cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k14t77p
title: Data from: Replanting of first-cycle oil palm results in a second wave of biodiversity loss

description: 1. Conversion of forest to oil palm plantations results in a significant
 loss of biodiversity. Despite this, first-cycle oil palm plantations can
 sustain relatively high biodiversity compared to other crops. However, the
 long-term effects of oil palm agriculture on flora and fauna are unknown.
 Oil palm has a 25-year commercial lifespan before it must be replanted,
 due to reduced productivity and difficulty of harvesting. Loss of the
 complex vegetation structure of oil palm plantations during the replanting
 process will likely have impacts on the ecosystem at a local and landscape
 scale. However, the effect of replanting on biodiversity is poorly
 understood. 2 Here, we investigate the effects of replanting oil palm on
 soil macrofauna communities. We assessed ordinal richness, abundance and
 community composition of soil macrofauna in first (25-27-years-old) and
 second-cycle oil palm (freshly cleared, 1-year-old, 3-year-old and
 7-year-old mature). 3. Macrofauna abundance and richness drastically
 declined immediately after replanting. Macrofauna richness showed some
 recovery 7-years after replanting, but was still 19% lower than
 first-cycle oil palm. Macrofauna abundance recovered to similar levels to
 that of first-cycle oil palm plantations, one-year after replanting. This
 was mainly due to high ant abundance, possibly due to the increased
 understory vegetation as herbicides are not used at this age. However,
 there were subsequent declines in macrofauna abundance 3 and 7-years after
 replanting, resulting in a 59% drop in macrofauna abundance compared to
 first-cycle levels. Furthermore, soil macrofauna community composition in
 all ages of second-cycle oil palm was different to first-cycle
 plantations, with decomposers suffering particular declines. 4. After
 considerable biodiversity loss due to forest conversion for oil palm;
 belowground invertebrate communities suffer a second wave of biodiversity
 loss due to replanting. This is likely to have serious implications for
 soil invertebrate diversity and agricultural sustainability in oil palm
 landscapes, due to the vital ecosystem functions that soil macrofauna
 provide.
description: arthropod biodiversity
 oil palm replantingarthropod abundance by
 taxonomic group for first-cycle and second-cycle oil palm
 agesarthropodreplanting.csv
DOI: 10.5061/dryad.f3r6799
title: Data from: Natural history of limb girdle muscular dystrophy R9 over 6 years: searching for trial endpoints

description: Objective: Limb girdle muscular dystrophy type R9 (LGMD R9) is an
 autosomal recessive muscle disease for which there is currently no
 causative treatment. The development of putative therapies requires
 sensitive outcome measures for clinical trials in this slowly progressing
 condition. This study extends functional assessments and MRI muscle fat
 fraction measurements in an LGMD R9 cohort across 6 years. Methods:
 Twenty‐three participants with LGMD R9, previously assessed over a 1‐year
 period, were re‐enrolled at 6 years. Standardized functional assessments
 were performed including: myometry, timed tests, and spirometry testing.
 Quantitative MRI was used to measure fat fraction in lower limb skeletal
 muscle groups. Results: At 6 years, all 14 muscle groups assessed
 demonstrated significant increases in fat fraction, compared to eight
 groups in the 1‐year follow‐up study. In direct contrast to the 1‐year
 follow‐up, the 6‐min walk test, 10‐m walk or run, timed up and go, stair
 ascend, stair descend and chair rise demonstrated significant decline.
 Among the functional tests, only FVC significantly declined over both the
 1‐ and 6‐year studies. Interpretation: These results further support fat
 fraction measurements as a primary outcome measure alongside functional
 assessments. The most appropriate individual muscles are the vastus
 lateralis, gracilis, sartorius, and gastrocnemii. Using composite groups
 of lower leg muscles, thigh muscles, or triceps surae, yielded high
 standardized response means (SRMs). Over 6 years, quantitative fat
 fraction assessment demonstrated higher SRM values than seen in functional
 tests suggesting greater responsiveness to disease progression.
description: LGMD R9 Murphy Annals
 Clin Trans Neurol 2019 public 200319Anonymised MRI
 measurements (fat fraction), physical function tests and basic subject
 characteristics as described in the Data Availability statement of Murphy
 et al. (2019)
DOI: 10.5061/dryad.dt17v7m
title: Data from: Alternative reproductive tactics shape within-species variation in behavioural syndromes

description: Multiple behaviours can correlate with each other at the individual level
 (behavioural syndrome), and behavioural syndromes can vary in their
 direction between populations within a species. Within-species variation
 in behavioural syndromes is predicted to be associated with alternative
 reproductive tactics (ARTs) which evolve under different selection
 regimes. Here we tested this using a water strider species, Gerris
 gracilicornis, in which males employ two ARTs that are fixed for life:
 signalling males (producing courtship ripples) versus non-signalling males
 (producing no courtship ripples). We measured multiple behaviours in males
 with both of these ARTs and compared behavioural syndromes between them.
 Our results showed that signalling males were more active and attempted to
 mate more frequently than non-signalling males. This shaped an overall
 behavioural syndrome between activities in mating and non-mating contexts
 when we pooled both ARTs. In addition, the behavioural syndromes between
 cautiousness and mating activity differed significantly between ARTs. In
 signalling males, the syndrome was significantly negative: signalling
 males more eager to mate tended to leave their refuges more rapidly.
 However, mating activity and cautiousness were not correlated in
 non-signalling males. This might be because active males, in the context
 of predation risk and mating, were favoured during the evolution and
 maintenance of the unique intimidating courtship tactic of G.
 gracilicornis males. Thus, our findings suggest that ARTs facilitate
 behavioural divergence and also contribute to the evolution of
 tactic-specific behavioural syndromes. We also show that research on ARTs
 and behavioural syndromes can be harmonised to study behavioural
 variation.
description: Datafiledata_han.txt
DOI: 10.5061/dryad.dn28cn6
title: Data from: Within-individual canalization contributes to age-related increases in trait repeatability: a longitudinal experiment in red knots

description: Abstract: Age-related increases in the repeatable expression of labile
 phenotypic traits are often assumed to arise from an increase in
 among-individual variance due to differences in developmental plasticity
 or by means of state-behaviour feedbacks. However, age-related increases
 in repeatability could also arise from a decrease in within-individual
 variance as a result of stabilizing trait expression, i.e. canalization.
 Here we describe age-related changes in within- and among-individual
 variance components in two correlated traits, gizzard mass and exploration
 behavior, in a medium-sized shorebird, the red knot (Calidris canutus).
 Increased repeatability of gizzard mass came about due to an increase in
 among-individual variance, unrelated to differences in developmental
 plasticity, together with decreases in within-individual variance,
 consistent with canalization. We also found canalization of exploration,
 but no age-related increase in overall repeatability, which suggests that
 showing predictable expression of exploration behaviour may be
 advantageous from a very young age onward. Contrasts between juveniles and
 adults in the first year after their capture provide support for the idea
 that environmental conditions play a key role in generating
 among-individual variation in both gizzard mass and exploration behavior.
 Our study shows that stabilization of traits occurs under constant
 conditions: with increased exposure to predictable cues, individuals may
 become more certain in their assessment of the environment allowing traits
 to become canalized.
description: kok et al2019_AmNat data
 within-indiv canalization datafileData
 filekok et
 al2019_AmNat data within-indiv
 canalization.txtkok et al2019_AmNat
 within-indiv canalization_RscriptR
 scriptkok
 et al2019_AmNat within-indiv
 canalization.R
DOI: 10.5281/zenodo.18391450
title: ZAMONAVIY TA'LIMDA FAOL METODLAR ORQALI CHUQURLASHTIRILGAN BILIMLARNI SHAKLLANTIRISH MODELI

description: Mazkur maqolada zamonaviy ta’lim tizimida faol ta’lim metodlari asosida chuqurlashtirilgan bilimlarni shakllantirish modeli ilmiy-nazariy jihatdan tahlil qilinadi. Tadqiqotda faol metodlarning kognitiv rivojlanish, bilimlarni transformatsiya qilish, mustaqil va tanqidiy fikrlashni shakllantirishdagi o‘rni asoslab beriladi. Shuningdek, kompetensiyaviy va shaxsga yo‘naltirilgan yondashuvlar asosida faol ta’lim metodlarining ta’lim samaradorligini oshirishdagi ahamiyati yoritiladi. Ilmiy tahlillar va zamonaviy pedagogik tadqiqotlar natijalari asosida faol metodlarning chuqur va barqaror bilimlarni shakllantirishdagi transformatsion imkoniyatlari aniqlanadi.
DOI: 10.5281/zenodo.18391451
title: ZAMONAVIY TA'LIMDA FAOL METODLAR ORQALI CHUQURLASHTIRILGAN BILIMLARNI SHAKLLANTIRISH MODELI

description: Mazkur maqolada zamonaviy ta’lim tizimida faol ta’lim metodlari asosida chuqurlashtirilgan bilimlarni shakllantirish modeli ilmiy-nazariy jihatdan tahlil qilinadi. Tadqiqotda faol metodlarning kognitiv rivojlanish, bilimlarni transformatsiya qilish, mustaqil va tanqidiy fikrlashni shakllantirishdagi o‘rni asoslab beriladi. Shuningdek, kompetensiyaviy va shaxsga yo‘naltirilgan yondashuvlar asosida faol ta’lim metodlarining ta’lim samaradorligini oshirishdagi ahamiyati yoritiladi. Ilmiy tahlillar va zamonaviy pedagogik tadqiqotlar natijalari asosida faol metodlarning chuqur va barqaror bilimlarni shakllantirishdagi transformatsion imkoniyatlari aniqlanadi.
DOI: 10.57745/smujec
title: A specific metabolomic and lipidomic signature reveals the post-partum resolution of gestational diabetes mellitus or its evolution to Type 2 Diabetes in rat Supplementary data

description: Gestational Diabetes Mellitus represents a major public health concern due to adverse maternal post-partum and long-term outcome. Current strategies to manage Gestational Diabetes Mellitus fail to reduce the maternal risk to develop later impaired glucose tolerance and type 2 diabetes . In a rodent model of diet-induced gestational diabetes mellitus without obesity, we explored the perinatal metabolic adaptations in dams with gestational diabetes mellitus followed by either persistent or resolved post-partum impaired glucose tolerance . Female Sprague-Dawley rats were fed a High-Fat High-Sucrose or a Chow diet, one week before mating and throughout gestation. Following parturition, High-Fat High-Sucrose dams were randomized to two subgroups: one switched to Chow diet and the other one maintained on High-Fat High-Sucrose diet throughout lactation. Oral glucose tolerance tests were performed and plasma metabolome-lipidome were characterized at Gestation_day 12 and Lactation_day 12. We found that: 1_in gestational diabetes mellituspregnant-dams, impaired glucose tolerance was associated with incomplete fatty acid oxidation, enhanced gluconeogenesis, altered insulin signaling and oxidative stress; 2_improved glucose tolerance post-partum seemed to restore complete fatty acid oxidation along with elevation of nervonic acid-containing sphingomyelins, assumed to impart beta-cell protection; and 3_persistence of impaired glucose tolerance after delivery was associated with metabolites known to predict the early onset of insulin and leptin resistance, with maintained liver dysfunction. Our findings shed light on the impact of post-partum impaired glucose tolerance evolution on maternal metabolic outcome after an episode of gestational diabetes mellitus. They suggest innovative strategies, implemented shortly after delivery and targeted on these biomarkers, should be explored to curb or delay the transition from gestational diabetes mellitus to type 2 diabetes in these mothers.
DOI: 10.5061/dryad.26036h6
title: Data from: Conodont size, trophic level and the evolution of platform elements.

description: Conodonts are among the first vertebrates to have evolved mineralized
 tooth-like structures. Among these, the so-called P1 elements are known to
 have been used to break down food, and display a wide variety of
 morphologies. In particular, the repeated independent evolution of
 platform-like P1 elements have been suggested to correspond to similar
 functional constraints linked to diet. To test this hypothesis of
 convergence, we measured size (as element length) for various conodont
 taxa, and used it as a proxy for trophic level. We then tested the
 correlation between size and platform presence/absence, both on raw data
 and in a phylogenetic context. Retaining or excluding the platform traits
 from the character matrix has limited impact on the resulting phylogeny.
 Contrary to platform presence/absence, size shows no phylogenetic signal.
 Using the raw data, size and platform presence appear positively
 correlated. That correlation however is no longer significant if one
 corrects for the phylogeny. We conclude that platform presence cannot be
 explained by an enlargement of the conodont element, be it via a trophic
 level change or developmental constraints. This suggests that conodonts as
 a whole, and in particular platform-bearing conodonts, were an
 ecologically diverse group and that the various known platform types are
 likely to reflect different, rather than convergent, ecological niches.
description: Length measurements for
 P1 conodont elements and their space / time contextLength measurement for
 P1 elements were obtained from the bibliography (references in table),
 using measurement tool from the GIMP software. All studied material were
 complete enough that total length could be measured. data associated to
 each element include genera and species name, presence of a
 'platform' morphology, the reference, the stratigraphic context
 as defined in the reference and the geographic location of the specimen
 collection. NB: Coordinates are for the most part VERY approximate, and
 are not raw data from the reference, but our estimation based on what
 information the original authors gave.supp_table_1.xlsx
DOI: 10.5061/dryad.322gd5p
title: Data from: The genome of blue-capped cordon-bleu uncovers hidden diversity of LTR retrotransposons in zebra finch

description: Avian genomes have perplexed researchers by being conservative in both
 size and rearrangements, while simultaneously holding the blueprints for a
 massive species radiation during the last 65 My. Transposable elements
 (TEs) in bird genomes are relatively scarce but have been implicated as
 important hotspots for chromosomal inversions. In zebra finch (Taeniopygia
 guttata), long terminal repeat (LTR) retrotransposons have proliferated
 and are positively associated with chromosomal breakpoint regions. Here,
 we present the genome, karyotype and transposons of blue-capped
 cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged
 from zebra finch at the root of estrildid finches 10 Mya. This constitutes
 the third linked-read sequenced genome assembly and fourth in-depth
 curated TE library of any bird. Exploration of TE diversity on this brief
 evolutionary timescale constitutes a considerable increase in resolution
 for avian TE biology and allowed us to uncover 4.5 Mb more LTR
 retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we
 likewise observed a recent LTR accumulation indicating that this is a
 shared feature of Estrildidae. Curiously, we discovered 25 new endogenous
 retrovirus-like LTR retrotransposon families of which at least 21 are
 present in zebra finch but were previously undiscovered. This highlights
 the importance of studying close relatives of model organisms.
description: uraCya_heart_0.8Genome assembly of an adult male blue-capped cordon-bleu (Uraeginthus cyanocephalus). NCBI BioProject (PRJNA531762) and NCBI BioSample (SAMN11381998). Note that this a "pseudohaploid" assembly created with Supernova 2.0 assembly software.uraCya_heart_0.8.phasedGenome assembly of an adult male blue-capped cordon-bleu (Uraeginthus cyanocephalus). NCBI BioProject (PRJNA531762) and NCBI BioSample (SAMN11381998). Note that this a phased diploid assembly created with Supernova 2.0 assembly software.
DOI: 10.5061/dryad.52kd8tg
title: Data from: Lifetime fitness, sex-specific life history, and the maintenance of a polyphenism

description: Polyphenisms, alternative morphs produced through plasticity, can reveal
 the evolutionary and ecological processes that initiate and maintain
 diversity within populations. We examined lifetime fitness consequences of
 two morphs in a polyphenic population of Arizona Tiger Salamanders using a
 27-year data set with 1,317 adults and 6,862 captures across eight
 generations. Larval salamanders develop into either an aquatic paedomorph
 that retains larval traits and stays in its natal pond or a terrestrial
 metamorph that undergoes metamorphosis. To evaluate the adaptive
 significance of this polyphenism, we compared lifetime reproductive
 success of each morph and assessed how life history strategies and
 spatiotemporal variation explained fitness. We found sex-specific
 differences in lifetime fitness between morphs. For males, paedomorphs had
 more reproductive opportunities than metamorphs when we accounted for the
 potential mating advantage of larger males. For females, in contrast,
 metamorphs had higher estimated egg production than paedomorphs. Life
 history strategies differed between morphs largely because the morphs
 maximize different ends of the trade-off between age at first reproduction
 and longevity. Spatiotemporal variation affected larval more than adult
 life history traits with little to no effect on lifetime fitness. Thus,
 environmental variation likely explains differences in morph production
 across time and space but contributes little to lifetime fitness
 differences between morphs and sexes. Our long-term study and measures of
 lifetime fitness provide unique insight into the complex selective regimes
 potentially acting on each morph and sex. Our findings motivate future
 work to examine how sex-specific selection may contribute to the
 maintenance of polyphenism.
description: Lackey_LifetimeFitnessTigerSalamanders_LifeHistoryData_2019.04.11Life history data for 1,317 adult salamanders (description of column names is in separate file)Lackey_LifetimeFitnessTigerSalamanders_LifeHistoryData_2019.04.11_ColumnNamesColumn names for Lackey_LifetimeFitnessTigerSalamanders_LifeHistoryData_2019.04.11.csv
DOI: 10.5061/dryad.9kc572m
title: Data from: Phenotype-by-environment interactions influence dispersal

description: 1. Numerous studies have demonstrated that dispersal is dependent on both
 disperser phenotype and the local environment. However, there is
 substantial variability in the observed strength and direction of
 phenotype- and environment-dependent dispersal. This has been hypothesized
 to be the result of interactive effects among the multiple phenotypic and
 environmental factors that influence dispersal. 2. Here, our goal was to
 test the hypothesis that these interactions are responsible for generating
 variation in dispersal behaviour. 3. We achieved these goals by conducting
 a large, 2-year, mark-release-recapture study of the backswimmer
 (Notonecta undulata) in an array of 36 semi-natural ponds. We measured the
 effects of multiple phenotypic (sex, body size) and environmental
 (population density, sex ratio) factors, on both dispersal probability and
 dispersal distance. 4. We found support for the hypothesis that
 interactive effects influence dispersal and produce variability in
 phenotype- and environment-dependent dispersal: dispersal probability was
 dependent on the three-way interaction between sex, body mass, and
 population density. Small males displayed strong, positive density
 dependence in their dispersal behaviour, while large males and females
 overall did not respond strongly to density. Small notonectids, regardless
 of sex, were more likely to disperse, but this effect was strongest at
 high population densities. Finally, the distance dispersed by backswimmers
 was a negative function of population density, a pattern which we
 hypothesize could be related to i) individuals from high and low density
 patches having different dispersal strategies, or ii) the effect of
 density on dispersal capacity. 5. These results suggest that
 phenotype-by-environment interactions strongly influence dispersal. Since
 phenotype- and environment-dependent dispersal has different consequences
 for ecological and evolutionary dynamics (e.g. metapopulation persistence
 and local adaptation) than random dispersal, interactive effects may have
 wide-reaching impacts on populations and communities. We therefore argue
 that more investment should be made into estimating the effects of
 multiple, interacting factors on dispersal, and determining whether
 similar interactive effects are acting across systems.
description: Dispersal data for
 Baines, Ferzoco & McCauley. 2019. Phenotype-by-environment
 interactions influence dispersal.Data from the
 mark-release-recapture study conducted in 2016 and 2017. Data includes
 only individuals that were recaptured at least once in either
 year.Baines, Ferzoco & McCauley.
 2019. Dispersal dataset.xlsx
DOI: 10.5061/dryad.t35r32q
title: Data from: Genome analysis reveals genetic admixture and signature of selection for productivity and environmental traits in Iraqi cattle

description: The Near East cattle are adapted to different agro-ecological zones
 including desert areas, mountains habitats as well as humid regions along
 the Tigris and Euphrates rivers system. The region was one of the earliest
 and most significant areas of cattle husbandry. Currently four main breeds
 of Iraqi cattle are recognized. Among these, the Jenoubi is found in the
 southern more humid part of Iraq while the Rustaqi is found in the middle
 and drier region of the country. Despite their importance, Iraqi cattle
 have up to now been poorly characterized at genome level. Here, we report
 at genome-wide level the diversity and signature of positive selection in
 these two breeds. Thirty-five unrelated Jenoubi cattle, sampled in the
 Maysan and Basra regions, and 60 Rustaqi cattle, from around Baghdad and
 Babylon, were genotyped using the Illumina Bovine HD BeadChip (700K).
 Genetic population structure and diversity level were studied using
 principal component analysis (PCA), expected heterozygosity (He), observed
 heterozygosity (Ho) and admixture. Signatures of selection were studied
 using Extended Haplotype Homozygosity (EHH) (iHS and Rsb) and
 inter-population Wright’s Fst. The results of PCA and admixture analysis,
 including European taurine, Asian indicine, African indicine and taurine
 indicate that the two breeds are crossbreed zebu x taurine, with more zebu
 background in Jenoubi cattle compared to Rustaqi. The Rustaqi has the
 greatest mean heterozygosity (He = 0.37) among all breeds. iHS and Rsb
 signature of selection analyses identify 68 candidate genes under positive
 selection in the two Iraqi breeds, while Fst analysis identifies 220
 candidate genes including genes related to the innate and acquired
 immunity responses, different environmental selection pressures (e.g. tick
 resistance, heat stress) and genes of commercial interest (e.g. marbling
 score).
description: Iraqi_cattleIraqi_cattle