cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hdr7sqvdc
title: Data from: Broad-scale patterns of the Afro-Palearctic landbird migration

description: Aim: Animal migration strategies balance trade-offs between mortality and
 reproduction in seasonal environments. Knowledge of broad-scale
 biogeographical patterns of animal migration is important for
 understanding ecological drivers of migratory behaviours. Here we present
 a flyway-scale assessment of the spatial structure and seasonal dynamics
 of the Afro-Palearctic bird migration system and explore how phenology of
 the environment guides long-distance migration. Location: Europe and
 Africa. Time period: 2009–2017. Major taxa studied: Birds. Methods: We
 compiled an individual-based dataset comprising 23 passerine and
 near-passerine species of 55 European breeding populations where a total
 of 564 individuals were tracked migrating between Europe and sub-Saharan
 Africa. In addition, we used remote sensed observations on primary
 productivity (NDVI) to estimate the timing of vegetation green-up in
 spring and senescence in autumn across Europe. First, we described how
 individual breeding and non-breeding sites and the migratory flyways link
 geographically. Second, we examined how migration timing along the two
 major Afro-Palearctic flyways is tuned with vegetation phenology en route
 and at the breeding sites. Results: While we found the longitudes of
 individual breeding and non-breeding sites to be strongly positively
 related, the latitudes of breeding and non-breeding sites were negatively
 related. In autumn, timing of migration was similar along the Western and
 the Eastern flyways and happened ahead of the autumnal senescence of
 vegetation. In spring, migration timing was approximately two weeks later
 along the Eastern flyway than on the Western flyway which coincided with
 the later spring green-up in Eastern Europe. Main Conclusions: Migration
 of the Afro-Palearctic landbirds follows a longitudinally parallel
 leap-frog migration pattern where migrants track vegetation green-up in
 spring and depart before vegetation senescence in autumn. However, the
 ongoing global change have the potential to disrupt this spatiotemporal
 synchronization between migration timing and spring green-up with variable
 effects on different migrant populations.
DOI: 10.5061/dryad.sf7m0cg25
title: Tunicate bulb size variation in monocots explained by temperature and phenology

description: Plants bulbs are modified shoot systems comprised of short internodes with
 apical bud(s) surrounded by layers of leaf bases. Bulb diameters can vary
 greatly, with overall bulb size playing a role in flower formation as well
 as resource allocation. Despite the importance of bulb size to the overall
 fitness of an individual, evolutionary and ecological aspects of this
 trait have been almost completely neglected. Examining over 2500 herbarium
 vouchers for 115 selected species, we analyzed monocot tunicate bulb size
 within a phylogenetic context in order to investigate its evolutionary
 significance. We recorded two bulb diameter optima and observed that as
 bulb size increases taxa inhabit warmer areas with less temperature
 seasonality. Furthermore, we found that hysteranthous taxa, a habit where
 leaves emerge separately from flowers, exhibit overall larger bulbs
 potentially due to reliance upon belowground stored resources to flower
 rather than on current environmental inputs. This work highlights the
 importance of including the belowground portion of plants into ecological
 and evolutionary studies in order to gain a more complete understanding of
 the evolution of plant forms and functions.
description: Data collected from herbarium specimens and available climatic
 data
DOI: 10.5061/dryad.rv15dv44w
title: Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout (Salvelinus fontinalis) populations of Nova Scotia

description: Many populations of freshwater fishes are threatened with losses, and
 increasingly, the release of hatchery individuals is one strategy being
 implemented to support wild populations. However, stocking of hatchery
 individuals may pose long-term threats to wild populations, particularly
 if genetic interactions occur between wild and hatchery individuals. One
 highly prized sport fish that has been heavily stocked throughout its
 range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada,
 hatchery brook trout have been stocked since the early 1900s, and despite
 continued stocking efforts, populations have suffered declines in recent
 decades. Before this study, the genetic structure of brook trout
 populations in the province was unknown; however, given the potential
 negative consequences associated with hatchery stocking, it is possible
 that hatchery programs have adversely affected the genetic integrity of
 wild populations. To assess the influence of hatchery supplementation on
 wild populations, we genotyped wild brook trout from 12 river systems and
 hatchery brook trout from two major hatcheries using 100 microsatellite
 loci. Genetic analyses of wild trout revealed extensive population genetic
 structure among and within river systems and significant
 isolation-by-distance. Hatchery stocks were genetically distinct from wild
 populations, and most populations showed limited to no evidence of
 hatchery introgression (&lt;5% hatchery ancestry). Only a single
 location had a substantial number of hatchery-derived trout and was
 located in the only river where a local strain is used for
 supplementation. The amount of hatchery stocking within a watershed did
 not influence the level of hatchery introgression. Neutral genetic
 structure of wild populations was influenced by geography with some
 influence of climate and stocking indices. Overall, our study suggests
 that long-term stocking has not significantly affected the genetic
 integrity of wild trout populations, highlighting the variable outcomes of
 stocking and the need to evaluate the consequences on a case-by-case basis
description: Details on data processing are provided in the manuscript. 
description: Dataset of 100 microsatellite loci for wild and hatchery brook
 trout from Nova Scotia, Canada. Genetic data is provided as genepop format
 (Lehnert_Brooktrout_100Microsatellites.txt). Population code
 information are provided in a seperate csv file and in the manuscript
 (Pop_Names_Lehnert_Brooktrout_100micros.csv). Environmental and
 anthropogenic data are also included in csv format
 (Introgression_AnthroEnviro_data.csv) with a seperate csv describing
 variables (Introgression_AnthroEnviro_Description.csv). Proportion of
 hatchery introgression is provided with environemental and anthropogenic
 data. Least cost distance between sites is also provided in a csv file
 (LCDist_measured.csv).
DOI: 10.5061/dryad.kprr4xh19
title: Emulating a target trial of statin use and risk of dementia using cohort data

description: Objective: Observational data can be used to attempt to emulate a target
 trial of statin use and estimate analogues of intention-to-treat and
 per-protocol effects on dementia risk. Methods: Using data from a
 prospective cohort study in the Netherlands, we conceptualized a sequence
 of “trials” in which eligible individuals ages 55-80 years were classified
 as statin initiators or non-initiators for every consecutive month between
 1993 and 2007 and were followed until diagnosis of dementia, death, loss
 to follow-up, or the end of follow-up. We estimated two types of effects
 of statin use on dementia and a combined endpoint of dementia or death:
 the effect of initiation versus no initiation and the effect of sustained
 use versus no use. We estimated risk by statin treatment strategy over
 time via pooled logistic regression. We used inverse-probability weighting
 to account for treatment-confounder feedback in estimation of per-protocol
 effects. Results: Of 233,526 eligible person-trials (6,373 individuals),
 there were 622 initiators and 232,904 non-initiators. Comparing statin
 initiation with no initiation, the 10-year risk differences (95% CI) were
 -0.1% (-2.3%, 1.8%) for dementia and 0.3% (-2.7%, 3.3%) for dementia or
 death. Comparing sustained statin use versus no use, the 10-year risk
 differences were -2.2% (-5.2%, 1.6%) for dementia and -5.1% (-10.5%,
 -1.1%) for dementia or death. Conclusions: Individuals with sustained
 statin use, but not statin initiation alone, had reduced 10-year risks of
 dementia and dementia or death. Our results should be interpreted with
 caution due to the small number of initiators and events, and potential
 for residual confounding.
DOI: 10.5061/dryad.8gtht76k3
title: Re-imagining fMRI for awake behaving infants

description: Thousands of functional magnetic resonance imaging (fMRI) studies have
 provided important insight into the human brain. However, only a handful
 of these studies tested infants while they were awake, because of the
 significant and unique methodological challenges involved. We report our
 efforts to address these challenges, with the goal of creating methods for
 awake infant fMRI that can reveal the inner workings of the developing,
 preverbal mind. We use these methods to collect and analyze two fMRI
 datasets obtained from infants during cognitive tasks, released publicly
 with this paper. In these datasets, we explore and evaluate data quantity
 and quality, task-evoked activity, and preprocessing decisions. We
 disseminate these methods by sharing two software packages that integrate
 infant-friendly cognitive tasks and eye-gaze monitoring with fMRI
 acquisition and analysis. These resources make fMRI a feasible and
 accessible technique for cognitive neuroscience in awake and behaving
 human infants.
description: Extensive details are provided in the manuscript: Ellis,
 Skalaban, Yates, Bejjanki, Cordova, & Turk-Browne.
 "Re-imagining fMRI for awake behaving infants".
description: Refer to the README.md file included with the data.
 Note from Aug 19th, 2021: Note that the burn-in information for
 each of the raw runs was not previously provided. This has now also been
 uploaded. The README was edited to include this information but otherwise,
 nothing else was changed.
DOI: 10.5061/dryad.9zw3r229n
title: Development and testing of a novel Killer-Rescue self-limiting gene drive system in Drosophila melanogaster

description: Here we report the development and testing of a novel self-limiting gene
 drive system, Killer-Rescue, in Drosophila melanogaster. This system is
 composed of an auto-regulated Gal4 Killer (K) and a Gal4-activated Gal80
 Rescue (R). Overexpression of Gal4 is lethal, but in the presence of R
 activation of Gal80 leads to much lower levels of Gal4 and rescue of
 lethality. We demonstrate that with a single 2:1 engineered to wildtype
 release, K drives R through the population and after nine generations more
 than 98% of the population carry R and less than 2% of the population are
 wildtype flies. We discuss how this simple Killer-Rescue gene drive system
 may be readily adapted for population replacement in a human health pest,
 Aedes aegypti, or for population suppression in an agricultural pest,
 Drosophila suzukii
description: Methods as described in the paper
DOI: 10.5061/dryad.m905qftxb
title: Asymmetric acoustic signal recognition led to asymmetric genetic introgression between two parapatric rhacophorid treefrogs

description: Correct discrimination between courtship signals could help maintain
 genetic integrity between closely related species. However, asymmetric
 usage of signals might cause asymmetric magnitude of gene flow across the
 contact zone. Buergeria japonica and B. otai are sibling species with
 parapatric distribution pattern in Taiwan, forming two narrow contact
 zones in eastern and western sides of the island. Both species use a
 shared acoustic signal of calls (Type 1a/1b), whereas B. otai presents
 another unique call type (Type 2) which never appears in B. japonica.
 Combining behavioral experiments with genome-wide RAD-seq analyses, we aim
 to test whether the ability of signal recognition influences genetic
 introgression across their species boundary. The playback experiments
 showed that the western population of B. otai has evolved a stronger level
 of reproductive character displacement by showing the inclusive usage of
 their unique Type 2 signal. In contrast, the eastern population used both
 unique and shared signals and has a stronger preference for the latter.
 Consistent with behavioral difference, genetic introgression across the
 contact zone was detected only in the eastern boundary but not in the
 western one. Furthermore, the gene flow in this contact zone tends to be
 unidirectional from B. japonica toward B. otai. Our results support the
 prediction that a more specialized signal user might have a higher
 probability to maintain their genetic integrity compared to a generalized
 signal user.
DOI: 10.5061/dryad.t4b8gthxx
title: Environmental and ecological correlates of avian field metabolic rate and water flux

description: 1. The field metabolic rate (FMR) of an endothermic animal represents its
 energy expenditure in a natural environment, or its energy budget, and its
 field water flux (FWF) reflects the animal’s water requirements. 2. We
 examined FMR of 103 species and FWF of 75 species of adult birds from
 direct field measurements by the doubly-labelled water method, and used
 the phylogenetic generalised least squares method to conduct a
 phylogenetically-informed, comprehensive analysis of the relationship
 between FMR, FWF, and multiple environmental and biological variables. 3.
 FMR was strongly positively associated with body mass with an allometric
 exponent of 0.66, and seabirds had lower FMR than terrestrial species.
 Birds consuming plant matter had lower FMR compared to omnivores,
 carnivores or nectarivores, and low ambient temperature was associated
 with higher FMR. There was little evidence for phylogenetic covariance in
 FMR, even though previous studies identified a phylogenetic signal for
 BMR. Life history traits, such as fecundity and migration, were also not
 strongly associated with FMR. 4. FWF was strongly positively associated
 with body mass with an allometric exponent of 0.61, and was strongly
 related to precipitation but not to temperature. Diet and habitat use had
 significant effects on FWF, with nectarivores and marine species
 exhibiting higher values than granivores and forest birds. 5. Thus, FMR
 and FWF are affected similarly by body size and differently by
 environmental temperature and precipitation, while the roles of diet, life
 history traits and habitat are more nuanced and generalities remain
 elusive.
DOI: 10.5061/dryad.b2rbnzs9m
title: The effect of proprioception training on knee kinematics after anterior cruciate ligament reconstruction

description: Background Proprioception is essential for the normal movement of joint
 knees. The degree of functional recovery after ACL reconstruction is
 related with the degree of postoperative recovery of proprioception. The
 current study aimed to investigate the effect of proprioception training
 on functional level of activity and knee kinematics after anterior
 cruciate ligament reconstruction. Methods Forty patients who underwent ACL
 reconstruction between January 2017 and June 2019 were included. The
 patients were divided into proprioception group (n=20) and control group
 (n=20). All the patients followed common postoperative rehabilitation
 program. The proprioception group were given proprioception enhancement
 program besides common postoperative rehabilitation program. All the
 patients were assessed preoperatively, 6 months and 1 year after
 operation. The lymsolm scores, hop distances, and knee kinematics during
 unanticipated jump–cut maneuver were compared at different follow-up time
 points. Results There were no significant differences preoperative and
 postoperative Lysholm scores between two groups.  After surgery,
 the proprioception group showed significantly higher hop distance (133.9 ±
 26.2 cm) when compared with the control group (81.2 ± 17.2 cm, P=0.026) in
 6-months and one-year follow-up (153.1 ± 19.3 vs 105.8 ± 20.7cm, P=0.034).
 For knee joint kinematics, the proprioception training group showed
 reduced knee abduction (valgus) angles and external rotations, and
 increased knee flexion when compared with the common training group.
 Conclusions We conclude that proprioceptive rehabilitation training
 enhance the kinematic performance and single leg hop distance in
 ACL-reconstructed populations during jump-stop, unanticipated cut
 maneuver. The findings will be scientific evidences to help clinicians and
 physiotherapists to evaluate the patients’ readiness for exercises and
 sports, especially in the cases of loading and extreme rotation
 conditions.
description: <b>Trial registration </b>This study was
 retrospectively registered on<b> Clnicaltrails.gov</b> on 24
 December.
DOI: 10.5061/dryad.s1rn8pk43
title: The longer the better: evidence that narwhal tusks are sexually selected

description: Once thought to be the magical horn of a unicorn, narwhal tusks are one of
 the most charismatic structures in biology. However, narwhals spend most
 of their lives hidden underneath the Arctic ice, which makes testing the
 function of the tusks nearly impossible. Over the course of 35 years, we
 collected morphology data on 245 adult male narwhals to shed light on the
 function and selection pressures that have acted on this exaggerated
 trait. Based on the disproportional growth and immense variation in tusk
 length that we found, we demonstrate that narwhal tusks are indeed
 sexually selected, and believe that they likely function as signals during
 male-male aggression or mate choice.
DOI: 10.5061/dryad.7wm37pvpb
title: Data from: Big fishery, big data, and little crabs: using genomic methods to examine the seasonal recruitment patterns of early life stage Dungeness crab (Cancer magister) in the California current ecosystem

description: The California Current Ecosystem (CCE) is a dynamic marine ecosystem from
 which many socioeconomically important fisheries species are harvested.
 Here, a genotypingby-sequencing (GBS) approach was used to examine genomic
 variation in an early life stage (megalopae) of the Dungeness crab (Cancer
 magister), which constitutes the most valuable single-species commercial
 fishery in the CCE. Variation in abundance and timing of megalopae
 recruitment has been extensively studied for over two decades in Coos Bay,
 Oregon, United States. Within the CCE, documented timing of Dungeness crab
 life history events indicates that coastal megalopae recruitment is
 expected to occur April through July; however, long-term studies in Coos
 Bay have observed late-season recruitment from August to October. Based on
 variation at 1,913 presumably neutral loci, evidence was found for weak,
 yet significant differentiation (FST estimate = 0.0011) between the 2014
 expected-season recruits (n = 47) and lateseason recruits (n = 47)
 collected in Coos Bay. However, two putatively adaptive loci with a high
 FST estimate (0.2036) between expected-season and late-season recruits
 were identified. These findings support the hypothesis that
 expected-season and lateseason megalopae recruiting to Coos Bay within the
 same year may have originated from different locations or from different
 breeding groups. Understanding marine species connectivity between
 ecosystems is important when considering how future changes in ocean
 conditions may impact fishery harvests.
DOI: 10.5061/dryad.r4xgxd288
title: The origins of acoustic communication in vertebrates

description: Acoustic communication is crucial to humans and many other tetrapods,
 including birds, frogs, crocodilians, and mammals. However, large-scale
 patterns in its evolution are largely unstudied. Here, we address several
 fundamental questions about the origins of acoustic communication in
 terrestrial vertebrates (tetrapods), using phylogenetic methods. We show
 that origins of acoustic communication are significantly associated with
 nocturnal activity. We find that acoustic communication does not increase
 diversification rates, a surprising result given the many
 speciation-focused studies of frog calls and bird songs. We also
 demonstrate that the presence of acoustic communication is strongly
 conserved over time. Finally, we find that acoustic communication evolved
 independently in most major tetrapod groups, often with remarkably ancient
 origins (~100–200 million years ago). Overall, we show that the role of
 ecology in shaping signal evolution applies to surprisingly deep
 timescales, whereas the role of signal evolution in diversification may
 not.
DOI: 10.5061/dryad.t1g1jwsz7
title: Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics

description: Amplicon metabarcoding is an established technique to analyse the
 taxonomic composition of communities of organisms using high-throughput
 DNA sequencing, but there are doubts about its ability to quantify the
 relative proportions of the species, as opposed to the species list. Here,
 we bypass the enrichment step and avoid the PCR-bias, by directly
 sequencing the extracted DNA using shotgun metagenomics. This approach is
 common practice in prokaryotes, but not in eukaryotes, because of the low
 number of sequenced genomes of eukaryotic species. We tested the
 metagenomics approach using insect species whose genome is already
 sequenced and assembled to an advanced degree. We shotgun-sequenced, at
 low-coverage DNA, 18 species of insects in 22 single-species and 6
 mixed-species libraries and mapped the reads against 110 reference genomes
 of insects. We used the single-species libraries to calibrate the process
 of assignation of reads to species and the libraries created from species
 mixtures to evaluate the ability of the method to quantify the relative
 species abundance. Our results showed that the shotgun metagenomic method
 is easily able to set apart closely-related insect species, like four
 species of Drosophila included in the artificial libraries. However, to
 avoid the counting of rare misclassified reads in samples, it was
 necessary to use a rather stringent detection limit of 0.001, so species
 with a lower relative abundance are ignored. We also identified that
 approximately half the raw reads were informative for taxonomic purposes.
 Finally, using the mixed-species libraries, we showed that it was feasible
 to quantify with confidence the relative abundance of individual species
 in the mixtures.
description: Speciments of 18 different species were captured and stored in 70 % ethanol at 4ºC. We used the DNeasy Blood & Tissue Kit (Qiagen) to extract the DNA from ca. 20 mg of fresh material of each species. We prepared two kinds of libraries: 22 libraries with DNA of a single-species and 6 libraries with a mixture of DNA of several species at known relative concentrations. All libraries were prepared using the TruSeq DNA PCR-Free LT Kit of Illumina following the manufacturer’s instructions (Ref. 15037063) and sequenced using an Illumina MiSeq with the 2x150 chemistry in three different runs.