cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vv277
title: Data from: Contemporary population structure and post-glacial genetic demography in a migratory marine species, the blacknose shark, Carcharhinus acronotus

description: Patterns of population structure and historical genetic demography of
 blacknose sharks in the western North Atlantic Ocean were assessed using
 variation in nuclear-encoded microsatellites and sequences of
 mitochondrial (mt)DNA. Significant heterogeneity and/or inferred barriers
 to gene flow, based on microsatellites and/or mtDNA, revealed the
 occurrence of five genetic populations localized to five geographic
 regions: the southeastern U.S Atlantic coast, the eastern Gulf of Mexico,
 the western Gulf of Mexico, Campeche Bay in the southern Gulf of Mexico,
 and the Bahamas. Pairwise estimates of genetic divergence between sharks
 in the Bahamas and those in all other localities were more than an order
 of magnitude higher than between pairwise comparisons involving the other
 localities. Demographic modelling indicated that sharks in all five
 regions diverged after the last glacial maximum and, except for the
 Bahamas, experienced post-glacial, population expansion. The patterns of
 genetic variation also suggest that the southern Gulf of Mexico may have
 served as a glacial refuge and source for the expansion. Results of the
 study demonstrate that barriers to gene flow and historical genetic
 demography contributed to contemporary patterns of population structure in
 a coastal migratory species living in an otherwise continuous marine
 habitat. The results also indicate that for many marine species, failure
 to properly characterize barriers in terms of levels of contemporary gene
 flow could in part be due to inferences based solely on equilibrium
 assumptions. This could lead to erroneous conclusions regarding levels of
 connectivity in species of conservation concern.
description: mtDNA
 haplotypesHaplotypes.txtFull data, blacknose sharkLocations, mtdNA haplotypes and microsatellite genotypesMicrosatellite genotypes of blacknose sharks.xlsx
DOI: 10.5061/dryad.dj828
title: Data from: Costs and benefits of lifetime exposure to mating rivals in male Drosophila melanogaster

description: Theory predicts that males should evolve mechanisms to assess competition
 and allocate resources accordingly. This requires phenotypic plasticity,
 to accurately match responses to the environment. Plastic responses in
 males to sexual competition are diverse and widespread. However, our
 ability to understand and predict how they evolve is limited because their
 benefits are rarely measured, and costs are, as yet, entirely
 unquantified. In the fruit fly Drosophila melanogaster, males that
 anticipate strong competition for matings or fertilisations subsequently
 mate for longer and transfer more of two key seminal fluid proteins. This
 results in significantly elevated reproductive output. In this study we
 examined the fitness effects of male responses to rivals across the entire
 male lifespan. Males were exposed to rivals or not throughout life whilst
 controlling mating opportunities. Males showed significant responses to
 rivals throughout their lifetimes, associated with significant early-life
 fitness benefits. However, these disappeared after the third mating. There
 were also significant costs – males exposed to rivals took significantly
 fewer mating opportunities in later life and had significantly shorter
 lifespans than controls. The data suggest that there are substantial costs
 for males of mounting plastic responses to the threat of sexual
 competition.
description: Bretman et al 2013
 Evolution DryadOriginal data file
 including metadata.
DOI: 10.5061/dryad.j5cf0
title: Data from: Local adaptation and oceanographic connectivity patterns explain genetic differentiation of a marine diatom across the North Sea-Baltic Sea salinity gradient

description: Drivers of population genetic structure are still poorly understood in
 marine micro-organisms. We exploited the North Sea–Baltic Sea transition
 for investigating the seascape genetics of a marine diatom, Skeletonema
 marinoi. Eight polymorphic microsatellite loci were analysed in 354
 individuals from ten locations to analyse population structure of the
 species along a 1500-km-long salinity gradient ranging from 3 to 30 psu.
 To test for salinity adaptation, salinity reaction norms were determined
 for sets of strains originating from three different salinity regimes of
 the gradient. Modelled oceanographic connectivity was compared to
 directional relative migration by correlation analyses to examine
 oceanographic drivers. Population genetic analyses showed distinct genetic
 divergence of a low-salinity Baltic Sea population and a high-salinity
 North Sea population, coinciding with the most evident physical dispersal
 barrier in the area, the Danish Straits. Baltic Sea populations displayed
 reduced genetic diversity compared to North Sea populations. Growth optima
 of low salinity isolates were significantly lower than those of strains
 from higher native salinities, indicating local salinity adaptation.
 Although the North Sea–Baltic Sea transition was identified as a barrier
 to gene flow, migration between Baltic Sea and North Sea populations
 occurred. However, the presence of differentiated neutral markers on each
 side of the transition zone suggests that migrants are maladapted. It is
 concluded that local salinity adaptation, supported by oceanographic
 connectivity patterns creating an asymmetric migration pattern between the
 Baltic Sea and the North Sea, determines genetic differentiation patterns
 in the transition zone.
description: growth
 ratesThis file contains data
 on growth rates (intrinsic rate of increase, µ) of Skeletonema marinoi
 strains isolated from the Baltic Sea and the Swedish west coast. The
 average values are based on measured growth rates of 10 monoclonal strains
 grown in f/4+Si for 5-7 days in +10 C in a light intensity of 40 µmol s-1
 m-2. Strains were acclimatized to respective salinity during one week
 prior to the growth experiment.Microsatellite genotypes
 (Skeletonema marinoi)This file contains
 allelic information on 354 individuals (8 loci) of Skeletonema marinoi
 isolated from the Baltic Sea and NE North Sea.genotypes.xlsxsampling locationsThis file contains the exact coordinates of the ten sampling stations in this study.directional relative migrationThis file contains the raw data for directional relative migration between the ten Skeletonema marinoi populations. More information in the ReadMe file.oceanographic connectivityThis file contains matrices of oceanographic connectivity between the ten sampling stations. More information in the associated ReadMe file.
DOI: 10.5061/dryad.dh05q
title: Data from: Survival relative to new and ancestral host plants, phytoplasma infection and genetic constitution in host races of a polyphagous insect disease vector

description: Dissemination of vectorborne diseases depends strongly on the
 vector's host range and the pathogen's reservoir range. Because
 vectors interact with pathogens, the direction and strength of a
 vector's host shift is vital for understanding epidemiology and is
 embedded in the framework of ecological specialization. This study
 investigates survival in host-race evolution of a polyphagous insect
 disease vector, Hyalesthes obsoletus, whether survival is related to the
 direction of the host shift (from field bindweed to stinging nettle), the
 interaction with plant-specific strains of obligate vectored
 pathogens/symbionts (stolbur phytoplasma), and whether survival is related
 to genetic differentiation between the host races. We used a twice
 repeated, identical nested experimental design to study survival of the
 vector on alternative hosts and relative to infection status. Survival was
 tested with Kaplan–Meier analyses, while genetic differentiation between
 vector populations was quantified with microsatellite allele frequencies.
 We found significant direct effects of host plant (reduced survival on
 wrong hosts) and sex (males survive longer than females) in both host
 races and relative effects of host (nettle animals more affected than
 bindweed animals) and sex (males more affected than females). Survival of
 bindweed animals was significantly higher on symptomatic than
 nonsymptomatic field bindweed, but in the second experiment only.
 Infection potentially had a positive effect on survival in nettle animals
 but due to low infection rates the results remain suggestive. Genetic
 differentiation was not related to survival. Greater negative
 plant-transfer effect but no negative effect of stolbur in the derived
 host race suggests preadaptation to the new pathogen/symbiont strain
 before strong diversifying selection during the specialization process.
 Physiological maladaptation or failure to accept the ancestral plant will
 have similar consequences, namely positive assortative mating within host
 races and a reduction in the likelihood of oviposition on the alternative
 plant and thus the acquisition of alternative stolbur strains.
description: DRYAD_SurvivalExcel table with individual survival dataDRYAD_genotypesGenotype data file for survival analysis of Hyalethes obsoletus - Structure input file.
DOI: 10.5061/dryad.c09b0
title: Data from: Morphological clocks in palaeontology, and a mid-Cretaceous origin of crown Aves

description: The limited fossil evidence for modern (crown) birds during the Cretaceous
 is consistent with a recent (Palaeogene) radiation; however, molecular
 clock studies have consistently suggested that modern birds radiated deep
 in the Mesozoic, with the paucity of fossils prior to the latest
 Cretaceous explainable by preservational bias. This issue is here
 addressed using Bayesian methods which integrate stratigraphical and
 morphological data to simultaneously infer evolutionary relationships and
 divergence times. These analyses place the diversification of modern birds
 in the mid-Cretaceous (~100-110Ma), only slightly more recent than many
 genetic studies, and congruent with latest molecular estimates.
description: S1_FullStratigraphic Ages and SourcesS2_CharacterMatrixChangesAdditions to Published Character MatrixS3_MrBayesMatrixData Matrix with all MrBayes commands
DOI: 10.5061/dryad.m01st7p0
title: Data from: Testing of the effect of missing data estimation and distribution in morphometric multivariate data analyses

description: Missing data are an unavoidable problem in biological datasets and the
 performance of missing data deletion and estimation techniques in
 morphometric datasets are poorly understood. Here a novel method is used
 to measure the introduced error of multiple techniques on a representative
 sample. A large sample of extant crocodilian skulls was measured and
 analyzed with principal components analysis (PCA). Twenty-three different
 proportions of missing data were introduced into the dataset, estimated,
 analyzed, and compared to the original result using Procrustes
 superimposition. Previous work investigating the effects of missing data
 input missing values randomly, a non-biological phenomenon. Here, missing
 data were introduced into the dataset using three methodologies: purely at
 random, as a function of the Euclidean distance between respective
 measurements (simulating anatomical regions), and as a function of the
 portion of the sample occupied by each taxon (simulating unequal missing
 data in rare taxa). Gower’s distance was found to be the best performing
 non-estimation method, and Bayesian PCA the best performing estimation
 method. Specimens of the taxa with small sample sizes and those most
 morphologically disparate had the highest estimation error. Distribution
 of missing data had a significant effect on the estimation error for
 almost all methods and proportions. Taxonomically biased missing data
 tended to show similar trends to random, but with higher error rates.
 Anatomically biased missing data showed a much greater deviation from
 random than the taxonomic bias, and with magnitudes dependent on the
 estimation method.
description: Online
 Appendix1_BrownetalDescription of the
 cranial morphometric variables and data used for in Brown et al. Syst.
 Biol., originally from Dodson, 1975. For illustration see Figure 1. For
 justification of variables see Dodson, 1975. All variables measured to the
 nearest mm.Online
 Appendix2_BrownetalR Scripts for functions
 in - Brown, Arbour and Jackson, Testing of the Effect of Missing Data
 Estimation and Distribution in Morphometric Multivariate Data Analyses,
 Systematic Biology.
DOI: 10.5061/dryad.411mv
title: Data from: Sizing ocean giants: patterns of intraspecific size variation in marine megafauna

description: What are the greatest sizes that the largest marine megafauna obtain? This
 is a simple question with a difficult and complex answer. Many of the
 largest-sized species occur in the world’s oceans. For many of these,
 rarity, remoteness, and quite simply the logistics of measuring these
 giants has made obtaining accurate size measurements difficult. Inaccurate
 reports of maximum sizes run rampant through the scientific literature and
 popular media. Moreover, how intraspecific variation in the body sizes of
 these animals relates to sex, population structure, the environment, and
 interactions with humans remains underappreciated. Here, we review and
 analyze body size for 25 ocean giants ranging across the animal kingdom.
 For each taxon we document body size for the largest known marine species
 of several clades. We also analyze intraspecific variation and identify
 the largest known individuals for each species. Where data allows, we
 analyze spatial and temporal intraspecific size variation. We also provide
 allometric scaling equations between different size measurements as
 resources to other researchers. In some cases, the lack of data prevents
 us from fully examining these topics and instead we specifically highlight
 these deficiencies and the barriers that exist for data collection.
 Overall, we found considerable variability in intraspecific size
 distributions from strongly left- to strongly right-skewed. We provide
 several allometric equations that allow for estimation of total lengths
 and weights from more easily obtained measurements. In several cases, we
 also quantify considerable geographic variation and decreases in size
 likely attributed to humans.
description: Sizing Ocean Giants Data
 and ScriptsBalaenoptera musculus
 and Physeter macrocephalus data were provided by the International Whaling
 Commission (IWC). These data are not included in sizingoceangiants.zip,
 and must be obtained from IWC directly.sizingoceangiants.zip
DOI: 10.5061/dryad.gd126
title: Data from: Effects of water level and grassland management on alpha and beta diversity of wet grassland birds in restored wetlands

description: Nearly 60% of European wetlands have been lost to drainage or to the
 cessation of grassland management. Large amounts of resources are put into
 wetland restoration with the aim to recover biodiversity. However, few
 studies have simultaneously evaluated effects of management, wetness and
 flooding dynamics on biodiversity of restored wetlands such as seasonally
 flooded wet grasslands. We inventoried bird communities over 4 years at
 137 sites (each 3·1 ha) within five restored wet grassland areas in Sweden
 to investigate whether species richness and occurrence of 12 common wet
 grassland species were related to (i) local conditions such as management
 (grazing, mowing and unmanaged areas), basic wetness and spring flooding
 dynamics. Further, we investigated whether (ii) the composition of the
 adjacent landscape (20 ha) related to local bird diversity and (iii)
 species turnover (i.e. beta diversity) differed between sites
 characterized by their basic wetness, degree of flooding and predominant
 management regime. Local species richness was positively linked to degree
 of flooding and basic wetness of grasslands but not to type of grassland
 management. Species richness tended also to be negatively linked to
 proportion of forest at the landscape scale. Although variable, the same
 results were also true concerning the probability of the occurrence of a
 single species at the local scale. Species turnover between sites, and
 thus total species richness, was distinctly higher in (i) grazed as
 compared to mowed grasslands except in dry non-flooded grasslands and (ii)
 flooded as compared to non-flooded sites. Similar patterns held for the
 subset of 12 red-listed species. We suggest that the high beta diversity
 in grazed and flooded grasslands is driven by the heterogeneous vegetation
 structure, resulting in good conditions for foraging and nesting for
 several wet grassland bird species. Synthesis and applications. The
 selection of wetlands for conserving wet grassland birds should prioritize
 temporary flooded grasslands of moderate wetness, preferably far from
 forest edges. Restoration and management of wet grasslands should include
 water level management, removal of shrubs and trees, and low-intensity
 grazing, whereas mowing could be used in non-flooded grasslands of low
 basic wetness.
description: Wet grassland birds in
 SwedenData.txt
DOI: 10.5061/dryad.7jd83
title: Data from: The utility of normalized difference vegetation index for predicting African buffalo forage quality

description: Many studies of mammalian herbivores have employed remotely sensed
 vegetation greenness, in the form of Normalized Difference Vegetation
 Index (NDVI) as a proxy for forage quality. The assumption that reflected
 greenness represents forage quality often goes untested, and limited data
 exist on the relationships between remotely sensed and traditional forage
 nutrient indicators. We provide the first study connecting NDVI and forage
 nutrient indicators within a free-ranging African herbivore ecosystem. We
 examined the relationships between fecal nutrient levels (nitrogen and
 phosphorus), forage nutrient levels, body condition, and NDVI for African
 buffalo (Syncerus caffer) in a South African savanna ecosystem over a
 2-year period (2001 and 2002). We used an information-theoretic approach
 to rank models of fecal nitrogen (Nf) and phosphorus (Pf) as functions of
 geology, season, and NDVI in each year separately. For each year, the
 highest ranked models for Nf accounted for 61% and 65% of the observed
 variance, and these models included geology, season, and NDVI. The
 top-ranked model for Pf in 2001, although capturing 54% of the
 variability, did not include NDVI. In 2002, we could not identify a top
 ranking model for phosphorus (i.e., all models were within 2 AICc of each
 other). Body condition was most highly correlated (equation image;
 P ≤ 0.001) with NDVI at a 1 month time lag and with Nf at a 3 months time
 lag (equation image; P ≤ 0.001), but was not significantly correlated with
 Pf. Our findings suggest that NDVI can be used to index nitrogen content
 of forage and is correlated with improved body condition in African
 buffalo. Thus, NDVI provides a useful means to assess forage quality where
 crude protein is a limiting resource. We found that NDVI accounted for
 more than a seasonal effect, and in a system where standing biomass may be
 high but of low quality, understanding available nutrients is useful for
 management.
description: NP_01-02_KNPThese data comprise the mean fecal Nitrogen and Phosphorous values, for herds sampled in Kruger National Park, South Africa, in 2001 and 2002. These data were used in analyses in Ryan, S.J., Cross, P.C., Winnie, J, Jr, Hay, C., Bowers, J., Getz, W.M. 2012. The utility of NDVI for predicting African buffalo forage quality. Journal of Wildlife Management. 76(7):1499-1508Buffalo Body Condition DataThese data comprise African buffalo body condition scores created from video files in Kruger National park in 2001-2002; a subset of these data were used in Ryan et al, 2012, as described in methods therein. This dataset contains 5,327 observations. DO NOT open this file in Excel, as the age ranges will be read incorrectly.ConditionData.csvVegetation and fecal indicators of Nitrogen and PhosphorousThese vegetation and fecal data were used to describe the relationship between fecal and vegetation Nitrogen (N) and Phosphorous (P) content, in 2002-2003 in Kruger National Park, as described in Ryan et al, 2012veg_fecal.csv
DOI: 10.5061/dryad.dg58v
title: Data from: Does coevolution with a shared parasite drive hosts to partition their defences among species?

description: When mimicry imposes costs on models, selection may drive the model's
 phenotype to evolve away from its mimic. For example, brood parasitism
 often drives hosts to diversify in egg appearance among females within a
 species, making mimetic parasitic eggs easier to detect. However, when a
 single parasite species exploits multiple host species, parasitism could
 also drive host egg evolution away from other co-occurring hosts, to
 escape susceptibility to their respective mimics. This hypothesis predicts
 that sympatric hosts of the same parasite should partition egg phenotypic
 space (defined by egg colour, luminance and pattern) among species to
 avoid one another. We show that eggs of warbler species parasitized by the
 cuckoo finch Anomalospiza imberbis in Zambia partition phenotypic space
 much more distinctly than do eggs of sympatric but unparasitized warblers.
 Correspondingly, cuckoo finch host-races better match their own specialist
 host than other local host species. In the weaver family, parasitized by
 the diederik cuckoo Chrysococcyx caprius, by contrast, parasitized species
 were more closely related and overlapped extensively in phenotypic space;
 correspondingly, cuckoos did not match their own host better than others.
 These results suggest that coevolutionary arms races between hosts and
 parasites may be shaped by the wider community context in which they
 unfold.
description: Egg_Phenotypes_CisticolidaeThis file provides standardized values for ten phenotypic attributes (five pattern, four color, one luminance) from the Cisticolidae family.Egg_Phenotypes_PloceidaeThis file provides standardized values for ten phenotypic attributes (five pattern, four color, one luminance) from the Ploceidae family.
DOI: 10.5061/dryad.m2tj3
title: Data from: Larger brain size indirectly increases vulnerability to extinction in mammals

description: Although previous studies have addressed the question of why large brains
 evolved, we have limited understanding of potential beneficial or
 detrimental effects of enlarged brain size in the face of current threats.
 Using novel phylogenetic path analysis, we evaluated how brain size
 directly and indirectly, via its effects on life-history and ecology,
 influences vulnerability to extinction across 474 mammalian species. We
 found that larger brains, controlling for body size, indirectly increase
 vulnerability to extinction by extending the gestation period, increasing
 weaning age, and limiting litter sizes. However, we found no evidence of
 direct, beneficial or detrimental, effects of brain size on vulnerability
 to extinction, even when we explicitly considered the different types of
 threats that lead to vulnerability. Order-specific analyses revealed
 qualitatively similar patterns for Carnivora and Artiodactyla.
 Interestingly, for Primates, we found that larger brain size was directly
 (and indirectly) associated with increased vulnerability to extinction.
 Our results indicate that under current conditions the constraints on
 life-history imposed by large brains outweigh the potential benefits,
 undermining the resilience of the studied mammals. Contrary to the
 selective forces that have favoured increased brain size throughout
 evolutionary history, at present, larger brains have become a burden for
 mammals.
description: Full
 datasetThis file records all
 data analysed in the published study, describing species-level traits
 including brain size.Gonzalez-Voyer_et_al_Evolution_Brain_Data.csv