cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5p6b1
title: Data from: Population genetic structure and its implications for adaptive variation in memory and the hippocampus on a continental scale in food-caching black-capped chickadees

description: Food-caching birds rely on stored food to survive the winter and spatial
 memory has been shown to be critical in successful cache recovery. Both
 spatial memory and the hippocampus, an area of the brain involved in
 spatial memory, exhibit significant geographic variation linked to
 climate-based environmental harshness and the potential reliance on food
 caches for survival. Such geographic variation has been suggested to have
 a heritable basis associated with differential selection. Here, we ask
 whether population genetic differentiation and potential isolation among
 multiple populations of food-caching black-capped chickadees is associated
 with differences in memory and hippocampal morphology by exploring
 population genetic structure within and among groups of populations that
 are divergent to different degrees in hippocampal morphology. Using
 mitochondrial DNA and 583 AFLP loci, we found that population divergence
 in hippocampal morphology is not significantly associated with neutral
 genetic divergence or geographic distance, but instead is significantly
 associated with differences in winter climate. These results are
 consistent with variation in a history of natural selection on memory and
 hippocampal morphology that creates and maintains differences in these
 traits regardless of population genetic structure and likely associated
 gene flow.
description: PravosudovAFLPs.txtAFLP data; columns are loci, rows are individuals (2 rows per individual). Row 1 is locus labels. Column A = population names; column B = population abbreviation with individual numbers; column C = population numbers.
DOI: 10.15468/dl.ufnq2r
title: Occurrence Download

description: A dataset containing 4570132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Canada",
 "Geometry POLYGON((-79.24992 43.65862,-79.29978 43.83218,-79.51282 43.8379,-79.6821 43.81013,-79.70929 43.68242,-79.61864 43.58071,-79.45999 43.52158,-79.24992 43.65862))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Animalia",
 "Year 2016-2026"
 ]
}

 The dataset includes 4570132 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000503-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4pn03
title: Data from: Evolution of displays within the pair bond

description: Although sexual selection is an important cause of display evolution, in
 socially monogamous species (e.g. many birds), displays continue after
 formation of the pair bond. Here, we consider that these displays evolve
 because they stimulate the partner to increase investment in offspring.
 Our study is motivated by elaborate mutual displays in species that are
 largely monomorphic and have long-term pair bonds (e.g. the great crested
 grebe, Podiceps cristatus) and by many empirical results evidencing that
 display manipulation affects parental investment. Using population genetic
 models, we show that a necessary condition for the permanent establishment
 of mutual displays in the pair bond is that the benefit of investment by
 the pair is more than twice that resulting from investment by a single
 individual. Pre-existing biases to respond to displays by increased
 investment are a necessary component of display evolution. We also
 consider examples where one sex (e.g. males) stimulates increased
 investment in offspring by the other sex. Here, display and additional
 investment cannot evolve permanently, but can increase and linger at high
 frequency for a long time before loss. We discuss how such transient
 effects may lead to the evolution of permanent displays as a result of
 evolution at additional loci.
description: asymmetric
 modelC code, parameter file,
 and Mathematica file for the asymmetric model. The positions of entries in
 the parameter file can be found in the "getinfo" function in the
 C file.asymmetric feedback
 modelC code, parameter file,
 and Mathematica file for the asymmetric feedback model. The positions of
 entries in the parameter file can be found in the "getinfo"
 function in the C file.symmetric
 modelC code, parameter file,
 and Mathematica file for the symmetric model. The positions of entries in
 the parameter file can be found in the "getinfo" function in the
 C file.symmetric model with
 fertility selC code, parameter file,
 and Mathematica file for the symmetric model with fertility selection. The
 positions of entries in the parameter file can be found in the
 "getinfo" function in the C file.asymmetric model with
 fertility selC code, parameter file,
 and Mathematica file for the asymmetric model with fertility selection.
 The positions of entries in the parameter file can be found in the
 "getinfo" function in the C file.
DOI: 10.5061/dryad.8b063
title: Data from: Ranging behaviour of badgers Meles meles vaccinated with Bacillus Calmette Guerin

description: Because biological systems are complex, management interventions
 occasionally have unintended adverse consequences. For example, attempts
 to control bovine tuberculosis (TB) by culling badgers Meles meles have,
 under some circumstances, inadvertently increased cattle TB risks. Such
 harmful effects occur because culling profoundly alters badger movement
 behaviour, increasing pathogen transmission both between badgers and from
 badgers to cattle. It has recently been suggested that another TB
 management tool, badger vaccination with Bacillus Calmette Guerin, might
 provoke similar behavioural changes and hence similar harmful effects for
 cattle. We therefore took advantage of an existing project, which
 monitored 54 GPS-collared badgers across four study sites in southwest
 Britain, to explore whether vaccination, or live trapping to administer
 vaccine, influenced badger movement behaviour. We detected no significant
 effects of either vaccination or trapping on badgers’ monthly home range
 size, nightly distance travelled, or frequency of trespassing in
 neighbouring territories. The estimated effect of vaccination on badger
 home range size [2% reduction, 95% confidence interval (CI) 18% reduction
 – 17% increase] was statistically non-significant, but significantly
 smaller than that associated with both widespread (180% increase, 95% CI
 70–362% increase; P &lt; 0·001) and localised badger culling (74%
 increase, 95% CI 4–191% increase; P = 0·038). Synthesis and applications.
 In contrast with culling, live trapping and vaccinating badgers did not
 measurably alter their movement behaviour, fuelling optimism that
 vaccination might contribute positively to cattle tuberculosis control.
 Our study illustrates how existing monitoring can be exploited to assess
 potentially adverse effects of wildlife management.
description: monthly_home_range_size_31Oct16Estimates of monthly home range size for individual GPS-collared badgers, both vaccinated and unvaccinated.nightly_distances_travelled_31Oct16Distances travelled each night by individual GPS-collared badgers, both vaccinated and unvaccinated. Restricted to nights with complete data, i.e. no locations missed or excluded by filtering.trespassing_31Oct16Indication of whether, for each night of tracking, individual GPS-collared badgers (both vaccinated and unvaccinated) were located within the territory of another social group.RBCT_bait_return_distances_31Oct16Estimates of badger home range size from areas with and without culling, within the Randomised Badger Culling Trial (RBCT)
DOI: 10.5061/dryad.sn058
title: Data from: Abundance and morphometry changes across the high-mountain lake-size gradient in the tropical Andes of Southern Ecuador

description: The number, size, and shape of lakes are key determinants of the
 ecological functionality of a lake district. The lake area scaling
 relationships with lake number and volume enable upscaling biogeochemical
 processes and spatially considering organisms' metapopulation
 dynamics. These relationships vary regionally depending on the
 geomorphological context, particularly in the range of lake area &lt;1
 km2 and mountainous regions. The Cajas Massif (Southern Ecuador) holds a
 tropical mountain lake district with 5955 water bodies. The number of
 lakes deviates from a power law relationship with the lake area at both
 ends of the size range; similarly to the distributions found in temperate
 mountain ranges. The deviation of each distribution tail does not respond
 to the same cause. The marked relief limits the size of the largest lakes
 at high altitudes, whereas ponds are prompt to a complete infilling. A
 bathymetry survey of 202 lakes, selected across the full-size range,
 revealed a volume-area scaling coefficient larger than those found for
 other lake areas of glacial origin but softer relief. Water renewal time
 is not consistently proportional to the lake area due to the volume-area
 variation in midsize lakes. The 85% of the water surface is in lakes
 &gt;104 m2 and 50% of the water resources are held in a few ones (∼10)
 deeper than 18 m. Therefore, midlakes and large lakes are by far more
 biogeochemically relevant than ponds and shallow lakes in this tropical
 mountain lake district.
description: Inventory and
 morphometry of Cajas Massif lakes (Andes, Ecuador)Lake inventory and area
 of the lakes in the Cajas Massif and volume, depth, and watershed area of
 a selection of lakes in the Cajas National Park based on a bathymetric
 survey.Cajas Massif lakes inventory
 and morphometry.xlsx
DOI: 10.5061/dryad.vg313
title: Data from: Basal metabolism in tropical birds: latitude, altitude, and the “pace of life”

description: 1. Life history varies across latitudes, with the ‘pace of life’ being
 ‘slower’ in tropical regions. Because life history is coupled to energy
 metabolism via allocation tradeoffs and links between performance capacity
 and energy use, low metabolic intensity is expected in tropical animals.
 Low metabolism has been reported for lowland tropical birds, but it is
 unclear if this is due to ‘slow’ life history or to a warm, stable
 environment. 2. We measured Basal Metabolic Rates (BMR) of 253 bird
 species across a 2.6 km altitude gradient in Peru. We predicted higher BMR
 at high altitude due to lower temperatures leading to elevated
 thermoregulatory costs. We also tested for BMR differences between widely
 separated tropical regions (Peru and Panama), and between tropical- and
 temperate-breeding birds. 3. We found no effect of altitude on BMR in
 Peruvian species and no difference in BMR between Peruvian and Panamanian
 birds, suggesting that BMR in Neotropical birds is consistent and
 independent of environmental temperature. In a dataset encompassing more
 than 500 species, tropical birds had significantly lower BMR than
 temperate-breeding birds. 4. In contrast to several recent analyses, we
 found higher BMR in passerine birds than in non-passerines, independent of
 breeding latitude. 5. Breeding latitude affects BMR, but diversity in
 avian life history within and between temperate and tropical regions may
 explain some of the residual variation in BMR after accounting for body
 mass and breeding latitude. Future studies of links between life history,
 metabolism, and environmental factors might benefit from examining these
 variables within individual species as well as across broad geographic
 contrasts.
description: MCC_base
 on_5000_treesThis tree is the summary
 of 5000 trees downloaded from http://birdtree.org. The birdtree.org
 website accompanies the following study: Jetz W, Thomas GH, Joy JB,
 Hartmann K, Mooers AO (2012) The global diversity of birds in space and
 time. Nature 491: 444-448. http://dx.doi.org/10.1038/nature11631, and the
 Jetz et al. article in Nature should be cited in the primary reference
 list of any publication that uses data culled from
 birdtree.orgSuplementary
 Material_Tables
DOI: 10.25919/htcm-zy88
title: Parkes observations for project P1183 semester 2025OCTS_18

description: After nearly three years of monitoring, comprising with the Parkes telescope and the FAST telescopes, FRB 20220529 is proven to be an extremely interesting repeater. It exhibits one of the longest activity durations and a potential ~200-day RM period. Due to frequent observations scheduled with both Parkes and FAST, an abrupt rotation measure (RM) flare has been observed in this source. This is the first detection of such an ``RM flare'' in a fast radio burst (FRB), suggesting that the source is in an environment with occasionally erupting coronal mass ejection. This presents a unique opportunity to study the eruption environment of FRBs and investigate the relation between burst activity and other burst parameters. If confirmed, the periodicity and the ``RM flare'' of FRB 20220529 would corroborate each other and become a ``smoking gun'' of the binary origin of FRB. In previous analysis, both Parkes and FAST observations have proven essential. While FAST's higher sensitivity has enabled the capture of many bursts, Parkes' wideband receiver has provided a good burst detection rate even during low-rate phases. Notably, during the RM flare, two high signal-to-noise ratio bursts from Parkes have been crucial in understanding the RM variations. To further investigate FRB 20220529, we have scheduled regular FAST observations every fortnight, monitoring the source for 20 minutes each time. Therefore, we also propose to monitor FRB 20220529 using the Parkes UWL receiver, ensuring high-time resolution and employing full-polarization observations.
DOI: 10.5061/dryad.s26qt314
title: Data from: Regional divergence and mosaic spatial distribution of two closely related damselfly species (Enallagma hageni and Enallagma ebrium)

description: North American Enallagma damselflies radiated during the Pleistocene, and
 species differ mainly by reproductive structures. Although morphologically
 very different, Enallagma hageni and Enallagma ebrium are genetically very
 similar. Partitioning of genetic variation (AFLP), isolation by distance
 and clustering analyses indicate that these morphospecies are locally
 differentiated genetically. Spatial analyses show that they are rarely
 sympatric at local sites, and their distributions form a mosaic of patches
 where one is clearly dominant over hundreds of square kilometers. However,
 these morphospecies are also not genetically more similar when they are
 sympatric, indicating that hybridization is probably not occurring. Given
 that these morphospecies are ecologically equivalent, strong assortative
 mating, reproductive interference and fast post-glacial recolonization may
 explain the origin and maintenance of these distributional patches across
 eastern North America. By limiting opportunities for gene flow,
 reproductive interference may play an unsuspected role in accelerating
 genetic differentiation in the early phases of nonecological speciation.
description: AFLP genotypes for
 Enallagma hageni and E. ebriumAFLP genotype (120
 locus) for Enallagma hageni (H) and E. ebrium (E) from 20 sites in QO, PE
 and NE.Genotypes_AFLP.xlsField sampling data for Enallagma hageni and E. ebriumField sampling data for Enallagma hageni (H) and E. ebrium (E) used for spatial analysis.Field_sampling_data.xlsx
DOI: 10.5061/dryad.95t87
title: Data from: Beyond mean allelic effects: a locus at the major color gene MC1R associates also with differing levels of phenotypic and genetic (co)variance for coloration in barn owls

description: The mean phenotypic effects of a discovered variant help to predict major
 aspects of the evolution and inheritance of a phenotype. However,
 differences in the phenotypic variance associated to distinct genotypes
 are often overlooked despite being suggestive of processes that largely
 influence phenotypic evolution, such as interactions between the genotypes
 with the environment or the genetic background. We present empirical
 evidence for a mutation at the melanocortin-1-receptor gene, a major
 vertebrate coloration gene, affecting phenotypic variance in the barn owl,
 Tyto alba. The white MC1R allele, which associates with whiter plumage
 coloration, also associates with a pronounced phenotypic and additive
 genetic variance for distinct color traits. Contrarily, the rufous allele,
 associated with a rufous coloration, relates to a lower phenotypic and
 additive genetic variance, suggesting that this allele may be epistatic
 over other color loci. Variance differences between genotypes entailed
 differences in the strength of phenotypic and genetic associations between
 color traits, suggesting that differences in variance also alter the level
 of integration between traits. This study highlights that addressing
 variance differences of genotypes in wild populations provides interesting
 new insights into the evolutionary mechanisms and the genetic architecture
 underlying the phenotype.
description: ColorData1ColorData2ColorData3gInverseARScriptReadMe
DOI: 10.5061/dryad.9067
title: Data from: Temperature-related natural selection in a wind-pollinated tree across regional and continental scales

description: Adaptive genetic variation is a key factor in evolutionary biology, but
 the detection of signatures of natural selection remains challenging in
 non-model organisms. We used a genome scan approach to detect signals of
 natural selection in the Black alder (Alnus glutinosa), a widespread
 wind-pollinated tree. Gene flow through pollen dispersal is believed to be
 high in this species, and we therefore expected to find a clear response
 to natural selection. In combination with two different landscape genetic
 approaches, we determined which environmental variables were most
 associated with the inferred selection. This analysis was performed on a
 regional scale (northern Belgium) and on a continental scale (Europe).
 Because climate-related differences are much more pronounced at the
 continental scale, we expected to find more selection-sensitive genetic
 markers across Europe than across northern Belgium. At both spatial scales
 a substantial number of genetic loci were considered outliers, with
 respect to neutral expectations, and were therefore identified as
 selective. Based on results from our combined approach, four putative
 selective loci (or 2.5 %) were recovered with high statistical support.
 Although these loci seemed to be associated with different environmental
 variables, they were mainly temperature-related. Our study demonstrates
 that the use of complementary methods in landscape genetics allows the
 discovery of selective loci which otherwise might stay hidden. In
 combination with a genome scan, the selective loci can be verified and the
 nature of the selection pressure can be identified.
description: AFLP matrix Alnus
 glutinosaThe data file contains
 two spread sheets. The first shows the AFLP data - in the first column the
 sample codes and in the second the population codes. The next 163 columns
 represent the different markers, named according to the primer combination
 and fragment size. Marker presence is noted as "1", marker
 absence is noted as "0". Missing values are given as
 "-1". The second spread sheet contains population information:
 country, location name, population code, latitude and
 longitude.
DOI: 10.5061/dryad.6kn23
title: Data from: Zika virus in the Americas: early epidemiological and genetic findings

description: Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV),
 with ~30,000 cases reported to date. ZIKV was first detected in Brazil in
 May 2015 and cases of microcephaly potentially associated with ZIKV
 infection were identified in November 2015. Using next generation
 sequencing we generated seven Brazilian ZIKV genomes, sampled from four
 self-limited cases, one blood donor, one fatal adult case, and one newborn
 with microcephaly and congenital malformations. Phylogenetic and molecular
 clock analyses show a single introduction of ZIKV into the Americas,
 estimated to have occurred between May-Dec 2013, more than 12 months prior
 to the detection of ZIKV in Brazil. The estimated date of origin coincides
 with an increase in air passengers to Brazil from ZIKV endemic areas, and
 with reported outbreaks in Pacific Islands. ZIKV genomes from Brazil are
 phylogenetically interspersed with those from other South American and
 Caribbean countries. Mapping mutations onto existing structural models
 revealed the context of viral amino acid changes present in the outbreak
 lineage; however no shared amino acid changes were found among the three
 currently available virus genomes from microcephaly cases.
 Municipality-level incidence data indicate that reports of suspected
 microcephaly in Brazil best correlate with ZIKV incidence around week 17
 of pregnancy, although this does not demonstrate causation. Our genetic
 description and analysis of ZIKV isolates in Brazil provide a baseline for
 future studies of the evolution and molecular epidemiology in the Americas
 of this emerging virus.
description: Epidemiological Data:
 Numbers of suspected ZIKV cases and suspected microcephaly cases per state
 and per epidemiological week.Contains 1) CSV file
 with number suspected ZIKV cases from January 2015 to the end of December
 2015; 2) CSV file with number of suspected microcephaly cases from January
 2015 to the first week of January 2016. Numbers correspond to suspected
 microcephaly cases at week 20 of pregnancy; 3) CSV file with codes of
 state of residence and municipality of residence in Brazil; and 4) R
 scripts for correlation analysis described in SI Section
 1.5.Epidemiological
 Data.zipSequence data details
 and alignments for dataset A and B.Contains (1) table with
 accession numbers, isolate names, cell passage history, publication
 details, country/location of sampling, sampling dates and (2) Fasta format
 sequence alignments of datasets A and B.Sequence
 Data.zipBEAST XML input file
 used for genetic analysis.BEAST XML input file
 used to generate Figure 3 under a strict clock model, a Bayesian skyline
 coalescent prior and a CTMC prior on the clock rate.ZIKV_with1966_strict_skyline_ctmc.xml