cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.11vj2
title: Data from: Timing of morphological and ecological innovations in the cyanobacteria – a key to understanding the rise in atmospheric oxygen

description: When cyanobacteria originated and diversified, and what their ancient
 traits were, remain critical unresolved problems. Here, we used a
 phylogenomic approach to construct a well-resolved 'core'
 cyanobacterial tree. The branching positions of four lineages
 (Thermosynechococcus elongatus, Synechococcus elongatus, Synechococcus PCC
 7335 and Acaryochloris marina) were problematic, probably due to long
 branch attraction artifacts. A consensus genomic tree was used to study
 trait evolution using ancestral state reconstruction (ASR). The early
 cyanobacteria were probably unicellular, freshwater, had small cell
 diameters, and lacked the traits to form thick microbial mats. Relaxed
 molecular clock analyses suggested that early cyanobacterial lineages were
 restricted to freshwater ecosystems until at least 2.4 Ga, before
 diversifying into coastal brackish and marine environments. The resultant
 increases in niche space and nutrient availability, and consequent
 sedimentation of organic carbon into the deep oceans, would have generated
 large pulses of oxygen into the biosphere, possibly explaining why oxygen
 rose so rapidly. Rapid atmospheric oxidation could have destroyed the
 methane-driven greenhouse with simultaneous drawdown in pCO(2),
 precipitating 'Snowball Earth' conditions. The traits associated
 with the formation of thick, laminated microbial mats (large cell
 diameters, filamentous growth, sheaths, motility and nitrogen fixation)
 were not seen until after diversification of the LPP, SPM and PNT clades,
 after 2.32 Ga. The appearance of these traits overlaps with a global
 carbon isotopic excursion between 2.2 and 2.1 Ga. Thus, a massive
 re-ordering of biogeochemical cycles caused by the appearance of complex
 laminated microbial communities in marine environments may have caused
 this excursion. Finally, we show that ASR may provide an explanation for
 why cyanobacterial microfossils have not been observed until after 2.0 Ga,
 and make suggestions for how future paleobiological searches for early
 cyanobacteria might proceed. In summary, key evolutionary events in the
 microbial world may have triggered some of the key geologic upheavals on
 the Paleoproterozoic Earth.
description: Blank&S-B2010.SSURpoCMesquite file containing phylogenetic trees and character matrix.Blank&S-B2010.SSULSUMesquite file containing phylogenetic tree and character matrix.
DOI: 10.5061/dryad.sg095
title: Data from: Behavioral elements and sensory cues involved in sexual isolation between Drosophila melanogaster strains

description: Sensory cues exchanged during courtship are crucial for mate choice: if
 they show intraspecific divergence this may cause or reinforce sexual
 isolation between strains, ultimately leading to speciation. There is a
 strong asymmetric sexual isolation between Drosophila melanogaster females
 from Zimbabwe (Z) and males from all other populations (M). While M and Z
 flies of both sexes show different cuticular pheromones, this variation is
 only partly responsible for the intraspecific isolation effect. Male
 acoustic signals are also partly involved in sexual isolation. We examined
 strain-specific courtship behaviour sequences to determine which body
 parts and sensory appendages may be involved in sexual isolation. Using
 two strains representative of the Z- and M-types, we manipulated sensory
 cues and the social context; we then measured the consequence of these
 manipulations on courtship and copulation. Our data suggest that Z females
 mated best with males whose sensory characteristics matched those of Z
 males in both quantity and quality. M females were less choosy and much
 less influenced by the sensory and social contexts. Differences in
 emission and reception of sensory signals seen between Z and M flies may
 lead to the concerted evolution of multiple sensory channel, thereby
 shaping a population-specific mate recognition system.
description: Raw-Data in Xlsx
 formatData are organised
 according to Figures and Supplementary FiguresRaw-Data.zip
DOI: 10.5061/dryad.cc630
title: Data from: Population density, not host competence, drives patterns of disease in an invaded community

description: Generalist parasites can strongly influence interactions between native
 and invasive species. Host competence can be used to predict how an
 invasive species will affect community disease dynamics; the addition of a
 highly competent, invasive host is predicted to increase disease. However,
 densities of invasive and native species can also influence the impacts of
 invasive species on community disease dynamics. We examined whether
 information on host competence alone could be used to accurately predict
 the effects of an invasive host on disease in native hosts. We first
 characterized the relative competence of an invasive species and a native
 host species to a native parasite. Next, we manipulated species
 composition in mesocosms and found that host competence results did not
 accurately predict community dynamics. While the invasive host was more
 competent than the native, the presence of the native (lower competence)
 host increased disease in the invasive (higher competence) host. To
 identify potential mechanisms driving these patterns, we analyzed a
 two-host, one-parasite model parameterized for our system. Our results
 demonstrate that patterns of disease were primarily driven by relative
 population densities, mediated by asymmetry in intra- and interspecific
 competition. Thus, information on host competence alone may not accurately
 predict how an invasive species will influence disease in native species.
description: Data and code for
 "Population density, not host competence, drives patterns of disease
 in an invaded community"This zip file includes
 data and non-trivial code for the mathematical model in "Population
 density, not host competence, drives patterns of disease in an invaded
 community" by Searle et al. for The American Naturalist. A
 description of the files is included.SearleComputationalFiles.zip
DOI: 10.5061/dryad.96d55
title: Data from: Likelihood of tree topologies with fossils and diversification rate estimation

description: Since the diversification process cannot be directly observed at the human
 scale, it has to be studied from the information available, namely the
 extant taxa and the fossil record. In this sense, phylogenetic trees
 including both extant taxa and fossils are the most complete
 representations of the diversification process that one can get. Such
 phylogenetic trees can be reconstructed from molecular and morphological
 data, to some extent. Among the temporal information of such phylogenetic
 trees, fossil ages are by far the most precisely known (divergence times
 are inferences calibrated mostly with fossils). We propose here a method
 to compute the likelihood of a phylogenetic tree with fossils in which the
 only considered time information is the fossil ages, and apply it to the
 estimation of the diversification rates from such data. Since it is
 required in our computation, we provide a method for determining the
 probability of a tree topology under the standard diversification model.
 Testing 21 our approach on simulated data shows that the maximum
 likelihood rate estimates from the phylogenetic tree topology and the
 fossil dates are almost as accurate as those obtained by taking into
 account all the data, including the divergence times. Moreover, they are
 substantially more accurate than the estimates obtained only from the
 exact divergence times (without taking into account the fossil record). We
 also provide an empirical example composed of 50 Permo-carboniferous
 eupelycosaur (early synapsid) taxa ranging in age from about 315 Ma (Late
 Carboniferous) to 270 Ma (shortly after the end of the Early Permian). Our
 analyses suggest a speciation (cladogenesis, or birth) rate of about 0.1
 per lineage and per My, a marginally lower extinction rate, and a
 considerable hidden paleobiodiversity of early synapsids.
description: AppendixA pdf file with results and proofs referred in the article.Diversificationhttps://github.com/gilles-didier/DiversificationLink to source code
DOI: 10.5061/dryad.7h4s265
title: Data from: Adaptation in temporally variable environments: stickleback armor in periodically breaching bar-built estuaries

description: The evolutionary consequences of temporal variation in selection remain
 hotly debated. We explored these consequences by studying threespine
 stickleback in a set of bar-built estuaries along the central California
 coast. In most years, heavy rains induce water flow strong enough to break
 through isolating sand bars, connecting streams to the ocean. New sand
 bars typically re-form within a few weeks or months, thereby re-isolating
 populations within the estuaries. These breaching events cause severe and
 often extremely rapid changes in abiotic and biotic conditions, including
 shifts in predator abundance. We investigated whether this strong temporal
 environmental variation can maintain within-population variation while
 eroding adaptive divergence among populations that would be caused by
 spatial variation in selection. We used neutral genetic markers to explore
 population structure, and then analyzed how stickleback armor traits, the
 associated genes Eda and Pitx1, and elemental composition (%P) varies
 within and among populations. Despite strong gene flow, we detected
 evidence for divergence in stickleback defensive traits and Eda genotypes
 associated with predation regime. However, this among-population variation
 was lower than that observed among other stickleback populations exposed
 to divergent predator regimes. In addition, within-population variation
 was very high as compared to populations from environmentally stable
 locations. Elemental composition was strongly associated with armor
 traits, Eda genotype, and the presence of predators; thus suggesting that
 spatiotemporal variation in armor traits generates corresponding variation
 in elemental phenotypes. We conclude that gene flow, and especially
 temporal environmental variation, can maintain high levels of
 within-population variation while reducing, but not eliminating,
 among-population variation driven by spatial environmental variation.
description: JEB-2017-00599_phenoPhenotypic dataJEB-2017-00599_NeutralNeutral markersJEB-2017-00599_EDA-PITX1EDA-Pitx1 markersJEB-2017-00599_Morpho2D morphometrics data tablesJEB-2017-00599_stoichStoichiometry data
DOI: 10.5061/dryad.s44s8
title: Data from: A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys

description: Premise of the Study: Several members of Selaginella are renowned for
 their ability to survive extreme drought and “resurrect” when conditions
 improve. Many of these belong to subgenus Tetragonostachys, a group of ∼45
 species primarily found in North and Central America, with substantial
 diversity in the Sonoran and Chihuahuan Deserts. We evaluated the
 monophyly and the age of subgenus Tetragonostachys and assess how drought
 tolerance contributed to the evolution of this clade. Methods: Our study
 included most Tetragonostachys species, using plastid and nuclear
 sequences, fossil and herbarium records, and climate variables to describe
 the species diversity, phylogenetic relationships, divergence times, and
 climatic niche evolution in the subgenus. Key Results: We found that
 subgenus Tetragonostachys forms a monophyletic group sister to Selaginella
 lepidophylla and may have diverged from other Selaginella because of a
 Gondwanan–Laurasian vicariance event ca. 240 mya. The North American
 radiation of Tetragonostachys appears to be much more recent and to have
 occurred during the Early Cretaceous–late Paleocene interval. We
 identified two significant and nested ecological niche shifts during the
 evolution of Tetragonostachys associated with extreme drought tolerance
 and a more recent shift to cold climates. Our analyses suggest that
 drought tolerance evolved in the warm deserts of southwest North America
 and may have been advantageous for colonization of cold and dry boreal
 climates. Conclusions: Our investigation provides a foundation for future
 research addressing the genomics of ecological niche evolution and the
 potential role of reticulate evolution in Selaginella subgenus
 Tetragonostachys.
description: SelaginellaData_Dryad
DOI: 10.5061/dryad.v10k0
title: Data from: Hydrology, shore morphology and species traits affect seed dispersal, germination and community assembly in shoreline plant communities

description: 1.Seed dispersal and germination are two primary processes influencing
 plant community assembly. On freshwater shores, water levels regulate both
 processes. However, it is still unclear how water levels, shore morphology
 and species traits interactively affect seed dispersal and germination,
 and how these interactions determine plant community assembly. We
 hypothesize that a drawdown water regime enhances seed establishment
 compared to a year-round stable water level, that this increases species
 richness and diversity, and that this is modulated by species traits and
 shore morphology. 2.Germination of 20 wetland plant species with different
 dispersal capacities (floating capacity expressed as seed floatation
 half-time) and soil moisture preferences for germination (Ellenberg F) was
 tested on artificial shores in 24 outdoor ponds in 2 complementary
 experiments over 8 weeks. The “dispersal experiment” tested the effect of
 water regime on recruitment of hydrochorously dispersing seeds. The “seed
 bank experiment” tested the effect of water regime on germination from a
 sown seed bank, on steep and gradual shores. 3.In the dispersal
 experiment, the drawdown regime increased recruitment and species
 richness. Longer floating species colonised a larger shoreline section.
 Soil moisture preference for germination did not determine colonisation
 patterns. 4.In the seed bank experiment, the drawdown regime increased the
 number of seedlings on gradual sloping shores, but not on steep shores.
 The number of germinating seedlings corresponded to the area subjected to
 the drawdown regime in both shore types. Species richness was not affected
 by water regime or shore morphology, and species traits did not determine
 shoreline colonisation. Most seeds germinated in moist soil conditions for
 all species. 5.Synthesis. A spring drawdown instead of stable water regime
 stimulates establishment of hydrochorously dispersing seeds in temperate
 wetlands, leading to higher species richness and diversity. Germination
 from the seed bank is more affected by water regime and shore surface than
 by the tested species traits. Species traits, water levels and shore
 morphology together determine wetland plant community assembly, with
 dispersal as the main driver of seedling community diversity. Water level
 regulations and shore morphology can be used to influence plant
 communities in wetland restoration.
description: Dispersal experiment
 dataData from the seed
 release experimentDispersal Jrl Ecol
 2014.xlsxSeed bank experiment
 dataData on the number of
 germinating seeds sown on the mats subjected to different water
 regimesSeed
 bank Jrl Ecol 2014.xlsx
DOI: 10.5061/dryad.438q3
title: Data from: Multi-scale temporal patterns in fish presence in a high-velocity tidal channel

description: The natural variation of fish presence in high-velocity tidal channels is
 not well understood. A better understanding of fish use of these areas
 would aid in predicting fish interactions with marine hydrokinetic (MHK)
 devices, the effects of which are uncertain but of high concern. To
 characterize the patterns in fish presence at a tidal energy site in
 Cobscook Bay, Maine, we examined two years of hydroacoustic data
 continuously collected at the proposed depth of an MHK turbine with a
 bottom-mounted, side-looking echosounder. The maximum number of fish
 counted per hour ranged from hundreds in the early spring to over 1,000 in
 the fall. Counts varied greatly with tidal and diel cycles in a seasonally
 changing relationship, likely linked to the seasonally changing fish
 community of the bay. In the winter and spring, higher hourly counts were
 generally confined to ebb tides and low slack tides near sunrise and
 sunset. In summer and fall of each year, the highest fish counts shifted
 to night and occurred during ebb, low slack, and flood tides. Fish counts
 were not linked to current speed, and did not decrease as current speed
 increased, contrary to observations at other tidal power sites. As fish
 counts may be proportional to the encounter rate of fish with an MHK
 turbine at the same depth, highly variable counts indicate that the risk
 to fish is similarly variable. The links between fish presence and
 environmental cycles at this site will likely be present at other
 locations with similar environmental forcing, making these observations
 useful in predicting potential fish interactions at tidal energy sites
 worldwide.
description: Viehman and Zydlewski
 2017 Fish Count DataThis .csv file contains
 the two-year time series of the hourly counts of fish that were used in
 the publication, with corresponding tidal and diel
 stages.Viehman Zydlewski Fish Counts
 3-24-2017.csv
DOI: 10.5061/dryad.pm162
title: Data from: Reproductive character displacement of female mate preferences for male cuticular hydrocarbons in Drosophila subquinaria

description: Several lines of evidence implicate sexual isolation in both initiating
 and completing the speciation process. While its existence is
 straightforward to demonstrate, understanding the evolution of sexual
 isolation requires identifying the underlying phenotypes responsible so
 that we can determine how these have diverged. Here we study geographic
 variation in female mate preferences for male sexual displays in the fly
 Drosophila subquinaria. Female D. subquinaria that are sympatric with its
 sister species D. recens discriminate strongly against both D. recens and
 allopatric conspecific males, whereas females from allopatric populations
 do not. Furthermore, female mate preferences target at least in part a
 suite of cuticular hydrocarbons (CHCs) in males and geographic variation
 in CHCs mirrors the pattern of mate discrimination. In this study we
 quantify female mate preferences for male CHCs from populations that span
 the geographic range of D. subquinaria. We find that the direction of
 linear sexual selection varies significantly between populations that are
 sympatric vs. allopatric with D. recens in a pattern of reproductive
 character displacement. Differences in preference partially align with
 existing differences in CHCs and patterns of sexual isolation, although
 discrepancies remain that suggest the involvement of additional traits
 and/and more complex, nonlinear preference functions.
description: D. serrata mating trial
 CHC dataThis file contains the
 gas chromatography data for the epicuticular hydrocarbons (i.e. CHCs) of
 Drosophila subquinaria ‘mixed stock’ males that were used in binomial
 choice mating trials with females from each of eight geographic
 populations. Each row is the data for one male. The columns indicate the
 day of the mating trial (Day), the replicate vial number (Vial), whether
 the male was chosen (i.e. mated) or not by the female during the trial
 (Chosen) and denoted as 1 vs. 0 respectively, the population of the female
 used in the trial (Pop), and whether this population is sympatric or
 allopatric to Drosophila recens (Type), with inland allopatric and coastal
 allopatric regions further denoted. Line denotes the isofemale line from
 which the female derived. See Table 1 of the paper for a description of
 the population abbreviations. GC data has had outliers removed but is
 untransformed and therefore represents the raw, integrated values. Peaks
 are numbered as described in Curtis et al. 2013. Epicuticular compounds of
 Drosophila subquinaria and D. recens: Identification, quantification, and
 their role in female mate choice. Journal of Chemical Ecology: 39:
 579–590.Preference_dryad.csv
DOI: 10.5061/dryad.bh4kt
title: Data from: Poor infant and young child feeding practices and sources of caregivers’ feeding knowledge in rural Hebei Province, China: findings from a cross-sectional survey

description: Objectives: To obtain a general overview of infant and young child feeding
 practices in one rural county in China and identify current delivery
 channels and challenges. Design: A cross-sectional study. Setting: A rural
 county, Zhao County, in Hebei Province, China. Participants: 10 clusters
 were first selected within each township (16 townships in total) with
 proportional to population size sampling. In each cluster, a name list was
 used to select 13 children aged 0–23 months. We interviewed caregivers of
 all the selected children. Primary and secondary outcomes measures:
 Coverage of infant feeding practices, reasons for low coverage of infant
 feeding practices and current delivery channels of infant feeding
 practices. Results: Findings from our survey indicated that infant feeding
 practices were poor. Early initiation of breastfeeding was only 22.4%,
 exclusive breastfeeding for 6 months was less than 10% and continued
 breastfeeding up to the age of two was just 38.2%. Only 32.5% of children
 were given iron-rich or iron-fortified foods. The leading sources of
 infant feeding information were family members, neighbours, friends and
 popular media. Only around 20% of the information came from health
 facilities and nearly none came from communities. Household property data
 showed that 99.9% of households owned televisions and 99.4% owned mobile
 phones. In addition, 61.2% of the households owned computers, with 54.8%
 having access to the internet. Conclusions: Few caregivers of children in
 Zhao County received feeding information during pregnancy and after
 delivery. Moreover, their feeding knowledge and practices were poor.
 Multi-channel approaches, delivered through health facilities, community
 resources, popular media, the internet and mobile phones, hold potential
 to improve infant feeding practices and should be explored in future
 studies. Strengths and limitations: Although this study took place only
 within one county, a full range of globally standard feeding indicators
 was used to assess the feeding practices of caregivers in our study. The
 name lists of children in some villages may not be complete, and therefore
 selection bias may have occurred. Some indicators may have recall bias due
 to long recall time. Trial registration number: ChiCTR-PRC-11001446.
description: The maternal, newborn
 and child health (MNCH) household survey dataThe data include
 household information, antenatal care, delivery and neonatal care,
 breastfeeding and nutrition, immunization, etc.Household survey data upload to
 BMJ open- rev2.xlsxRead Me (Explanation of all the
 variables in the database)-rev2.xlsx