cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3fj52
title: Data from: Petrocodon retroflexus sp. nov. (Gesneriaceae) from a karst cave in Guizhou, China

description: Petrocodon retroflexus Q. Zhang & J. Guo, a new species of
 Gesneriaceae from Guizhou, China, is described and illustrated. The new
 species is morphologically similar to Petrocodon viridescens W. H. Chen,
 Mich. Möller & Y. M. Shui, but differs by its leaf blade being
 ovate, broadly ovate to elliptic, 8–20 × 5–15 cm and densely pilose on
 both surfaces, narrowly triangular, 9 mm long, densely pilose bracts,
 white corolla that is decurved near the middle, with adaxial lip shallowly
 4-partitioned and retroflexed, and pistil ca 1.3 cm long and densely
 pilose and glandular-pilose.
description: ConcatenatedThe matrix of ITS and trnL-F.
DOI: 10.5061/dryad.48012
title: Data from: Cuckoo parasitism in a cavity nesting host: near absent egg-rejection in a northern redstart population under heavy apparent (but low effective) brood parasitism

description: Brood parasite - host systems continue to offer insights into species
 coevolution. A notable system is the redstart Phoenicurus phoenicurus
 parasitized by the “redstart-cuckoo” Cuculus canorus gens. Redstarts are
 the only regular cuckoo hosts that breed in cavities, which challenges
 adult cuckoos in egg laying and cuckoo chicks in host eviction. We
 investigated parasitism in this system and found high overall parasitism
 rates (31.1% of 360 redstart nests), but also that only 33.1% of
 parasitism events (49 of 148 eggs) were successful in laying eggs into
 redstart nest cups. The majority of cuckoo eggs were mislaid and found on
 the rim of the nest; outside the nest cup. All available evidence suggests
 these eggs were not ejected by hosts. The effective parasitism rate was
 therefore only 12.8% of redstart nests. Redstarts responded to natural
 parasitism by deserting their nests in 13.0% of cases, compared to
 desertion rates of 2.8% for non-parasitized nests. Our egg parasitism
 experiments found low rates (12.2%) of rejection of artificial non-mimetic
 cuckoo eggs. Artificial mimetic and real cuckoo eggs added to nests were
 rejected at even lower rates, and were always rejected via desertion.
 Under natural conditions, only 21 cuckoo chicks fledged of 150 cuckoo eggs
 laid. Adding to this low success, is that cuckoo chicks are sometimes
 unable to evict all host young, and were more likely to die as a result
 compared to cuckoo chicks reared alone. This low success seems to be
 mainly due to the cavity nesting strategy of the redstart which is a
 challenging obstacle for the cuckoo. The redstart-cuckoo system appears to
 be a fruitful model system and we suggest much more emphasis should be
 placed on frontline defences such as nest site selection strategies when
 investigating brood parasite-host coevolution.
description: All basic
 dataIncludes data worksheet
 that detail: 1. the natural nest data and parasitism rates, 2. the laying
 fate of the cuckoo eggs documented, 3. the outcome of the artificial
 parasitism experiments, and 4. the fates of the cuckoo
 chicksCuckoo-redstart data for
 archiving.xlsx
DOI: 10.5061/dryad.0578v
title: Data from: Genetic and phenotypic differentiation among Galaxias maculatus populations in a Patagonian postglacial lake system

description: Understanding the influence of landscape features on population
 differentiation is fundamental to evolutionary biology studies. We
 examined spatial patterns of genetic and phenotypic variability among
 Galaxias maculatus populations in a complex of four postglacial lakes in
 northwestern Patagonia differing in size and connectivity among them. A
 hierarchical Bayesian analysis grouped the individuals collected from 11
 localities into 3 genetic clusters, first defining the populations of the
 two large lakes and separating the two small lakes in subsequent analysis.
 Genetic structuring was restricted within large lakes. It is known that
 the larval stage of Galaxias maculatus migrate to the limnetic zone of
 Patagonian lakes, possibly exerting an homogenizing effect on gene flow
 within lakes. Gene flow asymmetry and divergences among lakes can be
 explained by a combination of landscape characteristics and the presence
 of predators in the short streams that connect them. Individuals from the
 small lakes are the most divergent morphologically and genetically. The
 population in the isolated Redonda Lake, exhibit meristic differences as
 well, suggesting strong drift and environmental effects. This population
 is likely to have been isolated following the decline in water level of a
 paleolake that existed in this region approximately 13.2 kya BP.
description: Convert_Nahuel
DOI: 10.5061/dryad.862h5
title: Data from: New host and lineage diversity of avian haemosporidia in the Northern Andes

description: The northern Andes, with their steep elevational and climate gradients,
 are home to an exceptional diversity of flora and fauna, particularly rich
 in avian species that have adapted to divergent ecological conditions.
 With this diversity comes the opportunity for parasites to exploit a wide
 breadth of avian hosts. However, little research has focused on examining
 the patterns of prevalence and lineage diversity of avian parasites in the
 Andes. Here, we screened a total of 428 birds from 19 species
 (representing nine families) and identified 133 infections of avian
 haemosporidia (31%), including lineages of Plasmodium, Haemoproteus, and
 Leucocytozoon. We document a higher prevalence of haemosporidia at higher
 elevations and lower temperatures, as well as an overall high diversity of
 lineages in the northern Andes, including the first sequences of
 haemosporidians reported in hummingbirds (31 sequences found in 11 species
 within the family Trochilidae). Double infections were distinguished using
 PHASE, which enables the separation of distinct parasite lineages. Results
 suggest that the ecological heterogeneity of the northern Andes that has
 given rise to a rich diversity of avian hosts may also be particularly
 conducive to parasite diversification and specialization.
description: AvianMalariaSequences-EcuadorList of locations, hosts, and sequences of each positive malaria positive found in Ecuador, South America.
DOI: 10.5061/dryad.t6s441n0
title: Data from: Recent speciation between sympatric Tanganyikan cichlid color morphs

description: Lake Tanganyika, Africa’s oldest lake, harbors an impressive diversity of
 cichlid fishes. Although diversification in its radiating groups is
 thought to have been initially rapid, cichlids from Lake Tanganyika show
 little evidence for ongoing speciation. In contrast, examples of recent
 divergence among sympatric color morphs are well known in haplochromine
 cichlids from Lakes Malawi and Victoria. Here we report genetic evidence
 for recent divergence between two sympatric Tanganyikan cichlid color
 morphs. These Petrochromis morphs share mitochondrial haplotypes, yet
 microsatellite loci reveal that their sympatric populations form distinct
 genetic groups. Nuclear divergence between the two morphs is equivalent to
 that which arises geographically within one of the morphs over short
 distances, and is substantially smaller than that among other sympatric
 species in this genus. These patterns suggest that these morphs diverged
 only recently, yet that barriers to gene flow exist which prevent
 extensive admixture despite their sympatric distribution. The morphs
 studied here provide an unusual example of active diversification in Lake
 Tanganyika’s generally ancient cichlid fauna and enable comparisons of
 speciation processes between Lake Tanganyika and other African lakes.
description: Petrochromis_microsats.strMicrosatellite dataset in STRUCTURE format, consisting of genotypes from 11 microsatellite loci for 4 Petrochromis species in the Kigoma region of Lake Tanganyika. Sample names correspond with Individual IDs listed in Supplementary Table 1 of the paper published in Molecular Ecology. Microsatellite locus information can be found in Supplementary Table 2.AllPetros122410.str
DOI: 10.5061/dryad.2538mj0
title: Data from: Replicated evolutionary inhibition of a complex ancestral behaviour in an adaptive radiation

description: Adaptive radiations often exhibit high levels of phenotypic replication, a
 phenomenon that can be explained by selection on standing variation in
 repeatedly divergent environments or by the influence of ancestral
 plasticity on selection in divergent environments. Here, we offer the
 first evidence that plastic loss of expression of a complex display in a
 novel environment, followed by selection against expression, could lead to
 replicated evolutionary inhibition of the phenotype. In both ancestral
 (oceanic) and benthic (freshwater) populations of the threespine
 stickleback fish, cannibalism is common and males defending nests respond
 to approaching groups with a complex diversionary display. This display is
 not exhibited by males in allopatric, limnetic (freshwater) populations
 from which cannibalistic groups are absent. Laboratory-reared males from
 three limnetic populations exhibit a reduced tendency to respond to
 cannibalistic foraging groups relative to laboratory-reared ancestral and
 benthic males, but still are capable of producing a similar array of forms
 of the display despite many generations of disuse. Thus, replication in
 adaptive radiations can reflect reduced expression of an ancestral trait
 followed by evolutionary inhibition while the population retains the
 capacity to express the trait under extreme ancestral conditions.
description: Diversionary display
 dataData used in analyses, 4
 Excel sheets
DOI: 10.5061/dryad.45bc0
title: Data from: A computational model of flow between the microscale respiratory structures of fish gills

description: The gills of most teleost fishes are covered by plate-like structures, the
 secondary lamellae, that provide the bulk of the respiratory surface area.
 Water passing over the secondary lamellae exchanges gases with blood
 passing through the secondary lamellae, forming a system that has served
 as a classic model of counter-current exchange. In this study, a
 computational model of flow around the secondary lamellae is used to
 examine the hydrodynamic consequences of changes to the lamellar
 morphology. Consistent with previous studies, the interlamellar distance
 is found to strongly affect the hydrodynamic resistance of the gills.
 However, the presence of a small gap between the tips of the secondary
 lamellae is found to have a similar strong effect on the hydrodynamic
 resistance and flow patterns within the gills. The results from this model
 have been generally formulated, allowing the calculation of the
 hydrodynamic resistance for measured morphometric parameters. These
 results provide a new basis for comparing theoretical predictions of the
 gill resistance with measured values, and provide a general model for
 examining the diversity gill morphologies observed in teleost fishes.
description: Source Code for
 Hydrodynamic ModelsThis file contains
 source code implementing each of the hydrodynamic models discussed in the
 manuscript. Models are implemented using MATLAB and all relevant source
 data is included.strother_jtb_2013.zip
DOI: 10.5061/dryad.8c7s0
title: Data from: Stability and generalization in seed dispersal networks: a case study of frugivorous fish in Neotropical wetlands

description: When species within guilds perform similar ecological roles, functional
 redundancy can buffer ecosystems against species loss. Using data on the
 frequency of interactions between fish and fruit, we assessed whether
 co-occurring frugivores provide redundant seed dispersal services in three
 species-rich Neotropical wetlands. Our study revealed that frugivorous
 fishes have generalized diets; however, large-bodied fishes had greater
 seed dispersal breadth than small species, in some cases, providing seed
 dispersal services not achieved by smaller fish species. As overfishing
 disproportionately affects big fishes, the extirpation of these species
 could cause larger secondary extinctions of plant species than the loss of
 small specialist frugivores. To evaluate the consequences of frugivore
 specialization for network stability, we extracted data from 39 published
 seed dispersal networks of frugivorous birds, mammals and fish (our
 networks) across ecosystems. Our analysis of interaction frequencies
 revealed low frugivore specialization and lower nestedness than analyses
 based on binary data (presence–absence of interactions). In that case,
 ecosystems may be resilient to loss of any given frugivore. However,
 robustness to frugivore extinction declines with specialization, such that
 networks composed primarily of specialist frugivores are highly
 susceptible to the loss of generalists. In contrast with analyses of
 binary data, recently developed algorithms capable of modelling
 interaction strengths provide opportunities to enhance our understanding
 of complex ecological networks by accounting for heterogeneity of
 frugivore–fruit interactions.
description: Datasets not included in
 supplementsSeed dispersal
 interaction frequencies retrieved from the literature; robustness to
 frugivores extinction, presence-absence of intact seeds in fish digestive
 tracts at each site, species specialization, dispersal and body size. A
 Meta-data file includes variable names and description for each
 file.Datasets.zip
DOI: 10.5061/dryad.bm562
title: Data from: Abrupt shortening of bird W chromosomes in ancestral Neognathae

description: As a result of suppressed recombination, heterogametic sex chromosomes
 (either Y or W) are usually assumed to gradually shorten over evolutionary
 time as a way to remove accumulated mutations. However, suppressed
 recombination removes the most obvious mechanism for excising portions of
 sex chromosomes. We examined ratios of W/Z chromosome size across 224 bird
 species from 146 genera. Much of the data were obtained from a previous
 study (Rutkowska et al. 2012. Biology Letters 8: 636–638), who, similar to
 ourselves, found no gradual decrease in W chromosome length over
 evolutionary time. However, we show an abrupt decrease in W chromosome
 length at or just after the phylogenetic split between the two extant bird
 superorders, Paleognathae and Neognathae, indicating that the key to
 understanding sex chromosome evolution may have little to do with gradual
 suppression of recombination.
description: Avian WZ Supplemental
 Table and ReferencesW/Z chromosome size
 ratios from karyotypes, also listing number of substitutions per site from
 Hackett et al. (2008) and source files for karyotypes. Data presented for
 size ratios include length, area, and optical density
 ratios.Avian WZ Supplemental Table and
 Refs.docx
DOI: 10.5061/dryad.fk2nh
title: Data from: Structural habitat predicts functional dispersal habitat of a large carnivore: how leopards change spots

description: Natal dispersal promotes inter-population linkage, and is key to spatial
 distribution of populations. Degradation of suitable landscape structures
 beyond the specific threshold of an individual's ability to disperse
 can therefore lead to disruption of functional landscape connectivity and
 impact metapopulation function. Because it ignores behavioral responses of
 individuals, structural connectivity is easier to assess than functional
 connectivity and is often used as a surrogate for landscape connectivity
 modeling. However using structural resource selection models as surrogate
 for modeling functional connectivity through dispersal could be erroneous.
 We tested how well a second-order resource selection function (RSF) models
 (structural connectivity), based on GPS telemetry data from resident adult
 leopard (Panthera pardus L.), could predict subadult habitat use during
 dispersal (functional connectivity). We created eight non-exclusive
 subsets of the subadult data based on differing definitions of dispersal
 to assess the predictive ability of our adult-based RSF model extrapolated
 over a broader landscape. Dispersing leopards used habitats in accordance
 with adult selection patterns, regardless of the definition of dispersal
 considered. We demonstrate that, for a wide-ranging apex carnivore,
 functional connectivity through natal dispersal corresponds to structural
 connectivity as modeled by a second-order RSF. Mapping of the adult-based
 habitat classes provides direct visualization of the potential linkages
 between populations, without the need to model paths between a priori
 starting and destination points. The use of such landscape scale RSFs may
 provide insight into predicting suitable dispersal habitat peninsulas in
 human-dominated landscapes where mitigation of human–wildlife conflict
 should be focused. We recommend the use of second-order RSFs for landscape
 conservation planning and propose a similar approach to the conservation
 of other wide-ranging large carnivore species where landscape-scale
 resource selection data already exist.
description: External validation data
 for leopard resource selection function, South Africa,
 2002-2012For each of the 10
 external validation sets, a Spearman's rank correlation is run
 between the observed number of locations and the ordinal rank of the
 corresponding RSF bins, and a linear regression between observed and
 expected number of locations in each bin is run to assess the predictive
 ability of the RSF.Validation
 data_dyrad.xlsx
DOI: 10.5061/dryad.3jb68
title: Data from: Copy-when-uncertain: bumblebees rely on social information when rewards are highly variable

description: To understand the relative benefits of social and personal information use
 in foraging decisions, we developed an agent-based model of social
 learning that predicts social information should be more adaptive where
 resources are highly variable and personal information where resources
 vary little. We tested our predictions with bumblebees and found that
 foragers relied more on social information when resources were variable
 than when they were not. We then investigated whether socially salient
 cues are used preferentially over non-social ones in variable
 environments. Although bees clearly used social cues in highly variable
 environments, under the same conditions they did not use non-social cues.
 These results suggest that bumblebees use a ‘copy-when-uncertain’
 strategy.
description: beeLandingsPrimary data from observing bees throughout the test phase (group=test_easy OR test_diff) and last round of the cue training (group=dummy_last). Further columns include: Cue types: bee model (=clay), craft foam (=green); Landed: at which of the 12 flowers did the bee land and in which sequence; Cue: describes which of the 12 flowers had an additional cue attached; reward: which of the 12 flowers were rewarding; firstLanding and lastLanding: time in minutes between a bee entering the arena and first/last landing on a flower.code_figures_statisticsR code to create figures and perform statistical tests that reused for the main text and the supplemental information of the article. It requires the 'beeLandings', 'simulation_results_1', and 'simulation_results_2' file. Depending on where the files are saved to, the path to the files has to be changed in the R code (be default files are assumed to be located at the desktop).simulation_results_1Results from first simulation (RData file, can be opened with R)simulation1simulation_results_2Results from second simulation (RData file, can be opened with R)simulation2
DOI: 10.5061/dryad.88896
title: Data from: Peripheral blood mitochondrial DNA copy number is associated with prostate cancer risk and tumor burden

description: Alterations of mitochondrial DNA (mtDNA) have been associated with the
 risk of a number of human cancers; however, the relationship between mtDNA
 copy number in peripheral blood leukocytes (PBLs) and the risk of prostate
 cancer (PCa) has not been investigated. In a case-control study of 196 PCa
 patients and 196 age-paired healthy controls in a Chinese Han population,
 the association between mtDNA copy number in PBLs and PCa risk was
 evaluated. The relative mtDNA copy number was measured using quantitative
 real-time PCR; samples from three cases and two controls could not be
 assayed, leaving 193 cases and 194 controls for analysis. PCa patients had
 significantly higher mtDNA copy numbers than controls (medians 0.91 and
 0.82, respectively; P&lt;0.001). Dichotomized at the median value of
 mtDNA copy number in the controls, high mtDNA copy number was
 significantly associated with an increased risk of PCa (adjusted odds
 ratio = 1.85, 95% confidence interval: 1.21–2.83). A significant
 dose-response relationship was observed between mtDNA copy number and risk
 of PCa in quartile analysis (Ptrend = 0.011). Clinicopathological analysis
 showed that high mtDNA copy numbers in PCa patients were significantly
 associated with high Gleason score and advanced tumor stage, but not serum
 prostate-specific antigen level (P = 0.002, 0.012 and 0.544,
 respectively). These findings of the present study indicate that increased
 mtDNA copy number in PBLs is significantly associated with an increased
 risk of PCa and may be a reflection of tumor burden.
description: Data of a case-control
 study of mtDNA copy numberExcel file containing
 epidemiological and experimental data on a case-control study of 196
 prostate cancer patients and 196 age-paired healthy controls in a Chinese
 Han population.Data.xlsx
DOI: 10.15468/dl.z2z7ct
title: Occurrence Download

description: A dataset containing 2312 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation)",
 "GadmGid is FRA.13.3_1",
 "Geometry POLYGON((5.44639 43.3244,5.65701 43.3244,5.65701 43.47025,5.44639 43.47025,5.44639 43.3244))",
 "OccurrenceStatus is Present",
 "TaxonKey is Arthropoda",
 "Year 2021-2026"
 ]
}

 The dataset includes 2312 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001434-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.