cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3j9kd51kw
title: Lagged effects of herbivory impact host-choice but not nymphal survivorship in an ant-protected treehopper

description: Theoretical studies have shown that in protection mutualism, modification
 of top-down control by protectors may be destabilizing. Central to this
 prediction are the assumptions that 1) protection mutualism increases the
 abundance of protected partners, 2) this increased abundance generates a
 lagged effect on partner resources, and 3) spatial dynamics can be
 ignored. Although a number of studies have confirmed that protection
 mutualism can increase the abundance of protected herbivores, the evidence
 for a negative effect of protected herbivores on plant quality is mixed,
 and we are unaware of any studies that have explored the effect of
 protected herbivores on plant quality across growing seasons. Here, we use
 the protection mutualism between ants and the treehopper Publilia concava
 to evaluate the assumption that treehopper herbivory has a lagged effect
 on plant quality. We also evaluated whether ant-protection exacerbated the
 negative effect of treehoppers on their host plants. We used a two-way
 factorial design that manipulated ant and treehopper presence on goldenrod
 host plants in one year, and assessed oviposition and survivorship on
 those same plants in the subsequent year. Treehopper herbivory was
 associated with a decrease in the probability of oviposition and female
 treehoppers laid significantly fewer egg masses on plants that had been
 fed on the previous year, regardless of ant-tending. In contrast, a prior
 history of herbivory had no impact on future treehopper performance as
 measured by nymph survival. Ant tending increased treehopper abundance and
 exacerbated the risk of plant mortality but otherwise did not
 significantly modify the negative effect of treehopper herbivory on plant
 quality or future treehopper performance. Although the increase in
 treehopper abundance associated with ant-tending and the lagged
 oviposition response of treehoppers is consistent with the core
 assumptions of a model showing that mutualism can be destabilizing, the
 avoidance of previously occupied plants for oviposition is not. These
 results highlight the importance of future modeling studies that explore
 spatiotemporal dynamics in protection mutualism, and long-term field
 studies that track the effect of mutualism across years.
DOI: 10.5061/dryad.7pvmcvdvk
title: Palaeoecological data of KTG core, Katingan, Central Kalimantan, Borneo, Indonesia

description: Southeast Asian peatlands, along with their various important ecosystem
 services, are mainly distributed in the coastal areas of Sumatra and
 Borneo. These ecosystems are threatened by coastal development, global
 warming and sea level rise (SLR). Despite receiving growing attention for
 their biodiversity and as massive carbon stores, there is still a lack of
 knowledge on how they initiated and evolved over time, and how they
 responded to past environmental change, i.e., precipitation, sea level and
 early anthropogenic activities. To improve our understanding thereof, we
 conducted multi-proxy palaeoecological studies in the Kampar Peninsula and
 Katingan peatlands in the coastal area of Riau and Central Kalimantan,
 Indonesia. The results indicate that the initiation timing and environment
 of both peatlands are very distinct, suggesting that peat could form under
 various vegetation as soon as there is sufficient moisture to limit
 organic matter decomposition. The past dynamics of both peatlands were
 mainly attributable to natural drivers, while anthropogenic activities
 were hardly relevant. Changes in precipitation and sea level led to shifts
 in peat swamp forest vegetation, peat accumulation rates, and fire regimes
 at both sites. We infer that the simultaneous occurrence of El
 Niño-Southern Oscillation (ENSO) events and SLR resulted in synergistic
 effects which led to the occurrenceere fires in a pristine coastal
 peatland ecosystem, however, it did not interrupt peat accretion. In the
 future, SLR, combined with the projected increase in frequency and
 intensity of ENSO, can potentially amplify the negative effects of
 anthropogenic peatland fires. This prospectively stimulates massive carbon
 release, thus could, in turn, contribute to worsening the global climate
 crisis especially once an as yet unknown threshold is crossed and peat
 accretion is halted, i.e., peatlands lose their carbon sink function.
 Given the current rapid SLR, coastal peatland managements should start
 develop fire risk reduction or mitigation strategies.
description: The investigation including pollen and spore, loss-on-ignition,
 total organic carbon, stable carbon isotope and micro- and macrocharcoal
 was carried out on a peat core collected from coastal area in southern
 Borneo. Pollen, spore and charcoal extraction and
 identification, as well as Loss-On-Igntition analysis were conducted at
 the Dept. Palynology and Climate Dynamics, University of
 Goettingen. Organic carbon content and isotopes were
 determined in Euro EA3000 elemental analyzer and Thermo Finnigan Delta
 Plus mass spectrometer, respectively, at the Leibniz Centre for Tropical
 Marine Research (ZMT), Bremen.
description: Fossil pollen and spore are in
 counts.
DOI: 10.5061/dryad.sf7m0cg7z
title: Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population

description: Interest in the genetic basis of variation in skin pigmentation in Native
 American populations led us to seek indigenous populations of the Western
 Hemisphere with African and minimal European admixture to study the effect
 of Native American ancestry on skin color. Admixture analysis from DNA
 collected from 458 individuals in the Kalinago territory of the
 Commonwealth of Dominica showed shared ancestry with East Asians at K=3
 and 55% Native American, 32% African, and 11% European ancestry at K=6,
 the highest Native American ancestry of Caribbean populations. Skin
 pigmentation was 20 to 80 melanin units, averaging 46. Three albino
 individuals were homozygous for multi-nucleotide polymorphism OCA2NW273KV
 of African origin, whose population allele frequency was 0.03 and single
 allele effect size was -8 melanin units. Hypopigmenting allele frequencies
 for SLC24A5A111T and SLC45A2L374F were 0.14 and 0.05, whose single allele
 effect sizes were -6 and -3, respectively. Skin color plots of individuals
 lacking known hypopigmenting alleles suggests that Native American
 Ancestry reduced pigmentation by more than 20 melanin units (low and high
 estimates 21.8 and 28.5). Shared ancestry with East Asians at K=3 suggests
 potential sharing of one or more pigmentation alleles.
description:  Saliva samples were collected after consents were given. Skin
 color measurement was collected by measuring the inner arm of the
 participants.
DOI: 10.5061/dryad.ngf1vhhw7
title: Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral

description: Dinoflagellates are a diverse group of protists that possess many unique
 traits. These include (but are not limited to) expansive genomes packaged
 into permanently condensed chromosomes, photosynthetic or cryptic plastids
 acquired vertically or horizontally in serial endosymbioses, and a
 ruffle-like transverse flagellum attached along its length to the cell.
 When reconstructing character evolution, early branching lineages with
 unusual features that distinguish them from the rest of the group have
 proven useful for inferring ancestral states. The Noctilucales are one
 such lineage, possessing relaxed chromosomes in some life stages and a
 trailing, thread-like transverse flagellum. However, most of the cellular
 and molecular data for the entire group come from a single cultured
 species, Noctiluca scintillans, and because its phylogenetic position is
 unresolved, it remains unclear if these traits are ancestral or derived.
 Here, we use single cell transcriptomics to characterize three diverse
 Noctilucales genera: Spatulodinium, Kofoidinium, and a new lineage,
 Fabadinium gen. nov. We also provide transcriptomes for undescribed
 species in Amphidinium and Abediniales, critical taxa for clarifying the
 phylogenetic position of Noctilucales. Phylogenomic analyses suggest that
 the Noctilucales are sister to Amphidinium rather than an independent
 branch outside the core dinoflagellates. This topology is consistent with
 observations of shared characteristics between some members of
 Noctilucales and Amphidinium and provides the most compelling evidence to
 date that the unusual traits within this group are derived rather than
 ancestral. We also confirm that Spatulodinium plastids are photosynthetic
 and of ancestral origin, and show that all non-photosynthetic Noctilucales
 retain plastid genes indicating a cryptic organelle.
DOI: 10.5061/dryad.2280gb5tv
title: Out of the temperate zone: a phylogenomic test of the biogeographical conservatism hypothesis in a contrarian clade of ants (Hymenoptera: Formicidae: Stenammini)

description: Aim: The standard latitudinal diversity gradient (LDG), in which
 species richness decreases from equator to pole, is a pervasive pattern
 observed in most organisms. Some lineages, however, exhibit inverse LDGs.
 Seemingly problematic, documenting and studying contrarian groups can
 advance understanding of LDGs generally. Here, we identify the ant tribe
 Stenammini as a contrarian clade and use a historical approach to evaluate
 alternative hypotheses that might explain the group’s atypical diversity
 pattern. We focus on the biogeographical conservatism hypothesis (BCH) and
 the diversification rate hypothesis (DRH). Location: Global.
 Taxon: Ants. Methods: We examined the shape of the LDG
 in Stenammini by plotting latitudinal midpoints for all described, extant
 species. We then inferred a genome-scale phylogeny and used the tree to
 estimate divergence dates and ancestral areas. We also examined
 diversification rate heterogeneity across the tree and tested for a
 correlation between rate and latitude. Results: Stenammini has a
 skewed inverse LDG with a richness peak in the northern temperate zone.
 Phylogenomic analyses revealed five major clades and several instances of
 non-monophyly among genera (Goniomma, Aphaenogaster). Stenammini
 and all its major lineages arose in the northern temperate zone. The tribe
 originated ~51 Ma during a climatic optimum and then diversified and
 dispersed southward as global climate cooled. Stenammini invaded the
 tropics at least seven times, but these events occurred more recently and
 were not linked with increased diversification. There is evidence for a
 diversification rate increase in
 Holarctic Aphaenogaster + Messor, but we found
 no significant correlation between latitude and diversification rate
 generally. Main Conclusions: Our results largely support the BCH
 as an explanation for the inverse latitudinal gradient in Stenammini. The
 clade originated in the Holarctic and likely became more diverse there due
 to the combined effects of center-of-origin, time-for-speciation, and
 niche conservatism, rather than latitudinal differences in diversification
 rate.
DOI: 10.5061/dryad.4tmpg4fbw
title: Plasticity in floral longevity and sex-phase duration of Lobelia siphilitica in response to simulated pollinator declines

description: Premise: Pollinator declines can reduce the quantity and quality of
 pollination services, resulting in less pollen deposited on flowers and
 lower seed production by plants. In response to these reductions, plants
 can increase the opportunity for pollination by plastically adjusting
 their floral traits, including floral longevity and sex-phase duration.
 However, studies of plant responses to pollinator declines have primarily
 focused on floral evolution across generations rather than plasticity in
 floral traits within a generation. Methods: To test whether plants can
 respond to pollinator declines by plastically adjusting their floral
 traits, we simulated declines by experimentally reducing pollinator access
 to Lobelia siphilitica plants, and measuring floral longevity and male-
 and female-phase duration. We also measured daily display size and
 phenotypic gender to test whether plasticity in floral longevity and
 sex-phase duration affected inflorescence traits. Results: We found that
 experimentally reducing pollination extended the male-phase duration of
 early-season flowers and the longevity of late-season flowers. However,
 plants with an extended male phase did not have a more male-biased
 phenotypic gender, and plants with an extended floral longevity did not
 have a larger daily display. Conclusions: Our results suggest that L .
 siphilitica plants can respond to pollinator declines by plastically
 adjusting both the longevity and sex-phase duration of their flowers.
 Consequently, plasticity in floral traits could be one mechanism by which
 plants respond to decreases in pollination services caused by pollinator
 declines.
description: A ReadMe file is attached.
DOI: 10.5061/dryad.8kprr4xqf
title: Data from: Price equations for understanding the response of ecosystem function to community change

description: Biodiversity-ecosystem function research in natural ecosystems would
 benefit from new theoretical and analytical tools that match common
 characteristics of observational community data. To this end, we developed
 a novel, abundance-based version of the ecological Price equation in both
 discrete and continuous forms. As part of the presentation of this new
 method, we conducted two demonstration analyses. The first analysis
 focuses on pollination of watermelon by wild bees. We net-collected wild
 pollinator specimens from standard areas of flowering watermelon crop at
 16 replicated farms in 2012. We also measured how many pollen grains each
 bee species deposited per visit. These per-visit pollen deposition rates
 were estimated as a genus-level property, as is common for landscape
 pollination studies. To determine total pollination for each bee species
 at each site, we multiplied pollinator visitation rates and per-visit
 pollen deposition. The attached data includes site by species matrices for
 the abundance (watermelon_com.csv) and per-capita pollen deposition
 (watermelon_fun.csv) of bee species. The second analysis focuses on
 changes in total community biomass of stream invertebrates collected from
 25 sites along a strong, continuous pollution gradient. These data were
 previously published by Pomeranz et al. (2019), accessible at the Dryad
 link given below. Specimens were individually measured and assigned to one
 of six functional groups. Finer taxonomic resolution is available in the
 original study, but we use functional groups here to get enough data to
 effectively model. The attached data includes site by functional group
 matrices for the abundance (stream_inverts.csv) and per-capita biomass
 (stream_invert_size.csv) of stream invertebrate functional groups, and a
 third .csv which describes the level of pollution at each site
 (steam_data.csv). The code is a single R code file which produces the
 results and figures found in the manuscript. We have also included a
 README and several .csv files (those described above) that need to be read
 in. These data may be useful for other analyses of variation in ecosystem
 function across sites. We stress that the stream invertebrate data were
 collected by Pomeranz et al. (2019) and they should be cited for any use
 those data. The relevant link to access their data is:
 https://datadryad.org/stash/dataset/doi:10.5061/dryad.v6g985s
description: No new data collection. See the main manuscript for details of
 where data were obtained.
description: Using the code and data should be mostly self-explanatory. Please
 contact the author if needed.
DOI: 10.5061/dryad.qnk98sfjk
title: Data from: Evidence of low within-pair genetic relatedness in a relict population of Thorn-tailed Rayadito despite long-term isolation

description: Investigating whether mating patterns are biased in relation to kinship in
 isolated populations can provide a better understanding of the occurrence
 of inbreeding avoidance mechanisms in wild populations. Here we report on
 the genetic relatedness (r) among breeding pairs in a relict population of
 Thorn-tailed Rayadito (Aphrastura spinicauda) in north-central Chile that
 has experienced a long-term history of isolation. We used simulations
 based on eight years of data to assess whether mating is random with
 respect to relatedness. We found that mean and median population values of
 pair relatedness tended to be lower than randomly generated values,
 suggesting that mating is not random with respect to kinship. We
 hypothesize that female-biased dispersal is the main mechanism reducing
 the likelihood of mating among kin, and that the proportion of related
 pairs (i.e., r &gt; 0.125) in the study population (25%) would
 presumably be higher in the absence of sex-biased dispersal. The
 occurrence of other mechanisms such as extra-pair copulations, delayed
 breeding and active inbreeding avoidance through kin discrimination cannot
 be dismissed and require further study.
description: All instructions regarding the dataset can be found in the
 ReadMe.txt file. Code for replicating all analyses is provided in the
 RelatedScript.txt and SimulationsScript.txt files.
DOI: 10.5061/dryad.jm63xsjct
title: Leaf, stem, and root stable carbon isotope ratios and gas exchange data for 452 plants

description: This dataset contains a compilation of stable carbon isotope ratios in
 leaves, stems, and roots for tree saplings and associated gas exchange
 data. It was used in a book chapter to test whether the relationship
 between carbon isotope discrimination and the ratio of intercellular to
 ambient carbon dioxide concentrations differs between leaves and woody
 tissues. The book chapter is entitled 'Carbon isotope effects in
 relation to CO2 assimilation by tree canopies' authored by Lucas A.
 Cernusak and Nerea Ubierna. It is part of the book entitled 'Stable
 Isotopes in Tree Rings' edited by Rolf T. Siegwolf, J. Renee Brooks,
 John Roden, and Matthias Saurer. The publisher of the book is Springer
 International Publishing, with publication in April 2022.
description: Plants were grown from seed in a variety of conditions until the
 sapling stage. At sapling stage, gas exchange was measured on several
 leaves for each plant using a LiCor 6400 portable photosynthesis system,
 and averaged for each plant. Plants were then harvested, oven dried,
 ground to a fine powder, and stable carbon isotope ratios measured for
 leaves, stems, and roots separately using an isotope ratio mass
 spectrometer. Full details of the experiments and methods can be found in
 the following publications: Cernusak LA (2020) Gas
 exchange and water-use efficiency in plant canopies. Plant Biology 22
 (Suppl. 1):52-67. Cernusak LA, Winter K, Aranda J,
 Turner BL (2008) Conifers, angiosperm trees, and lianas: growth,
 whole-plant water and nitrogen use efficiency, and stable isotope
 composition (δ<sup>13</sup>C and δ<sup>18</sup>O)
 of seedlings grown in a tropical environment. Plant Physiology
 148:642-659. Cernusak LA, Winter K, Aranda J, Turner
 BL, Marshall JD (2007) Transpiration efficiency of a tropical pioneer tree
 (<em>Ficus insipida</em>) in relation to soil fertility.
 Journal of Experimental Botany 58:3549-3566. Cernusak
 LA, Winter K, Martinez C, Correa E, Aranda J, Garcia M, Jaramillo C,
 Turner BL (2011) Responses of legume versus nonlegume tropical tree
 seedlings to elevated CO<sub>2</sub> concentration. Plant
 Physiology 157:372-385. Cernusak LA, Winter K, Turner
 BL (2009) Physiological and isotopic (δ<sup>13</sup>C and
 δ<sup>18</sup>O) responses of three tropical tree species to
 water and nutrient availability. Plant Cell & Environment
 32:1441-1455. Garrish V, Cernusak LA, Winter K, Turner
 BL (2010) Nitrogen to phosphorus ratio of plant biomass versus soil
 solution in a tropical pioneer tree, <em>Ficus insipida</em>.
 Journal of Experimental Botany 61:3735-3748.
description: Cells in the worksheet containing NA indicate data not
 available.
DOI: 10.5061/dryad.j0zpc86gk
title: Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations

description: Genetic data are useful for detecting sudden population declines in
 species that are difficult to study in the field. Yet this indirect
 approach has its own drawbacks, including population structure, mutation
 patterns, and generation overlap. The ivory gull (Pagophila eburnea), a
 long-lived Arctic seabird, is currently suffering from rapid alteration of
 its primary habitat (i.e., sea ice), and dramatic climatic events
 affecting reproduction and recruitment. However, ivory gulls live in
 remote areas, and it is difficult to assess the population trend of the
 species across its distribution. Here we present complementary
 microsatellite- and SNP-based genetic analyses to test a recent bottleneck
 genetic signal in ivory gulls over a large portion of their distribution.
 With attention to the potential effects of population structure, mutation
 patterns, and sample size, we found no significant signatures of
 population decline worldwide. At a finer scale, we found a significant
 bottleneck signal at one location in Canada. These results were compared
 with predictions from simulations showing how generation time and
 generation overlap can delay and reduce the bottleneck microsatellite
 heterozygosity excess signal. The consistency of the results obtained with
 independent methods strongly indicates that the species shows no genetic
 evidence of an overall decline in population size. However, drawing
 conclusions related to the species' population trends will require a
 better understanding of the effect of age structure in long-lived species.
 In addition, estimates of the effective global population size of ivory
 gulls were surprisingly low (approximately 1000 ind.), suggesting that the
 evolutionary potential of the species is not assured.
DOI: 10.7272/q6sx6bfr
title: Data from: Subsets of tissue CD4 T cells display different susceptibilities to HIV infection and death: Analysis by CyTOF and single cell RNA-seq

description: CD4 T lymphocytes belong to diverse cellular subsets whose sensitivity or
 resistance to HIV-associated killing remains to be defined. Working with
 lymphoid cells from human tonsils, we characterized the HIV-associated
 depletion of various CD4 T cell subsets using mass cytometry and
 single-cell RNA-seq. CD4 T cell subsets preferentially killed by HIV are
 phenotypically distinct from those resistant to HIV-associated cell death,
 in a manner not fully accounted for by their susceptibility to productive
 infection. Preferentially-killed subsets express CXCR5 and CXCR4 while
 preferentially-infected subsets exhibit an activated and exhausted
 effector memory cell phenotype. Single-cell RNA-seq analysis reveals that
 the subsets of preferentially-killed cells express genes favoring abortive
 infection and pyroptosis. These studies emphasize a complex interplay
 between HIV and distinct tissue-based CD4 T cell subsets, and the
 important contribution of abortive infection and inflammatory programmed
 cell death to the overall depletion of CD4 T cells that accompanies
 untreated HIV infection.
description: mass cytometry; single-cell RNA-seq mass
 cytometry data has been pre-gated on live singlets and normalized by CD8
 cell number single-cell RNA-seq data are raw
 data