cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bg79cnp7q
title: Modern termites inherited the potential of collective construction from their common ancestor

description: Animal collective behaviors give rise to various spatial patterns, such as
 the nests of social insects. These structures are built by individuals
 following a simple set of rules, slightly varying within and among
 species, to produce a large diversity of shapes. However, little is known
 about the origin and evolution of the behavioral mechanisms regulating
 nest structures. In this study, we discuss the perspective of inferring
 the evolution of collective behaviors behind pattern formations using a
 phylogenetic framework. We review the collective behaviors that can be
 described by a single set of behavioral rules, and for which variations of
 the environmental and behavioral parameter values produce diverse
 patterns. We propose that this mechanism could be at the origin of the
 pattern diversity observed among related species, and that, when they are
 placed in the proper conditions, species have the behavioral potential to
 form patterns observed in related species. The comparative analysis of
 shelter-tube construction by lower termites is consistent with this
 hypothesis. Although the use of shelter-tubes in natural conditions is
 variable among species, most modern species have the potential to build
 shelter-tubes, suggesting that the behavioral rules for shelter-tube
 construction evolved once in the common ancestor of modern termites. Our
 study emphasizes that comparative studies of behavioral rules have the
 potential to shed light on the evolution of collective behaviors.
DOI: 10.5061/dryad.2fqz612kv
title: Data from: Contemporary and future distributions of cobia, Rachycentron canadum

description: Aim: Climate change has influenced the distribution and phenology of
 marine species, globally. However, knowledge of the impacts of climate
 change are lacking for many species that support valuable recreational
 fisheries. Cobia (Rachycentron canadum) are the target of an important
 recreational fishery along the U.S. east coast that is currently the
 subject of a management controversy regarding allocation and stock
 structure. Further, the current and probable future distributions of this
 migratory species are unclear, further complicating decision-making. The
 objectives of this study are to better define the contemporary
 distribution of cobia along the U.S. east coast and to project potential
 shifts in distribution and phenology under future climate change
 scenarios. Location: Chesapeake Bay and the U.S. east coast. Methods: We
 developed a depth-integrated habitat suitability model using archival
 tagging data from cobia that were caught and tagged in Chesapeake Bay
 during summer months and coupled those data with high-resolution ocean
 models to project the contemporary and future distributions of cobia along
 U.S. east coast. Results: During the winter months, suitable cobia habitat
 currently occurs in offshore waters off North Carolina and further south,
 whereas during the summer months, suitable habitat occurs in waters from
 Florida to southern New England. In warmer years, the availability of
 suitable habitat increases in northern latitudes. Under continued climate
 change over the next 40-80 years, suitable habitat is projected to shift
 northward and decrease over the shelf. Main conclusions: Habitat
 distributions suggest cobia overwinter offshore and could inhabit waters
 further north during warmer months, into state jurisdictions that do not
 have strict management regulations for cobia. When waters are warmer,
 distributions are projected to shift poleward and seasonal migrations may
 begin earlier. These results can inform resource allocation discussions
 between fishery managers and resource users.
DOI: 10.15468/dl.m25nsj
title: Occurrence Download

description: A dataset containing 45308 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-73.44 46.36,-47.12 46.36,-47.12 60.71,-73.44 60.71,-73.44 46.36))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Ochrophyta"
 ]
}

 The dataset includes 45308 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002237-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2ngf1vhjs
title: Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade

description: ABSTRACTSatellite DNAs (satDNAs) are among the most dynamically evolving
 components of eukaryotic genomes and play important roles in genome
 regulation, genome evolution, and speciation. Despite their abundance and
 functional impact, we know little about the evolutionary dynamics and
 molecular mechanisms that shape satDNA distributions in genomes. Here we
 use high-quality genome assemblies to study evolutionary dynamics of two
 complex satDNAs, Rsp-like and 1.688 gm/cm3, in Drosophila melanogaster and
 its three nearest relatives in the simulans clade. We show that large
 blocks of these repeats are highly dynamic in the heterochromatin, where
 their genomic location varies across species. We discovered that small
 blocks of satDNA that are abundant in X chromosome euchromatin are
 similarly dynamic, with repeats changing in abundance, location, and
 composition among species. We detail the proliferation of a rare satellite
 (Rsp-like) across the X chromosome in D. simulans and D. mauritiana.
 Rsp-like spreads by inserting into existing clusters of the older, more
 abundant 1.688 satellite, in events that were likely facilitated by
 microhomology-mediated repair pathways. We show that Rsp-like is abundant
 on extrachromosomal circular DNA in D. simulans, which may have
 contributed to its dynamic evolution. Intralocus satDNA expansions via
 unequal exchange and the movement of higher-order repeats also contribute
 to the fluidity of the repeat landscape. We find evidence that euchromatic
 satDNA repeats experience cycles of proliferation and diversification
 somewhat analogous to bursts of transposable element proliferation. Our
 study lays a foundation for mechanistic studies of satDNA proliferation
 and the functional and evolutionary consequences of satDNA movement.
description: Please see methods here: https://doi.org/10.1101/846238
description: This archive includes data files and custom scripts used in our
 study. We organize the repository by figure number, and include additional
 directories with scripts and general data files not associated with
 specific figures.
DOI: 10.5061/dryad.vmcvdncpx
title: Metapopulation dynamics and foraging plasticity in a highly vagile seabird, the southern rockhopper penguin

description: Population connectivity is driven by individual dispersal potential and
 modulated by natal philopatry. In seabirds, high vagility facilitates
 dispersal yet philopatry is also common, with foraging area overlap often
 correlated with population connectivity. We assess the interplay between
 these processes by studying past and current connectivity and foraging
 niche overlap among southern rockhopper penguin colonies of the coast of
 southern South America using genomic and stable isotope analyses. We found
 two distinct genetic clusters and detected low admixture between northern
 and southern colonies. Stable isotope analysis indicated niche variability
 between colonies, with Malvinas/Falklands colonies encompassing the
 species entire isotopic foraging niche, while the remaining colonies had
 smaller, nonoverlapping niches. A recently founded colony in continental
 Patagonia differed in isotopic niche width and position with
 Malvinas/Falklands colonies, its genetically identified founder
 population, suggesting the exploitation of novel foraging areas and/or
 prey items. Additionally, dispersing individuals found dead across the
 Patagonian shore in an unusual mortality event were also assigned to the
 northern cluster, suggesting northern individuals reach southern
 localities, but do not breed in these colonies. Facilitated by variability
 in foraging strategies, and especially during unfavorable conditions, the
 number of dispersing individuals may increase and enhance the probability
 of founding new colonies. Metapopulation demographic dynamics
 in seabirds should account for interannual variability in
 dispersal behavior and pay special attention to extreme climatic events,
 classically related to negative effects on population trends.
DOI: 10.5061/dryad.rfj6q5772
title: Data from: Stasis of functionally versatile specialists

description: A classic hypothesis posits that lineages exhibiting long-term stasis are
 broadly adapted generalists that remain well-adapted despite environmental
 change. However, lacking constraints that steepen adaptive peaks and
 stabilize the optimum, generalists’ phenotypes might drift around a broad
 adaptive plateau. We propose that stasis would be likely for morphological
 specialists that behave as ecological generalists much of the time because
 specialists’ functional constraints stabilize the optimum, but those with
 a broad niche can, like generalists, persist despite environmental change.
 Tree squirrels (Callosciurinae and Sciurini) exemplify ecologically
 versatile specialists, being extreme in adaptations for forceful biting
 that expand rather than limit niche breadth. Here, we examine the
 structure of disparity and the evolutionary dynamics of their trophic
 morphology (mandible size and shape) to determine if they exhibit stasis.
 In both lineages, a few dietary specialists disproportionately account for
 disparity; excluding them, we find compelling evidence for stasis of jaw
 shape but not size. The primary optima of these lineages diverge little,
 if at all over approximately 30 million years. Once their trophic
 apparatus was assembled, their morphological specialization steepened the
 slopes of their adaptive peak and constrained the position of the optima
 without limiting niche breadth.
description: The data consist of Centroid Size(CS) and coordinates of
 landmarks and semilandmarks (V1:V196), digitized from photographs,
 superimposed by a Generalized Procrustes Analysis. Each individual's
 data occupies a row in the datafile. The "Image_Name" refers to
 the name of the photograph.
DOI: 10.5061/dryad.prr4xgxhq
title: Data from: Consequences of multiple simultaneous opportunities to exploit others’ efforts on free riding

description: Individuals within a group do not all act in the same way: typically the
 investors (or producers) put efforts into producing resources while the
 free riders (or scroungers) benefit from these resources without
 contributing. In behavioural ecology, the prevalence of free riders can be
 predicted by a well-known game-theoretical model -the Producer-Scrounger
 (PS) model- where group members have the options to either search for
 resources (producers) or exploit the efforts of others (scroungers). The
 PS model has received some empirical support, but its predictions,
 surprisingly, are based on the strict assumption that only one resource
 can be exploited at a time. Yet, multiple simultaneous opportunities to
 exploit others’ efforts should frequently occur in nature. Here, we
 combine analytic and simulation approaches to explore the effect of
 multiple simultaneous scrounging opportunities on tactic use. Our analyses
 demonstrate that scrounging rates should increase with the number of
 simultaneous opportunities. As such, the amount and spatial distribution
 (i.e. clumped versus dispersed) of resources as well as the risk of
 predation are key predictors of scrounging behaviour. Because scroungers
 contribute to reducing the speed of resource exploitation, the model
 proposed here has direct relevance to the exploitation and sustainability
 of renewable resources.
description: Code of the simulation model implemented in C++
DOI: 10.5061/dryad.qnk98sfcd
title: Data from: Passive acoustic monitoring effectively detects Northern Spotted Owls and Barred Owls over a range of forest conditions

description: Passive acoustic monitoring using autonomous recording units (ARUs) is a
 fast-growing area of wildlife research especially for rare, cryptic
 species that vocalize. Northern Spotted Owl (Strix occidentalis caurina)
 populations have been monitored since the mid-1980s using mark-recapture
 methods. To evaluate an alternative survey method, we used ARUs to detect
 calls of Northern Spotted Owls and Barred Owls (S. varia), a congener that
 has expanded its range into the Pacific Northwest and threatens Northern
 Spotted Owl persistence. We set ARUs at 30, 500-ha hexagons (150 ARU
 stations) with recent Northern Spotted Owl activity and high Barred Owl
 density within Northern Spotted Owl demographic study areas in Oregon and
 Washington, and set ARUs to record continuously each night from March-July
 2017. We reviewed spectrograms (visual representations of sound) and
 tagged target vocalizations to extract calls from ~160,000 hours of
 recordings. Even in a study area with low occupancy rates on historical
 territories (Washington’s Olympic Peninsula), the probability of detecting
 a Northern Spotted Owl when it was present in a hexagon exceeded 0.95
 after 3 weeks of recording. Environmental noise, mainly from rain, wind,
 and streams, decreased detection probabilities for both species over all
 study areas. Using demographic information about known Northern Spotted
 Owls, we found that weekly detection probabilities of Northern Spotted
 Owls were higher when ARUs were closer to known nests and activity centers
 and when owls were paired, suggesting passive acoustic data alone could
 help locate Northern Spotted Owl pairs on the landscape. These results
 demonstrate that ARUs can effectively detect Northern Spotted Owls when
 they are present, even in a landscape with high Barred Owl density,
 thereby facilitating the use of passive, occupancy-based study designs to
 monitor Northern Spotted Owl populations.
description: This dataset contains two encounter histories and associated
 environmental covariates for analysis in an occupancy modeling framework.
 Encounter histories for northern spotted owls and barred owls were
 generated using passive acoustic monitoring data summarized to a weekly
 scale. In the encounter histories, dots (.) indicate weeks in which
 stations were not surveyed, zeros represent weeks in which stations were
 surveyed but the species was not detected, and ones indicate weeks in
 which stations were surveyed and the species was detected.
 Environmental covariates are untransformed values from field
 measurements or remote sensed data. Site covariates are those that do not
 vary through the season (e.g. distance from stream), while survey
 covariates vary within season (e.g. weekly temperature) and can be used to
 model within-season heterogeneity in detection probability.
DOI: 10.5061/dryad.m0cfxpp0d
title: DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies

description: Taxa are frequently labeled incertae sedis when their placement is debated
 at ranks above the species level, such as their subgeneric, generic, or
 subtribal placement. This is a pervasive problem in groups with complex
 systematics due to difficulties in identifying suitable synapomorphies. In
 this study, we propose combining DNA barcodes with a multilocus backbone
 phylogeny in order to assign taxa to genus or other higher-level
 categories. This sampling strategy generates molecular matrices containing
 large amounts of missing data that are not distributed randomly: barcodes
 are sampled for all representatives, and additional markers are sampled
 only for a small percentage. We investigate the effects of the degree and
 randomness of missing data on phylogenetic accuracy using simulations for
 up to 100 markers in 1000-tips trees, as well as a real case: the subtribe
 Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous
 species with unresolved taxonomy. Our simulation tests show that when a
 strategic and representative selection of species for higher-level
 categories has been made for multigene sequencing (approximately one per
 simulated genus), the addition of this multigene backbone DNA data for as
 few as 5–10% of the specimens in the total data set can produce
 high-quality phylogenies, comparable to those resulting from 100%
 multigene sampling. In contrast, trees based exclusively on barcodes
 performed poorly. This approach was applied to a 1365-specimen data set of
 Polyommatina (including ca. 80% of described species), with nearly 8% of
 representative species included in the multigene backbone and the
 remaining 92% included only by mitochondrial COI barcodes, a phylogeny was
 generated that highlighted potential misplacements, unrecognized major
 clades, and placement for incertae sedis taxa. We use this information to
 make systematic rearrangements within Polyommatina, and to describe two
 new genera. Finally, we propose a systematic workflow to assess
 higher-level taxonomy in hyperdiverse groups. This research identifies an
 additional, enhanced value of DNA barcodes for improvements in
 higher-level systematics using large data sets.
DOI: 10.5061/dryad.c2fqz614r
title: Caterpillars on a phytochemical landscape: the case of alfalfa and the Melissa blue butterfly

description: Modern metabolomic approaches that generate more comprehensive
 phytochemical profiles than were previously available are providing new
 opportunities for understanding plant-animal interactions. Specifically,
 we can characterize the phytochemical landscape by asking how a larger
 number of individual compounds affect herbivores and how compounds covary
 among plants. Here we use the recent colonization of alfalfa (Medicago
 sativa) by the Melissa blue butterfly (Lycaeides melissa) to quantify
 plant metabolites and the performance of caterpillars as affected by both
 individual compounds and suites of covarying phytochemicals. We find that
 survival, development time and adult weight are all associated with
 variation in nutrition and toxicity, including biomolecules associated
 with plant cell function as well as putative anti-herbivore action. The
 plant-insect interface is complex, with clusters of covarying compounds in
 many cases encompassing divergent effects on different aspects of
 caterpillar performance. Individual compounds with the strongest
 associations are largely specialized metabolites, including alkaloids,
 phenolic glycosides and saponins. The saponins are represented in our data
 by more than 25 individual compounds with beneficial and detrimental
 effects on L. melissa caterpillars, which highlights the value of
 metabolomic data as opposed to approaches that rely on total
 concentrations within broad defensive classes.
DOI: 10.5061/dryad.c2fqz614s
title: ­­Evolution of floral morphology and symmetry in the Miconieae (Melastomataceae): multiple generalization trends within a specialized family

description: Premise of the Research:Analyses of evolution of floral morphology and
 symmetry broaden our understanding of the drivers of angiosperm
 diversification. Integrated within a flower, labile floral characters
 produce different phenotypes that promote variable interactions with
 pollinators. Thus, investigation of floral evolution may help infer
 potential historic transitions in pollinator modes and ecological
 pressures that generated present diversity. This study aims to explore
 morphological evolution of flowers in Miconieae, a species-rich
 Neotropical tribe within the Melastomataceae. Despite a constrained floral
 plan, Melastomataceae manage to achieve a variety of floral phenotypes
 appealing to diverse pollinator types, with majority of the species
 requiring specialized “buzz pollination” by bees. However, previous
 research in Miconieae documented several instances of convergent evolution
 of phenotypes associated with generalized pollination strategies. We
 explore floral morphological evolution of Miconieae in a phylogenetic
 context to understand how diversification relates to different phenotypes,
 and how common evolution of generalized pollination systems is within this
 tribe. Methodology: We constructed the largest species-level phylogeny of
 the Miconieae, and combined it with morphological data on a variety of
 floral characteristics for over 350 species scored from field photographs.
 Trait evolution was then analyzed using ancestral state reconstruction
 with stochastic character mapping. Trait correlation was estimated with
 Pagel’s statistical method for discrete characters and with regression
 analysis of phylogenetically independent contrasts of continuous
 characters. We analyzed diversification in the tribe with Bayesian
 Analysis of Macroevolutionary Mixtures (BAMM) and explored the effect of
 character state evolution on diversification with the Binary State
 Speciation and Extinction (BiSSE) approach. Pivotal Results: Our analyses
 reveal rampant convergent and correlated evolution of multiple characters
 indicative of pollinator-mediated selective pressures. Conclusions: We
 confirm several parallel trends in evolution of generalized floral
 phenotypes and find an association between generalization trends and
 increased diversification rates that may be related to colonization of
 highland environments.
DOI: 10.15468/dl.r7vqu4
title: Occurrence Download

description: A dataset containing 363 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mylodon darwini"
 ]
}

 The dataset includes 363 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002238-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6086/d12x00
title: Signature of a pair of Majorana zero modes in superconducting gold surface states

description: Under certain conditions, a fermion in a superconductor can separate in
 space into two parts known as Majorana zero modes, which are immune to
 decoherence from local noise sources and are attractive building blocks
 for quantum computers. Promising experimental progress has been made to
 demonstrate Majorana zero modes in materials with strong spin-orbit
 coupling proximity coupled to superconductors. Here we show direct
 evidence of the split Majorana pair in a new material platform utilizing
 the two-dimensional surface states of gold, which is intrinsically
 scalable for building the complex nanowire circuits for topological
 qubits. Using scanning tunneling microscope to probe EuS islands grown on
 top of gold nanowires, we confirm the Majorana pair by demonstrating two
 spatially well separated zero bias tunneling conductance peaks aligned
 along the direction of the applied magnetic field. Our work opens the door
 towards scalable and robust Majorana based topological qubits.
description: Data is collected using scanning tunneling microscopy. It is
 processed using Origin software.