cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n6k72
title: Data from: Patterns of ecological diversification in thelodonts

description: Here we explore the spatial, temporal and phylogenetic patterns of
 ecological diversification for the entire clade of thelodonts, one of the
 earliest groups of vertebrates and longest lasting of the Palaeozoic
 agnathans in the fossil record. Parsimony and maximum-likelihood methods
 are used to reconstruct ancestral states of their geographical
 distributions, habitats and lifestyles. Our results support the concept
 that thelodonts originated during the Middle?–Late Ordovician probably in
 marine open waters of Laurasia, with a demersal lifestyle on hard
 substrates being the ancestral condition for the whole clade. Later,
 thelodonts underwent a complex ecological diversification and
 palaeobiogeographical history, comparable in many aspects to those of some
 major groups of living fishes. Different modes of life evolved repeatedly
 and a wide range of habitats were colonized by distinct groups, including
 deep waters and brackish marine and/or freshwater environments. Diadromous
 strategies presumably appeared on nine different occasions. The
 palaeobiogeographical history of thelodonts reveals significant
 differences in the dispersal potential of some major groups. Dispersal of
 thelodontiforms entailed displacements over long distances and the
 crossing of deep-water biogeographical barriers, whereas those of
 furcacaudiforms were always limited to areas interconnected by shallow
 platforms. We propose that the evolution of pelagic larval stages in
 thelodontiforms might explain this biogeographical pattern and could
 satisfactorily account for the greater evolutionary success of this group.
description: Detailed information of
 the lifestyles, habitats and fossil occurrences of each thelodont
 species.Appendix
 S1.xlsxSupporting information
 references.Appendix
 S2.docx
DOI: 10.5061/dryad.70np2513
title: Data from: Genetic architecture in a marine hybrid zone: comparing outlier detection and genomic clines analysis in the bivalve Macoma balthica

description: The role of natural selection in speciation has received increasing
 attention and support in recent years. Different types of approaches have
 been developed that can detect genomic regions influenced by selection.
 Here we address the question whether two highly different methods - Fst
 outlier analysis and admixture analysis - detect largely the same set of
 non-neutral genomic elements or, instead, complementary sets. We study
 genetic architecture in a natural secondary contact zone where extensive
 admixture occurs. The marine bivalves Macoma balthica rubra and M. b.
 balthica descend from two independent trans-Arctic invasions of the north
 Atlantic and hybridize extensively where they meet, for example in the
 Kattegat - Danish Straits - Baltic Sea region. The Kattegat - Danish
 Straits region forms a steep salinity cline and is the only entrance to
 the recently (ca 8000 years ago) established brackish water basin the
 Baltic Sea. Salinity along the contact zone drops from 30‰ (Skagerrak,
 M.b.rubra) to 3‰ (Baltic, M.b.balthica). Both outlier analysis and genomic
 clines analysis suggest that large parts of the genome are influenced by
 non-neutral effects. Contrasting samples from well outside the hybrid
 zone, outlier analysis detects 16 of 84 amplified fragment length
 polymorphism (AFLP) markers as significant Fst outliers. Genomic clines
 analysis detects 31 out of 84 markers as non-neutral inside the hybrid
 zone. Remarkably, only three markers are detected by both methods. We
 conclude that the two methods together identify a suite of markers that
 are under the influence of non-neutral effects.
description: Luttikhuizen_et_al_MolEcol_2012_datadryadAFLP data for field collected marine bivalves in shallow intertidal locations in NW Europe. The species is Macoma balthica, the Baltic clam. Please refer to the original publication for further information such as exact locations and local habitat characteristics. File contains data on 644 individuals from 21 different locations scored (presence/absence) for 90 AFLP markers.
DOI: 10.5061/dryad.45kd1
title: Data from: Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa

description: The production of beneficial public goods is common in the microbial
 world, and so is cheating – the exploitation of public goods by
 non-producing mutants. Here, we examine co-evolutionary dynamics between
 cooperators and cheats and ask whether cooperators can evolve strategies
 to reduce the burden of exploitation, and whether cheats in turn can
 improve their exploitation abilities. We evolved cooperators of the
 bacterium Pseudomonas aeruginosa, producing the shareable iron-scavenging
 siderophore pyoverdine, together with cheats, defective in pyoverdine
 production but proficient in uptake. We found that cooperators managed to
 co-exist with cheats in 56% of all replicates over approximately 150
 generations of experimental evolution. Growth and competition assays
 revealed that co-existence was fostered by a combination of general
 adaptions to the media and specific adaptions to the co-evolving opponent.
 Phenotypic screening and whole-genome re-sequencing of evolved clones
 confirmed this pattern, and suggest that cooperators became less
 exploitable by cheats because they significantly reduced their pyoverdine
 investment. Cheats, meanwhile, improved exploitation efficiency through
 mutations blocking the costly pyoverdine-signalling pathway. Moreover,
 cooperators and cheats evolved reduced motility, a pattern that likely
 represents adaptation to laboratory conditions, but at the same time also
 affects social interactions by reducing strain mixing and pyoverdine
 sharing. Overall, we observed parallel evolution, where co-existence of
 cooperators and cheats was enabled by a combination of adaptations to the
 abiotic and social environment and their interactions.
description: Kuemmerli_etal_JEvolBiol_all_dataThis file contains all data presented in Kuemmerli et al. Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa.Kuemmerli_etal_JEvolBiol_Co-evolutionary_dynamics.xlsx
DOI: 10.5061/dryad.83605
title: Data from: Hierarchical polygyny in multiparous lesser flat-headed bats

description: How males gain access to mates and the potential for female choice will
 determine whether polygyny can operate at several levels, from within
 litters and groups to the wider population. Female lesser flat-headed bats
 (Tylonycteris pachypus) form maternity groups in bamboo stems. Unusually
 for bats, they are multiparous, providing the opportunity to test whether
 multi-level polygyny differs among males depending on whether they roost
 with females, with males, or are solitary. We genotyped 662 individuals
 from 54 internodes and undertook parentage of 165 litters. Our results
 revealed 170 sets of paternal twins/triplets, of which 96 were full-sibs
 and 74 were half-sibs. We found that males captured roosting with females
 typically sired more offspring overall than did other males, and also
 showed a greater tendency to monopolise paternity within both litters and
 roosting groups. In comparison, males that sired fewer full sibs were
 assigned more maternal half sibs. These latter individuals, which included
 solitary males and those from all-male groups might gain copulations
 either via roaming with furtive mating or during visits by females.
 Indeed, female lesser flat-headed bats store sperm, so could benefit from
 multiple mating to reduce genetic incompatibilities. At the same time,
 however, we found no evidence our outbreeding. Finally, relatedness and
 mtDNA analyses revealed that polygyny also operated within matrilineal
 kin, suggesting a system that might promote social cohesiveness. Future
 studies of individual movements will help to determine the extent to which
 mixed paternities in litters, matrilines and groups are driven by male or
 female behaviour.
description: microsatellite data
 upload-hpymicrosatellite data of
 the lesser flat-headed bats (Tylonycteris pachypus).
DOI: 10.5061/dryad.5ds70
title: Data from: Host specificity in subarctic aphids

description: The specificity of parasitic interaction depends on the adaptations of
 both the host and the parasite. Over time, these interactions evolve and
 change as a result of an “arms race” between host and parasite, and the
 resulting species-specific adaptations may be maintained, perpetuating
 these interactions across speciation events. With speciation and species
 sorting over time, complex systems of interactions evolve. Here, we
 elucidate some of these interactions using the aphids (Hemiptera:
 Aphididae) of Churchill as a model system. We analyzed these interactions
 by testing for two patterns in host-specificity: monophagy and
 phylogenetic clustering. We defined monophagy as one species feeding upon
 a single host plant species, an association which is driven by arms races
 in morphology, chemical resistance/tolerance, and camouflage; this pattern
 was observed in 7 of 22 aphid species. Secondly, we observed three
 separate cases where groups of closely related aphid species fed upon
 individual plant species (examples of phylogenetic clustering). One
 explanation for uncovering species-specific interactions in a recently
 deglaciated, sub-arctic locality is that the species involved in the
 associations moved north together. Testing different levels of specificity
 in species interactions allows us to accurately elucidate these patterns
 and gives us insight into where to direct future research.
description: Aphid
 dataAccession, collection
 and sequence data for the aphids associated with this publication. Data
 http://dx.doi.org/10.5883/DS-ASAPHPlant data associated
 with this manuscript.Accession, collection
 and sequence data for the plant species used in this manuscript. Public
 data originally derived from
 https://dx.doi.org/10.1186%2F1472-6785-12-25Plant
 data.xlsxPlant tree (all) Mar
 11To
 create a phylogeny of locally occurring plants in Churchill, we used the
 existing DNA barcode library derived from the majority of the vascular
 plants of Churchill (Kuzmina et al. 2012) (Supp. Appendix 1). Each plant
 species targeted in our study had three DNA barcode gene regions (ITS2,
 rbcLa, and matK; Hollingsworth et al. 2009) represented with the exception
 of Larix laricina, which lacked a matK sequence. For each plant species,
 and each gene region, the highest quality sequence (longest sequence
 containing the lowest number of ambiguous bases) was selected. The three
 genes were concatenated using FaBox (Villesen 2007), and the resulting
 contiguous sequence was used to create a Maximum-Likelihood tree (500
 bootstrap replicates) in MEGA6.aphid tree 1000
 bootstrap GTR tree consensus
DOI: 10.5061/dryad.tp3g0
title: Data from: Levels of clonal mixing in the black bean aphid Aphis fabae, a facultative ant mutualist

description: Aphids are a worldwide pest and an important model in ecology and
 evolution. Little is known, however, of the genetic structure of their
 colonies at a microgeographic level. For example, it remains largely
 unknown whether most species form monoclonal or polyclonal colonies. Here,
 we present the first detailed study on levels of clonal mixing in a
 nonsocial facultative ant mutualist, the black bean aphid Aphis fabae. In
 contrast to the earlier suggestion that colonies of this species are
 generally monoclonal, we found that across two subspecies of the black
 bean aphid, A. fabae cirsiiacanthoidis and A. fabae fabae, 32% and 77% of
 the aphid colonies were in fact polyclonal, consisting of a mix of up to 4
 different clones, which resulted in an overall average relatedness within
 colonies of 0.90 and 0.79 in the two subspecies. Data further show that
 the average relatedness in A. f. cirsiiacanthoidis remained relatively
 constant throughout the season, which means that clonal erosion due to
 clonal selection more or less balanced with the influx of new clones from
 elsewhere. Nevertheless, relatedness tended to decrease over the lifetime
 of a given colony, implying that clonal mixing primarily resulted from the
 joining of preexisting colonies as opposed to via simultaneous host
 colonisation by several foundresses. Widespread clonal mixing is argued to
 affect the ecology and evolution of the aphids in various important ways,
 for example with respect to the costs and benefits of group living, the
 evolution of dispersal and the interaction with predators as well as with
 the ant mutualists.
description: microsatellites data
 aphis fabae
DOI: 10.5061/dryad.j464h
title: Data from: Skin sloughing in susceptible and resistant amphibians regulates infection with a fungal pathogen

description: The fungal pathogen Batrachochytrium dendrobatidis (Bd) has been
 implicated in amphibian population declines globally. Given that Bd
 infection is limited to the skin in post-metamorphic amphibians, routine
 skin sloughing may regulate infection. Skin sloughing has been shown to
 reduce the number of cultivatable microbes on amphibian skin, and Bd
 infection increases skin sloughing rates at high loads. However, it is
 unclear whether species specific differences in skin sloughing patterns
 could regulate Bd population growth on the skin, and influence subsequent
 infection dynamics. We exposed five Australian frog species to Bd, and
 monitored sloughing rates and infection loads over time. Sloughing reduced
 Bd load on the ventral skin surface, in all five species, despite wide
 variation in susceptibility to disease. In the least susceptible species,
 an increase in sloughing rate occurred at lower infection loads, and
 sloughing reduced Bd load up to 100%, leading to infection clearance.
 Conversely, the drop in Bd load with sloughing was only temporary in the
 more susceptible species. These findings indicate that the ability of
 sloughing to act as an effective immune defence is species specific, and
 they have implications for understanding the pattern of Bd population
 growth on individual hosts, as well as population-level effects.
description: Data from: Skin
 sloughing in susceptible and resistant amphibians regulates infection with
 a fungal pathogenAll sloughing rate,
 infection load, and swab timing data analyzed in this publication. Please
 see README file for description of all sheets and columns contained in
 this Excel file.Ohmer et al 2017
 data.xlsx
DOI: 10.5061/dryad.d0p47
title: Data from: Using a ‘time machine’ to test for local adaptation of aquatic microbes to temporal and spatial environmental variation

description: Local adaptation occurs when different environments are dominated by
 different specialist genotypes, each of which is relatively fit in its
 local conditions and relatively unfit under other conditions. Analogously,
 ecological species sorting occurs when different environments are
 dominated by different competing species, each of which is relatively fit
 in its local conditions. The simplest theory predicts that spatial, but
 not temporal, environmental variation selects for local adaptation (or
 generates species sorting), but this prediction is difficult to test.
 Although organisms can be reciprocally transplanted among sites, doing so
 among times seems implausible. Here we describe a reciprocal transplant
 experiment testing for local adaptation or species sorting of lake
 bacteria in response to both temporal and spatial variation in water
 chemistry. The experiment used a −80 °C freezer as a ‘time machine’.
 Bacterial isolates and water samples were frozen for later use, allowing
 transplantation of older isolates ‘forward in time’ and newer isolates
 ‘backward in time’. Surprisingly, local maladaptation predominated over
 local adaptation in both space and time. Such local maladaptation may
 indicate that adaptation, or the analogous species sorting process, fails
 to keep pace with temporal fluctuations in water chemistry. This
 hypothesis could be tested with more finely-resolved temporal data.
description: Growth rate of lake
 bacteria in water samples from Alberta lakes, with data on water chemistry
 and taxonomic identityPlease see readme
 file.data
 for dryad.xlsx
DOI: 10.5061/dryad.6839bg5
title: Data from: A map-based approach to assessing genetic diversity, structure, and connectivity in the seagrass Halodule wrightii

description: Seagrass cover has declined in many areas of the world in a trend that has
 accelerated over the past several decades. This raises concern for both
 the impact the decline in cover has on coastal ecosystems and the effect
 it may have on seagrass evolutionary potential, as genotypic and genomic
 variation is lost. We used 8 microsatellite loci to investigate genetic
 diversity, structure, and connectivity in the seagrass Halodule wrightii
 from the Gulf of Mexico (Texas, USA) and western Atlantic (Bermuda). We
 examined how estimates correlated with changes in H. wrightii abundance
 and distribution on the Texas Gulf coast over the past 50 yr. Results show
 that, compared to other species, H. wrightii from this region exhibits
 variable clonal diversity (R = 0.02-0.81), moderate allelic diversity
 (mean AR = 4.09), and relatively high heterozygosity (mean He = 0.56). The
 patterns of genetic diversity and structure, however, do not entirely
 coincide with either geography or recent historical trends in seagrass
 distribution in this region. Results from a basin in which seagrasses have
 recently been expanding were consistent with expectations, as they were
 for an isolated site near the limit of H. wrightii’s range. Results from
 basins in which seagrasses have been experiencing decline and/or
 fragmentation, however, were mixed. Genetic structure on the Texas coast
 was relatively weak and coincided more strongly with tidal range than with
 geographic barriers or distance. Rapid expansion and the discovery of
 identical multi-locus genotypes at several sites raises the possibility of
 migration via drifting vegetative fragments, as the geographic distance
 among certain multi-locus genotypes cannot be explained by rhizome growth
 models.
description: Halodule wrightii
 Microsatellite ScoresThis file contain a
 dataset with microsatellite allele scores to accompany the 2017 ms A
 map-based approach to assessing genetic diversity, structure, and
 connectivity in the seagrass Halodule wrightii.Larkin_Hwrightii_2017_MicrosatelliteScores.xlsxHalodule wrightii Genclone-formatted microsatellite scoresThis zip file contains Genclone-formatted datasets to accompany the 2017 ms A map-based approach to assessing genetic diversity, structure, and connectivity in the seagrass Halodule wrightii.Larkin_2017_Genclone.zipHalodule wrightii Structure formatted fileThis file contains the Structure-formatted dataset to accompany the 2017 ms A map-based approach to assessing genetic diversity, structure, and connectivity in the seagrass Halodule wrightii.Larkin_2017_Hwrightii_Structure_input.txtHalodule wrightii Migrate-formatted data filesThis file contains Migrate-n formatted datasets to accompany the 2017 ms A map-based approach to assessing genetic diversity, structure, and connectivity in the seagrass Halodule wrightii.Larkin_2017_Migrate.zip
DOI: 10.5061/dryad.0tt5k
title: Data from: The incidental response to uniform natural selection

description: When populations are exposed to novel conditions of growth they often
 become adapted to a similar extent, and at the same time evolve some
 degree of impairment in their original environment. They may also come to
 vary widely with respect to characters which are uncorrelated with
 fitness, as the result of chance genetic associations among the founders,
 when these are a small sample from a large and variable ancestral
 population. I report an experiment in which 240 replicate lines of the
 unicellular chlorophyte Chlamydomonas were derived from primarily
 photoautotrophic ancestors and cultured as heterotrophs in the dark. All
 adapted to the dark and were impaired in the light after several hundred
 generations of culture. They also displayed a wide range of colony
 morphologies that were uncorrelated with fitness. This incidental response
 to selection probably arose through random variation in the initial
 composition of the lines. The differences between closely related species
 or varieties may likewise arise, in similar circumstances, by sampling
 error rather than natural selection.
description: Supplementary Table
 1Visual description of
 coloniesAcAgExpt Incidental Mass
 1Colony morphology and
 selection coefficient for Anc 1AcAgExpt Incidental Mass
 2Colony morphology and
 selection coefficient Anc 2AcAgExpt Incidental Mass
 3Colony morphology and
 selection coefficient Anc 3
DOI: 10.5061/dryad.f8f8h
title: Data from: Are aphid parasitoids locally adapted to the prevalence of defensive symbionts in their hosts?

description: Background: Insect parasitoids are under strong selection to overcome
 their hosts’ defences. In aphids, resistance to parasitoids is largely
 determined by the presence or absence of protective endosymbionts such as
 Hamiltonella defensa. Hence, parasitoids may become locally adapted to the
 prevalence of this endosymbiont in their host populations. To address
 this, we collected isofemale lines of the aphid parasitoid Lysiphlebus
 fabarum from 17 sites in Switzerland and France, at which we also
 estimated the frequency of infection with H. defensa as well as other
 bacterial endosymbionts in five important aphid host species. The
 parasitoids’ ability to overcome H. defensa-mediated resistance was then
 quantified by estimating their parasitism success on a single aphid clone
 (Aphis fabae fabae) that was either uninfected or experimentally infected
 with one of three different isolates of H. defensa. Results: The five
 aphid species (Aphis fabae fabae, A. f. cirsiiacanthoides, A. hederae, A.
 ruborum, A. urticata) differed strongly in the relative frequencies of
 infection with different bacterial endosymbionts, but there was also
 geographic variation in symbiont prevalence. Specifically, the frequency
 of infection with H. defensa ranged from 22 to 47 % when averaged across
 species. Parasitoids from sites with a high prevalence of H. defensa
 tended to be more infective on aphids possessing H. defensa, but this
 relationship was not significant, thus providing no conclusive evidence
 that L. fabarum is locally adapted to the occurrence of H. defensa. On the
 other hand, we observed a strong interaction between parasitoid line and
 H. defensa isolate on parasitism success, indicative of a high specificity
 of symbiont-conferred resistance. Conclusions: This study is the first, to
 our knowledge, to test for local adaptation of parasitoids to the
 frequency of defensive symbionts in their hosts. While it yielded useful
 information on the occurrence of facultative endosymbionts in several
 important host species of L. fabarum, it provided no clear evidence that
 parasitoids from sites with a high prevalence of H. defensa are better
 able to overcome H. defensa-conferred resistance. The strong genetic
 specificity in their interaction suggests that it may be more important
 for parasitoids to adapt to the particular strains of H. defensa in their
 host populations than to the general prevalence of this symbiont, and it
 highlights the important role symbionts can play in mediating
 host-parasitoid coevolution.
description: data_infectivity_for_dryadsymbiont_data_for_dryad