cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g42qs
title: Data from: The rate test of speciation: estimating the likelihood of non-allopatric speciation from reproductive isolation rates in Drosophila

description: Among the most debated subjects in speciation is the question of its mode.
 Although allopatric (geographical) speciation is assumed the null model,
 the importance of parapatric and sympatric speciation is extremely
 difficult to assess and remains controversial. Here I develop a novel
 approach to distinguish these modes of speciation by studying the
 evolution of reproductive isolation (RI) among taxa. I focus on the
 Drosophila genus, for which measures of RI are known. First, I incorporate
 RI into age-range correlations. Plots show that almost all cases of weak
 RI are between allopatric taxa whereas sympatric taxa have strong RI. This
 either implies that most reproductive isolation (RI) was initiated in
 allopatry or that RI evolves too rapidly in sympatry to be captured at
 incipient stages. To distinguish between these explanations, I develop a
 new “rate test of speciation” that estimates the likelihood of
 non-allopatric speciation given the distribution of RI rates in allopatry
 versus sympatry. Most sympatric taxa were found to have likely initiated
 RI in allopatry. However, two putative candidate species pairs for
 non-allopatric speciation were identified (5% of known Drosophila). In
 total, this study shows how using RI measures can greatly inform us about
 the geographical mode of speciation in nature.
description: Supl. Table
 S1Supl. Table
 S2
DOI: 10.5061/dryad.bp20k
title: Data from: Mutations in COL1A1 and COL1A2 and dental aberrations in children and adolescents with osteogenesis imperfecta - a retrospective cohort study

description: Osteogenesis imperfecta (OI) is a heterogeneous group of disorders of
 connective tissue, caused mainly by mutations in the collagen I genes
 (COL1A1 and COL1A2). Dentinogenesis imperfecta (DGI) and other dental
 aberrations are common features of OI. We investigated the association
 between collagen I mutations and DGI, taurodontism, and retention of
 permanent second molars in a retrospective cohort of 152 unrelated
 children and adolescents with OI. The clinical examination included
 radiographic evaluations. Teeth from 81 individuals were available for
 histopathological evaluation. COL1A1/2 mutations were found in 104
 individuals by nucleotide sequencing. DGI was diagnosed clinically and
 radiographically in 29% of the individuals (44/152) and through isolated
 histological findings in another 19% (29/152). In the individuals with a
 COL1A1 mutation, 70% (7/10) of those with a glycine substitution located
 C-terminal of p.Gly305 exhibited DGI in both dentitions while no
 individual (0/7) with a mutation N-terminal of this point exhibited DGI in
 either dentition (p = 0.01). In the individuals with a COL1A2 mutation,
 80% (8/10) of those with a glycine substitution located C terminal of
 p.Gly211 exhibited DGI in both dentitions while no individual (0/5) with a
 mutation N-terminal of this point (p = 0.007) exhibited DGI in either
 dentition. DGI was restricted to the deciduous dentition in 20
 individuals. Seventeen had missense mutations where glycine to serine was
 the most prevalent substitution (53%). Taurodontism occurred in 18% and
 retention of permanent second molars in 31% of the adolescents. Dental
 aberrations are strongly associated with qualitatively changed collagen I.
 The varying expressivity of DGI is related to the location of the collagen
 I mutation. Genotype information may be helpful in identifying individuals
 with OI who have an increased risk of dental aberrations.
description: Dataset
 1703312017-03-31 List of the
 variables in the supplementary dataset and explanation of the
 coding
DOI: 10.5061/dryad.2n96q
title: Data from: Song structure, not high-frequency song content, determines high-frequency auditory sensitivity in nine species of New World sparrows (Passeriformes: Emberizidae)

description: 1. The evolution of vocal signals can be constrained by a host of factors
 including habitat effects on sound propagation, morphology of
 sound-producing structures, and phylogenetic relationships among species.
 Here, we asked whether auditory sensitivity over a broad range of
 frequencies correlates with the spectral content of conspecific
 vocalizations, or whether it is constrained by the overall structure of
 vocalizations, habitat effects on sound propagation, or relatedness among
 species. 2. We studied nine New World sparrows (Passeriformes:
 Emberizidae) including three open-habitat species, three scrub-like
 habitat species, and three forest species. For each habitat, one species
 had pure trilled songs, another had tonal songs, and another had complex
 songs with tones, trills, and amplitude-modulated buzzes. 3. As predicted
 by the acoustic adaptation hypothesis, song spectral properties
 (specifically frequency and entropy) had the highest values in
 open-habitat species and the lowest values in forest species. 4. Based on
 our results from song analyses, and the sender-receiver matching
 hypothesis, we predicted that open-habitat species would be more sensitive
 to high-frequency sounds compared to forest species. Contrary to this
 prediction, habitat and high-frequency song content had little effect on
 audiogram shape. Song type, however, had a strong effect, with species
 that produce complex songs showing higher sensitivity to high-frequency
 sounds than all other species. 5. Our results suggest that the use of song
 frequency by receivers depends on song structure and not necessarily on
 song spectral content. Therefore, our current understanding of how
 signal-processing mechanisms should match signal properties appears to be
 too simple. When thinking about the evolution of signal-processing
 mechanisms, the multidimensionality of signals, and how the different
 dimensions can interact, should be considered.
description: Song spectral properties
 and hearing sensitivity dataThe excel file contains
 data on song spectral properties and auditory sensitivity of nine species
 of New world sparrows. The spreadsheet labeled as “Metadata” contains the
 abbreviations of species names used in the “Acoustical Analyses” and
 “Auditory Evoked Potentials” spreadsheets. The dates in the “Auditory
 Evoked Potentials” spreadsheet correspond to the date in which each
 subject was tested.Song_and_Hearing_data_for_archiving.xlsx
DOI: 10.5061/dryad.72c40
title: Data from: Increased soluble IL-7 receptor concentrations associate with improved IL-7 therapy outcomes in SIV-infected ART-treated Rhesus macaques

description: The use of interleukin-7 (IL-7) as an immunorestorative therapeutic has
 proven effective in HIV infection, cancer and bone marrow transplantation.
 Mediating its activity through membrane-bound IL-7 receptor α (mCD127),
 IL-7 therapy increases T-cell numbers and survival. A soluble form,
 sCD127, is found in plasma, and we have previously identified increased
 plasma sCD127 concentrations in HIV infection. Furthermore, patients with
 high sCD127 exhibited the best viral control, implicating a role for IL-7
 or sCD127 directly in improved virologic/immunologic outcomes. The role of
 the cytokine IL-7 in elevating sCD127 levels was addressed here through
 assessment of retrospective samples obtained from SIV-infected
 antiretroviral (ART)-treated Rhesus macaques. IL-7 was administered in
 clustered weekly doses, allowing for an assessment prior, during and
 following IL-7 administration. The levels of sCD127 remained relatively
 unchanged during both early SIV infection and following initiation of ART.
 However, treatment with IL-7 increased sCD127 concentrations in most
 animals, transiently or persistently, paralleling increased T-cell
 numbers, correlating significantly with CD8+ T-cell levels. In addition,
 proliferating CD4+ or CD8+ T-cells (measured by Ki67) increased in
 association with elevated sCD127 concentrations. Finally, a high
 concentration of sCD127 in IL7-treated animals was associated with
 increased retention of T-cells (measured by BrDU). In addition, a lack, or
 loss of viral control was associated with more pronounced and frequent
 elevations in plasma sCD127 concentrations with IL-7 therapy. In summary,
 plasma sCD127 levels in SIV-infected ART-treated macaques was associated
 with therapeutic IL-7 administration, with higher sCD127 levels in
 macaques demonstrating the best T-cell responses. This study furthers our
 knowledge regarding the interrelationship between increased IL-7 levels
 and elevated sCD127 levels that may have implications for future IL-7
 immunotherapeutic approaches in HIV-infected patients.
description: Raw data for online
 uploadThis file contains the
 raw data for all of the data figures in this
 manuscript.
DOI: 10.5061/dryad.hm054m5
title: Data from: Does batrachotoxin autoresistance co-evolve with toxicity in Phyllobates poison-dart frogs?

description: Toxicity is widespread among living organisms, and evolves as a multimodal
 phenotype. Part of this phenotype is the ability to avoid
 self-intoxication (autoresistance). Evolving toxin resistance can involve
 fitness tradeoffs, so autoresistance is often expected to evolve gradually
 and in tandem with toxicity, resulting in a correlation between the
 degrees of toxicity and autoresistance among toxic populations. We
 investigate this correlation in Phyllobates poison frogs, notorious for
 secreting batrachotoxin (BTX), a potent neurotoxin that targets sodium
 channels, using ancestral sequence reconstructions of BTX-sensing areas of
 the muscular voltage-gated sodium channel. Reconstructions suggest that
 BTX resistance arose at the root of Phyllobates, coinciding with the
 evolution of BTX secretion. After this event little or no further
 evolution of autoresistance seems to have occurred, despite large
 increases in toxicity throughout the history of these frogs. Our results
 therefore provide no evidence in favor of an evolutionary correlation
 between toxicity and autoresistance, which conflicts with previous work.
 Future research on the functional costs and benefits of mutations
 putatively involved in BTX resistance, as well as their prevalence in
 natural populations should shed light on the evolutionary mechanisms
 driving the relationship between toxicity and autoresistance in
 Phyllobates frogs.
description: MarquezBTXEvolution2018Alignments, trees, and other input files used.
DOI: 10.5061/dryad.g5g43
title: Data from: On the Coyne and Orr-igin of species: effects of intrinsic postzygotic isolation, ecological differentiation, X-chromosome size, and sympatry on Drosophila speciation

description: Coyne and Orr found that mating discrimination (premating isolation)
 evolves much faster between sympatric than allopatric Drosophila species
 pairs. Their meta-analyses established that this pattern, expected under
 reinforcement, is common and that Haldane's rule is ubiquitous in
 Drosophila species divergence. We examine three possible contributors to
 the reinforcement pattern: intrinsic postzygotic isolation, dichotomized
 as to whether hybrid males show complete inviability/sterility; host-plant
 divergence, as a surrogate for extrinsic postzygotic isolation; and X
 chromosome size, whether roughly 20% or 40% of the genome is X-linked. We
 focus on “young” species pairs with overlapping ranges, contrasted with
 allopatric pairs. Using alternative criteria for “sympatry” and tests that
 compare either level of prezygotic isolation in sympatry or frequency of
 sympatry, we find no statistically significant effects associated with X
 chromosome size or our coarse quantifications of intrinsic postzygotic
 isolation or ecological differentiation. Although sympatric speciation
 seems very rare in animals, the pervasiveness of the reinforcement pattern
 and the commonness of range overlap for close relatives indicate that
 speciation in Drosophila is often not purely allopatric. It remains to
 determine whether increased premating isolation with sympatry results from
 secondary contact versus parapatric speciation and what drives this
 pattern.
description: CoynOrriginDat_funkRaw data for all analyses using data from Funk et al 2006 (PNAS 103 : 3209–3213) when Funk and Yukilevich data conflict.CoynOrriginDat_romanRaw data for all analyses using data from Yukilevich 2012 (Evolution 66: 1430-1446) when Funk and Yukilevich data conflict.FitzpatrickControlAn R script with a simple implementation of the Fitzpatrick and Turelli 2006 (Evolution 60:601-615) control for phylogenetic non-independence of pairwise interspecific comparisons.minFTexampleA minimal example to run FitzpatrickControl.
DOI: 10.15468/dl.jujzhf
title: Occurrence Download

description: A dataset containing 2209 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.18.10_1",
 "OccurrenceStatus is Present",
 "Year 2000-2024"
 ]
}

 The dataset includes 2209 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001016-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8jr73
title: Data from: Trait responses to AM fungi are stronger and more consistent than fixed differences among populations of Asclepias speciosa

description: Premise of the study: Arbuscular mycorrhizal (AM) fungi can promote plant
 growth and reproduction, but other plant physiological traits or traits
 that provide defense against herbivores can also be affected by AM fungi.
 However, whether responses of different traits to AM fungi are correlated,
 and whether these relationships vary among plants from different
 populations is unresolved. Methods: We assessed whether different
 populations of the perennial forb, Asclepias speciosa, grown from seed
 collected from different environmental conditions across its
 distributional range respond differently to AM fungi, and if the responses
 of six growth and defense traits are correlated. Key Results: Although
 there was strong genetic differentiation in mean trait values among
 populations, AM fungi consistently increased expression of most growth and
 defense traits across all populations. Responses of biomass and root:shoot
 ratio to AM fungi were positively correlated, suggesting that plants that
 are more responsive to AM fungi allocated more biomass belowground.
 Responses of biomass and trichome density to AM fungi were negatively
 correlated, indicating a trade-off in responsiveness between a growth and
 defensive trait. Conclusions: Our results suggest that while there is
 substantial population differentiation in many traits of A. speciosa,
 populations respond similarly to AM fungi, and both positive and negative
 correlations among trait responses occur.
description: Waller_AJB_DataData from the greenhouse experiment. All data were collected by the authors.Waller_AJB_RcodeR code to conduct analyses presented in the paper.
DOI: 10.5061/dryad.34m83
title: Data from: The impact of salinity on mycorrhizal colonization of a rare legume in south Florida pine rocklands

description: Objectives: The success of restoration plantings depends on the capacity
 of transplanted individuals or seeds to establish and reproduce. It is
 increasingly recognized that restoration success depends quite heavily
 upon biotic interactions and belowground processes. Under stressful
 abiotic conditions, such as soils salinized by storm surge and sea level
 rise, symbiotic interactions with soil microbes such as mycorrhizae may be
 critically important. In this study, we investigate the impact of salinity
 on percent colonization of roots by arbuscular mycorrhizal fungi, in
 addition to the impacts of this colonization on plant fitness under saline
 conditions. Fifty Galactia smallii plants from an ex situ collection were
 subjected to a salinity treatment for six weeks, and fifty plants were
 untreated. Plants were harvested and assessed for percent colonization by
 arbuscular mycorrhizal fungi, nodule number, shoot and root dry biomass,
 and micronutrient content. Results: Colonization by arbuscular mycorrhizae
 (AMF) was higher in plants in the salinity treatment than in untreated
 plants; plants in the salinity treatment were also found to have a lower
 root:shoot ratio, and higher phosphorus and nitrogen levels. These results
 support the importance of arbuscular mycorrhizal fungi in restoration
 efforts of endangered plants in fragmented and threatened ecosystems, such
 as pine rocklands.
description: Galactia
 DatasetsThis file contains four
 data sheets, with raw data on plant size under the two treatments
 (saline/non-saline), spore identifications, plant elemental contents, and
 an overall datafile.
DOI: 10.5061/dryad.69ph0
title: Data from: Seed size and the evolution of leaf defences

description: 1. Leaf defences vary widely among tree species, affecting rates of
 herbivory, survival and reproduction. 2. Two contrasting hypotheses
 account for variation in leaf defences among species. The first predicts
 that a slow life history, which is characteristic of larger seeded species
 adapted to resource-limited environments, is associated with well-defended
 leaves. The second, apparency theory, predicts that elevated leaf defences
 are necessitated for species that are more detectable to herbivores. 3.
 Here we use comparative methods and a global data set to test (i) the
 relationship between seed size and leaf defences and (ii) the relationship
 between clumping (spatial apparency) and leaf defences. 4. We found that
 seed size was positively related to leaf fracture toughness, but not
 phenolics or tannin concentration and that spatial aggregation was
 unrelated to leaf defences. 5. Synthesis. Our results suggest that larger
 seed size and increased leaf toughness are correlated as part of a trait
 syndrome associated with a slow, resource-limited life history, not
 clumped dispersion and increased spatial apparency.
description: Plant functional trait
 data: BCIThis file contains data
 on plant functional traits and spatial dispersion. Data were collected by
 Joe Wright and colleagues at Barro Colorado Island,
 Panama.BCI
 data.csvPlant functional trait
 data: Kibale, Bukit Timah, PNM-SLPAThis file contains data
 on plant functional traits and spatial dispersion collected from Kibale,
 Uganda, Bukit Timah, Singapore, and PNM-SLPA, Panama. Data were collected
 by Nathaniel J. Dominy.Kraft_et_al
 data.csv
DOI: 10.5061/dryad.6v774
title: Data from: The rate of evolution of postmating-prezygotic reproductive isolation in Drosophila

description: Reproductive isolation (RI) is an intrinsic aspect of species, as
 described in the Biological Species Concept. For that reason, the
 identification of the precise traits and mechanisms of RI, and the rates
 at which they evolve, is crucial to understanding how species originate
 and persist. Nonetheless, precise measurements of the magnitude of
 reproductive isolation are rare. Previous work has measured the rates of
 evolution of prezygotic and postzygotic barriers to gene flow, yet no
 systematic analysis has carried out the study of the rates of evolution of
 postmating-prezygotic (PMPZ) barriers. We systematically measured the
 magnitude of two barriers to gene flow that act after mating occurs but
 before zygotic fertilization and also measured a premating (female mating
 rate in nonchoice experiments) and two postzygotic barriers (hybrid
 inviability and hybrid sterility) for all pairwise crosses of species
 within the Drosophila melanogaster subgroup. Our results indicate that
 PMPZ isolation evolves faster than hybrid inviability but slower than
 premating isolation. We also describe seven new interspecific hybrids in
 the group. Our findings open up a large repertoire of tools that will
 enable researchers to manipulate hybrids and explore the genetic basis of
 interspecific differentiation, reproductive isolation, and speciation.
description: Raw data and analytical
 code. Turissini et al. 2017This .zip file contains
 all the analytical data and code used in Turissini et al.
 2017.dryad_MBE.zip
DOI: 10.5061/dryad.j72tt79
title: Data from: Predation shapes the evolutionary traits of cervid weapons

description: Sexually selected weapons evolved to maximize the individual reproductive
 success of males in many polygynous breeding species. Many weapons are
 also retained outside of reproductive periods for secondary reasons, but
 the importance of these secondary functions is poorly understood. Here we
 leveraged a unique opportunity from the predator–prey system in northern
 Yellowstone National Park, WY, USA to evaluate whether predation by a
 widespread, coursing predator (wolves) has influenced a specific weapon
 trait (antler retention time) in their primary cervid prey (elk). Male elk
 face a trade-off: individuals casting antlers early begin regrowth before
 other males, resulting in relatively larger antlers the following year,
 and thus greater reproductive success, as indicated by research with red
 deer. We show, however, that male elk that cast their antlers early are
 preferentially hunted and killed by wolves, despite early casters being in
 better nutritional condition than antlered individuals. Our results run
 counter to classic expectations of coursing predators preferring
 poorer-conditioned individuals, and in so doing, reveal an important
 secondary function for an exaggerated sexually selected weapon—predatory
 deterrence. We suggest this secondary function played a key evolutionary
 role in elk; uniquely among North American cervids, they retain their
 antlers long after they fulfil their primary role in reproduction.
description: Metz-et-al._2018_NEE_dataField collected data from northern Yellowstone National Park that describes the characteristics of wolf-killed male elk, the presence or absence of antlers for individual male elk in the population, and the characteristics of elk groups encountered by wolves.
DOI: 10.5061/dryad.87478
title: Data from: Diversifying selection and color-biased dispersal in the asp viper

description: Background: The presence of intraspecific color polymorphism can have
 multiple impacts on the ecology of a species; as a consequence, particular
 color morphs may be strongly selected for in a given habitat type. For
 example, the asp viper (Vipera aspis) shows a high level of color
 polymorphism. A blotched morph (cryptic) is common throughout its range
 (central and western Europe), while a melanistic morph is frequently found
 in montane populations, presumably for thermoregulatory reasons. Besides,
 rare atypical uniformly colored individuals are known here and there.
 Nevertheless, we found in a restricted treeless area of the French Alps, a
 population containing a high proportion (&gt;50%) of such specimens.
 The aim of the study is to bring insight into the presence and function of
 this color morph by (i) studying the genetic structure of these
 populations using nine microsatellite markers, and testing for (ii) a
 potential local diversifying selection and (iii) differences in dispersal
 capacity between blotched and non-blotched vipers. Results: Our genetic
 analyses support the occurrence of local diversifying selection for the
 non-blotched phenotype. In addition, we found significant color-biased
 dispersal, blotched individuals dispersing more than atypical individuals.
 Conclusion: We hypothesize that, in this population, the non-blotched
 phenotype possess an advantage over the typical one, a phenomenon possibly
 due to a better background matching ability in a more open habitat. In
 addition, color-biased dispersal might be partly associated with the
 observed local diversifying selection, as it can affect the genetic
 structure of populations, and hence the distribution of color morphs.
description: for
 Dryadfile in Structure format
 with the coloration, the sex, population ID where the sample was
 collected, and the length of 9 microsatellite markers