cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jc5616h
title: Data from: Large birds travel farther in homogeneous environments

description: Aim: Animal movement is an important determinant of individual survival,
 population dynamics, and ecosystem structure and function. Yet it is still
 unclear how local movements are related to resource availability and the
 spatial arrangement of resources. Using resident bird species and
 migratory bird species outside of the migratory period, we examined how
 the distribution of resources affect the movement patterns of both large
 terrestrial birds (e.g., raptors, bustards, hornbills) and waterbirds
 (e.g., cranes, storks, ducks, geese, flamingos). Location: Global Time
 Period: 2003 - 2015 Major taxa studied: Birds Methods: We compiled GPS
 tracking data for 386 individuals across 36 bird species. We calculated
 the straight-line distance between GPS locations of each individual at the
 1-hour and 10-day timescales. For each individual and timescale, we
 calculated the median and 0.95 quantile of displacement. We used linear
 mixed-effects models to examine the effect of the spatial arrangement of
 resources, measured as Enhanced Vegetation Index (EVI) homogeneity, on
 avian movements while accounting for mean resource availability, body
 mass, diet, flight type, migratory status and taxonomy and spatial
 autocorrelation. Results: We found a significant effect of resource
 spatial arrangement at the 1-hour and 10-day timescales. On average,
 individual movements were seven times longer in environments with
 homogeneously distributed resources compared with areas of low resource
 homogeneity. Contrary to previous work, we found no significant effect of
 resource availability, diet, flight type, migratory status or body mass on
 the non-migratory movements of birds. Main conclusions: We suggest that
 longer movements in homogeneous environments may reflect the need for
 different habitat types associated with foraging and reproduction. This
 highlights the importance of landscape complementarity, where habitat
 patches within a landscape include a range of different, yet complimentary
 resources. As habitat homogenisation increases, it may force birds to
 travel increasingly longer distances to meet their diverse needs.
description: Bird Movement and EVI
 Homogeneity DataData from Tucker et al.
 Large birds travel farther in homogeneous environments. Data includes
 species names, median displacement (km), 0.95 quantile displacement (km),
 body mass (g), mean EVI value and EVI homogeneity
 values.TuckerBirdData_DRYAD.csv
DOI: 10.5061/dryad.b5k79
title: Data from: Assessing the completeness of the fossil record: comparison of different methods applied to parareptilian tetrapods (Vertebrata: Sauropsida)

description: As paleontological studies are generally distorted by gaps and biases in
 the fossil record, it is important to assess its completeness. Here we
 address the fossil record of Parareptilia, a Permian–Triassic amniote
 clade, applying two measures of specimen completeness: the skeletal
 completeness metric (SCM) and the character completeness metric (CCM). The
 SCM quantifies how much of the skeletal material of a taxon is preserved,
 whereas the CCM measures the amount of phylogenetic information available.
 The latter was implemented using two different approaches. In this study,
 we compare three completeness metrics. Two CCM implementations show a
 strong correlation with each other, but only the second implementation of
 the CCM correlates significantly with the SCM, possibly due to character
 selection in phylogenetic data sets. There is no correlation between
 diversity of parareptiles and their completeness, implying that the
 observed fluctuations in diversity are not driven by the completeness of
 the fossils. The mean completeness of parareptiles through time is
 consistently high compared with previously studied tetrapod clades,
 suggesting that most parareptile taxa are based on reasonably complete
 specimens. Clade-specific differences reveal no link between body size and
 completeness. However, the analyses confirm the impact of ecology, with
 aquatic mesosaurids being better preserved than terrestrial taxa.
description: Supplementary Table
 1Completeness scores of
 main skeletal sections. Abbreviations: Bol: Bolosauria; Lan:
 Lanthanosuchoidea; Mes: Mesosauridae; Mil: Millerosauria; Nyc:
 Nycteroleteroidea; Par: Pareiasauria; Pro: Procolophonoidea. SCM and CCMa
 columns are the main values (same as in table 4).Verriere_et_al_SuppTab1.xlsxSupplementary Table 2Results of the three completeness metrics, assigned stratigraphical age, completeness model and clade for the 76 parareptile genera considered in this study. Abbreviations used for stratigraphical ages are the same as in Figs. 4 and 6 except for Induan (IND) and Changhsingian (CHA). Abbreviations used for model used and clade assignment are the same as in Fig. 7.Verriere_et_al_SuppTab2.xlsx
DOI: 10.5061/dryad.b7k26
title: Data from: A rare exception to Haldane’s rule: Are X chromosomes key to hybrid incompatibilities?

description: The prevalence of Haldane’s rule suggests that sex chromosomes commonly
 have a key role in reproductive barriers and speciation. However, the
 majority of research on Haldane’s rule has been conducted in species with
 conventional sex determination systems (XY and ZW) and exceptions to the
 rule have been understudied. Here we test the role of X-linked
 incompatibilities in a rare exception to Haldane’s rule for female
 sterility in field cricket sister species (Teleogryllus oceanicus and T.
 commodus). Both have an XO sex determination system. Using three
 generations of crosses, we introgressed X chromosomes from each species
 onto different, mixed genomic backgrounds to test predictions about the
 fertility and viability of each cross type. We predicted that females with
 two different species X chromosomes would suffer reduced fertility and
 viability compared with females with two parental X chromosomes. However,
 we found no strong support for such X-linked incompatibilities. Our
 results preclude X–X incompatibilities and instead support an
 interchromosomal epistatic basis to hybrid female sterility. We discuss
 the broader implications of these findings, principally whether deviations
 from Haldane’s rule might be more prevalent in species without dimorphic
 sex chromosomes.
description: Fertility data from
 three generations of hybridisation crossesNumbers of eggs and
 offspring from three generations of hybridisation crosses (F1, BC1,
 BC2).The cross types are labelled based on the species X chromosome
 identity, C= T . commodus, O = T. oceanicus, while hybrid individuals have
 a prefix either F1 or BC1 and the species identity of their X chromosomes.
 The first letter represents the maternal species and the second the
 paternal species identity. (H) indicates an inter-species recombinant
 X.Three_generations_cross_data.xlsx
DOI: 10.5061/dryad.3f0v5
title: Data from: Flying the nest: male dispersal and multiple paternity enables extrafamilial matings for the invasive bark beetle Dendroctonus micans

description: There is an evolutionary trade-off between the resources that a species
 invests in dispersal versus those invested in reproduction. For many
 insects, reproductive success in patchily-distributed species can be
 improved by sibling-mating. In many cases, such strategies correspond to
 sexual dimorphism, with males–whose reproductive activities can take place
 without dispersal–investing less energy in development of dispersive
 resources such as large body size and wings. This dimorphism is
 particularly likely when males have little or no chance of mating outside
 their place of birth, such as when sperm competition precludes successful
 fertilisation in females that have already mated. The economically
 important bark beetle pest species Dendroctonus micans (Coleoptera:
 Curculionidae, Scolytinae) has been considered to be exclusively
 sibling-mating, with 90% of females having already mated with their
 brothers by emergence. The species does not, however, show strong sexual
 dimorphism; males closely resemble females, and have been observed flying
 through forests. We hypothesised that this lack of sexual dimorphism
 indicates that male D. micans are able to mate with unrelated females, and
 to sire some or all of their offspring, permitting extrafamilial
 reproduction. Using novel microsatellite markers, we carried out
 cross-breeding laboratory experiments and conducted paternity analyses of
 resulting offspring. Our results demonstrate that a second mating with a
 less-related male can indeed lead to some offspring being sired by the
 latecomer, but that most are sired by the first, sibling male. We discuss
 these findings in the context of sperm competition versus possible
 outbreeding depression.
description: Cross-breed experiment
 results and 454 microsatellite testsIn this file are two
 sheets.The first sheet is labelled 'cross breed' and contains
 the genotyping results from the cross-breeding experiments in this study -
 females, eggs, larvae and males. The allele/s for each locus are given, as
 well as the area under the allele peak (used to estimate relative paternal
 contribution, as described in the paper). The second sheet provides the
 alleles found for each microsatellite locus identified from the 454
 sequencing analysis, tested on 95 samples. Only those loci that showed any
 polymorphism are included here. All alleles were identified by sequencing,
 with identification and allele peak area estimation done using the
 software PeakScanner (see paper for more details).Cross-breed experiment
 results.xlsx
DOI: 10.5061/dryad.rs6h2
title: Data from: A 3,000 year record of Caribbean reef urchin communities reveals causes and consequences of long-term decline in Diadema antillarum

description: Urchins are the last abundant grazers of macroalgae on most Caribbean
 reefs following the historical overexploitation of herbivorous fishes. The
 long-spined urchin Diadema antillarum was particularly effective at
 controlling macroalgae and facilitating coral dominance on Caribbean reefs
 until its ecological extinction from a catastrophic disease epidemic in
 the early 1980s. Despite their important role in the structure and
 functioning of Caribbean reef ecosystems, the natural dynamics of
 Caribbean reef urchin communities are poorly known due to the paucity of
 ecological survey data prior to large-scale human disturbances and the
 Diadema dieoff. To help resolve the baseline abundances and ecological
 roles of common urchin taxa, we track changes in urchin abundance and
 composition over the past 3,000 years from analysis of subfossil urchin
 spines preserved in reef matrix cores collected in Caribbean Panama.
 Echinometra consistently dominated the subfossil spine assemblage, while
 Diadema was consistently rare in the subfossil record in this region.
 Rather than increasing during a period of heightened human exploitation of
 their fish competitors and predators, Diadema began declining over a
 millennium ago. Convergent cross mapping (CCM) causality analyses reveal
 that Diadema abundance is causally related to coral community composition.
 Diadema is negatively affected by Acropora cervicornis dominance, likely
 due to the tight association between this coral and the threespot
 damselfish, an effective Diadema competitor. Conversely, Diadema
 positively affects the abundance of the coral Madracis mirabilis, possibly
 via its control of macroalgae. Causal relationships were not detected
 among abundances of individual urchin taxa, indicating that inter-specific
 echinoid competition is not a factor limiting Diadema recovery. Our
 detailed record of prehistorical and historical urchin community dynamics
 suggests that the failure of Diadema to recover over 30 years after its
 mass mortality event may be due in part to the prey release of damselfish
 following the long-term overfishing of piscivorous fishes.
description: Urchin and coral fossil
 data from reef coresContains absolute
 abundances of urchin and coral fossil data (by species) within each sample
 for each of four reef sediment cores. Samples are 5cm slices of each core.
 For urchin species, corrected abundances can be computed by dividing
 urchin spine weight by weight of 500um-2mm sediment size fraction. For
 coral species, relative abundances can be computed by dividing coral
 skeletal weight by total coral weight.DryadData2.csv
DOI: 10.5061/dryad.1mn40
title: Data from: PCR-based isolation of multigene families: lessons from the avian MHC class IIB

description: The amount of sequence data available today highly facilitates the access
 to genes from many gene families. Primers amplifying the desired genes
 over a range of species are readily obtained by aligning conserved gene
 regions, and laborious gene isolation procedures can often be replaced by
 quicker PCR-based approaches. However, in the case of multigene families,
 PCR-based approaches bear the often ignored risk of incomplete isolation
 of family members. This problem is most prominent in gene families with
 highly variable and thus unpredictable number of gene copies among
 species, such as in the major histocompatibility complex (MHC). In the
 present study we (i) report new primers for the isolation of the MHC class
 IIB (MHCIIB) gene family in birds, and (ii) share our experience with
 isolating MHCIIB genes from an unprecedented number of avian species from
 all over the avian phylogeny. We report important and usually
 underappreciated problems encountered during PCR-based multigene family
 isolation, and provide a collection of measures to help significantly
 improving the chance of successfully isolating complete multigene families
 using PCR-based approaches.
description: MHCIIB alignments by
 groupSanger sequence data,
 obtained by PCR, cloning and sequencing. Sequences sorted in alignments
 based on higher taxonomic groups (family/order). Each sequence name
 includes species abreviation (first two letters of the genus name and
 first two letters of species name), gene name and sequence
 ID.for
 dryad.zip
DOI: 10.5061/dryad.pb74r
title: Data from: Connecting proximate mechanisms and evolutionary patterns: pituitary gland size and mammalian life history

description: At the proximate level, hormones are known to play a critical role in
 influencing the life history of mammals, including humans. The pituitary
 gland is directly responsible for producing several hormones, including
 those related to growth and reproduction. Although we have a basic
 understanding of how hormones affect life history characteristics, we
 still have little knowledge of this relationship in an evolutionary
 context. We used data from 129 mammal species representing 14 orders to
 investigate the relationship between pituitary gland size and life history
 variation. Because pituitary gland size should be related to hormone
 production and action, we predicted that species with relatively large
 pituitaries should be associated with fast life histories, especially
 increased fetal and postnatal growth rates. Phylogenetic analyses revealed
 that total pituitary size and the size of the anterior lobe of the
 pituitary significantly predicted a life history axis that was correlated
 with several traits including body mass, and fetal and postnatal growth
 rates. Additional models directly examining the association between
 relative pituitary size and growth rates produced concordant results. We
 also found that relative pituitary size variation across mammals was best
 explained by an Ornstein-Uhlenbeck model of evolution, suggesting an
 important role of stabilizing selection. Our results support the idea that
 the size of the pituitary is linked to life history variation through
 evolutionary time. This pattern is likely due to mediating hormone levels
 but additional work is needed. We suggest that future investigations
 incorporating endocrine gland size may be critical for understanding life
 history evolution.
description: Kamilar&Tecot-AppendixS1Data used in analyses
DOI: 10.5061/dryad.nm021
title: Data from: Genetic variation in social influence on mate preferences

description: Patterns of phenotypic variation arise in part from plasticity owing to
 social interactions, and these patterns contribute, in turn, to the form
 of selection that shapes the variation we observe in natural populations.
 This proximate–ultimate dynamic brings genetic variation in social
 environments to the forefront of evolutionary theory. However, the extent
 of this variation remains largely unknown. Here, we use a member of the
 Enchenopa binotata species complex of treehoppers (Hemiptera: Membracidae)
 to assess how mate preferences are influenced by genetic variation in the
 social environment. We used full-sibling split-families as ‘treatment’
 social environments, and reared focal females alongside each treatment
 family, describing the mate preferences of the focal females. With this
 method, we detected substantial genetic variation in social influence on
 mate preferences. The mate preferences of focal females varied according
 to the treatment families along with which they grew up. We discuss the
 evolutionary implications of the presence of such genetic variation in
 social influence on mate preferences, including potential contributions to
 the maintenance of genetic variation, the promotion of divergence, and the
 adaptive evolution of social effects on fitness-related traits.
description: Female responses to
 signal stimuliThese data represent the
 responses of focal females to 19 signal stimuli that varied in their
 frequency. Each signal was presented 3 times, such that females could
 respond from 0 to 3 times to each stimulus. Females were reared alongside
 full-sibling split-families that were used as the treatment social
 environments.Rebar female
 responses.xlsx
DOI: 10.5061/dryad.8tf05
title: Data from: Individual differences are consistent across changes in mating status and mediated by biogenic amines

description: Although aspects of an individual’s state are well-known to influence the
 expression of behavior, it is still unclear how elements of state affect
 consistent among-individual differences in behavior. With binary,
 irreversible elements of state, such as mating status, there may be
 optimal behavioral phenotypes before and after mating, with individuals
 often prioritizing mate acquisition before and resource acquisition after.
 Yet, limited plasticity may prevent optimal behavior in both contexts.
 Additionally, it remains largely unknown if some consistencies in neural
 or physiological traits may limit the ability of the organism to respond
 to state changes. In this study, we investigated how changes in a binary
 state variable, mating status, affected both the mean expression and
 among-individual variation in behavior and web structure of the redback
 spider, Latrodectus hasselti. Furthermore, we explored the role of
 biogenic amines in potentially mediating individual differences in
 behavior and web structure. We found that mated females were overall more
 aggressive than virgin females and also built webs structured primarily
 for capturing prey rather than safety. We also found that individual
 differences in behavior and web structure were maintained across mating
 statuses, which indicates the stability of these traits and may drive
 personality-specific state-dependent fitness trade-offs. Finally, we found
 that aggressive spiders had higher central nervous system dopamine levels.
 Interestingly, web structure was often correlated with a catabolite of
 tyramine (N-acetyltyramine), suggesting that variation in amine
 catabolism, and not the concentrations of the amines themselves, may drive
 individual differences in some traits.
description: Data from DiRienzo and
 Aonuma BEAS 2017DiRienzo_BEAS.rar
DOI: 10.15468/dl.pj3zen
title: Occurrence Download

description: A dataset containing 299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Enteroctopus megalocyathus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 10",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 299 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001191-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.65q20
title: Data from: Modified low-salt CTAB extraction of high-quality DNA from contaminant rich tissues

description: The increasing use of high-throughput sequencing platforms has made the
 isolation of pure, high molecular weight DNA a primary concern for studies
 of a diverse range of organisms. Purification of DNA remains a significant
 challenge in many tissue and sample types due to various organic and
 inorganic molecules that co-precipitate with nucleic acids. Molluscs, for
 example, contain high concentrations of polysaccharides which often
 co-precipitate with DNA and can inhibit downstream enzymatic reactions. We
 modified a low-salt CTAB (MoLSC) extraction protocol to accommodate
 contaminant rich animal tissues and compared this method to a standard
 CTAB extraction protocol and two commercially available animal tissue DNA
 extraction kits using oyster adductor muscle. Comparisons of purity and
 molecular integrity showed that our in-house protocol yielded genomic DNA
 generally free of contaminants and shearing, whereas the traditional CTAB
 method and some of the commercial kits yielded DNA unsuitable for some
 applications of massively parallel sequencing (MPS). Our open-source MoLSC
 protocol provides a cost-effective, scalable, alternative DNA extraction
 method that can be easily optimized and adapted for sequencing
 applications in other contaminant rich samples.
description: Oyster NanoDrop DNA
 dataNanoDrop A260/280,
 A260/230, and yield estimates for genomic DNA of 24 adductor muscle
 samples extracted with 4 different methods.Oyster_DNA_data_MER_DRYAD.csvOyster NanoDrop and Qubit dataNanoDrop A260/280, A260/230, and yield estimates for genomic DNA of 24 adductor muscle samples extracted with 4 different methods. Qubit-based yield estimates are also included in this file.Oyster_DNA_data_with_qubit_MER_DRYAD.csvR scriptsR scripts for statistical analyses and figure generation.R_scripts_Arsenau_et_al_2016_for_Dryad.R