cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1fs13
title: Data from: One step ahead: a parasitoid disperses farther and forms a wider geographic population than its fig wasp host

description: The structure of populations across landscapes influences the dynamics of
 their interactions with other species. Understanding the geographic
 structure of populations can thus shed light on the potential for
 interacting species to coevolve. Host – parasitoid interactions are
 widespread in nature, and also represent a significant force in the
 evolution of plant – insect interactions. However, there have been few
 comparisons of population structure between an insect host and its
 parasitoid. We used microsatellite markers to analyse the population
 genetic structure of Pleistodontes imperialis sp. 1, a fig-pollinating
 wasp of Port Jackson fig (Ficus rubiginosa), and its main parasitoid,
 Sycoscapter sp. A, in eastern Australia. Besides exploring this host –
 parasitoid system, our study also constitutes, to our knowledge, the first
 study of population structure in a non-pollinating fig wasp species. We
 collected matched samples of pollinators and parasitoids at several sites
 in two regions separated by up to 2000 km. We found that pollinators
 occupying the two regions represent distinct populations, but, in
 contrast, parasitoids formed a single population across the wide
 geographic range sampled. We observed genetic isolation by distance for
 each species, but found consistently lower FST and RST values between
 sites for parasitoids compared with pollinators. Previous studies have
 indicated that pollinators of monoecious figs can disperse over very long
 distances, and we provide the first genetic evidence that their
 parasitoids may disperse as far, if not farther. The contrasting
 geographic population structures of host and parasitoid highlight the
 potential for geographic mosaics in this important symbiotic system.
description: data file P. imperialis
 sp. 1 and Sycoscapter sp. A_revisedmicrosatellite
 genotypes, sampling locations and dates for Pleistodontes imperialis sp. 1
 and Sycoscapter sp. AP. imperialis_cytb
 sequencesAlignment of cytb
 sequences for Pleistodontes imperialis sp. 1P.
 imperialis_cytb.txtSycoscapter sp. A_cytb
 sequencescytb sequence alignment
 for Sycoscapter sp. A samplesSycoscapter_sp_A_cytb_revised.txtP. imperialis geographic and genetic distancesGeographic and genetic distances matrices used for IBD analyses for Pleistodontes imperialis sp. 1. Distance matrices were produced using the SPAGeDI software from geographic coordinates (lat/long).Sycoscapter sp. A geographic and genetic distancesgeographic and genetic distances matrices used for IBD analyses for Sycoscapter sp. A. Distance matrices were produced using the SPAGeDI software from geographic coordinates (lat/long)P. imperialis TESS inputinput file for TESS analysis of microsatellite data for P. imperialis sp. 1Sycoscapter sp. A TESS inputinput file for TESS analysis of microsatellite data for Sycoscapter sp. A
DOI: 10.5061/dryad.1jd40
title: Data from: Similarity in temporal variation in sex-biased dispersal over short and long distances in the dark-eyed junco, Junco hyemalis

description: Patterns of sex-biased dispersal are typically consistent within taxa,
 e.g., female-biased in birds and male-biased in mammals, leading to
 theories about the evolutionary pressures that lead to sex-biased
 dispersal. However, generalizations about the evolution of sex biases tend
 to overlook that dispersal is mediated by ecological factors that vary
 over time. We examined potential temporal variation in between- and
 within-population dispersal over an 11-year period in a bird, the
 dark-eyed junco (Junco hyemalis). We measured between-population dispersal
 patterns using genetic assignment indices and found yearly variation in
 which sex was more likely to have immigrated. When we measured
 within-population spatial genetic structure and mark-recapture dispersal
 distances, we typically found yearly sex-biased dispersal patterns that
 mirrored between–population dispersal, indicating common eco-evolutionary
 causes despite expected differences due to the scale of dispersal.
 However, in years without detectable between-population sex biases, we
 found genetic similarity between nearby males within our population. This
 suggests that, in certain circumstances, ecological pressures may act on
 within-population dispersal without affecting dispersal between
 populations. Alternatively, current analytical tools may be better able to
 detect within-population sex-biased dispersal. Future work will
 investigate potential causes of the observed temporal variation in
 dispersal patterns and whether they have greater effects on
 within-population dispersal.
description: Junco hyemalis
 microsatellite dataThis file includes
 microsatellite data for adult male and female juncos captured on Salt Pond
 Mountain from 1997-2007. Also included are sex and age of these adult
 nesting birds and their nest locations (UTMs).Liebgold-ME-13-0604-corrected.xlsxMark-recapture locations (Junco hyemalis)This file includes mark-recapture locations for nestlings banded in the nest on Salt Pond Mountain, VA from 1996-2006 that were also recaptured or nested the next year as adults. Included are band number, hatch year, sex of the individual, natal nest location, capture location, and first nest location.Liebgold-MEC-13-0604-Mark-recapture.xls
DOI: 10.5061/dryad.56360
title: Data from: Intraspecific niche variation drives abundance-occupancy relationships in freshwater fish communities

description: A positive relationship between occupancy and average local abundance of
 species is found in a variety of taxa, yet the mechanisms driving this
 association between abundance and occupancy are still enigmatic. Here we
 show that freshwater fishes exhibit a positive abundance-occupancy
 relationship across 125 Swedish lakes. For a subset of 9 species from 11
 lakes, we estimated species-specific diet breadth from stable isotopes,
 within-lake habitat breadth from catch data for littoral and pelagic nets,
 adaptive potential from genetic diversity, abiotic niche position, and
 dispersal capacity. Average local abundance was mainly positively
 associated with both within-lake habitat and diet breadth, that is,
 species with larger intraspecific variation in niche space had higher
 abundances. No measure was a good predictor of occupancy, indicating that
 occupancy may be more directly related to abundance or abiotic conditions
 than to niche breadth per se. This study suggests a link between
 intraspecific niche variation and a positive abundance-occupancy
 relationship and implies that management of freshwater fish communities,
 whether to conserve threatened or control invasive species, should
 initially be aimed at niche processes.
description: AFLP scores for each
 species (csv-files)These spreadsheets
 (csv-files) contain the raw peak height data of AFLPs as described in the
 text. The top rows of each file contain replicate data. Each column is a
 particular AFLP locus, with Megabace dye and size
 indicated.AFLP per
 species.zipStable Isotope data of N
 & CRaw data of stable
 isotopes of N and C of all species. Read the README-file for information
 on abbrevations.Stable Isotope All
 sp.csvAbundances and
 occupancies per speciesMean CPUE and occupancy
 for each species amon all 125 lakes or the subset of 11
 lakes.Ab-Occ.csvLake and fish data from 125 monitoring lakes in SwedenData on fish abundance from gill net monitoring and water chemistry and lake connectivity for the 125 monitoring lakes in SwedenData_fish_connectivity.csv
DOI: 10.15468/da30il
title: University of Tennessee Fungal Herbarium

description: The University of Tennessee fungal herbarium (TENN FU) comprises over 75,000 barcoded and databased specimens emphasizing the southeastern North America but with significant collections from New Zealand and China. Approximately 54,000 specimens are pertinent to this project and include voucher specimens for studies of Hesler, Petersen and students.
DOI: 10.5061/dryad.rp7qv
title: Data from: Maximum likelihood inference of small trees in the presence of long branches

description: The statistical basis of maximum likelihood (ML), its robustness and the
 fact that it appears to suffer less from biases lead to it being one of
 the most popular methods for tree reconstruction. Despite its popularity,
 very few analytical solutions for ML exist, so biases suffered by ML are
 not well understood. One possible bias is long branch attraction (LBA), a
 regularly-cited term generally used to describe a propensity for long
 branches to be joined together in estimated trees. Although initially
 mentioned in connection to inconsistency of parsimony, LBA has been
 claimed to affect all major phylogenetic reconstruction methods, including
 ML. Despite the widespread use of this term in the literature, exactly
 what LBA is and what may be causing it is poorly-understood, even for
 simple evolutionary models and small model trees. Studies looking at LBA
 have focused on the effect of two long branches on tree reconstruction.
 However, to understand the effect of two long branches it is also
 important to understand the effect of just one long branch. If ML
 struggles to reconstruct one long branch then this may have an impact on
 LBA. In this study we look at the effect of one long branch on three-taxon
 tree reconstruction. We show that, counterintuitively, long branches are
 preferentially placed at the tips of the tree. This can be understood
 through the use of analytical solutions to the ML equation and distance
 matrix methods. We go on to look at the placement of two long branches on
 four-taxon trees, showing that there is no attraction between long
 branches, but that for extreme branch lengths long branches are joined
 together disproportionally often. These results illustrate that even small
 model trees are still interesting to help understand how ML phylogenetic
 reconstruction works, and that LBA is a complicated phenomenon that
 deserves further study.
description: Supplementary Methods -
 3rd RevisionLBPaperVersion_sm.pdfSupplementary Figures - 2nd RevisionLBPaperVersion_sf.pdf
DOI: 10.18746/bmth.data.00000489
title: Knowledge and attitudes of Bournemouth University students towards breastfeeding
DOI: 10.5061/dryad.tf81g
title: Data from: Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity and turnover rates are disconnected

description: The magnitude and extent of global change during the Cenozoic are
 remarkable, yet the impacts of these changes on biodiversity and the
 evolutionary dynamics of species diversification remain poorly understood.
 To investigate this question we combine palaeontological and neontological
 data for the angiosperm order Fagales, an ecologically important clade of
 c. 1370 species of trees with an exceptional fossil record. We show
 differences in patterns of accumulation of generic diversity, species
 richness, and turnover rates for Fagales. Generic diversity evolved
 rapidly from the Late Cretaceous and peaked in the Eocene or Oligocene.
 Turnover rates were high during periods of extreme global climate change,
 but relatively low when the climate remained stable. Species richness
 accumulated gradually throughout the Cenozoic, possibly at an accelerated
 pace after the Middle Miocene. Species diversification was into new
 environments: Quercoids radiating in Oligocene subtropical seasonally arid
 habitats, Casuarinaceae in Australian pyrophytic biomes, and Betula into
 late Neogene holarctic habitats. These radiations were counterbalanced by
 regional extinctions in late-Neogene mesic warm-temperate forests. Thus
 overall diversification at species level is linked to regional radiations
 of clades with appropriate ecologies exploiting newly available habitats.
description: Fagales_MCC_uniform_treeFagales MCC tree using uniform priorsFagales_BEAST_MCC_TREEFagales_MCC_lognormalFagales MCC tree using lognormal priorsFagales_fossilFagales fossils used in the analysis
DOI: 10.5061/dryad.h75fp2q8
title: Data from: Parallel allochronic divergence in a winter moth due to disruption of reproductive period by winter harshness

description: The disruption of reproductive timing by climatic harshness may result in
 the temporal isolation of conspecific populations and, ultimately, in
 speciation. However, whether temporal isolation alone can act as the force
 initiating speciation and how often the same type of climatic disruption
 results in the divergence of allochronic populations in a lineage is
 largely unknown. The reproductive period of the winter geometrid moth
 Inurois punctigera is separated into early and late winter in habitats
 with severe winters, but not in habitats with mild winters, suggesting
 that the reproductive season is disrupted by the harshness of the
 mid-winter period. Here, we show that sympatric pairs of early- and
 late-winter populations that differ in origin exist in different regions,
 suggesting a parallel divergence of reproductive timing. In each region,
 significant genetic differentiation exists between these early- and
 late-winter populations, suggesting that the temporal reproductive
 isolation has persisted. Moreover, we demonstrate that the temporal
 isolation, in comparison with geographic isolation, contributes greatly to
 the genetic differentiation among geographic and temporal populations by
 an analysis of molecular variances and a comparison of genetic
 differentiations (Fst) between geographic populations with and without
 difference in reproductive season. Thus, adaptive divergence of
 allochronically reproducing populations occurred independently in
 different regions, implying the generality of speciation by temporal
 isolation in a winter moth lineage.
description: AFLP_data_for_AFLP_SURVAFLP data of Inurois punctigeracorrespondence_AFLPdata_to_COIShows the COI haplotypes (GenBank accession number) of individuals using in AFLP data analysis.
DOI: 10.5061/dryad.s43f8
title: Data from: Geomolecular dating and the origin of placental mammals

description: In modern evolutionary divergence analysis the role of geological
 information extends beyond providing a timescale, to informing molecular
 rate variation across the tree. Here I consider the implications of this
 development. I use fossil calibrations to test the accuracy of models of
 molecular rate evolution for placental mammals, and reveal substantial
 misspecification associated with life history rate correlates. Adding
 further calibrations to reduce dating errors at specific nodes
 unfortunately tends to transfer underlying rate errors to adjacent
 branches. Thus, tight calibration across the tree is vital to buffer
 against rate model errors. I argue that this must include allowing maximum
 bounds to be tight when good fossil records permit, otherwise divergences
 deep in the tree will tend to be inflated by the interaction of rate
 errors and asymmetric confidence in minimum and maximum bounds. In the
 case of placental mammals I sought to reduce the potential for
 transferring calibration and rate model errors across the tree by focusing
 on well-supported calibrations with appropriately conservative maximum
 bounds. The resulting divergence estimates are younger than others
 published recently, and provide the long-anticipated molecular signature
 for the placental mammal radiation observed in the fossil record near the
 66 Ma Cretaceous-Paleogene extinction event.
description: Philllips Geomolecular
 Dating SIFossil calibration
 sources Alternative Phylogenetic trees Analysis conditions and
 supplemental results Figures S1-S2 Tables S1-S2Phillips_SystBiol_SI_final.pdf
DOI: 10.5061/dryad.46m4b
title: Data from: Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach

description: Chromosome number is a key feature of the higher-order organization of the
 genome, and changes in chromosome number play a fundamental role in
 evolution. Dysploid gains and losses in chromosome number, as well as
 polyploidization events, may drive reproductive isolation and lineage
 diversification. The recent development of probabilistic models of
 chromosome number evolution in the groundbreaking work by Mayrose et al.
 (2010, ChromEvol) have enabled the inference of ancestral chromosome
 numbers over molecular phylogenies and generated new interest in studying
 the role of chromosome changes in evolution. However, the ChromEvol
 approach assumes all changes occur anagenetically (along branches), and
 does not model events that are specifically cladogenetic. Cladogenetic
 changes may be expected if chromosome changes result in reproductive
 isolation. Here we present a new class of models of chromosome number
 evolution (called ChromoSSE) that incorporate both anagenetic and
 cladogenetic change. The ChromoSSE models allow us to determine the mode
 of chromosome number evolution; is chromosome evolution occurring
 primarily within lineages, primarily at lineage splitting, or in
 clade-specific combinations of both? Furthermore, we can estimate the
 location and timing of possible chromosome speciation events over the
 phylogeny. We implemented ChromoSSE in a Bayesian statistical framework,
 specifically in the software RevBayes, to accommodate uncertainty in
 parameter estimates while leveraging the full power of likelihood based
 methods. We tested ChromoSSE's accuracy with simulations and
 re-examined chromosomal evolution in Aristolochia, Carex section
 Spirostachyae, Helianthus, Mimulus sensu lato (s.l.), and Primula section
 Aleuritia, finding evidence for clade-specific combinations of anagenetic
 and cladogenetic dysploid and polyploid modes of chromosome evolution.
description: ChromoSSEScripts and data needed to run ChromoSSE analyses.Freyman_SysBio_Chromosome_Evolution_Supplementary
DOI: 10.5061/dryad.k1v34cf
title: Data from: Pelvis morphology suggests that early Mesozoic birds were too heavy to contact incubate their eggs

description: Numerous new fossils have driven an interest in reproduction of early
 birds but direct evidence remains elusive. No Mesozoic avian eggs can be
 unambiguously assigned to a species, which hampers our understanding of
 the evolution of contact incubation, which is a defining feature of extant
 birds. Compared to living species eggs of Mesozoic birds are relatively
 small, but whether the eggs of Mesozoic birds could actually have borne
 the weight of a breeding adult has not yet been investigated. We estimated
 maximal egg breadth for a range of Mesozoic avian taxa from the width of
 the pelvic canal defined by the pubic symphysis. Known elongation ratios
 of Mesozoic bird eggs allowed us to predict egg mass and hence the load
 mass an egg could endure before cracking. These values were compared to
 the predicted body masses of the adult birds based on skeletal remains.
 Based on 21 fossil species, we show that for non-ornithothoracine birds
 body mass was 130% of the load mass of the eggs. For Enantiornithes body
 mass and egg load mass were comparable to extant birds, but some early
 Cretaceous ornithuromorphs were 110% heavier than their eggs could
 support. Our indirect approach provides the best evidence yet that early
 birds could not have sat on their eggs without running the risk of causing
 damage. We suggest that contact incubation evolved comparatively late in
 birds.
description: Deeming & Mayr JEB
 Online Supplementary MaterialsIncludes additional
 graphs plus datasets used in the analysis.
DOI: 10.5061/dryad.vd0nn
title: Data from: Successional status, seed dispersal mode and overstorey species influence tree regeneration in tropical rain-forest fragments in Western Ghats, India

description: The effects of fragmentation and overstorey tree diversity on tree
 regeneration were assessed in tropical rain forests of the Western Ghats,
 India. Ninety plots were sampled for saplings (1–5 cm diameter at breast
 height (dbh); 5×5-m plots) and overstorey trees (&gt;9.55 cm dbh;
 20×20-m plots) within two fragments (32 ha and 18 ha) and two continuous
 forests. We tested the hypotheses that fragmentation and expected
 seed-dispersal declines (1) reduce sapling densities and species richness
 of all species and old-growth species, and increase recruitment of
 early-successional species, (2) reduce the prevalence of dispersed
 recruits and (3) increase influence of local overstorey on sapling
 densities and richness. Continuous forests and fragments had similar
 sapling densities and species richness overall, but density and richness
 of old-growth species declined by 62% and 48%, respectively, in fragments.
 Fragments had 39% lower densities and 24% lower richness of immigrant
 saplings (presumed dispersed into sites as conspecific adults were absent
 nearby), and immigrant densities of old-growth bird-dispersed species
 declined by 79%. Sapling species richness (overall and old-growth)
 increased with overstorey species richness in fragments, but was unrelated
 to overstorey richness in continuous forests. Our results show that while
 forest fragments retain significant sapling diversity, losses of immigrant
 recruits and increased overstorey influence strengthen barriers to natural
 regeneration of old-growth tropical rain forests.
description: Plots and traits
 dataThis zip file contains
 three data files, corresponding to regeneration plot data, adult tree plot
 data and tree species traits data reported in Osuri et al. (2017).
 Successional status, seed dispersal mode and overstorey species influence
 tree regeneration in tropical rain-forest fragments in Western Ghats,
 India. Journal of Tropical Ecology, 33(4), 270-284. doi:
 https://doi.org/10.1017/S0266467417000219osuri_et_al_plots_traits_data.ziposuri_et_al_metadata.txt
DOI: 10.5061/dryad.n193d
title: Data from: Effects of fire regime on the population genetics of natural pine stands, in Genetic structure of forest trees in biodiversity hotspots at different spatial scales (Ph.D. thesis).

description: The recurrence of wildfires is predicted to increase worldwide due to
 climate change, resulting in severe impacts on biodiversity and ecosystem
 functioning. We used simple sequence repeat (SSR) and single nucleotide
 polymorphism (SNP) markers to examine the effects of fire regime on
 genetic diversity, demographic history and fine-scale spatial genetic
 structure (SGS) of Pinus pinaster and P. halepensis, two conifers with
 similar adaptations to fire in the eastern Iberian Peninsula. Stands
 growing under high (HiFi) or low (LoFi) frequency of crown fires had
 similar levels of genetic diversity and similar demographic history, with
 bottlenecks detected in all stands in both species. HiFi populations were
 not genetically depleted, suggesting that adaptations such as a diverse
 canopy seed bank due to serotinous cones, an early age of first flowering
 and high gene flow buffer against possible reductions of genetic
 diversity. Significantly stronger SGS at SNPs in HiFi than LoFi stands of
 P. halepensis suggested fire-related altered dispersal possibly combined
 with microenvironmental selection in this fire-sensitive “seeder” species.
 In contrast, SGS at SNP markers was unrelated to fire regime in P.
 pinaster. This could be a consequence of more pronounced fire-resistance
 in this species enabling some adults to survive fire, hence causing a
 lower dependence on post-fire regeneration. Our results highlight that the
 impact of fire differs in species with similar life-history traits.
 Therefore, species-specific studies are needed to understand the role of
 wildfires for the evolution of future forests
description: Pinus halapensis, 8pops,
 369 samples, 251SNPsPh_8Pops_251SNPs_corrected.xlsxPinus halepensis, 8pops, 366 samples, 9 nSSRsPh_8pops_micros_corrected.xlsx