cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.98sf7m0hr
title: Relative influences of microhabitat incubation conditions and genetic parentage effects on lake sturgeon (Acipenser fulvescens) offspring traits during early ontogeny (DATA)

description: Knowledge on factors influencing traits during critical early growth
 periods is essential for predicting population persistence. Genetic
 effects and microhabitat stream conditions at female selected oviposition
 sites influence larval phenotypes. However, limited work has examined
 contributions of both factors across sequential ontogenetic stages for
 larvae of wild origin. Using a wild population of lake sturgeon (Acipenser
 fulvescens) from Black Lake, Michigan (USA), fertilized eggs were
 collected from stream substrate just prior to hatch at one-meter intervals
 along seven transect lines at an adult-selected spawning area.
 Microhabitat variables (depth, discharge, substrate size) were recorded at
 egg collection points. Body length, body area, and yolk-sac area were
 quantified for yolk-sac larvae (N = 359) at the time of hatch.
 Following the onset of exogenous feeding, larval growth was measured
 weekly for four weeks. Parentage was assigned using genetic-based
 analysis. Inter-individual variation in phenotypic traits quantified at
 hatch were attributed to stream microhabitat variables; mean depth had the
 largest influence. No additive genetic effects were detected at hatch.
 Post-emergence larval growth significantly varied within and among
 half-sibling groups with the greatest range in body size observed at
 33 days post-hatch. Additive genetic variance and heritability
 increased with age. Results demonstrate that female-selected incubation
 habitats influenced traits at hatch for wild-origin fish, but effects do
 not persist to a sequential ontogenetic stage. Alternatively, growth after
 the onset of exogenous feeding was largely influenced by intrinsic
 (genetic) factors which must be considered when designing and implementing
 rehabilitation strategies for lake sturgeon and potentially other
 threatened riverine fishes.
description: Data was collected at the Black River located in the state of
 Michigan. See manuscript for further details.
DOI: 10.5061/dryad.1rn8pk0sq
title: Postcopulatory sexual selection as a driver of sex- and population-specific kidney mass in garter snakes?

description: In lizards and snakes, the kidneys produce seminal fluid in addition to
 having osmoregulatory functions. Therefore, in response to polyandry,
 kidney mass should be under selection regimes like those influencing
 testes. Male red-sided garter snakes deposit a kidney-derived copulatory
 plug that functions in sperm competition. We first tested for intersexual
 differences in kidney mass and allometry in one population and found that
 males had kidneys twice as heavy as those of females, consistent with
 stronger selection on male kidney mass. Previous studies have shown that
 male size enhances mating success in one-on-one competition prevalent in
 small mating aggregations. We then examined the relationship between body
 size, kidney mass, and testes mass in two populations with low (LD) and
 high (HD) mating aggregation densities. Males from the HD population had
 heavier testes and heavier kidneys than did males from the LD population;
 HD males were also smaller in body size. Our results suggest that the
 strength of sexual selection, and possibly the balance between pre- and
 postcopulatory selection, varies in response to population size or
 density. However, more replication is needed to confirm the generality of
 these results within red-sided garter snakes and other squamate reptiles.
DOI: 10.5061/dryad.d7wm37q0v
title: Developmental change in predators drives different community configurations

description: Theoreticians who first observed alternative stable states in simple
 ecological models warned of grave implications for unexpected and
 irreversible collapses of natural systems (i.e., regime shifts). Recent
 ecosystem-level shifts engendering considerable economic losses have
 validated this concern, positioning bistability at the vanguard of coupled
 human-environment systems management. While the perturbations that induce
 regime shifts are known, the ecological forces that uphold alternative
 stable states are often unresolved or complex and system-specific. Thus,
 the search continues for general mechanisms that can produce alternative
 stable states under realistic conditions. Integrating model predictions
 with long-term zooplankton community experiments, we show that the core
 feature of ontogenetic development, food-dependent maturation, enables a
 single community to reach different configurations within the same
 constant environment. In one configuration, predators regulate prey to
 foster coexistence, while in the other, prey counterintuitively exclude
 their predator via maturation-limiting competition. The concordance of
 these findings with the unique outcome and underlying mechanism of a
 general model provides empirical evidence that developmental change, a
 fundamental property of life, can support bistability of natural systems.
description: See ReadMe file (Toscano_Rudolf_longterm_zooplankton_readme.txt)
 and the manuscript resulting from this data set.
description: See ReadMe file (Toscano_Rudolf_longterm_zooplankton_readme.txt)
 and the manuscript resulting from this data set.
DOI: 10.6086/d1c39x
title: Data from: Rapid nitrate reduction produces pulsed NO and N2O emissions following wetting of dryland soils

description: Soil drying and wetting cycles can produce pulses of nitric oxide (NO) and
 nitrous oxide (N2O) emissions with substantial effects on both regional
 air quality and Earth’s climate. While pulsed production of N emissions is
 ubiquitous across ecosystems, the processes governing pulse magnitude and
 timing remain unclear. We studied the processes producing pulsed NO and
 N2O emissions at two contrasting drylands, desert and chaparral, where
 despite the hot and dry conditions known to limit biological processes,
 some of the highest NO and N2O flux rates have been measured. We measured
 N2O and NO emissions every 30 minutes for 24 hours after wetting soils
 with isotopically-enriched nitrate and ammonium solutions to determine
 production pathways. Nitrate was reduced to N2O within 15 minutes of
 wetting, with emissions exceeding 1000 ng N-N2O m-2 s-1 and returning to
 background levels within four hours, but the pulse magnitude did not
 increase in proportion to the amount of ammonium or nitrate added. In
 contrast to N2O, NO was emitted over 24 hours and increased in proportion
 to ammonium addition, exceeding 600 ng N-NO m-2 s-1 in both desert and
 chaparral soils. Nitrogen and oxygen isotopes suggest nitrifier
 denitrification and nitrate reduction produced NO. Taken together, our
 measurements demonstrate that rapid nitrate reduction following wetting
 dry soils produces large pulsed N2O emissions, and that both
 denitrification and nitrifier denitrification contribute to longer lasting
 NO emissions. These mechanisms are substantial pathways of ecosystem N
 loss that also contribute to regional air quality and global climate
 dynamics.
description: Please see ReadMe file as well as methods section in the
 manucript.
DOI: 10.5061/dryad.k6djh9w5n
title: Epigenetic regulation of the autonomous pathway mediates the flowering of Arabidopsis thaliana

description: Studies have shown that plant flowering time is affected by endogenous and
 exogenous factors, but the role of DNA methylation in flowering still
 remains unclear. Here, 27 Arabidopsis thaliana populations were used to
 determine how autonomous pathway gene methylation affects flowering
 differences by regulating gene expression patterns. DNA methylation
 analysis, qPCR and transgenic verification were performed. The flowering
 time of the Arabidopsis populations ranged from 19 to 55 days. Methylation
 of the coding regions of six upstream genes in the autonomous pathway,
 FVE, FY, FLD, PEP, HDA5 and PPR 39-1, was significantly correlated with
 flowering time and relative expression levels (P &lt; 0.05).
 Expression of FVE and FVE(CS) separately through codon degeneracy
 substitution (resulting in a reduction in cytosine) led to early flowering
 (by 8 days and 25 days, respectively). The flowering times of the FVE and
 FVE(CS) transgenic plants and the Col-0 plants were associated with the
 number of methylated sites of FVE and FVE(CS), resulting in the
 differential expression of FVE and FVE(CS). Our findings suggest that the
 methylation of six key upstream transcription factors of the autonomous
 pathway in Arabidopsis regulates the expression level of these genes,
 leading to phenotypic differences in flowering.
DOI: 10.5061/dryad.wpzgmsbmc
title: Geographic homogenization but little net change in the local richness of Canadian butterflies

description: Aim: Recent studies have found that local-scale plots measured through
 time exhibit marked variation in the change in species richness. However,
 the overall effect often reveals no net change. Most studies thus far have
 been agnostic about the identities of the species lost/gained, as well as
 the processes that may lead to these changes. Generalist traits may be
 crucial in allowing species to colonize new plots or remain resilient in
 situ, whereas environmental filtering may remove specialists. We test
 whether plots are changing in species richness, whether they are becoming
 more similar (i.e. becoming homogenized) through time, as well as whether
 several generalist traits can predict gains or losses from local plots.
 Location: Canada Time period: 1945-2015 Major taxa studied: 265 species of
 butterflies Methods: We measured i. species richness change and ii.
 pairwise beta diversity across 96 well-sampled 10x10 km plots across
 Canada between two time periods: 1945-1975 and 1985-2015. We looked at the
 effects of wingspan, mobility, diet breadth and range size on the number
 of grid cells each species gained and lost between time periods. Results:
 We observed a slight increase in plot-level species richness, and that
 these communities are becoming homogenized through time. We note that most
 butterfly species in Canada have large North American ranges, but the
 widest-ranged species are better able to colonize new plots than
 narrower-ranged species, but also experience higher frequencies of local
 extinctions. In sum, the median range size of species within a plot
 increased through time. Main conclusions: We highlight that, even when
 local species richness exhibits very little change, other potentially
 important biodiversity changes, such as geographic homogenization due to
 the colonization dynamics of already widely distributed species, can
 occur. Such patterns can reconcile observed global losses of species with
 the simultaneous lack of change in local diversity.
DOI: 10.5061/dryad.bg79cnp9j
title: Evolutionary effects of geographic and climatic isolation between Rhododendron tsusiophyllum populations on the Izu Islands and mainland Honshu of Japan

description: Geographic and environmental isolations of islands and the mainland offer
 excellent opportunity to investigate colonization and survival dynamics of
 island populations. We inferred and compared evolutionary processes and
 the demographic history of Rhododendron tsusiophyllum, in the Izu Islands
 and the much larger island Honshu, treated here as the mainland, using
 thousands of nuclear SNPs obtained by ddRAD-seq from eight populations of
 R. tsusiophyllum and three populations of R. tschonoskii as an outgroup.
 Phylogenetic relationships and their habitats suggest that R.
 tsusiophyllum had evolved and migrated from cold north to warm south
 regions. We detected clear genetic divergence among populations in three
 regions of Honshu and the Izu Islands, suggesting restricted migration
 between them due to isolated habitats on mountains even in the mainland.
 The three regions have different changes in effective population size,
 especially, genetic diversity and population size of the Izu Islands are
 small compared to the others. Further, habitats of populations in the Izu
 Islands are warmer than those in Honshu, suggesting that they have
 undergone adaptive evolution. Our study provides evidences of montane
 rather than insular isolation on genetic divergence, survival of
 populations and significance of adaptive evolution for island populations
 with small population size and low genetic diversity, despite close
 proximity to mainland populations.
DOI: 10.5061/dryad.9ghx3ffgj
title: Persistence of tropical herbivores in temperate reefs constrain kelp resilience to cryptic habitats

description: 1. Global warming is facilitating the range-expansion of tropical
 herbivores, causing a tropicalization of temperate marine ecosystems,
 where tropical herbivores can suppress habitat-forming macrophytes,
 supporting the resilience of canopy-free ecosystem states. However,
 currently we lack a thorough understanding of the mechanisms that, on one
 hand, support the persistence of tropical herbivores and on the other
 support the recovery of temperate foundation species in tropicalized
 ecosystems, a required knowledge to predict potential regime-shifts and
 reversals to the baseline state of the ecosystem. 2. This study tested
 processes behind the persistence of the tropicalization of temperate reefs
 which experienced a complete loss of their kelp forests and an influx of
 tropical herbivores following a marine heatwave in 2011. For this, we
 assessed the feedback mechanisms that maintain turf-dominated states
 (recruitment of tropical herbivores, browsing and grazing rates and turf
 cover) and those that resist it (kelp recruitment, survival, and
 reproductiveness). 3. We found that the reefs remained tropicalized with
 high cover of turf and high abundance of tropical herbivores after nine
 years from the regime shift. The most important herbivores, the rabbitfish
 Siganus fuscescens and the chub Kyphosus bigibbus, persisted with high
 abundances. This was supported by the adjacent reef lagoon, where seagrass
 meadows and the backreef habitats hosted juveniles of both species,
 particularly rabbitfish. Tropical herbivores exerted a strong top-down
 control on turf seaweed and kelp during herbivory assays, rapidly
 consuming kelp individuals in open areas. However, in topographical
 refuges in the reefs, herbivory was low and we found kelp individuals that
 had re-established, with some having reproductive tissue. 4. Synthesis.
 Our findings incorporate the importance of nursery grounds for tropical
 herbivores and herbivory refugia for kelp individuals into the
 tropicalization model, where the former increases the resilience of
 canopy-free states and the latter might facilitate recovering kelp
 populations. The restoration of abundant warm-resistant kelp populations
 in shelters could provide local sources of propagules to recolonize open
 spaces, however, our results suggest that the reduction of herbivory and
 the provision of turf-free substratum would be necessary to boost the
 recovery of kelp forests.
DOI: 10.5061/dryad.stqjq2c2r
title: Complex reticulate evolution of the speckled brush-furred rats (Lophuromys) in the Ethiopian centre of endemism

description: The Ethiopian highlands represent a remarkable biodiversity “hotspot” with
 a very high number of endemic species, even among vertebrates.
 Ethiopian representatives of a species complex of speckled brush-furred
 rats (Lophuromys flavopunctatus sensu
 lato) inhabit highland habitats ranging from low-elevation
 forests to Afroalpine grasslands. These may serve as a suitable model for
 understanding evolutionary processes leading to high genetic and
 ecological diversity in montane biodiversity hot-spots. Here, we analyze
 the most comprehensive genetic dataset of this group, comprising 315
 specimens (all nine putative Ethiopian Lophuromys taxa
 sampled acrysross most of their distribution ranges) genotyped at one
 mitochondrial and four nuclear markers, and thousands of SNPs from ddRAD
 sequencing. We performed phylogenetic analyses, delimited species and
 mapped their distribution
 and estimated  divergence time between species
 (under the species-tree framework) and mitochondrial lineages. We found
 significant incongruence between mitochondrial and nuclear phylogenies,
 most likely caused by multiple interspecific introgression events. We
 discuss alternative scenarios of
 Ethiopian Lophuromys evolution, from retention of
 ancestral polymorphism to hybridization upon secondary contact of
 partially reproductively isolated lineages leading to reticulate
 evolution. Finally, we use the diversity of the speckled brush-furred rats
 for the description of the main biogeographic patterns in the
 Ethiopian highland’s fauna.  
description: The files contain pair-end reads that were submitted to ipyrad
 (Eaton & Overcast, 2020) for denovo assembly of ddRAD loci. The
 reads were demultiplexed and barcodes removed in Skewer (Jiang, Lei, Ding
 & Zhu, 2014) and pre-processing of read ends in PEAR (Zhang,
 Kobert, Flouri & Stamatakis, 2014). Every pair of reads was merged
 (with minimum required overlap of 10 nucleotides) and cut in two halves.
 If they were not successfully merged, we trimmed off the last 10
 nucleotides from the reverse read. The PEAR-treatment was necessary to
 avoid poor quality mergers in a substantial proportion of loci.
 References: Eaton, D. A. R., &
 Overcast, I. (2020). ipyrad: Interactive assembly and analysis of RADseq
 datasets. Bioinformatics, 36(8), 2592–2594. doi:
 10.1093/bioinformatics/btz966<br> Jiang, H., Lei, R., Ding, S. W.,
 & Zhu, S. (2014). Skewer: a fast and accurate adapter trimmer for
 next-generation sequencing paired-end reads. BMC Bioinformatics, 15(1),
 182. doi: 10.1186/1471-2105-15-182<br> Zhang, J., Kobert, K.,
 Flouri, T., & Stamatakis, A. (2014). PEAR: a fast and accurate
 Illumina Paired-End reAd mergeR. Bioinformatics, 30(5), 614-20. doi:
 10.1093/bioinformatics/btt593
DOI: 10.15468/dl.sg5vd5
title: Occurrence Download

description: A dataset containing 828 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dermatophyllum secundiflorum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 828 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002775-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5mkkwh74z
title: Competition and facilitation among fungal plant parasites affect their life-history traits

description: Multi-infections may result in either competitive exclusion or coexistence
 on the same host of pathogen genotypes belonging to the same or different
 species. Epidemiological consequences of multiple infections, particularly
 how the development and transmission of a pathogen can be modified by the
 presence of another pathogen, are well documented. However, understanding
 how life history strategies of each pathogen modulate co-infection
 outcomes remains quite elusive. To analyze how co-infection drives changes
 in life history traits and affects co-existence in epidemic pathogens, we
 infected detached pea stipules with two fungal species, Peyronellaea
 pinodes and Phoma medicaginis var. pinodella (considering 2 strains per
 species), part of the ascochyta blight complex but presenting different
 life history strategies. All pairwise combinations (including self-pairs)
 between two strains of each species were tested. Strains were inoculated
 simultaneously, but apart from one another on the stipule. For each
 strain, four life history traits were measured: incubation period,
 necrosis area 6 days after inoculation, latent period and offspring
 production. Results show that, in co-infection, when resources are highly
 allocated to lesion development, the time between inoculation and the
 appearance of reproduction structures (latent period) and offspring
 production decreased, and vice -versa relative to single infections. The
 direction and/or magnitude of these responses to co-infection depend on
 the co-infecting strains. Moreover, these changes were always higher in
 self-pairs than in mixed co-infections. These results suggest facilitation
 between co-infecting strains, resulting in the selection of an
 intermediate level of virulence (here measured as the lesion development)
 at the expense of pathogen offspring production. This strategy allows the
 development and reproduction of each co-infecting strain when sharing
 limited resources. However, the direction and strength of these life
 history traits variations in co-infection depend on the life history
 strategy of the co-infecting strains, with a clear difference between
 ‘opportunists’, ‘scavengers’ and ‘pioneer colonisers’.
DOI: 10.5061/dryad.ns1rn8ps3
title: Why aren’t rabbits and hares larger?

description: Macroevolutionary consequences of competition among large clades have long
 been sought in patterns of lineage diversification. However,
 mechanistically clear examples of such effects remain elusive. Here we
 postulated that the limited phenotypic diversity and insular gigantism in
 lagomorphs could be explained at least in part by an evolutionary
 constraint placed on them by potentially-competing ungulate-type
 herbivores (UTHs). Our analyses yielded three independent lines of
 evidence supporting this hypothesis: (1) the minimum UTH body mass is the
 most influential predictor of the maximum lagomorph body mass in modern
 ecoregions; (2) the scaling patterns of local-population energy use
 suggest universal competitive disadvantage of lagomorphs weighing over
 ~6.3 kg against artiodactyls, closely matching their observed upper size
 limit in continental settings; and (3) the trajectory of maximum lagomorph
 body mass in North America from the late Eocene to the Pleistocene
 (37.5–1.5 Ma) was best modeled by the body mass ceiling placed by the
 smallest contemporary perissodactyl or artiodactyl. Body size evolution in
 lagomorphs has likely been regulated by the conflicting forces of
 competition within the clade, increased predation in open habitats, and
 importantly, competition from other ungulate-type herbivores. Our finding
 highlights the conditionally-coupled dynamics of phenotypic boundaries
 within an adaptive zone, offering a complementary, if nuanced, perspective
 to Van Valen’s Red Queen hypothesis.