cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2j08v
title: Data from: Phylogenetic diversity is a better measure of biodiversity than taxon counting

description: Biodiversity is most commonly measured in taxonomic richness. For example,
 it is common to describe how diverse a genus or a geographic area is by
 counting the number of species within them. Phylogenetic diversity (PD), a
 measurement of the branch lengths in a phylogenetic tree, is a better
 measure of biodiversity that provides a comparable, evolutionary measure
 of biodiversity not possible with species counts. Despite its advantages,
 PD is rarely used as the primary measure of biodiversity. We developed a
 genus‐level phylogeny for nearly 90% of taxonomically described Australian
 land plants and compared PD to genus richness in multiple clades. The
 proportion of PD per genera was skewed among clades. Non‐angiosperm clades
 had more PD than expected given the number of genera while angiosperm
 clades had less PD than expected. For example, ferns comprised only 4.7%
 of the genera yet 13.0% of the PD, while the angiosperms as a whole
 comprised 78.9% of the genera but only 62.7% of the PD. It is likely that
 cultural reasons, such as taxonomic biases, are more important than
 methodological and biological phenomena in explaining these discrepancies.
 Regardless of reasons for the observed results, we conclude that a shift
 towards the use of PD as the primary descriptor of biodiversity will
 promote an important conceptual shift in biodiversity studies as a
 quantitative science.
description: Australian Land Plant
 GeneraMaximum Likelihood,
 Figure S1Seven loci were used in this study: ITS, atpB, trnK, trnL, matK,
 ndhF, and rbcLfinal2363.tre
DOI: 10.5061/dryad.0015d
title: Data from: Rainfall during parental care reduces reproductive and survival components of fitness in a passerine bird

description: Adverse weather conditions during parental care may have direct
 consequences for offspring production, but longer-term effects on juvenile
 and parental survival are less well known. We used long-term data on
 reproductive output, recruitment, and parental survival in northern
 wheatears (Oenanthe oenanthe) to investigate the effects of rainfall
 during parental care on fledging success, recruitment success (juvenile
 survival), and parental survival, and how these effects related to
 nestling age, breeding time, habitat quality, and parental nest visitation
 rates. While accounting for effects of temperature, fledging success was
 negatively related to rainfall (days &gt; 10 mm) in the second half of
 the nestling period, with the magnitude of this effect being greater for
 breeding attempts early in the season. Recruitment success was, however,
 more sensitive to the number of rain days in the first half of the
 nestling period. Rainfall effects on parental survival differed between
 the sexes; males were more sensitive to rain during the nestling period
 than females. We demonstrate a probable mechanism driving the rainfall
 effects on reproductive output: Parental nest visitation rates decline
 with increasing amounts of daily rainfall, with this effect becoming
 stronger after consecutive rain days. Our study shows that rain during the
 nestling stage not only relates to fledging success but also has
 longer-term effects on recruitment and subsequent parental survival. Thus,
 if we want to understand or predict population responses to future climate
 change, we need to consider the potential impacts of changing rainfall
 patterns in addition to temperature, and how these will affect target
 species' vital rates.
description: FledgingSuccessData for analysis of fledging success as detailed in the Methods section of the paper. Variables are explained in the ReadMe file.RecruitmentSuccessData for analysis of recruitment success as detailed in the Methods section of the paper. Variables are explained in the ReadMe file.MaleSuvivalData for analysis of adult male survival as detailed in the Methods section of the paper. Variables are explained in the ReadMe file.FemaleSurvivalData for analysis of adult female survival as detailed in the Methods section of the paper. Variables are explained in the ReadMe file.
DOI: 10.5061/dryad.20617h5g
title: Data from: ALG11 – a new variable DNA marker for sponge phylogeny: comparison of phylogenetic performances with the 18S rDNA and the COI gene

description: Phylogenetic relationships within sponge classes are highly debated. The
 low phylogenetic signal observed with some current molecular data can be
 attributed to the use of few markers, usually slowly-evolving, such as the
 nuclear rDNA genes and the mitochondrial COI gene. In this study, we
 conducted a bioinformatics search for a new molecular marker. We sought a
 marker that (1) is likely to have no paralogs; (2) evolves under a fast
 evolutionary rate; (3) is part of a continuous exonic region; and (4) is
 flanked by conserved regions. Our search suggested the nuclear ALG11 as a
 potential suitable marker. We next demonstrated that this marker can
 indeed be used for solving phylogenetic relationships within sponges.
 Specifically, we successfully amplified the ALG11 gene from DNA samples of
 representatives from all four sponge classes as well as from several
 cnidarian classes. We also amplified the 18S rDNA and the COI gene for
 these species. Finally, we analyzed the phylogenetic performance of ALG11
 to solve sponge relationships compared to and in combination with the
 nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker
 seems to be superior to the widely-used COI marker. Our work thus
 indicates that the ALG11 marker is a relevant marker which can complement
 and corroborate the phylogenetic inferences observed with nuclear
 ribosomal genes. This marker is also expected to contribute to resolving
 evolutionary relationships of other apparently slow-evolving animal phyla,
 such as cnidarians.
description: ALG11 DNA
 alignmentDNA sequence alignment
 of the ALG11 gene in Nexus formatALG_paper.nexCOI DNA alignmentDNA sequence alignment of the COI gene in Nexus formatCOX_paper.nex18S rDNA alignmentDNA sequence alignment of the 18S rRNA gene in Nexus format18S_paper.nexCombined_ALG11_COI_18SrRNA_PhylobayesPhylogenetic tree presented in Figure 4: Bayesian consensus tree reconstructed using the CAT-GTR model for the concatenated DNA sequences of 18S rDNA, ALG11, and COI
DOI: 10.5061/dryad.gm005fg8
title: Data from: A connection between colony biomass and death in Caribbean reef-building corals

description: Increased sea-surface temperatures linked to warming climate threaten
 coral reef ecosystems globally. To better understand how corals and their
 endosymbiotic dinoflagellates (Symbiodinium spp.) respond to environmental
 change, tissue biomass and Symbiodinium density of seven coral species
 were measured on various reefs approximately every four months for up to
 thirteen years in the Upper Florida Keys, United States (1994–2007),
 eleven years in the Exuma Cays, Bahamas (1995–2006), and four years in
 Puerto Morelos, Mexico (2003–2007). For six out of seven coral species,
 tissue biomass correlated with Symbiodinium density. Within a particular
 coral species, tissue biomasses and Symbiodinium densities varied
 regionally according to the following trends: Mexico ≥ Florida Keys ≥
 Bahamas. Average tissue biomasses and symbiont cell densities were
 generally higher in shallow habitats (1–4 m) compared to deeper-dwelling
 conspecifics (12–15 m). Most colonies sampled displayed seasonal
 fluctuations in biomass and endosymbiont density related to annual
 temperature variations. During the bleaching episodes of 1998 and 2005,
 five out of seven species exposed to unusually high temperatures exhibited
 significant decreases in symbiotic algae that, in certain cases, preceded
 further diminishment of tissue biomass. Following bleaching, Montastraea
 spp. colonies with low relative biomass levels died, whereas colonies with
 higher biomass levels survived. Bleaching- or disease-associated mortality
 was also observed in Acropora cervicornis colonies; compared to A.
 palmata, all A. cervicornis colonies experienced low biomass values. Such
 patterns suggest that Montastraea spp. and possibly other coral species
 with relatively low biomass experience increased susceptibility to death
 following bleaching or other stressors than do conspecifics with higher
 tissue biomass levels.
description: Thornhill_etal_DRYAD_datafile
DOI: 10.5061/dryad.65tt7
title: Data from: Feed or fight: testing the impact of food availability and intraspecific aggression on the functional ecology of an island lizard

description: Body size often varies among insular populations relative to continental
 conspecifics – the ‘island rule’ – and functional, context-dependent
 morphological differences tend to track this body size variation on
 islands. Two hypotheses are often proposed as potential drivers of insular
 population differences in morphology: one relating to diet and the other
 involving intraspecific competition and aggression. We directly tested
 whether differences in morphology and maximum bite capacity were explained
 by interisland changes in hardness of both available and consumed prey,
 and levels of lizard-to-lizard aggression among small-island populations.
 Our study included 11 islands in the Greek Cyclades and made use of a
 gradient in island area spanning five orders of magnitude. We focused on
 the widespread lizard Podarcis erhardii. We found that on smaller islands,
 P. erhardii body size was larger, head height was larger relative to body
 size, and maximum bite capacity became proportionally stronger. This
 pattern in morphology and performance was not related to differences in
 diet, but was highly correlated with proxies of intraspecific aggression –
 bite scars and missing toes. Our findings suggest that critical functional
 traits such as body size and bite force in P. erhardii follow the
 predictions of the island rule and are changing in response to changes in
 the competitive landscape across islands of different sizes.
description: Donihue et al. 2015 Feed
 or Fight DataAll data archived here
 were used for analyses in Donihue et al. "Feed or Fight: Testing the
 impact of food availability and intraspecific aggression on the functional
 ecology of an island lizard." Data is in five worksheets. Please see
 ReadMe file for additional information.
DOI: 10.5061/dryad.b8s71
title: Data from: Chloroplast DNA-based phylogeography of Tilia americana (Malvaceae)

description: A comprehensive picture of how plant species and communities move and
 evolve over time will require that a variety of species be studied,
 including plants with different life histories, rarity, and distributions.
 Relatively few phylogeographic studies have focused on trees. In the
 present study, the phylogeographic history of Tilia americana, American
 basswood, was investigated. Samples were collected from throughout the
 United States and Mexican ranges of basswood, and a phylogenetic analysis
 was conducted based on sequence data from two non-coding chloroplast DNA
 regions. The results showed no evidence for the various hypotheses of
 multiple basswood species within the U. S. A., but there is evidence for a
 divergence between a Mexican and U. S. A. clade within basswood.
 Population genetics and spatial statistical analyses were also performed,
 and supported the conclusion that the only significant geographic barrier
 within the North American basswoods is found between U. S. A. and Mexico.
 An attempt was also made to interpret the anomalous geographic
 distribution of certain chloroplast haplotypes, raising further questions
 about past migration routes of North American temperate forest trees.
description: Preliminary screening of
 chloroplast markersMarkers showing a high
 level of intraspecific variability are required for phylogeographic
 analysis. Eleven chloroplast markers and one nuclear marker were
 identified from the literature and screened for variation among
 individuals of Tilia americana s.l. (ranging from n = 5 to n = 14) in
 North America. Supplementary Table 1 lists the locations where T.
 americana specimens were collected for the screening. Supplementary Table
 2 summarizes the screening results, and indicates that chloroplast markers
 rpL32-trnL and ndhF-rpL32 produced the largest amount of informative
 variation. These two markers were then sequenced across a much broader
 sampling of T. americana for the present study.Supplementary Data
 1.pdf
DOI: 10.5061/dryad.017t8
title: Data from: Malat1 as an evolutionarily conserved lncRNA, plays a positive role in regulating proliferation and maintaining undifferentiated status of early-stage hematopoietic cells

description: Background: The metastasis-associated lung adenocarcinoma transcription 1
 (Malat1) is a highly conserved long non-coding RNA (lncRNA) gene. Previous
 studies showed that Malat1 is abundantly expressed in many tissues and
 involves in promoting tumor growth and metastasis by modulating gene
 expression and target protein activities. However, little is known about
 the biological function and regulation mechanism of Malat1 in normal cell
 proliferation. Results: In this study we conformed that Malat1 is highly
 conserved across vast evolutionary distances amongst 20 species of mammals
 in terms of sequence, and found that mouse Malat1 expresses in tissues of
 liver, kidney, lung, heart, testis, spleen and brain, but not in skeletal
 muscle. After treating erythroid myeloid lymphoid (EML) cells with
 All-trans Retinoic Acid (ATRA), we investigated the expression and
 regulation of Malat1 during hematopoietic differentiation, the results
 showed that ATRA significantly down regulates Malat1 expression during the
 differentiation of EML cells. Mouse LRH (Lin-Rhodamine low Hoechst low )
 cells that represent the early-stage progenitor cells show a high level of
 Malat1 expression, while LRB (Lin − Hoechst Low Rhodamine Bright ) cells
 that represent the late-stage progenitor cells had no detectable
 expression of Malat1. Knockdown experiment showed that depletion of Malat1
 inhibits the EML cell proliferation. Along with the down regulation of
 Malat1, the tumor suppressor gene p53 was up regulated during the
 differentiation. Interestingly, we found two p53 binding motifs with help
 of bioinformatic tools, and the following chromatin immunoprecipitation
 (ChIP) test conformed that p53 acts as a transcription repressor that
 binds to Malat1’s promoter. Furthermore, we testified that p53 over
 expression in EML cells causes down regulation of Malat1. Conclusions: In
 summary, this study indicates Malat1 plays a critical role in maintaining
 the proliferation potential of early-stage hematopoietic cells. In
 addition to its biological function, the study also uncovers the
 regulation pattern of Malat1 expression mediated by p53 in hematopoietic
 differentiation. Our research shed a light on exploring the Malat1
 biological role including therapeutic significance to inhibit the
 proliferation potential of malignant cells.
description: matree-fastaData used for Figure 1C, "Evolutionary Tree of Malat1 in Mammals"matree.nwkData used for Figure 1C, "Evolutionary Tree of Malat1 in Mammals"matree.pdfmatree.megData used for Figure 1C, "Evolutionary Tree of Malat1 in Mammals". File created in MEGA 6.06Figure 1
DOI: 10.5061/dryad.50070
title: Data from: Rise and fall of a hybrid zone: implications for the roles of aggression, mate choice, and secondary succession

description: Hybridization can be an important evolutionary force by generating new
 species and influencing evolution of parental species in multiple ways,
 including introgression and the consequences of hybrid vigor. Determining
 the ecological processes underlying evolution in hybrid zones is difficult
 however because it requires examining changes in both genotypic
 frequencies over time and corresponding ecological information, data that
 are rarely collected together. Here, we describe genetic and ecological
 aspects of a hybrid zone between the Eastern Fence Lizard, Sceloporus
 undulatus, and the Florida Scrub Lizard, Sceloporus woodi, occurring over
 at least 23 generations. The hybrid zone, discovered greater than 35 years
 ago using morphological characters, originally consisted of nearly even
 proportions of parental species and hybrids. Now, using genetic markers
 (species-diagnostic mtDNA sites and 6 nDNA microsatellite loci across a
 total of n = 117 individuals), we confirm not only that hybridization
 occurred but also that subsequent backcrossing has resulted in highly
 introgressed hybrids, with many hybrids containing mitochondrial DNA from
 one species on a nuclear DNA background of the other. Ecological aspects
 explaining these shifts in genetic composition include female mate choice,
 changes in habitat associated with secondary succession, and, most
 strongly, a hierarchy of male territorial advantage—ecological mechanisms
 likely to be involved in the emergence and disappearance of many animal
 hybrid zones. Our results suggest that genetic assimilation is not a
 significant threat to either species and that rather transient hybrid
 zones such as this may serve to increase genetic diversity and are
 candidates for causing genetic discordance in phylogeographic analyses.
description: Species-diagnostic mtDNA
 assignment data - BanII and BstBIRobbins et al 2014 JOH
 Dryad-mtDNA data.xlsxMicrosatelite data -
 base pair sizes Sceloporus woodi and S. undulatus Ocala
 FLRobbins et
 al 2014 JOH Dryad-nDNA microsat data.xlsxResults of Structure
 analysis - assignment to Sceloporus woodi, Sceloporus undulatus, or Hybrid
 q-valuesRobbins et al 2014 JOH
 Dryad-Microsat StructureResults.xlsxMorphology, phenetics
 and scale counts, with assignments to Sceloporus undulatus, Sceloporus
 woodi, or hybrid z-scoresSex, scale counts and
 species assignment data. Followed methods by Jackson 1973 Evolution
 27:58-68Robbins et al 2014 JOH
 Dryad-MorphCharactersAssignments.xlsx
DOI: 10.5061/dryad.22rm1728
title: Data from: Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches

description: The effective population size (Ne) could be the ideal parameter for
 monitoring populations of conservation concern as it conveniently
 summarizes both the evolutionary potential of the population and its
 sensitivity to genetic stochasticity. However, tracing its change through
 time is difficult in natural populations. We applied four new methods for
 estimating Ne from a single sample of genotypes to trace temporal change
 in Ne for bears in the Northern Dinaric Mountains. We genotyped 510 bears
 using 20 microsatellite loci, and determined their age. The samples were
 organized into cohorts with regard to the year when the animals were born
 and yearly samples with age categories for every year when they were
 alive. We used the Estimator by Parentage Assignment (EPA) to directly
 estimate both Ne and generation interval for each yearly sample. For
 cohorts, we estimated the effective number of breeders (Nb) using Linkage
 Disequilibrium, Sibship Assignment and Approximate Bayesian Computation
 methods, and extrapolated these estimates to Ne using the generation
 interval. The Ne estimate by EPA is 276 (183-350 95% CI), meeting the
 inbreeding-avoidance criterion of Ne &gt; 50 but short of the
 long-term minimum viable population goal of Ne &gt; 500. The results
 obtained by the other methods are highly consistent with this result, and
 all indicate a rapid increase in Ne probably in the late 1990s and early
 2000s. The new single-sample approaches to estimation of Ne provide
 efficient means for including Ne in monitoring frameworks, and will be of
 great importance for future management and conservation.
description: Genotypes of bears from
 SloveniaThe dataset contains
 genotypes of 510 brown bears genotyped on 22 microsatellite loci. They
 were obtained by genotyping tissue samples of legally killed bears between
 2003 and 2008. Genotype on locus G10H is unrealiable (genotyping
 problems), and locus Mu26 has null alleles. Both were excluded from
 analysis, and have some missing data. All genotypes are complete on all
 other loci. Additional information is the age data (determined by tooth
 cross-section), sex and the date of mortality. Columns in the table:
 sample - laboratory name of the sample; sex - sex of the animal (recorded
 by the field crew and rechecked by genotyping the SRY marker); date_killed
 - the date on which the animal was killed; born - year of birth, estimated
 using the age data; age_months - age of the animal in months, calculated
 from the age determined by tooth cross-section, Feb 1 as the birthday and
 the recorded date of death. Genotypes: alleles at each locus are recorded
 in two columns, e.g. Cxx20_1, Cxx20_2. Missing data at loci G10H and Mu26
 are recorded as "NA".Genotypes_BearsSlovenia.txt
DOI: 10.5061/dryad.b5837
title: Data from: Disruptive viability selection on a black plumage trait associated with dominance

description: Traits used in communication, such as colour signals, are expected to have
 positive consequences for reproductive success, but their associations
 with survival are little understood. Previous studies have mainly
 investigated linear relationships between signals and survival, but both
 hump-shaped and U-shaped relationships can also be predicted, depending on
 the main costs involved in trait expression. Furthermore, few studies have
 taken the plasticity of signals into account in viability selection
 analyses. The relationship between signal expression and survival is of
 particular interest in melanin-based traits, because their main costs are
 still debated. Here, we first determined the main factors explaining
 variability in a melanin-based trait linked to dominance: the bib size of
 a colonial bird, the sociable weaver Philetairus socius. We then used
 these analyses to obtain a measure representative of the individual mean
 expression of bib size. Finally, we used capture-recapture models to study
 how survival varied in relation to bib size. Variation in bib size was
 strongly affected by year and moderately affected by age, body condition
 and colony size. In addition, individuals bearing small and large bibs had
 higher survival than those with intermediate bibs, and this U-shaped
 relationship between survival and bib size appeared to be more pronounced
 in some years than others. These results constitute a rare example of
 disruptive viability selection, and point towards the potential importance
 of social costs incurred by the dominance signalling function of badges of
 status.
description: Data for
 capture-recapture analysesThis dataset contains
 individual encounter histories (2002-2012) starting the year of first
 photography, with covariates: sex, raw bib size measurements and their
 squared values (taken the year of first photography), standardized bib
 size measurements and their squared values (taken the year of first
 photography, and standardized within this year), mean adjusted bib sizes
 and their squared values, and individual identities (band numbers). The
 file format is "headed" (i.e. containing explicit label for each
 column) with "txt" extension, which is compatible with E-SURGE
 and easily convertible with EXCEL (or equivalent) or R for any other
 use.SW CR -
 BIB DATA.txtData for variability
 analysesThis dataset contains
 all bib size measurements obtained from photographies taken at captures
 and recaptures events in the field (without any transformation). The
 dataset also contains covariates used to model bib size variation with
 mixed models: sex, year, colony size, age, body mass, tarsus length,
 colony identity and individual identity. The file format is
 "csv" which can be easily opened with EXCEL (or equivalent) and
 R for processing.SW BIB SIZE -
 COVARIATES.csv