cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.76hdr7ssj
title: Divergent neurogenomic responses shape social learning of both personality and mate preference

description: Behavior plays a fundamental role in shaping the origin and fate of
 species. Mating decisions can act to promote or restrict gene flow, as can
 personality traits that influence dispersal and niche use. Mate choice and
 personality are often both learned and therefore influenced by an
 individual’s social environment throughout development. Likewise, the
 molecular pathways that shape these behaviors may also be co-expressed. In
 this study on swordtail fish (Xiphophorus birchmanni), we show that female
 mating preferences for species-typical pheromone cues are entirely
 dependent on social experience with adult males. Experience with adults
 also shapes development along the shy-bold personality axis, with shy
 behaviors arising from exposure to risk-averse heterospecifics as a
 potential stress-coping strategy. In maturing females, conspecific
 exposure results in a strong upregulation of olfaction and vision genes
 compared to heterospecific exposure, as well as immune response genes
 previously linked to anxiety, learning and memory. Conversely,
 heterospecific exposure involves an increased expression of genes
 important for neurogenesis, synaptic plasticity and social
 decision-making.  We identify subsets of genes within the social
 decision-making network and with known stress-coping roles that may be
 directly coupled to the olfactory processes females rely on for social
 communication. Based on these results, we conclude that the social
 environment affects the neurogenomic trajectory through which
 socially-sensitive behaviors are learned, resulting in adult phenotypes
 adapted for specific social groupings.
description: This data set contains the main behavioral data files used for
 analyses on personality-related and preference behaviors in this
 manuscript. These files can be directly used in R. Note that, in the
 personality data file, females with net preferences of "0" were
 defined as non-responsive and excluded from mating preference analyses.
 Please feel free to contact me if you have suggestions or find any errors
 or inconsistencies in the files. Furthermore, please let me know about
 your uses of the data.
DOI: 10.5061/dryad.3bk3j9kfm
title: Complex relationship between tunneling patterns and individual behaviors in termites

description: The nests built by social insects are complex group-level structures that
 emerge from interactions among individuals following simple behavioral
 rules. Nest patterns vary among species, and the theory of complex systems
 predicts that there is no simple one-to-one relationship between
 variations in collective patterns and variation in individual behaviors.
 Therefore, a species-by-species comparison of the actual building process
 is essential to understand the mechanism producing diverse nest patterns.
 Here we compare tunnel formation of three termite species, and reveal two
 mechanisms producing interspecific variation: in one, a common behavioral
 rule yields distinct patterns via parameter-tuning; in the other, distinct
 rules produce similar patterns. We found that two related species
 transport sand in the same way using mandibles but build tunnels with
 different degree of branching. The variation arises from different
 probabilities of choosing between two behavioral options at crowded tunnel
 faces: excavating the sidewall to make a new branch or waiting for
 clearance to extend the current tunnel. We further discovered that a third
 species independently evolved low-branched patterns using different
 building rules; namely a bucket-brigade that can excavate a crowded
 tunnel. Our findings emphasize the importance of direct comparative study
 of collective behaviors at both individual- and group-levels.
description: All data is collected through image analysis and video analysis.
 See the method section of the paper and readme.txt.
DOI: 10.5061/dryad.d2547d807
title: Translocated native pine martens Martes martes alter short-term space use by invasive non-native grey squirrels Sciurus carolinensis

description: 1. Predators can shape the distributions and dynamics of their prey
 through direct and indirect mechanisms. Where prey animals are regarded as
 pests, the augmentation of predator populations might offer a potential
 tool in their management. 2. Declines in invasive non-native grey squirrel
 Sciurus carolinensis populations in Ireland and Scotland have been related
 to an increase in range and density of native pine marten Martes martes
 populations. These reductions in grey squirrel abundance have, in turn,
 been linked to recovery of native red squirrels Sciurus vulgaris. 3.
 Taking the opportunity presented by a conservation translocation of pine
 martens from Scotland to Wales, we investigated the short-term effects of
 exposure to translocated martens on the space use and survival of resident
 grey squirrels. 4. Grey squirrel range size and daily distance travelled
 increased significantly with increasing exposure to martens but we found
 no effect of marten exposure on the recapture probability (i.e. apparent
 survival) of the sampled squirrels within the study timeframe. This is
 suggestive of contemporary, non-lethal effects changing the ranging or
 foraging regimes of squirrels, due either to predator avoidance and/or
 earlier lethal effects associated with a reduction in intraspecific
 competition. 5. Synthesis and applications. Our evaluation mimics the
 conditions experienced by grey squirrels at the front edge of
 naturally-recovering pine marten populations and presents direct evidence
 that pine marten translocations could play an influential role in the
 behaviour and dynamics of invasive non-native grey squirrel populations.
 Translocations of native predators, undertaken primarily for biodiversity
 conservation, could therefore find additional application in managing the
 ecological and economic impacts of invasive non-native prey.
description: GPS and radio telemetry of squirrels and pine martens
 following translocation of pine martens. Raw tracking data and working
 dataset are provided.
description: Details contained in ReadMe file.
DOI: 10.5061/dryad.h70rxwdfq
title: Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

description: Premise : Discordance between nuclear and organellar phylogenies
 (cytonuclear discordance) is a well-documented phenomenon at shallow
 evolutionary levels, but has been poorly investigated at deep levels of
 plant phylogeny. Determining the extent of cytonuclear discordance across
 major plant lineages is essential not only for elucidating evolutionary
 processes but also for evaluating the currently used framework of plant
 phylogeny, which is largely based on the plastid genome. Methods : We
 present a phylogenomic examination of a major angiosperm clade ( Asteridae
 ) based on sequence data from the nuclear, plastid, and mitochondrial
 genomes as a means of evaluating currently accepted relationships inferred
 from the plastome and exploring potential sources of genomic conflict in
 this group. Results : We recovered at least five instances of
 well-supported cytonuclear discordance concerning the placements of major
 asterid lineages (i.e., Ericales, Oncothecaceae, Aquifoliales, Cassinopsis
 , and Icacinaceae). We attribute this conflict to a combination of
 incomplete lineage sorting and hybridization, the latter supported in part
 by previously inferred whole-genome duplications (WGDs). Conclusions : Our
 results challenge several long-standing hypotheses of asterid
 relationships and have implications for morphological character evolution
 and for the importance of ancient WGDs in early asterid evolution. These
 findings also highlight the value of reevaluating broad-scale angiosperm
 and green plant phylogeny with nuclear genomic data. 
description: This dataset comprises nuclear, plastid, and mitochondrial gene
 sequences generated through a variety methods (target enrichment, genomic
 skimming, transcriptome sequencing, and sanger sequencing). Many of the
 sequences were obtained from publically available sources (1KP, GenBank).
 New sequences were generated using target enrichment (for nuclear genes)
 and genome skimming on the Illumina sequencing platform. Methods of gene
 assembly, alignment, and phylogenetic analysis are outlined in the
 paper.
description: Three alignments are provided, one each for the nuclear,
 chloroplast, and mitochondrial genome. Each (concatenated) alignment file
 has an assocaited partition file listing the starting and stopping
 positions of each gene. This can be used to split the concatenated
 alignements into individual gene alignments as needed.
DOI: 10.5061/dryad.vx0k6djn7
title: Juvenile rank acquisition is associated with fitness independent of adult rank

description: Social rank has been identified as a significant determinant of fitness in
 a variety of species. The importance of social rank suggests that the
 process by which juveniles come to establish their position in the social
 hierarchy is a critical component of development. Here, we use the highly
 predictable process of rank acquisition in spotted hyenas to study the
 consequences of variation in rank acquisition in early life. In spotted
 hyenas, rank is ‘inherited’ through a learning process called ‘maternal
 rank inheritance.’ This pattern is highly predictable: ~80% of juveniles
 acquire the exact rank predicted by the rules of maternal rank
 inheritance. This predictable nature of rank acquisition in these
 societies allows the process of rank acquisition to be studied
 independently from the ultimate rank that each juvenile attains. In this
 study, we use Elo-deviance scores, a novel application of the Elo-rating
 method, to calculate each juvenile’s deviation from expected pattern of
 maternal rank inheritance during development. Despite variability in rank
 acquisition among juveniles, most of these juveniles come to attain the
 exact rank expected of them according to the rules of maternal rank
 inheritance. Nevertheless, we find that transient variation in rank
 acquisition in early life is associated with long term fitness
 consequences for these individuals: juveniles ‘underperforming’ their
 expected ranks show reduced survival and lower lifetime reproductive
 success than better-performing peers, and this relationship is independent
 of both maternal rank and rank achieved in adulthood. We also find that
 multiple sources of early life adversity have cumulative, but not
 compounding, effects on fitness. Future work is needed to determine
 variation in rank acquisition directly affects fitness, or if some other
 variable, such as maternal investment or juvenile condition, causes
 variation in both of these outcomes.
DOI: 10.5061/dryad.hx3ffbgb1
title: Data from: Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of Viburnum

description: Phylogeny, molecular sequences, fossils, biogeography, and biome occupancy
 are all lines of evidence that reflect the singular evolutionary history
 of a clade, but they are most often studied separately, by first inferring
 a fossil-dated molecular phylogeny, then mapping on ancestral ranges and
 biomes inferred from extant species. Here we jointly model the evolution
 of biogeographic ranges, biome affinities, and molecular sequences,
 incorporating fossils to estimate a dated phylogeny for all of the 163
 extant species of the woody plant clade Viburnum (Adoxaceae) that we are
 recognizing now in our ongoing worldwide monographic treatment of the
 group. Our analyses indicate that while the major Viburnum lineages
 evolved in the Eocene, the majority of extant species originated since the
 Miocene. Viburnum radiated first in Asia, in warm, broad-leaved evergreen
 (lucidophyllous) forests. Within Asia we infer several early shifts into
 more tropical forests, and multiple shifts into forests that experience
 prolonged freezing. From Asia we infer two early movements into the New
 World. These two lineages probably first occupied warm temperate forests
 and adapted later to spreading cold climates. One of these lineages
 (Porphyrotinus) occupied cloud forests and moved south through the
 mountains of the Neotropics. Several other movements into North America
 took place more recently, facilitated by prior adaptations to freezing in
 the Old World. We also infer four disjunctions between Asia and Europe:
 the Tinus lineage is the oldest and probably occupied warm forests when it
 spread, while the other three were more recent and in cold-adapted
 lineages. These results variously contradict published accounts,
 especially the view that Viburnum radiated initially in cold forests and,
 accordingly, maintained vessel elements with scalariform perforations. We
 explored how the location and biome assignments of fossils affected our
 inference of ancestral areas and biome states. Our results are sensitive
 to, but not entirely dependent upon, the inclusion of fossil biome data.
 It will be critical to take advantage of all available lines of evidence
 to decipher events in the distant past. The joint estimation approach
 developed here provides cautious hope even when fossil evidence is
 limited.
description: The main text and the supplement describe how the data were
 collected in detail. The zip file containing the data also contains a
 README.md file that overviews its contents.
description: RevBayes code for the phylogenetic analysis and plotting scripts
 for the figures are hosted on GitHub:
 https://github.com/mlandis/vib_div.
DOI: 10.5061/dryad.mgqnk98wb
title: Phylogeny and biogeographic history of the Chiropotes (Pitheciidae, Platyrrhini)

description: Pitheciidae is a New Word primate family composed of two subfamilies
 (Callicebinae and Pitheciinae). The three extant pitheciine genera,
 Pithecia, Cacajao and Chiropotes are all endemic to the Amazon region.
 Because of the uncertainties about intraspecific relationships, we
 reviewed the systematics and taxonomy of the genus Chiropotes. The
 phylogenetic analyses were performed based on Maximum Likelihood and
 Bayesian Inference, while species delimitation analyses were carried out
 using multispecies coalescent methods. In addition, we estimated genetic
 distances, divergence time and the probable ancestral distribution of this
 genus. Our results support the taxonomic classification of Chiropotes into
 five species that have emerged during the Plio-Pleistocene. Biogeographic
 estimates suggest that the ancestor of the current Chiropotes species
 occupied the endemism areas from Rondonia and Tapajos. Later, subsequent
 radiation and founder effects associated with the formation of the
 Amazonian basins have probably determined the speciation events within
 Chiropotes.
description: Twenty samples of blood and muscle
 tissue preserved in alcohol were analyzed in the present study. These
 included four <i>Chiropotes </i>taxa, <i>C. albinasus
 </i>(n = 04 samples), <i>C. satanas </i>(n = 03),
 <i>C. utahicki </i>(n = 05), and <i>C. sagulatus
 </i>(n = 03), as well as <i>Cacajao melanocephalus
 </i>(n = 03), <i>Pithecia pithecia</i> (n = 01), and
 <i>Plecturocebus moloch </i>(n = 01). These samples were
 obtained from the DNA databanks at the Federal University of Pará (UFPA)
 in Belém and from the Federal University of Amazonas (UFAM) in Manaus,
 both in Brazil. The UFPA samples are referenced in previous papers (Rocha
 et al., 1990; Sampaio et al., 1991; Schneider et al., 1994). Samples from
 UFAM were obtained from the wild under permits 40217-1 and 5135-1,
 supplied by the Instituto Chico Mendes de Conservação da Biodiversidade -
 ICMBio. The sequences were aligned using
 ClustalW (Thompson et al., 1994) and edited manually in BioEdit v.7.2.5
 (Hall, 1999). PartitionFinder v.1.1.0 (Lanfear et al., 2012) was used to
 identify the optimal data partitioning and evolutionary
 models. Phylogenetic analyses were based on Maximum Likelihood (ML) and
 Bayesian Inference (BI) approaches. Species were delimited using the
 software Bayesian Phylogenetics and Phylogeography (BPP). In order to
 estimate the biogeographic history of distributional ranges of cuxius, we
 used BioGeoBEARS ‘Biogeography with Bayesian (and likelihood) Evolutionary
 Analysis’ in R Scripts (Matzke, 2013). Six
 discrete biogeographic areas were
 defined: Belem (BE), Xingu (XI), Tapajos (TA), Rondonia (RO), Guyana (GU)
 and Tepui (PA).
DOI: 10.5061/dryad.4f4qrfj83
title: Time travelling seeds reveal that plant regeneration and growth traits are responding to climate change

description: Studies assessing the biological impacts of climate change typically rely
 on long-term, historic data. Here, we overcame the problem of absent
 historical data by using resurrected plant seeds. We collected seed and
 seedling trait measurements from resurrected historic seeds and modern
 seeds from the same species in the same geographic location. Our
 modern/historic seed pairs for each species were selected from a range of
 regions that have undergone different amounts o climate change. In regions
 where climate has changed to a greater degree (across a number of climate
 change variables), we found plant regeneration and growth traits to have
 changed more than in regions where climate changes have been marginal.
 Statistical model predictors of regeneration and growth trait changes
 (except stem density) combined at least two measures of climate change,
 indicating that these changes are correlated to climate change and that
 compounded changes, rather than change in a single climate metric, lead to
 plant regeneration and growth trait responses. Synthesis: plant trait
 responses to climate change are positive news for the future of plants,
 hinting at their ability to respond relatively swiftly as the climate
 continues to change.
description: All data was collected through historic records of the older
 seeds (where they were collected, how they were stored) and also by lead
 author Susan Everingham. All data was collected by measuring seeds and
 seedlings in the experiment and no data has been processed in the uploaded
 files. All data processing occurred in R studio and code is freely
 available at (https://github.com/SEveringham/regeneration-and-growth-plant-trait-responses-to-climate-change).
description: No missing values.
DOI: 10.5061/dryad.08kprr4zk
title: Longer is not always better: optimizing barcode length for large-scale species discovery and identification

description: New techniques for the species-level sorting of millions of specimens are
 needed in order to accelerate species discovery, determine how many
 species live on earth, and develop efficient biomonitoring techniques.
 These sorting methods should be reliable, scalable and cost-effective, as
 well as being largely insensitive to low-quality genomic DNA, given that
 this is usually all that can be obtained from museum specimens.
 Mini-barcodes seem to satisfy these criteria, but it is unclear how well
 they perform for species-level sorting when compared to full-length
 barcodes. This is here tested based on 20 empirical datasets covering ca.
 30,000 specimens (5,500 species) and six clade-specific datasets from
 GenBank covering ca. 98,000 specimens (&gt;20,000 species). All
 specimens in these datasets had full-length barcodes and had been sorted
 to species-level based on morphology. Mini-barcodes of different lengths
 and positions were obtained in silico from full-length barcodes using a
 sliding window approach (3 windows: 100-bp, 200-bp, 300-bp) and by
 excising nine mini-barcodes with established primers (length: 94 –
 407-bp). We then tested whether barcode length and/or position reduces
 species-level congruence between morphospecies and molecular Operational
 Taxonomic Units (mOTUs) that were obtained using three different species
 delimitation techniques (PTP, ABGD, objective clustering). Surprisingly,
 we find no significant differences in performance for both species- or
 specimen-level identification between full-length and mini-barcodes as
 long as they are of moderate length (&gt;200-bp). Only very short
 mini-barcodes (&lt;200-bp) perform poorly, especially when they are
 located near the 5’ end of the Folmer region. The mean congruence between
 morphospecies and mOTUs was ca. 75% for barcodes &gt;200-bp and the
 congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused
 by ca. 10% of the specimens that can be identified and should be targeted
 for re-examination in order to efficiently resolve conflict. Our study
 suggests that large-scale species discovery, identification, and
 metabarcoding can utilize mini-barcodes without any demonstrable loss of
 information compared to full-length barcodes.
description: gi/gb numbers and sample IDs of DNA sequences downloaded from
 GenBank and BOLDSystems. Gel images generated with
 313-bp and 658-bp PCR products of the same sample in each lane.
 Supplementary figures and tables.
DOI: 10.5061/dryad.v9s4mw6rg
title: Coping with branch excision when measuring leaf net photosynthetic rates in a lowland tropical forest

description: Measuring leaf gas exchange from canopy leaves is fundamental for our
 understanding of photosynthesis and for a realistic representation of
 carbon uptake in vegetation models. Since canopy leaves are often
 difficult to reach, especially in tropical forests with emergent trees up
 to 60 meters at remote places, canopy access techniques such as canopy
 cranes or towers have facilitated photosynthetic measurements. These
 structures are expensive and therefore not very common. As an alternative,
 branches are often cut to enable leaf gas exchange measurements. The
 effect of branch excision on leaf gas exchange rates should be minimised
 and quantified to evaluate possible bias. We compared light-saturated leaf
 net photosynthetic rates measured on excised and intact branches. We
 selected branches positioned at three canopy positions, estimated relative
 to the top of the canopy: upper sunlit foliage, middle canopy foliage, and
 lower canopy foliage. We studied the variation of the effects of branch
 excision and transport amongst branches at these different heights in the
 canopy. After excision and transport, light-saturated leaf net
 photosynthetic rates were close to zero for most leaves due to stomatal
 closure. However, when the branch had acclimated to its new environmental
 conditions – which took on average 20 minutes –light-saturated leaf net
 photosynthetic rates did not significantly differ between the excised and
 intact branches. We therefore conclude that branch excision does not
 affect the measurement of light-saturated leaf net photosynthesis,
 provided that the branch is recut under water and is allowed sufficient
 time to acclimate to its new environmental conditions.
description: For methods we refer to the manuscript.
description: See info file