cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.95x69p8jr
title: Leucostegia amplissima, the third species of the genus (Hypodematiaceae)

description: Leucostegia has been long recognized as a small fern genus with only two
 species, L. immersa and L. pallida. Here we elevate a variety of L.
 immersa to species level and make the new combination Leucostegia
 amplissima based on morphological and molecular phylogenetic evidence.
 Morphologically, Leucostegia amplissima differs from L. immersa by having
 larger evergreen fronds, smaller indusia, and glandular hairs on the basal
 stipes. The study of Taiwanese populations further suggested an ecological
 divergence between L. immersa and L. amplissima.
DOI: 10.5061/dryad.3ffbg79hd
title: Speciation along the elevation gradient: divergence of Roscoea species within the south slope of the Himalayas

description: The Himalayas with dramatic elevation gradient is one of the global
 biodiversity hotspots. Although origin of biodiversity of the Himalayas is
 of great concern, the speciation process within the Himalayas is poorly
 known. Roscoea within the Himalayas serve as a good model system to test
 the speciation process along an elevation gradient. 32375 unlinked SNPs
 were used to reconstruct phylogenetic relationships and introgression
 analyses in D-statistics and Fastsimicoal2. Species distribution modeling
 (SDM) was used to simulate habitat shift of Roscoea species during climate
 changes. Phylogeny suggested that the speciation order, except R.
 capitata, was from highland to lowland. D-statistics analyses suggested
 significant bidirectional ancient introgression between
 elevation-neighboring clades but no introgression between R. capitata and
 othern clades and no introgression among extant species. Fastsimicoal2
 suggested interspecific introgressions were asymmetric. SDM predicted that
 habitats of Roscoea shifted to low elevation during cooling age. These
 results suggested that the sudden uplift of the Himalayas likely promoted
 speciation by vicariance, and climate cooling drove species divergence
 towards lower elevation. This study provides explanations for the origin
 of biodiversity within the Himalayas, and an insight to understand
 speciation along elevation in the mountainous regions.
description: Climate data from the CHELSA and coordinates of
 <i>Roscoea</i>  were collected from previous study (Li
 <em>et al. </em>2020) Li DB, Ou XK, Zhao JL
 & Li QJ. 2020 An ecological barrier between the Himalayas and the
 Hengduan Mountains maintains the disjunct distribution of
 <i>Roscoea</i>. <i>J. Biogeogr.</i>
 <b>47</b>, 326–341. (doi:10.1111/jbi.13729).
DOI: 10.5061/dryad.547d7wm7f
title: Local ancestry to identify selection in response to trypanosome infection in Baoulé x Zebu crossbred cattle in Burkina Faso

description: The genomes of crossbred (admixed) individuals are a mosaic of ancestral
 haplotypes formed by recombination in each generation. The proportion of
 these ancestral haplotypes in certain genomic regions can be responsible
 for either susceptibility or resistance against pathogens, and for
 performances in production traits. Using dense genomic markers from the
 Illumina Bovine SNP50 BeadChip, we estimated individual admixture
 proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were
 tested for trypanosome infection by direct ELISA from blood samples.
 Furthermore, we calculated local ancestry deviation from average for each
 SNP across 29 autosomes to identify potential regions under selection in
 the trypanotolerant Baoulé cattle and their crossbreds. We identified
 significant deviation from the local average ancestry (above 5% and 10%
 genome-wide thresholds) on chromosomes 8 and 19 in the positive animals,
 while the negative ones showed higher deviation on chromosomes 6, 19, 21
 and 22. Screening for FST outliers in trypanosome positive/ negative
 animals we detected seven variants putatively under selection. Finally, we
 identified a minimum set of highly ancestry informative SNPs for routine
 admixture testing.  Generally, results will serve as basis for
 further characterization, conservation and improvement strategies for
 purebred and crossbred populations. Our results are important not only for
 conserving the genetic integrity in the indigenous Baoulé cattle, but also
 for improving community-based breeding programs to increase
 trypanotolerance in crossbred populations.
DOI: 10.5061/dryad.t4b8gtj19
title: Divergence in life history and behaviour between hybridizing Phymata

description: Life history variation plays a central role in evolutionary and ecological
 processes, and may be especially pertinent to divergence in closely
 related species.  We investigated life history differences in a
 pair of parapatric species of ambush bugs (Phymata) and a putative hybrid
 population. Despite the evidence of gene flow among these species, we
 found clear divergence between these parapatric populations for a suite of
 juvenile and adult life history traits including components of fitness.
 The higher latitude species was also less active, suggestive of potential
 divergence in dispersal. Increased melanism was correlated with longevity
 in one species, though it is unclear whether this relationship is causal.
  Observed life history differences between species were
 consistent with expectations of high-latitude species putting a premium on
 early or rapid development and increased reproductive rates. However,
 these results were not consistent with ‘pace-of-life syndromes’ at the
 species level. Individuals from the putative hybrid zone exhibited
 intermediate values for most traits though they had slower development,
 and reduced mobility, consistent with some previous work suggesting
 natural selection via hybrid breakdown.
DOI: 10.5061/dryad.rn8pk0p8q
title: Effectiveness and feasibility of convalescent blood transfusion to reduce COVID-19 fatality ratio

description: As of December 2020,  COVID-19 has spread all over the world with
 more than 81 million cases and more than 1.8 million deaths. The rapidly
 increasing number of patients mandates the consideration of potential
 treatments for patients under severe and critical conditions. Convalescent
 plasma (CP) treatment refers to the approach of infusing patients with
 plasma from recently recovered patients. CP appears to be a possible
 therapeutic option to manage patients suffering from severe or even lethal
 infectious disorders, in which “traditional therapies” have failed to
 obtain any result. In the present study, we develop a mathematical model
 on the treatment-donation-stockpile dynamics for an optimal implementation
 of CP therapy to examine potential benefits and complications in the
 logistic realization of this therapy in a large-scale population. We
 parameterize the model with COVID-19 epidemics in Italy, and conduct
 scenario analyses to estimate outcomes of population-wide CP therapy and
 to examine the maximum number of CP donation processions per day. Under
 the assumption that the efficacy of CP is 90%, we show that by the end of
 year 2020, initiating the population-wide CP therapy from April 2020 can
 save as many as 19,215 lives (ranging from 5000 - 28,000 depending on
 donor availability), while the demand for apheresis use is manageable in
 all scenarios: the maximum daily demand is 156 (ranging from 27 - 519
 depending on donor availability) for the first outbreak wave and 1,434
 (ranging from 224 - 4,817 depending on donor availability) for the second
 wave. Given that Italy has 61 centers with apheresis this maximum demand
 level corresponds to a daily average of 2.5 and 23.5 processions of CP
 donation being performed by each center with respect to each outbreak
 wave. Our analyses show that population-wide CP therapy can contribute to
 curbing COVID-19 related deaths, and the logistic implementation is
 feasible for developed countries. The reduction of deaths can be very
 significant if the CP therapy is started earlier at the outbreak, and
 remains significant even if it is implemented during the outbreak peak
 time.
DOI: 10.5061/dryad.2bvq83bph
title: Molecular gut content analysis indicates the inter- and intra-guild predation patterns of spiders in conventionally managed vegetable fields

description: Inter- and intra-guild interactions are important in the coexistence of
 predators and their prey, especially in highly disturbed vegetable
 cropping systems with sporadic food resources. Assessing the dietary range
 of a predator taxon characterized by diverse foraging behavior using
 conventional approaches, such as visual observation and conventional
 molecular approaches for prey detection, has serious logistical problems.
 In this study, we investigated the trophic interactions of a functionally
 diverge group of predators -spiders- to accomplish the ultimate goal that
 is the predation of spiders on major crop pests. We used high-throughput
 sequencing (HTS) and biotic interaction networks to precisely annotate the
 predation spectrum and highlight the predator–predator and predator-prey
 interactions in Brassica fields. The prey taxa in the gut of spiders were
 mainly enriched with insects (including dipterans, coleopterans,
 orthopterans, hemipterans and lepidopterans) and arachnids (such as
 Araneae) along with a wide range of other prey factions. Despite the
 generalist foraging behavior of spiders, the community structure analysis
 and interaction networks highlighted the overrepresentation of particular
 prey taxa in the gut of each spider family, as well as showed the
 intra-family predation between different spiders. Identifying the diverse
 trophic niche proportions underpins the importance of spiders as predators
 of pests in highly disturbed agroecosystems. More specifically, combining
 HTS with advanced ecological community analysis reveals the preferences
 and biological control potential of particular spider taxa, so provides a
 valuable evidence base for targeted conservation biological control
 efforts in complex trophic networks.
description: DNA extracted from spiders for DNA metabarcoding; amplified using
 primer pairs mlCOlintF and HCO2198; sequenced using Illumina
 MiSeq.
DOI: 10.5061/dryad.wdbrv15n9
title: Common kinematic synergies of various human locomotor behaviours

description: Humans show a variety of locomotor behaviours in daily living, varying in
 locomotor modes and interaction styles with the external environment.
 However, how this excellent motor ability is formed, whether there are
 some invariants underlying various locomotor behaviours and simplifying
 their generation, and what factors contribute to the invariants remain
 unclear. Here we find three common kinematic synergies that form the six
 joint motions of one lower limb during walking, running, hopping,
 and sitting-down-standing-up (movement variance accounted for &gt;
 90%), through identifying the coordination characteristics of thirty-six
 lower limb motor tasks in diverse environments. This finding supports the
 notion that humans simplify the generation of various motor behaviours
 through reusing several basic motor modules, rather than developing
 entirely new modules for each behaviour. Moreover, a potential link is
 also found between these synergies and the unique biomechanical
 characteristics of the human musculoskeletal system (muscular-articular
 connective architecture and bone shape), and the patterns of inter-joint
 coordination are consistent with the energy-saving mechanism in locomotion
 by using biarticular muscles as efficient mechanical energy transducers
 between joints. Altogether, our work helps understand the formation
 mechanisms of human locomotion from a holistic viewpoint, and evokes
 inspirations for the development of artificial limbs imitating human motor
 ability.
DOI: 10.5061/dryad.8sf7m0cm7
title: Conservation of the glycogen metabolism pathway underlines a pivotal function of storage polysaccharides in Chlamydiae

description: The order Chlamydiales includes obligate intracellular pathogens capable
 of infecting mammals, fishes and amoeba. Unlike other intracellular
 bacteria for which intracellular adaptation led to the loss of glycogen
 metabolism pathway, all chlamydial families maintained the
 nucleotide-sugar dependent glycogen metabolism pathway i.e. the
 GlgC-pathway with the notable exception of both Criblamydiaceae and
 Waddliaceae families. Through detailed genome analysis and biochemical
 investigations, we have shown that genome rearrangement events have
 resulted in a defective GlgC-pathway and more importantly we have
 evidenced a distinct trehalose-dependent GlgE-pathway in both
 Criblamydiaceae and Waddliaceae families. Altogether, this study strongly
 indicates that the glycogen metabolism is retained in all Chlamydiales
 without exception, highlighting the pivotal function of storage
 polysaccharides, which has been underestimated to date. We propose that
 glycogen degradation is a mandatory process for fueling essential
 metabolic pathways that ensure the survival and virulence of extracellular
 forms i.e. elementary bodies of Chlamydiales.
description: Homologous sequences of TreS-Mak and GlgE were carried out by
 BLAST against the nr databasefrom NCBI with, respectively, WP_098038072.1
 and WP_098038073.1 sequences of Estrellalausannensis. We retrieved the top
 2000 homologs with an E-value cut off ≤ 10 -5 and aligned themusing MAFFT
 with the fast alignment settings. Block selection was then performed using
 BMGE61 with a block size of four and the BLOSUM30 similarity matrix.
 Preliminary trees were generatedusing Fasttree and ‘dereplication’ was
 applied to robustly supported monophyletic clades usingTreeTrimmer in
 order to reduce sequence redundancy. For each protein, the final set of
 sequenceswas selected manually. Proteins were realigned with MUSCLE and
 block selection was carriedout using BMGE with a block size of four and
 the matrix BLOSUM30. Phylogenetic trees wereinferred using Phylobayes
 under the catfix C20 + Poisson model with the two chains stoppedwhen
 convergence was reached (maxdiff&lt;0.1) after at least 500 cycles,
 discarding 100 burn-intrees. Bootstrap support values were estimated from
 100 replicates using IQ-TREE under theLG4X model and mapped onto the
 Bayesian tree.
description: This data file is composed of sequence data used for phylogenies
 of both GlgE and TreS-MAK proteins. Inside, you will find the raw
 sequences, the aligned sequences as well as blocks selected to perform
 phylogenies. Finally, the raw tree found in the publication for each one
 is provided. In addition, for GlgE the tree performed with the same
 dataset under LG model with 1000 ultrafastbootstraps is provided as a raw
 tree and with a pdf version, too.
DOI: 10.5061/dryad.70rxwdbwq
title: Synchronization of seasonal acclimatization and short-term heat hardening improves physiological resilience in a changing climate

description: Summary 1. Animal survival and species distribution in the face of global
 warming and increasing occurrences of heatwave largely depend on how heat
 tolerance shifts with plastic responses at different spatiotemporal
 scales, including long-term acclimation/acclimatization and short-term
 heat hardening. However, knowledge about the interaction of these plastic
 responses is still unclear. 2. To understand how plastic responses at
 different timescales work together to adjust heat tolerance of organisms,
 we examined the effect of heat hardening on the upper thermal limits of an
 intertidal mudflat bivalve, the razor clam Sinonovacula constricta, for
 different seasons by using heart rate as a proxy. 3. We observed a
 stronger heat hardening response of S. constricta in warm seasons,
 implying that heat hardening worked synchronously with seasonal
 acclimatization to increase resistance of the clams to high temperatures
 in warm seasons. In warm seasons, heat hardening increased heat tolerance
 by 2-4°C and showed a 24-h temporal dependence, suggesting an adaptation
 to the diel fluctuation of thermal regimes in summer. 4. Furthermore,
 thermal stress resembling seasonal maximum environmental temperature
 induced stronger heat hardening effects, indicating that heat hardening is
 an essential plastic response to extreme hot weather, complementing
 seasonal acclimatization. 5. Our results suggest that high temperature
 risk can be alleviated jointly by seasonal acclimatization and heat
 hardening, and emphasize the importance of considering physiological
 plasticity on both long-term and short-term temporal scales in evaluating
 and forecasting vulnerability of organisms to climate change.
DOI: 10.5061/dryad.2547d7wpt
title: Supplementary tables for Low-density lipoprotein cholesterol is associated with insulin secretion

description: Objective: Pharmacological lowering of LDL cholesterol potently reduces
 cardiovascular risk while concurrently increasing type 2 diabetes risk.
 The aim of this study was to investigate the relationship between LDL
 cholesterol concentrations and insulin secretion and glucagon levels.
 Methods: 3,039 subjects without cholesterol lowering therapy, but with
 increased risk for diabetes, underwent routine blood tests and a 5-point
 oral glucose tolerance test (OGTT). Glucagon concentrations, insulin
 secretion and insulin clearance indices were derived from the OGTT.
     Results: There was no association
 between LDL cholesterol and fasting glucagon (p=0.7, ß=-0.01) or post
 glucose load glucagon levels (p=0.7, ß=-0.07), but we detected significant
 positive associations of LDL cholesterol and C-peptide-based indices of
 insulin secretion (AUCC-Peptide(0-30min)/AUCGlucose(0-30min): p=0.0001,
 ß=0.06; AUCC-Peptide(0-120min)/AUCGlucose(0-120min): p&lt;0.0001,
 ß=-0.08). In contrast we found a negative association of insulin-based
 insulin secretion indices with LDL concentrations (Insulinogenic index:
 p=0.014, ß=-0.04; disposition index: p=0.0005, ß=-0.06). Though, LDL
 cholesterol levels were positively associated with insulin clearance
 assessed from C-peptide and insulin concentrations, both in the fasting
 state and post glucose load (p&lt;0.0001, ß=0.09 and p&lt;0.0001,
 ß=0.06, respectively). Conclusion: As C-peptide based indices reflect
 insulin secretion independent of hepatic clearance, our results indicate
 lower insulin secretion in case of lesser LDL cholesterol. This could
 explain deteriorating glycemic control in response to cholesterol lowering
 drugs.
description: <sub> </sub>
DOI: 10.5061/dryad.bk3j9kd9x
title: Geographic variation and temporal trends in ice phenology in Norwegian lakes during a century

description: The physical characteristics of ice formation in water courses are ideal
 for studying climatic variation in space and time. We used a large set of
 observations for 9-116 years (1890-2019) of the timing of freeze-up and
 break-up, and the length of ice-free season for 99 Norwegian lakes to
 elucidate variation in ice phenology across space and time. The dataset of
 Norwegian lakes is unusual, covering considerable variation in altitude (4
 – 1401 m above sea level) and climate (varying from oceanic to
 continental) within a large latitudinal and longitudinal gradient (58.2 –
 69.9 °N; 4.9 – 30.2 °E). The average date of ice break-up occurred later
 in spring with increasing altitude and latitude, but earlier in spring
 with increasing longitude. The average date of freeze-up and the length of
 the ice-free period decreased significantly with altitude and longitude.
 No correlation with distance from the ocean was detected. The geographical
 gradients are related to regional climate due to adiabatic processes
 (altitude), solar radian (latitude) and the degree of continentality
 (longitude).  There was a significant lake area effect as small
 lakes froze-up earlier due to less volume. There was also a significant
 trend that lakes were completely frozen over later in the autumn in recent
 years. After accounting for the effect of long-term trends in the
 large-scale NAO index, a significant but weak trend over time for earlier
 ice break-up was detected. An understanding of the relationship between
 ice phenology and geographical parameters is a prerequisite for predicting
 the potential consequences of climate change on ice phenology. Changes in
 ice phenology will have consequences for the behaviour and life cycle
 dynamics of the aquatic biota.
description: We collated observations
 from 101 Norwegian lakes, covering a wide range in latitude (58.2 – 69.9
 °N), longitude (4.9 – 30.2 °E) and altitude (4 – 1401 m a.s.l.). The lakes
 are situated in three major climatic zones (boreal, subalpine, alpine) and
 with varying distances from the ocean. Thus, they differ in several
 geographic characteristics (Figure 1, Appendix 1). Most of the lakes are
 relatively small (median area 6.9 km<sup>2</sup>), although
 the dataset also includes Norway’s largest lake, Mjøsa (369.3
 km<sup>2</sup>). The catchment area varies between 7.1 and
 18101.9 km<sup>2</sup> (median 235 km<sup>2</sup>)
 and mean annual inflow to the lakes varies between 5.6 10<sup>6
 </sup>and 9935.7 10<sup>6</sup>
 m<sup>3</sup> year<sup>-1</sup> (median 256
 10<sup>6</sup> m<sup>3</sup>
 year<sup>-1</sup>). About 50 % of the lakes (N = 53) were
 developed for hydropower production with an annual water level variation
 varying from 1 to 30.3 m. The lake and catchment information were
 extracted from www.nve.no.  
description: See the Read me file.txt
DOI: 10.5061/dryad.np5hqbzs1
title: From glacial refugia to hydrological microrefugia: factors and processes driving the persistence of the climate relict tree Zelkova sicula

description: With only two tiny populations, the climate relict Zelkova sicula (Sicily,
 Italy) is one of the rarest trees in the world. It also represents the
 most marginal member of genus Zelkova that was widespread in the
 broadleaved forests thriving in warm-temperate climates throughout Eurasia
 until the Last Glacial Age. Occurring at the westernmost range of the
 genus under typical Mediterranean climate, the micro-topographic settings
 have always appeared crucial for the survival of this Sicilian relict.
 However, the factors and processes actually involved in its persistence in
 the current refugia, as well as the response of similar relict trees in
 arid environments are poorly understood worldwide. In the aim to elucidate
 these aspects, in the two sites hosting Z. sicula analyses of
 topographical attributes were combined with investigations on soil
 moisture dynamics. Additionally, plants’ growth and spatial distribution
 patterns were analysed to detect fine-scale differences between
 populations and assess the possible ecological amplitude of the species.
 Results revealed that convergent topographies are basic determinants of
 microrefugia in arid environments. Within the investigated sites,
 underground moisture never decreases below 25%, buffering seasonal
 rainfall fluctuations. Therefore, hydrological microrefugia play a
 key-role in decoupling from regional climate, supporting the target
 species in coping with an unsuitable climatic envelope. Additionally, the
 inter-population variability of biometric attributes showed that
 individual growth is site-dependent and the species retains a relative
 ecological plasticity, whereas the strongly clumped spatial patterns
 confirmed the exclusive vegetative propagation and the common clonal
 growth. On one hand, deeply incised landforms have acted as effective
 hydrologic microrefugia, on the other clonality coupled with triploidy
 supposedly improved the resistance of Z. sicula to harsh environments,
 though entailing inability to reproduce sexually. Most likely, sterility
 and environmental/physical barriers prevent since millennia this relict
 from leaving the last suitable microrefugia, resulting in the two current
 rear-edge populations.
description: This data is supplemented to: Garfì et al., From glacial refugia
 to hydrological microrefugia: factors and processes driving the
 persistence of the climate relict tree <i>Zelkova sicula.
 </i>Ecology and Evolution