cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4f4qrfjd2
title: Ancient volcanos as species pumps: A case study of freshwater amphipods in Northeast Asia

description: Volcano-tectonic processes have been viewed as primary divers in the
 formation of present-day diversity. Volcanos associated with mountain
 uplifts drives allopatric speciation through vicariance and may impact the
 surrounding areas like species pump or species attractor. However, the
 application of these hypotheses to aquatic fauna has rarely been tested
 explicitly. We conducted this research in the Changbai Mountains (Mts),
 which are one of the most typical, active volcanic ranges in Northeast
 (NE) Asia with a long and turbulent geological history. The Gammarus
 nekkensis species complex of amphipod crustaceans, widely distributed
 throughout NE Asia with poor dispersal abilities and a long evolutionary
 history, is a suitable model for testing these hypotheses. Phylogenetic
 and ancestral range reconstructions demonstrated that the studied amphipod
 originated from the Changbai Mts approximately 27 Ma and diverged into
 eastern (Clade I) and western (Clade II) clades, which corresponds well
 with the initial volcanic eruption of the Changbai Mts in the Late
 Oligocene. The subsequent diversifications of subclades CI-3, CII-1a and
 CII-2a were likely driven by second and third eruptions of the Changbai
 Mts during the Miocene. In particular, the Changbai lineages had spread to
 the Russian Far East multiple times since the Early Miocene, and widely
 colonized the region during the Pleistocene. Our discoveries suggest that
 the ancient volcanos of the Changbai Mts act as species pumps in NE Asia,
 resulted in burst of diversification around the Changbai Mts and
 subsequent dispersals into adjacent regions.
description: Alignments Aligned sequences of the five
 genes used in analysis <strong>R scripts used in
 this analysis</strong> The r scripts about bGMYC,
 LTT, Laser, BioGeoBEARS, GeoSSE
 <strong>Trees</strong> All trees
 generated for the publication in editable formats (nexus and
 newick). 1.Figure 2 The species-level Maximum clade
 credibility tree from the BEAST analysis 2.The 1000
 species-level time-calibrated trees with outgroups removed from the BEAST
 analysis 3.Figure S4 The time calibrated Maximum
 clade credibility tree based on full data set.
 4.Multiple-gene phylogeny based on the BI analysis in
 MrBayes. 5.Multiple-gene phylogeny based on the ML
 analysis in RAxML.
DOI: 10.5281/zenodo.18398259
title: Discreteness from continuity
DOI: 10.5281/zenodo.18398260
title: Discreteness from continuity
DOI: 10.5061/dryad.prr4xgxn4
title: Data on streamer initiation from charged hydrometeors

description: This dataset contains data from a series of simulations of streamers
 Initiation from spherical and column hydrometeors in thundercloud fields.
 The corresponding simulation experiments are described in paper “Jinjin
 Hu, Yikai Ma, Xin Gao, and Ningyu Liu(2021) Study on Dominant Parameters
 Determining Streamer Initiation from Hydrometeors in Thundercloud Fields.
 Journal of Geophysical Research: Atmospheres, doi: 10.1029/2021JD034936”.
 The simulation mainly investigated the three factors affecting streamers
 Initiation: the size of hydrometeors, the shape of hydrometeors (spherical
 and column), and the quantity of electric charge carried on the surface of
 hydrometeors (0pC, 180pC, 200pC, 300pC, 400pC). In addition, the
 simulation of streamers initiation at different initial electron densities
 is also studied. That is, this dataset includes two parts of simulated
 experimental data: one is the simulated data of spherical hydrometeors
 with different sizes and electric charges; the other is the simulated data
 of column hydrometeors with different sizes and electric charges. Based on
 the simulation results, the Meek criterion was used to analyze the lowest
 background electric field causing the streamers from spherical and column
 hydrometeors, and the condition of streamer initiation from spherical and
 column hydrometeors was compared. The main results of the simulation
 experiment are as follows:（1）A larger hydrometeor is more likely to
 initiate a streamer discharge at a lower ambient field for noncharged
 hydrometeors.（2）The charge on hydrometeor plays a prominent role when a
 charged hydrometeor has a smaller size, and it is easier to initiate a
 streamer in this case. (3) The charge on hydrometeor plays a dominant role
 in streamer initiation when hydrometeor is smaller, but hydrometeor shape
 becomes more important for larger hydrometeor.(4) Streamer discharge can
 be predicted by Meek number, but stable streamer can not be ensured.(5)
 Initial electron and ion pair density has little effects on the streamer
 initiation. Only the moments starting to form streamer discharge depend on
 the initial density.
description: The dataset is collected from our numerical simulation results.
 The data relating to the figures presented in the manuscript have been
 presented.
DOI: 10.5061/dryad.z8w9ghxd4
title: Variation in intraspecific demography drives localised concordance but species-wide discordance in responses to Plio-Pleistocene climatic change

description: Understanding how species biology may facilitate resilience to climate
 change remains a critical factor in detecting and protecting species at
 risk of extinction. Many studies have focused on the role of particular
 ecological traits in driving species responses, but less so on demographic
 history and levels of standing genetic variation. We used environmental
 and genomic datasets to reconstruct the phylogeographic histories of two
 ecologically similar and largely co-distributed freshwater fishes to
 assess the degree of concordance in their responses to Plio-Pleistocene
 climatic changes. Although several co-occurring populations demonstrated
 concordant demographic histories, idiosyncratic population size changes
 were found at the range edges of the more spatially restricted species.
 Discordant responses between species were associated with low standing
 genetic variation in peripheral populations. This might have hindered
 adaptive potential, as documented in recent population declines and
 extinctions of the two species. Our results highlight both the role of
 spatial scale in the degree of concordance in species responses to climate
 change, and the importance of standing genetic variation in facilitating
 range shifts. Even when ecological traits are similar between species,
 long-term genetic diversity and historical population demography may lead
 to discordant responses to ongoing and future climate change
DOI: 10.5061/dryad.2bvq83br4
title: Functional traits reveal the dominant drivers of long‐term community change across a North American Great Lake

description: The datasets here were used to determine annual sentinel fish species and
 trait composition in Lake Erie's western and central basins during
 1969–2018 in relation to multiple anthropogenic stressors. Here, we
 provide three datasets, which are used in the paper by Sinclair et al.
 titled: "Functional traits reveal the dominant drivers of long-term
 community change across a North American Great Lake". Each dataset is
 provided as a separate tab in a single Excel worksheet. The first dataset
 ("Western basin") provides the annual catch-per-unit-effort
 (CPUE; individuals per trawl minute) for all sentinel fish species caught
 in Lake Erie's western basin during 1969–2018 in fall
 (September-October) trawl surveys conducted by the Ohio Department of
 Natural Resources - Division of Wildlife. The second dataset
 ("Central basin") provides the CPUE values for Lake Erie's
 central basin. The third dataset ("Environmental stressors")
 provides the annual values for nutrient inputs, water transparency,
 temperature, white perch abundances, and goby abundances for the western
 and central basins. A summary and explanation of each variable are also
 provided in the "Info" tab. Further information on how fish CPUE
 and stressor values were calculated is provided in the methods and
 supporting information of the associated article.
description: Please refer to the associated article for data collection
 methods.
description: Please refer to the associated article for information on
 variable transformations and data usage.
DOI: 10.5061/dryad.r7sqv9scv
title: Data from: Warming alters juvenile carp effects on macrophytes resulting in a shift to turbid conditions in freshwater mesocosms

description: 1. Multiple stressors such as climate change and eutrophication are
 responsible for the global decline of macrophytes in lakes. The loss of
 this key component can result in turbid conditions and a loss of important
 ecosystem functions and services, particularly in shallow lakes.
 Benthivorous fish, which can increase in abundance during eutrophication,
 can adversely affect macrophytes through physical disturbance, cascading
 effects on turbidity, suspended and attached algae (phytoplankton and
 periphyton) and direct consumption. However, whether warming amplifies
 their effects on macrophytes and can trigger regime shifts remains
 unexplored. 2. Here, we tested the single and combined effects of warmer
 water (+4.5°C) and the widespread benthivorous juvenile common carp
 (Cyprinus carpio) on two different types of aquatic macrophytes in 24
 mesocosms (2500 L each). We monitored phytoplankton, periphyton, turbidity
 and the abundance of the submerged curly-leafed pondweed (Potamogeton
 crispus) and the floating-leaved water chestnut (Trapa bispinosa) during
 their growing season. These species dominated successively in spring and
 summer. 3. Warming alone advanced the growing season of P. crispus by 17
 days. Juvenile carp decreased the abundance of the more palatable P.
 crispus, but promoted the abundance of T. bispinosa, supporting an
 ecosystem shift to a dominance of floating-leaved macrophytes. Fish also
 substantially increased water turbidity and the biomass of phytoplankton
 and periphyton. Warming amplified juvenile carp effects on turbidity and
 submerged macrophytes, but also decreased the abundance of floating-leaved
 macrophytes leading to an overall macrophyte decline and increase in water
 turbidity. 4. Synthesis and applications. Our study provides the first
 experimental evidence for a warming-induced regime shift from clear water
 conditions dominated by submerged or floating/floating-leaved macrophytes
 to a turbid state in shallow aquatic ecosystems. The regime shift was
 triggered by impacts of warming on benthivorous fish (juvenile common
 carp) rather than on macrophytes. Lowering nutrient loading and other
 measures to reduce the abundance of benthivorous fish (e.g., fish removal
 and piscivorous fish restocking) thus may become increasingly important
 for the management of shallow lakes under global climate change.
description: Data were collected during the experiment.
DOI: 10.5061/dryad.w6m905qqh
title: Data from: Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protist Tetrahymena thermophila

description: 1. Populations that expand their range can undergo rapid evolutionary
 adaptation of life-history traits, dispersal behaviour, and adaptation to
 the local environment. Such adaptation may be aided or hindered by sexual
 reproduction, depending on the context. 2. However, few empirical and
 experimental studies have investigated the genetic basis of adaptive
 evolution during range expansions. Even less attention has been given to
 the question how sexual reproduction may modulate such adaptive evolution
 during range expansions. 3. We here studied genomic adaptation during
 experimental range expansions of the protist Tetrahymena thermophilain
 landscapes with a uniform environment or a pH-gradient. Specifically, we
 investigated two aspects of genomic adaptation during range expansion.
 Firstly, we investigated adaptive genetic change in terms of the
 underlying numbers of allele frequency changes from standing genetic
 variation and de novo variants. We focused on how sexual reproduction may
 alter this adaptive genetic change. Secondly, we identified genes subject
 to selection caused by the expanding range itself, and directional
 selection due to the presence or absence of the pH-gradient. We focused
 this analysis on alleles with large frequency changes that occurred in
 parallel in more than one population to identify the most likely candidate
 targets of selection. 4. We found that sexual reproduction altered
 adaptive genetic change both in terms of de novo variants and standing
 genetic variation. However, sexual reproduction affected allele frequency
 changes in standing genetic variation only in the absence of long-distance
 gene flow. Adaptation to the range expansion affected genes involved in
 cell divisions and DNA repair, whereas adaptation to the pH-gradient
 additionally affected genes involved in ion balance, and oxidoreductase
 reactions. These genetic changes may result from selection on growth and
 adaptation to low pH. 5. In the absence of gene flow, sexual reproduction
 may have aided genetic adaptation. Gene flow may have swamped expanding
 populations with maladapted alleles, thus reducing the extent of
 evolutionary adaptation during range expansion. Sexual reproduction also
 altered the genetic basis of adaptation in our evolving populations via de
 novo variants, possibly by purging deleterious mutations or by
 revealing fitness benefits of rare genetic variants.
DOI: 10.5061/dryad.xsj3tx9gc
title: Microbiome diversity and reproductive incompatibility induced by the prevalent endosymbiont Arsenophonus in two species of African cassava Bemisia tabaci whiteflies

description: This dataset contains data from two-part experiments described in the
 paper: “El Hamss, H., Ghosh, S., M. N., M., Delatte, H., & Colvin,
 J. (2021). Microbiome diversity and reproductive incompatibility induced
 by the prevalent endosymbiont Arsenophonus in two species of African
 cassava Bemisia tabaci whiteflies. Ecology and Evolution, 00, 1–10.
 https://doi.org/10.1002/ece3.840”. The experiment investigates the effects
 of Arsenophonus on whitefly reproduction and microbiome diversity. In the
 first experiment (“crossing experiment”), the effect of Arsenophonus is
 studied on number of eggs, nymphs, males, and females on different
 whitefly species at intraspecies level (SSA1-SG3A+ with SSA1-SG3A-) and at
 interspecies level (SSA2A+ with SSA1-SG3A- and SSA1-SG3A+). Arsenophonus
 infection A+ means the presence of Arsenophonus in related whitefly
 colony, A- means the absence of Arsenophonus. In the second experiment
 (“microbiome diversity”), whitefly colonies of crossed parents and
 generated progenies were sequenced to check Arsenophonus threshold (number
 of reads) and the presence of other bacteria in those crossed whiteflies.
 The main results of this work are: (i) Arsenophonus did not induce
 reproductive incompatibility within SSA1-SG3 but reduced the number of
 eggs, nymphs and female ratios, (ii) complete RI was observed between
 SSA1-SG3 and SSA2 indicating the lack of gene flow between the two
 whitefly species, (iii) many new ‘other bacteria’ in SSA B. tabaci have
 been identified, whose role remains to be investigated.
description: The DNA of the microbiome dataset was extracted from single
 whitefly after the crossing experiment in insectary in NRI, University of
 Greenwich, UK. The DNA has been then sequenced by Illumina Hiseq, then the
 final filtered reads were clustered and assigned. The statistical analyses
 were subsequently carried out using the attached excel sheet of a series
 of bacteria. One-way ANOVA test was carried out to investigate bacterial
 diversity parameters such as Simpson index and observed OTUs. Bray–Curtis
 dissimilarities between all pairwise combinations of whitefly samples were
 ordinated following a non-metric multidimensional scaling (nMDS). The
 methods are well described and accepted for publication in Ecology and
 Evolution journal.
description: The readme file contains an
 explanation of each of the variables in the dataset, the way it was
 collected from the primary data. Information on how the crossing
 experiments and microbiome analyses were done can be found in the
 associated manuscript referenced above.
DOI: 10.5061/dryad.xpnvx0kgc
title: Lophozia svalbardensis (Lophoziaceae) in continental North America, Greenland and Siberia, its identity, variation, and differentiation

description: Lophozia excisa var. succulenta (≡ Lophoziopsis excisa var. succulenta) is
 a synonym of Lophozia svalbardensis. This conclusion is based on
 morphological investigation and a subsequent molecular-genetic study which
 revealed an absence of variability amon nucleotide sequences of ITS1-2
 nrDNA and trnL-F cpDNA in specimens from Arctic Alaska, west Siberian
 Arctic and Svalbard. Lophozia svalbardensis is reported for the first time
 for continental North America, Greenland and Siberia based on revised data
 on the distribution of Lophozia excisa var. succulenta. An expanded
 description of Lophozia svalbardensis, its variation, differentiation and
 photomicrographs of specimens from the Seward and Gydanskiy peninsulas are
 provided. The variability of pigmentation pattern, cell walls, perianth
 structure and gemmae is described.
description: Representative specimens examined: Norway, Svalbard,
 Nordaustlandet, Gustav V Land, Murchisonfjorden, south– east slope on
 north–west coast of Nordvika Bay, 80°03′13″N, 18°48′26″E, 196 m a.s.l.,
 bank of lake, rock field, on covered by bryophytes nonsorted circles among
 crushed rocks, 17 Aug 2007, Konstantinova N.A. & A.N. Savchenko
 K135-3-07 (isotype of L. svalbardensis, LE); Denmark, West Greenland,
 Agpat [Appat Island], R.M. Schuster & K. Damsholt 66-1465 (C,
 paratype of L. excisa var. succulenta); Russia, West Siberia, Yamal
 Peninsula, Neromoyakha watershed slope, on bare soil among Solarina
 crocea, 20 Jul 1990, V. Golubkov (LE); GYDANSKIY PENINSULA, cotton
 grassdwarf shrub-moss tundra, 71.9082°N, 78.6625°E, on loamy wet soil,
 2017, E. I. Troeva G2-4 (LE); USA, Alaska, Seward Peninsula, Southern
 Killeak Lake, lake shore, ca 66°20′N, 164°08′E, on bare ground, 24 Jul
 1992, Potemkin 92-90-04 (LE). To provide a molecular
 comparison with DNA data from the type specimen of L. svalbardensis
 (GenBank accession numbers MW298768 and MW297149) the ITS1-2 nrDNA and
 trnL-F cpDNA sequences were produced for the two abovecited specimens
 (Potemkin 92-90-04 from Alaska and Troeva G2-4 from Gydanskiy Peninsula).
 The procedures of DNA extraction and amplification followed protocols
 described in Konstantinova et al. (2020). Obtained sequences were
 assembled and aligned in BioEdit ver. 7.0.1 (Hall 1999). The molecular
 variability of the tested samples was evaluated as the value of
 p-distances for both ITS1-2 and trnL-F in Mega ver. 5.1 (Tamura et al.
 2011).
DOI: 10.5061/dryad.ht76hdrgp
title: Changes in body surface temperature play an under-appreciated role in the avian immune response

description: Fever and hypothermia are well characterized components of systemic
 inflammation. However, our knowledge of the mechanisms underlying such
 changes in body temperature is largely limited to rodent models and other
 mammalian species. In mammals, high dosages of an inflammatory agent
 (e.g., lipopolysaccharide, LPS) typically leads to hypothermia (decrease
 in body temperature below normothermic levels), which is largely driven by
 a reduction in thermogenesis, and not changes in peripheral vasomotion
 (i.e., changes in blood vessel tone). In birds, however, hypothermia
 occurs frequently, even at lower dosages, but the thermoeffector
 mechanisms associated with the response remain unknown. We
 immune-challenged zebra finches (Taeniopygia guttata) with LPS and
 monitored changes in subcutaneous temperature and energy balance (i.e.,
 body mass, food intake), and assessed surface temperatures of, and heat
 loss across, the eye region, bill, and legs. We hypothesized that if birds
 employ similar thermoregulatory mechanisms to similarly-sized mammals,
 LPS-injected individuals would reduce subcutaneous body temperature and
 maintain constant surface temperatures when compared with saline-injected
 individuals. Instead, LPS-injected individuals showed a slight elevation
 in body temperature, and this response coincided with a reduction in
 peripheral heat loss, particularly across the legs, as opposed to changes
 in energy balance. However, we note that our interpretations should be
 taken with caution due to small sample sizes within each treatment. We
 suggest that peripheral vasomotion, allowing for heat retention, is an
 underappreciated component of the sickness-induced thermoregulatory
 response of small birds.
description: The attached files contain the necessary descriptions for
 understanding and working with data used in the construction of Tapper et
 al. 2021 (Physiological and Biochemical Zoology). The
 PBZ_dryad_readme.docx file contains descriptions of each file name
 attached to this data repository and descriptions of the data contained
 within each column of a data file. Information pertaining to the R code,
 which has been provided in this data repository as a .R file, has not been
 provided within this readme file, because necessary descriptions for
 understanding our code are provided within the R code file
 itself.
DOI: 10.5061/dryad.n02v6wwz8
title: Type specimen information of Primula longistyla

description: Primula longistyla, a new species of Primulaceae is described and
 submitted to the Nordic Journal of Botany. This species is
 similar to P. densa, but clearly differs in its leaves,
 corollas and styles. In this dataset, we provide details
 of the type specimens of the new species.
DOI: 10.5061/dryad.qbzkh18hv
title: Community-level leaf N:P Ratios in terrestrial ecosystems in China

description: Community-level leaf N:P ratios in terrestrial ecosystems (e.g. forests,
 grasslands, and deserts) in China were calculated using the
 biomass-weighted mean and species-arithmetic mean.
DOI: 10.5061/dryad.mcvdnck25
title: Effects of chronic and acute predation risk on sexual ornamentation and mating preferences

description: Phenotypic plasticity is wide-spread in animals, but how plastic responses
 to predation threat affect traits under sexual selection and influence
 mating preferences is not well understood. Here, we examined how chronic
 predation risk during development and acute predation risk during mate
 choice affect the expression of male secondary sexual traits and female
 mating preference in the three-spined stickleback, Gasterosteus aculeatus.
 Males reared under chronic predation risk developed less intense red
 breeding colouration but showed higher courtship activity than males that
 grew up in a predator-free environment. Acute predation risk during mate
 choice did not influence male behaviour or ornamentation. Predation risk
 experienced during development did not affect female mating preferences,
 while acute predator presence induced a switch in preferences for male
 courtship activity. Male body size and eye colouration influenced the
 intensity of female mating preferences, while the trait changing most in
 response to predation risk during development (red colouration) had no
 significant impact. The observed interplay between developmental
 plasticity in male ornamental traits and environment-dependent female
 mating preferences may lead to dynamic processes altering the strength and
 direction of sexual selection depending on both the chronic and acute risk
 of predation. These processes may contribute to the maintenance of within-
 and among-population variation in secondary sexual traits, and may,
 ultimately, facilitate speciation.