cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n13hn
title: Data from: Modelling plant species distribution in alpine grasslands using airborne imaging spectroscopy

description: Remote sensing using airborne imaging spectroscopy (AIS) is known to
 retrieve fundamental optical properties of ecosystems. However, the value
 of these properties for predicting plant species distribution remains
 unclear. Here, we assess whether such data can add value to topographic
 variables for predicting plant distributions in French and Swiss alpine
 grasslands. We fitted statistical models with high spectral and spatial
 resolution reflectance data and tested four optical indices sensitive to
 leaf chlorophyll content, leaf water content and leaf area index. We found
 moderate added-value of AIS data for predicting alpine plant species
 distribution. Contrary to expectations, differences between species
 distribution models (SDMs) were not linked to their local abundance or
 phylogenetic/functional similarity. Moreover, spectral signatures of
 species were found to be partly site-specific. We discuss current limits
 of AIS-based SDMs, highlighting issues of scale and informational content
 of AIS data.
description: Floristic data Swiss
 siteSpData_CH.csvFloristic data French siteSpData_FR.csvRemotely sensed reflectance, vegetation indices and topographic data (Swiss Site)PlotData_CH.csvRemotely sensed reflectance, vegetation indices and topographic data (French Site)PlotData_FR.csvPlant trait data Swiss siteTraits_CH.csvPlant trait data French siteTraits_FR.csvPhylogenetic data Swiss sitePhyloTree_CH.trePhylogenetic data French sitePhyloTree_FR.tre
DOI: 10.5061/dryad.87815
title: Data from: Effects of mammalian herbivores and termites on performance of native and exotic plantation tree seedlings

description: Invasion of exotic species is a global challenge and the potential for
 adverse effects on local biodiversity is particularly high in protected
 areas. Protected African savanna areas support globally important
 biodiversity. At the same time, forest plantations are widespread
 throughout Africa and exotic tree species frequently invade natural areas.
 To evaluate the potential invasiveness of plant species, it is pertinent
 to know to what extent, if at all, consumption by native herbivore
 assemblages differentially affects exotic and indigenous plants. We
 studied how two globally widespread exotic trees Eucalyptus grandis and
 Grevillea robusta and two common indigenous trees Milicia excelsa and
 Maesopsis eminii responded to natural herbivory by large herbivores and
 termites. We experimentally exposed 720 tree seedlings to: (i) no large
 herbivores or termites; (ii) termites only; (iii) large herbivores only;
 and (iv) both large herbivores and termites. When exposed to large
 herbivores and termites, the total survival was much higher for the
 exotics with 45% (E. grandis) and 63% (G. robusta) compared to the
 indigenous species (both 20%). Exposure to large herbivores affected early
 seedling survival of natives more than the exotics. Apart from the
 indigenous M. excelsa, survival did not decrease when seedlings were
 exposed to termites. Large herbivores retarded seedling growth for all
 species. The exotic E. grandis was the only species capable of growth when
 exposed to large herbivores. Exposure to termites had only a small, but
 significant effect resulting in a 7% size difference in all species.
 Synthesis and applications. Our results highlight how browsing might, for
 some tree species, adversely affect native seedling survival and growth
 more than exotic species in protected African savanna. If exotic species
 are to be used in plantations, managers should consider planting tree
 species and varieties that are sensitive to ungulate browsing. This will
 not compromise economic gain because large herbivores are generally less
 common in plantations. Consequently, local ungulates could function as
 biological control agents outside plantations and reduce the potential
 risk of exotic plants proliferating in protected areas.
description: Exotic Species Data in
 Lake MburoFile contain data from
 the field experiment.JAPPL-2015-00412_data.xlsx
DOI: 10.5061/dryad.kp296
title: Data from: Dmrt1 polymorphism covaries with sex-determination patterns in Rana temporaria

description: Patterns of sex-chromosome differentiation and gonadal development have
 been shown to vary among populations of Rana temporaria along a
 latitudinal transect in Sweden. Frogs from the northern-boreal population
 of Ammarnäs displayed well-differentiated X and Y haplotypes, early
 gonadal differentiation, and a perfect match between phenotypic and
 genotypic sex. In contrast, no differentiated Y haplotypes could be
 detected in the southern population of Tvedöra, where juveniles
 furthermore showed delayed gonadal differentiation. Here, we show that
 Dmrt1, a gene that plays a key role in sex determination and sexual
 development across all metazoans, displays significant sex differentiation
 in Tvedöra, with a Y-specific haplotype distinct from Ammarnäs. The
 differential segment is not only much shorter in Tvedöra than in Ammarnäs,
 it is also less differentiated and associates with both delayed gonadal
 differentiation and imperfect match between phenotypic and genotypic sex.
 Whereas Tvedöra juveniles with a local Y haplotype tend to ultimately
 develop as males, those without it may nevertheless become functional XX
 males, but with strongly female-biased progeny. Our findings suggest that
 the variance in patterns of sex determination documented in common frogs
 might result from a genetic polymorphism within a small genomic region
 that contains Dmrt1. They also substantiate the view that recurrent
 convergences of sex determination toward a limited set of chromosome pairs
 may result from the co-option of small genomic regions that harbor key
 genes from the sex-determination pathway.
description: Genotypes of linkage
 mapThis file includes
 genotyping data of linkage map for several families from each population,
 Ammarnas and Tvedora.genotype_linkagemap.xlsxGenotypes for Dxy calculationThis file includes genotypes of all progeny and parents. Each individual is assigned the relative maleness score to indicate the phenotypic sex.genotype_Dxy_calculation.xlsxGenotype for adultsThis file includes the genotypes of dmrt1 region for all adults from the two populations: Ammarnas and Tvedora.genotype_adults.xlsx
DOI: 10.5061/dryad.j2063
title: Data from: Standing genetic variation in host preference for mutualist microbial symbionts

description: Many models of mutualisms show that mutualisms are unstable if hosts lack
 mechanisms enabling preferential associations with mutualistic symbiotic
 partners over exploitative partners. Despite the theoretical importance of
 mutualism-stabilizing mechanisms, we have little empirical evidence to
 infer their evolutionary dynamics in response to exploitation by
 non-beneficial partners. Using a model mutualism—the interaction between
 legumes and nitrogen-fixing soil symbionts—we tested for quantitative
 genetic variation in plant responses to mutualistic and exploitative
 symbiotic rhizobia in controlled greenhouse conditions. We found
 significant broad-sense heritability in a legume host's preferential
 association with mutualistic over exploitative symbionts and selection to
 reduce frequency of associations with exploitative partners. We failed to
 detect evidence that selection will favour the loss of
 mutualism-stabilizing mechanisms in the absence of exploitation, as we
 found no evidence for a fitness cost to the host trait or indirect
 selection on genetically correlated traits. Our results show that genetic
 variation in the ability to preferentially reduce associations with an
 exploitative partner exists within mutualisms and is under selection,
 indicating that micro-evolutionary responses in mutualism-stabilizing
 traits in the face of rapidly evolving mutualistic and exploitative
 symbiotic bacteria can occur in natural host populations.
description: Standing genetic
 variation in host preference for mutualist microbial
 symbiontsSimonsenStinchcombe_Proc.Roy.Soc.B_2014_rawdata.csv
DOI: 10.5061/dryad.8g59456
title: Data from: Do replicates of independent guppy lineages evolve similarly in a predator-free laboratory environment?

description: The Trinidadian guppy is emblematic of parallel and convergent evolution,
 with repeated demonstrations that predation regime is a driver of adaptive
 trait evolution. A classic and foundational experiment in this system was
 conducted by John Endler 40 years ago, where male guppies placed into
 low-predation environments in the laboratory evolved increased color in a
 few generations. However, Endler’s experiment did not employ the now
 typical design for a parallel/convergent evolution study, which would
 employ replicates of different ancestral lineages. We therefore
 implemented an experiment that seeded replicate mesocosms with small
 founding populations of guppies originating from high-predation
 populations of two very different lineages. The different mesocosms were
 maintained identically, and male guppy color was quantified every four
 months. After one year, we tested whether male colour had increased,
 whether replicates within a lineage had parallel phenotypic trajectories,
 and whether the different lineages converged on a common phenotype.
 Results showed that male guppy color generally increased through time,
 primarily due to changes in melanic color; whereas the other colors showed
 inconsistent and highly variable trajectories. Most of the non-parallelism
 in phenotypic trajectories was among mesocosms containing different
 lineages. In addition to this mixture of parallelism and non-parallelism,
 convergence was not evident in that the variance in colour among the
 mesocosms actually increased through time. We suggest that our results
 reflect the importance of high variation in female preference and founder
 effects, both of which could be important in nature.
description: Colour
 DataRaw data of male guppy
 colour quantification2016-05-05
 AmyDF.csv
DOI: 10.5061/dryad.k247v
title: Data from: Size of dominant diatom species can alter their evenness

description: Traditionally, biodiversity has often been estimated on the basis of
 abundance partly due to the need for complicated measurements of biomass.
 Here, we conducted robust measurements of the community composition and of
 the size structure of diatoms in the North Pacific to evaluate the
 importance of biomass on the biodiversity. We found that the two most
 useful evenness indices increased in most cases where small species were
 numerically dominant when calculations were based on biomass compared with
 those on abundance. Size-abundance spectra of diatoms revealed that
 numerically dominant small species rarely dominated in terms of biomass.
 On the other hand, intermediate to large diatom species generally played a
 dominant role in terms of biomass in diatom community. The results suggest
 that the size of the dominant species is a crucial factor in determining
 the role of diatoms in the ecosystem functioning. Because such size
 variability can also be observed in other organisms, we need to pay
 attention to the effect of size structures on biodiversity.
description: Data_Sugie_and_SuzukiFigure 2. Species accumulation curves of 6 samples obtained during the KH12-3 cruise. Sample information is provided as follows: sample 1: 5 m, 28°00’ N, 138°00’ E; sample 2: 75 m, 32°19’ N, 133°33’ E; sample 3: 43 m, 33°05’ N, 133°40’ E; sample 4: 75 m, 35°00’ N, 160°00’ E; sample 5: 5 m, 43°31’ N, 160°00’ E; sample 2: 75 m, 15°00’ N, 160°00’ E. Figure 3. Relationships between (a) J′ calculated based on abundance (J′cell) and biomass (J′bio), and (b) 2E calculated based on abundance (2Ecell) and biomass (2Ebio). The dotted lines in (a) and (b) represent the 1:1 line. (c) Boxplot of J′bio/J′cell and 2Ebio/2Ecell. The upper and lower lines of the box represent the 75% and 25% values. The middle line in the box and circle represents the median and average of the ratios. Crosses represent maximum and minimum values. The ratio = 1 (dotted line), has the same meaning as the 1:1 line shown in Fig. 3a and 3b. Figure 4. Rank order of (a) biomass and (b) abundance of diatoms from the North Pacific. (a-1) and (b-1) show the rank order (line, left axis) and corresponding equivalent spherical diameter (ESD: dots, right axis). Histograms (lower panels) represent the ESD distribution depending on the dominancy shown in (a-1) and (b-1); data were assembled (a-2) and (b-2) 10–100%, (a-3) and (b-3) 1–10%, (a-4) and (b-4) 0.1–1%, and (a-5) and (b-5) &lt;0.1% groups.
DOI: 10.5061/dryad.vh396
title: Data from: Wolbachia in the Drosophila yakuba complex: pervasive frequency variation and weak cytoplasmic incompatibility, but no apparent effect on reproductive isolation

description: Three hybridizing species-the clade ((Drosophila yakuba, D. santomea), D.
 teissieri) -comprise the yakuba complex in the D. melanogaster subgroup.
 Their ranges overlap on Bioko and São Tomé, islands off west Africa. All
 three species are infected with Wolbachia, maternally inherited,
 endosymbiotic bacteria, best known for manipulating host reproduction to
 favor infected females. Previous analyses reported no cytoplasmic
 incompatibility (CI) in these species. However, we discovered that
 Wolbachia from each species cause intra- and interspecific CI. In D.
 teissieri, analyses of F1 and backcross genotypes show that both host
 genotype and Wolbachia variation modulate CI intensity. Wolbachia-infected
 females seem largely protected from intra- and interspecific CI,
 irrespective of Wolbachia and host genotypes. Wolbachia do not affect host
 mating behavior or female fecundity, within or between species. The latter
 suggests little apparent effect of Wolbachia on premating or gametic RI
 between host species. In nature, Wolbachia frequencies varied spatially
 for D. yakuba in 2009, with 76% (N = 155) infected on São Tomé, and only
 3% (N = 36) infected on Bioko; frequencies also varied temporally in D.
 yakuba and D. santomea on São Tomé between 2009 and 2015. These temporal
 frequency fluctuations could generate asymmetries in interspecific mating
 success, and contribute to postzygotic RI. However, the fluctuations in
 Wolbachia frequencies that we observe also suggest that asymmetries are
 unlikely to persist. Finally, we address theoretical questions that our
 empirical findings raise about Wolbachia persistence when conditions
 fluctuate and about the stable coexistence of Wolbachia and host variants
 that modulate Wolbachia effects.
description: CI_scanData related to population scans for cytoplasmic incompatibility (CI).Fecundity_scanData related to population scans for Wolbachia effects on host fecundity.teis_CI_natural_backgroundsData related to analysis of CI in D. teissieri with Wolbachia in their natural host backgrounds.teissieri_F1_CIData related to analysis of CI in D. teissieri with Wolbachia in F1 backgrounds.teis_backcrossData related to analysis of CI in D. teissieri with Wolbachia backcrossed into different host backgrounds.teis_CI_ixiData related to analysis of female protection from CI in D. teissieri.eggs_laid_and_viabilityData related to analysis of Wolbachia effects on intraspecific and interspecific fecundity and egg to adult viability in all three host species.infection_statusData related to analysis of Wolbachia infection frequencies in all three host species, in Bioko and Sao Tome.prop_matedData related to analysis of Wolbachia effects on intraspecific and interspecific mating in all three host species.
DOI: 10.5061/dryad.429vh
title: Data from: Intraspecific and interspecific variation in thermotolerance and photoacclimation in Symbiodinium dinoflagellates

description: Light and temperature are major drivers in the ecology and biogeography of
 symbiotic dinoflagellates living in corals and other cnidarians. We
 examined variations in physiology among 11 strains comprising five species
 of clade A Symbiodinium. We grew cultures at 26°C (control) and 32°C (high
 temperature) over a duration of 18 days while measuring growth and
 photochemical efficiency (Fv/Fm). Responses to thermal stress ranged from
 susceptible to tolerant across species and strains. Most strains exhibited
 a decrease in cell densities and Fv/Fm when grown at 32°C. Tolerance to
 high temperature (T32) was calculated for all strains, ranging from 0
 (unable to survive at high temperature) to 1 (able survive at high
 temperature). There was substantial variation in thermotolerance across
 species and among strains. One strain had a T32 close to 1, indicating
 that growth was not reduced at 32°C for only this one strain. To evaluate
 the combined effect of temperature and light on physiological stress, we
 selected three strains with different levels of thermotolerance (tolerant,
 intermediate and susceptible) and grew them under five different light
 intensities (65, 80, 100, 240 and 443 µmol quanta m−2 s−1) at 26 and 32°C.
 High irradiance exacerbated the effect of high temperature, particularly
 in strains from thermally sensitive species. This work further supports
 the recognition that broad physiological differences exist not only among
 species within Symbiodinium clades, but also among strains within species
 demonstrating that thermotolerance varies widely between species and among
 strains within species.
description: ArchiveCell densities and Fv/Fm measurements
DOI: 10.5061/dryad.sh537
title: Data from: Phage selection for bacterial cheats leads to population decline

description: While predators and parasites are known for their effects on bacterial
 population biology, their impact on the dynamics of bacterial social
 evolution remains largely unclear. Siderophores are iron-chelating
 molecules that are key to the survival of certain bacterial species in
 iron-limited environments, but their production can be subject to cheating
 by non-producing phenotypes. In a selection experiment conducted over c 20
 bacterial generations and involving 140 populations of the pathogenic
 bacterium Pseudomonas aeruginosa PAO1, we assessed the impact of a lytic
 phage on competition between siderophore producers and non-producers. We
 show that the presence of lytic phages favours the non-producing genotype
 in competition, regardless of whether iron use relies on siderophores.
 Interestingly, phage pressure resulted in higher siderophore production,
 which constitutes a cost to the producers and may explain why they were
 outcompeted by non-producers. At the end of the experiment, however,
 cheating load reduced the fitness of mixed populations relative to
 producer monocultures, and only monocultures of producers managed to grow
 in the presence of phage in situations where siderophores were necessary
 to access iron. These results suggest that public goods production may be
 modulated in the presence of natural enemies with consequences for the
 evolution of social strategies.
description: Datasets_Vasse_et_al_2015Contains all datasets from the experiments and assays conducted in the paper "Phage selection for bacterial cheats leads to population decline". Each dataset is on a separate spredsheet. Includes (i) densities and frequencies over the evolution experiment, (ii) resistance to phages, (iii) phage fitness, (iv) pyoverdin measurements in evolved populations and (v) growth and pyoverdin assays.
DOI: 10.5061/dryad.0qr3g
title: Data from: Genetic parentage analysis confirms a polygynandrous breeding system in the European grayling (Thymallus thymallus)

description: Knowing the breeding system of a species is important in order to
 understand individual variation in reproductive success. Large variation
 in reproductive success and thus reproductive skew strongly impacts on the
 effective number of breeders and thus the long-term effective population
 size (Ne). Fishes, in particular species belonging to the salmonid family,
 exhibit a wide diversity of breeding systems. In general, however,
 breeding systems are rarely studied in detail in the wild. Here we examine
 the breeding system of the spring-spawning European grayling Thymallus
 thymallus from a small Norwegian stream using parentage assignment based
 on the genotyping of 19 polymorphic microsatellite loci. In total 895
 individual grayling fry and 154 mature grayling (57 females and 97 males)
 were genotyped. A total of 466 offspring were assigned a father, a mother,
 or a parent pair with a confidence of 90% or higher. Successfully
 reproducing males had on average 11.9 ± 13.3 (SD) offspring with on
 average 2.1 ± 1.2 partners, whereas successful females had on average 9.5
 ± 12.8 offspring and 2.3 ± 1.5 partners. Parents with more partners also
 produced more offspring. Thus the grayling breeding system within this
 small stream revealed a polygynandrous breeding system, similar to what
 has been observed for many other salmonid fish species. The present study
 thus unambiguously corroborates a polygynadrous breeding system in the
 European grayling. This knowledge is critical for managing populations of
 this species, which has suffered significant local population declines
 throughout its range over the last several decades.
description: Haddeland et
 al._genotypes_and_metadatathe excel file contains
 2 sheets: sheet1 contains a description of the data in sheet2, sheet2
 contains the microsatellite genotypes, length and sex information for 994
 individuals of Thymallus thymallus
DOI: 10.5061/dryad.bt348
title: Data from: Social affiliation matters: both same-sex and opposite-sex relationships predict survival in wild female baboons

description: Social integration and support can have profound effects on human
 survival. The extent of this phenomenon in non-human animals is largely
 unknown, but such knowledge is important to understanding the evolution of
 both lifespan and sociality. Here, we report evidence that levels of
 affiliative social behaviour (i.e. ‘social connectedness’) with both
 same-sex and opposite-sex conspecifics predict adult survival in wild
 female baboons. In the Amboseli ecosystem in Kenya, adult female baboons
 that were socially connected to either adult males or adult females lived
 longer than females who were socially isolated from both sexes—females
 with strong connectedness to individuals of both sexes lived the longest.
 Female social connectedness to males was predicted by high dominance rank,
 indicating that males are a limited resource for females, and females
 compete for access to male social partners. To date, only a handful of
 animal studies have found that social relationships may affect survival.
 This study extends those findings by examining relationships to both sexes
 in by far the largest dataset yet examined for any animal. Our results
 support the idea that social effects on survival are evolutionarily
 conserved in social mammals.
description: Archie_social_connectednessData to estimate the correlation between adult female social connectedness and survival.Archie_data_for_Dryad.xlsx