cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vp4q518
title: Data from: Time for a rethink: time sub-sampling methods in disparity-through-time analyses

description: Disparity-through-time analyses can be used to determine how morphological
 diversity changes in response to mass extinctions, and to investigate the
 drivers of morphological change. These analyses are routinely applied to
 palaeobiological datasets, yet although there is much discussion about how
 to best calculate disparity, there has been little consideration of how
 taxa should be sub-sampled through time. Standard practice is to group
 taxa into discrete time bins, often based on stratigraphic periods.
 However, this can introduce biases when bins are of unequal size, and
 implicitly assumes a punctuated model of evolution. In addition, many time
 bins may have few or no taxa, meaning that disparity cannot be calculated
 for the bin and making it harder to complete downstream analyses. Here we
 describe a different method to complement the disparity-through-time
 tool-kit: time-slicing. This method uses a time-calibrated phylogenetic
 tree to sample disparity-through-time at any fixed point in time rather
 than binning taxa. It uses all available data (tips, nodes and branches)
 to increase the power of the analyses, specifies the implied model of
 evolution (punctuated or gradual), and is implemented in R. We test the
 time-slicing method on four example datasets and compare its performance
 in common disparity-through-time analyses. We find that the way you time
 sub-sample your taxa can change your interpretations of the results of
 disparity-through-time analyses. We advise using multiple methods for time
 sub-sampling taxa, rather than just time binning, to gain a better
 understanding disparity-through-time.
description: Appendix S3: Additional
 TablesAdditional Table S1 to
 support the paper.S3-time-slice-additional-tables.docxAppendix S1: Additional details of datasetsAdditional details of the datasets, and how these were processed prior to analysis. Also contains images of the phylogenies used for interest.S1-time-slice-appendices.pdfAppendix S2: Additional figuresAdditional figures to support the paperS2-time-slice-additional-figures.pdf
DOI: 10.5061/dryad.g85fb
title: Data from: Understanding the formation of ancient intertropical disjunct distributions using Asian and Neotropical hinged-teeth snakes (Sibynophis and Scaphiodontophis: Serpentes: Colubridae)

description: Numerous taxa show ancient intertropical disjunct distributions. Many can
 be explained by well-known processes of historical vicariance, such as the
 breakup of Gondwanaland. Others, such as Asian–Neotropical divergences are
 not as well understood. To clarify the phylogenetic position and
 understand biogeographic and temporal origins the geographically disjunct
 and morphologically unique genera of hinged-teeth snakes, Scaphiodontophis
 (n = 1) and Sibynophis (n = 9; Colubridae), we inferred a time-calibrated
 phylogeny with additional 107 taxa representing the superfamily
 Colubroidea using four genes (c-mos, cyt-b, ND2, RAG-1; 3085 bp). We used
 this tree to estimate ancestral areas for the group. The results show that
 Scaphiodontophis is sister to Sibynophis, which both originated in the
 late Eocene/Oligocene in Asia and likely dispersed through Beringia to the
 New World, but unlike other snake groups left no extant species in
 temperate North America. Current recognition of Scaphiodontophiinae
 renders Colubrinae paraphyletic, and we resurrect the previously named
 subfamily Sibynophiinae to encompass both genera and use the tribes
 Sibynophiini (Sibynophis) and Scaphiodontophiini (Scaphiodontophis) to
 highlight the geographically distinct areas occupied by these taxa. These
 results suggest that intercontinental dispersal with extinction in
 intermediate areas can explain puzzling patterns of ancient intertropical
 disjunct distributions.
description: XMLcodexml code for running BSSVS in program BEASTsibyreview16.xml
DOI: 10.5061/dryad.b4t60
title: Data from: NREM2 and sleep spindles are instrumental to the consolidation of motor sequence memories

description: Although numerous studies have convincingly demonstrated that sleep plays
 a critical role in motor sequence learning (MSL) consolidation, the
 specific contribution of the different sleep stages in this type of memory
 consolidation is still contentious. To probe the role of stage 2 non-REM
 sleep (NREM2) in this process, we used a conditioning protocol in three
 different groups of participants who either received an odor during
 initial training on a motor sequence learning task and were re-exposed to
 this odor during different sleep stages of the post-training night (i.e.,
 NREM2 sleep [Cond-NREM2], REM sleep [Cond-REM], or were not conditioned
 during learning but exposed to the odor during NREM2 [NoCond]). Results
 show that the Cond-NREM2 group had significantly higher gains in
 performance at retest than both the Cond-REM and NoCond groups. Also, only
 the Cond-NREM2 group yielded significant changes in sleep spindle
 characteristics during cueing. Finally, we found that a change in
 frequency of sleep spindles during cued-memory reactivation mediated the
 relationship between the experimental groups and gains in performance the
 next day. These findings strongly suggest that cued-memory reactivation
 during NREM2 sleep triggers an increase in sleep spindle activity that is
 then related to the consolidation of motor sequence memories.
description: Behavioral and Sleep
 DataData are related to
 associated tab names in the manuscript and supplemental information.
 Groups are numbered as follow (1: Cond-NREM2; 2: Cond-REM; 3:
 NoCond).Data
 S1.xlsx
DOI: 10.5061/dryad.f5n5c
title: Data from: Differential introgression and reorganization of retrotransposons in hybrid zones between wild wheats

description: The maintenance of species integrity despite pervasive hybridization is
 ruled by the interplay between reproductive barriers. Endogenous
 postzygotic isolation will shape the patterns of introgression in hybrid
 zones, leading to variable outcomes depending on the genetic mechanism
 involved. Here, we analysed experimental and natural hybrid populations of
 Aegilops geniculata and Aegilops triuncialis to examine the genetics of
 species boundaries in the face of gene flow. Because long-terminal repeat
 retrotransposons (LTR-RTs) showing differential evolutionary trajectories
 are probably to affect hybrid dysgenesis and reproductive isolation
 between these wild wheat species, we addressed the impact of LTR-RTs in
 shaping introgression between them. Experimental settings involving
 artificial sympatry and enforced crossings quantified strong, but
 incomplete reproductive isolation, and highlighted asymmetrical endogenous
 postzygotic isolation between the two species. Natural hybrid zones
 located in the northern Golan Heights were analysed using plastid DNA,
 amplified fragment length polymorphisms (AFLP) marking random sequences,
 and sequence-specific amplified polymorphisms (SSAP) tracking insertions
 from six LTR-RT families. This analysis demonstrated asymmetrical
 introgression and genome reorganization. In comparison with random
 sequences and quiescent LTR-RTs, those LTR-RTs predicted to be activated
 following conflicting interactions in hybrids revealed differential
 introgression across the hybrid zones. As also reported for synthetic F1
 hybrids, such LTR-RTs were specifically reorganized in the genomes of
 viable hybrids, confirming that conflicts between selfish LTR-RTs may
 represent key incompatibilities shaping species boundaries and fostering
 long-term species integrity in the face of gene flow.
description: AFLP and SSAP
 DatasetsContains binary scores
 for 3 AFLP combinations as well as 2 SSAP combinations for each family of
 retrotransposon (BARE1, Claudia, Egug, Fatima, Romani, Sabine). Details
 are provided on the first sheet of the Excell file.Senerchia_Datasets.xlsxAlignment of plastid sequencescpDNA_Alignment.fastaHybrdization_datasetRaw data used to estimate spontaneous and artificial rates of hybridizationSampleCodeCode used to describe sampled individuals according to their population of origin
DOI: 10.5061/dryad.j18g0
title: Data from: XY females do better than the XX in the African pygmy mouse, Mus minutoides

description: All therian mammals have a similar XY/XX sex determination system except
 for a dozen species. The African pygmy mouse, Mus minutoides, harbors an
 unconventional system in which all males are XY, and there are three types
 of females: the usual XX but also XX* and X*Y ones (the asterisk
 designates a sex reversal mutation on the X chromosome). The long-term
 evolution of such a system is a paradox, since X*Y females are expected to
 face high reproductive costs (e.g. meiotic disruption and loss of unviable
 YY embryos), which should prevent invasion and maintenance of a
 sex-reversal mutation. Hence, mechanisms for compensating for the costs
 could have evolved in M. minutoides. Data gathered from our laboratory
 colony revealed that X*Y females do compensate and even show enhanced
 reproductive performance in comparison to the XX and XX*; they produce
 significantly more offspring due to (i) a higher probability of breeding,
 (ii) an earlier first litter, and (iii) a larger litter size, linked to
 (iv) a greater ovulation rate. These findings confirm that rare conditions
 are needed for an atypical sex determination mechanism to evolve in
 mammals, and provide valuable insight into understanding modifications of
 systems with highly heteromorphic sex chromosomes.
description: Kinship
 matrixKinship matrix used as a
 correlation structure to describe relatedness between females in the
 statistical models.kinship_matrix.csvfemale_dataData about all females that were raised in the lab colony: genotype, date of birth, age at contact, overall progeny number, first litter age, mean litter size, mean interbirth interval...corpora_lutea_count_dataCorpora lutea count for all females dissected to estimate the ovulation rate.Contains information on female identity, genotype, corpora lutea count and age of female at the time of the dissection.Full_pedigreeThe full pedigree of all individuals (females and males) considered in the study, along with their genotype and the identity of both maternal and paternal chromosomes.pedigree_full.csv
DOI: 10.5061/dryad.040h9t7
title: Data from: A neural mechanism underlying failure of optimal choice with multiple alternatives

description: Despite widespread interest in neural mechanisms of decision-making, most
 investigations focus on decisions between just two options. Here we adapt
 a biophysically plausible model of decision-making to predict how a key
 decision variable, the value difference signal—encoding how much better
 one choice is than another—changes with the value of a third, but
 unavailable, alternative. The model predicts a surprising failure of
 optimal decision-making: greater difficulty choosing between two options
 in the presence of a third very poor, as opposed to very good,
 alternative. Both investigation of human decision-making and functional
 magnetic resonance imaging–based measurements of value difference signals
 in ventromedial prefrontal cortex (vmPFC) bore out this prediction. The
 vmPFC signal decreased in the presence of low-value third alternatives,
 and vmPFC effect sizes predicted individual variation in suboptimal
 decision-making in the presence of multiple alternatives. The effect
 contrasts with that of divisive normalization in parietal cortex.
description: behav_fmri
 Behavioral data
 of the main experiment (matlab data)     
 behav_pilot1
 Behavioral data
 of Pilot Study 1 reported in SI.6 (matlab data)     
 behav_pilot2
 Behavioral data
 of Pilot Study 2 reported in SI.6 (matlab data)     
 behav_pilot3
 Behavioral data
 of Pilot Study 3 reported in SI.6 (matlab data)     
 behav_3options Behavioral data of the three-option experiment reported in SI.7 and 8 (matlab data)     behav_hk Unpublished data of a new experiment. The experiment involved the identical task paradigm that is published in Chau et al., Nature Neursocience, 2014, except: 1. It contained only distractor trials. 2. It contained new trials where all options were associated with negative reward magnitudes (i.e. losses). behav_hk.mat (Updated in Feb 2020)
DOI: 10.5061/dryad.dk4t694
title: Data from: Multiple stages of tree seedling recruitment are altered in tropical forests degraded by selective logging

description: Tropical forest degradation is a global environmental issue. In degraded
 forests, seedling recruitment of canopy trees is vital for forest
 regeneration and recovery. We investigated how selective logging, a
 pervasive driver of tropical forest degradation, impacts canopy tree
 seedling recruitment, focusing on an endemic dipterocarp Dryobalanops
 lanceolata in Sabah, Borneo. During a mast-fruiting event in intensively
 logged and nearby unlogged forest, we examined four stages of the seedling
 recruitment process: seed production, seed predation, and negative
 density-dependent germination and seedling survival. Our results suggest
 that each stage of the seedling recruitment process is altered in logged
 forest. The seed crop of D. lanceolata trees in logged forest was
 one-third smaller than that produced by trees in unlogged forest. The
 functional role of vertebrates in seed predation increased in logged
 forest while that of non-vertebrates declined. Seeds in logged forest were
 less likely to germinate than those in unlogged forest. Germination
 increased with local-scale conspecific seed density in unlogged forest,
 but seedling survival tended to decline. However, both germination and
 seedling survival increased with local-scale conspecific seed density in
 logged forest. Notably, seed crop size, germination and seedling survival
 tended to increase for larger trees in both unlogged and logged forests,
 suggesting that sustainable timber extraction and silvicultural practices
 designed to minimize damage to the residual stand are important to prevent
 seedling recruitment failure. Overall, these impacts sustained by several
 aspects of seedling recruitment in a mast-fruiting year suggest that
 intensive selective logging may affect long-term population dynamics of D.
 lanceolata. It is necessary to establish if other dipterocarp species,
 many of which are threatened by the timber trade, are similarly affected
 in tropical forests degraded by intensive selective logging.
description: Tree size, seed trap,
 natural plot and experimental plot data for Dryobalanops lanceolata in
 BorneoThis xlsx workbook
 contains four worksheets that encompass the complete dataset for all
 analyses described in the paper. These include tree size measurements,
 seed trap data, and seed germination and seedling survival data from
 natural and experimental plots.Dryobalanops_lanceolata_AllData.xlsx
DOI: 10.5061/dryad.s0948
title: Data from: Evidence for adaptive divergence of thermal responses among Bemisia tabaci populations from tropical Colombia following a recent invasion

description: There is an increasing evidence that populations of ectotherms can diverge
 genetically in response to different climatic conditions, both within
 their native range and (in the case of invasive species) in their new
 range. Here, we test for such divergence in invasive whitefly Bemisia
 tabaci populations in tropical Colombia, by considering heritable
 variation within and between populations in survival and fecundity under
 temperature stress, and by comparing population differences with patterns
 established from putatively neutral microsatellite markers. We detected
 significant differences among populations linked to mean temperature (for
 survival) and temperature variation (for fecundity) in local environments.
 A QST − FST analysis indicated that phenotypic divergence was often larger
 than neutral expectations (QST &gt; FST). Particularly, for survival
 after a sublethal heat shock, this divergence remained linked to the local
 mean temperature after controlling for neutral divergence. These findings
 point to rapid adaptation in invasive whitefly likely to contribute to its
 success as a pest species. Ongoing evolutionary divergence also provides
 challenges in predicting the likely impact of Bemisia in invaded regions.
description: Survival data in
 response to heat shocks in populations of B. tabaci from Colombian
 Southwest and CaribbeanHere are the data for
 survival of B. tabaci after heat shocks performed at two treatments: Basal
 tolerance (45°C: 45°C/1h and then a recovery at 25°C/1h) and induced
 treatment (40-45°C: 40-45°C/1h, then 40°C/1h and then a recovery time at
 25°C/1h). Survival was measured from groups of 10 adults (males and
 females). These data were assessed from isofemales of B. tabaci belonging
 to nine populations: six from the Southwest and three in the Caribbean
 region in Colombia.Survival after heat shocks in
 B. tabaci.xlsFecundity data in
 response to heat shocks in populations of B. tabaci from Colombian
 Southwest and CaribbeanHere are the data for
 fecundity of B. tabaci after heat shocks performed at two treatments:
 Basal tolerance (45°C: 45°C/1h and then a recovery at 25°C/1h) and induced
 treatment (40-45°C: 40-45°C/1h, then 40°C/1h and then a recovery time at
 25°C/1h). Couples (males and females) were lead to mate for seven days and
 then the number of eggs was count. These data were assessed from
 isofemales of B. tabaci belonging to nine populations: six from the
 Southwest and three in the Caribbean region in
 Colombia.Fecundity after heat shocks in
 B. tabaci.xlsMicrosatellites data in
 B. tabaciHere are the data for
 the molecular weigth of ten microsatellites from B. tabaci. These data
 were assessed from eight populations: five from the Southwest and three in
 the Caribbean region in Colombia.
DOI: 10.5061/dryad.rr85h
title: Data from: Resurrection and new species of the Neotropical genus Adelonema (Araceae: Philodendron clade)

description: Previous studies have shown Homalomena as traditionally defined to be
 polyphyletic, with Neotropical species phylogenetically distinct from
 Asian species. This study of 29 accessions of 10 Neotropical taxa, and a
 total of 135 accessions representing 92 taxa of Homalomena, Furtadoa, and
 Philodendron for nuclear ITS and plastid matK regions, supports
 resurrection of the genus Adelonema for Neotropical species currently
 assigned to Homalomena. Adelonema is here delimited as a Neotropical genus
 of 16 species divided into two new sections: sect. Adelonema and sect.
 Curmeria, based on morphologically supported molecular results. The genus
 Adelonema is distinguished by a hypogeal rhizome, crushed vegetative
 tissues smelling of anise, an extensively sheathing, sometimes prickly
 petiole, chartaceous often variegated leaf blades, a spadix either
 obliquely inserted on the spathe/peduncle (sect. Adelonema), or stipitate
 (sect. Curmeria), ovaries with 2–4-pluriovulate locules, and anatropous
 ovules on an axile placenta. Four new species are described: Adelonema
 orientalis, A. palidinervia, A. panamensis, and A. yanamonoensis. Eleven
 new combinations are made: Adelonema allenii, A. crinipes, A. hammelii, A.
 kvistii, A. moffleriana, A. peltata, A. picturata, A. roezlii, A.
 speariae, A. wallisii, and A. wendlandii.
description: Supp Fig. 1 Adelonema
 ITS MLThe maximum likelihood
 tree of 116 taxa based on the ITS1, ITS2, and the 5.8S regions of the
 nuclear rRNA gene. Bootstrap (BS) values are shown above/below next to
 each internal branch.Supp Fig. 2 Adelonema
 matK MLThe maximum likelihood
 tree of 55 taxa (Adelonema, Homalomena, Philodendron and outgroup) based
 on matK and partial trnK (matK) plastid region. Bootstrap (BS) values are
 shown above/below/next to the branch.Supp Fig. 3 Adelonema
 combined MLThe maximum likelihood
 tree of 38 taxa (Adelonema, Homalomena, Philodendron and outgroup) based
 on combined ITS and matK regions. Bootstrap (BS) values are shown
 above/below/next to the branch.
DOI: 10.5061/dryad.7b87b
title: Data from: The extreme disjunction between Beringia and Europe in Ranunculus glacialis s. l. (Ranunculaceae) does not coincide with the deepest genetic split – a story of the importance of temperate mountain ranges in arctic-alpine phylogeography

description: The arctic–alpine Ranunculus glacialis s. l. is distributed in
 high-mountain ranges of temperate Europe and in the North, where it
 displays an extreme disjunction between the North Atlantic Arctic and
 Beringia. Based on comprehensive sampling and employing plastid and
 nuclear marker systems, we (i) test whether the European/Beringian
 disjunction correlates with the main evolutionary diversification, (ii)
 reconstruct the phylogeographic history in the Arctic and in temperate
 mountains and (iii) assess the susceptibility of arctic and mountain
 populations to climate change. Both data sets revealed several
 well-defined lineages, mostly with a coherent geographic distribution. The
 deepest evolutionary split did not coincide with the European/Beringian
 disjunction but occurred within the Alps. The Beringian lineage and North
 Atlantic Arctic populations, which reached their current distribution via
 rapid postglacial colonization, show connections to two divergent pools of
 Central European populations. Thus, immigration into the Arctic probably
 occurred at least twice. The presence of a rare cpDNA lineage related to
 Beringia in the Carpathians supports the role of these mountains as a
 stepping stone between temperate Europe and the non-European Arctic, and
 as an important area of high-mountain biodiversity. The temperate and
 arctic ranges presented contrasting phylogeographic histories: a largely
 static distribution in the former and rapid latitudinal spread in the
 latter. The persistence of ancient lineages with a strictly regional
 distribution suggests that the ability of R. glacialis to survive repeated
 climatic changes within southern mountain ranges is greater than what
 recently was predicted for alpine plants from climatic envelope modelling.
description: Plastid DNA sequence
 alignment (non-coding regions rpl32-trnL and rps12-rpl20) of Ranunculus
 glacialis s.l.The file contains the
 alignment of sequences used for the BEAST analysis of plastid DNA
 variation (concatenated sequences of non-coding regions rpl32-trnL and
 rps12-rpl20)in Ranunculus glacialis s.l.Rglacialis_plastid_BEAST_alignment.fasNuclear ribosomal ITS DNA sequence alignment of Ranunculus glacialis s.l.The file contains the alignment of sequences used for the BEAST analysis of nuclear ribosomal ITS (Internal transcribed Spacer region containing ITS1, 5.8S gene and ITS 2) DNA variation in Ranunculus glacialis s.l.Rglacialis_its_BEAST_alignment.fas