cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.681q5
title: Data from: Chronological and biological age predict seasonal reproductive timing: an investigation of clutch initiation and telomeres in birds of known age

description: Female vertebrates that breed earlier in the season generally have greater
 reproductive success. However, evidence suggests that breeding early may
 be costly, thus leading to the prediction that females with fewer future
 reproductive events will breed earlier in the season. While chronological
 age is a good indicator of remaining lifespan, telomere lengths may also
 be good biomarkers of longevity as they potentially reflect lifetime
 'wear and tear' (i.e. "biological age"). We examined
 whether variation in the timing of the first seasonal clutch was related
 to age and telomere length in female dark-eyed juncos (Junco hyemalis),
 predicting that older females and those with shorter telomeres would breed
 earlier. Both predictions held true and were independent of each other, as
 telomere length did not significantly vary with age. These results suggest
 that females may adjust their reproductive effort based on both
 chronological and biological age.
description: Migrant_and_Resident_Dark-eyed_Junco_Telomere_LengthsThis file contains breeding, female junco banding data, year of collection, date of first clutch initiation (the number of days after the first clutch of the year), age (in years), T/S ratio (note: this is a comparative metric- these values can only be compared to other T/S ratios that were run on the same plates), tarsus length (mm), and body weight (in grams).DataForDryad.xlsx
DOI: 10.5061/dryad.ht4t3
title: Data from: Host phenology and potential saprotrophism of ectomycorrhizal fungi in the boreal forest

description: Phenology-induced changes in carbon assimilation by trees may affect
 carbon stored in fine roots and as a consequence, alter carbon allocated
 to ectomycorrhizal fungi. Two competing models exist to explain carbon
 mobilization by ectomycorrhizal fungi. Under the ‘saprotrophy model’,
 decreased allocation of carbon may induce saprotrophic behaviour in
 ectomycorrhizal fungi, resulting in the decomposition of organic matter to
 mobilize carbon. Alternatively, under the ‘nutrient acquisition model’,
 decomposition may instead be driven by the acquisition of nutrients locked
 within soil organic matter compounds, with carbon mobilization a secondary
 process. We tested whether phenology-induced shifts in carbon reserves of
 fine roots of aspen (Populus tremuloides) affect potential activity of
 four carbon-compound degrading enzymes, β-glucuronidase, β-glucosidase,
 N-acetylglucosaminidase and laccase, by ectomycorrhizal fungi.
 Ectomycorrhizal roots from mature aspen were collected across eight stands
 in north-eastern Alberta, Canada, and analysed during tree dormancy, leaf
 flush, full leaf expansion and leaf abscission. We predicted potential
 extracellular enzyme activity to be highest when root carbon reserves were
 lowest, should host phenology induce saprotrophism. Further, we
 anticipated enzyme activity to be mediated by invertase, a plant-derived
 enzyme which makes carbon available to fungal symbionts in the
 plant–fungus interface. Root carbon reserves were positively correlated
 with invertase, suggesting phenology may affect carbon allocation to
 ectomycorrhizal fungi. However, of the four enzymes, host phenology had
 the largest effect on β-glucuronidase, but activity of this enzyme was not
 correlated with root carbon reserves or invertase. Low-biomass
 ectomycorrhizas had greater potential laccase activity than high-biomass
 ectomycorrhizas, highlighting discrete functional traits in fungi for
 litter decomposition. Our results suggest that the decomposition of
 organic matter may be driven by foraging by fungi for nutrients locked
 within organic compounds rather than for mobilizing carbon. Furthermore,
 the potential ability to degrade lignin was more common in low-biomass
 ectomycorrhizas when compared to high-biomass ectomycorrhizas.
description: Potential enzyme
 activity - NSCs - env - allPotentential enzyme
 activity, nonstructural carbohydrates, and environmental
 measurements.Potential enzyme
 activity - exploration typePotential enzyme
 activity of contact and distance exploration types.
DOI: 10.5061/dryad.40gg7
title: Data from: Population-level effects of fitness costs associated with repressible female-lethal transgene insertions in two pest insects

description: Genetic control strategies offer great potential for the sustainable and
 effective control of insect pests. These strategies involve the field
 release of transgenic insects with the aim of introducing engineered
 alleles into wild populations, either permanently or transiently. Their
 efficacy can therefore be reduced if transgene-associated fitness costs
 reduce the relative performance of released insects. We describe a method
 of measuring the fitness costs associated with transgenes by analyzing
 their evolutionary trajectories when placed in competition with wild-type
 alleles in replicated cage populations. Using this method, we estimated
 lifetime fitness costs associated with two repressible female-lethal
 transgenes in the diamondback moth and olive fly as being acceptable for
 field suppression programs. Furthermore, using these estimates of
 genotype-level fitness costs, we were able to project longer-term
 evolutionary trajectories for the transgenes investigated. Results from
 these projections demonstrate that although transgene-associated fitness
 costs will ultimately cause these transgenes to become extinct, even when
 engineered lethality is repressed, they may persist for varying periods of
 time before doing so. This implies that tetracycline-mediated transgene
 field persistence in these strains is unlikely and suggests that realistic
 estimates of transgene-associated fitness costs may be useful in trialing
 ‘uncoupled’ gene drive system components in the field.
description: Raw Data for
 submission
DOI: 10.5061/dryad.2204v
title: Data from: Social discrimination by quantitative assessment of immunogenetic similarity

description: Genes of the major histocompatibility complex (MHC) that underlie the
 adaptive immune system may allow vertebrates to recognise their kin. True
 kin-recognition genes should produce signalling products to which
 organisms can respond. Allelic variation in the peptide-binding region
 (PBR) of MHC molecules determines the pool of peptides that can be
 presented to trigger an immune response. To examine whether these MHC
 peptides also might underlie assessments of genetic similarity, we tested
 whether Xenopus laevis tadpoles socially discriminate between pairs of
 siblings with which they differed in PBR amino acid sequences. We found
 that tadpoles (4 sibships, N=854) associated preferentially with siblings
 with which they were more similar in PBR amino acid sequence. Moreover,
 the strength of their preference for a conspecific was directly
 proportional to the sequence similarity between them. Discrimination was
 graded, and correlated more closely with functional sequence differences
 encoded by MHC class I and class II alleles than with numbers of shared
 haplotypes. Our results thus suggest that haplotype analyses may fail to
 reveal fine-scale behavioural responses to divergence in functionally
 expressed sequences. We conclude that MHC-PBR gene products mediate
 quantitative social assessment of immunogenetic similarity that may
 facilitate kin recognition in vertebrates.
description: PBR raw data
 archiveSpreadsheet of raw
 tadpole assiciation time data and MHC-PBR amino acid stimulus
 differentials.
DOI: 10.6084/m9.figshare.30413173.v1
title: Phase-tuned modulation during reward expectancy in human anterior insular cortex

description: We analyzed intracranial electroencephalographic (iEEG) data from 13 presurgical epilepsy patients navigating a virtual T-maze with predetermined reward zones. During the reward expectancy stage, which is the period immediately before entering the reward zone, we examined AIC signals using representational similarity analysis, phase-amplitude coupling (PAC), and phase precession analysis.
DOI: 10.5061/dryad.rj408
title: Data from: Genetic evidence for prevalence of alloparental care in a socially monogamous biparental cichlid fish, Perissodus microlepis, from Lake Tanganyika supports the "selfish shepherd effect" hypothesis

description: Alloparental care – care for unrelated young – is rare in animals, and its
 ecological or evolutionary advantages or, alternative maladaptive nature,
 remain unclear. We investigate alloparental care in the socially
 monogamous cichlid fish Perissodus microlepis from Lake Tanganyika that
 exhibits bi-parental care. In a genetic parentage analysis, we discovered
 a surprisingly high percentage of alloparental care represented by brood
 mixing, extra-pair paternity and extra-pair maternity in all broods that
 we investigated. The percentage of nondescendant juveniles of other
 parents, i.e., brood mixing, ranged from 5% to 57% (mean = 28%). The
 distribution of genetic parentage also suggests that this socially
 monogamous species has, in fact, polygamous mating system. The prevalence
 of genetically mixed broods can be best explained by two, not mutually
 exclusive hypotheses on farming-out and fostering behaviors. In the
 majority of broods, the sizes of the parents’ own (descendant) offspring
 were significantly larger than those of the adopted (nondescendant)
 juveniles, supporting the ‘selfish shepherd effect’ hypothesis, i.e., that
 foster parents preferentially accept unrelated “smaller or not larger”
 young since this would tend to lower the predation risks for their own
 larger offspring. There was also a tendency for larger parents
 particularly mothers, more so than smaller parents, to care predominantly
 for their own offspring. Larger parents might be better at defending
 against cuckoldry and having foreign young dumped into their broods
 through farming-out behavior. This result might argue for maladaptive
 effects of allopatric care for the foster parents that only larger and
 possibly more experienced pairs can guard against. It needs to be
 determined why, apparently, the ability to recognize one's own young
 has not evolved in this species.
description: Raw dataset of six
 microsatellite loci for the 46 population samples
 genotypedDataset of body sizes of
 genetic parents and proportion of his and her own
 offspringDataset of body sizes
 (skull length) of descendant and nondescendant juveniles
DOI: 10.5061/dryad.gh28q
title: Data from: The cost of growing large: sex-specific costs of post-weaning growth on body mass senescence in a wild mammal

description: Individual body mass often positively correlates with survival and
 reproductive success, whereas fitness costs of growing large are rarely
 detected in vertebrates in the wild. Evidence that adult body mass
 progressively declines with increasing age is accumulating across
 mammalian populations. Growing fast to a large body can increase the
 cellular damage accumulated throughout life, leading body growth in early
 life to be negatively associated with the rate of body mass senescence.
 Moreover, the onset of mass senescence may strongly depend on both
 sex-specific reproductive tactics and environmental conditions. Assessing
 the timing and the rate of body mass decline with increasing age thus
 offers an opportunity to look for costs of having grown fast, especially
 after a poor start during early life, in both sexes and in different
 environments. Using a unique dataset including 30 years of longitudinal
 data on age-specific body mass collected in two roe deer Capreolus
 capreolus populations subjected to contrasted environmental conditions, we
 looked for potential costs of high post-weaning growth rate in terms of
 steeper rate of body mass senescence. Our analyses of body mass senescence
 accounted for the potential variation in the onset of senescence and
 allowed explicit comparisons of this variable between sexes and
 populations. Higher growth rates late in the growing period (after
 weaning) were associated with a steeper rate of body mass senescence,
 regardless of early mass (gained before weaning), but at different extents
 depending on sex and environmental conditions. Body mass senescence
 occurred earlier in males than in females, especially in the population
 facing limiting resources. In the wild, although heavy individuals
 generally survive better than small ones, the costs of growing large late
 in the growing period only became apparent late in life through mass
 senescence.
description: Characteristics of
 individual lifetime measurements of roe deer body massData and variables
 description are reported in the two different sheets.Data_Douhard_et_al.xlsx
DOI: 10.5061/dryad.8rf538cp
title: Data from: Model-based comparisons of phylogeographic scenarios resolve the intraspecific divergence of cactophilic Drosophila mojavensis

description: The cactophilic fly Drosophila mojavensis exhibits considerable
 intraspecific genetic structure across allopatric geographic regions and
 shows associations with different host cactus species across its range.
 The divergence between these populations has been studied for more than 60
 years, yet their exact historical relationships have not been resolved. We
 analysed sequence data from 15 intronic X-linked loci across populations
 from Baja California, mainland Sonora-Arizona and Mojave Desert regions
 under an isolation-with-migration model to assess multiple scenarios of
 divergence. We also compared the results with a pre-existing sequence
 dataset of 8 autosomal loci. We derived a population tree with Baja
 California placed at its base and link their isolation to Pleistocene
 climatic oscillations. Our estimates suggest the Baja California
 population diverged from an ancestral Mojave Desert/mainland
 Sonora-Arizona group around 230-270 Kya, while the split between the
 Mojave Desert and mainland Sonora-Arizona populations occurred one glacial
 cycle later, 117-135 Kya years ago. Although we found these three
 populations to be effectively allopatric, model ranking could not rule out
 the possibility of a low-level of gene flow between two of them. Finally,
 the Mojave Desert population showed a small effective population size,
 consistent with a historical population bottleneck. We show that
 model-based inference from multiple loci can provide accurate information
 on the historical relationships of closely related groups allowing us to
 set into historical context a classic system of incipient ecological
 speciation.
description: IMa2 input
 filesInput files for sequence
 analysis in IMa2. Files in the archive include 3 pairwise comparisons of
 populations from Smith et al data and 3 from Machado et al (2007),
 labelled by population comparison (see manuscript) and data source. The
 last file is for comparison of all populations for the Smith et al data.
 All files contain locus ID, DNA sequence (aligned using MAFFT - see
 manuscript for details) and locus specific mutation rates. Line 1= general
 info, line 2 = number of populations, line 3 = tree topology, line 4 =
 number of loci, thereafter = sequence data.
DOI: 10.5061/dryad.h95h0
title: Data from: The influence of feeding on the evolution of sensory signals: a comparative test of an evolutionary trade-off between masticatory and sensory functions of skulls in southern African Horseshoe bats (Rhinolophidae)

description: The skulls of animals have to perform many functions. Optimization for one
 function may mean another function is less optimized resulting in
 evolutionary trade-offs. Here we investigate whether a trade-off exists
 between the masticatory and sensory functions of animal skulls using
 echolocating bats as model species. Several species of rhinolophid bats
 deviate from the allometric relationship between body size and
 echolocation frequency. Such deviation may be the result of selection for
 increased bite force resulting in a decrease in snout length which could
 in turn lead to higher echolocation frequencies. If so, there should be a
 positive relationship between bite force and echolocation frequency. We
 investigated this relationship in several species of southern African
 rhinolophids using phylogenetically informed analyses of the allometry of
 their bite force and echolocation frequency and of the 3-dimensional shape
 of their skulls. As predicted, echolocation frequency was positively
 correlated with bite force, suggesting that its evolution is influenced by
 a trade-off between the masticatory and sensory functions of the skull. In
 support of this, variation in skull shape was explained by both
 echolocation frequency (80%) and bite force (20%). Furthermore, it appears
 that selection has acted on the nasal capsules which have a
 frequency-specific impedance matching function during vocalization. There
 was a negative correlation between echolocation frequency and capsule
 volume across species. Optimization of the masticatory function of the
 skull may have been achieved through changes in the shape of the mandible
 and associated musculature, elements not considered in this study.
description: External
 measurements_Nov 2014Individual size, bite
 force and call frequency measurements for ten species of horseshoe bats
 (Rhinolophidae).Data for
 archiving_submitted_Nov
 2014.xlsxSkull measurements_Nov
 2014Skull measurements for
 individuals from ten species of horseshoe bats
 (Rhinolophidae).Data for
 archiving_Skull_submitted_Nov 2014.xlsx
DOI: 10.5061/dryad.2kq65
title: Data from: Forecasting potential emergence of zoonotic diseases in Southeast Asia: network analysis identifies key rodent hosts

description: 1. Within complex ecological systems, identifying animal species likely to
 play a key role in the emergence of infectious zoonotic diseases remains a
 major challenge. One approach consists of using information on current
 ecological and parasitological similarities among host species in order to
 predict the most likely pathways for future pathogen spillover. 2. Using
 field data acquired from 15 sympatric rodent species in various habitats
 in Thailand, Cambodia and Laos, we built networks based on shared
 parasites (17 helminth and 15 microparasite species) and shared habitats
 among rodent species and humans. We investigated the architectures of
 bipartite and unipartite networks using modularity, subgroups partitioning
 or node centrality, to assess the relative epidemiological importance of
 particular rodent species. 3. Our results showed that Rattus tanezumi,
 Bandicota savilei and R. exulans were consistently found to be members of
 subgroups that included humans in unipartite and bipartite networks on
 zoonotic agents and shared habitats. High values of centrality in shared
 zoonotic agents were found for the same three rodent species, whereas high
 values of shared habitats were observed for two of them. Although
 phylogenetically related rodent species likely shared both habitats and
 parasites, a lack of habitat specialisation was associated with increased
 zoonotic parasite sharing. 4. Our results emphasize the disproportionate
 importance of these three rodent species, through their high degree of
 connectivity with humans, which may represent a high risk for direct
 zoonotic spillover. Moreover, due to its high centrality in habitats, R.
 tanezumi may also play a key role as a bridge host. 5. The recent
 discovery of new arenaviruses in rodents in Southeast Asia, with
 associated disease in humans in Cambodia, provides an opportunity to test
 this empirically. The three rodent species identified using our network
 approach are some of the potential maintenance hosts for these new
 emerging arenaviruses. 6. Synthesis and applications. Our results on
 rodents and their pathogens in Southeast Asia show that network analysis
 has a high potential to improve the surveillance of emerging zoonotic
 pathogens by targeting key host species and potential “emerging’
 pathogen–rodent interactions in complex and heterogeneous landscapes.
description: data_parasites_habitatsSurvey of infection by virus, protists, bacteria and helminths of 15 rodent species occurring in 19 main habitats of Thailand, Lao PDR
DOI: 10.5061/dryad.3m2n4
title: Data from: Measuring the immune system of the three-spined stickleback - examining natural variation in the laboratory and the wild

description: Current understanding of the immune system comes primarily from
 laboratory-based studies. There has been substantial interest in examining
 how it functions in the wild, but studies have been limited by a lack of
 appropriate assays and study species. The three-spined stickleback
 (Gasterosteus aculeatus L.) provides an ideal system in which to advance
 the study of wild immunology, but requires the development of suitable
 immune assays. We demonstrate that meaningful variation in the immune
 response of stickleback can be measured using real-time PCR to quantify
 the expression of eight genes, representing the innate response and Th1-,
 Th2- and Treg-type adaptive responses. Assays are validated by comparing
 the immune expression profiles of wild and laboratory-raised stickleback,
 and by examining variation across populations on North Uist, Scotland. We
 also compare the immune response potential of laboratory-raised
 individuals from two Icelandic populations by stimulating cells in
 culture. Immune profiles of wild fish differed from laboratory-raised fish
 from the same parental population, with immune expression patterns in the
 wild converging relative to those in the laboratory. Innate measures
 differed between wild populations, whilst the adaptive response was
 associated with variation in age, relative size of fish, reproductive
 status and S. solidus infection levels. Laboratory-raised individuals from
 different populations showed markedly different innate immune response
 potential. The ability to combine studies in the laboratory and in the
 wild underlines the potential of this toolkit to advance our understanding
 of the ecological and evolutionary relevance of immune system variation in
 a natural setting.
description: Wild_Lab_DataSampling and gene expression data for all individuals used in the study of immune variation in the wild, and the accompanying laboratory raised fish. All sampling data used during the analysis are included, including the relative expression values (DeltaDeltaCt) for eight immune genes, and the PC1 scores for each immune grouping type.Responsiveness_DataData used in the study of innate immune response potential of laboratory fish from two different Icelandic populations. All data used during analysis is included, along with relative expression values (DeltaDeltaCt) for control and stimulated cells, along with the relative change in expression.