cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b2rbnzsck
title: Allopatry, hybridization, and reproductive isolation in Arctostaphylos: phenology and field morphology

description: Premise of the study: Hybridization plays a key role in introgressive
 adaptation, speciation, and adaptive radiation as a source of evolutionary
 innovation. Hybridization is considered common in Arctostaphylos,
 yet species boundaries are retained in stands containing multiple
 species. Arctostaphylos contains diploids and
 tetraploids, and recent phylogenies indicate two clades; we hypothesize
 combinations of these traits limit or promote hybridization
 rates.  Methods: We statistically analyzed co-occurrence patterns
 of species by clade membership and ploidy level from 87-0.1 ha plots. We
 sampled multiple sites to analyze for percent hybridization based on
 morphology. Finally, phenophases were analyzed by scoring herbarium sheets
 for a large number of taxa from both clades as well as tetraploids, and
 second, surveying three field sites over two years for divergence in
 phenological stages between co-occurring taxa. Key results: Most taxa
 in Arctostaphylos are allopatric relative to other
 congenerics. When two taxa co-occur, the patterns are a diploid with a
 tetraploid, or two diploids from different clades. When three taxa
 co-occur, the pattern is two diploids from different clades and a
 tetraploid. Field and herbarium data both indicate flowering phenology is
 displaced between diploids from the two clades; one of the diploid clades
 and tetraploids overlap considerably.  Conclusions: The two deep
 clades in Arctostaphylos are genetically distant, with
 hybrids rare or non-existent when taxa co-occur. Reproductive isolation
 between clades is enhanced by displaced flowering phenology for
 co-occurring species. Within clades, taxa appear to have few reproductive
 barriers other than an allopatric distribution or different ploidy levels.
description: 1. Field morphology: random transects were used to collect
 specimens that were then measured for morphology traits. Sites contained
 two species of Arctostaphylos, usually from different phylogenetic clades.
 Data were used for estimating hybridization rates and used in PCA figures
 in publication. 2. Field phenology: 3 sites containing
 2 Arctostaphylos species from different clades were monitored for
 phenology over two seasons. Peak flowering dates were statistically
 compared; one table and one figure were in manuscript.
 3. Herbarium phenology: Over 1800 herbarium sheets of
 Arctostaphylos species were scored for different phenological phases to
 estimate  peak flowering times for species of different phylogenetic
 clades and ploidy. Data analysis published as one figure and one table in
 manuscript.
DOI: 10.5061/dryad.z08kprr9s
title: Testing for adaptive radiation: a new approach applied to Madagascar frogs

description: Adaptive radiation is a key topic at the intersection of ecology and
 evolutionary biology. Yet the definition and identification of adaptive
 radiation both remain contentious. Here, we introduce a new approach for
 identifying adaptive radiations which combines key aspects of two widely
 used definitions. Our approach compares evolutionary rates in morphology,
 performance, and diversification between the candidate radiation and other
 clades. We then apply this approach to a putative adaptive radiation of
 frogs from Madagascar (Mantellidae). We collect new data on morphology and
 performance from mantellid frogs and compare rates of diversification and
 multivariate evolution of size, shape, and performance between mantellids
 and other frogs. We find that mantellids potentially pass our test for
 accelerated rates of evolution for shape, but not for size, performance,
 or diversification. Our results demonstrate that clades can have
 accelerated phenotypic evolution without rapid diversification (dubbed
 “adaptive non-radiation”). We also highlight general issues in testing for
 adaptive radiation, including taxon sampling and the problem of including
 another adaptive radiation in the comparison clades. Finally, we suggest
 that similar tests should be conducted on other putative adaptive
 radiations on Madagascar, comparing their evolutionary rates to those of
 related clades outside Madagascar. Based on our results, we speculate that
 older Madagascar clades may show evolutionary patterns more similar to
 those on a continent than an island.
description: See methods of manuscript.
DOI: 10.5061/dryad.p8cz8w9nf
title: Pollinator-mediated facilitation alleviates pollen limitation through effects on the quality of plant reproduction

description: Facilitation and competition among plants sharing pollinators have
 contrasting consequences for each species' fitness. However, it is
 unclear whether pollinator-mediated indirect interactions between plants
 affect plant fitness in a multispecies context. Here, we investigated how
 pollinator sharing affects pollen limitation (contribution of pollination
 to fitness) in a tropical hummingbird-pollinated community marked by
 facilitation. We employed indices describing how much a plant species is
 important to shared pollinators (acting degree) and have its shared
 pollinators influenced by other plants (target degree) within the
 plant-hummingbird network. Since facilitation often increases pollination
 quantity but not necessarily quality, we expected both indices to be
 associated with reductions in pollen limitation estimates that depend on
 pollination quantity (fruit set and seed number) rather than estimates
 more strictly related to quality (seed weight and germination). Instead,
 we found that both indices were associated with reductions in pollen
 limitation only for seed weight and germination. Thus, facilitation acted
 on qualitative estimates of pollen limitation. Our results suggest that
 facilitation may enhance plant fitness even if quantitative components of
 plant fecundity are already saturated. Overall, we showed that
 pollinator-mediated indirect effects in a multispecies context are
 important drivers of plant fitness with consequences for coexistence in
 diverse communities.
DOI: 10.6078/d1bx2f
title: Particle-in-cell modeling of Martian magnetic cusps

description: Datasets supporting the manuscript, "Particle-in-cell modeling of
 Martian magnetic cusps and their role in enhancing nightside ionospheric
 ion escape", published in Geophysical Research Letters. All
 datasets are output from a 1.5-dimensional, particle-in-cell model of
 magnetospheric-ionospheric particle interactions along an open magnetic
 field line in a Martian magnetic cusp region. Particles are
 self-consistently traced according to the combined magnetic mirror force,
 parallel electrostatic fields, and Martian gravity. Particle densities,
 velocity distributions, and domain potentials are printed out at the end
 of simulations, after the establishment of steady-state conditions.
description: All files are in simple ASCII format, with descriptive
 headers.
DOI: 10.5061/dryad.9p8cz8wdk
title: High elevation increases the risk of Y chromosome loss in Alpine skink populations with sex reversal

description: The view genotypic sex determination (GSD) and environmental sex
 determination (ESD) are mutually exclusive states has been contradicted by
 the discovery that chromosomal sex and environmental influences can
 co-exist within the same species, hinting at a continuum of intermediate
 states. Systems where genes and the environment interact to determine sex
 present the opportunity for sex reversal to occur, where the phenotypic
 sex is the opposite of that predicted by their sex chromosome complement.
 The skink Bassiana duperreyi has XX:XY sex chromosomes with sex reversal
  of the  XX genotype to a male phenotype in response to
 exposure to cold incubation temperatures. Here we studied the frequency of
 sex reversal in B. duperreyi in response to climatic variation, using
 elevation as a surrogate for environmental temperatures. We demonstrate
 sex reversal for the first time in free-ranging adults of a reptile
 species with XX/XY sex determination. The highest frequency of sex
 reversal occurred at the highest elevation location, Mount Ginini (18.64%)
 and decreases in frequency with elevation. We model the impact of this
 under Fisher's frequency dependent selection to show that, only at
 the highest elevations, populations risk the loss of the Y chromosome and
 a transition to TSD. This study contributes to our understanding of the
 risks of extinction from climate change in species subject to sex reversal
 by temperature, and will provide focus for future research to test
 on-the-ground management strategies to mitigate the effects of climate in
 local populations.  
description: Tail tissue samples of a
 total of 100 <i>B. duperreyi</i> from the 10 populations (10
 samples per location) were passed to Diversity Arrays Technology Pty Ltd
 (Canberra) (DArT) for reduced representational sequencing. Genomic DNA
 (gDNA) was extracted using a NucleoMag® 96 Tissue kit (Macherey‐ Nagel,
 Düren, Germany) coupled with NucleoMag SEP (Ref. 744900) to allow
 automated separation of high‐quality DNA on a Freedom Evo robotic liquid
 handler (TECAN, Männedorf, Switzerland). Four combinations of restriction
 enzymes were evaluated for <i>B. duperreyi</i> (PstI enzyme
 combined with either HpaII, SphI, NspI, and MseI) and the restriction
 enzyme combination of PstI (recognition sequence 5’-CTGCA| G-3’) and SphI
 (5’ -GCATG|C-3’) was selected for complexity reduction by double
 digestion. A full account of the process of generating SNP genotypes for
 these samples is given by Georges et al. 2018, Molecular Ecology 27:5195-5213. The data comprised
 a matrix of SNP loci by individuals, with the contents stored as 0,
 homozygote, reference state; 1, heterozygote; and 2, homozygote, alternate
 state.
description: Refer to the README file.
DOI: 10.5061/dryad.m37pvmd0j
title: Genome-wide SNPs detect no evidence of genetic population structure for reef manta rays (Mobula alfredi) in southern Mozambique

description: Little is known about the extent of genetic connectivity along continuous
 coastlines in manta rays or whether site visitation is influenced by
 relatedness. Such information is pertinent to defining population
 boundaries and understanding localised dispersal patterns and behaviour.
 Here, we use 3057 genome-wide single nucleotide polymorphisms (SNPs) to
 evaluate population genetic structure and assess levels of relatedness at
 aggregation sites of reef manta rays (Mobula alfredi) in southern
 Mozambique (n = 114). Contrary to indications of limited dispersal along
 the southern Mozambican coastline inferred from photo identification and
 telemetry studies, our results show no evidence of population structure
 (non-significant FST &lt;0.001) for M. alfredi along this coast. We
 also found no evidence that individuals sampled at the same site were more
 related than expected by chance for males, females or across both sexes,
 suggesting kinship may not influence visitation pattern s at these sites.
 We estimated the effective population size (Ne) of this population to be
 375 (95% CI = 369-380). Comparison to a distant eastern Indian Ocean site
 (Western Australia; n = 15) revealed strong genetic differentiation
 between Mozambique and Western Australia (FST = 0.377), identifying the
 Indian Ocean basin as a barrier to dispersal. Our findings show that
 genetic connectivity in M. alfredi extends for several hundred kilometres
 along continuous coastlines. We therefore recommend the population in
 Mozambique be considered a discrete management unit and future
 conservation plans should prioritize integrated strategies along the
 entire southern coastline.
description: <em>M. alfredi</em> DArTseq SNP data (Diversity
 Arrays Technology, Canberra)
DOI: 10.5061/dryad.bzkh1896r
title: Blow to the Northeast? Intraspecific differentiation of Populus davidiana suggests a northeastward skew of a phylogeographic break boundary in East Asia

description: Aim: There is increasing interest in the role that biological traits, and
 historical and biogeographic processes, play in the formation of
 phylogeographic patterns. An arid belt that once existed in
 northern China might have affected many plants, but this has yet to be
 untested in an arid-tolerant, wind-dispersed species. Here we tested how
 intrinsic and extrinsic factors have affected the phylogeography of
 Populus davidiana. Location: East Asia Methods: Genetic variation was
 surveyed across 40 populations (555 individuals) covering the Chinese
 range of P. davidiana, using 16 nuclear microsatellite loci (nSSRs) and
 four chloroplast fragments (cpDNA). Demographic and migration hypotheses
 were tested using coalescent-based approaches, and the present and past
 potential distributions were predicted using species distribution
 modelling. Results: Molecular data divides P. davidiana into two lineages,
 northeastern China (NECR), and central and northern China (CNCR); however,
 the dividing line is around 118ºE for nSSRs, but 122ºE for cpDNA. The
 range and habitat of the two lineages barely overlap at present, and their
 ecological separation may have initiated around the Pliocene-Quaternary
 boundary, when major infraspecific cpDNA clades diverged. NECR and CNCR
 experienced postglacial northeastward and northward range shifts,
 respectively. Bi-directional historical gene flow was detected
 between NECR and CNCR for both bi-parentally inherited nSSRs and
 maternally inherited cpDNA. Demographic inferences suggest a severe
 bottleneck for CNCR and especially NECR, around the latest Pleistocene.
 Main conclusions: The phylogeographic break within P.
 davidiana reflects the impacts of biogeographic history, climate
 and biological traits. Its plumed, wind-dispersed seeds might be
 especially significant, because prevailing southwestern spring winds may
 have moved the NECR-CNCR boundary further east than similar phylogenetic
 breaks in other species, and also moved the cpDNA boundary relative to
 that for nuclear markers. Biological traits, therefore, should also be
 considered when examining the genetic and ecological differentiation
 between closely related taxa.
description: We sampled 555 individuals
 from 40 populations throughout the main range of <i>Populus
 </i><i>davidiana</i>,
 in northern China<i> </i>, including the 170 individuals from
 33 populations sampled by Zheng et al. . Between three and 27 trees were
 sampled from each population, with all sampled individuals at least 100 m
 apart from one another. All individuals were genotyped using a set of 16
 nuclear microsatellite loci, and four chloroplast DNA (cpDNA) regions
 (<i>mat</i>K,
 <i>t</i><i>rn</i>G-<i>psb</i>K, <i>ps</i>bK-<i>psb</i>I, and <i>ndh</i>C-<i>trn</i>V) were sequenced for 379 individuals across all sampled populations, plus one <i>P. adenopoda</i> individual as outgroup.
DOI: 10.15468/dl.g4x55x
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Calamus manan"
 ]
}

 The dataset includes 60 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002572-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5mkkwh742
title: Seek and learn: automated identification of microevents in animal behaviour using envelopes of acceleration data and machine learning

description: 1. Animal-borne accelerometers have been used across more than 120 species
 to infer biologically significant information such as energy expenditure
 and broad behavioural categories. While the accelerometer’s high
 sensitivity to movement and fast response times present the unprecedented
 opportunity to resolve fine-scale behaviour, leveraging this opportunity
 will require overcoming the challenge of developing general, automated
 methods to analyse the nonstationary signals generated by nonlinear
 processes governing erratic, impulsive movement characteristic of
 fine-scale behaviour. 2. We address this issue by conceptualising
 fine-scale behaviour in terms of characteristic microevents: impulsive
 movements producing brief (&lt;1 s) shock signals in accelerometer
 data. We propose a ‘seek-and-learn’ approach: a novel microevent detection
 step first locates where shock signals occur (‘seek’) by searching for
 peaks in envelopes of acceleration data. Robust machine learning (‘learn’)
 employing meaningful features then separates microevents. We showcase the
 application of our method on tri-axial accelerometer data collected on ten
 free-living meerkats (Suricata suricatta) for four fine-scale foraging
 behaviours – searching for digging sites, one-armed digging, two-armed
 digging, and head jerks during prey ingestion. Annotated videos served as
 groundtruth, and performance was benchmarked against that of a variety of
 classical machine-learning approaches. 3. Microevent identification
 (μEvId) with eight features in a three-node hierarchical classification
 scheme employing logistic regression at each node achieved a mean overall
 accuracy of &gt;85% during leave-one-individual-out cross-validation,
 and exceeded that of the best classical machine learning approach by 9%.
 μEvId was found to be robust not only to inter-individual variation but
 also to large changes in model parameters. 4. Our results show that
 microevents can be modelled as impulse responses of the animal
 body-and-sensor system. The microevent detection step retains only
 informative regions of the signal, which results in the selection of
 discriminative features that reflect biomechanical differences between
 microevents. Moving-window-based classical machine learning approaches
 lack this prefiltering step, and were found to be suboptimal for capturing
 the nonstationary dynamics of the recorded signals. The general, automated
 technique of μEvId, together with existing models that can identify broad
 behavioural categories, provides future studies with a powerful toolkit to
 exploit the full potential of accelerometers for animal behaviour
 recognition.
DOI: 10.5061/dryad.tht76hdxc
title: Causes and consequences of an unusually male-biased adult sex ratio in an unmanaged feral horse population

description: 1. The adult sex ratio (ASR) is important within ecology due to its
 predicted effects on behaviour, demography, and evolution, but research
 examining the causes and consequences of ASR bias have lagged behind
 studies of sex ratios at earlier life stages. Although ungulate ASR is
 relatively well-studied, exceptions to the usual female-biased ASR
 challenge our understanding of the underlying drivers of biased ASR, and
 provide an opportunity to better understand its consequences. 2. Some
 feral ungulate populations, including multiple horse populations, exhibit
 unusually male-biased ASR. For example, research suggests that the feral
 horse (Equus ferus caballus) population on Sable Island, Nova Scotia,
 Canada, may exhibit a male-biased ASR. Such exceptions to the rule provide
 a valuable opportunity to reveal the contributions of environmental
 context and trait differences to ASR bias. 3. We aimed to test for bias in
 Sable Island horse ASR, identify the demographic drivers of bias, and
 explore its demographic and social consequences. To do this, we used
 life-history, movement, and group membership information for hundreds of
 horses followed through a long-term individual-based study between 2007
 and 2018. 4. Sable Island horse ASR is male-biased, and this skew has
 increased over time, reaching 62% male in 2018. Our life table response
 experiment suggested that ASR skew was driven predominantly by male-biased
 adult survival. Further analyses pointed to sex-biased survival being
 driven by reduced female survival post-reproduction. Male-biased ASR was
 associated with reduced harem sizes, an increase in the number of social
 groups on the island, and reduced reproduction in young females. 5. Our
 results support the idea that male-biased ASR in feral ungulate
 populations may be caused by a combination of high population density and
 high reproductive output. We suggest that female-biased mortality may be
 caused by females continuing to reproduce at high density, and thus being
 more susceptible to resource shortages. Thus, our results highlight the
 strong context-dependence of ASR. Furthermore, our work indicates the
 potential for ASR to substantially alter a population's social
 organisation. Such changes in social structure could have knock-on
 consequences for demography by altering the formation/stability of social
 relationships, or competition for matings.
DOI: 10.5061/dryad.0cfxpnw0b
title: Field‐based individual plant phenotyping of herbaceous species by unmanned aerial vehicle

description: 1. Recent advances in Unmanned Aerial Vehicle (UAVs) and image processing
 have made high-throughput field phenotyping possible at plot/canopy level
 in the mass grown experiment. Such techniques are now expected to be used
 for individual level phenotyping in the single grown experiment. 2. We
 found two main challenges of phenotyping individual plants in the single
 grown experiment: plant segmentation from weedy backgrounds and the
 estimation of complex traits that are difficult to measure manurally. 3.
 In this study, we proposed a methodological framework for field-based
 individual plant phenotyping by UAV. Two contributions, which are weed
 elimination for individual plant segmentation, and complex traits (volume
 and outline) extraction, have been developed. The framework demonstrated
 its utility in the phenotyping of Helianthus tuberosus(Jerusalem
 artichoke), an herbaceous perennial plant species. 4. The proposed
 framework can be applied to either small and large scale phenotyping
 experiments.
description: Please check the paper for more details.
description: This is a support page of paper : Guo, W., Fukano1,Y., Noshita,
 K., Ninomiya, S..(2020) Field-based individual plant phenotyping of
 herbaceous species by unmanned aerial vehicle. Before
 testing the source code, the following dirctory of files should be
 downloaded to your PC. Then, 
 Run "step1_copyexperimentRe.m" if you need to copy the
 related files from Pix4Dmapper. open folder
 "makeSegModel", follow the steps to generate the color-based
 segmentation model. run
 "step2_weips.m" play with "*.CSV"
 files to get results needed. Check more
 details here: https://github.com/oceam/WEIPS.
DOI: 10.5061/dryad.hdr7sqvg3
title: Data from: Extra-pair paternity in two populations of the socially monogamous Thorn-tailed Rayadito Aphrastura spinicauda (Passeriformes: Furnariidae)

description: Studies on extra-pair paternity (EPP) are key to understanding the
 ecological and evolutionary drivers of variation in avian mating
 strategies, but information is currently lacking for most tropical and
 sub-tropical taxa. We describe the occurrence of EPP in two populations of
 a South American socially monogamous bird, the Thorn-tailed Rayadito,
 based on data from 266 broods and 895 offspring that were sampled during
 six breeding seasons in north-central and southern Chile. In the northern
 population, 21% of the broods contained at least one extra-pair young and
 14% of all offspring were sired by an extra-pair male, while in the
 southern population, we detected extra-pair offspring (EPO) in 14% of the
 broods, and 6% of all offspring were EPO. Variation in the frequency of
 EPP could stem from population differences in the duration of the breeding
 season or the density of breeding individuals. Other factors such as
 differences in breeding synchrony and variation in food availability need
 to be evaluated. More reports on EPP rates are necessary to determine the
 patterns of taxonomic and geographic variation in mating strategies in
 Neotropical birds, and to better understand the differences in ecological
 dynamics between northern and southern hemisphere populations.
description: All instructions regarding the dataset can be found in the
 ReadMe.txt file.