cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rf5bj
title: Data from: Timing of head movements is consistent with energy minimization in walking ungulates

description: Many ungulates show a conspicuous nodding motion of the head when walking.
 Until now, the functional significance of this behaviour remained unclear.
 Combining in vivo kinematics of quadrupedal mammals with a computer model,
 we show that the timing of vertical displacements of the head and neck is
 consistent with minimizing energy expenditure for carrying these body
 parts in an inverted pendulum walking gait. Varying the timing of head
 movements in the model resulted in increased metabolic cost estimate for
 carrying the head and neck of up to 63%. Oscillations of the head–neck
 unit result in weight force oscillations transmitted to the forelimbs.
 Advantageous timing increases the load in single support phases, in which
 redirecting the trajectory of the centre of mass (COM) is thought to be
 energetically inexpensive. During double support, in which—according to
 collision mechanics—directional changes of the impulse of the COM are
 expensive, the observed timing decreases the load. Because the head and
 neck comprise approximately 10% of body mass, the effect shown here should
 also affect the animals' overall energy expenditure. This mechanism,
 working analogously in high-tech backpacks for energy-saving load
 carriage, is widespread in ungulates, and provides insight into how
 animals economize locomotion.
description: Maple
 worksheetThe .zip folder contains
 the Maple worksheet used for the publication "Timing of head
 movements is consistent with energy minimization in walking
 ungulates".Maple.zipLoscher et al Matlab CodeThe .zip folder contains all Matlab code used for the publication "Timing of head movements is consistent with energy minimization in walking ungulates". SEE README FILE FOR FURTHER EXPLANATION
DOI: 10.5061/dryad.b89k7
title: Data from: When new human-modified habitats favor the expansion of an amphibian pioneer species: evolutionary history of the natterjack toad (Bufo calamita) in a coal basin

description: Human activities affect microevolutionary dynamics by inducing
 environmental changes. In particular, land cover conversion and loss of
 native habitats decrease genetic diversity and jeopardize the adaptive
 ability of populations. Nonetheless, new anthropogenic habitats can also
 promote the successful establishment of emblematic pioneer species. We
 investigated this issue by examining the population genetic features and
 evolutionary history of the natterjack toad (Bufo [Epidalea] calamita) in
 northern France, where populations can be found in native coastal habitats
 and coalfield habitats shaped by European industrial history, along with
 an additional set of European populations located outside this focal area.
 We predicted contrasting patterns of genetic structure, with newly settled
 coalfield populations departing from migration–drift equilibrium. As
 expected, coalfield populations showed a mosaic of genetically divergent
 populations with short-range patterns of gene flow, and native coastal
 populations indicated an equilibrium state with an isolation-by-distance
 pattern suggestive of postglacial range expansion. However, coalfield
 populations exhibited (i) high levels of genetic diversity, (ii) no
 evidence of local inbreeding or reduced effective population size and
 (iii) multiple maternal mitochondrial lineages, a genetic footprint
 depicting independent colonization events. Furthermore, approximate
 Bayesian computations suggested several evolutionary trajectories from
 ancient isolation in glacial refugia during the Pleistocene, with
 biogeographical signatures of recent expansion probably confounded by
 human-mediated mixing of different lineages. From an evolutionary and
 conservation perspective, this study highlights the ecological value of
 industrial areas, provided that ongoing regional gene flow is ensured
 within the existing lineage boundaries.
description: Population coordiantes
 and genotyping dataThis file contains the
 coordinates of sample locations and nuclear and mitochondrial genetic data
 for 68 populations of the Natterjack toad (Bufo
 calamita).Data_MEC-17-0131.R1.xlsx
DOI: 10.5061/dryad.d227g
title: Data from: ‘Fix me another marguerite!’: species delimitation in a group of intensively hybridising lineages of ox-eye daisies (Leucanthemum Mill., Compositae-Anthemideae)

description: Delineating species boundaries in the framework of the multi-species
 coalescent (MSC) proves to be a reliable, objective, and reproducible
 method in an increasing number of studies. However, the underlying model
 assumes the lack of gene flow after speciation; an assumption which may be
 frequently violated in plant evolution. The present study evaluates the
 robustness of currently available species delimitation methods implemented
 in BEAST (BFD, BFD, and DISSECT) in the closely-knit ox-eye daisy group
 around Leucanthemum ageratifolium Pau. Comprising five taxa being
 allopatrically distributed between northern Spain and southern Italy this
 study group shows signs of hybridisation with the widespread and
 co-distributed species Leucanthemum vulgare (Vaill.) Lam. to various
 extent. As expected, our empirical analyses based on both AFLP
 fingerprinting and sequence data demonstrate that the robustness of
 species delimitation results is considerably influenced by the intensity
 of hybridisation among species and the number of hybrid individuals
 included. Therefore, we set up a methodological pipeline with a first step
 of identification and subsequent removal of individuals showing admixed
 genetic patterns caused by actual interbreeding using AFLP-fingerprint and
 morphometric data, followed by application of different Bayesian MSC
 species delimitation methods based on the remnant individuals using both
 AFLP-fingerprint and sequence data (four nuclear markers, five
 concatenated intergenic spacer regions of the plastid genome). The results
 argue for acknowledgement of Leucanthemum laciniatum, L. legraeanum, and
 L. ligusticum as independent species, show the close relationship of L.
 ageratifolium, L. monspeliense, and L. vulgare, and give rise to the
 description of three nothospecies new to science.
description: AFLP data
 matricesAFLP-profile matrices
 from 87 individuals of the Leucanthemum ageratifolium group. Total
 AFLP-dataset (aflpdata1) and dataset without putative hybrid individuals
 (aflpdata2).AFLP_data_matrices.zipDNA sequence alignmentsDNA sequence alignments containing sequence information of individuals of the L. ageratifolium group for four nuclear (A39, C12, C33, D23) and five chloroplast (petN-psbM, psbA-trnH, trnC-petN, trnL-trnF, trnQ-rps16) loci. Datasets, providing sequence information of all populations under study are labeled by seqdata1. Datasets without individuals of putative hybrid origin are labeled by seqdata2.DNA_sequence_alignments.zipxml files for BEAST analysesxml files for BEAST analyses (DISSECT, SNAPP, Bayes Factor delimitation). File names of total datasets (seqdata1) and datasets without individuals of putative hybrid origin (seqdata2) are labeled by different species delimitation scenarios (A-H, see publication for details) or used priors (collapsing height and collapsing weight parameters, see publication for details).XML_files_BEAST.zip
DOI: 10.5061/dryad.44b50
title: Data from: The first half of tetrapod evolution, sampling proxies, and fossil record quality

description: The first half of tetrapod evolution witnessed substantial diversification
 of the clade and several major turnovers and mass extinctions. In the time
 since their origin, more than 380 Myr ago, to the beginning of the Middle
 Jurassic 175 Myr ago, tetrapods apparently diversified fitfully, reaching
 their highest level in the Middle Permian, and showing major diversity
 declines in the late Moscovian, Early Permian, Wordian, lower
 Wuchiapingian, end-Permian, lower Anisian, lower Ladinian, Late Triassic
 (lower Norian to upper Rhaetian), end-Triassic, and Early Jurassic (upper
 Sinemurian, lower Pliensbachian). Of these diversity drops, only the
 end-Permian and end-Triassic correspond to recognised mass extinctions,
 and the late Moscovian and early Norian drops to other previously
 identified environmental crises. The remainder could be real extinction or
 turnover events, or partially artefacts of biased sampling. There are
 strong correlations between formation counts and tetrapod palaeodiversity,
 suggesting a sampling component in the raw data, but the covariation is
 not uniform through the whole time span, being poor from Devonian to
 Middle Permian, and better from Late Permian to Early Jurassic. There is
 limited evidence for covariation between the tetrapod palaeodiversity time
 series and other putative sampling metrics, such as specimen completeness,
 numbers of publications, map areas, gap-bounded sedimentary units, rock
 volumes, formations, and fossil collections. Modelling by multiple
 correlations shows that formation count is generally the best explanatory
 model, either on its own, or combined with other ‘sampling’ time series.
 However, it is not clear that formation count is independent of the
 palaeodiversity time series, because rises and falls in both signals could
 reflect variations in original diversity or in preservation or in
 sampling.
description: Data_uploadListing of all tetrapod species, from Devonian to Early Jurassic inclusive, together with stratigraphic and geographic distribution. The data were compiled from the literature, up to February 2012.
DOI: 10.5061/dryad.3hp5v
title: Data from: Population structure over a broad spatial scale driven by non-anthropogenic factors in a wide-ranging migratory mammal, Alaskan caribou

description: Wide-ranging mammals face significant conservation threats, and knowledge
 of the spatial scale of population structure and its drivers is needed to
 understand processes that maintain diversity in these species. We analysed
 DNA from 655 Alaskan caribou (Rangifer tarandus granti) from 20 herds that
 vary in population size, used 19 microsatellite loci to document genetic
 diversity and differentiation in Alaskan caribou, and examined the extent
 to which genetic differentiation was associated with hypothesized drivers
 of population subdivision including landscape features, population size
 and ecotype. We found that Alaskan caribou are subdivided into two
 hierarchically structured clusters: one group on the Alaska Peninsula
 containing discrete herds and one large group on the Mainland lacking
 differentiation between many herds. Population size, geographic distance,
 migratory ecotype and the Kvichak River at the nexus of the Alaska
 Peninsula were associated with genetic differentiation. Contrary to
 previous hypotheses, small Mainland herds were often differentiated
 genetically from large interconnected herds nearby, and genetic drift
 coupled with reduced gene flow may explain this pattern. Our results raise
 the possibility that behaviour helps to maintain genetic differentiation
 between some herds of different ecotypes. Alaskan caribou show remarkably
 high diversity and low differentiation over a broad geographic scale.
 These results increase information for the conservation of caribou and
 other migratory mammals threatened by population reductions and landscape
 barriers and may be broadly applicable to understanding the spatial scale
 and ecological drivers of population structure in widespread species.
description: caribou_Mager_et_al_MolEcol_DRYADData is a single Excel workbook with multiple worksheets. Sheet 1: msats_Alaskan_caribou Microsatellite genotypes at 19 loci for 655 caribou from 20 populations (herds). Microsatellite allele sizes are in base pairs. Missing data is indicated by '0'. Sheet 2: CBfactors_herdpairs_n&gt;4 Pairwise data for genetic differentiation, geographic distance, harmonic mean population size, and landscape features. Includes 172 herd pairs representing all possible pairs of herds except Wolf Mountain (WOLF; n=4). Please read the Molecular Ecology manuscript by Mager et al., including the Supplementary Online Resources, for details on how these data were generated and how they were used in Mantel and Random Forests analyses.
DOI: 10.5061/dryad.10j18k2
title: Data from: Seed size regulates plant dispersal distances in flowing water

description: Dispersal is an essential component of plant life, especially under the
 current threats of anthropogenic habitat fragmentation and climate change.
 For many wetland species, water is a key dispersal vector, as it can
 presumably disperse seeds long distances and towards suitable sites for
 establishment. Seed dispersal distance is affected by stream
 characteristics and seed traits. Yet, the effect of relevant seed traits,
 such as size, remains largely unknown. Here, we report on an experimental
 field study examining the effect of seed size on dispersal distance in
 lowland streams. We released cork seed mimics of different sizes in four
 Dutch lowland streams in restored and channelized sections. After 24
 hours, we recorded their entrapment location, entrapment mechanism, and
 the vegetation type in which they were caught. Large seeds generally
 dispersed over longer distances than smaller seeds. This effect of seed
 size is likely caused by the different entrapment mechanisms – net
 trapping, surface tension and wake trapping – which were highly correlated
 with seed size. Especially net trapping was responsible for the capture of
 a large proportion of small seed mimics in vegetation such as aquatic and
 riparian grasses, starwort, and reed. Due to the prevalent occurrence of
 these vegetation types in lowland streams, particularly during summer,
 smaller seeds are more likely to become entrapped and, hence, disperse
 less far. Our analysis on existing seed data reveals that water-dispersed
 riparian plants have relatively large seeds and are thereby evolutionarily
 adapted to long-distance dispersal. Furthermore, our results indicate that
 median dispersal distances are 0.02-1.8 km (99-percentile &lt;8.5 km)
 in lowland streams in summer. In winter, less vegetation is present in and
 surrounding the streams, which leads to median dispersal distances of
 0.12-14.2 km (99-percentile &lt;65 km). Synthesis: This study
 demonstrates that (1) large seeds generally disperse further than smaller
 seeds in lowland steams and (2) distances depend strongly on stream
 vegetation. This information should inform future restoration by, for
 instance, planning efforts to coincide with times or conditions of open
 water which are more favourable for the dispersal of target plant species
 – especially those with small seeds (&lt;10 mm).
description: De Jager et al. 2018
 Field experiment dataThis file contains the
 raw data of our field experiments described in De Jager et al.
 2018.deJagerData.txt
DOI: 10.5061/dryad.k4m8t
title: Data from: Limits and relationships of Paracanthopterygii: a molecular framework for evaluating past morphological hypotheses

description: Gadiforms and percopsiforms have historically been treated as prototypical
 or core paracanthopterygians. As such, they are the keys to unlocking the
 evolutionary history and limits of a revised Paracanthopterygii;
 therefore, we address the taxonomic compositions of gadiforms and
 percopsiforms and how they are related to each other and other putative
 basal acanthomorphs. We address these questions by first constructing a
 phylogenetic hypothesis based on multiple molecular sequences. Both
 maximum likelihood and parsimony criteria strongly support a
 Paracanthopterygii comprised of Percopsiformes + [Zeiformes + (Gadiformes
 + Stylephorus)]. Polymixiids are sister to this clade. Polymixiids +
 paracanthopterygians are in turn sister to the acanthopterygians
 (batrachoidiforms, beryciforms, lophiiforms, ophidioids, percomorphs) in
 the parsimony analysis but sister to Acanthopterygii + Lampriformes (minus
 Stylephorus) in the likelihood analysis. A review of published
 morphological characters, putatively pertinent to paracanthopterygian
 systematics were evaluated by the direct examination of specimens. Results
 find high congruence between the molecular tree and character-state
 distributions for many of these internal relationships. New
 interpretations of homologies of published characters are proposed based
 on topological and phylogenetic data.
description: NEXUS alignment for
 Garli of all fragmentsCharacter set 1
 represents mitochondrial tRNA-Val and 16S (characters 1-1436). Character
 set 2 represents nuclear 28S (characters 1437-2147). Character set 3-5
 represent the three codon positions of nuclear ENC1 (characters
 2148-2937). Character set 6-8 represent the three codon positions of
 nuclear histone H3 (characters 2938-3270). character set 9 represents a
 portion of nuclear RAG1 that includes an intron (characters 3271-3429).
 character set 10-12 represent the three codon positions of nuclear RAG1
 (characters 3430-4027).ForGarli.nexus
DOI: 10.5061/dryad.d548646j
title: Data from: Dietary hardness, loading behavior, and the evolution of skull form in bats

description: The morphology and biomechanics of the vertebrate skull reflect the
 physical properties of diet and behaviors used in food acquisition and
 processing. We use phyllostomid bats, the most diverse mammalian dietary
 radiation, to investigate if and how changes in dietary hardness and
 loading behaviors during feeding shaped the evolution of skull morphology
 and biomechanics. When selective regimes of food hardness are modeled, we
 found that species consuming harder foods have evolved skull shapes that
 allow for more efficient bite force production. These species have shorter
 skulls and a greater reliance on the temporalis muscle, both of which
 contribute to a higher mechanical advantage at an intermediate gape angle.
 The evolution of cranial morphology and biomechanics also appears to be
 related to loading behaviors. Evolutionary changes in skull shape and the
 relative role of the temporalis and masseter in generating bite force are
 correlated with changes in the use of torsional and bending loading
 behaviors. Functional equivalence appears to have evolved independently
 among three lineages of species that feed on liquids and are not obviously
 morphologically similar. These trends in cranial morphology and
 biomechanics provide insights into behavioral and ecological factors
 shaping the skull of a trophically diverse clade of mammals.
description: Table 1_Diet, MA, PC,
 MomentsDiet, mechanical
 advantage, skull shape and biomechanical variables for the phyllostomid
 bat species studies. Morphological data collected from dry skulls and
 biomechanical variables generated through a 3D bite force
 modelTable
 S1_Diet, MA, PC, Moments.pdfTable 2_Strain
 values_Bilateral bitingValues of tensile and
 compressive strains during finite element simulations of bilateral molar
 bitingTable
 S2_Strain values_Bilateral
 biting.pdfTables 3_Strain
 values_Unilateral bitingValues of tensile and
 compressive strains during finite element simulations of unilateral molar
 bitingTables S3_Strain
 values_Unilateral biting.pdf
DOI: 10.5061/dryad.4m0v8474
title: Data from: Not all sequence tags are created equal: designing and validating sequence identification tags robust to indels

description: Ligating adapters with unique synthetic oligonucleotide sequences
 (sequence tags) onto individual DNA samples before massively parallel
 sequencing is a popular and efficient way to obtain sequence data from
 many individual samples. Tag sequences should be numerous and sufficiently
 different to ensure sequencing, replication, and oligonucleotide synthesis
 errors do not cause tags to be unrecoverable or confused. However, many
 design approaches only protect against substitution errors during
 sequencing and extant tag sets contain too few tag sequences. We developed
 an open-source software package to validate sequence tags for conformance
 to two distance metrics and design sequence tags robust to indel and
 substitution errors. We use this software package to evaluate several
 commercial and non-commercial sequence tag sets, design several large sets
 (maxcount=7,198) of edit metric sequence tags having different lengths and
 degrees of error correction, and integrate a subset of these edit metric
 tags to polymerase chain reaction (PCR) primers and sequencing adapters.
 We validate a subset of these edit metric tagged PCR primers and
 sequencing adapters by sequencing on several platforms and subsequent
 comparison to commercially available alternatives. We find that several
 commonly used sets of sequence tags or design methodologies used to
 produce sequence tags do not meet the minimum expectations of their
 underlying distance metric, and we find that PCR primers and sequencing
 adapters incorporating edit metric sequence tags designed by our software
 package perform as well as their commercial counterparts. We suggest that
 researchers evaluate sequence tags prior to use or evaluate tags that they
 have been using. The sequence tag sets we design improve on extant sets
 because they are large, valid across the set, and robust to the suite of
 substitution, insertion, and deletion errors affecting massively parallel
 sequencing workflows on all currently used platforms.
description: Data-Supporting-Figure4-and-FigureS14Number of Illumina HiSeq 2000 reads returned for TruSeq indexes versus indexes designed using EDITTAG and incorporated to TruSeq-style sequencing adapters.Data-Supporting-FigureS11Number of 454 FLX Titanium reads returned for PCR primers incorporating 10 nt edit distance sequence tags and amplifying RbcLa in land plants.Data-Supporting-FigureS12Number of Illumina GAIIx reads returned for Epicentre Nextera indexes versus indexes designed using EDITTAG and incorporated to Epicentre Nextera-style sequencing adapters.Data-Supporting-FigureS13Number of Illumina GAIIx reads returned for TruSeq-style adapters incorporating indexes designed using EDITTAG and ligated onto pooled DNA templates (Tab 1) versus the number of Illumina HiSeq 2000 reads returned for TruSeq-style adapters incorporating indexes designed using EDITTAG and ligated onto DNA individually. The variance in read number is the important difference to note.