cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s3r4hn4p
title: Data from: Ecologically relevant dispersal of corals on isolated reefs: implications for managing resilience

description: Coral reefs are in decline worldwide, and marine reserve networks have
 been advocated as a powerful management tool for maximizing the resilience
 of coral communities to an increasing variety, number, and severity of
 disturbances. However, the effective design of reserves must account for
 the spatial scales of larval dispersal that affect the demography of
 communities over ecological time frames. Ecologically relevant distances
 of dispersal were inferred from DNA microsatellite data in a
 broadcast-spawning (Acropora tenuis) and a brooding (Seriatopora hystrix)
 coral at isolated reef systems off northwest Australia. Congruent with
 expectations based on life histories, levels of genetic subdivision among
 populations were markedly higher in the brooder than in the broadcast
 spawner. Additionally, significant subdivision for both species between
 systems (&gt;100 km), and between (&gt;10 km) or within reefs
 (&lt;10 km) within systems, indicated that many reefs or reef patches
 are demographically independent. There was also a clear distinction in the
 scale of genetic structure between the different systems; at the more
 geographically complex of the systems, a much finer scale structure was
 detected in both species. This suggested that the hydrodynamics associated
 with these complex reefs restrict distances regularly traveled by larvae.
 The primary implication is that short-term recovery of these coral
 communities after severe disturbance requires the input of larvae from
 viable communities kilometers to a few tens of kilometers away. Therefore,
 to be self-sustaining, we suggest that coral reef protected areas need to
 be large enough to encompass these routine dispersal distances. Further,
 to facilitate recovery from severe disturbances, protected areas need to
 be replicated over these spatial scales. However, specific designs also
 need to account for size, complexity, and isolation of reefs, which will
 either restrict or enhance dispersal within this range.
description: ecologically relevant
 dispersal_Shystrix&Atenuis@offshoreNWA_rawdata
DOI: 10.5061/dryad.33bf108
title: Data from: Structural and defensive roles of angiosperm leaf venation network reticulation across an Andes-Amazon elevation gradient

description: 1.The network of minor veins of angiosperm leaves may include loops
 (reticulation). Variation in network architecture has been hypothesized to
 have hydraulic and also structural and defensive functions. 2.We measured
 venation network trait space in eight dimensions for 136 biomass-dominant
 angiosperm tree species along a 3,300 m elevation gradient in southeastern
 Peru. We then examined the relative importance of multiple ecological, and
 evolutionary predictors of reticulation. 3.Variation in minor venation
 network reticulation was constrained to three axes. These axes described
 branching vs. reconnecting veins, elongated vs. compact areoles, and high
 vs. low density veins. Variation in the first two axes was predicted by
 traits related to mechanical strength and secondary compounds, and in the
 third axis by site temperature. 4.Synthesis. Defensive and structural
 factors primarily explain variation in multiple axes of reticulation, with
 a smaller role for climate-linked hydraulic factors. These results suggest
 that venation network reticulation may be determined more by species
 interactions than by hydraulic functions.
description: Trait
 dataVenation, trait, and
 climate data for tree species on an Andes-Amazon transect in southeastern
 Peru (CHAMBASA project).Data
 S1.csv
DOI: 10.5061/dryad.88606
title: Data from: Paternal epigenetic effects of population density on locust phase-related characteristics associated with heat-shock protein expression

description: Many species exhibit transgenerational plasticity by which environmental
 cues experienced by either parent can be transmitted to their offspring,
 resulting in phenotypic variants in offspring to match ancestral
 environments. However, the manner by which paternal experiences affect
 offspring plasticity through epigenetic inheritance in animals generally
 remains unclear. In this study, we examined the transgenerational effects
 of population density on phase-related traits in the migratory locust
 Locusta migratoria. Using an experimental design that explicitly controls
 genetic background, we found that the effects of crowd or isolation
 rearing on phase plasticity could be inherited to the offspring. The
 isolation of gregarious locusts resulted in reduced weight in offspring
 eggs and altered morphometric traits in hatchlings, whereas crowding of
 solitarious locusts exhibited opposite effects. The consequences of
 density changes were transmitted by both maternal and paternal
 inheritance, although the expression of paternal effects was not as
 pronounced as that of maternal effects. Prominent expression of heat-shock
 proteins (Hsps), such as Hsp90, Hsp70, and Hsp20.6, could be triggered by
 density changes. Hsps were significantly upregulated upon crowding but
 downregulated upon isolation. The variation in parental Hsp expression was
 also transmitted to the offspring, in which the pattern of inheritance was
 consistent with that of phase characteristics. These results revealed a
 paternal effect on phase polyphenism and Hsp expression induced by
 population density, and defined a model system that could be used to study
 the paternal epigenetic inheritance of environmental changes.
description: Raw
 data_MEC-14-1210.R2Data for adult
 morphology and coloration, egg weight and larval morphormetric traits, and
 data for gene expression. Ten separate files plus one Readme file are
 included in the data.
DOI: 10.5061/dryad.k6516
title: Data from: Axial xylem architecture of Larix decidua exposed to CO2 enrichment and soil warming at the treeline

description: 1. Trees continuously adjust their axial xylem structure to meet changing
 needs imposed by ontogenetic and environmental changes. These axial
 structure-function responses need to be coordinated among competing
 biophysical constraints to avoid failure of the xylem system. Here, we
 investigated if ontogeny or experimental manipulation of CO2 and soil
 temperature influence these structure-function responses. 2. We performed
 detailed xylem cell anatomical quantification along the axis of
 40-year-old Larix decidua trees planted at the Swiss treeline and exposed
 to a combination of elevated CO2 (+200 ppm) and soil warming (+4 °C)
 between 2001 and 2012. We assessed how mean hydraulic tracheid diameter
 (Dh), the cell wall reinforcement ((t/b)2), tracheid wall thickness (CWT)
 and the percent area of ray parenchyma (PERPAR) – proxies for hydraulic
 efficiency, hydraulic safety, biomechanical support and metabolic xylem
 functions, respectively – co-vary along the tree axis. 3. Dh increased
 from the stem apex to base, strictly following a power function (R2=0.81),
 independent from ontogeny and experimental treatments. In contrast, axial
 trends of (t/b)2 and CWT were either influenced by treatment and/or
 ontogeny, or showed no axial trend (PERPAR). Additionally, we found that a
 larger Dh only at the stem apex promoted primary and secondary growth. 4.
 Our approach of analyzing xylem anatomical traits along the tree axis and
 across tree-rings provides novel insights into xylem functional
 architecture and allows reconstructing xylem function over time. We
 conclude that the maintenance of hydraulic efficiency during ontogeny is
 very robust, as the conduit diameter undergoes a strong apical control,
 and plays a fundamental role for assimilation and tree growth. Instead,
 the other functional traits more plastically vary with ontogeny and
 environmental changes.
description: Dataset-fileThis file includes the data used to analyze: i) the axial scaling of the hydraulic diameter (Dh), the 5th percentile of cell wall reinforcement ((t/b)2), the mean wall thickness of latewood tracheids (CWTLW) and the percent of ray parenchyma (PERPAR); ii) the treatment effect on the axial scaling of the above mentioned functional traits; iii) the functional traits trade-off during ontogeny and under different treatments; iv) the hydraulic efficiency in terms of costs and effects on tree growth. Variables are organized in columns and named with the acronyms described in Table 1 and Table 2. The first two columns identify the tree and the disc respectively. Every row corresponds to the value of an individual ring.Dataset_FE_29.08.2017.xlsx
DOI: 10.5061/dryad.jq203737
title: Data from: Determination of the cost of worker reproduction via diminished lifespan in the ant Diacamma sp.

description: Workers of social Hymenoptera can usually produce male offspring, but
 rarely do so in the presence of a queen despite the potential individual
 fitness benefit. Various mechanisms have been hypothesized to regulate
 worker reproduction, including avoiding the colony-level cost of worker
 reproduction. However, firm quantitative evidence is lacking to support
 that hypothesis. Here, we accurately quantified this cost by studying an
 ant species (Diacamma sp.) in which worker reproduction is rare in the
 presence of the gamergate (the functional queen). A series of experiments
 to manipulate worker–gamergate contact revealed that short-term
 brood-production efficiency is not changed by the presence of worker
 reproduction. However, when workers reproduce, their average lifespan is
 reduced to between 74% and 88% of that in the absence of reproduction,
 indicating a long-term cost to the colony. In theory, this cost can
 explain the policing of worker reproduction under a queen-single mating
 system, but the cost does not appear to be high enough to stop worker
 reproduction. When contact with the gamergate is lost, it is only the
 non-reproductive workers whose lifespan was reduced; the reproductive
 workers lived as long as non-orphaned workers. We suggest that an
 increased workload can account for the reduction in lifespan better than a
 trade-off between reproduction and longevity.
description: DiaBroodproduction
 PupaeRaw data that correspond
 to those used in the analysis summarized in Table 1(A) and Table 2(A) of
 Tsuji et al.DiaBroodproduction
 AdultsRaw data used ion the
 analysis summarized Tables 1(B) and 2(B) in Tsuji et
 al.Dialifespan Colony
 IMO-1Raw data used in the
 analysis summarized in Figure 1(A) and (C) of Tsuji et
 al.Dialifespan Colony
 IMO-4Raw data used in the
 analysis summarized in Figure 1(A) and (C) of Tsuji et
 al.Dialifespan Colony
 UENO-4Raw data used in the
 analysis summarized in Figure 1(A) and (C) of Tsuji et
 al.Dialifespan Colony
 AGO-1Raw data used in the
 analysis summarized in Figure 1(B) and (C) of Tsuji et
 al.Dialifespan Colony
 Sasaki-1Raw data used in the
 analysis summarized in Figure 1(B) and Figure 1(C) of Tsuji et
 al.BehavioralChangedata
 Colony M1Raw data used in the
 analysis summarized in Figure 2 of Tsuji et al.BehavioralChangedata
 Colony N1Raw data used in the
 analysis summarized in Figure 2 of Tsuji et al.BehavioralChangedata
 Colony N4Raw data used in the
 analysis summarized in Figure 2 of Tsuji et al.BehavioralChangedata
 Colony N5Raw data used in the
 analysis summarized in Figure 2 of Tsuji et al.BehavioralChangedata
 Y1Raw
 data used in the analysis summarized in Figure 2 of Tsuji et
 al.
DOI: 10.5061/dryad.8qs7bv5
title: Data from: Whole-plant metabolic allocation under water stress

description: Trade-offs between plant growth and defense depend on environmental
 resource availability. Plants are predicted to prioritize growth when
 environmental resources are abundant and defense when environmental
 resources are scarce. Nevertheless, such predictions lack a whole-plant
 perspective-they do not account for potential differences in plant
 allocation above- and belowground. Such accounting is important because
 leaves and roots, though both critical to plant survival and fitness,
 differ in their resource-uptake roles and, often, in their vulnerability
 to herbivores. Here we aimed to determine how water availability affects
 plant allocation to multiple metabolic components of growth and defense in
 both leaves and roots. To do this, we conducted a meta-analysis of data
 from experimental studies in the literature. We assessed plant metabolic
 responses to experimentally reduced water availability, including changes
 in growth, nutrients, physical defenses, primary metabolites, hormones,
 and other secondary metabolites. Both above- and belowground, reduced
 water availability reduced plant biomass but increased the concentrations
 of primary metabolites and hormones. Importantly, however, reduced water
 had opposite effects in different organs on the concentrations of other
 secondary metabolites: reduced water increased carbon-based secondary
 metabolites in leaves but reduced them in roots. In addition, plants
 suffering from co-occurring drought and herbivory stresses exhibited
 dampened metabolic responses, suggesting a metabolic cost of multiple
 stresses. Our study highlights the needs for additional empirical studies
 of whole-plant metabolic responses under multiple stresses and for
 refinement of existing plant growth-defense theory in the context of whole
 plants.
description: Mundim&Pringle_RcodesR codes for the meta-analysisMundim&Pringle_metadata_forExcelFilesmetadata explaining the excel files (the data files)Mundim&Pringle_general_info_dataAll information extracted from the studies used in the meta-analysisMundim&Pringle_metaAnalysis_datathe meta-analysis data
DOI: 10.5061/dryad.970qg720
title: Data from: Support for the immunocompetence handicap hypothesis in the wild: hormonal manipulation decreases survival in sick damselflies

description: The immunocompetence handicap hypothesis (ICHH) states that hormones
 enhance sexual trait expression but impair immunity. Previous tests of the
 ICHH have been hampered by experimental design problems. Here we report on
 an experimental test of the ICHH that includes manipulations of both
 hormones and infections in males of the territorial damselfly, Hetaerina
 americana, with accurate survival measurements. We conducted a fully
 factorial experiment subjecting each individual to one of three topical
 treatments: methoprene (a juvenile hormone analog), acetone, or control,
 and one of three injection treatments: bacteria, PBS, or control. We
 measured survival of manipulated males in both the wild and in captivity.
 As predicted, survival was most heavily impaired in methoprene-bacteria
 males than in the other groups in the wild, and no survival differences
 emerged in captive animals. This result confirms that survival is one cost
 an animal pays for increased hormonal levels. This corroborates
 theoretical predictions of the ICHH.
description: SurvivalFieldMARKEncounter histories of Hetaerina americana males exposed to a topical and an injected treatmentSurvivalCaptivitySurvival of Hetaerina americana males exposed to a topical and an injected treatment in captivity
DOI: 10.5061/dryad.10154
title: Data from: The effect of inbreeding rate on fitness, inbreeding depression and heterosis over a range of inbreeding coefficients

description: Understanding the effects of inbreeding and genetic drift within
 populations and hybridization between genetically differentiated
 populations is important for many basic and applied questions in ecology
 and evolutionary biology. The magnitudes and even the directions of these
 effects can be influenced by various factors, especially by the current
 and historical population size (i.e., inbreeding rate). Using Drosophila
 littoralis as a model species, we studied the effect of inbreeding rate
 over a range of inbreeding levels on 1) mean fitness of a population
 (relative to that of an outbred control population), 2) within-population
 inbreeding depression (reduction in fitness of offspring from inbred vs.
 random mating within a population), and 3) heterosis (increase in fitness
 of offspring from inter-population vs. within-population random mating).
 Inbreeding rate was manipulated by using three population sizes (2, 10,
 and 40), and fitness was measured as offspring survival and fecundity.
 Fast inbreeding (smaller effective population size) resulted in greater
 reduction in population mean fitness than slow inbreeding, when
 populations were compared over similar inbreeding coefficients.
 Correspondingly, populations with faster inbreeding expressed more
 heterosis upon inter-population hybridization. Inbreeding depression
 within the populations did not have a clear relationship with either the
 rate or the level of inbreeding.
description: Fitness
 measurementsSee ReadMe
 fileData
 Pekkala et al EVOL APPL.xlsx
DOI: 10.5061/dryad.30320
title: Data from: Genes underlying altruism

description: William D. Hamilton postulated the existence of 'genes underlying
 altruism', under the rubric of inclusive fitness theory, a
 half-century ago. Such genes are now poised for discovery. In this article
 we develop a set of intuitive criteria for the recognition and analysis of
 genes for altruism, and describe the first candidates for altruism genes
 from social insects and humans. We also provide evidence from a human
 population for genetically-based tradeoffs, underlain by oxytocin-system
 polymorphisms, between alleles for altruism and alleles for non-social
 cognition. Such tradeoffs between self-oriented and altruistic behaviour
 may influence the evolution of phenotypic diversity across all social
 animals.
description: ThompsonHurdCrespi-SNPdataData for the three SNPsThompsonHurdCrespi-MRTDataMRT data
DOI: 10.5061/dryad.vr666
title: Data from: Heritable variation in maternally-derived yolk androgens, thyroid hormones and immune factors

description: Maternal reproductive investment can critically influence offspring
 phenotype, and thus these maternal effects are expected to be under strong
 natural selection. Knowledge on the extent of heritable variation in the
 physiological mechanisms underlying maternal effects is however limited.
 In birds, resource allocation to eggs is a key mechanism for mothers to
 affect their offspring and different components of the egg may or may not
 be independently adjusted. We studied the heritability of egg components
 and their genetic and phenotypic covariation in great tits (Parus major),
 using captive-bred full siblings of wild origin. Egg mass, testosterone
 (T) and androstenedione (A4) hormone concentrations showed moderate
 heritability, in agreement with earlier findings. Interestingly, yolk
 triiodothyronine hormone (T3), but not its precursor, thyroxine hormone
 (T4), concentration was heritable. An immune factor, albumen lysozyme,
 showed moderate heritability, but yolk immunoglobulins (IgY) did not. The
 genetic correlation estimates were moderate but statistically
 nonsignificant; a trend for a positive genetic correlation was found
 between A4 and egg mass, T and lysozyme and IgY and lysozyme,
 respectively. Interestingly, phenotypic correlations were found only
 between A4 and T, and T4 and T3, respectively. Given that these egg
 components are associated with fitness-related traits in the offspring
 (and mother), and that we show that some components are heritable, it
 opens the possibility that natural selection may shape the rate and
 direction of phenotypic change via egg composition.
description: Ruuskanen: heritability
 of egg componentsRuuskanen_Heredity_NIOO20062010TempAviaries_treat.xlsx
DOI: 10.5061/dryad.gk880
title: Data from: A new Hyperodapedon (Archosauromorpha, Rhynchosauria) from the Upper Triassic of India: implications on Rynchosaur phylogeny

description: A new species of the rhynchosaur genus Hyperodapedon, namely H. tikiensis,
 is described from well-preserved skeletal elements that were collected
 from the Upper Triassic Tiki Formation of India. Hyperodapedon tikiensis
 is diagnosed on the basis of several cranial and postcranial features
 including longer than wide basipterygoid process, crest-shaped maxillary
 cross section lateral to the main longitudinal groove, deeply excavated
 neural arches of mid-dorsal vertebrae, long scapular blade, a pronounced
 deltopectoral crest, proximal humeral end much broader than distal end,
 iliac length greater than iliac height, equal pre- and postacetabular
 iliac lengths and circular femoral cross section. Two distinct morphotypes
 of the maxillary tooth plates can be discerned, which are attributed to
 ontogenetic variations. A maximum-parsimony analysis was carried out to
 show that the order Rhynchosauria is characterized by nine cranial and one
 postcranial character states. The analysis reveals that Otischalkia
 elderae is invalid and the basal forms, Howesia and Mesosuchus, are
 closely related. The Mid-Triassic genus Ammorhynchus is more derived and
 forms a sister group to the Late Triassic subfamily Hyperodapedontinae.
 Isalorhynchus and Teyumbaita are basal to the pandemic genus
 Hyperodapedon. Twenty-four characters that are not homoplasious document
 major patterns of skeletal evolution in rhynchosaurs. From laterally
 oriented scapula and slender propodials, the postcranial skeleton evolved
 into a more robust form as is evident from nearly vertical scapula and
 increase in the robustness of the propodials. Shortening of the femur is
 noted in the derived Late Triassic forms as exemplified in Hyperodapedon
 gordoni, Hyperodapedon huxleyi and H. tikiensis.
description: Mukherjee_Ray_AppendixS1-R2Mukherjee_Ray_AppendixS2-R1Mukherjee_Ray_AppendixS3-R2Mukherjee_Ray_AppendixS4_R2
DOI: 10.5061/dryad.362r0
title: Data from: The linking of plate tectonics and evolutionary divergences

description: It is exciting to be living at a time when the big questions in biology
 can be investigated using modern genetics and computing. Bauzà-Ribot et
 al. take on one of the fundamental drivers of biodiversity, the effect of
 continental drift in the formation of the world’s biota, employing
 next-generation sequencing of whole mitochondrial genomes and modern
 Bayesian relaxed molecular clock analysis. Bauzà-Ribot et al. conclude
 that vicariance via plate tectonics best explains the genetic divergence
 between subterranean metacrangonyctid amphipods currently found on islands
 separated by the Atlantic Ocean. This finding is a big deal in
 biogeography, and science generally, as many other presumed biotic
 tectonic divergences have been explained as probably due to more recent
 transoceanic dispersal events. However, molecular clocks can be
 problematic and we have identified three issues with the analyses of
 Bauzà-Ribot et al. that cast serious doubt on their results and
 conclusions. When we reanalyzed their mitochondrial data and attempted to
 account for problems with calibration [5,6], modeling rates across
 branches and substitution saturation, we inferred a much younger date for
 their key node. This implies either a later trans-Atlantic dispersal of
 these crustaceans, or more likely a series of later invasions of
 freshwaters from a common marine ancestor, but either way probably not
 ancient tectonic plate movements.
description: Sequence data from
 Phillips et al, Current Biology (2013)amphipods30_12_rlc3.xml