cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.05qfttf1h
title: Neurovascular evidence for a co-occurrence of teeth and baleen in an Oligocene mysticete and the transition to filter-feeding in baleen whales

description: Extant baleen whales (Mysticeti) have a deciduous foetal dentition, but
 are edentulous at birth. Fossils reveal that the earliest mysticetes
 possessed an adult dentition. Aetiocetids, a diverse clade of Oligocene
 toothed mysticetes, have a series of small palatal foramina and associated
 sulci medial to the postcanine dentition. The openings have been
 homologized with lateral palatal foramina that transmit neurovascular
 structures to baleen in extant mysticetes, thereby implying a
 co-occurrence of teeth and baleen in aetiocetids. However, homology of the
 foramina and sulci have been questioned. Using CT-imaging, we report that
 the lateral palatal foramina of Aetiocetus weltoni are connected
 internally to the superior alveolar canal, which transmits neurovascular
 structures to baleen in extant mysticetes and to teeth in extant
 odontocetes. Furthermore, the lateral palatal foramina of Aetiocetus are
 separate from the more medially positioned canals for the greater palatine
 arterial system. These results provide critical evidence to support the
 hypothesis that the superior alveolar neurovasculature was co-opted in
 aetiocetids and later diverging mysticetes to serve a new function
 associated with baleen. We evaluate competing hypotheses for the
 transition from teeth to baleen, and explore the transition from raptorial
 feeding in early mysticetes to filter-feeding in extant species.
description: The skull and partial right dentary (attached to rostrum)
 of <i>Aetiocetus weltoni </i>(UCMP 122900) were CT scanned by
 YXLON International in San Jose, CA using a Y.CT Modular cone-beam system.
 A total of 3866 slices were acquired with a slice thickness of 0.27 mm and
 pixel dimensions of 0.14 mm by 0.14 mm. 
description: The data are a merging of two scans, one of which contains most
 of the cranium, and the other a small portion of the left zygomatic arch.
 Unfortunately, the section with the zygomatic arch was not matched well
 with the other dataset. However, this does not affect the internal
 structure of the cranium and rostrum.
DOI: 10.5061/dryad.qbzkh18g6
title: Data from: Montane meadows: A soil carbon sink or source?

description: As the largest biogeochemically active terrestrial reserve of carbon (C),
 soils have the potential to either mitigate or amplify rates of climate
 change. Ecosystems with large C stocks and high rates of soil C
 sequestration, in particular, may have outsized impacts on regional and
 global C cycles. Montane meadows have large soil C stocks relative to
 surrounding ecosystems. However, anthropogenic disturbances in many
 meadows may have altered the balance of C inputs and outputs, potentially
 converting these soils from net C sinks to net sources of C to the
 atmosphere. Here, we quantified ecosystem-level C inputs and outputs to
 estimate the annual net soil C flux from 13 montane meadows spanning a
 range of conditions throughout the California Sierra Nevada. Our results
 suggest that meadow soils can be either large net C sinks (577.6 ± 250.5 g
 C m−2 y−1) or sources of C to the atmosphere (− 391.6 ± 154.2 g C m−2
 y−1). Variation in the direction and magnitude of net soil C flux appears
 to be driven by belowground C inputs. Vegetation species and functional
 group composition were not associated with the direction of net C flux,
 but climate and watershed characteristics were. Our results demonstrate
 that, per unit area, montane meadows hold a greater potential for C
 sequestration than the surrounding forest. However, legacies of
 disturbance have converted some meadows to strong net C sources. Accurate
 quantification of ecosystem-level C fluxes is critical for the development
 of regional C budgets and achieving global emissions goals.
DOI: 10.7272/q6028psc
title: The onset and offset of noxious stimuli robustly modulate perceived pain intensity

description: Reported pain intensity depends not only on stimulus intensity but also on
 previously experienced pain. A painfully hot temperature applied to the
 skin evokes a lower subjective pain intensity if immediately preceded by a
 higher temperature, a phenomenon called offset analgesia. 
 Previous work indicated that prior pain experience can also increase
 subsequent perceived pain intensity. Therefore, we examined whether a
 given noxious stimulus is experienced as more intense when it is preceded
 by an increase from a lower temperature. Using healthy volunteer subjects,
 we observed a disproportionate increase in pain intensity at a given
 stimulus intensity when this intensity is preceded by a rise from a lower
 intensity. This disproportionate increase is similar in magnitude to that
 of offset analgesia. We call this effect onset hyperalgesia. 
 Control stimuli, in which a noxious temperature is held constant,
 demonstrate that onset hyperalgesia is distinct from receptor or central
 sensitization. The absolute magnitudes of offset analgesia and onset
 hyperalgesia correlate with each other but not with the noxious stimulus
 temperature. Finally, the magnitude of both offset analgesia and onset
 hyperalgesia depends on preceding temperature changes. Overall, this study
 demonstrates that the perceptual effect of a noxious thermal stimulus is
 influenced in a bidirectional manner depending upon both the intensity and
 direction of change of the immediately preceding thermal stimulus.
DOI: 10.6086/d14t2b
title: Impact of uncertainty in precipitation forcing datasets on the hydrologic budget of an integrated hydrologic model in mountainous terrain

description: Precipitation is a key input variable in distributed surface
 water-groundwater models, and its spatial variability is expected to
 impact watershed hydrologic response via changes in subsurface flow
 dynamics. Gridded precipitation datasets based on gauge observations,
 however, are plagued by uncertainty, especially in mountainous terrain
 where gauge networks are sparse. To examine the mechanisms via which
 uncertainty in precipitation data propagates through a watershed, we
 perform a series of numerical experiments using an integrated surface
 water-groundwater hydrologic model, ParFlow.CLM. The Kaweah River
 watershed in California, USA is used as our virtual catchment laboratory
 to characterize watershed response to variable precipitation forcing from
 headwaters to groundwaters. By applying the three cornered hat method, we
 quantify the spatially distributed uncertainty in four publically
 available precipitation forcing datasets and their simulated hydrology.
 Simulations demonstrate that uncertainty in the simulated groundwater
 storage is primarily a result of topographic redistribution of uncertainty
 in precipitation forcing. Soil water redistribution is the primary pathway
 that redistributes uncertainty downslope. We also find that topography
 exerts a larger impact than variable subsurface parameters on propagating
 uncertainty in simulated fluxes. Finally, we find that improvement in
 model performance metrics is higher for a single simulation forced with
 the mean precipitation from the available datasets than the averaged
 simulated results of separate simulations forced with each dataset.
 Results from this study highlight the importance of topography-moderated
 flow through the critical zone in shaping the groundwater response to
 climate variability.
description: See README for Usage Notes
DOI: 10.5061/dryad.sn02v6x2q
title: Raw data used in: Variations in effects of ectosymbiotic microbes on the growth rates among different species and genotypes of Daphnia fed different algal diets

description: Several recent studies have shown that ectosymbiotic bacterial microbiota,
 including gut microbes, affect the growth and reproduction of Daphnia, a
 key organism in lake ecosystems. However, these studies examined specific
 species, such as the model organism, D. magna, and used green algae as
 food. It is unclear if symbiotic bacteria affect fitness in other Daphnia
 species common in lakes and ponds in Japan. In this study, we examined the
 growth rates of sterilized individuals of two D. pulex genotypes with D.
 magna using the green algae Scenedesmus and the diatom Cyclotella as algal
 diets. In addition, we examined the growth rate of the sterilized Daphnia
 pulex individuals infected by Limnohabitans spp., previously reported to
 promote the fitness of D. magna as ectosymbiotic bacteria. We found that
 the effects of ectosymbiotic bacteria on growth rate differed not only
 between different genotypes of D. pulex but also between individuals fed
 the different algal diets. The results suggest that the genotype- and
 diet-specific differences in fitness-dependency on the ectosymbiotic
 microbiota can be factors affecting the genetic structures of D. pulex
 populations.
description: Detailed methods are described in the paper published in
 Ecological Research.
DOI: 10.5061/dryad.g79cnp5nv
title: Full data for: Predators, prey or temperature? Mechanisms driving niche use of a foundation plant species by specialist lizards

description: Foundation species interact strongly with other species to profoundly
 influence communities, such as by providing food, refuge from predators,
 or beneficial microclimates. We tested relative support for these
 mechanisms using spinifex grass (Triodia spp.), which is a foundation
 species of arid Australia that provides habitat for diverse lizard
 communities. We first compared the attributes of live and dead spinifex,
 bare ground and a structurally similar plant (Lomandra effusa), and then
 tested the relative strength of association of two spinifex specialist
 lizard species (Ctenophorus spinodomus and Ctenotus atlas) with spinifex
 using a mesocosm experiment. Temperatures were coolest within spinifex
 compared to bare ground and Lomandra. Invertebrate abundance and the
 threat of predation were indistinguishable between treatments, suggesting
 temperature attenuation may be a more important driver. Overall, the
 dragon C. spinodomus preferred live over dead spinifex, while the skink C.
 atlas preferred dead spinifex, particularly at warmer air temperatures.
 However, both species displayed individual variability in
 their use of available microhabitats, with some individuals
 rarely using spinifex. Our results provide an example of temperature
 attenuation by a foundation species driving niche use by ectothermic
 animals.
DOI: 10.5061/dryad.fqz612jr9
title: Influences of climatic and social environment on variable maternal allocation among offspring in Alpine marmots

description: 4 dataset corresponding to the four models described.
DOI: 10.5061/dryad.c59zw3r5s
title: Trophic resource partitioning drives fine-scale coexistence in cryptic bat species

description: Understanding the processes that enable species coexistence has important
 implications for assessing how ecological systems will respond to global
 change. Morphology and functional similarity increase the potential for
 competition, and therefore, co-occurring morphologically similar but
 genetically unique species are a good model system for testing coexistence
 mechanisms. We used DNA metabarcoding and High Throughput Sequencing to
 characterise for the first time the trophic ecology of two
 recently-described cryptic bat species with parapatric ranges, Myotis
 escalerai and Myotis crypticus. We collected faecal samples from
 allopatric and sympatric regions and from syntopic and allotopic locations
 within the sympatric region to describe the diets both taxonomically and
 functionally and compare prey consumption with prey availability. The two
 bat species had highly similar diets characterised by high arthropod
 diversity, particularly Lepidoptera, Diptera and Araneae, and a high
 proportion of prey that is not volant at night, which points to extensive
 use of gleaning. Diet overlap at the prey-item level was lower in syntopic
 populations, supporting trophic shift under fine-scale co-occurrence.
 Furthermore, the diet of M. escalerai had a marginally lower proportion of
 not nocturnally volant prey in syntopic populations, suggesting that the
 shift in diet may be driven by a change in foraging mode. Our findings
 suggest that fine-scale coexistence mechanisms can have implications for
 maintaining broad-scale diversity patterns. This study highlights the
 importance of including both allopatric and sympatric populations and
 choosing meaningful spatial scales for detecting ecological patterns. We
 conclude that a combination of high taxonomic resolution with a functional
 approach helps identify patterns of niche shift.
description: Sequencing data generated from metabarcoding and high throughput
 sequencing on Illumina MiSeq of arthropod DNA in faecal smaples from
 Myotis escalerai and Myotis crypticus in the Iberian Peninsula in 2017.
 Raw sequencing data post removal of primers and low quality reads. Two
 different generic arthropod primers were used: ZBJ (Zeale et al. 2011,
 Mol. Ecol. Resour. 11: 236-244) and CFMRA (ANML; Jusino et al. 2019, Mol.
 Ecol. Resour. 19: 176–190).   
description: Dataset includes sample list with species identification and
 capture site location (Sample_ID_location.csv), and list of arthropod BINs
 identified in bat faecal samples and their presence in each of the two bat
 species (Novell-Fernandez_EcolEvol_Data file S1.csv).
DOI: 10.5061/dryad.wpzgmsbk9
title: Assembly of Aegilops comosa chromosomes

description: We sequenced and assembled seven chromosomes of Aegilops comosa. The
 assembly with Meraculous resulted in ~ 50k - 186k scaffolds per chromosome
 with N50 size 6.4kb - 20.2kb. The scaffold sequences were used for
 development of molecular markers specific for cDNAs sequences mapped on
 Ae. comosa chromosomes Pairwise alignment of wheat cDNA-sequences and the
 chromosomal scaffolds of Ae. comosa identified candidate sequences. In
 order to analyze the structure and homeology of Aegilops chromosomes,
 forty-three mapped wheat cDNAs covering all seven chromosome groups were
 localized by FISH.
description: The flow-sorted chromosomes 1M-7M were used for preparation of
 libraries for sequencing. Chromosome samples were purified according to
 (Šimková et al. 2008, BMC Genomics) and 20 ng DNA was fragmented and used
 to prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.
 Size selection was directed for larger final library size (~1000 bp) and
 PCR enrichment was done in 9 cycles. Libraries were sequenced on NovaSeq
 6000 (Illumina) and 2x150 bp paired-end reads were produced. The raw data
 were trimmed for low-quality bases using Trimmomatic (Bolger et al. 2014,
 Bioinformatics) and assembled to scaffolds with Meraculous v2.0.5 (Chapman
 et al. 2011, PLoS One) using 111 bp k-mers. Scaffolds shorter than 1 kb
 were eliminated.
DOI: 10.5061/dryad.573n5tb5t
title: Data from: Dryopithecine palaeobiodiversity in the Iberian Miocene revisited on the basis of molar endostructural morphology

description: Extensive fieldwork at Abocador de Can Mata (NE Iberian Peninsula) has
 uncovered a previously unsuspected diversity of catarrhine primates in the
 middle Miocene (12.5–11.6 Ma) of Europe. However, the distinction of the
 great ape genera Pierolapithecus and Anoiapithecus from
 Dryopithecus—supported by craniodental differences—has been disputed by
 some authors. Here we revisit the diversity of great apes (dryopithecines)
 from the Iberian Miocene based on molar 3D endostructural morphology
 (relative enamel thickness, enamel distribution, and enamel-dentine
 junction [EDJ]). Using microtomography, we inspected an extensive sample
 of 49 hominoid molars representing at least five species from 12
 localities. 2D and 3D relative enamel thickness values indicate that
 Dryopithecus and “Sivapithecus” occidentalis (species inquirenda) display
 the thinnest and thickest enamel, respectively, while the remaining taxa
 (Hispanopithecus, Anoiapithecus, Pierolapithecus) show intermediate
 values. Upper molar enamel distribution maps exhibit a similar pattern in
 P. catalaunicus, A. brevirostris, D. fontani, H. laietanus and H.
 crusafonti whereas for the lower molars they reveal differences between
 Hispanopithecus laietanus and Hispanopithecus crusafonti. Lower molar
 enamel distribution and EDJ morphology of “S.” occidentalis support the
 distinction of this species but do not resolve if it is a junior synonym
 of Anoiapithecus brevirostris or Pierolapithecus catalaunicus. Overall our
 results support the distinction of middle Miocene dryopithecins from late
 Miocene hispanopithecins, the distinction of Pierolapithecus and
 Anoiapithecus from Dryopithecus among the former, and the distinct species
 status of H. crusafonti compared to H. laietanus among the latter. Our
 results highlight the potential of inner tooth morphology for hominoid
 alpha-taxonomy.
DOI: 10.5061/dryad.q83bk3jgg
title: Cellular and whole‐organism effects of prolonged versus acute heat stress in a montane, desert lizard

description: Global climate change involves both prolonged periods of
 higher-than-normal temperatures, and short but extreme heat
 waves.  Both types of temperature increases are likely to be
 detrimental to ectotherms, and even if such temperature increases do not
 cause mortality directly, compensating for such temperature increases will
 likely entail costs to organisms.  We tested the effects of
 prolonged periods of higher-than-average temperatures and short-term,
 acute heat stress in wild populations of greater short-horned lizards
 (Phrynosoma hernandesi), a temperate, montane lizard of the Colorado
 Plateau, U.S.A.  We transplanted one group of lizards from a
 high- to a low-elevation site, exposing them to a prolonged period of
 warmer temperatures.  These lizards, exposed to prolonged periods
 of higher-than-average temperatures, experienced no change in sprint
 speed, endurance, or heat shock protein production after treatment
 compared to baseline levels; however, they had lower water content after
 the transplant to a warmer climate compared to before the
 transplant.  We exposed a second group of lizards to acute heat
 stress by exposing them to thermally stressful temperatures for four
 hours.  These lizards, exposed to a short period of acute heat
 stress, had no change in endurance, water content, or heat shock protein
 production following acute heat stress; however, lizards exposed to acute
 heat stress had slower sprint speeds than control lizards.  Our
 results demonstrate that both prolonged temperature increases and acute
 heat stress, each of which are predicted to occur with climate change, had
 different cellular and/or whole organismal-level effects on lizards.
description: Ex1.HSP-Acute:  Comparison of heat shock protein 70 production by
 lizards after being exposed to acute heat stress for 4 hours, and control
 lizards that were not exposed to acute heat stress.
 Ex1-Acute:  Comparison of tissue water content, sprint speed, and
 endurance in lizards after being exposed to acute heat stress for 4 hours,
 and control lizards that were not exposed to acute heat stress.
 Ex2.HSP-Prolonged:  Comparison of heat shock protein 70
 production by lizards after being transplanted from high-elevation to
 low-elevation, thereby being exposed to a prolonged period (1 week) of
 higher-than-normal temperatures, and control lizards that were not
 transplanted to a different climate.
 Ex2-Prolonged:  Comparison of tissue water content, sprint speed,
 and endurance in lizards after being transplanted from high-elevation to
 low-elevation, thereby being exposed to a prolonged period (1 week) of
 higher-than-normal temperatures, and control lizards that were not
 transplanted to a different climate.
DOI: 10.5061/dryad.np5hqbzr7
title: Probiotic-prebiotic therapy improved constipation and gut motility in Parkinson’s disease: Randomised controlled trial

description: Objective: We determined the effectiveness of a multi-strain
 probiotic-prebiotic combination on constipation symptoms and gut motility
 in PD patients with constipation. Methods: PD patients with constipation
 (ROME III criteria) were randomized to receive a multi-strain probiotic
 (Lactobacillus sp and Bifidobacterium sp at 30 X 109 CFU) with
 fructo-oligosaccaride (prebiotic) or placebo (fermented milk) twice daily
 for 8 weeks. Primary outcomes were changes in the presence of constipation
 symptoms using 9 items of Garrigues Questionnaire (GQ), which included an
 item on bowel opening frequency. Secondary outcomes were whole gut transit
 time (WGTT), quality of life (PDQ39-SI), motor (MDS-UPDRS) and non-motor
 symptoms (NMSS). Results: Of 55 recruited, 48 patients completed the
 study: 22 received probiotic and 26 received placebo. At 8 weeks, the item
 on bowel opening frequency (BOF) of GQ showed  a higher mean
 weekly BOF in the probiotic group compared to placebo [4.18 (SD 1.44) vs
 2.81(SD 1.06), (mean difference 1.37, 95% CI 0.68, 2.07, uncorrected
 p&lt;0.001). Patients in the probiotic group reported five times
 higher odds (odds ratio=5.48, 95% CI 1.57, 19.12, uncorrected p=0.008) for
 increasing BOF (&lt; 3 to 3-5 to &gt;5 times/week) compared to the
 placebo group. Between-group differences were observed in the WGTT [77.32
 (SD 55.35) hours vs 113.54 (SD 61.54) hours], (mean difference -36.22, 95%
 CI -68.90, -3.54, uncorrected p=0.030) and the mean change in WGTT [58.05
 (SD 59.30) vs 20.73 (60.48) hours], (mean difference 37.32, 95% CI 4.00,
 70.63, uncorrected p=0.028). No between-groups differences were observed
 in the NMSS, PDQ39-SI, MDS-UPDRS II, III, scores. Four patients in the
 probiotics group experienced mild reversible side effects. Conclusion:
 This study provides Class I evidence that consumption of multi-strain
 probiotics with prebiotic over 8 weeks improved bowel opening frequency
 and whole gut transit time.
DOI: 10.5061/dryad.mpg4f4qx8
title: Temporal and spatial changes in benthic invertebrate trophic networks along a salinity gradient

description: Species interactions underlie all ecosystem goods and services and are
 important for understanding ecosystem changes. Representing one type of
 species interaction, trophic networks are able to be constructed from
 biodiversity monitoring data and known trophic links to understand how
 ecosystems have changed over time. The Baltic Sea is subject to high
 anthropogenic pressures, and its low species diversity makes it an ideal
 candidate for understanding how pressures change food webs. In this study,
 we used benthic monitoring data from 20 years (1980-1989 and 2010-2019)
 from the Swedish coast of the Baltic Sea and Skagerrak to investigate
 changes in benthic invertebrate trophic interactions. We constructed food
 webs and calculated traditional food web metrics that we compared over
 space and time. Our results show that the west coast of Sweden (Skagerrak)
 showed a reduction in benthic invertebrate biodiversity by 40% between the
 1980’s and 2010’s, and that the number of links, linkage diversity,
 generality of predators, and vulnerability of prey have been significantly
 reduced. However, connectance has not significantly changed in the
 Skagerrak. The other basins (Bothnian Sea, Baltic Proper and Bornholm
 Basin) do not show any consistent significant trends in any food web
 metrics investigated, demonstrating resilience at a lower species
 diversity. The decreased complexity of the Skagerrak food webs indicates
 vulnerability to further perturbations and pressures should be limited as
 much as possible to ensure continued ecosystem functions.