cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6q6r5
title: Data from: Competition decreases with relatedness and lek size in mole crickets: a role for kin selection?

description: Twenty years ago, Kokko & Lindstrom (1996) introduced the
 hypothesis that kin selection may drive the evolution of leks, shifting
 the lek-paradigm away from a competitive framework and spurring research
 on the relatedness of males on leks. However, support for Kokko &
 Lindstrom’s kin selection hypothesis has been sparse; most studies have
 shown related males to occur on leks no more than expected by chance.
 Additionally, evidence supporting the proposed mechanism is mixed; by
 joining a lek males do not always increase the female visitation rate on a
 per-capita basis. The prairie mole cricket Gryllotalpa major is a lekking
 cricket in which male relatives advertise in close proximity. We reject
 the Kokko-Lindstrom hypothesis for this species because G. major females
 do not preferentially visit larger leks. Interestingly, more females
 visited smaller leks, where the presence of larger, more highly related
 males suggest reduced levels of local competition. Although the mechanism
 continues to be explored, these results provide an alternative inclusive
 fitness scenario to consider for lekking species – the existence of kin
 benefits between related neighbors rather than spread across the lek as a
 whole.
description: Individual
 Microsatellite Genotypes and Geographic CoordinatesFirst column represents
 unique individual identifier with population abbreviation. WA=White Oak
 2013, WB=White Oak 2014, WO=White Oak 2015, see paper for additional
 abbreviations. Individuals whose identifier ends with a letter are females
 who were attracted to the male with the same number without the letter
 suffix (for example, LL-10A is the first female who was attracted to male
 LL-10). Column headings show the name of the loci/marker
 used.alleles_location.csvSex RatiosIncludes sex ratios and length of time where female trapping occurred at several different lekssex_ratios.csvMale Mass DataIncludes data on male mass and lek sizemale_mass_combined.csvMale Size DataSpreadsheet of male mass, size, and lek sizemale_size.xlsx2009-2015 female attractionsRepresents number of female attractions by each male on several different leks
DOI: 10.5061/dryad.pp26q
title: Data from: Ontogenetic variability in old and new collections of Dicranophyllum gallicum Grand’Eury from the late Palaeozoic of Europe

description: Dicranophyllum gallicum Grand’Eury is described by means of a morphometric
 analysis of eighty two samples from various old and new localities in
 western and central Europe. Stem, leaf cushions, leaf scars, leaves,
 axillary structures and potential seeds are described in detail, and
 discussed in comparison to earlier studies. The encountered variability in
 size and structure is shown to be higher than what was described earlier.
 The organisation of the leaf cushion and scar density vary gradually with
 the stem width, while stratigraphic position and ecology do not relate to
 it. It is concluded that the described variability represents an
 ontogenetic feature rather than a phylogenetic or ecologic one. The
 juvenile plants are characterised by small stems, a high leaf scar density
 and elongated leaf cushions with a dominant apical field, while mature
 specimens are characterized by a wide stem, a relatively low leaf scar
 density and relatively wide leaf cushions with a pronounced basal field.
 Axillary shoots and potential seeds of D. gallicum are described and
 illustrated in detail for the first time. A reconstruction based on the
 studied material is presented.
description: Supplementary file 1-
 Considered samplesList of samples holding
 the Dicranophyllum gallicum specimen considered. The samples are listed by
 collection, by sample number and by locality.Supplementary file 2 -
 Stem measurementsMeasurements on
 Dicranophyllum gallicum stem: stem width, leaf scar length and width, leaf
 cushion length and width and apical and basal leaf cushion length in mm
 and leaf scar density in number per cm2.Supplementary file 3 -
 Leaf measurementsMeasurements of
 Dicranophyllum gallicum leaves: length second segment, width first, second
 and third segment in mm.Supplementary file 4 -
 Axillary shoots measurementsMeasurements of
 Dicranophyllum gallicum axillary shoots: maximal length, maximal width,
 apex width in mm.Supplementary file 5 -
 Seeds measurementsMeasurements of
 co-occurring seeds: seeds length and width and nucellus length and width
 in mm.
DOI: 10.5061/dryad.p7c6p
title: Data from: Genetic diversity and drivers of dwarfism in extinct island emu populations

description: Australia’s iconic emu (Dromaius novaehollandiae novaehollandiae) is the
 only living representative of its genus, but fossil evidence and reports
 from early European explorers suggest that three island forms (at least
 two of which were dwarfs) became extinct during the 19th century. While
 one of these - the King Island emu - has been found to be conspecific with
 Australian mainland emus, little is known about how the other two forms -
 Kangaroo Island and Tasmanian emus - relate to the others, or even the
 size of Tasmanian emus. We present a comprehensive genetic and
 morphological analysis of Dromaius diversity, including data from one of
 the few definitively genuine Tasmanian emu specimens known. Our genetic
 analyses suggest that all the island populations represent sub-populations
 of mainland D. novaehollandiae. Further, the size of island emus and those
 on the mainland appears to scale linearly with island size but not time
 since isolation, suggesting that island size—and presumably concomitant
 limitations on resource availability—may be a more important driver of
 dwarfism in island emus, though its precise contribution to emu dwarfism
 remains to be confirmed.
description: Fasta alignment of emu
 dataAlignment of all emu
 dataEmu_Thomson_2018.fasta
DOI: 10.5061/dryad.f84d3
title: Data from: Fungal effects on plant-plant interactions contribute to grassland plant abundances: evidence from the field

description: 1. Plant-fungal interactions can have strong effects on plant abundances,
 both through direct effects on plant performance and indirect effects on
 competition and facilitation. Most evidence linking fungi to plant
 abundances derives from direct fungal effects on initial growth, with
 little evidence linking fungal effects on plant-plant interactions in
 intact communities to plant abundances for any plant life history stage.
 2. We transplanted 4320 individuals belonging to 18 plant species into
 plots where we removed neighbouring vegetation and suppressed fungi using
 fungicide in a factorial design. We monitored plant survival and growth
 for three years, using this data to test whether fungi had net effects on
 how plant-plant interactions affected different plant life history
 components (initial survival/growth, adult survival/growth). We then
 tested whether these indirect fungal effects or direct fungal effects on
 plant performance best explained plant commonness (frequency of
 occurrence) and local density (percent cover). Finally, we measured
 differences in root-associated fungi following fungal suppression and
 associated these differences with fungal effects on plant performance. 3.
 Overall, fungi increased competitive effects on survival (i.e. lower
 survival with fungi intact), but reduced competitive effects on growth of
 adult plants (i.e. higher growth when fungi intact). Among the focal
 species, these indirect fungal effects increased survival for more common
 species relative to rarer species. However, indirect fungal effects on
 adult growth benefitted rarer species more than common species. Local
 plant densities were unassociated with indirect fungal effects, but were
 negatively associated with direct fungal effects on survival and adult
 growth. This suggests that fungi limit local dominance, thereby indirectly
 increasing the establishment of common species and the growth of rare
 species. 4. Synthesis. By using a variety of plant species and suppressing
 both fungi and neighbours, we show that fungi have net indirect effects,
 through plant-plant interactions, within intact plant communities.
 Variation among species in both direct and indirect fungal effects
 contributed to plant abundances, yet fungal effects did not consistently
 benefit either common or rare species. However, regardless of commonness,
 fungi directly reduced growth and survival for species with high local
 densities, consistent with plant-soil feedbacks limiting species
 dominance.
description: Bennett and Cahill
 Multi-year competition data with and without fungicideThis file contains data
 on growth and survival for 18 species in a factorial experiment that
 removed neighbouring plants and applied fungicide in a factorial
 combination. These treatments and plant measurements were taken from years
 one and three of the experiment.Bennett and Cahill Multiyear
 competition data with and without
 fungicide.xlsx
DOI: 10.5061/dryad.73s36
title: Data from: Diet quality determines interspecific parasite interactions in host populations

description: The widespread occurrence of multiple infections and the often vast range
 of nutritional resources for their hosts allow that interspecific parasite
 interactions in natural host populations might be determined by host diet
 quality. Nevertheless, the role of diet quality with respect to
 multispecies parasite interactions on host population level is not clear.
 We here tested the effect of host population diet quality on the parasite
 community in an experimental study using Daphnia populations. We studied
 the effect of diet quality on Daphnia population demography and the
 interactions in multispecies parasite infections of this freshwater
 crustacean host. The results of our experiment show that the fitness of a
 low-virulent microsporidian parasite decreased in low, but not in
 high-host-diet quality conditions. Interestingly, infections with the
 microsporidium protected Daphnia populations against a more virulent
 bacterial parasite. The observed interspecific parasite interactions are
 discussed with respect to the role of diet quality-dependent changes in
 host fecundity. This study reflects that exploitation competition in
 multispecies parasite infections is environmentally dependent, more in
 particular it shows that diet quality affects interspecific parasite
 competition within a single host and that this can be mediated by host
 population-level effects.
description: Host
 populationshost_pop.csvParasite spore countsparasite.csv
DOI: 10.15468/dl.byza49
title: Occurrence Download

description: A dataset containing 229 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Metternichia principis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 229 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000950-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.527
title: Data from: Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae)

description: Cladistic analyses of the nuclear ribosomal DNA (nrDNA) internal
 transcribed spacer (ITS) sequences from 55 samples corresponding to 34
 taxa in the genus Armeria reveal that ITS sequence diversity among and
 within species utterly conflicts with patterns of morphological
 similarity. Three facts are apparent from the results here reported: (1)
 different samples of a single subspecies, A. villosa subsp. longiaristata,
 appear in three of the five major clades; (2) samples of at least one of
 the six subspecies of A. villosa appear in four of the five major clades;
 and (3) composition of major clades shows greater congruence with the
 geographic origin of plants than with the traditional systematic
 arrangement based primarily on morphology. Specifically, the clades here
 termed Ia, II, III, and IV each encompass terminals restricted to
 geographically delimited areas. There are alternative explanations for the
 ITS pattern, but the most likely one is that nucleotide positions
 supporting the major clades are due, in some of the samples, to concerted
 evolution following horizontal transfer (gene flow) rather than to recency
 of common ancestry. This interpretation is consistent with previous
 systematic and experimental evidence and implies that reticulation in
 Armeria may be extensive. Harlan and de Wet (1963, Evolution 17:497-501)
 proposed the compilospecies concept to account for situations in which a
 genetically "aggressive" species captures portions of the genome
 of other sympatric species via extensive introgression. Evidence of
 extensive reticulation, ecological diversification, and geographic pattern
 indicates that A. villosa may fit the compilospecies concept, which is
 here supported on molecular grounds for the first time.
description: Fuentes Aguilar et al
 Data SetAguilar.txt
DOI: 10.5061/dryad.7s8h7
title: Data from: High opsin diversity in a non-visual infaunal brittlestar

description: Background: In metazoans, opsins are photosensitive proteins involved in
 both vision and non-visual photoreception. Echinoderms have no
 well-defined eyes but several opsin genes were found in the purple sea
 urchin (Strongylocentrotus purpuratus) genome. Molecular data are lacking
 for other echinoderm classes although many species are known to be light
 sensitive.Results: In this study focused on the European brittle star
 Amphiura filiformis, we first highlighted a blue-green light sensitivity
 using a behavioural approach. We then identified 13 new putative opsin
 genes against eight bona fide opsin genes in the genome of S. purpuratus.
 Six opsins were included in the rhabdomeric opsin group (r-opsins). In
 addition, one putative ciliary opsin (c-opsin), showing high similarity
 with the c-opsin of S. purpuratus (Sp-opsin 1), one Go opsin similar to
 Sp-opsins 3.1 and 3.2, two basal-branch opsins similar to Sp-opsins 2 and
 5, and two neuropsins similar to Sp-opsin 8, were identified. Finally, two
 sequences from one putative RGR opsin similar to Sp-opsin 7 were also
 detected. Adult arm transcriptome analysis pinpointed opsin mRNAs
 corresponding to one r-opsin, one neuropsin and the homologue of Sp-opsin
 2. Opsin phylogeny was determined by maximum likelihood and Bayesian
 analyses. Using antibodies designed against c- and r-opsins from S.
 purpuratus, we detected putative photoreceptor cells mainly in spines and
 tube feet of A. filiformis, respectively. The r-opsin expression pattern
 is similar to the one reported in S. purpuratus with cells labelled at the
 tip and at the base of the tube feet. In addition, r-opsin positive cells
 were also identified in the radial nerve of the arm. C-opsins positive
 cells, expressed in pedicellariae, spines, tube feet and epidermis in S.
 purpuratus were observed at the level of the spine stroma in the brittle
 star. Conclusion: Light perception in A. filiformis seems to be mediated
 by opsins (c- and r-) in, at least, spines, tube feet and in the radial
 nerve cord. Other non-visual opsin types could participate to the light
 perception process indicating a complex expression pattern of opsins in
 this infaunal brittle star.
description: Truncated Opsin
 Alignment (including New Amphiura opsins)Fasta file of the
 truncated opsin alignment used for phylogenetic
 analyses.Delroisse_et_al_2014_Truncated_Alignment_Opsin_AmphiuraFASTABayesian tree of new Amphiura opsinsTree files obtained in Bayesian analyses (modified with FigTree software, http://tree.bio.ed.ac.uk/software/figtree/)Bayesian_tree_Delroisse_et_al_2014_Opsin_Amphiura.treeML tree of new Amphiura opsinsTREE files obtained in Maximum Likelihood Analyses (modified with FigTree software, http://tree.bio.ed.ac.uk/software/figtree/)ML_tree_Delroisse_et_al_2014_Opsin_Amphiura.tree
DOI: 10.5061/dryad.4qr34
title: Data from: The value of an egg: resource reallocation in ladybirds (Coleoptera: Coccinellidae) infected with male-killing bacteria

description: Male-killing bacteria (MKs) are thought to persist in host populations by
 vertical transmission, and conferring direct and/or indirect fitness
 benefits to their hosts. Here, we test the role of indirect fitness
 benefits accrued from resource reallocation in species that engage in
 sibling egg cannibalism. We found that a single-egg meal significantly
 increased larval survival in 12 ladybird species, but the value of an egg
 (to survival) differed substantially between species. Next we tested the
 impact of three MKs on larval survival in one ladybird species, Adalia
 bipunctata. Spiroplasma reduced larval survival, whereas Wolbachia and
 Rickettsia had no effect. However, Spiroplasma-infected larvae showed the
 greatest response to a single-egg meal. The indirect fitness benefit
 obtained from a single egg is thus so large, that even MKs with direct
 fitness costs can persist in host populations. This study supports the
 hypothesis that fitness compensation via resource reallocation can explain
 MK persistence.
description: Elnagdy et al 2011
 dataSurvival data for three
 experiments to investigate resource reallocation in coccinellids
 (Coleoptera: Coccinellidae) infected with male-killing
 bacteria
DOI: 10.5061/dryad.qn514810
title: Data from: Parental genetic effects in a cavefish adaptive behavior explain disparity between nuclear and mitochondrial DNA

description: Epigenetic parental genetic effects are important in many biological
 processes but their roles in the evolution of adaptive traits and their
 consequences in naturally evolving populations remain to be addressed. By
 comparing two divergent blind cave-dwelling cavefish populations with a
 sighted surface-dwelling population (surface fish) of the teleost Astyanax
 mexicanus, we report here that convergences in vibration attraction
 behavior (VAB), the lateral line sensory receptors underlying this
 behavior, and the feeding benefits of this behavior are controlled by
 parental genetic effects, either maternal or paternal inheritance. From
 behavioral studies and mathematical evolutionary simulations, we further
 demonstrate that disparity in nuclear and mitochondrial DNA in one of
 these cavefish populations that has hybridized with surface fish can be
 explained by paternal inheritance of VAB. The results suggest that
 parental genetic effects in adaptive behaviors may be important factors in
 biasing mitochondrial DNA inheritance in natural populations that are
 subject to introgression.
description: Yoshizawa et al_archived
 data_0209-2012Raw data from the
 laboratory experiments. Abbreviations are described in the main
 manuscript.processMitoSim_allThis perl code calculates the stats of the data produced by Yoshizawa_etal_simuPOP_code.py. Further descriptions are seen at the comments in this file.Yoshizawa_etal_simuPOP_codeThe python code is to simulate the introgression event of mitochondria by running simuPOP program. Detailed description are seen in 'comments' in this code.
DOI: 10.5061/dryad.tc3415t
title: Data from: Systematics and macroevolution of extant and fossil scalopine moles (Mammalia, Talpidae)

description: Scalopini is one of the two fully fossorial mole tribes in the family
 Talpidae, with remarkable adaptations to subterranean lifestyles. Most
 living Scalopini species are distributed in North America while a sole
 species occurs in China. On the other hand, scalopine fossils are found in
 both Eurasia and North America from upper Oligocene strata onwards,
 implying a complex biogeographical history. The systematic relationships
 of both extant and fossil Scalopini across North America and Eurasia are
 revised by conducting phylogenetic analyses using a comprehensive
 morphological character matrix together with 2D geometric–morphometric
 analyses of the humeral shape, with a specific emphasis on Mioscalops, a
 genus commonly found in North America and formerly known as Scalopoides.
 Our phylogenetic analyses support the monophyly of the tribe Scalopini as
 well as a proposed two‐subtribe‐division scenario of Scalopini (i.e.
 Scalopina and Parascalopina), although Proscapanus could not be assigned
 to either subgenus. Our geometric–morphometric analyses indicate that the
 European Mioscalops from southern Germany should be allocated to
 Leptoscaptor, which in turn implies that Mioscalops may be endemic to
 North America and never arrived in Europe. Examination of biogeographical
 patterns does not unambiguously determine the geographical origin of
 Scalopini. Nevertheless, it does support multiple transcontinental
 colonization events across Asia, Europe and North America. Scapanulus
 oweni, distributed in central China, is the only remaining representative
 of one of those out‐of‐North‐America migrations, whereas scalopine moles
 are common in North America nowadays with up to five species.
description: Schwermann_He_et_al_2018_Systematis_and_macroevolution_of_extant_and_fossil_scalopine_moles_supplS1: Dental Formular f Yunoscaptor scalprum and Scapanulus oweni; S2: Matrix and characters for phylogenetic Analysis; S3: List of species used in this study, and their sample sizes; S4: Published North American Mioscalops-findings; S5: Notes on Mioscalops-findings from the Hemphillian
DOI: 10.5061/dryad.9s5p4k1
title: Data from: Developmental shifts in social cognition: socio-emotional biases across the lifespan in rhesus monkeys

description: Humans exhibit a suite of developmental changes in social cognition across
 the lifespan. To what extent are these developmental patterns unique? We
 first review several social domains in which humans undergo critical
 ontogenetic changes in socio-cognitive processing, including social
 attention and theory of mind. We then examine whether one human
 developmental transition—a shift in socioemotional preferences—also occurs
 in nonhuman primates. Specifically, we experimentally measured
 socioemotional processing in a large population of rhesus macaques (Macaca
 mulatta) ranging from infancy to old age. We tested whether macaques, like
 humans, also exhibited developmental shifts from a negativity bias at
 younger ages, indicating preferential attention to negative socioemotional
 stimuli, to a positivity bias at older ages. We first assessed monkeys’ (n
 = 337) responses to negative socioemotional stimuli by comparing their
 duration of looking towards photos of negative conspecific signals (threat
 displays) versus matched neutral expressions. In contrast to the pattern
 observed in humans, we found that older monkeys were more attentive to
 negative emotional stimuli than were younger monkeys. In a second study,
 we used the same method to examine monkeys’ (n = 132) attention to
 positive (affiliative displays) versus matched neutral expressions.
 Monkeys did not exhibit an overall preference for positive stimuli, nor
 major age-related changes in their attention. These results indicate that
 while monkeys show robust ontogenetic shifts in social preferences, they
 differ from humans by exhibiting an increasing negativity bias with age.
 Studies of comparative cognitive development can therefore provide insight
 into the evolutionary origins of human socio-cognitive development.
description: Rosati, Arre, Platt,
 & Santos - Study 1Trial data from Rosati,
 Arre, Platt, & Santos Study 1 (Negative socioemotional stimuli). Key
 for variables included as a separate tab in file.Rosati-Arre-Platt-Santos-Emotions-Study1-DRYAD.xlsxRosati, Arre, Platt, & Santos - Study 2Trial data from Rosati, Arre, Platt, & Santos Study 2 (Positive socioemotional stimuli). Key for variables included as a separate tab in file.Rosati-Arre-Platt-Santos-Emotions-Study2-DRYAD.xlsx