cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3b56d
title: Data from: We happy few: using structured population models to identify the decisive events in the lives of exceptional individuals

description: In any population, some individuals make it big: they are among the few
 that produce many offspring, grow to large size, and so on. What
 distinguishes the lives of these happy few? We present three approaches
 for identifying what factors distinguish those "lucky"
 individuals who come to dominate reproduction in a population without
 fixed differences between individuals (genotype, site quality, etc.):
 comparing life-history trajectories for lucky and unlucky individuals and
 calculating the elasticity of the probability of becoming lucky to
 perturbations in demographic rates at a given size or a given age. As
 examples we consider published size-structured integral projection models
 for the tropical tree Dacrydium elatum and the semiarid shrub Artemisia
 ordosica and an age-size-structured matrix model for the tropical tree
 Cedrela ordosica. We find that good fortune (e.g., rapid growth) when
 small and young matters much more than good fortune when older and larger.
 Becoming lucky is primarily a matter of surviving while others die. For
 species with more variable growth (such as Cedrela and Ordosica), it is
 also a matter of growing fast. We focus on reproductive skew, but our
 methods are broadly applicable and can be used to investigate how
 individuals come to be exceptional in any aspect.
description: R scripts for figures in
 Snyder, Ellner, Am. Nat. 2016Snyder, Ellner, Am. Nat.
 2016 presents methods for analyzing structured population models (integral
 projections models or matrix models) to determine what makes an individual
 more likely to become of the few who dominate reproductive output. It
 assumes that all individuals are identical: some are lucky, most are not.
 These files contain all that is necessary to generate the figures in that
 paper. They include both the functions and data that define the models and
 the analysis scripts. Each figure caption references the R script which
 generated it.SnyderEllnerAmNat2016Scripts.zip
DOI: 10.15468/dl.q33nyt
title: Occurrence Download

description: A dataset containing 1352 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Costus speciosus"
 ]
}

 The dataset includes 1352 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001433-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8525
title: Data from: What makes a leaf tough? Patterns of correlated evolution between leaf toughness traits and demographic rates among 197 shade-tolerant woody species in a neotropical forest

description: Slow-growing juveniles of shade-tolerant plant species are predicted to
 have tough leaves because of the high cost of leaf replacement in shade
 relative to potential carbon gain. We assessed the degree of correlated
 evolution among eight traits associated with leaf toughness and their
 relationships with growth and mortality rates of 197 tree and shrub
 species from the understory of the 50-hectare forest dynamics plot on
 Barro Colorado Island, Panama. Path analysis with phylogenetically
 independent contrasts revealed that leaves attained material toughness
 (resistance to fracture per unit fracture area) through increases in
 tissue density, percent cellulose per unit dry mass, and vein fracture
 toughness. Lamina density and cellulose content evolved independently, and
 thus represent different paths to material toughness. Structural toughness
 (resistance to fracture per unit fracture length) depended on material
 toughness and lamina thickness. Mortality rates of individuals 1-10 cm in
 stem diameter were negatively correlated with material toughness and
 lamina density, but were independent of structural toughness and cell wall
 fiber contents. Leaf toughness traits were uncorrelated with relative
 growth rates. These results imply that material toughness enhances
 resistance to natural enemies, which increases survival and offsets the
 biomass allocation cost of producing tough leaves in the shaded
 understory.
description: BCI_leaf_toughness_data
DOI: 10.5061/dryad.551
title: Data from: Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses

description: The horseshoe crabs, known as living fossils, have maintained their
 morphology almost unchanged for the past 150 million years. The little
 morphological differentiation among horseshoe crab lineages has resulted
 in substantial controversy concerning the phylogenetic relationship among
 the extant species of horseshoe crabs, especially among the three species
 in the Indo-Pacific region. Previous studies suggest that the three
 species constitute a phylogenetically unresolvable trichotomy, the result
 of a cladogenetic process leading to the formation of all three
 Indo-Pacific species in a short geological time. Data from two
 mitochondrial genes (for 16S ribosomal rRNA and cytochrome oxidase subunit
 I) and one nuclear gene (for coagulogen) in the four species of horseshoe
 crabs and outgroup species were used in a phylogenetic analysis with
 various substitution models. All three genes yield the same tree topology,
 with Tachypleus-gigas and Carcinoscorpius-rotundicauda grouped together as
 a monophyletic taxon. This topology is significantly better than all the
 alternatives when evaluated with the RELL (resampling estimated
 log-likelihood) method.
description: Xia Data
 SetXiadata.wd
DOI: 10.5061/dryad.k8m7b
title: Data from: Adaptive and selective seed abortion reveals complex conditional decision making in plants

description: Behaviour is traditionally attributed to animals only. Recently, evidence
 for plant behaviour is accumulating, mostly from plant physiological
 studies. Here, we provide ecological evidence for complex plant behaviour
 in the form of seed abortion decisions conditional on internal and
 external cues. We analysed seed abortion patterns of barberry plants
 exposed to seed parasitism and different environmental conditions. Without
 abortion, parasite infestation of seeds can lead to loss of all seeds in a
 fruit. We statistically tested a series of null-models with Monte-Carlo
 simulations to establish selectivity and adaptiveness of the observed seed
 abortion patterns. Seed abortion was more frequent in parasitized fruits
 and fruits from dry habitats. Surprisingly, seed abortion occurred with
 significantly greater probability if there was a second intact seed in the
 fruit. This strategy provides a fitness benefit if abortion can prevent a
 sibling seed from co-infestation and if non-abortion of an infested, but
 surviving single seed saves resources invested in the fruit coat.
 Ecological evidence for complex decision making in plants thus includes a
 structural memory (the second seed), simple reasoning (integration of
 inner and outer conditions), conditional behaviour (abortion), and
 anticipation of future risks (seed predation).
description: Observed number of
 fruitsData were collected in
 the fieldData_Meyer_et_al_Seed_abortion_in_Berberis.doc
DOI: 10.5061/dryad.jk34r
title: Data from: White Syndrome in Acropora muricata: Non-specific bacterial infection and ciliate histophagy

description: Selective antibiotic treatment of White Syndrome (WS)-affected corals
 (Acropora muricata) from Fiji was used to identify 3 potential bacterial
 pathogens of the disease. Interestingly, the suite of bacterial associates
 of the disease was different to that recently identified using identical
 primer sets for WS on the GBR and in the Solomon Islands. In addition to
 the three bacterial pathogenic candidates and as previously shown for WS
 and more recently for White Band Disease (WBD) in the Caribbean, all
 samples of the disease were specifically associated with the histophagous
 ciliate Philaster lucinda. From the pattern of disease progression and
 histopathology in relation to the selective elimination of microbial
 groups, we conclude that these ‘white’ diseases are a result of a
 non-specific bacterial infection and a ‘secondary’ infection by the P.
 lucinda ciliate. Although we have not observed the initiation of
 infection, a non-specific, multi-species bacterial infection appears to be
 a co-requirement for WS lesion progression and we hypothesize that the
 bacterial infection occurs initially, weakening the defences of the host
 to predation by the ciliates. Such ciliate histophagy, gives rise to the
 characteristic white band of denuded coral skeleton that gives these
 diseases their names. The characteristics of the microbial communities of
 WBD and WS appear identical, and since the bacterial associates of WS vary
 geographically (and/or temporally), there appears to be no logical
 distinction between WS in the Indo-Pacific and WBD in the Caribbean.
description: 454 OTU RAW data
 filesOTU data from 454
 sequencing 4 samples per treatment. H = healthy WS = controls showing
 signs of white syndrome MET = treated corals with Metronidazole, AMP =
 treated coral with Ampicillin, PARA = treatment with Paromomycin
 sulfate
DOI: 10.5061/dryad.c301h
title: Data from: Widespread forest vertebrate extinctions induced by a mega hydroelectric dam in lowland Amazonia

description: Mega hydropower projects in tropical forests pose a major emergent threat
 to terrestrial and freshwater biodiversity worldwide. Despite the
 unprecedented number of existing, under-construction and planned
 hydroelectric dams in lowland tropical forests, long-term effects on
 biodiversity have yet to be evaluated. We examine how medium and
 large-bodied assemblages of terrestrial and arboreal vertebrates
 (including 35 mammal, bird and tortoise species) responded to the drastic
 26-year post-isolation history of archipelagic alteration in landscape
 structure and habitat quality in a major hydroelectric reservoir of
 Central Amazonia. The Balbina Hydroelectric Dam inundated 3,129 km2 of
 primary forests, simultaneously isolating 3,546 land-bridge islands. We
 conducted intensive biodiversity surveys at 37 of those islands and three
 adjacent continuous forests using a combination of four survey techniques,
 and detected strong forest habitat area effects in explaining patterns of
 vertebrate extinction. Beyond clear area effects, edge-mediated surface
 fire disturbance was the most important additional driver of species loss,
 particularly in islands smaller than 10 ha. Based on species-area models,
 we predict that only 0.7% of all islands now harbor a species-rich
 vertebrate assemblage consisting of ≥80% of all species. We highlight the
 colossal erosion in vertebrate diversity driven by a man-made dam and show
 that the biodiversity impacts of mega dams in lowland tropical forest
 regions have been severely overlooked. The geopolitical strategy to deploy
 many more large hydropower infrastructure projects in regions like lowland
 Amazonia should be urgently reassessed, and we strongly advise that
 long-term biodiversity impacts should be explicitly included in
 pre-approval environmental impact assessments.
description: Matrix of surveyed sites
 versus vertebrate species detected by at least one sampling
 techniqueMatrix of surveyed sites
 versus vertebrate species detected by at least one sampling technique,
 including the geographical coordinate of each site.Plos_data.xls
DOI: 10.5061/dryad.qb35fd8
title: Data from: Seed traits, not density or distance from parent, determine seed predation and establishment in an Afrotropical forest

description: Seed predators drive patterns in seed mortality and seedling establishment
 and are posited to contribute to the maintenance of plant species
 diversity through several mechanisms. Negative density dependence and
 spatially-restricted recruitment are apparently widespread in Neotropical
 forests, but are little studied in Afrotropical forests, where generalist
 vertebrates may contribute more to seed mortality than do specialized
 invertebrates and fungi. We experimentally assessed the roles of seed
 density and distance from the parent tree for ten tree species in a forest
 in northeastern Gabon, using exclosures to isolate the effects of
 different seed predator types. Vertebrates caused greater seed losses than
 all other mortality agents combined. Unexpectedly, seeds under fruiting
 conspecific trees had significantly lower removal and higher seedling
 establishment than those under heterospecific trees or in neutral
 non-fruiting locations. Seed density did not significantly affect seedling
 establishment. Vertebrate seed removal ranged from 0% to 100% among focal
 species, and was positively correlated with seed mass but had no
 relationship with species commonness (adult tree density). Seed traits
 strongly affected patterns of seed removal and seedling establishment, and
 may contribute more to the likelihood of success for an individual seed
 than do its density or distance from parent. Our results highlight an
 apparent divergence in patterns of seed mortality and seedling
 establishment between tropical forest regions, and emphasize the need for
 further comparative study.
description: Rosin_SeedSwap_AllDataAll data from the project, with each row representing a single seed, and columns representing the conditions under which that seed was placed (density, canopy location, treatment type), as well as its fate. Species identifier codes use the first two letters of the genus and the first two letters of the specific epithet.
DOI: 10.5061/dryad.768
title: Data from: Evolution of Male Tail Development in Rhabditid Nematodes Related to Caenorhabditis Elegans

description: The evolutionary pathway that has led to male tails of diverse morphology
 among species of the nematode family Rhabditidae was reconstructed. This
 family includes the well-studied model species Caenorhabditis elegans. By
 relating the steps of male tail morphological evolution to the phenotypic
 changes brought about by developmental mutations induced experimentally in
 C. elegans, the goal is to identify genes responsible for morphological
 evolution. The varying morphological characters of the male tails of
 several rhabditid species have been described previously (Fitch and
 Emmons, 1995, Dev. Biol. 170:564--582). The developmental events preceding
 differentiation of the adult structures have also been analyzed; in many
 cases the origins of varying adult morphological characters were traced to
 differences during ontogeny. In the present work, the evolutionary changes
 producing these differences were reconstructed in the context of the four
 possible phylogenies supported independently by sequences of 18S ribosomal
 RNA genes (rDNA). Two or more alternative states were defined for 36
 developmental and adult morphological characters. These characters alone
 do not provide sufficient data to resolve most species relationships;
 however, when combined with the rDNA characters, they provide stronger
 support for one of the four rDNA phylogenies. Assuming a model of ordered
 transformations for multistate developmental characters generally results
 in greater resolution. Transformations between character states can be
 assigned unequivocally by parsimony to unambiguous branches for most of
 the characters. Correlations are thereby revealed for some of the
 developmental characters, indicating a probability of a shared
 developmental or genetic regulatory pathway. Four of the unequivocal
 character state changes on unambiguously supported branches closely
 resemble the phenotypic changes brought about by known mutations in C.
 elegans. These mutations define genes that are known to act in genetic
 regulatory hierarchies controlling pattern formation, differentiation, and
 morphogenesis. Although these studies are still at an early stage, these
 results strongly suggest that parallel studies of developmental mutants in
 C. elegans and of morphological and developmental evolution among related
 nematodes will help define genetic changes underlying the evolution of
 form.
description: Fitch Paup Data
 Setfitch1.paupFitch MacClade Data Setfitch2.mc
DOI: 10.5061/dryad.596
title: Data from: Timing transantarctic disjunctions in the Atherospermataceae (Laurales): evidence from coding and noncoding chloroplast sequences

description: Previous studies of the small Southern Hemisphere family
 Atherospermataceae have drawn contradictory conclusions regarding the
 number of transantarctic disjunctions and role of transoceanic dispersal
 in its evolution. Clarification of intergeneric relationships is critical
 to resolving (1) whether the two Chilean species, Laurelia sempervirens
 and Laureliopsis philippiana, are related to different Australpacific
 species, implying two transantarctic disjunctions as suggested by
 morphology; (2) where the group is likely to have originated; and (3)
 whether observed disjunctions reflect the breakup of Gondwana. We analyzed
 chloroplast DNA sequences from six regions (the rbcL gene, the rpl16
 intron, and the trnL-trnF, trnT-trnL, psbA-trnH, and atpB-rbcL spacer
 regions; together 4,338 bp) for all genera and most species of
 Atherospermataceae, using parsimony and maximum likelihood (ML). The
 family's sister group, the Chilean endemic Gomortega nitida
 (Gomortegaceae), was used to root the tree. Parsimony and ML yielded
 identical single best trees that contain three well supported clades
 (&gt;80% bootstrap): Daphnandra and Doryphora from south-eastern
 Australia; Atherosperma and Nemuaron from Australia-Tasmania and New
 Caledonia, respectively; and Laurelia novae-zelandiae and Laureliopsis
 philippiana from New Zealand and Chile, respectively. The second Chilean
 species, Laurelia sempervirens, is sister to this last clade. A likelihood
 ratio test rejects the molecular clock for the full rbcL data set, but the
 clock assumption holds for the ingroup. The atherosperm fossil record goes
 back to the Upper Cretaceous and includes pollen, wood, and leaf fossils
 from Europe, Africa, South America, Antarctica, New Zealand, and Tasmania.
 Calibration of rbcL substitution rates with the fossils suggest an initial
 diversification of the family at 100-140 million years ago (MYA), likely
 in West Gondwana, early entry into Antarctica, and long distance dispersal
 to New Zealand and New Caledonia at 50-30 MYA by the ancestors of L.
 novae-zelandiae and Nemuaron.
description: Renner et al Data
 Setrenner.nexus
DOI: 10.5061/dryad.vc44v
title: Data from: Male choice in the stream-anadromous stickleback complex

description: Studies of mating preferences and pre-mating reproductive isolation have
 often focused on females, but the potential importance of male preferences
 is increasingly appreciated. We investigated male behavior in the context
 of reproductive isolation between divergent anadromous and stream-resident
 populations of threespine stickleback, Gasterosteus aculeatus, using
 size-manipulated females of both ecotypes. Specifically, we asked if male
 courtship preferences are present, and if they are based on relative body
 size, non-size aspects of ecotype, or other traits. Because male behaviors
 were correlated with each other, we conducted a principal components
 analysis on the correlations and ran subsequent analyses on the principal
 components. The two male ecotypes differed in overall behavioral
 frequencies, with stream-resident males exhibiting consistently more
 vigorous and positive courtship than anadromous males, and an otherwise
 aggressive behavior playing a more positive role in anadromous than
 stream-resident courtship. We observed more vigorous courtship toward
 smaller females by (relatively small) stream-resident males and the
 reverse pattern for (relatively large) anadromous males. Thus
 size-assortative male courtship preferences may contribute to reproductive
 isolation in this system, although preferences are far from absolute. We
 found little indication of males responding preferentially to females of
 their own ecotype independent of body size.
description: Raw
 DataThese are the raw data
 from which one can calculate the PC's etc.SizeManipTests02,03behSingleDRYAD.xlsx
DOI: 10.5061/dryad.2p164
title: Data from: Statistical analysis of dental variation in the Oligocene equid Miohippus (Mammalia, Perissodactyla) of Oregon

description: As many as eight species of the “anchitherine” equid Miohippus have been
 identified from the John Day Formation of Oregon, but no statistical
 analysis of variation in these horses has yet been conducted to determine
 if that level of diversity is warranted. Variation of the
 anterior-posterior length and transverse width of upper and lower teeth of
 Turtle Cove Member Miohippus was compared to that of M. equinanus,
 Mesohippus bairdii, Equus quagga, and Tapirus terrestris using t tests of
 their coefficients of variation (V). None of the t tests are significant,
 indicating that the variation seen in Turtle Cove Miohippus is not
 significantly different from any of the populations of other
 perissodactyls examined in this study. Data also indicate that Mesohippus
 is present in the Turtle Cove Member. Additionally, hypostyle condition,
 used to diagnose all species of Miohippus, was found to be related to
 stage of wear using an ordered logistic regression. Only two species of
 equid, one Miohippus and one Mesohippus, in the Turtle Cove Member can be
 identified, therefore only Miohippus annectens, the genotype and first
 species described from the region, can be recognized as the sole Miohippus
 species known from the Turtle Cove assemblage. There are insufficient data
 to determine which species of Mesohippus is present. The dependence of
 hypostyle condition on crown height in Miohippus implies that wear stage
 must also be considered in investigations of dental morphology in the
 “Anchitheriinae.”
description: Supplemental_Data_1Raw data used in the analysis and coefficients of variation calculations.Supplemental_Data_2R code used in this analysis