cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9418j
title: Data from: Microsatellite marker development by multiplex Ion Torrent PGM sequencing: a case study of the endangered Odorrana narina complex of frogs

description: The endangered Ryukyu tip-nosed frog Odorrana narina and its related
 species, Odorrana amamiensis, Odorrana supranarina, and Odorrana
 utsunomiyaorum, belong to the family Ranidae and are endemically
 distributed in Okinawa (O. narina), Amami and Tokunoshima (O. amamiensis),
 and Ishigaki and Iriomote (O. supranarina and O. utsunomiyaorum) Islands.
 Because of varying distribution patterns, this species complex is an
 intrinsic model for speciation and adaptation. For effective conservation
 and molecular ecological studies, further genetic information is needed.
 For rapid, cost-effective development of several microsatellite markers
 for these and 2 other species, we used next-generation sequencing
 technology of Ion Torrent PGM™. Distribution patterns of repeat motifs of
 microsatellite loci in these modern frog species (Neobatrachia) were
 similarly skewed. We isolated and characterized 20 new microsatellite loci
 of O. narina and validated cross-amplification in the three-related
 species. Seventeen, 16, and 13 loci were cross-amplified in O. amamiensis,
 O. supranarina, and O. utsunomiyaorum, respectively, reflecting close
 genetic relationships between them. Mean number of alleles and expected
 heterozygosity of newly isolated loci varied depending on the size of each
 inhabited island. Our findings suggested the suitability of Ion Torrent
 PGM™ for microsatellite marker development. The new markers developed for
 the O. narina complex will be applicable in conservation genetics and
 molecular ecological studies.
description: genotypicdataGenotypic data of Odorrana narina complex in Convert file format (plain text).
DOI: 10.5061/dryad.2t02070
title: Data from: Uncoordinated dances associated to high reproductive success in the crane

description: Coordinated mutual displays by two individuals are believed to play
 important roles in social and sexual communication. Although previous
 studies have described mutual displays in birds, few have conducted
 quantitative analyses. To understand the role of mutual signals, we
 investigated the reproductive function of pair dances in the red-crowned
 crane (Grus japonensis). We used an information theory approach to
 quantify the characteristics of the pair dance and tested the classical
 “pair bond hypothesis,” which states that the elaborate dance is related
 to reproductive success. We found that characteristics of the pair dances
 were related to reproductive success, but the results were not always
 consistent with the predictions. Dance duration increased as the breeding
 season approached. However, the past reproductive success of an individual
 was negatively related to dance coordination (i.e. mutual information) of
 a pair. These results partially support the pair bond hypothesis, but more
 importantly, also suggest the need to define the vague concept of a “pair
 bond” in a biologically reasonable, measurable way.
description: dance-raw-dataraw data of analyses for pair dances in the red-crowned crane
DOI: 10.5061/dryad.307c3n10
title: Data from: Complex patterns of multivariate selection on the ejaculate of a broadcast spawning marine invertebrate

description: Assessing how selection operates on several, potentially interacting,
 components of the ejaculate is a challenging endeavour. Ejaculates can be
 subject to natural and/or sexual selection, which can impose both linear
 (directional) and nonlinear (stabilizing, disruptive and correlational)
 selection on different ejaculate components. Most previous studies have
 examined linear selection of ejaculate components and, consequently, we
 know very little about patterns of nonlinear selection on the ejaculate.
 Even less is known about how selection acts on the ejaculate as a
 functionally integrated unit, despite evidence of covariance among
 ejaculate components. Here we assess how selection acts on multiple
 ejaculate components simultaneously in the broadcast spawning sessile
 invertebrate Mytilus galloprovincialis using the statistical tools of
 multivariate selection analyses. Our analyses of relative fertilization
 rates revealed complex patterns of selection on sperm velocity, motility
 and morphology. Interestingly, the most successful ejaculates were made up
 of slower-swimming sperm with relatively low percentages of motile cells,
 and sperm with smaller head volumes that swam in highly pronounced curved
 swimming trajectories. These results are consistent with an emerging body
 of literature on fertilization kinetics in broadcast spawners, and shed
 light on the fundamental nature of selection acting on the ejaculate as a
 functionally integrated unit.
description: Fitzpatrick_et_al_Selection_DataRaw data used in multivariate selection analysis. Data include: proportion eggs fertilized, sperm density, mean sperm head volume (measured as spheroid ovoid volume), mean sperm flagellum length, composite sperm motility PC1 and PC2 scores, sperm age and egg age.
DOI: 10.5061/dryad.98c7s
title: Data from: Plasma carotenoid concentrations of incubating American kestrels (Falco sparverius) show annual, seasonal, and individual variation and explain reproductive outcome

description: In wild birds, the proximate and ultimate factors that affect circulating
 carotenoid concentrations remain poorly understood. We studied variation
 in plasma carotenoid concentrations across several scales: annual,
 seasonal, pair, territory and individual, and evaluated whether plasma
 carotenoid concentrations explained reproductive outcome of wild American
 kestrels (Falco sparverius). We sampled plasma carotenoid concentrations
 of 99 female and 80 male incubating kestrels from April to June in 2008 to
 2012. Plasma carotenoid concentrations were explained by an interaction
 between year and sex, date, and random effects for pair and individual
 identity. In general, plasma carotenoid concentrations of males were
 significantly higher than females, but this depended on year. Within a
 breeding season, earlier nesting kestrels had higher carotenoid
 concentrations than later nesting kestrels, a pattern that is coincident
 with seasonal trends in local fitness. Pair and individual identity
 explained variation in carotenoid concentrations suggesting that
 carotenoid concentrations of mated birds were correlated, and some
 individuals consistently maintained higher carotenoid levels than others.
 Male carotenoid concentrations were positively associated with number of
 young fledged per pair. These results are consistent with the hypothesis
 that higher quality individuals have higher carotenoid levels compared to
 lower quality individuals, despite annual variations in carotenoid
 availability.
description: ak_carots_ES2012_proofedThis file contains data on American kestrel carotenoid concentrations and associated information collected from kestrels in the field during the breeding seasons 2008-2012. All information was collected from adult kestrels that were in incubating eggs in nest boxes in southern Idaho. Columns are variables, and each row represents 1 bird. Variable: "record" : unique line identifier; Variable: "ID" : individual identifier for each bird; Variable: "sex" : sex of the bird determined from plumage; Variable: "carotenoid con" : plasma carotenoid concentrations of kestrels (see Sassani et al. for methods); Variable: "Year" : year the bird was captured and sample collected; Variable: "Jcap" : Julian date of capture. Jan 1 = 1; Variable: "Box" : Nest box identifier used to represent territory identity; Variable: "Mass" : Mass of the bird in grams (digital scale) Note: some birds are missing data on mass; Variable: "nevent" : individual identifier for the pair of birds or nest event; Variable: "Box" : Nest box identifier used to represent territory identity Variable: "Mass" : Mass of the bird in grams (digital scale) Note: some birds are missing data on mass. Variable: "nevent" : individual identifier for the pair of birds or nest event
DOI: 10.5061/dryad.731
title: Data from: Phylogenies and physiological processes--the evolution of sexual dimorphism in Southeast Asian frogs

description: There are a number of species of Southeast Asian Rana that are
 characterized by an unusual suite of sexually dimorphic features and
 derived reproductive modes. These frogs lack the usual secondary sexual
 characteristics of ranid frogs: nuptial pads, vocal sacs, and enlarged
 flexor muscles. Secondary sexual characteristics in frogs are under
 androgenic control. Phylogenetic analyses using morphological and
 molecular data indicate that a drop in androgen level and/or a shift in
 androgen sensitivity may have been involved in the evolution of male
 parental care and the loss of the common suite of secondary sexual
 characteristics in these Asian frogs. Phylogenetic analyses also provide
 important information on experimental design by indicating the most
 appropriate taxa to use in the exploration of physiological processes
 controlling the expression of sexual dimorphism. This work is an example
 of how emergent properties from phylogenetic analyses can be used to
 formulate and test hypotheses of process and pattern of evolutionary
 change.
description: Emerson Data
 Setemerson.app
DOI: 10.5061/dryad.19n37d1
title: Data from: Predator prey games in multiple habitats reveal mixed strategies in diel vertical migration

description: Prey and predators continuously react to each other and to their
 environment, adjusting their behaviour to maximize their fitness. In a
 pelagic environment, organisms can optimize their fitness by performing
 diel vertical migrations (DVM). We applied a game theoretic approach to
 investigate the emergent patterns of optimal habitat selection strategies
 in a multiple habitat arena. Our set-up allows both players to choose
 their position at day and at night in the water column. The model
 reproduces features of vertical migrations observed in nature, including
 residency at depth or at the surface, vertical migrations, mixed
 strategies and bimodal distributions within a population. The mixed
 strategies appear as a consequence of frequency-dependent processes and
 not of any intra-species difference between individuals. The model also
 reveals a curious feature, where natural selection on individuals can
 provoke distinct regime shifts and precipitate an irreversible collapse in
 fitness. In the case presented here, the increasing voracity of the
 predator triggers a behavioural shift in the prey reducing the fitness of
 all members of the predator population.
description: Matlab code - Diel
 Vertical migrationThis matlab code solves
 the replicator equation for two players (prey and predator) in a water
 column. Running the code with no modification will provide day-night
 positions for both prey and predator for a range of predator clearance
 rates.DVM_code.m
DOI: 10.34894/e48c9m
title: TICCL version of F. Leviticus,Geillustreerde encyclopaedie der diamantnijverheid plus documentation

description: F. Leviticus, Geillustreerde encyclopaedie der diamantnijverheid (1908) is used to make a concept list for the Diamonds in Borneo project. The OCR of the text is converted to Folia XML and then analyzed and corrected with help of TICCL. This data set contains the corrected paragraphs from the encyclopaedia as well as the complete TICCL archive as zip file.
DOI: 10.5061/dryad.623hq
title: Data from: The flashing Brownian ratchet and Parrondo’s paradox

description: A Brownian ratchet is a one-dimensional diffusion process that drifts
 towards a minimum of a periodic asymmetric sawtooth potential. A flashing
 Brownian ratchet is a process that alternates between two regimes, a
 one-dimensional Brownian motion and a Brownian ratchet, producing directed
 motion. These processes have been of interest to physicists and biologists
 for nearly 25 years. The flashing Brownian ratchet is the process that
 motivated Parrondo’s paradox, in which two fair games of chance, when
 alternated, produce a winning game. Parrondo’s games are relatively
 simple, being discrete in time and space. The flashing Brownian ratchet is
 rather more complicated. We show how one can study the latter process
 numerically using a random walk approximation.
description: 0 initial n=100
 lambda=1-5Mathematica code used to
 generate Tables 1, 2 and Figure 40 initial
 nstationarity initial
 n=100 lambda=5Mathematica code used to
 generate Figure 5stationarity initial
 n
DOI: 10.5061/dryad.4188b
title: Data from: Social manipulation of sperm competition intensity reduces seminal fluid gene expression

description: A considerable body of evidence supports the prediction that males should
 increase their expenditure on the ejaculate in response to sperm
 competition risk. The prediction that they should reduce their expenditure
 with increasing sperm competition intensity is less well supported.
 Moreover, most studies have documented plasticity in sperm numbers. Here
 we show that male crickets Teleogryllus oceanicus exhibit reduced seminal
 fluid gene expression and accessory gland mass in response to elevated
 sperm competition intensity. Together with previous research, our findings
 suggest that strategic adjustments in seminal fluid composition contribute
 to competitive fertilization success in this species.
description: Data from Sloan et
 alExcel spreadsheet
 containing gene expression and morphometric data for males from two
 treatment groups
DOI: 10.5061/dryad.r8s59
title: Data from: Background matching ability and the maintenance of a colour polymorphism in the red devil cichlid

description: The evolution and maintenance of colour polymorphisms remains a topic of
 considerable research interest. One key mechanism thought to contribute to
 the coexistence of different colour morphs is a bias in how conspicuous
 they are to visual predators. Although individuals of many species
 camouflage themselves against their background to avoid predation,
 differently coloured individuals within a species may vary in their
 capacity to do so. However, to date, very few studies have explicitly
 investigated the ability of different colour morphs to plastically adjust
 their colouration to match their background. The red devil (Amphilophus
 labiatus) is a Neotropical cichlid fish with a stable colour polymorphism,
 with the gold morph being genetically dominant and having a myriad of
 documented advantages over the dark morph. However, gold individuals are
 much rarer, which may be related to their heightened conspicuousness to
 would-be predators. Here, we tested the ability of differently coloured
 individuals to phenotypically adjust the shade of their body colour and
 patterns to match their background. In particular, we filmed dark, gold
 and mottled (a transitioning phase from dark to gold) individuals under an
 identical set-up on light vs. dark-coloured substrates. We found that, in
 contrast to individuals of the dark morph, gold and mottled individuals
 were less capable of matching their body colouration to their background.
 As a result, gold individuals appeared to be more conspicuous. These
 results suggest that a difference in background matching ability could
 play an important role in the maintenance of colour polymorphisms.
description: Background matching
 ability and the maintenance of a colour polymorphism in the red devil
 cichlidThis is an excel file
 containing RGB scores that we used to analyse the background matching
 ability of color morphs in a polymorphic species. The file contains the
 raw data, the sum of RGB values and the grey standard
 values.
DOI: 10.34894/cy5liw
title: Diamonds in Borneo: Commodities as Concepts in Context

description: Diamonds in Borneo: Commodities as Concepts in Context, article written for Datech Conference, May 2019,Brussels
DOI: 10.5061/dryad.r05k616
title: Data from: The great Indian joint families of free-ranging dogs

description: Cooperative breeding is an excellent example of altruistic cooperation in
 social groups. Domestic dogs have evolved from cooperatively hunting and
 breeding ancestors, but have adapted to a facultatively social scavenging
 lifestyle on streets, and solitary living in human homes. Pets typically
 breed and reproduce under human supervision, but free-ranging dogs can
 provide insights into the natural breeding ecology of dogs. We conducted a
 five year-long field based behavioural study on parental care of
 free-ranging dogs in India. 23 mother-litter units, belonging to 15 groups
 were observed, which revealed the presence of widespread allo-parenting by
 both adult males and females. While all the females were known to be
 related to the pups receiving care, the relatedness with the males could
 not be determined. Hence, we coined the term "putative father"
 for caregiving males. Allomothers provided significantly less care than
 the mothers, but the putative fathers showed comparable levels of care
 with the mothers. Mothers invested more effort in nursing and
 allogrooming, while the putative fathers played and protected more. Our
 observations provide support for both the
 "benefit-of-philopatry" and "assured fitness returns"
 hypotheses. Free-ranging dogs are not cooperative breeders like wolves but
 are rather communal breeders; their breeding biology bearing interesting
 similarities with the human joint family system. This breeding strategy is
 likely to have played an important role in increasing pup survival in a
 stochastic environment and helping to adapt to living among humans during
 the domestication of dogs.
description: Paul and
 Bhadra_2018_data descriptorRaw
 dataPaul
 and Bhadra_2018_raw data.csv
DOI: 10.5061/dryad.1805c973
title: Data from: Neonicotinoid pesticide reduces bumblebee colony growth and queen production

description: Growing evidence for declines in bee populations has caused great concern
 because of the valuable ecosystem services they provide. Neonicotinoid
 insecticides have been implicated in these declines because they occur at
 trace levels in the nectar and pollen of crop plants. We exposed colonies
 of the bumble bee Bombus terrestris in the laboratory to field-realistic
 levels of the neonicotinoid imidacloprid, then allowed them to develop
 naturally under field conditions. Treated colonies had a significantly
 reduced growth rate and suffered an 85% reduction in production of new
 queens compared with control colonies. Given the scale of use of
 neonicotinoids, we suggest that they may be having a considerable negative
 impact on wild bumble bee populations across the developed world.
description: Whitehorn,
 O'Connor, Wackers, Goulson (2012) Data from 'Neonicotinoid
 pesticide reduces bumblebee colony growth and queen
 production'.csv
DOI: 10.5061/dryad.hp4b3
title: Data from: Assessing changes in distribution of the endangered snow leopard Panthera uncia and its wild prey over 2 decades in the Indian Himalaya through interview-based occupancy surveys

description: Understanding species distributions, patterns of change and threats can
 form the basis for assessing the conservation status of elusive species
 that are difficult to survey. The snow leopard Panthera uncia is the top
 predator of the Central and South Asian mountains. Knowledge of the
 distribution and status of this elusive felid and its wild prey is
 limited. Using recall-based key-informant interviews we estimated site use
 by snow leopards and their primary wild prey, blue sheep Pseudois nayaur
 and Asiatic ibex Capra sibirica, across two time periods (past: 1985–1992;
 recent: 2008–2012) in the state of Himachal Pradesh, India. We also
 conducted a threat assessment for the recent period. Probability of site
 use was similar across the two time periods for snow leopards, blue sheep
 and ibex, whereas for wild prey (blue sheep and ibex combined) overall
 there was an 8% contraction. Although our surveys were conducted in areas
 within the presumed distribution range of the snow leopard, we found snow
 leopards were using only 75% of the area (14,616 km2). Blue sheep and ibex
 had distinct distribution ranges. Snow leopards and their wild prey were
 not restricted to protected areas, which encompassed only 17% of their
 distribution within the study area. Migratory livestock grazing was
 pervasive across ibex distribution range and was the most widespread and
 serious conservation threat. Depredation by free-ranging dogs, and illegal
 hunting and wildlife trade were the other severe threats. Our results
 underscore the importance of community-based, landscape-scale conservation
 approaches and caution against reliance on geophysical and opinion-based
 distribution maps that have been used to estimate national and global snow
 leopard ranges.
description: DataSet_ParameterValues_AG_6Dec2017The data set has occupancy values and local extinction probability values for 88 grids/sites of 15km X 15km each, for snow leopard, blue sheep, Asiatic ibex and wild prey (blue sheep and ibex combined), across an area of 14,616 sq.km in the Himalaya and Trans-Himalaya mountains of Himachal Pradesh, India.
DOI: 10.5061/dryad.4t806
title: Data from: Intercontinental genetic structure and gene flow in Dunlin (Calidris alpina), a potential vector of avian influenza

description: Waterfowl (Anseriformes) and shorebirds (Charadriiformes) are the most
 common wild vectors of influenza A viruses. Due to their migratory
 behavior, some may transmit disease over long distances. Migratory
 connectivity studies can link breeding and nonbreeding grounds while
 illustrating potential interactions among populations that may spread
 diseases. We investigated Dunlin (Calidris alpina), a shorebird with a
 subspecies (C. a. arcticola) that migrates from nonbreeding areas endemic
 to avian influenza in eastern Asia to breeding grounds in northern Alaska.
 Using microsatellites and mitochondrial DNA, we illustrate genetic
 structure among six subspecies: C. a. arcticola, C. a. pacifica, C. a.
 hudsonia, C. a. sakhalina, C. a. kistchinski, and C. a. actites. We
 demonstrate that mitochondrial DNA can help distinguish C. a. arcticola on
 the Asian nonbreeding grounds with &gt;70% accuracy depending on their
 relative abundance, indicating that genetics can help determine if C. a.
 arcticola occurs where they may be exposed to highly pathogenic avian
 influenza (HPAI) during outbreaks. Our data reveal asymmetric
 intercontinental gene flow, with some C. a. arcticola short-stopping
 migration to breed with C. a. pacifica in western Alaska. Because C. a.
 pacifica migrates along the Pacific Coast of North America, interactions
 between these subspecies and other taxa provides route for transmission of
 HPAI into other parts of North America.
description: mtDNA and
 microsatellite_dataA zip file containing
 two data files plus a third text file containing descriptions of the data
 files. See file "File annotations.txt" included int the archive
 for more information.