cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.70rxwdbtk
title: Experimental facilitation of heat loss affects work rate and innate immune function in a breeding passerine bird

description: The capacity to get rid of excess heat produced during hard work is a
 possible constraint on parental effort during reproduction (heat
 dissipation limit [HDL] theory). We released hard-working blue tits
 (Cyanistes caeruleus) from this constraint by experimentally removing
 ventral plumage. We then assessed if this changed their reproductive
 effort (feeding rate and nestling size) and levels of self-maintenance
 (change in body mass and innate immune function). Feather-clipped females
 reduced the number of feeding visits and increased levels of constitutive
 innate immunity compared to unclipped females but did not fledge smaller
 nestlings. Thus, they increased self-maintenance without compromising
 current reproductive output. In contrast, feather-clipping did not affect
 the number of feeding visits or innate immune function in males, despite
 increased heat loss rate. Our results show that analyses of physiological
 parameters, such as constitutive innate immune function, can be important
 when trying to understand sources of variation in investment in
 self-maintenance versus reproductive effort and that risk of overheating
 can influence innate immune function during reproduction.
description: Field data (feeding frequency, biometrics and body temperature)
 and laboratory measurements on innate immune function collected during
 breeding season 2017. Feeding rates have been filtered according to
 methods described in the paper. 
description: The attached Excel-file should be self explanatory. Headings that
 could be hard to interpret are explained in a separate data
 sheet. See methods in the paper for sample sizes and
 missing data.
DOI: 10.5061/dryad.g4f4qrfmn
title: Variation in brown rat cranial shape shows directional selection over 120 years in New York City

description: Urbanization exposes species to novel environments and selection pressures
 that may change morphological traits within a population.  We
 investigated how the shape and size of crania and mandibles changed over
 time within a population of brown rats (Rattus norvegicus) living in
 Manhattan, New York, USA, a highly urbanized environment.  We
 measured 3D landmarks on the cranium and mandible of 62 adult individuals
 sampled in the 1890s and 2010s.  Static allometry explained
 approximately 22% of shape variation in crania and mandible datasets,
 while time accounted for approximately 14% of variation. We did not
 observe significant changes in skull size through time or between the
 sexes.  Estimating the P-matrix revealed that directional
 selection explained temporal change of the crania but not the
 mandible.  Specifically, rats from the 2010s had longer noses and
 shorter upper molar tooth rows, traits identified as adaptive to colder
 environments and higher quality or softer diets, respectively. 
 Our results highlight the continual evolution to selection
 pressures.  We acknowledge that urban selection pressures
 impacting cranial shape likely began in Europe prior to the introduction
 of rats to Manhattan.  Yet, our study period spanned changes in
 intensity of artificial lighting, human population density, and human
 diet, thereby altering various aspects of rat ecology and hence pressures
 on the skull.
description: 3D landmark data was taken with a microscribe on brown rat crania
 and mandibles.  Dorsal and ventral landmarks were merged into a single
 shape using MorphoJ.  Data were analyzed in R with the geomorph
 package. SFS of ddRAD-Seq data for 248 rats from NYC
 included for estimation of Ne.
description: Missing landmarkers in cranial and mandible datasets denoted by
 -999 -999 -999 (for x,y,z coordinates).
DOI: 10.5061/dryad.stqjq2c0q
title: Intercontinental long‐distance seed dispersal across the Mediterranean Basin explains population genetic structure of a bird‐dispersed shrub

description: Long-distance dispersal (LDD) is a pivotal process for plants determining
 their range of distribution and promoting gene flow among distant
 populations. Most fleshy-fruited species rely on frugivorous vertebrates
 to disperse their seeds across the landscape. While LDD events are
 difficult to record, a few ecological studies have shown that birds move a
 sizeable number of ingested seeds across geographic barriers, such as sea
 straits. The foraging movements of migrant frugivores across distant
 populations, including those separated by geographic barriers, creates a
 constant flow of propagules that in turn shapes the spatial distributions
 of the genetic variation in populations. Here, we have analysed the
 genetic diversity and structure of 74 populations of Pistacia lentiscus, a
 fleshy-fruited shrub widely distributed in the Mediterranean Basin, to
 elucidate whether the Mediterranean Sea acts as a geographic barrier or
 alternatively whether migratory frugivorous birds promote gene flow among
 populations located on both sides of the sea. Our results show reduced
 genetic distances among populations, including intercontinental
 populations, and they show a significant genetic structure across an
 eastern-western axis. These findings are consistent with known bird
 migratory routes that connect the European and African continents
 following a north-southwards direction during the fruiting season of many
 fleshy-fruited plants. Further, Approximate Bayesian Analysis failed to
 explain the observed patterns as a result of historical population
 migrations at the end of Last Glacial Maximum. Therefore, anthropic and/or
 climatic changes that would disrupt the migratory routes of frugivorous
 birds might have genetic consequences for the plant species they feed
 upon.
description: Genotypes obtained from microsatellite analysis for
 <em>Pistacia lentiscus</em> populations
DOI: 10.5061/dryad.hx3ffbgb9
title: Trophic cascades alter eco-evolutionary dynamics and body size evolution

description: Trait evolution in predator-prey systems can feed back to the dynamics of
 interacting species as well as cascade to impact the dynamics of
 indirectly linked species (eco-evolutionary trophic cascades; EETC). A key
 mediator of trophic cascades is body mass, as it both strongly influences
 and evolves in response to predator-prey interactions. Here we use
 Gillespie Eco-Evolutionary Models to explore EETCs resulting from top
 predator loss and mediated by body mass evolution. Our four trophic level
 food chain model uses allometric scaling to link body mass to different
 functions (ecological pleiotropy) and is realistically parameterized from
 the FORAGE database to mimic the parameter space of a typical freshwater
 system. To track real-time changes in selective pressures, we also
 calculated fitness gradients for each trophic level. As predicted, top
 predator loss generated alternating shifts in abundance across trophic
 levels, and depending on the nature and strength in changes to fitness
 gradients, also altered trajectories of body mass evolution. Although more
 distantly linked, changes in the abundance of top predators still affected
 the eco-evolutionary dynamics of the basal producers, in part because of
 their relatively short generation times. Overall, our results suggest that
 impacts on top predators can set off transient eco-evolutionary trophic
 cascades with the potential for widespread indirect impacts on food webs.
description: MatLab files used to create eco-evolutionary trophic cascades in
 the GEM model.
DOI: 10.5061/dryad.nvx0k6dp1
title: Morphological and molecular evidences to segregation disjunct species of Hymenophyllum ( Hymenophyllaceae ) from Southern South America

description: — Morphological studies and molecular phylogenetic analyses were carried
 out to examine the taxonomic position of Hymenophyllum caudiculatum , a
 species with disjunct distributions in South America. This species is
 found in tropical and subtropical forest of Brazil and in temperate forest
 of southern Argentina and Chile. Based on results obtained from
 morphological, molecular, and species delimitation analyses, Hymenophyllum
 caudatum , from the Valdivian forest of southern Chile and Argentina, is
 proposed as a species separate from H. caudiculatum , endemic of Brazil.
 Their diagnostic characters are respectively: nonalate stipe 1–5 cm long
 (vs. nonalate stipe 0.3–1 cm long in H. cuadiculatum ); stipe wings
 gradually ending (vs. stipe wings abruptly ending very near to the
 rhizome); margin entire to somewhat undulate (vs. margin undulate to
 crispate); soriferous segment alate, angostate or null (vs. soriferous
 segment with laminar constriction in the apex); widely obovoid receptacle
 with sessile sporangia (vs. flattened obovoid or globose receptacle with
 shortly pedunculated sporangia). A key to identify both species herein
 recognized, and a map containing geographical distribution of them are
 provided, together with nomenclatural revision, description, illustration
 and conservation status of the two recognized species.
DOI: 10.5061/dryad.1ns1rn8qq
title: Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution

description: The within-host evolutionary dynamics of TB remain unclear, and underlying
 biological characteristics render standard population genetic approaches
 based upon the Wright-Fisher model largely inappropriate. In addition, the
 compact genome combined with an absence of recombination is expected to
 result in strong purifying selection effects. Thus, it is imperative to
 establish a biologically-relevant evolutionary framework incorporating
 these factors in order to enable an accurate study of this important human
 pathogen. Further, such a model is critical for inferring fundamental
 evolutionary parameters related to patient treatment, including mutation
 rates and the severity of infection bottlenecks. We here implement such a
 model and infer the underlying evolutionary parameters governing
 within-patient evolutionary dynamics. Results demonstrate that the progeny
 skew associated with the clonal nature of TB severely reduces genetic
 diversity and that the neglect of this parameter in previous studies has
 led to significant mis-inference of mutation rates. As such, our results
 suggest an underlying de novo mutation rate that is
 considerably faster than previously inferred, and a progeny distribution
 differing significantly from Wright-Fisher assumptions. This inference
 represents a more appropriate evolutionary null model, against which the
 periodic effects of positive selection, associated with drug-resistance
 for example, may be better assessed.
description: Table S1. Simulation results. These data
 were generated using SLiM v.3. The script used for generating the data is
 also attached here. Simulations were run through R and
 statistics were estimated, from ms files, using the R-package
 PopGenome. Parameters simulated in the table
 are ordered by descending mutation rate (<i>μ</i>) and
 corresponding values of progeny skew (<i>Ψ</i>) and bottleneck
 severity (<i>N2</i>). Given are the mean and standard
 deviation of the summary statistics from 1000 replicates.
  
description: The last column from Table_S1 was not generated with PopGenome,
 but by counting the number of simulations that had zero segregating sites
 (given as percentage of invariables by parameter set).
DOI: 10.15468/dl.cy97nv
title: Occurrence Download

description: A dataset containing 1845 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Retropinna retropinna",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 1845 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002265-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zcrjdfn7c
title: Duncan and Rausher 2020

description: Data set for Figures 2-4 from Duncan and Rausher, Selection. favors loss
 of floral pigmentation in a highly selfing morning glory.  Data
 are for qPCR and pyrosequencing of anthocyanin pathway genes, and
 microsatellite genotypes for plants from various study sites.
description: Methods are described in the associated manuscript.
DOI: 10.5061/dryad.bzkh1895m
title: Fruit preferences by fishes in a Neotropical floodplain

description: The diets of frugivorous animals result from the interaction between
 feeding preference and ecological factors such as availability of
 alternative resources and interactions with other frugivores. A better
 understanding of frugivore diets will enable predictions about the
 vulnerability of plant populations to anthropogenic or natural
 environmental changes. In addition, frugivores with greater variation in
 diet (generalists) are potentially more resilient to habitat changes than
 specialists. Here, we combined data on diets of frugivorous fishes with
 visual censuses on fruit availability to evaluate if fishes are selective
 or opportunistic in their use of fruits in floodplain habitats. We found a
 high diversity of fruit species (74 species) frequently consumed by four
 common species of frugivorous fishes during the flooding season. The
 identity of preferred fruits, rather than their availability, had a
 stronger effect on the patterns of fruit consumed by fishes in this
 system. Fruit preferences by fish may influence the long-term persistence
 and the maintenance of plant diversity in floodplain habitats. Possible
 disturbances of fish populations with selective consumption and the plant
 populations on which they depend could increase the vulnerability of both
 populations involved. Thus, selectivity may affect ecological and
 evolutionary processes associated with frugivory by fish.
DOI: 10.5061/dryad.cfxpnvx2s
title: Phylogeny of the Eocene Antarctic Tapetinae Gray, 1851 (Bivalvia: Veneridae) from the La Meseta and Submeseta formations

description: Systematic analysis shows that the Southern Hemisphere bivalve genus
 Retrotapes includes the Antarctic species R. antarcticus, R. newtoni, and
 R. robustus and recognizes for the first time the presence of Katelysia
 represented by K. florentinoi. Two new genera were erected in this study:
 Marciachlys new genus to include M. inflata new combination, and Adelfia
 new genus, which includes A. austrolissa new combination and A. omega new
 species from the Eocene of Antarctica, and the late Eocene Chilean A.
 arenosa new combination. Eurhomalea carlosi was synonymized with K.
 florentinoi; Cyclorismina marwicki with R. antarcticus; Gomphina iheringi
 was considered an indeterminate species; and Cockburnia lunulifera was
 excluded from the Tapetinae. These systematic assignments are supported by
 a phylogenetic analysis, which recognizes an Austral clade of Tapetinae,
 comprising all the genera mentioned above, and additionally Marcia,
 Paleomarcia, Atamarcia, and Protapes.
description: During the 2014
 expedition to Marambio Island, more than 640 specimens of the studied
 species were collected at 33 localities (Fig. 1) distributed along all the
 allomembers defined by Marenssi (1998a). Precise information about the
 mentioned localities is available in Appendix 1. We also used the material
 donated by W. Zinsmeister to the MACN-Pi collection, which was collected
 during the field seasons 1990–1994. Most of the materials collected by W.
 Zinsmeister and J. Stilwell are housed at the Paleontological Research
 Institute (PRI), and were recently studied by CJR, who noted that said
 materials are currently being reclassified and renumbered. For this
 reason, we decided to not include these specimens in our analysis,
 considering that the materials housed at the MACN-Pi collection and the
 new materials collected in the Field Season 2014 deposited in the IAA are
 sufficient to perform the present study.            
 Geographic and stratigraphic distributions of each studied species are
 summarized in Supplementary Data Set 1, and the materials corresponding to
 taxa used for comparison and phylogenetic analysis are summarized in
 Supplementary Data Set 2.
DOI: 10.5061/dryad.931zcrjgp
title: Data from: Co-occurrence of bobcats, coyotes, and ocelots in Texas

description: Interspecific competition among carnivores has been linked to differences
 in behavior, morphology, and resource use. Insights into these
 interactions can enhance understanding of local ecological processes that
 can have impacts on the recovery of endangered species, such as the ocelot
 (Leopardus pardalis). Ocelots, bobcats (Lynx rufus), and coyotes (Canis
 latrans) share a small geographic range overlap from South Texas to
 south-central Mexico but relationships among the three are poorly
 understood. From May 2011 to March 2018, we conducted a camera trap study
 to examine co-occurrence patterns among ocelots, bobcats, and coyotes on
 the East Foundation’s El Sauz Ranch in South Texas. We used a novel
 multi-season extension to multi-species occupancy models with ≥2
 interacting species to conduct an exploratory analysis to examine
 interspecific interactions and examine the potential effects of
 patch-level and landscape-level metrics relative to the occurrence of
 these carnivores. We found strong evidence of seasonal mutual coexistence
 among all three species and observed a species-specific seasonal trend in
 detection. Seasonal coexistence patterns were also explained by increasing
 distance from a high-speed roadway. However, these results have important
 ecological implications for planning ocelot recovery in the rangelands of
 South Texas. This study suggests a coexistence among ocelots, bobcats, and
 coyotes under the environmental conditions on the El Sauz Ranch. Further
 research would provide a better understanding of the ecological mechanisms
 that facilitate coexistence within this community. As road networks in the
 region expand over the next few decades, large private working ranches
 will be needed to provide important habitat for ocelots and other
 carnivore species.
description: DataDryad_Lombardi_et_al- - Binary capture history used for
 analysis to conduct an exploratory analysis to examine interspecific
 interactions (avoidance/coexistence) and examine the potential effects of
 patch-level and landscape-level metrics relative to the occurrence of
 bobcats, coyotes and ocelots.  The binary capture history is based on 14
 seasons of five 4-week periods (five occasions) per season.
description: This dataset is for a multi-species, multi-season occupancy model
 of 2 or more interacting species. Spatial data - 1-m
 land cover classification for the study area used in the analysis for this
 research
DOI: 10.5061/dryad.w0vt4b8n1
title: Vasoactive intestinal peptide as a mediator of the effects of a supergene on social behavior

description: Supergenes, or linked groups of alleles that are inherited together,
 present excellent opportunities to understand gene-behavior relationships.
 In white-throated sparrows (Zonotrichia albicollis), a supergene on the
 second chromosome associates with a more aggressive and less parental
 phenotype. This supergene includes the gene for vasoactive intestinal
 peptide (VIP), a neuropeptide known to play a causal role in both
 aggression and parental behavior. Here, using a free-living population, we
 compared levels of VIP mRNA between birds with and without the supergene.
 We focused on the anterior hypothalamus and infundibular region, two brain
 regions containing VIP neurons known to play a causal role in aggression
 and parental behavior, respectively. First, we show that the supergene
 enhances VIP expression in the anterior hypothalamus and that expression
 positively predicts vocal aggression independently of genotype in both
 sexes. Next, we show that the supergene reduces VIP expression in the
 infundibular region, which suggests reduced secretion of prolactin, a
 pro-parental hormone. Thus, patterns of VIP expression in these two
 regions are consistent with the enhanced aggression and reduced parental
 behavior of birds with the supergene allele. Our results illustrate
 mechanisms by which elements of genomic architecture, such as supergenes,
 can contribute to the evolution of alternative behavioral phenotypes.
DOI: 10.5061/dryad.mcvdncjx7
title: Changes in multiple environmental factors additively enhance the dominance of an exotic plant with a novel trade-off pattern

description: 1. Whether global changes impact native and exotic species differently is
 unclear, because the changes may favour both native and exotic species
 over competitors. Previous studies have mainly focused on the separate
 effects of the different environmental changes, but plant communities are
 influenced by changes in multiple environmental factors, and it is still
 unclear whether native and exotic species respond similarly to the
 combined effects of these factors. 2. We hypothesized that differences in
 interspecific trade-offs between native and exotic species could lead to
 the dominance of exotic species when the species are simultaneously
 subjected to multiple environmental changes. 3. Using coastal saltmarsh
 plant communities as the study system, we experimentally manipulated
 flooding and nutrient enrichment, examined the interspecific trade-offs
 between competitiveness and stress tolerance for two native and one exotic
 species, and explored the combined effect of the two environmental changes
 on both native–native and native–exotic species interactions. 4. We found
 that flooding and nutrient enrichment oppositely affected native–native
 species interactions but additively affected native–exotic species
 interactions. The two factors together resulted in no net change in the
 relative advantages between the two native species but enhanced the
 dominance of the exotic species over the native species. This disparity
 occurred because the exotic species was not subject to the interspecific
 trade-off between competitiveness and stress tolerance that constrained
 the native species. 5. Synthesis. Our results suggest that changes in
 multiple environmental factors favour exotic species because of
 evolutionary novel trade-off patterns. Mechanisms underlying species
 coexistence in the invaded community such as interspecific trade-offs
 should be considered when researchers attempt to predict the effects of
 global changes on biological invasions.