cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h12kh08n
title: Data from: Host and habitat specialization of avian malaria in Africa

description: Studies of both vertebrates and invertebrates have suggested that
 specialists, as compared to generalists, are likely to suffer more serious
 declines in response to environmental change. Less is known about the
 effects of environmental conditions on specialist vs. generalist
 parasites. Here, we study the evolutionary strategies of malaria parasites
 (Plasmodium spp.) among different bird host communities. We determined the
 parasite diversity and prevalence of avian malaria in three bird
 communities in the lowland forests in Cameroon, highland forests in East
 Africa, and fynbos in South Africa. We calculated the host specificity
 index of parasites to examine the range of hosts parasitized as a function
 of the habitat, and investigated the phylogenetic relationships of
 parasites. First, using phylogenetic and ancestral reconstruction analyses
 we found an evolutionary tendency for generalist malaria parasites to
 become specialists. The transition rate at which generalists become
 specialists was nearly four times as great as the rate at which
 specialists become generalists. We also found more specialist parasites
 and greater parasite diversity in African lowland rainforests as compared
 to the more climatically variable habitats of the fynbos and the highland
 forests. Thus, with environmental changes, we anticipate a change in the
 distribution of both specialist and generalist parasites with potential
 impacts on bird communities.
description: Climate data 02 Oct
 2011
DOI: 10.5061/dryad.tj37s
title: Data from: Inferences on population history of a seed chalcid wasp: invasion success despite a severe founder effect from an unexpected source population

description: Most invasive species established in Europe originate from either Asia or
 North America, but little is currently known about the potential of the
 Anatolian Peninsula (Asia Minor) and/or the Near East to constitute
 invasion sources. Mediterranean forests are generally fragile ecosystems
 that can be threatened by invasive organisms coming from different regions
 of the Mediterranean Basin, but for which historical data are difficult to
 gather and the phylogeographic patterns are still poorly understood for
 most terrestrial organisms. In this study, we characterized the genetic
 structure of Megastigmus schimitscheki, an invasive seed-feeding insect
 species originating from the Near East, and elucidated its invasion route
 in Southeastern France in the mid 1990’s. To disentangle the evolutionary
 history of this introduction, we gathered samples from the main native
 regions (Taurus Mountains in Turkey, Lebanon and Cyprus) and from the
 invaded region, that we genotyped using five microsatellite markers and
 for which we sequenced the mitochondrial Cytochrome Oxidase I gene. We
 applied a set of population genetic statistics and methods, including
 approximate Bayesian computation. We proposed a detailed phylogeographic
 pattern for the Near East populations, and we unambiguously showed that
 the French invasive populations originated from Cyprus, although the
 available historical data strongly suggested that Turkey could be the most
 plausible source area. Interestingly, we could show that the introduced
 populations were founded from an extremely restricted number of
 individuals that realized a host switch from Cedrus brevifolia to C.
 atlantica. Evolutionary hypotheses are discussed to account for this
 unlikely scenario.
description: Microsatellite-dataThis file corresponds to the genotypes of the individual analysed in the paper. All were collected in the field.Auger-Rozenberg-MEC-12-0561_Microsat-data.pdfmtDNA-Sequences-dataThis file corresponds to the sequence and corresponding information on individuals analyzed in the documentAuger-Rozenberg-MEC-12-0561_Sequences-data.pdf
DOI: 10.5061/dryad.327v0
title: Data from: Anthropogenic selection enhances cancer evolution in Tasmanian devil tumours

description: The Tasmanian Devil Facial Tumour Disease (DFTD) provides a unique
 opportunity to elucidate the long-term effects of natural and
 anthropogenic selection on cancer evolution. Since first observed in 1996,
 this transmissible cancer has caused local population declines by
 &gt;90%. So far, four chromosomal DFTD variants (strains) have been
 described and karyotypic analyses of 253 tumours showed higher levels of
 tetraploidy in the oldest strain. We propose that increased ploidy in the
 oldest strain may have evolved in response to effects of genomic decay
 observed in asexually reproducing organisms. In this study, we focus on
 the evolutionary response of DFTD to a disease suppression trial. Tumours
 collected from devils subjected to the removal programme showed
 accelerated temporal evolution of tetraploidy compared with tumours from
 other populations where no increase in tetraploid tumours were observed.
 As ploidy significantly reduces tumour growth rate, we suggest that the
 disease suppression trial resulted in selection favouring slower growing
 tumours mediated by an increased level of tetraploidy. Our study reveals
 that DFTD has the capacity to rapidly respond to novel selective regimes
 and that disease eradication may result in novel tumour adaptations, which
 may further imperil the long-term survival of the world's largest
 carnivorous marsupial.
description: DFTD samples
 2006-2011Tumour tissue samples
 used in the study were collected between 2006 and 2011 at 12 sites within
 the DFTD affected areas of Tasmania.
DOI: 10.5061/dryad.3479r
title: Data from: Molecular mechanisms of 2, 3′, 4, 4′, 5-pentachlorobiphenyl-induced thyroid dysfunction in FRTL-5 cells

description: Polychlorinated biphenyls (PCBs) can severely interfere with multiple
 animals and human systems. To explore the molecular mechanisms underlying
 2, 3′, 4, 4′, 5- pentachlorobiphenyl (PCB118)-induced thyroid dysfunction,
 Fischer rat thyroid cell line-5(FRTL-5) cells were treated with either
 different concentrations of PCB118 or dimethyl sulfoxide (DMSO). The
 effects of PCB118 on FRTL-5 cells viability and apoptosis were assessed by
 using a Cell Counting Kit-8 assay and apoptosis assays, respectively.
 Quantitative real-time polymerase chain reaction was used to quantify
 protein kinase B (Akt), Forkhead box protein O3a (FoxO3a), and
 sodium/iodide symporter (NIS) mRNA expression levels. Western blotting was
 used to detect Akt, phospho-Akt (p-Akt), FoxO3a, phospho-FoxO3a
 (p-FoxO3a), and NIS protein levels. Luciferase reporter gene technology
 was used to detect the transcriptional activities of FoxO3a and NIS
 promoters. The effects of the constitutively active Akt (CA-Akt) and
 dominant-negative Akt (DN-Akt) plasmids on p-Akt, p-FoxO3a, and NIS levels
 were examined in PCB118-treated FRTL-5 cells. The effects of FoxO3a siRNA
 on FoxO3a, p-FoxO3a, and NIS protein levels were examined in the
 PCB118-treated FRTL-5 cells. The effects of pcDNA3 (plsmid vectors
 designed for high-level stable and transient expression in mammalian
 host)-FoxO3a on NIS promoter activity were examined in the PCB118-treated
 FRTL-5 cells. Our results indicated that relatively higher PCB118
 concentrations can inhibit cell viability in a concentration- and
 time-dependent manner. Akt, p-Akt, and p-FoxO3a protein or mRNA levels
 increased significantly in PCB118-treated groups and NIS protein and mRNA
 levels decreased considerably compared with the control groups. FoxO3a
 promoter activity increased significantly, whereas NIS promoter activity
 decreased. These effects on p-FoxO3a and NIS could be decreased by the
 DN-Akt plasmid, enhanced by the CA-Akt plasmid, and blocked by FoxO3a
 siRNA. The overexpressed FoxO3a could reduce NIS promoter activity. Our
 results suggested that PCB118 induces thyroid cell dysfunction through the
 Akt/FoxO3a/NIS signaling pathway.
description: Data from: Molecular
 mechanisms of 2, 3′, 4, 4′, 5- pentachlorobiphenyl -induced thyroid
 dysfunction in FRTL-5 cellsData from: Molecular
 mechanisms of 2, 3′, 4, 4′, 5- pentachlorobiphenyl -induced thyroid
 dysfunction in FRTL-5 cellsData.xls
DOI: 10.5061/dryad.8684
title: Data from: Plastic and evolutionary responses of cell size and number to larval malnutrition in Drosophila melanogaster

description: Both development and evolution under chronic malnutrition lead to reduced
 adult size in Drosophila. We studied the contribution of changes in size
 vs. number of epidermal cells to plastic and evolutionary reduction of
 wing size in response to poor larval food. We used flies from six
 populations selected for tolerance to larval malnutrition and from six
 unselected control populations, raised either under standard conditions or
 under larval malnutrition. In the control populations, phenotypic
 plasticity of wing size was mediated by both cell size and cell number. In
 contrast, evolutionary change in wing size, which was only observed as a
 correlated response expressed on standard food, was mediated entirely by
 reduction in cell number. Plasticity of cell number had been lost in the
 selected populations, and cell number did not differ between the sexes
 despite males having smaller wings. Results of this and other experimental
 evolution studies are consistent with the hypothesis that alleles which
 increase body size through prolonged growth affect wing size mostly via
 cell number, whereas alleles which increase size through higher growth
 rate do so via cell size.
description: body size data (dry
 weight, wing area, Cell size and cell number)The data was collected
 as described in the material and methods section of the paper. The body
 weight data gives average weight per fly per line while the data for the
 remaining three traits is per vial per line and is log transformed. The
 column heading line is equivalent to the replicate population described in
 the paper.
DOI: 10.5061/dryad.3qs21
title: Data from: Concordance in evolutionary history of threatened plant and insect populations warrant unified conservation management approaches

description: Threatened organisms may act as host to a suite of dependent organisms,
 which are potentially cothreatened, yet management is rarely coordinated
 between host and dependent species. Here, we test the congruency of
 patterns of genetic structure between two critically endangered
 interacting taxa; the feather-leaf banksia (Banksia brownii R.Br.), and
 its host-specific herbivorous plant-louse Trioza barrettae Taylor
 & Moir, to establish whether conservation actions should be
 implemented jointly for both species. We also examine the role of host
 population size and fire history on the density of psyllids on host
 plants. We show that the patterns of mtDNA variation in T barrettae and
 microsatellite variation in both species supports the presence of at least
 two conservation units across each species, with the microsatellites also
 showing a high evolutionary congruency between plant and insect
 populations. The extinction of divergent B. brownii populations,
 therefore, is likely to have resulted in the extinction of divergent
 plant-louse populations. Larger populations of host plant (&gt;150)
 and more recent fire history (&lt;20 years since fire) are important
 factors in maintaining T. barrettae densities. High molecular congruency
 indicates the importance of considering patterns of genetic diversity of
 source material from both host and dependent organisms for ex situ
 conservation, in situ supplementations and reintroductions. As dependents
 such as T. barrettae are often lost to extinction before their host,
 considering the conservation of dependent biota in the early stages of
 species management is paramount.
description: Trioza microsatellite
 dataAn excel file containing
 Trioza barrettae genotypes at 14 microsatellite loci.Trioza CO1
 dataAn excel file containing
 Trioza barrettae haplotype frequencies for the mitochondrial COI
 gene
DOI: 10.5061/dryad.2j3c8
title: Data from: The chicken or the egg? Adaptation to desiccation and salinity tolerance in a lineage of water beetles

description: Transitions from fresh to saline habitats are restricted to a handful of
 insect lineages, as the colonization of saline waters requires specialized
 mechanisms to deal with osmotic stress. Previous studies have suggested
 that tolerance to salinity and desiccation could be mechanistically and
 evolutionarily linked, but the temporal sequence of these adaptations is
 not well established for individual lineages. We combined molecular,
 physiological and ecological data to explore the evolution of desiccation
 resistance, hyporegulation ability (i.e., the ability to osmoregulate in
 hyperosmotic media) and habitat transitions in the water beetle genus
 Enochrus subgenus Lumetus (Hydrophilidae). We tested whether enhanced
 desiccation resistance evolved before increases in hyporegulation ability
 or vice versa, or whether the two mechanisms evolved in parallel. The most
 recent ancestor of Lumetus was inferred to have high desiccation
 resistance and moderate hyporegulation ability. There were repeated shifts
 between habitats with differing levels of salinity in the radiation of the
 group, those to the most saline habitats generally occurring more rapidly
 than those to less saline ones. Significant and accelerated changes in
 hyporegulation ability evolved in parallel with smaller and more
 progressive increases in desiccation resistance across the phylogeny,
 associated with the colonization of meso- and hypersaline waters during
 global aridification events. All species with high hyporegulation ability
 were also desiccation-resistant, but not vice versa. Overall, results are
 consistent with the hypothesis that desiccation resistance mechanisms
 evolved first and provided the physiological basis for the development of
 hyporegulation ability, allowing these insects to colonize and diversify
 across meso- and hypersaline habitats.
description: AlignmentsAlignments of the mitochondrial and nuclear genes (or gene fragments) sequenced to obtain the phylogeny of the subgenus Lumetus (genus Enochrus, family Hydrophilidae, order Coleoptera) in FASTA formatalignments.rar
DOI: 10.5061/dryad.c241p
title: Data from: Domestic dogs and puppies can use human voice direction referentially

description: Domestic dogs are particularly skilled at using human visual signals to
 locate hidden food. This is, to our knowledge, the first series of studies
 that investigates the ability of dogs to use only auditory communicative
 acts to locate hidden food. In a first study, from behind a barrier, a
 human expressed excitement towards a baited box on either the right or
 left side, while sitting closer to the unbaited box. Dogs were successful
 in following the human's voice direction and locating the food. In
 the two following control studies, we excluded the possibility that dogs
 could locate the box containing food just by relying on smell, and we
 showed that they would interpret a human's voice direction in a
 referential manner only when they could locate a possible referent (i.e.
 one of the boxes) in the environment. Finally, in a fourth study, we
 tested 8–14-week-old puppies in the main experimental test and found that
 those with a reasonable amount of human experience performed overall even
 better than the adult dogs. These results suggest that domestic dogs’
 skills in comprehending human communication are not based on visual cues
 alone, but are instead multi-modal and highly flexible. Moreover, the
 similarity between young and adult dogs’ performances has important
 implications for the domestication hypothesis.
description: Data_complete_VoiceFollowingDogsExcel sheet containing all subjects and conditions tested and all trials results for the Voice Following paper
DOI: 10.5061/dryad.3vg33
title: Data from: Application of wMelPop Wolbachia strain to crash local populations of Aedes aegypti

description: The endosymbiotic bacteria Wolbachia pipientis (wMel strain) has been
 successfully established in several populations of Aedes aegypti, the
 primary dengue vector. The virulent Wolbachia strain wMelPop is known to
 cause several pathological impacts (increased egg mortality, life
 shortening, etc.) reducing overall fitness in the mosquito Ae. aegypti.
 Increased egg mortality could substantially reduce egg banks in areas with
 a lengthy monsoonal dry season, and be employed to eliminate local
 populations. We tested this application under semi-field cage conditions.
 First, we determined that wMelPop infection significantly reduced the
 survival of desiccation-resistant eggs of the dengue vector Ae. aegypti,
 with shade and temperature having a significant impact; nearly all
 wMelPop-infected eggs failed to hatch after 6 and 10 weeks in summer and
 winter conditions, respectively. In laboratory selection experiments we
 found that egg desiccation resistance can be increased by selection, and
 that this effect of wMelPop infection is due to the nuclear background of
 the host rather than Wolbachia. We then conducted an invasion of wMelPop
 within a semi-field cage using sustained weekly releases of wMelPop
 infected mosquitoes, with fixation achieved after 9 weeks. The egg
 populations wMelPop infected and an uninfected control were then subjected
 to a simulated prolonged monsoonal dry season (2.5 months) before flooding
 to induce hatching. The wMelPop infected eggs suffered significantly
 greater mortality than the controls, with only 0.67% and 4.35% of
 respective infected and uninfected eggs held in 99% shade hatching after
 80 days. These studies suggest that wMelPop could be used to locally
 eliminate populations of Ae. aegypti that are exposed to prolonged dry
 conditions, particularly if combined with vector control.
description: Application of wMelPop
 Wolbachia strain to crash local populations of Aedes
 aegyptiStudies of the survival
 of Aedes aegypti eggs infected with the Wolbachia strain wMelPop
 "popcorn"Ritchie popcorn extinction data
 repository 2015.xlsx
DOI: 10.5061/dryad.kt8k2
title: Data from: Nectar bacteria affect life history of a generalist aphid parasitoid by altering nectar chemistry

description: 1. Nectar is a crucial energy resource that strongly mediates the
 interactions between plants and animal pollinators or plant defenders.
 Previous research has shown that nectar is commonly colonized by
 microorganisms, most commonly bacteria and yeasts, which can have a strong
 impact on nectar chemistry. However, at present little is known about the
 effects of microorganisms on the fitness of animals feeding on nectar. 2.
 We used three nectar bacteria representing different metabolic groups
 (Asaia sp., Lactococcus sp. and Rosenbergiella sp.) and the common
 generalist aphid parasitoid Aphidius ervi (Haliday) (Hymenoptera:
 Braconidae) to test the hypothesis that different nectar-dwelling bacteria
 affect nectar consumption and insect longevity differently by altering the
 chemistry of nectar. 3. Bacteria significantly affected nectar chemistry
 by altering its acidity, sugar and amino acids composition/concentration
 and by adding compounds synthesized by the microbes. Although inoculation
 with bacteria did not affect nectar consumption, a significant difference
 in insect longevity was observed. The impact on longevity was species
 specific, with Lactococcus being beneficial and Asaia having a detrimental
 effect. 4. Bacteria have a strong impact on nectar chemistry and changes
 in nectar chemistry may not only influence the foraging behavior of
 flower-visiting animals and impact on plant fitness, but also influence
 the fitness of nectar-consuming organisms. As effects were species
 dependent, changes in nectar chemistry induced by different bacteria may
 have contrasting effects on the interactions between plants and insects.
 It is therefore essential to know how different microbes alter nectar
 chemistry to understand the relationships between plants,
 nectar-inhabiting microbes and nectar-consuming animals.
description: Data Lenaerts et al.
 Functional Ecology
DOI: 10.5061/dryad.fb778jf2
title: Data from: Intertemporal choice in lemurs

description: Different species vary in their ability to wait for delayed rewards in
 intertemporal choice tasks. Models of rate maximization account for part
 of this variation, but other factors such as social structure and feeding
 ecology seem to underly some species differences. Though studies have
 evaluated intertemporal choice in several primate species, including Old
 World monkeys, New World monkeys, and apes, prosimians have not been
 tested. This study investigated intertemporal choices in three species of
 lemur (black-and-white ruffed lemurs, Varecia variegata, red ruffed
 lemurs, Varecia rubra, and black lemurs, Eulemur macaco) to assess how
 they compare to other primate species and whether their choices are
 consistent with rate maximization. We offered lemurs a choice between two
 food items available immediately and six food items available after a
 delay. We found that by adjusting the delay to the larger reward, the
 lemurs were indifferent between the two options at a mean delay of 17 s,
 ranging from 9-25 s. These data are comparable to data collected from
 common marmosets (Callithrix jacchus). The lemur data were not consistent
 with models of rate maximization. The addition of lemurs to the list of
 species tested in these tasks will help uncover the role of life history
 and socio-ecological factors influencing intertemporal choices.
description: Data on intertemporal
 choice in lemursThese data were
 collected from Nov 2007 to Jul 2009 as part of an intertemporal choice in
 lemurs. Citation: Stevens, J.R. & Mühlhoff, N. (in press).
 Intertemporal choice in lemurs. Behavioural Processes.stevens_data.zip
DOI: 10.5061/dryad.g41cj
title: Data from: Global population genetic dynamics of a highly migratory, apex predator shark

description: Knowledge of genetic connectivity dynamics in the world's
 large-bodied, highly migratory, apex predator sharks across their global
 ranges is limited. One such species, the tiger shark (Galeocerdo cuvier),
 occurs worldwide in warm temperate and tropical waters, uses remarkably
 diverse habitats (nearshore to pelagic) and possesses a generalist diet
 that can structure marine ecosystems through top-down processes. We
 investigated the phylogeography and the global population structure of
 this exploited, phylogenetically enigmatic shark by using 10 nuclear
 microsatellites (n = 380) and sequences from the mitochondrial control
 region (CR, n = 340) and cytochrome oxidase I gene (n = 100). All three
 marker classes showed the genetic differentiation between tiger sharks
 from the western Atlantic and Indo-Pacific ocean basins (microsatellite
 FST &gt; 0.129; CR ΦST &gt; 0.497), the presence of North vs.
 southwestern Atlantic differentiation and the isolation of tiger sharks
 sampled from Hawaii from other surveyed locations. Furthermore,
 mitochondrial DNA revealed high levels of intraocean basin matrilineal
 population structure, suggesting female philopatry and sex-biased gene
 flow. Coalescent- and genetic distance-based estimates of divergence from
 CR sequences were largely congruent (dcorr = 0.0015–0.0050), indicating a
 separation of Indo-Pacific and western Atlantic tiger sharks &lt;1
 million years ago. Mitochondrial haplotype relationships suggested that
 the western South Atlantic Ocean was likely a historical connection for
 interocean basin linkages via the dispersal around South Africa. Together,
 the results reveal unexpectedly high levels of population structure in a
 highly migratory, behaviourally generalist, cosmopolitan ocean predator,
 calling for management and conservation on smaller-than-anticipated
 spatial scales.
description: Genepop Input
 FileMicrosatellite allele
 sizes formatted for Genepop.Genepop.txt