cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3j8t5
title: Data from: Intrinsic and extrinsic factors act at different spatial and temporal scales to shape population structure, distribution and speciation in Italian Barbus (Osteichthyes: Cyprinidae)

description: Previous studies have given substantial attention to external factors that
 affect the distribution and diversification of freshwater fish in Europe
 and North America, in particular Pleistocene and Holocene glacial cycles.
 In the present paper we examine sequence variation at one mitochondrial
 and four nuclear loci (over 3 kbp) from populations sampled across several
 drainages of all species of Barbus known to inhabit Italian freshwaters
 (introduced B. barbus and native B. balcanicus, B. caninus, B. plebejus
 and B. tyberinus). By comparing species with distinct ecological
 preferences (rheophilic and fluvio-lacustrine) and using a
 fossil-calibrated phylogeny we gained considerable insight about the
 intrinsic and extrinsic processes shaping barbel distribution, population
 structure and speciation. We found that timescales of Italian barbel
 diversification are older than previously thought, starting in the Early
 Miocene, and involving local and regional tectonism and basin
 paleo-evolution rather than Pleistocene glacial cycles. Conversely, more
 recent environmental factors associated with glaciation–deglaciation
 cycles have influenced species distributions. These events had a more
 marked impact on fluvio-lacustrine than on rheophilic species by means of
 river confluence at low sea levels. We show that genetic structure is
 influenced by species ecology: populations of small rheophilic species
 inhabiting upper river stretches of large basins are less connected and
 more differentiated than large fluvio-lacustrine species that inhabit
 lower river courses. We report the existence of both natural and
 human-induced interspecific gene flow, which could have great impacts on
 the evolution and persistence of species involved. In addition, we provide
 evidence that B. tyberinus is genetically distinguishable from all other
 Italian taxa and that its morphological similarity to B. plebejus and
 intermediacy with B. caninus are best explained by recent common ancestry
 and similar ecology with the former, rather than by hybrid origin
 involving these two species as previously hypothesized.
description: Cytochrome_bCytochrome b sequencescytb.fasGrowth_Hormone_1Growth Hormone-1 sequences phasedgh1complete.fasGrowth_Hormone_2Growth Hormone-2 sequences phasedgh2complete2.fasS7_1S7-1 sequences phaseds71complete.fasS7_2S7-2 sequences phaseds7_2complete no usat.fas
DOI: 10.5061/dryad.66s7c
title: Data from: A major gene for bovine ovulation rate

description: Half-sib daughters sired by a bull believed to be a carrier of a major
 gene for high ovulation rate were evaluated for ovulation rate and
 genotyped in an effort to both test the hypothesis of segregation of a
 major gene and to map the gene’s location. A total of 131 daughters were
 produced over four consecutive years at a University of Wisconsin-Madison
 research farm. All were evaluated for ovulation rate over an average of
 four estrous cycles using transrectal ultrasonography. The sire and all
 daughters were genotyped using a 3K SNP chip and the genotype and
 phenotype data were used in a linkage analysis. Subsequently, daughters
 recombinant within the QTL region and the sire were genotyped successively
 with 50K and 777K SNP chips to refine the location of the causative
 polymorphism. Positional candidate genes within the fine-mapped region
 were examined for polymorphism by Sanger sequencing of PCR amplicons
 encompassing coding and 5’ and 3’ flanking regions of the genes. Sire DNA
 was used as template in the PCR reactions. Strong evidence of a major gene
 for ovulation rate was observed (p&lt;1x10-28) with the gene localized
 to bovine chromosome 10. Fine-mapping subsequently reduced the location to
 a 1.2 Mb region between 13.6 and 14.8 Mb on chromosome 10. The location
 identified does not correspond to that for any previously identified major
 gene for ovulation rate. This region contains three candidate genes,
 SMAD3, SMAD6 and IQCH. While candidate gene screening failed to identify
 the causative polymorphism, three polymorphisms were identified that can
 be used as a haplotype to track inheritance of the high ovulation rate
 allele in descendants of the carrier sire.
description: Ovulation rate
 phenotypesAverage ovulation rate
 of study animals over approximately four estrous
 cycles.Dataset_S1_phenotypes.txtGenotypesGenotype data for study animalsDataset_S2_genotypes.txt.zip
DOI: 10.5061/dryad.4tn05
title: Data from: Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using next-gen derived plastid sequences

description: Premise of the study: Several studies have incorporated molecular and
 morphological data to study the phylogeny of the palms (Arecaceae), but
 some relationships within the family remain ambiguous—particularly those
 within Arecoideae, the most diverse subfamily including coconut and oil
 palm. Here, two next-generation, targeted plastid-enrichment methods were
 compared and used to elucidate Arecoideae phylogeny. Methods:
 Next-generation sequencing techniques were used to generate a plastid
 genome data set. Long range PCR and hybrid gene capture were used to
 enrich for chloroplast targets. Ten taxa were enriched using both methods
 for comparison. Chloroplast sequence data were generated for 31
 representatives of the 14 Arecoideae tribes and five outgroup taxa. The
 phylogeny was reconstructed using maximum likelihood, maximum parsimony,
 and Bayesian analyses. Key results: Long range PCR and hybrid gene capture
 both enriched the plastid genome and provided similar sequencing coverage.
 Subfamily Arecoideae was resolved as monophyletic with tribe Chamaedoreeae
 as the earliest-diverging lineage, implying that the development of
 flowers in triads defines a synapomorphy for the Arecoideae clade
 excluding Chamaedoreeae. Three major clades within this group were
 recovered: Roystoneeae/Reinhardtieae/Cocoseae (RRC),
 Areceae/Euterpeae/Geonomateae/Leopoldinieae/Manicarieae/Pelagodoxeae (core
 arecoids), and Podococceae/Oranieae/Sclerospermeae (POS). An Areceae +
 Euterpeae clade was resolved within the core arecoids. The POS clade was
 sister to a RRC + core arecoids clade, implying a shared ancestral area in
 South America for these three clades. Conclusions: The plastome phylogeny
 recovered here provides robust resolution of previously ambiguous studies
 and new insights into palm evolution.
description: Nexus file of 114
 chloroplast genes and gene positionsNexus file containing
 the 114 genes data set followed by the position of each gene with the
 matrix.NEXUS file of 114 chloroplast
 genes and gene postion.txtM1 Langrange combined
 input and outputCombined Lagrange M1
 model input python script followed by the results output. This includes
 the dispersal constraints, geographic coding for taxa, concatenated 85
 genes ML tree, and inferred ancestral areas within two log-likelihoods of
 the most likely area with relative probabilities.
DOI: 10.5061/dryad.n64kk
title: Data from: Salt tolerance is evolutionarily labile in a diverse set of angiosperm families

description: Background: Salt tolerance in plants is rare, yet they it is found across
 a diverse set of taxonomic groups. This suggests that, although salt
 tolerance involves a complex set of traits, it has evolved many times
 independently in different angiosperm lineages. However, the pattern of
 evolution of salt tolerance can vary dramatically between families. A
 recent phylogenetic study of the Chenopodiaceae (goosefoot family)
 concluded that salt tolerance has a conserved evolutionary pattern, being
 gained early in the evolution of the lineage then retained by most species
 in the family. Conversely, a phylogenetic study of the Poaceae (grass
 family) suggested over 70 independent origins of salt tolerance, most
 giving rise to only one or a few salt tolerant species. Here, we use a
 phylogenetic approach to explore the macroevolutionary patterns of salt
 tolerance in a sample of angiosperm families, in order to ask whether
 either of these two patterns - deep and conserved or shallow and labile -
 represents a common mode of salt tolerance evolution. We analyze the
 distribution of halophyte species across the angiosperms and identify
 families with more or less halophytes than expected under a random model.
 Then, we explore the phylogenetic distribution of halophytes in 22
 families using phylogenetic comparative methods. Results: We find that
 salt tolerance species have been reported from over one-third of
 angiosperm families, but that salt tolerant species are not distributed
 evenly across angiosperm families. We find that salt tolerance has evolved
 hundreds of times over the history of the angiosperms. In a few families,
 we find deep and conserved origins of evolution of salt tolerance, but in
 the majority of families analyzed, we find that salt tolerance evolution
 is characterized by multiple independent origins that occur near the tips
 of the phylogeny and often give rise to only one or a few halophytes.
 Conclusions: Our results suggest that salt tolerance is evolutionarily
 labile in many different angiosperm families. Thus, the evolutionary
 pattern of many independent origins of salt tolerance near the tips of the
 phylogeny found previously in the grasses and observed in several other
 angiosperm families represents a common feature of salt tolerance
 evolution. Our findings add to the growing literature of the repeated
 evolution of complex ecological traits.
description: Data_salt_tolerance_angiosperms_Moray_et_al_BMC_Evo_BioPlease see ReadMe file.Data_salt_tolerance_angiosperms.zip
DOI: 10.5061/dryad.9k219
title: Data from: Composite collective decision making

description: Individual animals are adept at making decisions and have cognitive
 abilities, such as memory, which allow them to hone their decisions.
 Social animals can also share information. This allows social animals to
 make adaptive group-level decisions. Both individual and collective
 decision-making systems also have drawbacks and limitations, and while
 both are well studied, the interaction between them is still poorly
 understood. Here, we study how individual and collective decision-making
 interact during ant foraging. We first gathered empirical data on
 memory-based foraging persistence in the ant Lasius niger. We used these
 data to create an agent-based model where ants may use social information
 (trail pheromones), private information (memories) or both to make
 foraging decisions. The combined use of social and private information by
 individuals results in greater efficiency at the group level than when
 either information source was used alone. The modelled ants couple
 consensus decision-making, allowing them to quickly exploit high-quality
 food sources, and combined decision-making, allowing different individuals
 to specialize in exploiting different resource patches. Such a composite
 collective decision-making system reaps the benefits of both its
 constituent parts. Exploiting such insights into composite collective
 decision-making may lead to improved decision-making algorithms.
description: ESM 3 - complete model
 datasetThe complete model
 dataset used in this publicationEmpirical data for
 Lasius niger ants foraging persistenceThe raw empirical data
 collected for the study, and used to inform the behaviour of ants in the
 model.Empirical data - lasius niger
 foraging persistence.xlsxESM 2 - complete netlogo
 modelThe complete Netlogo
 model, and all files nececcary to run it. Netlogo must be installed in
 order to run the model. Netlogo is available for free from
 https://ccl.northwestern.edu/netlogo. Note that the two .nls files must be
 in the same folder as the .nlogo file in order for the model to work. A
 full description of the model is available in the "information"
 tab inside the model.
DOI: 10.5061/dryad.n3581
title: Data from: Molecular phylogeny of Squaliformes and first occurrence of bioluminescence in sharks

description: Background: Squaliform sharks represent approximately 27 % of extant shark
 diversity, comprising more than 130 species with a predominantly
 deep-dwelling lifestyle. Many Squaliform species are highly specialized,
 including some that are bioluminescent, a character that is reported
 exclusively from Squaliform sharks within Chondrichthyes. The
 interfamiliar relationships within the order are still not satisfactorily
 resolved. Herein we estimate the phylogenetic interrelationships of a
 generic level sampling of “squaloid” sharks and closely related taxa using
 aligned sequences derived from a targeted gene capture approach. The
 resulting phylogenetic estimate is further used to evaluate the age of
 first occurrence of bioluminescence in Squaliformes. Results: Our dataset
 comprised 172 putative ortholog exon sequences. Phylogenetic estimates
 result in a fully resolved tree supporting a monophyletic lineage of
 Squaliformes excluding Echinorhinus. Non-luminous Squalidae are inferred
 to be the sister to a clade comprising all remaining Squaliform families.
 Our results suggest that the origin of photophores is coincident with an
 elevated diversification rate and the splitting of families Dalatiidae,
 Etmopteridae, Oxynotidae and Somniosidae at the transition of the Lower to
 the Upper Cretaceous. The presence of luminous organs was confirmed for
 the Sleeper shark genus Zameus. These results indicate that
 bioluminescence in sharks is not restricted solely to the families
 Etmopteridae and Dalatiidae as previously believed. Conclusions: The
 sister-clade to non-luminous Squalidae comprises five families. The
 presence of photophores is reported for extant members of three out of
 these five families based on results of this study, i.e. Lantern sharks
 (Etmopteridae), Kitefin sharks (Dalatiidae) and Sleeper sharks
 (Somniosidae). Our results suggest that the origin of luminous organs
 arose during the rapid diversification event that gave rise to the extant
 Squaliform families. These inferences are consistent with the idea of
 diversification of Squaliform sharks being associated with the emergence
 of new deep-sea habitats in the Lower Cretaceous, which may have been
 facilitated by the evolution of bioluminescence.
description: Straube_et_al_Squaliform_phylogeny_dataThese files contain data supporting results from Straube et al. 2015. Please see also Additional file 1 of the article.
DOI: 10.5061/dryad.dc02b
title: Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture

description: Studies of species with continental distributions continue to identify
 intraspecific lineages despite continuous habitat. Lineages may form due
 to isolation by distance, adaptation, divergence across barriers, or
 genetic drift following range expansion. We investigated lineage
 diversification and admixture within American black bears (Ursus
 americanus) across their range using 22 k single nucleotide polymorphisms
 and mitochondrial DNA sequences. We identified three subcontinental
 nuclear clusters which we further divided into nine geographic regions:
 Alaskan (Alaska-East), eastern (Central Interior Highlands, Great Lakes,
 Northeast, Southeast), and western (Alaska-West, West, Pacific Coast,
 Southwest). We estimated that the western cluster diverged 67 ka, before
 eastern and Alaskan divergence 31 ka; these divergence dates contrasted
 with those from the mitochondrial genome where clades A and B diverged
 1.07 Ma, and clades A-east and A-west diverged 169 ka. We combined
 estimates of divergence timing with hindcast species distribution models
 to infer glacial refugia for the species in Beringia, Pacific Northwest,
 Southwest, and Southeast. Our results show a complex arrangement of
 admixture due to expansion out of multiple refugia. The delineation of the
 genomic population clusters was inconsistent with the ranges for 16
 previously described subspecies. Ranges for U. a. pugnax and U. a.
 cinnamomum were concordant with admixed clusters, calling into question
 how to order taxa below the species level. Additionally, our finding that
 U. a. floridanus has not diverged from U. a. americanus also suggests that
 morphology and genetics should be reanalyzed to assess taxonomic
 designations relevant to the conservation management of the species.
description: Puckett_etal-MaxEntInputGeographic coordinates used as input in MaxEnt species distribution model.Puckett_etal-mtDNA_HaplotypeListList of samples and the identified mitochondrial haplotype. See GenBank accessions: AY334363–AY334367 (Onorato et al 2004), FJ619652–FJ619659 (Van Den Bussche et al 2009), KJ406324-KJ406336 (Puckett et al 2014), and KM230048-KM230113 (this paper).Puckett_etal-SSR_DataMicrosatellite genotypes (15 loci) used for inference of effective population size by regional cluster.Puckett_etal-U_amer_29k_SNPsPED file with 29,213 SNPs for Ursus americanus. Data were clustered the following way: 1- AK-East, 2- Central Interior Highlands, 3- Great Lakes, 4- Northeast, 5- Southeast, 6- AK-West, 7- West, 8- Southwest, 9- Pacific Coast.Puckett_etal-U_amer_29k_SNPsMAP file that accompanies PED file for analyzing SNP data in PLINK.
DOI: 10.5878/000437
title: The Regional Skåne SOM Survey 2004
title: SOM-undersökningen i Skåne 2004
title: Syd-SOM 2004

description: This is the second SOM survey carried out in the Skåne region. Unlike Southern SOM 2001 - geographically limited to ten municipalities in the south western part of Skåne - the 2004 survey was carried out in the whole Skåne region. The questionnaire consists of nine coherent parts: press, radio and television; politics and society; society and service; traffic; holdings of technology and internet; questions about the closed down newspaper Arbetet; activities and leisure habits; working life; and background.

Purpose:
Study attitudes and behaviour linked to local and regional issues.
description: Detta är den andra SOM-undersökning som genomförts i Skåne. Till skillnad mot Syd-SOM 2001 - som var geografiskt begränsad till tio kommuner i sydvästra Skåne - har Syd-SOM 2004 genomförts i hela region Skåne. Frågeformuläret består av nio sammanhållna frågeområden: press, radio och TV; politik och samhälle; samhälle och service; trafik; teknikinnehav och internet; frågor kring den nedlagda tidningen Arbetet; aktiviter och fritidsvanor; arbetsliv; samt bakgrundsfrågor.

Syfte:
Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5878/002382
title: The Regional Skåne SOM Survey 2004
title: SOM-undersökningen i Skåne 2004
title: Syd-SOM 2004

description: This is the second SOM survey carried out in the Skåne region. Unlike Southern SOM 2001 - geographically limited to ten municipalities in the south western part of Skåne - the 2004 survey was carried out in the whole Skåne region. The questionnaire consists of nine coherent parts: press, radio and television; politics and society; society and service; traffic; holdings of technology and internet; questions about the closed down newspaper Arbetet; activities and leisure habits; working life; and background.

Purpose:
Study attitudes and behaviour linked to local and regional issues.
description: Detta är den andra SOM-undersökning som genomförts i Skåne. Till skillnad mot Syd-SOM 2001 - som var geografiskt begränsad till tio kommuner i sydvästra Skåne - har Syd-SOM 2004 genomförts i hela region Skåne. Frågeformuläret består av nio sammanhållna frågeområden: press, radio och TV; politik och samhälle; samhälle och service; trafik; teknikinnehav och internet; frågor kring den nedlagda tidningen Arbetet; aktiviter och fritidsvanor; arbetsliv; samt bakgrundsfrågor.

Syfte:
Studera attityder och beteenden som är knutna till lokala och regionala frågor och företeelser.
DOI: 10.5061/dryad.p1529
title: Data from: Assessment of disability among the elderly in Xiamen of China: a representative sample survey of 14,292 older adults

description: Background: The unprecedented number of elderly individuals in China
 presents a serious public health challenge. Limited data are available on
 the prevalence of disability or factors resulting in disability among the
 elderly in China. Objective: We aimed to assess the prevalence of
 disability and related risk factors among the elderly of Xiamen, China.
 Methods: A cross-sectional study was performed on individuals who were ≥60
 years of age. The subjects were recruited by multi-stage sampling; a total
 of 14,292 valid questionnaires were received. Study measurements included
 activities of daily living (ADL), demographics, and health status. The ADL
 was assessed by the Katz Index Scale to evaluate disability. Chi-square
 tests and binary logistic regression were used to identify factors
 associated with disabilities. Results: Among the valid participants, 4.27%
 had at least one disability. Bathing was the most frequently reported
 disability and feeding was the least frequently reported disability.
 Disabilities were significantly associated with female gender, older age,
 unmarried status, living with family, urban residence, illiteracy, poor
 economic status, self-rated bad health, chronic illnesses, lower life
 satisfaction, bad mood, and feelings of loneliness. Conclusion: Functional
 disability among the elderly requires more public attention. Culturally
 appropriate policies and programs are also needed to address the care for
 the disabled elderly.
description: Assessment of disability
 among the elderly in Xiamen of China a representative sample survey sample
 of 14,292 older adults
DOI: 10.5061/dryad.4b3cd
title: Data from: Evidence for a pervasive ‘idling-mode’ activity template in flying and pedestrian insects

description: Understanding the complex movement patterns of animals in natural
 environments is a key objective of ‘movement ecology’. Complexity results
 from behavioural responses to external stimuli but can also arise
 spontaneously in their absence. Drawing on theoretical arguments about
 decision-making circuitry, we predict that the spontaneous patterns will
 be scale-free and universal, being independent of taxon and mode of
 locomotion. To test this hypothesis, we examined the activity patterns of
 the European honeybee, and multiple species of noctuid moth, tethered to
 flight mills and exposed to minimal external cues. We also reanalysed
 pre-existing data for Drosophila flies walking in featureless
 environments. Across these species, we found evidence of common
 scale-invariant properties in their movement patterns; pause and movement
 durations were typically power law distributed over a range of scales and
 characterized by exponents close to 3/2. Our analyses are suggestive of
 the presence of a pervasive scale-invariant template for locomotion which,
 when acted on by environmental cues, produces the movements with
 characteristic scales observed in nature. Our results indicate that
 scale-finite complexity as embodied, for instance, in correlated random
 walk models, may be the result of environmental cues overriding innate
 behaviour, and that scale-free movements may be intrinsic and not limited
 to ‘blind’ foragers as previously thought.
description: Flight mill
 dataFlight mill data for
 wild British noctuid moths, African armyworms and the European
 honeybee