cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.89mv921
title: Data from: Is barotrauma an important factor in the discard mortality of yellow perch?

description: In physoclistous fishes, barotrauma caused by rapid decompression during
 capture may be an important source of fishing mortality that is
 unquantified for some fisheries. We developed a predictive logistic model
 for barotrauma incidence in Yellow Perch Perca flavescens and applied this
 model to Ohio's recreational and commercial fisheries in Lake Erie
 where discard mortality is implicitly considered to be negligible in
 current stock assessment. As expected, most of the variation in incidence
 was explained by capture depth with comparatively small effects of season,
 sex, and size categories. Measurements of whole body and gonad density
 provided limited explanation for the categorical effects. Both fisheries
 spanned a range of depths (7.6 to 16.8 m) that corresponded to a broad
 range of barotrauma incidence (13 to 74%). Using a recent example, we
 estimated that additional fishing mortality due to barotrauma in discards
 was approximately six-fold higher in the commercial than recreational
 fishery. Overall, this additional mortality was &lt;1% of lake wide
 population size estimates. Thus, the assumption that all discarded Yellow
 Perch survive is unlikely to result in a detectable bias in population
 estimates. One caveat is that we still do not understand how strong
 year-classes might influence discard mortality via increased discard rate
 and barotrauma incidence for small fish.
description: Incidence of barotrauma
 in Yellow PerchSee metatdata
 file.S2.062018-JFWM-056.incidence_table.csvSpecific gravity measurements from yellow perch.See metadata file.S3.062018-JFWM-056.density_table.csvRecreational fishery catch and discard data for yellow perch.See metadata file.S4.062018-JFWM-056.rec_discard_table.csvCommercial fishery catch and discard data for yellow perch.See metatdata file.S5.062018-JFWM-056.com_discard_table.csvAkaike Information Criteria results from logistic regression models of yellow perch barotrauma incidence.See metadata file.S6.062018-JFWM-056.AIC_results.csvVariable descriptions for data package.S1.062018-JFWM-056.txt
DOI: 10.5061/dryad.fm0j1
title: Data from: The geographic structure of selection on a coevolving interaction between social parasitic wasps and their hosts hampers social evolution

description: Social parasites exploit societies, rather than organisms, and rear their
 brood in social insect colonies at the expense of their hosts, triggering
 a coevolutionary process that may affect host social structure. The
 resulting coevolutionary trajectories may be further altered by selection
 imposed by predators, which exploit the abundant resources concentrated in
 these nests. Here, we show that geographic differences in selection
 imposed by predators affects the structure of selection on coevolving
 hosts and their social parasites. In a multi-year study, we monitored the
 fate of the annual breeding attempts of the solitary-founding females of
 Polistes biglumis social wasps in four geographically distinct populations
 that varied in levels of attack by the congeneric social parasite, P.
 atrimandibularis. Foundress fitness depended mostly on whether, during the
 long founding phase, a colony was invaded by social parasites or attacked
 by predators. Foundresses from each population differed in morphological
 traits and reproductive tactics that were consistent with selection
 imposed by their natural enemies and in ways that may affect host
 sociality. In turn, parasite traits were consistent with selection imposed
 locally by hosts, implying a geographic mosaic of coevolution in this
 brood parasitic interaction.
description: Founding_phase_dataThe data in this file describe Polistes biglumis nests at the end of the founding phase. Data were collected in the field, in years 2004-2008, in 4 populations (Mtg: Montgenèvre, French Hautes Alpes; Fer: Ferrere, Cuneo, Italy; Carì: Canton Ticino, Switzerland; MM: Monte Mare, Isernia, Italy). To avoid pseudoreplication, one census was used for each nest.foundress_fitnessThis file contains data of the fitness of Polistes biglumis foundresses. They were collected in the field, in years 2004-2008, in 4 populations (Mtg: Montgenèvre, French Hautes Alpes; Fer: Ferrere, Cuneo, Italy; Carì: Canton Ticino, Switzerland; MM: Monte Mare, Isernia, Italy).head_widthThis file contains the measures of the head width of foundresses, obligate parasites and usurpers in Polistes biglumis. Data were collected in the field, in years 2004-2008, in 4 populations (Mtg: Montgenèvre, French Hautes Alpes; Fer: Ferrere, Cuneo, Italy; Carì: Canton Ticino, Switzerland; MM: Monte Mare, Isernia, Italy).predationThis file contains data on whether colonies of Polistes biglumis were killed by predators at the end of the founding phase. Data were collected in the field, in years 2004-2008, in 4 populations (Mtg: Montgenèvre, French Hautes Alpes; Fer: Ferrere, Cuneo, Italy; Carì: Canton Ticino, Switzerland; MM: Monte Mare, Isernia, Italy).
DOI: 10.5061/dryad.2f4g2h90
title: Data from: Cost of cooperation rules selection for cheats in bacterial metapopulations

description: Bacteria secrete a large variety of beneficial metabolites into the
 environment, which can be shared as public goods among producing bacteria,
 but also be exploited by non-producing cheats. Here, we focus on
 cooperative production of iron-chelating molecules (siderophores) in the
 bacterium Pseudomonas aeruginosa to study how relevant ecological factors
 influence selection for cheating. We designed patch-structured
 metapopulations that allowed us introducing among-patch ecological
 variation. We found that cheating readily evolved in uniform iron-limited
 environments. This finding is explained by severe iron limitation
 demanding high siderophore-production efforts, which results in high
 metabolic costs accruing to cooperators, and thereby facilitates the
 spread of cheats. In contrast, we observed a significant reduction or even
 negation of selection for cheating in metapopulations where we introduced
 patches with increased iron availability and/or opportunities to recycle
 siderophores. These findings are compatible with the view that cheats are
 less likely to invade in environments that allow bacteria to reduce
 siderphore-production efforts, as this lowers the overall metabolic costs
 accruing to cooperators. Because we increased iron availability and
 siderophore recycling opportunities moderately, and only in some patches,
 our findings demonstrate that already small local variations in ecological
 conditions as occurring in nature can significantly affect selection for
 public-good secretion in microbes. In addition, we found that most (84.6%)
 of the evolved cheats were partially deficient for siderophore production
 and not loss-of-function mutants. Genetic considerations indicate that
 mutations leading to partial deficiency occur more frequent than mutations
 leading to loss of function, but also suggest that partially-deficient
 mutants might often be the more competitive cheats.
description: ZD_RK_CostOfCooperation_dataThis file contains three sheets. Sheet#1 contains all raw data related to the metapopulation analyses presented in Figures 2a, 3a, and 4a of the paper. Sheet#2 contains all raw data related to the individual clone analyses presented in figures 2b, 3b, and 4b of the paper. Sheet#3 contains the raw data related to the classification of clones presented in figure 5 of the paper.
DOI: 10.5061/dryad.g0d1d
title: Data from: Relationship between high serum cystatin C levels and the risk of gestational diabetes mellitus

description: Aims: Serum cystatinC (CysC) has recently been shown to be associated with
 the incidence of type 2 diabetes mellitus (T2DM) and progression to the
 pre-diabetic state. The aim of this study was to explore the relationship
 between serum CysC and the risk of gestational diabetes mellitus (GDM) in
 Chinese pregnant women. Methods: This cross-sectional study consisted of
 400 pregnant women including 111 with GDM and 289 with normal glucose
 tolerance at 24-28 weeks of gestation. The subjects were further divided
 into four groups according to the CysC quartiles, and their clinical
 characteristics were compared. The serum CysC concentration was measured
 using immunoturbidimetry and the degree of insulin resistance was assessed
 by the homeostasis model assessment of insulin resistance (HOMA-IR).
 Results: Serum CysC levels were significantly higher in pregnant women
 with GDM than in the healthy pregnant women [1.0(0.8-1.8) vs 0.7(0.6-1.0),
 P&lt;0.01). The Spearman's correlation analysis showed that serum
 CysC was positively associated with HOMA-IR(r=0.118, P&lt;0.05) and
 the occurrence of GDM (r=0.348, P&lt;0.01). The pregnant women were
 divided into quartiles according to their serum CysC concentrations.
 Compared to the first quartile, pregnant women in Q2 (OR, 2.441; P=0.025),
 Q3 (OR, 3.383; P=0.001) and Q4 (OR, 5.516; P&lt;0.001) had higher risk
 of GDM after adjusted for age, BMI, HbA1c and HOMA-IR. Further, with a
 rise in the serum CysC, there was an increasing trend in the HOMA-IR
 levels (P&lt;0.05). A binary logistic regression analysis after
 adjusting for other confounding variables revealed a significant and
 independent association between serum CysC and GDM [OR=14.269; 95%
 confidence interval, 4.977-40.908, P&lt;0.01]. The receiver operating
 characteristic curve analysis revealed that the optimal cutoff point for
 serum CysC to indicate GDM was 0.95mg/L. Conclusions: Serum CysC is
 significantly and independently associated with insulin resistance and
 GDM. It may be a helpful biomarker to identify the risk of GDM in Chinese
 pregnant women.
description: PONE-D-15-29188R1-S1_Dataset
DOI: 10.5061/dryad.6cc27
title: Data from: Early diving behaviour in juvenile penguins: improvement or selection processes

description: The early life stage of long-lived species is critical to the viability of
 population, but is poorly understood. Longitudinal studies are needed to
 test whether juveniles are less efficient foragers than adults as has been
 hypothesized. We measured changes in the diving behaviour of 17
 one-year-old king penguins Aptenodytes patagonicus at Crozet Islands
 (subantartic archipelago) during their first months at sea, using
 miniaturized tags that transmitted diving activity in real time. We also
 equipped five non-breeder adults with the same tags for comparison. The
 data on foraging performance revealed two groups of juveniles. The first
 group made shallower and shorter dives that may be indicative of early
 mortality while the second group progressively increased their diving
 depths and durations, and survived the first months at sea. This surviving
 group of juveniles required the same recovery durations as adults, but
 typically performed shallower and shorter dives. There is thereby a
 relationship between improved diving behaviour and survival in young
 penguins. This long period of improving diving performance in the juvenile
 life stage is potentially a critical period for the survival of deep avian
 divers and may have implications for their ability to adapt to
 environmental change.
description: juvskp_data_for_blJuveniles and Non-breeder Adults king penguins diving parameters by weeks for two different deployment years (2013/2014 and 2014/2015)
DOI: 10.5281/zenodo.13888278
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Henry Ogg Forbes, http://www.wikidata.org/entity/Q1349901. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q1349901
DOI: 10.5281/zenodo.18381761
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Henry Ogg Forbes, http://www.wikidata.org/entity/Q1349901. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q1349901
DOI: 10.5061/dryad.q3f2j
title: Data from: Hepatic Aryl hydrocarbon Receptor Nuclear Translocator (ARNT) regulates metabolism in mice

description: Background & Aims: Aryl hydrocarbon Receptor Nuclear Translocator
 (ARNT) and its partners hypoxia-inducible factors (HIF)-1α and HIF-2α are
 candidate factors for the well-known link between the liver, metabolic
 dysfunction and elevation in circulating lipids and glucose. Methods:
 Hepatocyte-specific ARNT-null (LARNT), HIF-1α-null (LHIF1α) and
 HIF-2α-null (LHIF2α) mice were created. Results: LARNT mice had increased
 fasting glucose, impaired glucose tolerance, increased glucose production,
 raised post-prandial serum triglycerides (TG) and markedly lower hepatic
 ATP versus littermate controls. There was increased expression of G6Pase,
 Chrebp, Fas and Scd-1 mRNAs in LARNT animals. Surprisingly, LHIF1α and
 LHIF2α mice exhibited no alterations in any metabolic parameter assessed.
 Conclusions: These results provide convincing evidence that reduced
 hepatic ARNT can contribute to inappropriate hepatic glucose production
 and post-prandial dyslipidaemia. Hepatic ARNT may be a novel therapeutic
 target for improving post-prandial hypertriglyceridemia and glucose
 homeostasis.
description: LARNT
 dataData for LARNT
 paperWeights 18 wk
 LARNT.zip
DOI: 10.5061/dryad.5kf38
title: Data from: Allopolyploidy, diversification, and the Miocene grassland expansion

description: The role of polyploidy, particularly allopolyploidy, in plant
 diversification is a subject of debate. Whole-genome duplications precede
 the origins of many major clades (e.g., angiosperms, Brassicaceae,
 Poaceae), suggesting that polyploidy drives diversification. However,
 theoretical arguments and empirical studies suggest that polyploid
 lineages may actually have lower speciation rates and higher extinction
 rates than diploid lineages. We focus here on the grass tribe
 Andropogoneae, an economically and ecologically important group of C4
 species with a high frequency of polyploids. A phylogeny was constructed
 for ca. 10% of the species of the clade, based on sequences of four
 concatenated low-copy nuclear loci. Genetic allopolyploidy was documented
 using the characteristic pattern of double-labeled gene trees. At least
 32% of the species sampled are the result of genetic allopolyploidy and
 result from 28 distinct tetraploidy events plus an additional six
 hexaploidy events. This number is a minimum, and the actual frequency
 could be considerably higher. The parental genomes of most Andropogoneae
 polyploids diverged in the Late Miocene coincident with the expansion of
 the major C4 grasslands that dominate the earth today. The well-documented
 whole-genome duplication in Zea mays ssp. mays occurred after the
 divergence of Zea and Sorghum. We find no evidence that polyploidization
 is followed by an increase in net diversification rate; nonetheless,
 allopolyploidy itself is a major mode of speciation.
description: Alignments of
 Orthologous and Paralogous Isolates for Allopolyploidy Identification in
 AndropogoneaeSee ReadMe
 file.Estepetal_PNAS_2014.tar.gz
DOI: 10.5061/dryad.s522m
title: Data from: Extinction-driven changes in frugivore communities on oceanic islands

description: Global change and human expansion have resulted in many species
 extinctions worldwide, but the geographic variation and determinants of
 extinction risk in particular guilds still remain little explored. Here,
 we quantified insular extinctions of frugivorous vertebrates (including
 birds, mammals and reptiles) across 74 tropical and subtropical oceanic
 islands within 20 archipelagos worldwide and investigated extinction in
 relation to island characteristics (island area, isolation, elevation and
 climate) and species’ functional traits (body mass, diet and ability to
 fly). Out of the 74 islands, 33 islands (45%) have records of frugivore
 extinctions, with one third (mean: 34%, range: 2–100%) of the
 pre-extinction frugivore community being lost. Geographic areas with more
 than 50% loss of pre-extinction species richness include islands in the
 Pacific (within Hawaii, Cook Islands and Tonga Islands) and the Indian
 Ocean (Mascarenes, Seychelles). The proportion of species richness lost
 from original pre-extinction communities is highest on small and isolated
 islands, increases with island elevation, but is unrelated to temperature
 or precipitation. Large and flightless species had higher extinction
 probability than small or volant species. Across islands with extinction
 events, a pronounced downsizing of the frugivore community is observed,
 with a strong extinction-driven reduction of mean body mass (mean: 37%,
 range: -18–100%) and maximum body mass (mean: 51%, range: 0–100%). The
 results document a substantial trophic downgrading of frugivore
 communities on oceanic islands worldwide, with a non-random pattern in
 relation to geography, island characteristics and species’ functional
 traits. This implies severe consequences for ecosystem processes that
 depend on mutualistic plant-animal interactions, including ecosystem
 dynamics that result from the dispersal of large-seeded plants by
 large-bodied frugivores. We suggest that targeted conservation and
 rewilding efforts on islands are needed to halt the defaunation of large
 and non-volant seed dispersers and to restore frugivore communities and
 key ecological interactions.
description: Data_Occurrences_IslandFrugivoresExtinct and extant occurrences of frugivorous birds, mammals and reptiles on 74 tropical and subtropical oceanic islands within 20 archipelagos worldwideData_Traits_IslandFrugivoresData on body size (body mass: g), flying (ability to fly: yes/no), and diet (amount of fruit in the diet: low/medium/high) of extant and extinct frugivorous birds, mammals and reptiles on 74 tropical and subtropical oceanic islands within 20 archipelagos worldwideData_Island_CharacteristicsData on island characteristics (island area, isolation, elevation and climate) of 74 tropical and subtropical oceanic islands within 20 archipelagos worldwide
DOI: 10.5061/dryad.ts569
title: Data from: Phylogenetic relationships among Old World Ruellia L.: a new classification and reinstatement of the genus Dinteracanthus Schinz

description: The genus Ruellia (Acanthaceae) consists of some ca. 350 species that are
 concentrated in tropical and subtropical regions of the world. Old World
 Ruellia have never been the focus of explicit phylogenetic study, yet
 comprise the earliest diverging lineages in the genus and contain upwards
 of 100 species. We sampled 52 accessions representing 29 OW species of
 Ruellia for phylogenetic analysis. Results yielded five clades that were
 strongly supported and marked by morphological synapomorphies. Analyses
 additionally recovered a newly recognized lineage within the tribe
 Ruellieae, a small radiation of plants in the deserts of Namibia and
 Angola, and the name Dinteracanthus is available for reinstatement.
 Divergence time analysis using a primary fossil calibration revealed
 relatively young estimates for crown ages of all five clades of OW Ruellia
 (2.5 Ma ‐ 630,000 ypb) as well as for Dinteracanthus (2.0 Ma). Ancestral
 state reconstruction of pollination systems among OW Ruellia suggest a
 minimum of two transitions from short-tongued insect pollination to
 nocturnal moth pollination, one from short-tongued insect to bird
 pollination, and one reversal from nocturnal moth pollination back to
 short-tongued insect pollination. We formally delimit the five clades of
 OW Ruellia as sections and present a key to aid in their identification:
 sect. Eusiphon, sect. Dipteracanthus, sect. Madagasikara, sect.
 Pseudoruellia, and sect. Discifolia. We provisionally treat 77 of 97
 species of OW Ruellia among these five sections, with the remaining names
 considered to be unresolved.
description: Ruellia_no_exclusions_OW_pruned taxaFull, aligned DNA matrix
DOI: 10.5061/dryad.19264
title: Data from: Parasite load and MHC diversity in undisturbed and agriculturally modified habitats of the ornate dragon lizard

description: MHC gene polymorphism is thought to be driven by host-parasite
 coevolution, but the evidence for an association between the selective
 pressure from parasites and the number of MHC alleles segregating in a
 population is scarce and inconsistent. Here, we characterized MHC class I
 polymorphism in a lizard whose habitat preferences (rock outcrops) lead to
 the formation of well-defined and stable populations. We investigated the
 association between the load of ticks, which were used as a proxy for the
 load of pathogens they transmit, and MHC class I polymorphism across
 populations in two types of habitat: undisturbed reserves and agricultural
 land. We hypothesized that the association would be positive across
 undisturbed reserve populations, but across fragmented agricultural land
 populations the relationship would be distorted by the loss of MHC
 variation due to drift. After controlling for habitat, MHC diversity was
 not associated with tick number, and the habitats did not differ in this
 respect. Neither did we detect a difference between habitats in the
 relationship between MHC and neutral diversity, which was positive across
 all populations. However, there was extensive variation in the number of
 MHC alleles per individual, and we found that tick number was positively
 associated with the average number of alleles carried by lizards across
 reserve populations, but not across populations from disturbed
 agricultural land. Our results thus indicate that local differences in
 selection from parasites may contribute to MHC copy number variation
 within species, but habitat degradation can distort this relationship.
description: MHC class I
 allelesCtenophorus ornatus MHC
 I putative functional allele sequences. Aligned fasta
 file.Ctenophorus_ornatus_MHC_I_putative_functional_alleles.fasIndividual tick count and number of MHC alllesCtenophorus ornatus Individual tick count and number of MHC allles. Information about habitat and population of origin is also included. Excel format.Ctenophorus_ornatus_tick_load_n_MHC_alleles.xlsxMHC and microsatellite genotypesMHC and microsatellite genotypes. MHC genotypes are in Structure-like dominant format (each allele trated as a separate locus). Microsatellite genotypes are in Structure-like one-line-per genotype format. Excel file.Ctenophorus_ornatus_MHC_msat_genotypes.xlsxCtenophorus_ornatus_expression_dataThis file contains results of MHC genotyping of 4 individuals using genomic DNA (gDNA) and cDNA synthesized from DNAse-treated RNA (cDNA); for one individual only cDNA data are available. Because in no gDNA/cDNA pair coverage in both samples was sufficient for rigorous genotyping (min 300 reads), we present raw read counts of putative true alleles (identified as such using the entire dataset). On the basis of the read counts in gDNA/cDNA samples we assign "expressed", "not_expressed" and in few cases "undetermined" expression status to those alleles.