cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xksn02vcs
title: Data from: Foundation species promote local adaptation and fine-scale distribution of herbaceous plants

description: 1) Interactions among neighbors can alter demography and traits of
 commingled species via adaptation or plasticity in phenotypic expression
 and understanding these two mechanisms in diverse communities is important
 for determining the ecological and evolutionary consequences of
 plant–plant interactions. 2) We reciprocally transplanted perennial
 species (Arenaria armerina and Festuca indigesta) among patches of two
 foundation shrub species and open ground to assess whether origin
 microsite (defined as the spatially distinct abiotic and biotic conditions
 associated with the two shrubs and open ground) determines germination,
 recruitment and growth that, in turn, promotes fine-scale distribution of
 species among microsites. In addition, we tested the effect of origin
 microsite on traits, competitive ability, drought tolerance and outlier
 loci to assess whether origin microsite conditions drove differences in
 traits, strategies and adaptive loci. 3) Germination was consistently
 greater for seeds planted back into their origin microsite relative to
 seeds sourced from foreign microsites, although this effect was weakened
 for recruitment. Plant growth was best in open sites regardless of origin
 microsite. In the greenhouse, A. armerina had conserved traits within
 origin microsite but distinct trait values among microsite conditions,
 specifically for plants originating from the most productive microsite
 (e.g. sufficient light and high nutrients and water availability). Festuca
 indigesta had conserved trait responses among microsites while within
 microsite, individuals had significant trait plasticity to different
 environmental conditions. The combined field and greenhouse results
 suggest that fine-scale distributions are supported by local adaptation
 among microsites of A. armerina and phenotypic plasticity of F. indigesta.
 Synthesis Adaptation or plasticity in phenotypic expression have different
 implications for demographic rate and persistence of species in changing
 environments. Local adaptation to neighbors suggests that reductions in
 foundation species diversity could concomitantly lead to reduced genetic
 diversity of commingled species while a plastic response indicates a more
 robust and broad response to changing climatic and biotic conditions.
description: These data sets represent work from two experiments: a reciprocal
 transplant in the Sierra Nevada, Spain (36.9845°N, 3.3232°W) and a
 greenhouse common garden at the University of Zurich. Data from the field
 experiment includes the biomass of plants after two growing seasons,
 germination from season 1 and season 2, recruitment after 2 seasons and
 the environmental conditions measured in the three microsites. Data from
 the greenhouse include traits (LMA and LDMC) from control and drought
 treatments.
description: There is a ReadME file with the data that provides all
 descriptions of the columns and units. The vcf file contains the raw SNP
 data (840652 SNPs).
DOI: 10.5061/dryad.59zw3r24z
title: Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos

description: 1. Reliable and accurate biodiversity census methods are essential for
 monitoring ecosystem health and assessing potential ecological impacts of
 future development projects. Although metabarcoding is increasingly used
 to study biodiversity across ecological research, morphology-based
 identification remains the preferred approach for marine ecological impact
 assessments. Comparing metabarcoding to morphology-based protocols
 currently used by ecological surveyors is essential to determine whether
 this DNA-based approach is suitable for the long-term monitoring of marine
 ecosystems. 2. We compared metabarcoding and morphology-based approaches
 for the analysis of invertebrates in low diversity intertidal marine
 sediment samples. We used a recently developed bioinformatics pipeline and
 two taxonomic assignment methods to resolve and assign amplicon sequence
 variants (ASVs) from Illumina amplicon data. We analysed the community
 composition recovered by both methods and tested the effects, on the
 levels of diversity detected by the metabarcoding method, of sieving
 samples prior to DNA extraction. 3. Metabarcoding of the mitochondrial
 marker cytochrome c oxidase I (COI) gene recovers the presence of more
 taxonomic groups than the morphological approach. We found that sieving
 samples results in lower alpha diversity detected and suggests a community
 composition that differs significantly from that suggested by un-sieved
 samples in our metabarcoding analysis. We found that whilst metabarcoding
 and morphological approaches detected similar numbers of species, they are
 unable to identify the same set of species across samples. 4. Synthesis
 and Applications We show that metabarcoding using the COI marker provides
 a more holistic, community-based, analysis of benthic invertebrate
 diversity than a traditional morphological approach. We also highlight
 current gaps in reference databases and bioinformatic pipelines for the
 identification of intertidal benthic invertebrates that need to be
 addressed before metabarcoding can replace traditional methods.
 Ultimately, with these limitations taken into consideration, resolving
 community-wide diversity patterns with metabarcoding could improve the
 management of non-protected marine habitats in the U.K.14-Jul-2020
DOI: 10.5061/dryad.6wwpzgmw5
title: Data from: Climate warming drives Himalayan alpine plant growth and recruitment dynamics

description: Understanding how climate influences plant reproduction and growth at
 contrasting range limits is crucial for predicting how species‘ ranges may
 shift in response to ongoing climate change. Trees and shrubs have shown
 warming-induced increases in performance at upper elevation limits but
 reduced performance at lower distributional limits due to warming-driven
 drought limitation. Whether these differential responses are also valid
 for alpine forbs exposed to accelerated warming remains largely unknown.
 We examined climate signal recorded in annual growth and recruitment over
 the past sixty years in the alpine forb Potentilla pamirica in Western
 Himalayas, and tested whether the responses to recent climate warming
 differ between dry steppe, wet alpine and cold subnival zone within the
 species 5250-5900 m elevation range. We reconstructed recruitment and
 growth chronologies from 1019 individuals spanning 1-73 years, and more
 than 21,500 annual growth rings. We identified contrasting climatic
 controls of recruitment and growth at opposite elevation range margins, as
 well as contrasting demographic trends identified from age distributions.
 In lower-elevation steppes, recruitment increased with high late-winter
 snowfall and decreased with high summer temperatures, while growth
 increased with high summer precipitation. Conversely, warm winters and
 summers in higher-elevation alpine and subnival zones support growth and
 recruitment, while snowy winters reduce them, especially at their upper
 elevation limit. The age distribution revealed greater numbers of younger
 individuals, indicating healthy growing populations, in the alpine
 habitat, while evidence of ageing plant populations was observed in steppe
 and subnival zones. Accelerated warming since the 1990s reduced growth and
 recruitment in dry steppes while supporting plant performance in the
 alpine habitat. The recruitment in the subnival zone did not peak during
 the past warmest decade due to concomitant extreme snowfall
 events.  Synthesis: Our results bring novel information on
 population-specific climate dependency of plant recruitment, growth, and
 population dynamics, suggesting a high vulnerability of high elevation
 Himalayan ecosystems to climate change. This is partly balanced by high
 species longevity and slow radial growth securing a long-term population
 persistence. Continuing trends of extreme snowfall events at higher
 elevations and droughts at lower elevations may lead to species range
 contraction.
DOI: 10.5061/dryad.08kprr509
title: Chironomid-based temperature reconstruction from Burgäschisee, Switzerland

description: The data herein presents a new chironomid record and associated
 chironomid-based temperature reconstruction covering the time interval
 18,000-14,000 cal. BP from the lacustrine sediments of a kettle hole lake
 Burgäschisee, Switzerland. Chironomid assemblages show ecological turnover
 beginning 1,300 years before the onset of the Oldest
 Dryas / Bølling transition at ca. 14,700 cal. BP and associated increases
 in chironomid-based temperature reconstructions. These data also
 include non-chironomid invertebrate remains, including Ceratopogonidae,
 Daphnia and Ephemeroptera as well as Characean oospores.
description: <strong>Sample processing</strong>: Sediment samples
 were soaked in room temeprature 10% KOH solution for 6 hours before being
 sieved through 100 and 200 micrometer sieves. Chironomids were picked from
 those samples using a Bogorov tray under a stereomicroscope (30 – 50 x
 magnification). Samples were dried and then mounted on microscope slides
 using Euparal and identified under at 40 – 100 x magnification  with a
 composund microscope. The full laboratory methods are presented in the
 associated manuscript. For post identification data
 processing and temperature reconstruction analysis please see the
 associated publication in Quaternary Science Reviews.
DOI: 10.5061/dryad.ttdz08kvh
title: Identification of GGC repeat expansion in the NOTCH2NLC gene in amyotrophic lateral sclerosis

description: Objective To determine whether the GGC repeats in the NOTCH2NLC gene
 contribute to amyotrophic lateral sclerosis (ALS). Methods In this study,
 545 ALS patients and 1305 healthy controls from mainland China were
 recruited. Several pathogenic mutations in known ALS-causative genes
 (including C9ORF72 and ATXN2) and polynucleotide repeat expansions in
 NOP56 and AR genes were excluded. Repeat-primed polymerase chain reaction
 PCR (RP-PCR) and GC-rich PCR were performed to determine the GGC repeat
 size in NOTCH2NLC. Systematic and targeted clinical evaluations and
 investigations, including skin biopsy and dynamic electrophysiological
 studies, were conducted in the genetically affected patients. Results GGC
 repeat expansion was observed in four patients (numbers of repeats: 44,
 54, 96, and 143), accounting for approximately 0.73% (4/545) of all ALS
 patients. A comparison with 1305 healthy controls revealed that GGC repeat
 expansion in NOTCH2NLC was associated with ALS (Fisher’s exact test, 4/545
 vs 0/1305, p=0.007). Compared to patients with the neuronal intranuclear
 inclusion disease (NIID) muscle-weakness-dominant subtype, patients with
 ALS phenotype carrying the abnormal repeat expansion tended to have a
 severe phenotype and rapid deterioration. Conclusion Our results suggest
 that ALS is a specific phenotype of NIID or that GGC expansion in
 NOTCH2NLC is a factor that modifies ALS. These findings may help clarify
 the pathogenic mechanism of ALS and may expand the known clinical spectrum
 of NIID.
DOI: 10.5061/dryad.76hdr7stk
title: Data from: Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

description: Background: Understanding the processes that lead to hybridization of
 wolves and dogs is of scientific and management importance, particularly
 over large geographical scales, as wolves can disperse great distances.
 However, a method to efficiently detect hybrids in routine wolf monitoring
 is lacking. Microsatellites offer only limited resolution due to the low
 number of markers showing distinctive allele frequencies between wolves
 and dogs. Moreover, calibration across laboratories is time-consuming and
 costly. In this study, we selected a panel of 96 ancestry informative
 markers for wolves and dogs, derived from the Illumina CanineHD
 Whole-Genome BeadChip (174K). We designed very short amplicons for
 genotyping on a microfluidic array, thus making the method suitable also
 for non-invasively collected samples. Results: Genotypes based on 93 SNPs
 from wolves sampled throughout Europe, purebred and non-pedigree dogs, and
 suspected hybrids showed that the new panel accurately identifies parental
 individuals, first-generation hybrids and first-generation backcrosses to
 wolves, while second- and third-generation backcrosses to wolves were
 identified as advanced hybrids in almost all cases. Our results support
 the hybrid identity of suspect individuals and the non-hybrid status of
 individuals regarded as wolves. We also show the adequacy of these markers
 to assess hybridization at a European-wide scale and the importance of
 including samples from reference populations. Conclusions: We showed that
 the proposed SNP panel is an efficient tool for detecting hybrids up to
 the third-generation backcrosses to wolves across Europe. Notably, the
 proposed genotyping method is suitable for a variety of samples, including
 non-invasive and museum samples, making this panel useful for wolf-dog
 hybrid assessments and wolf monitoring at both continental and different
 temporal scales.
description: Part of the data is genotyped with microfluidic 96.96 Dynamic
 Arrays™ (Fluidigm Corp., South San Francisco, USA) using the 93 SNP panel
 developed in the corresponding article. The remaining part of the data is
 genotyped with CanineHD Whole-Genome BeadChip microarray (Illumina, Inc.,
 San Diego, California, USA) and the 93 SNPs genotypes are extracted from
 the larger dataset.
description: SNP genotypes are in Plink (.ped, .map) file in CanFam2 forward
 format. Dataset consist of 288 wild wolves, 4 wolves from zoos, 314 dogs
 (including14 individuals from wolf-dog breeds), 12 suspected hybrids, 3
 golden jackals and 3 foxes.
DOI: 10.5061/dryad.tht76hdwz
title: Data from: Montane regions shape patterns of diversification in small mammals and reptiles from Madagascar’s moist evergreen forest

description: Aim Madagascar is renowned for its exceptional species diversity and
 endemism. The island’s mountainous regions are thought to have played a
 role in lineage and species diversification, but this has yet to be
 explored across taxonomic groups and a temporal context has not yet been
 identified. We tested whether montane regions have promoted population
 divergence in Madagascar’s vertebrate fauna and, if so, whether these
 divergence events were contemporaneous. Location Moist evergreen forests
 of Madagascar. Taxa Small mammals and reptiles. Methods We analyzed
 mitochondrial DNA data from 20 small-mammal and five reptile species
 widely distributed across Madagascar’s moist evergreen forests. We used
 phylogenetic and population genetic analyses to identify major
 phylogeographic patterns, then used linear regression to determine if the
 strength of phylogeographic structure is related to taxon, body size, or
 elevation. Finally, we tested whether or not divergence across highlands
 occurred synchronously in multiple species, and used simulations to assess
 the power of these analyses to accurately estimate divergence times.
 Results We observed a shared phylogeographic pattern across multiple
 species that suggests Madagascar’s northern, central, and southern
 highlands have served as important regions of diversification on
 Madagascar. This pattern was recovered across taxa with varying body sizes
 and elevational distributions. We also identified four pulses of
 divergence between the northern and central highlands since the late
 Miocene, although simulations suggest that our empirical data cannot
 recover the number or timing of divergence events with high certainty.
 Finally, we observed several instances of deep intraspecific genetic
 splits, suggesting that several of the species we evaluated may represent
 cryptic species complexes. Main Conclusions We identified a
 highland-driven phylogeographic pattern plus several cases of cryptic
 endemism and recent speciation, which have important evolutionary and
 conservation implications. This work presents a new phylogeographic
 hypothesis for recent diversification on Madagascar, reaffirms the urgent
 need for continued collection of voucher specimens, and illuminates areas
 of particular importance for safeguarding genetic diversity in one of the
 world’s foremost and threatened biodiversity hotspots.
DOI: 10.5061/dryad.cjsxksn3j
title: Data from: Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean

description: The Southern Ocean (SO) harbours some of the most intense phytoplankton
 blooms on Earth. Changes in temperature and iron availability are expected
 to alter the intensity of SO phytoplankton blooms, but little is known
 about how environmental change will influence community composition and
 downstream biogeochemical processes. We performed experimental
 manipulations on surface ocean microbial communities from McMurdo Sound in
 the Ross Sea, with and without iron addition, at -0.5 °C, 3 °C, and 6 °C.
 We then examined nutrient uptake patterns as well as the growth and
 molecular responses of two dominant diatoms, Fragilariopsis and
 Pseudo-nitzschia, to these conditions. We found that nitrate uptake and
 primary productivity were elevated at increased temperature in the absence
 of iron addition, and were even greater at high temperature with added
 iron. Pseudo-nitzschia became more abundant under increased temperature
 without added iron, while Fragilariopsis required additional iron to
 benefit from warming. We attribute the apparent advantage Pseudo-nitzschia
 shows under warming to upregulation of iron-conserving photosynthetic
 processes, utilization of iron-economic nitrogen assimilation mechanisms,
 and increased iron uptake and storage. These data identify important
 molecular and physiological differences between dominant diatom groups and
 add to the growing evidence for the increasingly important role of
 Pseudo-nitzschia in warming SO ecosystems. This study also suggests that
 temperature-driven shifts in SO phytoplankton assemblages may increase
 utilization of the vast pool of excess nutrients in iron-limited SO
 surface waters, and thereby influence global nutrient distributions and
 carbon cycle.
DOI: 10.5061/dryad.j3tx95xb1
title: Data from: Maxwell-Cattaneo magnetoconvection dataset

description: We study the instability of a Bénard layer subject to a vertical uniform
 magnetic field, in which the fluid obeys the Maxwell-Cattaneo (MC) heat
 flux-temperature relation. We extend the work of Bissell (Proc. R. Soc.
 A, 472: 20160649, 2016) to non-zero values of the magnetic
 Prandtl number pm. With non-zero pm, the order of the dispersion relation
 is increased, leading to considerably richer behaviour. An asymptotic
 analysis at large values of the Chandrasekhar
 number Q confirms that the MC effect becomes important
 when CQ1/2 is O(1), where C is the Cattaneo number. In
 this regime, we derive a scaled system that is independent of Q. When
 CQ1/2 is large, the results are consistent with those derived
 from the governing equations in the limit of the Prandtl number p →
 ∞ with pm finite; here we identify a new mode of
 instability, which is due neither to inertial nor induction effects. In
 the large pm regime, we show how a transition can occur between
 oscillatory modes of different horizontal scale. For Q &gt;&gt; 1
 and small values of the Prandtl number p, we show that the critical
 Rayleigh number is non-monotonic in p, provided that
 C &gt;1/6. While the analysis of this paper is performed for
 stress-free boundaries, it can be shown that other types of mechanical
 boundary conditions give the same leading order results.
description: MATLAB files for generating and plotting the figures. (The
 exception is that the data for figure 1 was produced by FORTRAN code: also
 included.)
description: Introductory comments at the head of each code.
DOI: 10.5061/dryad.3bk3j9kgm
title: Data from: Sequential co-infections drive parasite competition and the outcome of infection

description: 1) Co-infections by multiple parasites are common in natural populations.
 Some of these are likely to be the result of sequential rather than
 simultaneous infections. The timing of the co-infections may affect their
 competitive interactions, thereby influencing the success of the parasites
 and their impact on the host. This may have important consequence for
 epidemiological and eco-evolutionary dynamics. 2) We examined in two
 ecological conditions the effect of sequential co-infection on the outcome
 of infection by two microsporidians, Vavraia culicis and Edhazardia aedis,
 that infect the mosquito Aedes aegypti. The two parasites have different
 transmission strategies: V. culicis is transmitted horizontally either
 among larvae or from adults to larvae, while E. aedis can be transmitted
 horizontally among larvae or vertically from females to their eggs. 3) We
 investigated how the timing and order of the co-infection and how the
 host’s food availability affected the parasite’s transmission potential
 (the percentage of individuals that harboured transmissible spores) and
 the host’s juvenile survival, its age at emergence and its longevity. 4)
 The outcome of co-infection was strongly affected by the order at which
 the parasites arrived. In co-infections, V. culicis had greater horizontal
 transmission if it arrived early, whereas the transmission potential of E.
 aedis, either vertical or horizontal, was not affected by the competitor
 V. culicis. The availability of food determined the duration of infection
 leading to variation in mortality and in the transmission potential. For
 both parasites low food decreased juvenile survival, delayed emergence to
 adulthood and increased horizontal transmission potential. High food
 increased juvenile survival and the probability of emergence with higher
 vertical transmission for E. aedis. Overall, our results suggest that
 early infection favours transmission and that (i) V. culicis plastically
 responded to co-infection, (ii) E. aedis was not affected by co-infection
 but it was more susceptible to factors extending or decreasing the time it
 spent in the host (time of infection and food). 5) Our results emphasise
 the complexity of the impact of co-infection on host-parasite
 interactions. In particular, the timing and order of sequential
 co-infections can result in different within-host dynamic and modify
 infection outcomes.