cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ns1rn8pt7
title: Revealing cryptic interactions between large mammalian herbivores and plant-dwelling arthropods via DNA metabarcoding

description: In the past decade, it has become clear that omnivory, feeding on more
 than one trophic level, is important in natural and agricultural systems.
 Large mammalian herbivores (LMH) frequently encounter plant-dwelling
 arthropods (PDA) on their food plants. Yet, ingestion of PDA by LMH is
 only rarely addressed and the extent of this direct trophic interaction,
 especially at the PDA community level, remains unknown. Using a DNA
 metabarcoding analysis on feces of free-ranging cattle from a replicated
 field experiment of heavily and moderately grazed paddocks, we reveal that
 feeding cattle (incidentally) ingest an entire food-chain of PDA including
 herbivores, predators and parasites. Overall, 25 families of insects and 4
 families of arachnids were ingested, a pattern that varied over the
 season, but not with grazing intensity. We identified the functional
 groups of PDA vulnerable to ingestion, such as sessile species and
 immature life stages. Most of the fecal samples (76%) contained sequences
 belonging to PDA, indicating that direct interactions are frequent. This
 study highlights the complex trophic connections between LMH and PDA. It
 may even be appropriate to consider LMH as omnivorous enemies of PDA.
DOI: 10.5061/dryad.zw3r22882
title: Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure

description: Ecological, environmental, and geographic factors all influence genetic
 structure. Species with broad distributions are ideal systems because they
 cover a range of ecological and environmental conditions allowing us to
 test which components predict genetic structure. This study presents a
 novel, broad geographic approach using molecular markers, morphology, and
 habitat modelling to investigate rangewide and local barriers causing
 contemporary genetic differentiation within the geographical range of
 three white-crowned sparrow (Zonotrichia leucophrys) subspecies: Z. l.
 gambelii, Z. l. oriantha, and Z. l. pugetensis.  Three types of
 genetic markers showed geographic distance between sampling sites,
 elevation, and ecosystem type are key factors contributing to population
 genetic structure. Microsatellite markers revealed white-crowned sparrows
 do not group by subspecies, but instead indicated four groupings at a
 rangewide scale and two groupings based on coniferous and deciduous
 ecosystems at a local scale. Our analyses of morphological variation also
 revealed habitat differences; sparrows from deciduous ecosystems are
 larger than individuals from coniferous ecosystems based on principal
 component analyses. Habitat modeling showed isolation by distance was
 prevalent in describing genetic structure, but isolation by resistance
 also had a small but significant influence. Not only do these findings
 have implications concerning the accuracy of subspecies delineations, they
 also highlight the critical role of local factors such as habitat in
 shaping contemporary population genetic structure of species with high
 dispersal ability.
description: We genotyped 328 individuals at nine polymorphic microsatellite
 loci (Bensch et al., 1997; Dawson et al., 1997; Hanotte et al., 1994;
 Petren, 1998; Poesel et al., 2009; Stenzler et al., 2004).  Genomic DNA
 was amplified in 10 µL reaction volumes containing colourless GoTaq® Flexi
 buffer (Promega), 0.2 mM dNTP, and 0.8 mM or 1 mM
 MgCl<sub>2</sub>, 0.5 µM forward and reverse primer, 0.05 µM
 fluorescent M13 tag, 0.5 U GoTaq® Flexi DNA polymerase
 (Promega).
description: Missing values are scored as zero in this dataset
DOI: 10.5061/dryad.0vt4b8h07
title: Parental population range expansion before secondary contact promotes heterosis

description: Population genomic analysis of hybrid zones is instrumental to our
 understanding of the evolution of reproductive isolation. Many
 temperate hybrid zones are formed by the secondary contact between two
 parental populations that have undergone post-glacial range expansion.
 Here we show that explicitly accounting for historical parental isolation
 followed by range expansion prior to secondary contact is fundamental for
 explaining genetic and fitness patterns in these hybrid zones.
 Specifically, ancestral population expansion can result in allele surfing
 where neutral or slightly deleterious mutations drift to high frequency at
 the expansion front. If these surfed deleterious alleles are recessive,
 they can contribute to substantial heterosis in hybrids produced at
 secondary contact, counteracting negative effects of
 Bateson-Dobzhansky-Muller incompatibilities (BDMIs) hence weakening
 reproductive isolation. When BDMIs are linked to such recessive
 deleterious alleles the fitness benefit of introgression at these loci can
 facilitate introgression at the BDMIs. The extent to which this occurs
 depends on the strength of selection against the linked deleterious
 alleles and the distribution of recombination across the chromosome.
 Finally, surfing of neutral loci can alter the expected pattern of
 population ancestry, thus accounting for historical population expansion
 is necessary to develop accurate null genomic models of secondary-contact
 hybrid zones.
DOI: 10.5061/dryad.905qfttm1
title: Single-parentage analysis of Sockeye Salmon

description: Understanding reproductive patterns in endangered species is critical for
 supporting their recovery efforts. In this study we use a combination of
 paired-parent and single-parent assignments to examine the reproductive
 patterns in an endangered population of sockeye salmon (Oncorhynchus
 nerka) that uses Redfish Lake in central Idaho as a spawning and nursery
 lake. Recovery efforts include the release of maturing adults into the
 lake for volitional spawning. The lake is also inhabited by a population
 of resident O. nerka that is genetically indistinguishable, but
 phenotypically smaller, to the maturing adults released into the lake. The
 resident population is difficult to sample and the reproductive patterns
 between the two groups are unknown. We used results of paired- and
 single-parentage assignments to specifically examine the reproductive
 patterns of male fish released into the lake under an equal sex ratio and
 a male-biased sex ratio. Assignment results of offspring leaving the lake
 indicated a reproductive shift by males under the two scenarios. Males
 displayed an assortative mating pattern under an equal sex ratio and
 spawned almost exclusively with the released females. Under a male-biased
 sex ratio most males shifted to a negative-assortative mating pattern and
 spawned with smaller females from the resident population. These males
 were younger and smaller than males that spawned with released females
 suggesting they were unable to compete with larger males for spawning
 opportunities with the larger, released females. The results provided
 insights into the reproductive behavior of this endangered population and
 has implications for recovery efforts.
DOI: 10.5061/dryad.g4f4qrfqg
title: A phylogeny of white-eyes based on ultraconserved elements

description: White-eyes are an iconic radiation of passerine birds that have been the
 subject of studies in evolutionary biology, biogeography, and speciation
 theory. Zosterops white-eyes in particular are thought
 to have radiated rapidly across continental and insular regions of the
 Afro- and Indo-Pacific tropics, yet, their phylogenetic history remains
 equivocal. Here, we sampled 77% of the genera and 47% of known white-eye
 species and sequenced thousands of ultraconserved elements to infer the
 phylogeny of the avian family Zosteropidae. We used concatenated maximum
 likelihood and species tree methods and found strong support for seven
 clades of white-eyes and three clades within the
 species-rich Zosterops radiation.
description: Target-capture of ultraconserved elements, following Faircloth et
 al. 2012 Syst Biol 61, 717
DOI: 10.6078/d1s415
title: Population genetics, demographic and evolutionary history of the Dudley’s lousewort, a rare redwood forest specialist (Pedicularis dudleyi)

description: Pedicularis dudleyi (Dudley’s Lousewort, Orobanchaceae) is an
 extremely rare wildflower endemic to the redwood forests of Central
 California. Until recently the species was known only from three extant
 natural populations. However, one of those populations was recently
 described as a novel species (P. rigginsiae D.J. Keil) based on
 morphological and ecological data leaving only two populations described
 as P. dudleyi. While little is known about the past distribution
 of the species, historical records have led to speculation that the
 species was once more widespread and may have suffered from habitat
 destruction as a result of widespread logging during the early twentieth
 century. We utilized a combination of ddRAD SNP and Sanger sequencing data
 to: 1) Describe the genetic diversity and population structure
 of P. dudleyi; 2) Test the hypothesis that the species
 underwent a bottleneck corresponding with increased logging of redwood
 forests in the early twentieth century and; 3) Test the morphological
 hypothesis that P. rigginsiae is distinct
 from P. dudleyi. Genetic diversity statistics and
 analyses of genetic structure suggest that both populations of P.
 dudleyi are highly differentiated from each other. Demographic
 modeling supports a scenario where the contemporary rarity of the species
 is explained by a recent bottleneck. Finally, recognition of P.
 rigginsiae as distinct from P. dudleyi is
 supported, increasing the conservation priority of both species.
description: ddRADseq libraries were constructed following a modified version
 of the protocol described in Peterson et al.(2012)where amplification was
 performed prior to size selection. 500150 ng of genomic DNA were digested
 using the restriction enzymes EcoRI and SphI-HF.P1 and P2 flex adapters
 were ligated to the digested DNA. Ligation products with similar
 concentrations were combined into a total of eight pools with each pool
 containing 1024 samples. Each pool was then divided, and PCR amplified in
 eight separate 25ul reactions using dual indexed PCR primers as described
 in Meyer and Kircher(2010). After amplification, indexed libraries were
 then re-pooled, quantified using qPCR and combined in equimolar ratios.
 The final library was size-selected for 750bp and the final Illumina
 library was sequenced by Novogene at the UC Davis Sequencing Center on a
 single lane of Illumina HiSeq X Ten(150bp, paired-end). The files included
 here include the final SNP data set formatted for STRUCTURE, GENPOP, and
 DIYABC and VCF.a Phylogenetic data includes aligned
 gene sequences for the concatenated ITS and the matK-5trnK intron
 dataset.
DOI: 10.5061/dryad.rv15dv484
title: Stable species and interactions in plant-pollinator networks deviate from core position in fragmented habitats

description: Species and their interactions are more dynamic over time and space in
 fragmented habitats than in continuous habitats. In fragmented habitats,
 the low nestedness of mutualistic networks may be related to the position
 change of stable (high persistence over time/space) species and
 interactions in the networks. Previous studies have shown
 that stable species and interactions tend to be in the core
 position of mutualistic networks. However, in fragmented habitats, it
 remains unknown whether stable species or interactions still tend to be in
 the core position. To address this gap, here we evaluated the
 correlation between the position of proximity to the network core and the
 temporal/spatial stability of species and interactions, using the
 observation of 42 plant-pollinator networks conducted in a fragmented
 island landscape over 3 years. We showed that temporally/spatially stable
 species and interactions deviated from the network core to varying
 degrees. Temporally stable plants were most likely to deviate from the
 network core, followed by pollinators and interactions, while only
 spatially stable pollinators tend to deviate from the network core. When
 unstable species (present in few time/space points, typically specialists)
 and interactions occupy the network core, they cannot interact with most
 species in the network as generalists do, resulting in the decrease of
 network nestedness. Therefore, from the perspective of position and
 stability, stable species and interactions deviate from the network core
 in fragmented habitats, which is an important reason for the decrease of
 nestedness in mutualistic networks. Our study suggests that
 protecting plants that occupy the core in large plant-pollinator networks
 is essential for maintaining the network persistence in fragmented
 habitats.
description: The dataset contains 3 files:
 “1_linner_regression”, “2_null_model_background_data” and
 “3_span_1CV”. 1. File
 “1_linner_regression”: The file contains the data of the
 position-stability correlation of plants (Fig. 3a), pollinators (Fig. 3b)
 and interactions (Fig. 3c) over time and space on 41 studied islands and
 the mainland, and also contains R code of linear regressions for the
 position-stability correlation against island area (ln-transformed, ha)
 and island isolation (ln-transformed, m). In addition, for the stability
 of interactions, the data contains the data of the results using the
 method of removing rare interactions and using the previous method 1/CV.
 The corresponding R script file was
 “linner_regression.R”. 2. File
 “2_null_model_background_data”: The file contains the data and R code for
 null model networks. The corresponding R script files were
 “function_of_null_model_network.R” and
 “null_model_R_code.R”. 3. File
 “3_span_1CV”: The file contains the data and R code for calculating the
 stability using our proposed method 1/CV. The corresponding R script file
 was “temporal_spatial_span_CV.R”.
DOI: 10.5061/dryad.98sf7m0jd
title: Humpback whale adult females and calves balance acoustic contact with vocal crypsis during periods of increased separation

description: Acoustic communication is important for animals with dependent young,
 particularly when they are spatially separated. Maternal humpback whales
 (Megaptera novaeangliae) use acoustic calling to help minimise the risk of
 separation from their young calves during migration. These pairs also use
 acoustic crypsis to minimise detection by males. How they balance a
 restricted active space with the need to maintain acoustic contact during
 periods of separation is not yet understood. Here, we analysed movement
 metrics of tagged adult female-calf pairs during migration to identify two
 behavioural states, ‘resting/milling’ and ‘travelling’. When travelling,
 these pairs dived synchronously and exhibited little to no spatial
 separation. Alternatively, adult females had significantly longer dive
 durations (p &lt; 0.01) when resting, and while they spent prolonged
 times at depth, calves would surface several times independently. This
 demonstrated that these pairs are frequently separated during periods of
 rest. We then determined if the call rates and acoustic levels of these
 pairs increased with more frequent separation, finding that both adult
 females and calves significantly increased their call rates, but not
 levels, when resting. We also found that adult female-calf pairs have a
 restricted active space, with less than 15% of calls estimated to be
 detectable beyond 2 km. However, as with call level, detection distance
 did not differ significantly between the two behavioural states. In
 summary, adult female-calf pairs maintain successful communication during
 periods of separation by calling more frequently rather than by producing
 louder calls. This strategy aids in maintaining acoustic contact while
 simultaneously limiting detectability by conspecifics.
description: This dataset was collected using animal-borne recording tags and
 accompanying boat- and land-based visual observations, as well as
 recordings from a moored hydrophone array. The non-hierarchical
 partitioning clustering method ‘k-means’ was used to determine adult
 female-calf behavioural states; a <em>glmer</em> was used to
 examine whether fine-scale dive parameters of the adult females were
 significantly different between behavioural states;
 <i>GLMM'</i><em>s</em> were used to determine
 if call rate (calls per hour) varied per individual between behavioural
 states; an <em>lmer</em> was used to determine if adult
 females modified their received call levels (dB <em>re </em>1
 µPa) in response to the behavioural state of the pair; and a site-specific
 frequency- and distance-dependent transmission loss equation was used
 to determine the communication active space of adult female-calf vocal
 signals, while a <em>glmer </em>was used to determine whether
 these pairs modified this active space in response to their behavioural
 state.
description: Please see the README document for information regarding the data
 spreadsheets.
DOI: 10.5061/dryad.tdz08kq0j
title: Reversal learning in FTD (fMRI)

description: Objective: Frontotemporal Dementia (FTD) is a neurodegenerative disorder
 that results in disinhibition and difficulty with flexible responding when
 provided feedback. Inflexible responding is observed early in the course
 of the illness and contributes to the financial and social morbidities of
 FTD. Reversal learning is an established cognitive paradigm that
 indexes flexible responding in the face of feedback signaling a change in
 reinforcement contingencies, with components of reversal learning
 associated with specific neurotransmitter systems. The objective of the
 study was to evaluate the neural mechanisms underlying impaired flexible
 behavioural responding in FTD using a reversal learning paradigm combined
 with fMRI. Methods: Twenty-two patients meeting the diagnostic criteria
 for FTD and twenty-one healthy controls completed the study. Participants
 completed an fMRI-adapted reversal learning task that indexes behavioural
 flexibility when provided positive and negative feedback. Results:
 Patients with FTD demonstrated poorer behavioural flexibility relative to
 controls and abnormal BOLD responses within the left ventrolateral
 prefrontal cortex to incorrect responses made during the learning phase,
 and during correct responses when reward contingencies were reversed. As
 well, patients showed decreased activity within the left dorsal lateral
 prefrontal cortex to incorrect responses compared to controls.
 Conclusions: These findings suggest that reversal learning impairments in
 patients with FTD, in particular those with frontal predominant atrophy,
 may be related to impaired flexible motor responding when selecting among
 several choices and deficient attention to relevant stimuli during
 instances of conflict (i.e. receiving negative feedback). These results
 and the associated neurotransmitter systems mediating these regions may
 provide targets for future pharmacological or behavioural interventions
 mediating these cognitive deficits.
DOI: 10.6076/d14k5x
title: Mutualism-enhancing mutations dominate early adaptation in a two-species microbial community

description: Species interactions drive evolution while evolution shapes these
 interactions. The resulting eco-evolutionary dynamics, their outcomes and
 their repeatability depend on how adaptive mutations available to
 community members affect fitness and ecologically relevant traits.
 However, the diversity of adaptive mutations is not well characterized,
 and we do not know how this diversity is affected by the ecological
 milieu. Here we use barcode lineage tracking to address this gap in a net
 commensal relationship that contains both competitive and mutualistic
 aspects between the yeast Saccharomyces cerevisiae and the alga
 Chlamydomonas reinhardtii. We find that yeast has access to many adaptive
 mutations with diverse ecological consequences, in particular, those that
 increase and reduce the yields of both species. The presence of the alga
 does not change which mutations are adaptive in yeast (i.e., there is no
 fitness trade-off for yeast between growing alone or with alga), but
 rather shifts selection to favor yeast mutants that increase the yields of
 both species and make the mutualism stronger. Thus, in the presence of the
 alga, adaptations contending for fixation in yeast are more likely to
 enhance the mutualism, even though cooperativity is not directly favored
 by natural selection in our system. Our results demonstrate that
 ecological interactions not only alter the trajectory of evolution but
 also dictate its repeatability; in particular, weak mutualisms can
 repeatably evolve to become stronger.
DOI: 10.5061/dryad.k3j9kd57f
title: Temperature-mediated variation in selection on offspring size: a multi-cohort field study

description: Offspring size is a key life history trait that often covaries negatively
 with temperature. Most studies focus on how temperature alters selection
 on offspring size during early life history stages such as embryos or
 larvae. The degree to which temperature alters the relationship between
 offspring size and post-metamorphic performance remains unclear as field
 studies across multiple temperature regimes are rare. I deployed over 6000
 individuals of known offspring size, into the field across 28 cohorts
 spanning 4 years for the model marine invertebrate, Bugula
 neritina and monitored their survival, growth and reproduction.
 Offspring size closely tracked the local environmental temperature across
 cohorts. This offspring size-temperature covariance appeared to be
 adaptive, at least from the perspective of mothers. When temperatures were
 warmer, the relationship between offspring size and performance was weak;
 when temperatures were cooler, the relationship was strongly positive.
 Estimates of selection based on maternal fitness differed from those based
 on offspring fitness, suggesting temperature-mediated parent-offspring
 conflict over offspring provisioning exists. I also found evidence for
 temporal autocorrelation in temperature and selection on offspring size.
 That temperature affects the relationship between offspring size and
 post-metamorphic performance further complicates the challenge in
 understanding the ubiquitous covariance between offspring size and
 temperature.
DOI: 10.15468/dl.4gcskb
title: Occurrence Download

description: A dataset containing 182581 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence, Living Specimen)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Sabal, Schippia, Zombia, Trithrinax, Coccothrinax, Hemithrinax, Leucothrinax, Chelyocarpus, Cryosophila, Itaya, Sabinaria, Phoenix, Chamaerops, Guihaia, Trachycarpus, Rhapidophyllum, Maxburretia, Rhapis, Livistona, Licuala, Johannesteijsmannia, Pholidocarpus, Saribus, Lanonia, Acoelorrhaphe, Serenoa, Brahea, Colpothrinax, Copernicia, Pritchardia, Washingtonia, Chuniophoenix, Kerriodoxa, Nannorrhops, Tahina, Caryota, Arenga, Corypha, Bismarckia, Satranala, Hyphaene, Medemia, Latania, Lodoicea, Borassodendron, Borassus)"
 ]
}

 The dataset includes 182581 records from 582 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002831-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.