cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4q6b9
title: Data from: Molecular phylogeny and symbiotic selectivity of the green algal genus Dictyochloropsis sensu lato (Trebouxiophyceae): a polyphyletic and widespread group forming photobiont-mediated guilds in the lichen family Lobariaceae

description: Dictyochloropsis s.l. is an ecologically important, common but
 little-studied genus of green algae. Here, we examined the diversity and
 host selectivity of algae attributed to this genus at both
 species-to-species and species-to-community levels. We conducted a
 molecular investigation of 15 cultured strains and several lichen
 photobionts, using 18S rRNA, rbcL and ITS sequence data. We further used
 seven alga-specific microsatellite markers to study algal sharing among
 fungi of the family Lobariaceae in two populations in Madeira and Taiwan
 (454 lichens). We found that the genus Dictyochloropsis s.l. is
 polyphyletic. Dictyochloropsis clade 1 comprises only free-living algae
 whereas Dictyochloropsis clade 2 includes lichenized algae as well as
 free-living algae. Fungal selectivity towards algae belonging to
 Dictyochloropsis clade 2 is high. Selectivity varies geographically, with
 photobionts being restricted to a single region. Finally, we showed that
 Dictyochloropsis clade 2 individuals are shared among different fungal
 hosts in communities of lichens of the Lobariaceae. As for other green
 algal lineages, there is a high amount of cryptic diversity in
 Dictyochloropsis. Furthermore, co-evolution between Dictyochloropsis clade
 2 algae and representatives of the Lobariaceae is manifested at the
 community level, with several unrelated fungal species being horizontally
 connected by shared photobiont clones.
description: Multilocus SSR genotypes
 of the lichen symbiotic green alga Sym5Multilocus genotypes (7
 microsatellite markers: LPh1-LPh7) of the photobiont Sym5 in two lichen
 communities sampled from 10 trees in Madeira (249 thalli) and Taiwan (205
 thalli).DalGrande_et_al_New_Phytol.xlsxDNA alignment of the 18S gene in Fasta formatDNA alignment of the 18S gene in Fasta format18S_alignment.fastaPhylogenetic tree presented in Figure 1Maximum Likelihood tree of the green algae inferred from 18S rRNA sequencesRAxML_result.18S.reduced_raxout.treFig1: bootstrap values (1000 replicates)Maximum Likelihood tree of the green algae inferred from 18S rRNA sequences with bootstrap values (1000 replicates)RAxML_bipartitions.18S.reduced_raxout.treDNA alignment of the rbcL gene in Fasta formatDNA alignment of the rbcL gene in Fasta formatrbcL_alignment.fastaPhylogenetic tree presented in Figure S1Maximum Likelihood tree of the green algae inferred from rbcL sequencesRAxML_result.rbcL.reduced_raxout.treFigS1: bootstrap values (1000 replicates)Maximum Likelihood tree of the green algae inferred from rbcL sequences with bootstrap values (1000 replicates)RAxML_bipartitions.rbcL.reduced_raxout.tre
DOI: 10.5061/dryad.3k0d8
title: Data from: Hidden diversity in the freshwater planktonic diatom Asterionella formosa

description: Many freshwater and marine algal species are described as having
 cosmopolitan distributions. Whether these widely distributed
 morphologically similar algae also share a similar gene pool remains often
 unclear. In the context of island biogeography theory, stronger spatial
 isolation deemed typical of freshwater lakes should restrict gene flow and
 lead to higher genetic differentiation among lakes. Using nine
 microsatellite loci, we investigate the genetic diversity of a widely
 distributed freshwater planktonic diatom, Asterionella formosa, across
 different lakes in Switzerland and the Netherlands. We applied a
 hierarchical spatial sampling design to determine the geographical scale
 at which populations are structured. A subset of the isolates was
 additionally analysed using amplified fragment length polymorphism (AFLP)
 markers. Our results revealed complex and unexpected population structure
 in A. formosa with evidence for both restricted and moderate to high gene
 flow at the same time. Different genetic markers (microsatellites and
 AFLPs) analysed with a variety of multivariate methods consistently
 revealed that genetic differentiation within lakes was much stronger than
 among lakes, indicating the presence of cryptic species within A. formosa.
 We conclude that the hidden diversity found in this study is expected to
 have implications for the further use of A. formosa in biogeographical,
 conservation and ecological studies. Further research using species-level
 phylogenetic markers is necessary to place the observed differentiation in
 an evolutionary context of speciation.
description: MicrosatGenotypes_Asterionella_formosaExcel spreadsheet of genotypic data of 224 individuals of Asterionella formosa (freshwater diatom), from seven lakes in Switzerland and four lakes in The Netherlands, scored for nine microsatellite markers.AFLP_data_Asterionella_formosaAFLP fingerprint data of 91 isolates of Asterionella formosa (freshwater diatom) at 121 loci, from seven lakes in Switzerland and tree lakes in The Netherlands.Microsatellite sequences Asterionella formosaMicrosatellite sequences of Asterionella formosa, containing the repeat units and forward and reverse primer sites.Microsatellitesequences_Asterionella_formosa.doc
DOI: 10.5061/dryad.s03n4d1
title: Data from: Two decades of evolutionary changes in Brassica rapa in response to fluctuations in precipitation and severe drought

description: As climate changes at unprecedented rates, understanding population
 responses is a major challenge. Resurrection studies can provide crucial
 insights into the contemporary evolution of species to climate change. We
 used a seed collection of two Californian populations of the annual plant
 Brassica rapa made over two decades of dramatic precipitation
 fluctuations, including increasingly severe droughts. We compared
 flowering phenology, other drought response traits, and seed production
 among four generations, grown under drought and control conditions, to
 test for evolutionary change and to characterize the strength and
 direction of selection. Post-drought generations flowered earlier, with a
 reduced stem diameter, and lower water-use efficiency (WUE), while
 intervening wet seasons reversed these adaptations. There was selection
 for earlier flowering, which was adaptive, but delayed flowering after wet
 years resulted in reduced total seed mass, indicating a maladaptive
 response caused by brief wet periods. Furthermore, evolutionary changes
 and plastic responses often differed in magnitude between populations and
 drought periods, suggesting independent adaptive pathways. While B. rapa
 rapidly evolved a drought escape strategy, plant fitness was reduced in
 contemporary generations, suggesting that rapid shifts in flowering time
 may no longer keep up with the increasing severity of drought periods,
 especially when drought adaptation is slowed by occasional wet seasons.
description: Phenotypic data for
 Onset of flowering and stem diameter at floweringThis file contains data
 for onset of flowering and stem diameter at flowering for each individual.
 For each individual, factors are assigned, like population name, year
 collected, treatment, block, replicates etc.pheno_flow_diam.xlsxPhenotypic data for SLAThis file contains data for specific leaf area (SLA) measured on a subset of individuals. The file also contains individual information, like population, collection year, treatment, block, replicate etc.pheno_SLA.xlsxphenotypic data for WUEThis file contains the isotopic analyses as returned by the stabke isotope lab. For water-use efficiency, we used delta13C from the data file. The file also contains individual information, like population, collection year, treatment, block, replicate etc.pheno_isotopeWUE.xlspheno_seedmassThis file contains total seed mass measured for each individual. The file also contains individual information, like population, collection year, treatment, block, replicate etc.data for selection analysesThis file contains data for the selection analysis: seed mass, onset of flowering and stem diameter at flowering. From there we calculated standardized traits and relative fitness. The file also contains individual information, like population, collection year, treatment, block, replicate etc.pheno_selectionanal.xlsx
DOI: 10.5061/dryad.3583j
title: Data from: Evolutionary processes and its environmental correlates in the cranial morphology of western chipmunks (Tamias)

description: The importance of the environment in shaping phenotypic evolution lies at
 the core of evolutionary biology. Chipmunks of the genus Tamias (subgenus
 Neotamias) are part of a very recent radiation, occupying a wide range of
 environments with marked niche partitioning among species. One open
 question is if and how those differences in environments affected
 phenotypic evolution in this lineage. Herein we examine the relative
 importance of genetic drift versus natural selection in the origin of
 cranial diversity exhibited by clade members. We also explore the degree
 to which variation in potential selective agents (environmental variables)
 are correlated with the patterns of morphological variation presented. We
 found that genetic drift cannot explain morphological diversification in
 the group, thus supporting the potential role of natural selection as the
 predominant evolutionary force during Neotamias cranial diversification,
 although the strength of selection varied greatly among species. This
 morphological diversification, in turn, was correlated with environmental
 conditions, suggesting a possible causal relationship. These results
 underscore that extant Neotamias represent a radiation in which aspects of
 the environment might have acted as the selective force driving species’
 divergence.
description: Data from the chipmunk
 skull's measuredIn this file you can
 find the covariance matrices estimated for each chipmunk species and also
 the morphological and climatic estimates used in the study. The readMe
 file describes all the specimens used, and the respective museum where the
 data is deposited.covariance_matrices_neotamias.xls
DOI: 10.5061/dryad.0j4b2
title: Data from: Priority effects can persist across floral generations in nectar microbial metacommunities

description: The order of species arrival can influence how species interact with one
 another and, consequently, which species may coexist in local communities.
 This phenomenon, called priority effects, has been observed in various
 types of communities, but it remains unclear whether priority effects
 persist over the long term spanning multiple generations of local
 communities in metacommunities. Focusing on bacteria and yeasts that
 colonize floral nectar of the sticky monkey flower, Mimulus aurantiacus,
 via hummingbirds and other flower-visiting animals, we experimentally
 manipulated initial microbial dominance on plants (regarded as
 metacommunities) to examine whether its effects persisted across multiple
 generations of flowers (regarded as local microbial habitats). The
 experimental introduction of Neokomagataea (= Gluconobacter) bacteria and
 Metschnikowia yeasts into wild flowers showed that the effects of initial
 dominance were observable across multiple floral generations. Three weeks
 after introduction, corresponding approximately to three floral
 generations, Neokomagataea introduction led to exclusion of yeasts,
 whereas Metschnikowia introduction did not result in the exclusion of
 Neokomagataea. Our results suggest that, even when local habitats are
 ephemeral, priority effects may influence multiple generations of local
 communities within metacommunities.
description: Appendix S3 - Data
 matricesThis file includes
 sample x OTU tables, taxonomic information, meta data, etc. Same file as
 Appendix S3 of the paper.AppendixS3.xlsxAppendix S4 - Nucleotide sequencesNucleotide sequences of the OTUs obtained in the sequencing analysis. Same as Appendix S4 of the paper.AppendixS4.fasta
DOI: 10.5061/dryad.hc93j
title: Data from: Increased duration of aquatic resource pulse alters community and ecosystem responses in a subarctic plant community

description: Allochthonous resource movement across ecosystem boundaries creates
 episodic linkages between ecosystems. The sensitivity of the community to
 external resources of varying duration can alter the baseline upon which
 future pulses of allochthony can act. We explored the terrestrial
 ecosystem response to pulsed inputs of lake-derived resources with a
 manipulative experiment in a subarctic heathland where we assessed plant
 community and nutrient availability responses to additions of midge
 carcasses (Diptera: Chironomidae). Insect carcasses were added as either a
 one-time pulse or a 4-year press to simulate differing durations of
 allochthony, which is common in the area. We found that midge pulses
 significantly elevated soil inorganic [N] in the first year (7× over
 background levels) but were significantly diminished (1.5×) by the second
 year after the initial pulse. The press treatment continued to elevate
 total soil inorganic [N] to 13× over background levels by the fourth year
 of midge additions, but then declined to 3.6× background in year 5 when
 experimental midge additions had ceased. In contrast to the soil inorganic
 N response, plant biomass was similar in pulse-addition and control plots
 over the course of the experiment. However, by the second year of the
 study plant biomass in press-addition plots were significantly higher than
 controls (&gt;50%), and continued to increase over the 4 years of the
 press treatment. Midge addition stimulated dominance of graminoids and
 thatch litter in plots that had previously been primarily heathland
 vegetation, a response that persisted four years post-midge addition. Our
 findings suggest that soil and plant community responses to persistent
 insect carcass deposition (e.g., press) into heathland vegetation has the
 potential to carry forward in a way that modifies the baseline ecosystem
 conditions upon which additional allochthony may act.
description: HEL_Biomass_Data_2009_2015Plant biomass data from experimental plots, XLS formatHEL_Veg_PhotoQuadrat_Data_2011_2015Plant community composition data, XLS formatHEL_Nitrogen_Data_2008_2012Soil Nitrogen data from resin bags, XLS formatHEL_Biomass_Data_2009_2015Plant biomass data from experimental plots, CSV formatHEL_Nitrogen_Data_2008_2012Soil Nitrogen data from resin bags, CSV formatHEL_Veg_PhotoQuadrat_Data_2011Plant community composition 2011, CSV formatHEL_Veg_PhotoQuadrat_Data_2015Plant community composition 2015, CSV format
DOI: 10.5061/dryad.7dd62
title: Data from: Linear reaction norms of thermal limits in Drosophila: predictable plasticity in cold but not in heat tolerance

description: 1. Thermal limits of ectotherms have been studied extensively and are
 believed to be evolutionary constrained, leaving ectotherms at risk under
 future climate change. Phenotypic plasticity may extend the thermal
 limits, but we lack detailed characterizations of thermal limit reaction
 norms as well as an understanding of the interspecific variation of these
 reaction norms. 2. Here we investigated the interspecific variation in
 phenotypic plasticity of thermal limits in 13 Drosophila species. We
 obtained high-resolution reaction norms for upper and lower thermal limits
 across the permissive developmental thermal range (12.5 – 30°C). The
 estimated phenotypes were then associated (while accounting for phylogeny)
 with climatic parameters from the species’ distributional range. 3. All
 species showed linear reaction norms for cold tolerance (CTmin) and heat
 tolerance (CTmax) across developmental acclimation temperatures. We
 observed strong beneficial cold acclimation to lower temperatures in all
 species. Conversely, the heat acclimation response was non-existent in
 some species, and decreasing or increasing with increasing developmental
 acclimation temperatures in other species. The degree of phenotypic
 plasticity of CTmin and CTmax was neither related to the basal thermal
 limits (trade-off hypothesis) nor to climatic parameters connected to
 latitudinal distributions (latitudinal hypothesis). 4. A substantial and
 linear developmental plasticity of lower thermal limits is a general
 characteristic of Drosophila species, which allows for straightforward
 application in species distribution models. In general, upper thermal
 limits also show linear norms of reaction, but their adaptive significance
 is limited and highly variable among species, making general predictions
 across species rather impossible. 5. High resolution estimates of norms of
 reaction of thermal limits can considerably increase our understanding of
 the capacity of ectotherms to acclimate to different thermal environments.
 However, our understanding of the environmental drivers of the evolution
 of phenotypic plasticity and thus of the interspecific differences remains
 ambiguous, potentially constrained by limited microclimate information.
description: Climatic data for the
 distribution of each speciesThe gps coordinates for
 each species was obtained from http://www.taxodros.uzh.ch while the
 associated climatic variables was obtained from http://www.worldclim.org.
 See paper for details.Clim_Lat_All.csvCTmaxCritical thermal maximum across developmental temperatures for all species.CTminCritical thermal minimum across developmental temperatures for all species.Egg-to-adult viabilityEgg-to-adult viability across developmental temperatures.Viability.csv
DOI: 10.5061/dryad.v75c9
title: Data from: Resource tracking and its conservation implications for an obligate frugivore (Procnias tricarunculatus, the three-wattled bellbird)

description: In Monteverde, Costa Rica, the vulnerable Three-wattled Bellbird (Procnias
 tricarunculatus) feeds primarily upon the fruit of Lauraceae species
 during its reproductive and post-reproductive seasons. To understand and
 advance appropriate conservation measures, this study identified the
 bellbird’s foraging challenges in its search for a temporally and
 spatially fluctuating resource. Although there are at least 96 species of
 Lauraceae found in the five life zones of Monteverde, the distinct
 distributions of tree species both among and within life zones require the
 bellbirds to track seasonal fruiting across the various zones. In this
 six-year study, we monitored the fruiting of tree species and bellbird
 abundance in 24 study plots within its post-reproductive life zone, the
 Premontane Wet forest, in order to identify preferred bellbird food
 resources and how the fruiting of these species drives the spatial
 distribution of the bellbird. Our research revealed phenological patterns
 of annual, biennial, and triennial fruiting with high levels of fruiting
 synchrony within several identified key fruit species. Of critical
 conservation importance is that no single species of Lauraceae produced a
 consistent food supply for bellbirds each year. Therefore, even within
 life zones, the bellbird’s survival depends on its mobility to search for
 and obtain fruit, as well as the availability of fruits of multiple tree
 species. The conservation implications include focused attention on
 multiple core areas within given life zones, protection of existing forest
 and remnant trees, and forest restoration with plantings of multiple tree
 species. We suspect that other tropical frugivorous species face similar
 conservation challenges.
description: Resource_Tracking_by_the_Bellbird_dataData collected in the field in Monteverde, Costa Rica for the Hamilton et al. study titled "Resource Tracking and its Conservation Implications for an Obligate Frugivore (Procnias tricarunculatus, the Three-wattled Bellbird)." For full explanation, see README file.
DOI: 10.5061/dryad.14n6g
title: Data from: Post-glacial northward expansion and genetic differentiation between migratory and sedentary populations of the broad-tailed hummingbird (Selasphorus platycercus)

description: Unlike other migratory hummingbirds in North America, the broad-tailed
 hummingbird (Selasphorus platycercus) exhibits both long-distance
 migratory behaviour in the USA and sedentary behaviour in Mexico and
 Guatemala. We examined the evolution of migration linked to its northward
 expansion using a multi-perspective approach. We analysed variation in
 morphology, mitochondrial and nuclear DNA, estimated migration rates
 between migratory and sedentary populations, compared divergence times
 with the occurrence of Quaternary climate events, and constructed species
 distribution models to predict where migratory and sedentary populations
 resided during the Last Glacial Maximum (LGM) and Last Interglacial (LIG)
 events. Our results are consistent with a recent northward population
 expansion driven by migration from southern sedentary populations.
 Phylogeographical analyses and population genetics methods revealed that
 migratory populations in the USA and sedentary populations in Mexico of
 the platycercus subspecies form one admixed population, and that sedentary
 populations from southern Mexico and Guatemala (guatemalae) undertook
 independent evolutionary trajectories. Species distribution modelling
 revealed that the species is a niche tracker and that the climate
 conditions associated with modern obligate migrants in the USA were not
 present during the LIG, which provides indirect evidence for recent
 migratory behaviour in broad-tailed hummingbirds on the temporal scale of
 glacial cycles. The finding that platycercus hummingbirds form one genetic
 population and that suitable habitat for migratory populations was
 observed in eastern Mexico during the LIG also suggests that the
 conservation of overwintering sites is crucial for obligate migratory
 populations currently facing climate change effects.
description: Malpica&Ornelas_morphology_infoFour body measurements measurement obtained from 324 adult broad-tailed hummingbirds (281 with data for all variables were used in statistical analyses).Malpica&Ornelas_localities_informationThe file contains the collection localities for the Selasphorus platycercus samples examined in this study.Malpica&Ornelas_localities_info.docMalpica&Ornelas_microsatellites_informationMicrosatellite sizing for 118 hummingbirds samples genotyped at eight autosomal microsatellite loci.Malpica&Ornelas_microsatellites_info.docMalpica&Ornelas_IMafiles_informationFour IMa files are available depending on populations being compared and markers used.Malpica&Ornelas_IMafiles.zip