cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t7p41f4
title: Data from: Colour plasticity in response to social context and parasitic infection in a self-fertilizing fish

description: Many animal species rely on changes in body colouration to signal social
 dominance, mating readiness and health status to conspecifics, which can
 in turn influence reproductive success, social dynamics and pathogen
 avoidance in natural populations. Such colour changes are thought to be
 controlled by genetic and environmental conditions, but their relative
 importance is difficult to measure in natural populations, where
 individual genetic variability complicates data interpretation. Here, we
 studied shifts in melanin-related body colouration in response to social
 context and parasitic infection in two naturally inbred lines of a
 self-fertilizing fish to disentangle the relative roles of genetic
 background and individual variation. We found that social context and
 parasitic infection had a significant effect on body colouration that
 varied between genetic lines, suggesting the existence of genotype by
 environment interactions. In addition, individual variation was also
 important for some of the colour attributes. We suggest that the genetic
 background drives colour plasticity and that this can maintain phenotypic
 variation in inbred lines, an adaptive mechanism that may be particularly
 important when genetic diversity is low.
description: Colour plasticity
 data_infection and social colour changeRaw data provided for
 infection and social colour change experiments. Raw data obtained in
 CIELAB format before conversion to light, hue and
 chroma.Colour plasticity
 data.zip
DOI: 10.5061/dryad.c9p26
title: Data from: Batocrinidae (Crinoidea) from the lower Mississippian (lower Viséan) Fort Payne Formation of Kentucky, Tennessee, and Alabama: systematics, geographic occurrences, and facies distribution

description: The Batocrinidae are characteristic faunal elements in lower Mississippian
 shallow-marine settings in North America. Recent delineation of
 objectively defined genera allows a reexamination of batocrinid species
 and their distribution in the Fort Payne Formation (early Viséan, late
 Osagean), a well-studied array of carbonate and siliciclastic facies. The
 Fort Payne batocrinid fauna has fourteen species assigned to six genera,
 plus hybrid specimens. Magnuscrinus spinosus (Miller and Gurley, 1895a) is
 reassigned to its original placement in Eretmocrinus. Hybrid specimens
 (Ausich and Meyer, 1994) are regarded as Eretmocrinus magnificus X
 Eretmocrinus spinosus. Macrocrinus casualis is the dominant species of
 Macrocrinus in the Fort Payne, and M. mundulus and M. strotobasilaris are
 recognized in the Fort Payne Formation for the first time. Magnuscrinus
 cumberlandensis n. sp. is named, thirteen species are designated as junior
 synonyms, the name for the hybrid specimens is changed to Eretmocrinus
 magnificus × Eretmocrinus spinosus, and the previous occurrences of two
 species in the Fort Payne are rejected. The Eastern Interior Seaway was a
 mixed carbonate-siliciclastic setting with both shallow- and deep-water
 epicontinental sea facies ranging from relatively shallow autochthonous
 green shales to deep-water turbidite facies. Dizygocrinus was restricted
 to shallow-water carbonate and siliciclastic facies, Eutrochocrinus was
 restricted to shallow-water carbonate facies, and Magnuscrinus was
 restricted to deep-water facies. Species distributions varied from
 Abatocrinus steropes, Alloprosallocrinus conicus, Macrocrinus mundulus,
 and Uperocrinus nashvillae that occurred throughout the Eastern Interior
 Seaway to species that were restricted to a single facies. Eretmocrinus
 magnificus, Alloprosallocrinus conicus, and Uperocrinus robustus were the
 dominant batocrinids in the Fort Payne Formation.
description: AusichRhenbergMeyer-OnlineSupplement-Revised-10-06-17Methods, Synonomies, Localities, Measurements
DOI: 10.5061/dryad.71k17
title: Data from: A morphometric and genetic framework for the genus Gazella de Blainville, 1816 (Ruminantia: Bovidae) with special focus on Arabian and Levantine mountain gazelles

description: Gazella is one of the most species-rich genera within horned ruminants.
 Despite overall similarity in body size and morphology, gazelles show
 variability in coloration and horn morphology. Unfortunately, however,
 species differentiation based on these characters, or on discrete skull
 characters, is very difficult due to high intraspecific variability.
 Furthermore, most species have fragmented and allopatric distributions, so
 that species boundaries were hard to define in the past. Mitochondrial DNA
 sequences have proven useful for investigating gazelle taxonomy in recent
 years, but especially for old museum material, i.e. type specimens,
 destructive sampling is often impossible. We provide a comprehensive
 morphometric framework for the genus Gazella based on linear skull
 measurements reconciled with results from molecular phylogenetic analysis
 based on the largest dataset available so far. In particular for males,
 the skull morphology shows interspecific differences concurrent with DNA
 data and provides a reliable tool for species identification. Based on
 morphometric data we synonymize G. karamii with G. marica, and confirm the
 identification of the G. arabica and G. a. rueppelli type skulls from
 analyses of mitochondrial DNA sequences.
description: Gazella skull
 measurements, raw data (A morphometric and genetic framework for
 Gazella)This file includes the
 linear measurements of Gazella skulls from several museum specimens.
 Measurements were taken with callipers (except L F+P2 and HL2, these were
 measured with a tape measure) and are given in mm. Figure 2 in the
 original publication depicts the measurements taken.Gazella measurements_raw
 data.xlsx
DOI: 10.5061/dryad.q03c3
title: Data from: Melanin in a changing world: brown trout coloration reflects alternative reproductive strategies in variable environments

description: Melanins are the most widespread pigments in animals but their adaptive
 significance remains elusive. Recent studies suggest that intraspecific
 variation in melanin-based coloration reflects individual genetic-based
 alternative strategies to cope with environment variability, which could
 be crucial for their responses to climate changes. However, empirical
 evidence is still scarce. In this study, we tested how skin coloration in
 natural populations of brown trout Salmo trutta fario would reflect
 alternative reproductive strategies in different environments. We
 experimentally manipulated the flow regime (constant vs. variable) in
 artificial streams and compared the reproductive investment (body mass and
 plasma triglyceride variations), innate immunity (variations in plasma
 peroxidase and lysozyme activity) and reproductive success (number of
 mates and offspring) of differently colored brown trout over 2
 reproductive seasons. Results show that darker males had a higher
 reproductive investment, but similar immune variations during reproduction
 compared to paler males. In addition, this reproductive investment was
 higher in variable environments. However, this did not translate into a
 higher reproductive success in variable environments, as darker males had
 a similar number of mates and offspring compared to their paler
 counterparts under a variable water flow. Since climate change will likely
 lead to an increased flow variability in the next decades, this suggests
 that darker brown trout could incur a higher energetic cost of
 reproduction and could be more impacted by climate changes than their
 paler counterparts. This highlights the need to take into account
 intraspecific variability to better forecast the response of natural
 populations to climate changes.
description: DATA
 BEHECO-2016-0591
DOI: 10.5061/dryad.n774460
title: Data from: Implications of dimeric activation of PDE6 for rod phototransduction

description: We examine the implications of a recent report providing evidence that two
 transducins must bind to the rod phosphodiesterase to elicit significant
 hydrolytic activity. To predict the rod photoreceptor's electrical
 response, we use numerical simulation of the two-dimensional diffusional
 contact of interacting molecules at the surface of the disc membrane, and
 then we use the simulated PDE activity as the driving function for the
 downstream reaction cascade. The results account for a number of aspects
 of rod phototransduction that have previously been puzzling. For example,
 they explain the existence of a greater initial delay in rods than in
 cones. Furthermore, our analysis suggests that the ‘continuous’ noise
 recorded in rods in darkness is likely to arise from spontaneous
 activation of individual molecules of PDE at a rate of a few tens per
 second per rod, probably as a consequence of spontaneous activation of
 transducins at a rate of thousands per second per rod. Hence, the dimeric
 activation of PDE in rods provides immunity against spontaneous transducin
 activation, thereby reducing the continuous noise. Our analysis also
 provides a coherent quantitative explanation of the amplification
 underlying the single photon response. Overall, numerical analysis of the
 dimeric activation of PDE places rod phototransduction in a new light.
description: WalkMat_v4_RSOBZipped archive containing ‘WalkMat’ package of Matlab computer code used to run the stochastic simulations and to integrate the downstream reactions in support of the findings in the publication.
DOI: 10.5061/dryad.21mp3
title: Data from: Nutrient limitation of woody debris decomposition in a tropical forest: contrasting effects of N and P addition

description: Tropical forests represent a major terrestrial store of carbon (C), a
 large proportion of which is contained in the soil and decaying organic
 matter. Woody debris plays a key role in forest C dynamics because it
 contains a sizeable proportion of total forest C. Understanding the
 factors controlling the decomposition of organic matter in general, and
 woody debris in particular, is hence critical to assessing changes in
 tropical C storage. We conducted a factorial fertilization experiment in a
 tropical forest in South China to investigate the influence of nitrogen
 (N) and phosphorus (P) availability on woody debris decomposition using
 branch segments (5 cm diameter) of four species (Acacia auriculaeformis,
 Aphanamixis polystachya, Schefflera octophylla, and Carallia brachiata) in
 plots fertilized with +N, +P, or +NP, and controls. Fertilization with +P
 and +NP increased decomposition rates by 5–53%, and the magnitude was
 species specific. Contrary to expectations, we observed no negative effect
 of +N addition on decay rates or mass loss of woody debris in any of the
 four study species. Decomposition rates of woody debris were higher in
 species with lower C : P ratios regardless of treatment. We observed
 significant accumulation of P in the woody debris of all species in plots
 fertilized with +P and +NP during the early stages of decomposition. N
 release from woody debris of Acacia (N-fixing) was greater in the +P plots
 towards the end of the study, whereas fertilization with +N had no impact
 on the patterns of nutrient release during decomposition. Synthesis: Our
 results indicate that decomposition of woody debris is primarily
 constrained by P availability in this tropical forest. However, contrary
 to expectations, +N addition did not exacerbate P limitation. It is
 conceivable that decay rates of woody debris in tropical forests can be
 predicted by C : P or lignin : P ratios, but additional work with more
 tree species is needed to determine whether the patterns we observed are
 more generally applicable.
description: Chen Yao, Wang Faming-N
 and P addition on woody debris decompositon datasheetThe Raw data of this
 paper
DOI: 10.5061/dryad.72s5k
title: Data from: Y-chromosome evidence supports asymmetric dog introgression into eastern coyotes

description: Hybridization has played an important role in the evolutionary history of
 Canis species in eastern North America. Genetic evidence of coyote–dog
 hybridization based on mitochondrial DNA (mtDNA) is lacking compared to
 that based on autosomal markers. This discordance suggests dog
 introgression into coyotes has potentially been male biased, but this
 hypothesis has not been formally tested. Therefore, we investigated
 biparentally, maternally, and paternally inherited genetic markers in a
 sample of coyotes and dogs from southeastern Ontario to assess potential
 asymmetric dog introgression into coyotes. Analysis of autosomal
 microsatellite genotypes revealed minimal historical and contemporary
 admixture between coyotes and dogs. We observed only mutually exclusive
 mtDNA haplotypes in coyotes and dogs, but we observed Y-chromosome
 haplotypes (Y-haplotypes) in both historical and contemporary coyotes that
 were also common in dogs. Species-specific Zfy intron sequences of
 Y-haplotypes shared between coyotes and dogs confirmed their homology and
 indicated a putative origin from dogs. We compared Y-haplotypes observed
 in coyotes, wolves, and dogs profiled in multiple studies, and observed
 that the Y-haplotypes shared between coyotes and dogs were either absent
 or rare in North American wolves, present in eastern coyotes, but absent
 in western coyotes. We suggest the eastern coyote has experienced
 asymmetric genetic introgression from dogs, resulting from predominantly
 historical hybridization with male dogs and subsequent backcrossing of
 hybrid offspring with coyotes. We discuss the temporal and spatial
 dynamics of coyote–dog hybridization and the conditions that may have
 facilitated the introgression of dog Y-chromosomes into coyotes. Our
 findings clarify the evolutionary history of the eastern coyote.
description: Wheeldon et al ECE3_693
 Autosomal Microsatellite DataAutosomal microsatellite
 genotypes of historical (pop 1) and contemporary (pop 2) coyotes from
 southeastern Ontario, eastern wolves (pop 3) from Algonquin Provincial
 Park, gray wolves (pop 4) from northeastern Ontario, and domestic dogs
 (pop 5).Wheeldon et al ECE3_693 DRYAD
 entry.xlsx
DOI: 10.5061/dryad.tn90g
title: Data from: Risk factors and clinical features of ovarian pregnancy: a case-control study

description: Objective: To identify risk factors for ovarian pregnancy (OP) and compare
 clinical features between OP and tubal pregnancy (TP) patients. Design:
 Case–control study. Setting: University hospital. Participants: A
 case–control study was conducted from January 2005 to May 2014. Women
 diagnosed with OP were recruited as the case group (n=71), 145 women with
 TP and 146 with intrauterine pregnancy (IUP) were matched as controls at a
 ratio of 1:2:2. Women who refused interviews or provided incomplete
 information were excluded. Results: OP risk was lower than TP risk in
 women with serological evidence of Chlamydia trachomatis infection
 (adjusted OR1 0.17, 95% CI 0.06 to 0.52), previous adnexal surgery
 (adjusted OR1 0.25, 95% CI 0.07 to 0.95), and current levonorgestrel
 emergency contraceptive use (adjusted OR1 0.24, 95% CI 0.07 to 0.78). In
 vitro fertilisation-embryo transfer (IVF-ET) carried a higher risk of OP
 (adjusted OR1 12.18, 95% CI 2.23 to 66.58) than natural conception. When
 Controlled by IUP women, current users of intrauterine devices (IUDs)
 carried a higher risk of OP than non-users of any contraceptives (adjusted
 OR2 9.60, 95% CI 1.76 to 42.20). β-Human chorionic gonadotropin (hCG)
 levels on the day of surgery were higher in OP patients than in TP
 patients (p&lt;0.01). Women with OP were less likely to initially
 present with vaginal bleeding than those with TP (p=0.02). Moreover, shock
 (p=0.02), rupture (p&lt;0.01), haemoperitoneum (p&lt;0.01) and
 emergency laparotomy (p&lt;0.01) were more common in the OP group than
 in the TP group. Conclusions: IVF-ET and IUD use may be risk factors for
 OP, and OP patients tend to have high β-hCG levels and a poor clinical
 outcome (shock, rupture, haemoperitoneum and need for emergency
 laparotomy). Our findings may contribute to the prevention and early
 diagnosis of OP.
description: Data from: Risk factors
 and clinical features of ovarian pregnancy: a case-control
 studyData.rar
DOI: 10.6084/m9.figshare.31153790
title: Additional file 5 of Gender norms in sexual and reproductive health and rights: insights from young Angolan women and the development of a context-specific questionnaire (2021–2022)

description: Supplementary Material 5.
DOI: 10.6084/m9.figshare.31153790.v1
title: Additional file 5 of Gender norms in sexual and reproductive health and rights: insights from young Angolan women and the development of a context-specific questionnaire (2021–2022)

description: Supplementary Material 5.
DOI: 10.5061/dryad.1661m
title: Data from: Economic investment by ant colonies in searches for better homes.

description: Organisms should invest more in gathering information when the pay-off
 from finding a profitable resource is likely to be greater. Here we ask
 whether animal societies put more effort in scouting for a new nest when
 their current one is of low quality. We measured the scouting behaviour of
 Temnothorax albipennis ant colonies when they inhabit nest-sites with
 different combinations of desirable attributes. We show that the average
 probability of an ant scouting decreases significantly with an increase in
 the quality of the nest in which the colony currently resides. This means
 that the greater the potential gain from finding a new nest, the more
 effort a colony puts into gathering information regarding new nest-sites.
 Our results show for the first time, the ability of animal societies to
 respond collectively to the quality of a resource they currently have at
 their disposal (e.g. current nest-site) and regulate appropriately their
 information gathering efforts for an alternative (e.g. a potentially
 better nest-site).
description: ants_searching_for_a_better_home_comments_raw_dataNumber of ants counted according to the protocol described in the manuscript.
DOI: 10.5061/dryad.k2502d93
title: Data from: Long-term genetic monitoring reveals contrasting changes in the genetic composition of newly established populations of the intertidal snail Bembicium vittatum

description: Newly established populations are susceptible to founder events that
 reduce genetic variation. This may be counterbalanced by gene flow after
 populations become established or founders coming from genetically
 different populations. However, initial gains in genetic diversity may be
 short-lived if there is limited mixing between lineages and subsequent
 inbreeding or if one lineage sweeps to fixation through selection or
 genetic drift. Here, we report on the genetic changes taking place within
 two newly established populations of intertidal snail over a 15-year
 period (~ 10 generations). Each translocation was set up using multiple,
 genetically distinct source populations. Our data show that higher levels
 of variation in the translocated populations compared to the source
 populations were maintained over time for both nuclear (microsatellite)
 and mitochondrial genes. Small changes in allele and haplotype frequencies
 were observed in the source populations and in one of the translocated
 populations, but marked changes were evident in the other, where there was
 a dramatic shift towards the genetic make-up of one of the source
 populations. These genetic changes occurred despite relatively large
 numbers of founders (200- 374 adults) and no evidence of the population
 experiencing a severe reduction in effective population size. Our study
 shows that the genetic composition of newly established populations can
 vary greatly over time and that genetic outcomes can be highly variable,
 and significantly different to expectations, even when they are
 established using high numbers of individuals and involve source
 populations from the same geographic regions.
description: Msat
 dataMicrosatellite
 datamtdna
 data
DOI: 10.5281/zenodo.18218909
title: Proteins and ncRNAs across 352 species illuminate genome evolution

description: Transposable elements (TEs), nature’s genetic engineers’, are pivotal drivers of genome evolution, yet their precise mechanisms in shaping plant functional innovation remain elusive. This study presents a comprehensive analysis of TEs across 558 high-quality plant genomes, encompassing 352 species from 221 genera across five phyla, ranging from algae to angiosperms. We identified over 460 million TEs and 67 million transposase domains, systematically assessing their impact on host genomes through gene domestication, noncoding RNA generation, and gene duplication. Our analysis revealed 1,258,230 genes domesticated from TEs, 1,165,059 ncRNAs originating from TEs, and 10,488,967 TE-induced gene duplications. These genes affect more than 2,805 function families, likely planning crucial roles at key stages of plant evolution.
DOI: 10.5281/zenodo.18218910
title: Proteins and ncRNAs across 352 species illuminate genome evolution

description: Transposable elements (TEs), nature’s genetic engineers’, are pivotal drivers of genome evolution, yet their precise mechanisms in shaping plant functional innovation remain elusive. This study presents a comprehensive analysis of TEs across 558 high-quality plant genomes, encompassing 352 species from 221 genera across five phyla, ranging from algae to angiosperms. We identified over 460 million TEs and 67 million transposase domains, systematically assessing their impact on host genomes through gene domestication, noncoding RNA generation, and gene duplication. Our analysis revealed 1,258,230 genes domesticated from TEs, 1,165,059 ncRNAs originating from TEs, and 10,488,967 TE-induced gene duplications. These genes affect more than 2,805 function families, likely planning crucial roles at key stages of plant evolution.
DOI: 10.5061/dryad.8583t
title: Data from: Age, growth and fall diet of channel catfish in Cheat Lake, West Virginia

description: Acidification has historically impaired Cheat Lake's fish community,
 but recent mitigation efforts within the Cheat River watershed have
 improved water quality and species richness. Presently, channel catfish
 Ictalurus punctatus are abundant and attain desirable sizes for anglers.
 We evaluated the age, growth and fall diet of the population. A sample of
 155 channel catfish was collected from Cheat Lake from 5 August to 4
 December 2014, a subsample of which was aged (n = 148) using lapillus
 otoliths. Four growth models (von Bertalanffy, logistic, Gompertz and
 power) were fit to length at age data and compared using an information
 theoretic approach. Fall diets were collected from 55 fish sampled from 13
 October to 4 December 2014. Total lengths of individuals in the sample
 ranged from 154-721 mm and ages ranged from 2-19 years. The von
 Bertalanffy growth model was AICc -selected as the best approximating
 model, and the power and Gompertz models also had considerable support.
 Diets were numerically dominated by Diptera larvae, specifically
 Chironomidae and Chaoboridae, while 39% of stomachs contained terrestrial
 food items. This study provides baseline data for management of Cheat
 Lake's channel catfish population. Further, this study fills a
 knowledge gap in the scientific literature on channel catfish, as few
 published studies have examined the population ecology of channel catfish
 in the Central Appalachian region.
description: Hilling_et_al_Table_S1Details on individual sampling events for channel catfish Ictalurus punctatus in Cheat Lake, West Virginia. Dates provided were from the year 2014. Water temperatures presented were measured by the USGS water gauge on the Cheat River at Albright, West Virginia at 2400 hours. Gear was denoted as EGN (experimental gill nets), HN (hoop nets), GN (46 m gill nets) and BEF (boat electrofishing). See text for thorough explanations of net dimensions.Hilling_et_al_DataA1Data and working files for length-at-age, diet, relative weight and relative growth index from Cheat Lake, West Virginia channel catfish collected from 5 August to 4 December 2014.