cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.07mc1
title: Data from: Opportunities and challenges of Integral Projection Models for modeling host-parasite dynamics

description: Epidemiological dynamics are shaped by and may in turn shape host
 demography. These feedbacks can result in hard to predict patterns of
 disease incidence. Mathematical models that integrate infection and
 demography are consequently a key tool for informing expectations for
 disease burden and identifying effective measures for control. A major
 challenge is capturing the details of infection within individuals and
 quantifying their downstream impacts to understand population-scale
 outcomes. For example, parasite loads and antibody titres may vary over
 the course of an infection and contribute to differences in transmission
 at the scale of the population. To date, to capture these subtleties,
 models have mostly relied on complex mechanistic frameworks, discrete
 categorization and/or agent-based approaches. Integral Projection Models
 (IPMs) allow variance in individual trajectories of quantitative traits
 and their population-level outcomes to be captured in ways that directly
 reflect statistical models of trait–fate relationships. Given increasing
 data availability, and advances in modelling, there is considerable
 potential for extending this framework to traits of relevance for
 infectious disease dynamics. Here, we provide an overview of host and
 parasite natural history contexts where IPMs could strengthen inference of
 population dynamics, with examples of host species ranging from mice to
 sheep to humans, and parasites ranging from viruses to worms. We discuss
 models of both parasite and host traits, provide two case studies and
 conclude by reviewing potential for both ecological and evolutionary
 research.
description: Time-series of infected
 red blood cells for different Plasmodium chabaudi chabaudi clones in
 miceTime-series of infected
 red blood cells (×10−2 μl–1) for different Plasmodium chabaudi chabaudi
 clones in mice (column headings 5 onwards show days). Two treatments (IgG
 and hu-IgG) corresponding to the relevant control groups for different
 experimental designs are distinguished but do not result in differences in
 these time-courses. Original papers in which the data were first reported,
 and in which controls were compared with immune-depleted hosts, are shown
 in the first column.paraForDryad.csv
DOI: 10.5061/dryad.40s3m
title: Data from: Albian infaunal Pholadomyida (Cretaceous Bivalvia), Comanchean Carbonate Shelf, Texas

description: Species of the Megaorder Poromyata, although common and relatively diverse
 in Albian-lower Cenomanian Comanchean strata in Texas and northern Mexico,
 have been neglected as biostratigraphic markers and paleoecological
 indicators. Since 1852 more than a dozen species have been identified as
 Homomya Agassiz, Order Pholadomyida, Superfamily Pholadomyoidea, or
 Pleuromya Agassiz, Order Pholadida, Superfamily Pleuromyoidea. Because
 valve morphologies of both genera are similar in many ways, casts of both
 genera are difficult to separate. Statistical analysis of key
 morphological properties objectively defines species concepts and assesses
 synonymies. Eight species are retained in Homomya, four are synonymized
 with these; two species are provisionally retained in “Homomya” although
 they differ significantly. One species is re-assigned to Liopistha
 (Sergipemya) alta (Roemer). Pleuromya henselli (Hill) is re-assigned to
 Panopea. Homomyid species range from upper Aptian to lower Cenomanian of
 the Comanchean Series in Texas and Mexico. Their ranges vary in duration
 from one million years up to eight million years. Two sets of species are
 distinct morphotypes: a smaller-sized set of H. knowltoni, H.
 tarrantensis, H. tlahualiloensis, H. kellumi, and a larger-sized set of H.
 cymbiformis, H. austinensis, H. vulgaris, H. budaensis, and H.
 auroraensis. Two end-member morphotypes are represented by the
 ‘streamlined’ Homomya knowltoni, which is an elongate, slightly inflated
 form with a relatively high umbo, and the cylindrical Homomya budaensis;
 which is a very elongate, tubular, inflated form with a very low umbo.
 These infaunal suspension feeders occupied calcareous mud and carbonate
 shelf substrates.
description: Scott MS JPaleo data
 fileExcel file of species
 and measurements of morphological parameters
DOI: 10.5061/dryad.7hn24
title: Data from: Hybridization in the Drosophila melanogaster subgroup: incomplete isolation among the three species of the yakuba complex

description: In the Drosophila melanogaster subgroup, the yakuba species complex, D.
 yakuba, D. santomea and D. teissieri have identical mitochondrial genomes
 in spite of nuclear differentiation. The first two species can be readily
 hybridized in the laboratory, and produce fertile females and sterile
 males. They also form hybrids in natural conditions. Nonetheless, the
 third species, D. teissieri, was thought to be unable to produce hybrids
 with either D. yakuba or D. santomea. This in turn posed the conundrum of
 why the three species shared a single mitochondrial genome. In this report
 we show that D. teissieri can indeed hybridize with both D. yakuba and D.
 santomea. The resulting female hybrids from both crosses are fertile,
 while the hybrid males are sterile. We also characterize six isolating
 mechanisms that might be involved in keeping the three species apart. Our
 results open the possibility of studying the history of introgression in
 the yakuba species complex and dissecting the genetic basis of
 interspecific differences between these three species by genetic mapping.
description: Raw data and analytical
 code Turissini et al. 2015teissieri_raw_data.zip
DOI: 10.5061/dryad.m009s
title: Data from: Parasites and competitors suppress bacterial pathogen synergistically due to evolutionary trade-offs

description: Parasites and competitors are important for regulating pathogen densities
 and subsequent disease dynamics. It is, however, unclear to what extent
 this is driven by ecological and evolutionary processes. Here we used
 experimental evolution to study the eco-evolutionary feedbacks between
 Ralstonia solanacearum bacterial pathogen, Ralstonia-specific phage
 parasite and Bacillus amyloliquefaciens competitor bacterium in the
 laboratory and plant rhizosphere. We found that while the phage had a
 small effect on pathogen densities on its own, it considerably increased
 the R. solanacearum sensitivity to antibiotics produced by B.
 amyloliquefaciens. Instead of density effects, this synergy was due to
 phage-driven increase in phage resistance that led to trade-off with the
 resistance to B. amyloliquefaciens antibiotics. While no evidence was
 found for pathogen resistance evolution to B. amyloliquefaciens
 antibiotics, the fitness cost of adaptation (reduced growth) was highest
 when the pathogen had evolved in the presence of both parasite and
 competitor. Qualitatively similar patterns were found between laboratory
 and greenhouse experiments even though the evolution of phage resistance
 was considerably attenuated in the tomato rhizosphere. These results
 suggest that evolutionary trade-offs can impose strong constraints on
 disease dynamics and that combining phages and antibiotic-producing
 bacteria could be an efficient way to control agricultural pathogens.
description: All data for the
 manuscriptThe attached file is all
 the raw data for the manuscript which also including the
 arcsine-transformed proportional data and the average value for each
 treatment at the replicated population level.
DOI: 10.5061/dryad.1416
title: Data from: Passerine extrapair mating dynamics: a Bayesian modeling approach comparing four species

description: In many socially monogamous animals, females engage in extrapair
 copulation (EPC), causing some broods to contain both within‐pair and
 extrapair young (EPY). The proportion of all young that are EPY varies
 across populations and species. Because an EPC that does not result in EPY
 leaves no forensic trace, this variation in the proportion of EPY reflects
 both variation in the tendency to engage in EPC and variation in the
 extrapair fertilization (EPF) process across populations and species. We
 analyzed data on the distribution of EPY in broods of four passerines
 (blue tit, great tit, collared flycatcher, and pied flycatcher), with
 18,564 genotyped nestlings from 2,346 broods in two to nine populations
 per species. Our Bayesian modeling approach estimated the underlying
 probability function of EPC (assumed to be a Poisson function) and
 conditional binomial EPF probability. We used an information theoretical
 approach to show that the expected distribution of EPC per female varies
 across populations but that EPF probabilities vary on the above‐species
 level (tits vs. flycatchers). Hence, for these four passerines, our model
 suggests that the probability of an EPC mainly is determined by ecological
 (population‐specific) conditions, whereas EPF probabilities reflect
 processes that are fixed above the species level.
description: DataPlottedInFig1.xlsxRaw data for Figure 1 in original articleRawDataFile.txt
DOI: 10.5061/dryad.d61jk
title: Data from: Decoupled evolution of foliar freezing resistance, temperature-niche and morphological leaf traits in Chilean Myrceugenia

description: 1. Phylogenetic conservatism of tolerance to freezing temperatures has
 been cited to explain the tendency of plant lineages to grow in similar
 climates. However there is little information about whether or not
 freezing resistance is conserved across phylogenies, and whether
 conservatism of physiological traits could explain conservatism of
 realized climatic niches. Here we compared the phylogenetical lability of
 realized climatic niche, foliar freezing resistance, and four
 morphological leaf traits that are generally considered adaptations to
 frost resistance in Chilean species of Myrceugenia, which grow in a wide
 range of habitats. 2. We estimated the predicted niche occupancy profiles
 with respect to minimum temperature (minT) of all species. We measured
 foliar freezing resistance (using chlorophyll fluorescence), leaf size,
 leaf mass per area (LMA), stomatal and trichome densities of ten
 individuals per species. Finally, we estimated phylogenetic signal and we
 performed independent contrast analyses among all variables. 3. We found
 that both foliar freezing resistance and minT were subject to a
 significant phylogenetic signal, but the former had a stronger signal. We
 also detected a significant but weak correlation between them (r=0.49,
 pone tail= 0.04). Morphological traits evolved independent of any
 phylogenetic effect. Synthesis. Our results show that freezing resistance
 evolved in association with temperature niche, but with some delay that
 could result from phylogenetic inertia. Our results also show that
 morphological leaf traits are more labile than realized climatic niche and
 frost tolerance and the former probably evolved associated to microhabitat
 preferences.
description: Leaf traits, foliar
 freezing resistance and realized climatic niche oif chilean Myrceugenia
 speciesThe file contains three
 sheets of data. The first sheet contains morphological leaf traits,
 including leaf size, leaf mass per area, stomatal density and trichome
 density of 12 chilean species of Myrceugenia, as well location and GPS
 coordinates of study sites. Values indicate the mean ± SE obtained from 10
 individuals per species. The second sheet contains foliar freezing
 resistance of Myrceugenia species measured using chlorophyll fluorescence.
 Values indicate the mean freezing temperature producing 50% foliar damage
 (LT50) ± SE obtained from 10 individuals per species. The third sheet
 contains the probability of occurrence of each Myrceugenia species with
 respect to the minimum temperature of coldest month derived with
 MAXENT.leaf
 traits, foliar freezing resistance, climatic
 niche.xlsx
DOI: 10.5061/dryad.9p91h
title: Data from: Marine communities on oil platforms in Gabon, West Africa: high biodiversity oases in a low biodiversity environment

description: The marine biodiversity of Gabon, West Africa has not been well studied
 and is largely unknown. Our examination of marine communities associated
 with oil platforms in Gabon is the first scientific investigation of these
 structures and highlights the unique ecosystems associated with them. A
 number of species previously unknown to Gabonese waters were recorded
 during our surveys on these platforms. Clear distinctions in benthic
 communities were observed between older, larger platforms in the north and
 newer platforms to the south or closer to shore. The former were dominated
 by a solitary cup coral, Tubastraea sp., whereas the latter were dominated
 by the barnacle Megabalanus tintinnabulum, but with more diverse benthic
 assemblages compared to the northerly platforms. Previous work documented
 the presence of limited zooxanthellated scleractinian corals on natural
 rocky substrate in Gabon but none were recorded on platforms. Total
 estimated fish biomass on these platforms exceeded one ton at some
 locations and was dominated by barracuda (Sphyraena spp.), jacks
 (Carangids), and rainbow runner (Elagatis bipinnulata). Thirty-four
 percent of fish species observed on these platforms are new records for
 Gabon and 6% are new to tropical West Africa. Fish assemblages closely
 associated with platforms had distinct amphi-Atlantic affinities and
 platforms likely extend the distribution of these species into coastal
 West Africa. At least one potential invasive species, the snowflake coral
 (Carijoa riisei), was observed on the platforms. Oil platforms may act as
 stepping stones, increasing regional biodiversity and production but they
 may also be vectors for invasive species. Gabon is a world leader in
 terrestrial conservation with a network of protected areas covering
 &gt;10% of the country. Oil exploration and biodiversity conservation
 currently co-exist in terrestrial and freshwater ecosystems in Gabon.
 Efforts to increase marine protection in Gabon may benefit by including
 oil platforms in the marine protected area design process.
description: Gabon_dryad_fish_dataData description: Date – MM/DD/YYYY ; Reef – Gabon ; STATION – Rig1……Rig10 ; Latitude – Decimal degrees, WGS 1984 ; Longitude - Decimal degrees, WGS 1984 ; Depth_m- depth in meters ; Depth_stratum - DIVER – AMF = Alan Friedlander ; TRANSECT = A, B, C, D ; Taxon – lowest possible scientific name ; num_m^2 – numerical abundance in number per meter squared ; g_m^2 – biomass in grams per meter squared
DOI: 10.5061/dryad.gb122
title: Data from: Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus

description: The temporal origins of the extraordinary biodiversity of the Neotropical
 region are highly debated. Recent empirical work has found support for
 alternative models on the tempo of speciation in Neotropical species
 further fuelling the debate. However, relationships within many
 Neotropical lineages are poorly understood and it is unclear how this
 uncertainty impacts inferences on the evolution of taxa in the region. We
 examined the robustness of diversification patterns in the avian genus
 Forpus by testing whether the use of different units of biodiversity (i.e.
 biological species and statistically inferred species) impacted
 diversification rates and inferences regarding important biogeographic
 breaks in the genus. We found that the best-fit model of diversification
 for the biological species data set was a declining rate of
 diversification; whereas a model of constant diversification was the
 best-fit model for statistically inferred species or subspecies. Moreover,
 the relative importance of different landscape features in delimiting
 genetic structure across the landscape varied across data sets with
 differing units of biodiversity. Patterns based on divergence times among
 biological species indicated old speciation events across major geographic
 and river barriers, in contrast, data sets more inclusive of the diversity
 in Forpus illustrate the role of both old divergence across major
 landscape features as well as more recent divergences that are possibly
 attributed to Pleistocene climatic changes. Overall, these results
 indicate that conflicting models on the temporal origins of Neotropical
 birds may be attributable to sampling biases.
description: AlignmentsSequence alignments for complete mtDNA matrix and phased nuclear loci
DOI: 10.5061/dryad.hg61r
title: Data from: Unexpected pattern of pearl millet genetic diversity among ethno-linguistic groups in the Lake Chad Basin

description: Despite of a growing interest in considering the role of sociological
 factors in seed exchanges and their consequences on the evolutionary
 dynamics of agro-biodiversity, very few studies assessed the link between
 ethno-linguistic diversity and genetic diversity patterns in small-holder
 farming systems. This is key for optimal improvement and conservation of
 crop genetic resources. Here, we investigated genetic diversity at 17 SSR
 markers of pearl millet landraces (varieties named by farmers) in the Lake
 Chad Basin. 69 pearl millet populations, representing 27 landraces
 collected in eight ethno-linguistic farmer groups, were analyzed. We found
 that the farmers’ local taxonomy was not a good proxy for population’s
 genetic differentiation as previously shown at smaller scales. Our results
 show the existence of a genetic structure of pearl millet mainly
 associated with ethno-linguistic diversity in the western side of the lake
 Chad. It suggests there is a limit to gene flow between landraces grown by
 different ethno-linguistic groups. This result was rather unexpected,
 because of the highly outcrossing mating system of pearl millet, the high
 density of pearl millet fields all along the green belt of this Sahelian
 area and the fact that seed exchanges among ethno-linguistic groups are
 known to occur. In the eastern side of the Lake, the pattern of genetic
 diversity suggests a larger efficient circulation of pearl millet genes
 between ethno-linguistic groups that are less numerous, spatially
 intermixed and, for some of them, more prone to exogamy. Finally, other
 historical and environmental factors which may contribute to the observed
 diversity patterns are discussed.
description: Microsatellite_datamicrosatellite genotypes for the individuals of our study
DOI: 10.5061/dryad.g7d1r
title: Data from: Does population size affect genetic diversity? A test with sympatric lizard species

description: Genetic diversity is a fundamental requirement for evolution and
 adaptation. Nonetheless, the forces that maintain patterns of genetic
 variation in wild populations are not completely understood. Neutral
 theory posits that genetic diversity will increase with a larger effective
 population size and the decreasing effects of drift. However, the lack of
 compelling evidence for a relationship between genetic diversity and
 population size in comparative studies has generated some skepticism over
 the degree that neutral sequence evolution drives overall patterns of
 diversity. The goal of this study was to measure genetic diversity among
 sympatric populations of related lizard species that differ in population
 size and other ecological factors. By sampling related species from a
 single geographic location, we aimed to reduce nuisance variance in
 genetic diversity owing to species differences, for example, in mutation
 rates or historical biogeography. We compared populations of zebra-tailed
 lizards and western banded geckos, which are abundant and short-lived, to
 chuckwallas and desert iguanas, which are less common and long-lived. We
 assessed population genetic diversity at three protein-coding loci for
 each species. Our results were consistent with the predictions of neutral
 theory, as the abundant species almost always had higher levels of
 haplotype diversity than the less common species. Higher population
 genetic diversity in the abundant species is likely due to a combination
 of demographic factors, including larger local population sizes (and
 presumably effective population sizes), faster generation times and high
 rates of gene flow with other populations.
description: Lizard sample locality
 data with associated Genbank numbersThis data file contains
 the assigned Genbank numbers for three genes for four species of lizards
 from the Mojave National Preserve. Each individual lizard is identified by
 a number with a single letter prefix representing the gene. Autosomal
 genes have two entries. Also included is the locality data for each
 lizard.Dryad data file for
 Heredity.xlsx
DOI: 10.5061/dryad.0qg71
title: Data from: Preference for outbred host plants and positive effects of inbreeding on egg survival in a specialist herbivore

description: Inbreeding can profoundly affect the interactions of plants with
 herbivores as well as with the natural enemies of the herbivores. We
 studied how plant inbreeding affects herbivore oviposition preference, and
 whether inbreeding of both plants and herbivores alters the probability of
 predation or parasitism of herbivore eggs. In a laboratory preference test
 with the specialist herbivore moth Abrostola asclepiadis and inbred and
 outbred Vincetoxicum hirundinaria plants, we discovered that herbivores
 preferred to oviposit on outbred plants. A field experiment with inbred
 and outbred plants that bore inbred or outbred herbivore eggs revealed
 that the eggs of the outbred herbivores were more likely to be lost by
 predation, parasitism or plant hypersensitive responses than inbred eggs.
 This difference did not lead to differences in the realized fecundity as
 the number of hatched larvae did not differ between inbred and outbred
 herbivores. Thus, the strength of inbreeding depression in herbivores
 decreases when their natural enemies are involved. Plant inbreeding did
 not alter the attraction of natural enemies of the eggs. We conclude that
 inbreeding can significantly alter the interactions of plants and
 herbivores at different life-history stages, and that some of these
 alterations are mediated by the natural enemies of the herbivores.
description: Herbivore oviposition
 preferenceOviposition preference
 of Abrostola asclepiadis moths over inbred or outbred
 plantsdryad_data_preference.txtHerbivore egg survivalSurvival of inbred and outbred herbivore eggs (Abrostola asclepiadis) on inbred and outbred host plants (Vincetoxicum hirundinaria)dryad_data_eggs.txt