cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.xpnvx0kg5
title: Mimulus cardinalis plasticity analyses and R scripts for: Spatial variation in high temperature-regulated gene expression predicts evolution of plasticity with climate change in the scarlet monkeyflower

description: A major way that organisms can adapt to changing environmental conditions
 is by evolving increased or decreased phenotypic plasticity. In the face
 of current global warming, more attention is being paid to the role of
 plasticity in maintaining fitness as abiotic conditions change over time.
 However, given that temporal data can be challenging to acquire, a major
 question is whether evolution in plasticity across space can predict
 adaptive plasticity across time. In growth chambers simulating two thermal
 regimes, we generated transcriptome data for western North American
 scarlet monkeyflowers (Mimulus cardinalis) collected from different
 latitudes and years (2010 and 2017) to test hypotheses about how
 plasticity in gene expression is responding to increases in temperature,
 and if this pattern is consistent across time and space. Supporting the
 genetic compensation hypothesis, individuals whose progenitors were
 collected from the warmer-origin northern 2017 descendant cohort showed
 lower thermal plasticity in gene expression than their cooler-origin
 northern 2010 ancestors. This was largely due to a change in response at
 the warmer (40ºC) rather than cooler (20ºC) treatment. A similar pattern
 of reduced plasticity, largely due to a change in response at 40ºC, was
 also found for the cooler-origin northern versus the warmer-origin
 southern population from 2017. Our results demonstrate that reduced
 phenotypic plasticity can evolve with warming and that spatial and
 temporal changes in plasticity predict one another.
description: Leaf tissue was collected from individuals grown at 20°C day:5ºC
 night or 40°C day:25ºC night. Individuals were grown from seed collected
 from full-sibling families. Tissues from 18 individuals representing two
 collection localities (north and south), 3 biological replicates, two
 collection years (northern population only), and two growth conditions
 were used for RNA extraction and RNAseq. Pre-processing, alignment, and
 quantification were carried out with Partek® Flow® software v.7.0, and
 differential expression was conducted in DESeq2.
description: Please refer to the uploaded README file to undertand which files
 and scripts were used to generate each figure.
DOI: 10.5061/dryad.gxd2547mt
title: Data from: Phylogenomics and continental biogeographic disjunctions – insight from the Australian starflowers (Calytrix: Myrtaceae)

description: PREMISE OF THE STUDY: Continental-scale disjunctions and
 associated drivers is a core research interest in biogeographic studies.
 Here, we selected a species-rich Australian plant genus
 (Calytrix; Myrtaceae) as a case study to investigate
 these patterns in an Australian context. The endemic Australian starflower
 genus has a disjunct distribution across the mesic fringes of the
 continent and is absent from the arid centre. METHODS: We used
 high-throughput sequencing to generate unprecedented resolution and near
 complete species-level nuclear and plastid phylogenies
 for Calytrix. BioGeoBEARS and biogeographic stochastic
 mapping (BSM) were used to infer ancestral areas, the relative
 contributions of vicariance and dispersal events, and directionality of
 dispersal. KEY RESULTS: Present-day disjunctions
 in Calytrix are explained by a combination of scenarios:
 (1) retreat of multiple lineages from the continental centre to
 the more mesic fringes as Australia became progressively more arid, with
 subsequent extinction in the centre, and also (2) origination of ancestral
 lineages in southwestern Australia (SWA) for species-rich
 clades. The SWA biodiversity hotspot is a major diversification
 centre and the most common source area of dispersals, with multiple
 lineages originating in SWA and subsequently spreading to the adjacent
 arid Eremaean region.  CONCLUSIONS: Our results suggest
 major extinction as a result of cooling and drying of the Australian
 continent in the Eocene–Miocene shaped the present-day biogeography
 of Calytrix. We hypothesise that this peripheral
 vicariance pattern, which is similar to the African Rand flora, may
 explain the disjunctions of many other Australian plant groups. Further
 studies with densely sampled phylogenies are required to test this
 hypothesis.
description: Read me file contains description of the folders and associated
 files. The submission includes: BEAST_files:<br>
 Alignments of gene regions sourced from GenBank (outgroups) as well as
 newly sequenced NGS data from this study. This folder also includes the
 xml files with fossil calibrations and final trees from BEAST analyses
 found in the figures of the main manuscript as well as supplementary
 figures (as tree files). BioGeoBEARS_files:<br>
 Input files (tree, biogeographic states for each taxa, and time scale
 scenarios) for the BioGeoBEAR runs.
 ASTRAL_files:<br> Individual nuclear gene trees (RAxML) and
 species tree output from ASTRAL.
 IQTree_files:<br> alignment and partition files and output
 tree from IQTree for nuclear dataset (nr-CON).
 plastid-RAXML_files<br> Alignments of plastid gene regions
 and output tree file with bootstrap support.
DOI: 10.5061/dryad.wm37pvmns
title: Do human infrastructures shape nest distribution in the landscape depending on individual personality in a farmland bird of prey?

description: 1. Individuals´ distribution across habitats may depend on their
 personality. Human activities and infrastructures are critical elements of
 the landscape that may impact the habitat selection process. However,
 depending on their personality, individuals may respond differently to
 these unnatural elements. 2. In the present study, we first investigated
 whether some human infrastructures (buildings, roads and paths) shaped
 Montagu’s harrier nest spatial distribution in the landscape according to
 female personality (boldness). Second, we tested if the reproductive
 success of females depended on their boldness and nest location regarding
 infrastructures. 3. Using a long-term (19 years) data set, we calculated
 the distance from each nest to the nearest infrastructure type and the
 density of each infrastructure type around the nest. We tested the effects
 of female boldness (bold vs. shy) and its interaction with egg-laying date
 on these six metrics. 4. Nest location in the landscape depended on female
 personality and on some human infrastructures: the building density was
 smaller around nests from shy females than from bold ones. Nest
 distribution related to other infrastructure metrics did not depend on
 female boldness. The pattern related to building density is consistent
 with some habitat choice hypotheses which are discussed. Path density
 around nests negatively affected reproductive success regardless of female
 boldness, and late breeders nested further away from paths than early
 breeders. Human activities on paths (more common later in the season)
 could lead to disturbance and a decrease in parental care, reducing
 reproductive success. 5. Increasing human presence in farmlands implies a
 need to better understand its impact on population composition, in terms
 of personality. Our results suggest that individual behavioural
 differences should be taken into account in studies assessing the effects
 of human disturbance on animal populations, to propose more appropriate
 conservation measures.
description: For more information, please contact the authors.
DOI: 10.5061/dryad.8pk0p2nnr
title: From crypsis to masquerade: ontogeny changes the colour defences of a crab spider hiding as bird droppings

description: Selection imposed by visually-hunting predators has driven the evolution
 of colour-based antipredator defence strategies such as crypsis,
 masquerade, mimicry and aposematism. Individuals of many animals are
 generally considered to rely on a single type of defence strategy, but
 individuals of some species use multiple colour-based defences. Many
 animals switch between colour-based defences against visually-hunting
 predators during ontogeny. However, why this occurs remains poorly
 understood. The crab spider Phrynarachne ceylonica is an often-cited
 example of a bird dropping masquerade. It has recently been demonstrated
 that P. ceylonica crab spiders gain protection from their predators by
 being misidentified as bird droppings by their predators. P. ceylonica
 females show an ontogenetic shift in colour defences: early instars
 possess a dark and cryptic form, while at later instars and as adults, the
 spiders resemble bird droppings. We hypothesised that this shift may be
 driven by differential changes in predation risk of two defence strategies
 with increasing body size due to ontogeny. We tested this hypothesis by
 presenting naïve domestic chicks with 3D printed artificial spiders of two
 different sizes (small, large) and two colours (dark, bird dropping-like),
 and determined if larger bird dropping-like spiders are more readily found
 and attacked than cryptic forms by chicks. We found that small cryptic
 spiders were more difficult to detect than small bird dropping
 masquerading spiders, but large cryptic spiders were attacked much more
 quickly and more frequently than large bird dropping masquerading spiders.
 Increasing predation pressure on larger, cryptic spiders during ontogeny
 suggests that switching to bird dropping masquerade may be a more
 effective defence as spiders increase in size. We thus conclude that the
 ontogenetic shift from crypsis to masquerade is adaptive.
DOI: 10.5061/dryad.sbcc2fr6x
title: The adipokine FABP4 – A key regulator of neonatal glucose homeostasis

description: During pregnancy, fetal glucose production is suppressed, with rapid
 activation immediately post-partum. Fatty acid-binding protein 4 (FABP4)
 was recently demonstrated as a regulator of hepatic glucose production and
 systemic metabolism in animal models. Here we studied FABP4’s role in
 regulating neonatal glucose hemostasis. Serum samples were collected from
 pregnant women with normoglycemia or gestational diabetes at term, from
 the umbilical circulation, and from the newborns within 6 hours of life.
 FABP4 level was higher in the fetal vs. maternal circulation with a
 further rise in neonates after birth by ~3-fold. Neonatal FABP4 inversely
 correlated with blood glucose with ~10-fold increase in hypoglycemic
 neonates. When studied in mice, blood glucose of 12hr-old wild-type, Fabp4
 -/+ and Fabp4 -/- littermate mice was 59±13 ng/dL, 50±11 mg/dL and 43±11
 mg/dL, respectively (p&lt;0.05). Similar to our observations in
 humans, FABP4 levels in wild-type mice neonates was ~8-fold higher
 compared to adult mice. RNA-Seq of neonatal liver suggested altered
 expression of multiple glucagon-regulated pathways in Fabp4 -/- mice.
 Indeed, Fabp4 -/- liver glycogen was inappropriately intact, despite a
 significant hypoglycemia, with rapid restoration of normoglycemia upon
 injection of recombinant FABP4. Our data suggest an important biological
 role for the adipokine FABP4 in the orchestrated regulation of post-natal
 glucose metabolism.
DOI: 10.5061/dryad.0p2ngf220
title: Data from: A brief history and popularity of methods and tools used to estimate micro-evolutionary forces

description: Population genetics is a field of research that predates the current
 generations of sequencing technology. Those approaches, that were
 established before massively parallel sequencing methods, have been
 adapted to these new marker systems (in some cases involving the
 development of new methods) that allow genome-wide estimates of the four
 major micro-evolutionary forces – mutation, gene flow, genetic drift and
 selection. Nevertheless, classic population genetic markers are still
 commonly used and a plethora of analysis methods and programs is available
 for these and High Throughput Sequencing (HTS) data. These methods employ
 various and diverse theoretical and statistical frameworks, to varying
 degrees of success, to estimate similar evolutionary parameters making it
 difficult to get a concise overview across the available approaches.
 Presently, reviews on this topic generally focus on a particular class of
 methods to estimate one or two evolutionary parameters. Here, we provide a
 brief history of methods and a comprehensive list of available programs
 for estimating micro-evolutionary forces. We furthermore analyzed their
 usage within the research community based on popularity (citation bias)
 and discuss the implications of this bias for the software community. We
 found that a few programs received the majority of citations, with program
 success being independent of both the parameters estimated and the
 computing platform. The only deviation from a model of exponential growth
 in the number of citations was found for the presence of a graphical user
 interface (GUI). Interestingly, no relationship was found for the impact
 factor of the journals, when the tools were published, suggesting
 accessibility might be more important than visibility.
description: This dataset was collected from the records from the web of
 knowledge database and processed using both perl and R scripts for the
 analysis. These scripts are publicly available in the supplementary
 material of the publication titled: "A brief history and popularity
 of methods and tools used to estimate micro-evolutionary
 forces".
description: Please refer to the scripts in the paper titled "A brief
 history and popularity of methods and tools used to estimate
 micro-evolutionary forces" published in the journal of ecology and
 evolution by Wiley.
DOI: 10.5061/dryad.n02v6wwxw
title: Automated audio recording as a means of surveying Tinamous (Tinamidae) in the Peruvian Amazon

description: The use of machine learning technologies to process large quantities of
 remotely-collected audio data is a powerful emerging research tool in
 ecology and conservation. We applied these methods to a field study of
 tinamou (Tinamidae) biology in Madre de Dios, Peru, a region expected to
 have high levels of interspecies competition and niche partitioning as a
 result of high tinamou alpha diversity. We used autonomous recording units
 to gather environmental audio over a period of several months at lowland
 rainforest sites in the Los Amigos Conservation Concession and developed a
 Convolutional Neural Network-based data processing pipeline to detect
 tinamou vocalizations in the dataset.  The classified acoustic
 event data are comparable to similar metrics derived from an ongoing
 camera trapping survey at the same site, and it should be possible to
 combine the two datasets for future explorations of the target species’
 niche space parameters. Here we provide an overview of the methodology
 used in the data collection and processing pipeline, offer general
 suggestions for processing large amounts of environmental audio data, and
 demonstrate how data collected in this manner can be used to answer
 questions about bird biology.
description: This dataset has two components: training and testing data used
 to create an acoustic detection model, and a csv containing detections in
 the survey data. The acoustic dataset was derived from audio downloaded from the Macaulay Library of Natural Sounds (https://macaulaylibrary.org) and Xeno-Canto (http://www.xeno-canto.org) databases (S2) as well as from exemplar cuts in the audio we collected in the field. Effort was taken to ensure that the training examples covered the full breadth of the acoustic parameter space of tinamous, including for the two species in this study, <i>C. soui</i> and <i>C. variegatus</i>, that were observed to use distinct call and song types in the survey audio. All audio was checked to ensure correct assignment to species before use. Training and testing datasets were subsets of this larger dataset. Survey audio was collected using Swift recorders at sites in lowland Peruvian rainforest from July-October 2019 and processed using a convolutional neural network to obtain tinamou detections. The csv dataset includes all non-independent detections; independent detections as defined in the manuscript are all detections of a particular species separated from one another by more than an hour.
description: Deployments are labeled from 1-4; each was about two weeks long,
 though not every recorder recorded for the entire period due to battery
 issues. Swift recorders are labeled from 1-10, but recorders were deployed
 to different locations ("ct_code") in each deployment.
DOI: 10.5061/dryad.w0vt4b8rx
title: Posterior cervical brown fat and CXCL14 levels in the first year of life: sex differences and association with adiposity

description: Context: Brown adipose tissue (BAT) is particularly abundant in
 neonates but its association with measures of adiposity and metabolic
 health in early infancy is poorly delineated. Besides sustaining
 non-shivering thermogenesis, BAT secretes brown adipokines that act on
 systemic metabolism. The chemokine CXCL14 has been identified as a brown
 adipokine in experimental studies. Objective: To
 determine the relationships among BAT activity, adiposity and
 circulating CXCL14 levels in the first year of life in girls and boys.
 Design, setting and participants: Indices of fat accretion,
 circulating endocrine-metabolic parameters and serum CXCL14 levels were
 assessed longitudinally in a cohort of infants at birth and at 4 and 12
 months. BAT activity was estimated using infrared thermography only at age
 12 months. Main outcome measures: Weight and length Z-scores,
 total and abdominal fat content (by DXA), BAT activity at the
 posterior-cervical and supraclavicular regions, serum levels of glucose,
 insulin, insulin-like growth factor-I, high-molecular-weight adiponectin
 and CXCL14; CXCL14 transcript levels in neonatal BAT and liver.
 Results: Posterior-cervical BAT was more active in girls than in
 boys (p=0.02). BAT activity was negatively associated with adiposity
 parameters only in girls. CXCL14 levels were higher in girls than in boys
 at age 12 months and correlated positively with the area of active
 posterior-cervical BAT in girls. Neonatal BAT showed high CXCL14 gene
 expression levels. Conclusions: BAT activity and the levels of
 CXCL14 -a potential surrogate of BAT activity- are sex-specific
 in the first year of life. BAT activity associates negatively
 with indices of adiposity only in girls.
description: Here, we assessed for the first time brown adipose tissue (BAT) activity and the circulating levels of CXCL14 in a longitudinal cohort of infants in the first year of life, and determined their relationship with measures of adiposity (by DXA) and endocrine-metabolic parameters. The study cohort was composed of N= 43 infants (23 girls, 20 boys) who were recruited prenatally during the customary third-trimester visit among pregnant mothers consecutively seen in the outpatient clinics of Hospital Sant Joan de Déu and Hospital de Sant Boi – Parc Sanitari Sant Joan de Déu (Barcelona, Spain).
DOI: 10.5061/dryad.pk0p2ngp7
title: A highly invasive malaria parasite has expanded its range to non-migratory birds in North America

description: Parasite range expansions are a direct consequence of globalization and
 are an increasing threat to biodiversity. Here we report a recent range
 expansion of the SGS1 strain of a highly invasive parasite, Plasmodium
 relictum, to two non-migratory passerines in North America. Plasmodium
 relictum is considered one of the world’s most invasive parasites and
 causes the disease avian malaria: this is the first reported case of SGS1
 in wild birds of Western North America and wild non-migratory birds on the
 continent. Using a long-term database where researchers report avian
 malaria parasite infections, we summarized our current understanding of
 the geographic range of SGS1 and its known hosts. We also identified the
 most likely geographic region of this introduction event using the MSP1
 allele. We hypothesize that this introduction resulted from movements of
 captive birds and subsequent spillover to native bird populations, via
 ecological fitting. Further work should be conducted to determine the
 extent to which SGS1 has spread following its introduction in North
 America.
description: This data was collected across a time period spanning 4 years
 (2017-2020) in Boulder County, Colorado. DNA extractions were conducted on
 all blood samples. We conducted a nested PCR protocol on all DNA
 extractions to amplify a region of the cytb gene
 for <em>Plasmodium </em>parasites. In brief– we used primers
 HAEMNF1 and HAEMNR3 followed by the nested set of primers HAEMF and
 HAEMR2. Infections were further verified by an alternative set of primers–
 983R and 621F. We further identified the Pr2 variant for the SGS1
 infecting chickadees using an additional nested PCR protocol with primers
 MSP1-3F and MSP1-3R followed by the nested set of primers MSP1-3FN and
 MSP1-3RN. 
description: This dataset only includes infections in chickadees from our
 study with SGS1 but not other avian malaria parasites. Data from this
 study has also been reported to the MalAvi database. Some chickadees were
 recaptured and this is why their band number is listed more than once in
 the dataset.
DOI: 10.5061/dryad.vhhmgqntx
title: Origin of the species richness and composition of Caribbean aquatic entomofauna

description: From a literature review, we constructed a database yielding comprising
 &gt;1000 freshwater insect species (especially Odonata, Coleoptera,
 Trichoptera, Ephemeroptera; OCTE) in 26 Geographical Caribbean Units (GCU)
 and quantified local filtering (climate heterogeneity, annual rainfall,
 annual temperature), geography (area, distance from the mainland) and
 emergence age as a proxy for island ontogeny. We investigated the relative
 role of these variables on the species richness, endemism and composition
 of the units using island species-area relationship (ISAR), generalised
 linear modelling (GLM) and nonmetric multidimensional scaling (NMDS). In
 addition, we analysed the spatial patterns of species richness and
 composition using Moran’s I index. ISAR generally demonstrated one or two
 thresholds and continuous or discontinuous responses according to OCTE
 groups. A small island effect could be detected for Trichoptera and
 Ephemeroptera richness, whereas Odonata and Coleoptera only demonstrated
 differences in slope between smaller and larger GCUs. Area, climate
 heterogeneity, maximal rainfall and distance from mainland were major
 drivers of species composition in GCUs, whereas local climate variables
 were of main importance for the endemism rate. Due to the potential
 complexity of the Caribbean island ontogeny, middle-stage islands had an
 expected higher freshwater invertebrate richness than younger ones but an
 unexpected lower richness compared to older islands. Finally, the degree
 of colonization of islands was linked to the dispersal ability of species,
 with Odonata and Coleoptera having larger distribution ranges than
 Trichoptera and Ephemeroptera, which were more restricted by their
 comparatively narrow ecological niches. The high endemism (&gt;60%)
 found in the Caribbean freshwaters calls for more conservation effort in
 managing these highly threatened freshwater environments.To assess the
 relative contribution of geographical (area, distance from mainland) and
 local filtering variables (e.g., climate heterogeneity) to the species
 richness, endemism and composition of Caribbean aquatic entomofauna.
description: See the ReadMe File.
description: See the ReadMe File.