cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.440874g
title: Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence

description: Incongruence, or topological conflict, is prevalent in genome-scale data
 sets. Internode certainty (IC) and related measures were recently
 introduced to explicitly quantify the level of incongruence of a given
 internal branch among a set of phylogenetic trees and complement regular
 branch support measures (e.g., bootstrap, posterior probability) that
 instead assess the statistical confidence of inference. Since most
 phylogenomic studies contain data partitions (e.g., genes) with missing
 taxa and IC scores stem from the frequencies of bipartitions (or splits)
 on a set of trees, IC score calculation typically requires adjusting the
 frequencies of bipartitions from these partial gene trees. However, when
 the proportion of missing taxa is high, the scores yielded by current
 approaches that adjust bipartition frequencies in partial gene trees
 differ substantially from each other and tend to be overestimates. To
 overcome these issues, we developed three new IC measures based on the
 frequencies of quartets, which naturally apply to both complete and
 partial trees. Comparison of our new quartet-based measures to previous
 bipartition-based measures on simulated data shows that: (1) on complete
 data sets, both quartet-based and bipartition-based measures yield very
 similar IC scores; (2) IC scores of quartet-based measures on a given data
 set with and without missing taxa are more similar than the scores of
 bipartition-based measures; and (3) quartet-based measures are more robust
 to the absence of phylogenetic signal and errors in phylogenetic inference
 than bipartition-based measures. Additionally, the analysis of an
 empirical mammalian phylogenomic data set using our quartet-based measures
 reveals the presence of substantial levels of incongruence for numerous
 internal branches. An efficient open-source implementation of these
 quartet-based measures is freely available in the program QuartetScores
 (https://github.com/lutteropp/QuartetScores).
description: Zhou_etal_supplementary_figuresSupplementary FiguresZhou_etal_supplementary_textSupplementary Text
DOI: 10.5061/dryad.674g1f7
title: Data from: Litter quality and site characteristics interact to affect the response of priming effect to temperature in subtropical forests

description: 1.Forest litter inputs to soil can stimulate the decomposition of older
 soil organic matter (SOM) via a priming effect (PE). The magnitude and
 underlying mechanisms driving PE are poorly understood, with especially
 little know about how litter quality and site conditions affect PE in
 situ. Further, very few studies have examined PE in tropical and
 subtropical soils. 2.Here, we established low and high elevation sites
 (600 vs 1400 m a.s.l.) in the subtropical Wuyishan National Park, China
 that differed with respect to mean annual temperature (MAT; ∆MAT = 4.2°C),
 vegetation, soil texture, and soil moisture. We conducted a one‐year field
 incubation study at these two sites to compare PE induced by adding low‐
 and high‐quality 13C‐labelled leaf‐litter to soils. 3.At the low elevation
 site, additions of high‐quality (low C/N)litter caused a PE that was 140%
 greater than the PE observed following additions of low‐quality (high C/N)
 litter. In contrast, we saw no significant differences in PE between
 litter types at the high elevation site, perhaps because PE was not
 limited by substrate quality at this cooler, finer textured and higher
 soil moisture coniferous site. In addition, we found a negative
 relationship between home‐field advantage (HFA) for litter decomposition
 and PE, indicating that specialized litter decomposer community driving
 HFA may not accelerate SOM decomposition via PE in the same way. 4.In line
 with our observed strong relationship between PE and the efficiency of
 priming (PE size per unit of mineralized litter C), PEs induced by the
 high‐ and low‐quality litters were directed to microbial phosphorus (P)
 mining rather than nitrogen (N) mining. This interpretation aligns with
 observed increases in the activity of P‐acquiring extracellular enzymes,
 often described as phosphatases (P‐tases), as well as the positive
 relationship between the PE, P‐tase activity, and the activity of
 C‐acquiring extracellular enzymes. 5.Overall, this PE study across two
 contrasting sites highlights the important role of site characteristics
 and litter quality in regulating PE size. Further, we suggest that MAT may
 be a dominant driver of soil priming, through both the direct effects of
 litter quantity on labile substrate supply and indirect effects of litter
 quality changes on downstream decomposer communities.
description: Litter decom, PE,
 Enzyme, HFA
DOI: 10.5061/dryad.jc40j5v
title: Data from: Macro-to-nanoscale investigation of wall-plate joints in the acorn barnacle Semibalanus balanoides: correlative imaging, biological form and function, and bioinspiration

description: Correlative imaging combines information from multiple modalities
 (physical–chemical–mechanical properties) at various length scales
 (centimetre to nanometre) to understand the complex biological materials
 across dimensions (2D–3D). Here, we have used numerous coupled systems:
 X-ray microscopy (XRM), scanning electron microscopy (SEM), electron
 backscatter diffraction (EBSD), optical light microscopy (LM) and focused
 ion beam (FIB-SEM) microscopy to ascertain the microstructural and
 crystallographic properties of the wall-plate joints in the barnacle
 Semibalanus balanoides. The exoskeleton is composed of six interlocking
 wall plates, and the interlocks between neighbouring plates (alae) allow
 barnacles to expand and grow while remaining sealed and structurally
 strong. Our results indicate that the ala contain functionally graded
 orientations and microstructures in their crystallography, which has
 implications for naturally functioning microstructures, potential natural
 strengthening and preferred oriented biomineralization. Elongated grains
 at the outer edge of the ala are oriented perpendicularly to the contact
 surface, and the c-axis rotates with the radius of the ala. Additionally,
 we identify for the first time three-dimensional nanoscale ala pore
 networks revealing that the pores are only visible at the tip of the ala
 and that pore thickening occurs on the inside (soft bodied) edge of the
 plates. The pore networks appear to have the same orientation as the
 oriented crystallography, and we deduce that the pore networks are
 probably organic channels and pockets, which are involved with the
 biomineralization process. Understanding these multiscale features
 contributes towards an understanding of the structural architecture in
 barnacles, but also their consideration for bioinspiration of human-made
 materials. The work demonstrates that correlative methods spanning
 different length scales, dimensions and modes enable the extension of the
 structure–property relationships in materials to form and function of
 organisms.
description: Supplemental 1 - Avizo
 porosity dataPorosity data obtained
 from XRM scanssupplemental 2 -
 barnacle plate videoVideo illustrating the
 individual plates in the barnacle exoskeletonSupplemental 3 - ala
 VIDEOSupplemental 4 -
 opposite joint videoVideo highlighting the
 opposite ala joint of the barnacle structureIndividual plate XRM
 scanTiff stack of individual
 plate - images generated through XRM scanningWhole barnacles in resin
 XRM scanTiff stack of the three
 barnacle specimens set in a resin block
DOI: 10.5061/dryad.md243j3
title: Data from: Floodplains provide important amphibian habitat despite multiple ecological threats

description: Floodplain ponds and wetlands are productive and biodiverse ecosystems,
 yet they face multiple threats including altered hydrology, land use
 change, and non-native species. Protecting and restoring important
 floodplain ecosystems requires understanding how organisms use these
 habitats and respond to altered environmental conditions. We developed
 Bayesian models to evaluate occupancy of six amphibian species across 103
 off-channel aquatic habitats in the Chehalis River floodplain, Washington
 State, USA. The basin has been altered by changes in land use, reduced
 river-wetland connections, and the establishment of non-native American
 bullfrogs (Rana catesbeiana = Lithobates catesbeianus) and centrarchid
 fishes, all of which we hypothesized could influence native amphibian
 occupancy. Despite potential threats, the floodplain habitats had
 relatively high rates of native amphibian occupancy, particularly when
 compared to studies from non-floodplain habitats within the species’
 native ranges. The biggest challenge for native amphibians appears to be
 non-native centrarchid fishes, which strongly reduced occupancy of two
 native amphibians: the northern red-legged frog (Rana aurora) and the
 northwestern salamander (Ambystoma gracile). Emergent vegetative cover
 increased occupancy probability for all five native amphibian species,
 indicating that plant-management may offer a strategy to counter the
 negative effect of centrarchids by providing refuge from predation. We
 found that temporary and permanent hydroperiod sites supported different
 species, hence both should be conserved on the landscape. Lastly,
 human-created and natural ponds had similar amphibian occupancy patterns,
 suggesting that pond construction offers a viable strategy for adding
 habitats to the floodplain landscape. Overall, floodplain ponds and
 wetlands provide important amphibian habitat, and we offer management
 strategies that will bolster amphibian occupancy in an altered floodplain
 landscape.
description: Holgerson_Ecosphere_DatasetThis dataset represents naive detection of six amphibian species from ponds and wetlands within the Chehalis River Basin, Washington State, USA. In addition to amphibian observations, the dataset includes environmental covariates, such as fish presence, forested land use, emergent vegetation, and day of year.
DOI: 10.5061/dryad.104d626
title: Data from: Chemical defense over decadal scales: ontogenetic allocation trajectories and consequences for fitness in a foundation tree species

description: 1. Expression of herbivore defense traits can change dramatically during
 the course of plant development. Little is known, however, about the
 degree of genetic or sexual variation in these ontogenetic defense
 trajectories or whether the trajectories themselves are adaptive,
 especially in long‐lived species. 2. We used a 13‐year dataset of chemical
 defense traits, growth, and survivorship from a common garden of trembling
 aspen (Populus tremuloides) genotypes to document long‐term defense
 trajectories and their relationship to tree fitness during juvenile and
 early mature stages. 3. Overall, concentrations of the two principal
 classes of aspen defense compounds (salicinoid phenolic glycosides [SPGs]
 and condensed tannins [CTs]) decreased to differing degrees in foliage of
 juvenile trees and then remained relatively constant in maturity. Initial
 values, juvenile rates of change, and average mature values all exhibited
 significant genetic variation for both SPGs and CTs. 4. Relationships
 between defense trajectory parameters and metrics of tree fitness (growth
 and survivorship) depended on compound type and tree sex. Females with
 higher‐allocation SPG trajectories (high initial juvenile concentrations,
 slow juvenile declines, high mature concentrations) grew more slowly
 relative to females with lower‐allocation trajectories. In males,
 higher‐allocation SPG trajectories had a lesser effect on growth but were
 associated with reduced mortality. Juvenile CT trajectories were not
 correlated with tree fitness, but average CT concentration in maturity was
 positively related to growth in females. 5. These results suggest that
 ontogenetic defense trajectories are adaptive and subject to natural
 selection. Genotypic variation and ontogeny shape tree defensive
 chemistry, both independently and interactively. These patterns of defense
 expression have the potential to structure trophic interactions and the
 genetic composition of forests in both space and time.
description: Aspen Defense
 Ontogenetic Trajectory DataThis file contains data
 on trajectories of defense allocation. Each row is one individual tree.
 The second tab is has README information on each variable within the
 data.Cope_Ontogeny_Trajectories.xlsxAspen Yearly Trait DataThis file contains data on tree size, defense, and leaf traits. Each row is one year of observations for one individual tree. The second tab is has README information on each variable within the data.Cope_Ontogeny_Yearly_Data.xlsx
DOI: 10.6084/m9.figshare.28436015
title: Research_data_parasitism_analysis.xlsx

description: Common cuckoo (<i>Cuculus canorus</i>) females rely on host species to raise their young and therefore should benefit from targeting high-quality individuals that maximise their fitness. Empirical evidence for individual host selection is, however, mixed with some studies suggesting random choice. Nevertheless, it is possible that the lack of consistent evidence for host selection may be because spatio-temporal variation in host availability has rarely been accounted for, or because the implications of host choice on fitness outcomes have not been tested experimentally. Here we combined long-term monitoring data with an experiment to examine whether cuckoo females parasitising Common redstarts (<i>Phoenicurus phoenicurus</i>) target individual hosts of higher quality to optimise their nestlings´ growth. We first explored the scope for cuckoos to choose, finding spatial and temporal variation in host nest availability and host quality (using completed clutch size as a proxy). Cuckoos may choose hosts at different spatial scales, so we next investigated whether parasitism varied with host quality (i) across the study area and (ii) among nests within putative breeding areas; however, we found no evidence that redstarts laying larger clutches were more likely to be parasitised. Finally, we conducted a cross-fostering experiment to disrupt the cuckoo’s choice of nest. Moving cuckoo eggs to non-parasitised nests and between parasitised nests had no effect on morphometric growth of nestlings (mass, tarsus and wing length) but those raised by foster parents differing in quality (i.e. smaller/larger clutch size) from the original nest tended to grow faster but smaller in asymptotic mass and tarsus length. Together these results suggest that the potential fitness benefits of choosing high quality hosts do not compensate possible costs of searching for hosts in this system, although using different proxies for individual quality could help resolve the complexities inherent to understanding host choice.
DOI: 10.6084/m9.figshare.28436015.v1
title: Research_data_parasitism_analysis.xlsx

description: Common cuckoo (<i>Cuculus canorus</i>) females rely on host species to raise their young and therefore should benefit from targeting high-quality individuals that maximise their fitness. Empirical evidence for individual host selection is, however, mixed with some studies suggesting random choice. Nevertheless, it is possible that the lack of consistent evidence for host selection may be because spatio-temporal variation in host availability has rarely been accounted for, or because the implications of host choice on fitness outcomes have not been tested experimentally. Here we combined long-term monitoring data with an experiment to examine whether cuckoo females parasitising Common redstarts (<i>Phoenicurus phoenicurus</i>) target individual hosts of higher quality to optimise their nestlings´ growth. We first explored the scope for cuckoos to choose, finding spatial and temporal variation in host nest availability and host quality (using completed clutch size as a proxy). Cuckoos may choose hosts at different spatial scales, so we next investigated whether parasitism varied with host quality (i) across the study area and (ii) among nests within putative breeding areas; however, we found no evidence that redstarts laying larger clutches were more likely to be parasitised. Finally, we conducted a cross-fostering experiment to disrupt the cuckoo’s choice of nest. Moving cuckoo eggs to non-parasitised nests and between parasitised nests had no effect on morphometric growth of nestlings (mass, tarsus and wing length) but those raised by foster parents differing in quality (i.e. smaller/larger clutch size) from the original nest tended to grow faster but smaller in asymptotic mass and tarsus length. Together these results suggest that the potential fitness benefits of choosing high quality hosts do not compensate possible costs of searching for hosts in this system, although using different proxies for individual quality could help resolve the complexities inherent to understanding host choice.
DOI: 10.5061/dryad.53t3574
title: Data from: Genome sequence of Striga asiatica provides insight into the evolution of plant parasitism

description: Parasitic plants in the genus Striga, commonly known as witchweeds, cause
 major crop losses in sub-Saharan Africa and pose a threat to agriculture
 worldwide. An understanding of Striga parasite biology, which could lead
 to agricultural solutions, has been hampered by the lack of genome
 information. Here we report the draft genome sequence of Striga asiatica
 with 34,577 predicted protein-coding genes, which reflects gene family
 contractions and expansions that are consistent with a three-phase model
 of parasitic plant genome evolution. Striga seeds germinate in response to
 host-derived strigolactones (SLs) and then develop a specialised
 penetration structure, the haustorium, to invade the host root. A family
 of SL receptors has undergone a striking expansion, suggesting a molecular
 basis for the evolution of broad host range among Striga spp. We found
 that genes involved in lateral root development in non-parasitic model
 species are coordinately induced during haustorium development in Striga,
 suggesting a pathway that was partly co-opted during the evolution of the
 haustorium. In addition, we found evidence for horizontal transfer of host
 genes as well as retrotransposons, indicating gene flow to S. asiatica
 from hosts. Our results provide valuable insights into the evolution of
 parasitism and a key resource for the future development of Striga control
 strategies.
description: SGA.v2.0.final.scaffold.fastaA multifasta file including all Striga asiatica genome scaffolds.Sh14Contig_protein.fastaPredicted protein sequences from transcriptome assembly of Striga hermonthica mRNA isolated from seeds, seedlings, 1, 3 and 7-d haustoria. Note this sequences contain gaps.RT HGT sequencesHorizontally transferred retrotransposon sequences used in Figure 7E and Figure S4 in multifasta format together with phylogenetic tree files.HGTfile for Datadryad.zipSGA2.02_all_CDSA multifasta file containing predicted coding sequences from Striga asiatica genome assembly ver. 2.SGA2.02_all_proteinsA multifasta file containing predicted protein sequences from Striga asiatica genome assembly ver2.Sh14Contig.fastaTranscriptome assembly of Striga hermonthica mRNA isolated from seeds, seedlings, 1, 3 and 7-d haustoria. Note this sequences contain gaps.Sh14Contig_submit_ver2.fastaSGA_annotation.gffA gff3 file with gene annotation on Striga asiatica genome assembly ver2.SGA_functionalannot.gffSh14Contig_functionalannotationFunctional annotation and GO classification of transcriptome assembly of Striga hermonthica made by blast2GO program.
DOI: 10.5061/dryad.5n28c4q
title: Data from: Early-life conditions determine the between-individual heterogeneity in plasticity of calving date in reindeer

description: 1. Phenotypic plasticity has become a key-concept to enhance our ability
 to understand the adaptive potential of species to track the pace of
 climate change by allowing a relatively rapid adjustment of life history
 traits. 2. Recently, population-level trends of an earlier timing of
 reproduction to climate change have been highlighted in many taxa but only
 few studies have explicitly taken into consideration between-individual
 heterogeneity in phenotypic plasticity. 3. Using a long-term data of a
 semi-domesticated reindeer (Rangifer tarandus) population, we demonstrated
 that females differed greatly in their mean calving date but only slightly
 in the magnitude of their plastic response to the amount of precipitation
 in April. We also showed that despite the absence of a population trend,
 females individually responded to the amount of precipitation in April by
 delaying their calving dates. 4. Females’ calving date under average
 climatic conditions was best predicted by their birthdate, their physical
 condition in March-April-May before their first calving season and by
 their first calving date. The degree of their phenotypic plasticity was
 not dependent on any of the females’ attributes early in life tested in
 this study. However, females who delayed their calving dates in response
 to a higher amount of precipitation in April slightly produced less calves
 over their reproductive life. 5. These findings confirmed that early life
 conditions of female reindeer can shape their phenotypic value during
 reproductive life, supporting the importance of maternal effects in
 shaping individuals’ lifetime reproductive success. Whether females
 differed in the magnitude of their plastic response to climatic changes
 has received contrasted responses for various ungulate species. This calls
 for more research to enhance our understanding of the underlying
 mechanisms leading to the complexity of plastic responses among
 populations to cope with current climate change.
description: Full
 dataAll the abbreviated
 variable names are described in detail in the paper. Variables not
 provided in abbreviation in the paper are not abbreviated here, but
 provided in full text.data.csv
DOI: 10.5061/dryad.733455d
title: Data from: What makes motion dazzle markings effective against predation?

description: Motion dazzle markings comprise patterns such as stripes and zig-zags that
 are postulated to protect moving prey by making predators misjudge the
 prey’s speed or trajectory. Recent experiments have provided conflicting
 results on their effect on speed perception and attack success. We focus
 on motion dazzle stripes and investigate the influence of four parameters
 – stripe orientation, stripe contrast, target size, and target speed – on
 perceived speed and attack success using a common experimental paradigm
 involving human ‘predators’ attacking virtual moving targets on a computer
 touchscreen. We found high contrast stripes running parallel or
 perpendicular to the direction of motion reduce attack success compared to
 conspicuous uniform targets. Surprisingly, parallel stripes induced
 underestimation of speed, while perpendicular stripes induced
 overestimation of speed in relation to uniform black, suggesting that
 misjudgment of speed per se is sufficient to reduce attack accuracy.
 Across all the experiments, we found some support for parallel stripes
 inducing underestimation of target speed but these stripes reduced attack
 success only when targets were small, moved at an intermediate speed and
 had high internal contrast. We suggest that prey features (e.g., size or
 speed) are an important determinant of capture success and that distortion
 of speed perception by a color pattern does not necessarily translate to
 reduced capture success of the prey. Overall, our results support the idea
 that striped patterns in prey animals can reduce capture in motion but are
 effective under a limited set of conditions.
description: Data file for What makes
 motion dazzle markings effective against predation?CSV files that contain
 data for capture and speed perception experimentsfor_dryad.rar