first complete genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g. related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.
DOI: 10.5683/sp2/1zju98
title: The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements

description: Abstract Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain‐containing Gypsy LTR retrotransposons (‘chromoviruses’), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.
DOI: 10.5683/sp2/m1i3b4
title: Type 1 diabetes adolescent transition study

description: AbstractObjectives: Adolescents with type 1 diabetes experience dramatic excursions in blood sugars as they transition to adult care. Trials on single interventions have struggled to demonstrate lasting improvements in clinical outcomes. Thus, the purpose of this study was to evaluate the effect of a multi-component intervention on glycemic control, clinic attendance, and diabetes distress amongst adolescents with type 1 diabetes transitioning to adult health services. Design: Prospective controlled quasi-experimental study. Setting: Adolescents with type 1 diabetes from an urban academic pediatric hospital (control group) and a community regional hospital (intervention group) were recruited and followed for 1 year after their last pediatric diabetes visit. Participants: 101 adolescents with type 1 diabetes transitioning to adult care, including 68 from the control group and 33 from the intervention group. Interventions: The intervention group had access to (1) a diabetes nurse transition coordinator, (2) joint pediatric-adult diabetes clinic visits, and (3) pediatric and adult clinics being in the same building. Those in the control group were referred to an adult diabetes provider at their last pediatric diabetes visit without any formal transition program or additional supports. Primary and secondary outcome measures: The primary outcome was longitudinal change in A1C. The secondary outcomes were number of A1C tests obtained, number of adult diabetes visits attended, time gap between pediatric and adult visits, and diabetes distress. Results: There was a difference in A1C trajectory between the control and intervention groups (base model p=0.004, adjusted model p=0.003). A1C continued to rise in the control group after the transition to adult care, whereas A1C decreased in the intervention group. However, there were no statistically significant differences in the secondary outcomes between the two groups. Conclusion: A multi-component intervention can mitigate the glycemic excursions experienced by adolescents with type 1 diabetes transitioning to adult care.
DOI: 10.5683/sp2/q8aone
title: Incomplete reproductive isolation and strong transcriptomic signature of hybridization between sympatric sister species of salmon

description: AbstractGlobal change is altering ecosystems at an unprecedented rate. The resulting shifts in species ranges and reproductive timing are opening the potential for hybridization between closely-related species which could dramatically alter the genetic diversity, adaptive capacity, and evolutionary trajectory of interbreeding taxa. Here, we used behavioural breeding experiments, in vitro fertilization experiments, and whole-transcriptome gene expression data to assess the potential for and consequences of hybridization between Chinook and Coho salmon. We show that behavioural and gametic prezygotic barriers between socioeconomically valuable Chinook and Coho salmon are incomplete. Postzygotically, we demonstrate a clear transcriptomic response to hybridization among F1 Chinook-Coho offspring. Genes transgressively expressed within hybrids were significantly enriched with genes encoded in the nucleus but localized to the mitochindrion, suggesting a potential role for mito-nuclear incompatibilities as a postzygotic mechanism of hybrid breakdown. Chinook and Coho salmon are expected to continue to respond to climate change with shifts in migration timing and habitat use, potentiating hybridization between these species. The downstream consequences of hybridization on the future of these threatened salmon, and the ecosystems they inhabit, is unknown.
DOI: 10.5683/sp2/mwmvux
title: Data from: Forecasting the cumulative effects of multiple stressors on breeding habitat for a steeply declining aerial insectivorous songbird, the olive-sided flycatcher (Contopus cooperi)

description: AbstractTo halt ongoing loss in biodiversity, there is a need for landscape-level management recommendations that address cumulative impacts of anthropogenic and natural disturbances on wildlife habitat. We examined the cumulative effects of logging, roads, land-use change, fire, and bark beetle outbreaks on future habitat for olive-sided flycatcher (Contopus cooperi), a steeply declining aerial insectivorous songbird, in Canada's western boreal forest. To predict the occurrence of olive-sided flycatcher we developed a suite of habitat suitability models using point count surveys (1997–2011) spatially- and temporally-matched with forest inventory data. Flycatcher occurrence was positively associated with small (~10 ha) 10–20-year-old clearcuts, and with 10–100% tree mortality due to mountain pine beetle (Dendroctonus ponderosae) outbreaks, but we found no association with roads or distance to water. We used the parameter estimates from the best-fit habitat suitability models to inform spatially explicit state-and-transition simulation models to project change in habitat availability from 2020 to 2050 under six alternative scenarios (three management × two fire alternatives). The simulation models projected that the cumulative effects of land use conversion, forest harvesting, and fire will reduce the area of olive-sided flycatcher habitat by 16–18% under Business As Usual management scenarios and by 11–13% under scenarios that include protection of 30% of the land base. Scenarios limiting the size of all clearcuts to ≤ 10 ha resulted in a median habitat loss of 4–6%, but projections were highly variable. Under all three management alternatives, a 50% increase in fire frequency (expected due to climate change) exacerbated habitat loss. The projected losses of habitat in western boreal forest, even with an increase in protected areas, imply that reversing the ongoing population declines of olive-sided flycatcher and other migratory birds will require attention to forest management beyond protected areas. Further work should examine the effects of multiple stressors on the demographic mechanisms driving change in aerial insectivore populations, including stressors on the wintering grounds in South America, and should aim to adapt the design of protected areas and forest management policies to projected climate-driven increases in the size and frequency of wildfires.