cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1534j
title: Data from: Mutualistic mimicry and filtering by altitude shape the structure of Andean butterfly communities

description: Both the abiotic environment and abiotic interactions among species
 contribute to shaping species assemblages. While the roles of habitat
 filtering and competitive interactions are clearly established, less is
 known about how positive interactions, whereby species benefit from the
 presence of one another, affect community structure. Here we assess the
 importance of positive interactions by studying Andean communities of
 butterflies that interact mutualistically via Müllerian mimicry. We show
 that communities at similar altitudes have a similar phylogenetic
 composition, confirming that filtering by altitude is an important
 process. We also provide evidence that species that interact
 mutualistically (i.e., species that share the same mimicry wing pattern)
 coexist at large scales more often than expected by chance. Furthermore,
 we detect an association between mimicry structure and altitude that is
 stronger than expected even when phylogeny is corrected for, indicating
 adaptive convergence for wing pattern and/or altitudinal range driven by
 mutualistic interactions. Positive interactions extend far beyond
 Müllerian mimicry, with many examples in plants and animals, and their
 role in the evolution and assembly of communities may be more pervasive
 than is currently appreciated. Our findings have strong implications for
 the evolution and resilience of community structure in a changing world.
description: Presence/absence data
 and altitude data per Ithomiini species in the
 incidence-datasetPresence/absence data
 obtained from field inventories supplemented by specimen data from
 multiple museum and private collections for 15 sites from eastern Ecuador.
 Locations and altitudes of the sites are given in Chazot et al (2013,
 American Naturalist). Each species was assigned to a mimicry complex. Some
 species exhibit sexual dimorphism. In some cases different
 subspecies/forms belong to different mimicry complexes, and are considered
 as different taxa. Minimum, maximum, median and mean altitude of each
 species are also given (extracted from a database of 3193 species locality
 records, KRW unpublished data).Incidence_dataset.xlsxAbundance data per Ithomiini species in the abundance-datasetAbundance data obtained from field inventories for 7 sites from eastern Ecuador. Data for an additional site (JS) was obtained from the literature (Beccaloni 1997). Locations and altitudes of the sites are given in Chazot et al (2013, American Naturalist). Each species was assigned to a mimicry complex. Some species exhibit sexual dimorphism. In some cases different subspecies/forms belong to different mimicry complexes, and are considered as different taxa.Abundance_dataset.xlsxGenbank accession numbersGenBank accession numbers, locality and references of sequences used in the study.Genbank_accession_numbers.xlsx
DOI: 10.5061/dryad.26pm4
title: Data from: Spatial heterogeneity lowers rather than increases host-parasite specialization

description: Abiotic environmental heterogeneity can promote the evolution of diverse
 resource specialists, which in turn may increase the degree of
 host-parasite specialization. We coevolved Pseudomonas fluorescens and
 lytic phage ϕ2 in spatially structured populations, each consisting of two
 interconnected subpopulations evolving in the same or different nutrient
 media (homogeneous and heterogeneous environments, respectively). Counter
 to the normal expectation, host-parasite specialization was significantly
 lower in heterogeneous compared with homogeneous environments. This result
 could not be explained by dispersal homogenizing populations, as this
 would have resulted in the heterogeneous treatments having levels of
 specialization equal to or greater than that of the homogeneous
 environments. We argue that selection for costly generalists is greatest
 when the coevolving species are exposed to diverse environmental
 conditions and that this can provide an explanation for our results. A
 simple coevolutionary model of this process suggests that this can be a
 general mechanism by which environmental heterogeneity can reduce rather
 than increase host-parasite specialization.
description: Host-parasite
 specializationThis data file contains
 data on bacterial resistance in two subpopulations linked by migration.
 Homogeneous subpopulations are linked by 1% dispersal (where treatment A
 gives dispersal between 0.5-0.5 M9 and B gives dispersal between 5-5 M9).
 Hetergeneous populations (0.5-5 M9) are linked by either 1% (C) or 50% (D)
 dispersal. For each subpopulation 5 bacterial clones (A1-A5 and B1-B5)
 where tested for resistance (1 or 0) against infectivity by 5 phage clones
 (A1-A5 and B1-B5) isolated from each subpopulation.Hesse_etal.xlsx
DOI: 10.5061/dryad.kt3109v7
title: Data from: Distinguishing social from nonsocial navigation in moving animal groups

description: Many animals, such as migrating shoals of fish, navigate in groups.
 Knowing the mechanisms involved in animal navigation is important when it
 comes to explaining navigation accuracy, dispersal patterns, population
 and evolutionary dynamics and consequently the design of conservation
 strategies. When navigating towards a common target, animals could
 interact socially by sharing available information directly or indirectly,
 or each individual could navigate by itself and aggregations may not
 disperse because all animals are moving towards the same target. Here, we
 present an analysis technique that uses individual movement trajectories
 to determine the extent to which individuals in navigating groups interact
 socially, given knowledge of their target. The basic idea of our approach
 is that the movement direction of individuals arises from a combination of
 responses to the environment and to other individuals. We estimate the
 relative importance of these responses, distinguishing between social and
 non-social interactions. We develop and test our method using simulated
 groups and demonstrate its applicability to empirical data in a case study
 on groups of guppies moving towards shelter in a tank. Our approach is
 generic and can be extended to different scenarios of animal group
 movement.
description: data
DOI: 10.5061/dryad.7qj70
title: Data from: Dispersal and the transition to sympatry in vertebrates

description: Under allopatric speciation models, a key step in the build-up of species
 richness is population dispersal leading to the co-occurrence of
 previously geographically isolated forms. Despite its central importance
 for community assembly, the extent to which the transition from spatial
 segregation (allopatry or parapatry) to coexistence (sympatry) is a
 predictable process, or alternatively one governed by chance and the
 vagaries of biogeographic history, remains poorly understood. Here, we use
 estimated divergence times and current patterns of geographical range
 overlap among sister species to explore the evolution of sympatry in
 vertebrates. We show that rates of transition to sympatry vary predictably
 according to ecology, being faster in marine or strongly dispersive
 terrestrial clades. This association with organism vagility is robust to
 the relative frequency of geographical speciation modes and consistent
 across taxonomic scales and metrics of dispersal ability. These findings
 reject neutral models of dispersal assembly based simply on evolutionary
 age and are not predicted by the main alternative view that range overlap
 is primarily constrained by biotic interactions. We conclude that species
 differences in dispersal limitation are fundamental in organizing the
 assembly of ecological communities and shaping broad-scale patterns of
 biodiversity over space and time.
description: Dataset
 S1Sister species ages and
 range overlapDataset
 S2Verebrate Fst
 estimatesDataset
 S3Avian genbank accession
 numbers
DOI: 10.5061/dryad.j4489
title: Data from: Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae

description: Background: The plastid maturase MatK has been implicated as a possible
 model for the evolutionary “missing link” between prokaryotic and
 eukaryotic splicing machinery. This evolutionary implication has sparked
 investigations concerning the function of this unusual maturase. Intron
 targets of MatK activity suggest that this is an essential enzyme for
 plastid function. The matK gene, however, is described as a pseudogene in
 many photosynthetic orchid species due to presence of premature stop
 codons in translations, and its high rate of nucleotide and amino acid
 substitution. Results: Sequence analysis of the matK gene from orchids
 identified an out-of-frame alternative AUG initiation codon upstream from
 the consensus initiation codon used for translation in other angiosperms.
 We demonstrate translation from the alternative initiation codon generates
 a conserved MatK reading frame. We confirm that MatK protein is expressed
 and functions in sample orchids currently described as having a matK
 pseudogene using immunodetection and reverse-transcription methods. We
 demonstrate using phylogenetic analysis that this alternative initiation
 codon emerged de novo within the Orchidaceae, with several reversal events
 at the basal lineage and deep in orchid history. Conclusion: These
 findings suggest a novel evolutionary shift for expression of matK in the
 Orchidaceae and support the function of MatK as a group II intron maturase
 in the plastid genome of land plants including the orchids.
description: Nucleotide alignment
 supporting phylogenyNucleotide sequence
 alignment of matK used for generating RAxML phylogeny of the
 Orchidaceae.orhid species FF
 81814.fas
DOI: 10.5061/dryad.5167t
title: Data from: Sex-specific genotype-by-environment interactions for cuticular hydrocarbon expression in decorated crickets, Gryllodes sigillatus: implications for the evolution of signal reliability

description: Phenotypic traits that convey information about individual identity or
 quality are important in animal social interactions, and the degree to
 which such traits are influenced by environmental variation can have
 profound effects on the reliability of these cues. Using inbred genetic
 lines of the decorated cricket, Gryllodes sigillatus, we manipulated diet
 quality to test how the cuticular hydrocarbon (CHC) profiles of males and
 females respond across two different nutritional rearing environments.
 There were significant differences between lines in the CHC profiles of
 females, but the effect of diet was not quite statistically significant.
 There was no significant genotype-by-environment interaction (GEI),
 suggesting that environmental effects on phenotypic variation in female
 CHCs are independent of genotype. There was, however, a significant effect
 of GEI for males, with changes in both signal quantity and content,
 suggesting that environmental effects on phenotypic expression of male
 CHCs are dependent on genotype. The differential response of male and
 female CHC expression to variation in the nutritional environment suggests
 that these chemical cues may be under sex-specific selection for signal
 reliability. Female CHCs show the characteristics of reliable cues of
 identity: high genetic variability, low condition dependence, and a high
 degree of genetic determination. This supports earlier work showing that
 female CHCs are used in self-recognition to identify previous mates and
 facilitate polyandry. In contrast, male CHCs show the characteristics of
 reliable cues of quality: condition dependence and a relatively higher
 degree of environmental determination. This suggests that male CHCs are
 likely to function as cues of underlying quality during mate choice and/or
 male dominance interactions.
description: Weddle et
 alGas
 chromatographic analysis of CHCs of male and female decorated crickets,
 Gryllodes sigillatus from 9 inbred genetic lines reared on two different
 diet qualities. | Diet 1 = high-quality diet | Diet 2 = low-quality diet |
 Data represent raw peak areas for each of the 15 hydrocarbon peaks
 identified (Peak 1 - 15) by GC, and includes the raw peak area for the
 dodecane internal standard used in all samples.
DOI: 10.5061/dryad.88741
title: Data from: Microsatellite evidence for high frequency of multiple paternity in the marine gastropod Rapana venosa

description: Background: Inferring of parentage in natural populations is important in
 understanding the mating systems of a species, which have great effects on
 its genetic structure and evolution. Muricidae, a large group
 (approximately 1,600 species) of marine gastropods, are poorly
 investigated in patterns of multiple paternity and sperm competition based
 on molecular techniques. The veined Rapa whelk, Rapana venosa, a
 commercially important muricid species with internal fertilization, is an
 ideal species to study the occurrence and frequency of multiple paternity
 and to facilitate understanding of their reproductive strategies.
 Methodology/Principal Findings: We developed five highly polymorphic
 microsatellites in R. venosa and applied them to identify multiple
 paternity in 19 broods (1381 embryos) collected from Dandong, China.
 Multiple paternity was detected in 17 (89.5%) of 19 broods. The number of
 sires per brood ranged from 1 to 7 (4.3 on average). Of the 17 multiply
 sired broods, 16 (94.1%) were significantly skewed from equal paternal
 contributions, and had a dominant sire which was also dominant in each
 assayed capsule. Conclusions: Our results indicate that a high level of
 multiple paternity occurs in the wild population of R. venosa. Similar
 patterns of multiple paternity in the 2–6 assayed capsules from each brood
 imply that fertilization events within the body of a female occur mostly
 (but not entirely) as random draws from a “well-but-not-perfectly blended
 sperm pool” of her several mates. Strongly skewed distributions of
 fertilization success among sires also suggest that sperm competition
 and/or cryptic female choice might be important for post-copulatory
 paternity biasing in this species.
description: microsatellite genotypes
 of Rapana venosaThe Excel file
 microsatellite genotypes contains the genotypes at 4 or 5 microsatellite
 loci of all offspring of Rapana venosa used in the Colony
 analyses.microsatellite
 genotypes.xls
DOI: 10.5061/dryad.nr916
title: Data from: Evolution under changing climates: climatic niche stasis despite rapid evolution in a non-native plant

description: A topic of great current interest is the capacity of populations to adapt
 genetically to rapidly changing climates, for example by evolving the
 timing of life-history events, but this is challenging to address
 experimentally. I use a plant invasion as a model system to tackle this
 question by combining molecular markers, a common garden experiment and
 climatic niche modelling. This approach reveals that non-native Lactuca
 serriola originates primarily from Europe, a climatic subset of its native
 range, with low rates of admixture from Asia. It has rapidly refilled its
 climatic niche in the new range, associated with the evolution of
 flowering phenology to produce clines along climate gradients that mirror
 those across the native range. Consequently, some non-native plants have
 evolved development times and grow under climates more extreme than those
 found in Europe, but not among populations from the native range as a
 whole. This suggests that many plant populations can adapt rapidly to
 changed climatic conditions that are already within the climatic niche
 space occupied by the species elsewhere in its range, but that evolution
 to conditions outside of this range is more difficult. These findings can
 also help to explain the prevalence of niche conservatism among non-native
 species.
description: Microsatellite genotypes
 of Lactuca serriolaThis file contains
 information about the geographic origin and genotypes at 7 microsatellite
 loci of every individual included in the population genetics analysis of
 introduction history in Lactuca serriola. Data were obtained from
 molecular analyses of plants raised from wild-collected seeds (see paper
 for details), and includes data collected for an earlier study (Alexander
 et al. 2009, see references). Fragment lengths were scored using
 GeneMapper v.4.1 software (Applied Biosystems).Alexander_Lactuca_genotypes.xlsxPhenological and size traits of Lactuca serriolaThis file contains data about Lactuca serriola plants from 55 populations raised in a common garden (climate chamber) experiment. Data describe the geographic and climatic origin of plants, their flowering phenology, reproductive output and size at different developmental stages when raised under controlled environmental conditions.Alexander_Lactuca_phenology.xlsx
DOI: 10.5061/dryad.1n84v
title: Data from: Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome

description: Properly estimating genetic diversity in populations of non-model species
 requires a basic understanding of how diversity is distributed across the
 genome and among individuals. To this end we analysed whole-genome
 re-sequencing data from 20 collared flycatchers (genome size ≈1.1 Gb;
 10.13 million single nucleotide polymorphisms detected). Genome-wide
 nucleotide diversity was almost identical among individuals (mean =
 0.00394, range = 0.00384-0.00401) but diversity levels varied extensively
 across the genome (95% confidence interval for 200 kb windows =
 0.0013-0.0053). Diversity was related to selective constraint such that in
 comparison to intergenic DNA, diversity at fourfold degenerate sites was
 reduced to 85%, 3’ UTRs to 82%, 5’ UTRs to 70% and non-degenerate sites to
 12%. There was a strong positive correlation between diversity and
 chromosome size, probably driven by a higher density of targets for
 selection on smaller chromosomes increasing the diversity-reducing effect
 of linked selection. Simulations exploring the ability of sequence data
 from a small number of genetic markers to capture the observed diversity
 clearly demonstrated that diversity estimation from finite sampling of
 such data is bound to be associated with large confidence intervals.
 Nevertheless, we show that precision in diversity estimation in large
 outbred populations benefits from increasing the number of loci rather
 than the number of individuals. Simulations mimicking RAD sequencing
 showed that this approach gives accurate estimates of genome-wide
 diversity. Based on the patterns of observed diversity and the performed
 simulations we provide broad recommendations for how genetic diversity
 should be estimated in natural populations.
description: All
 dataThis folder contains the
 information related to the analyses as well as the important results and
 scripts. Folders are described in individual README within the
 subfolders.data_folder.zip
DOI: 10.5061/dryad.4q5k6
title: Data from: Phenotypic integration of the cervical vertebrae in the Hominoidea (Primates)

description: Phenotypic integration and modularity represent important factors
 influencing evolutionary change. The mammalian cervical vertebral column
 is particularly interesting in regards to integration and modularity
 because it is highly constrained to seven elements, despite widely
 variable morphology. Previous research has found a common pattern of
 integration among quadrupedal mammals, but integration patterns also
 evolve in response to locomotor selective pressures like those associated
 with hominin bipedalism. Here, I test patterns of covariation in the
 cervical vertebrae of three hominoid primates (Hylobates, Pan, Homo) who
 engage in upright postures and locomotion. Patterns of integration in the
 hominoid cervical vertebrae correspond generally to those previously found
 in other mammals, suggesting that integration in this region is highly
 conserved, even among taxa that engage in novel positional behaviors.
 These integration patterns reflect underlying developmental as well as
 functional modules. The strong integration between vertebrae suggests that
 the functional morphology of the cervical vertebral column should be
 considered as a whole, rather than in individual vertebrae. Taxa that
 display highly derived morphologies in the cervical vertebrae are likely
 exploiting these integration patterns, rather than reorganizing them.
 Future work on vertebrates without cervical vertebral number constraints
 will further clarify the evolution of integration in this region.
description: Homo sapiens
 morphological dataCranial base and
 cervical vertebral data collected from museum and medical school
 specimens, either extracted from 3D coordinate data or with
 calipers.hom_cb_cv.csvHylobates lar morphological dataCranial base and cervical vertebral data collected from museum specimens, either extracted from 3D coordinate data or with calipers.hyl_cb_cv.csvPan troglodytes morphological dataCranial base and cervical vertebral data collected from museum specimens, either extracted from 3D coordinate data or with calipers.pan_cb_cv.csv
DOI: 10.5061/dryad.5h6n5
title: Data from: Mitochondrial DNA (COI) analyses reveal that amphipod diversity is associated with environmental heterogeneity in deep-sea habitats

description: The relationship between species diversity and environmental parameters is
 poorly understood for the mobile macrofauna of deep-sea habitats due to
 under-sampling and subsequent lack of accurate taxonomic information. To
 redress this, cytochrome oxidase c subunit I (COI) DNA sequences were used
 to estimate species diversity and to compare phoxocephalid amphipod
 assemblages among 20 stations encompassing a range of environmental
 conditions. Two regions, east (Chatham Rise) and west (Challenger Plateau)
 of New Zealand were sampled to depths of 200 – 1200 m with an epibenthic
 sled. Using a comparison among identified morphospecies, we found a clear
 gap in sequence divergences between 6 and 13% and used a 6% threshold to
 designate molecular operational taxonomic units (MOTUs), as a surrogate to
 putative species. DNA sequences (n=297) revealed high total diversity
 (n=49 MOTUs), as well as high beta diversity (28 MOTUs found at single
 location only). Novel phoxocephalid MOTUs were found at most stations,
 especially on Challenger Plateau and the flanks of Chatham Rise. Analyses
 of inter-station assemblages revealed a major split between regions,
 indicating minimal overlap in taxon distributions. A cluster of highly
 similar stations was identified, broadly distributed over the crest of
 Chatham Rise, in association with elevated food availability, probably
 resulting from higher surface productivity and relatively shallow depth.
 Accordingly, multivariate analysis revealed a strong correlation between
 phoxocephalid assemblages and food supply. This study highlights the value
 of molecular approaches, in particular COI sequences, for quantifying and
 comparing diversity in under-sampled and/or under-studied taxa.
description: PHOXOCEPHALIDAE
 ALIGNMENTOriginal source: samples
 collected in field. Created in BoLD. Sequence names refer to species.
 replicate number then station. Bar | separates species from collection
 data.FINAL
 PHOX ALIGNMENTv2.fasta