cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v3m84
title: Data from: Tipping the scales: evolution of the allometric slope independent of average trait size

description: The scaling of body parts is central to the expression of morphology
 across body sizes and to the generation of morphological diversity within
 and among species. Although patterns of scaling-relationship evolution
 have been well documented for over one hundred years, little is known
 regarding how selection acts to generate these patterns. In part, this is
 because it is unclear the extent to which the elements of log-linear
 scaling relationships – the intercept or mean trait size and the slope –
 can evolve independently. Here, using the wing-body size scaling
 relationship in Drosophila melanogaster as an empirical model, we use
 artificial selection to demonstrate that the slope of a morphological
 scaling relationship between an organ (the wing) and body size can evolve
 independently of mean organ or body size. We discuss our findings in the
 context of how selection likely operates on morphological scaling
 relationships in nature, the developmental basis for evolved changes in
 scaling, and the general approach of using individual-based selection
 experiments to study the expression and evolution of morphological
 scaling.
description: ReadMeThis describes the files
 associated with the publication, and their contents.ALLDATAThis .txt file contains linage, sex, pupal size, wing size, and generation data for all flies in the experiment.SLOPE_ANALYSISThis file contains the annotated R scripts used in the main analysesVECTOR_PROJECTIONSThe .xlsx data file giving the inter-generational change in body (pupal) and wing size parallel and orthogonal to the allometry of the previous generation. Cells include formulae used to calculate the change.SELNDIF_ANALYSISThe annotated R scripts used to calculate realized heritabilities.SELNDIFThe data file giving the cumulative selection differentials for allometric slope in each sex/linage combination across generations.
DOI: 10.11588/duerer.online.6978eb579f938
title: Christus am Ölberg, 192861
DOI: 10.5061/dryad.b8m8g7s
title: Data from: Feeding ecology underlies the evolution of cichlid jaw mobility

description: The fish feeding apparatus is among the most diverse functional systems in
 vertebrates. While morphological and mechanical variation of feeding
 systems are well studied, we know far less about the diversity of the
 motions that they produce. We explored patterns of feeding movements in
 African cichlids from Lakes Malawi and Tanganyika, asking whether the
 degree of kinesis is associated with dietary habits of species. We used
 geometric morphometrics to measure feeding kinesis as trajectories of
 shape change, based on 326 high-speed videos in 56 species. Cranial
 morphology was significantly related to feeding movements, both of which
 were distributed along a dietary axis associated with prey evasiveness.
 Small-mouthed cichlids that feed by scraping algae and detritus from rocks
 had low kinesis strikes, while large-mouthed species that eat large,
 evasive prey (fishes and shrimps) generated the greatest kinesis. Despite
 having higher overall kinesis, comparisons of trajectory shape (linearity)
 revealed that cichlids that eat mobile prey also displayed more
 kinematically conserved, or efficient, feeding motions. Our work indicates
 that prey evasiveness is strongly related to the evolution of cichlid jaw
 mobility, suggesting that this same relationship may explain the origins
 and diversity of highly kinetic jaws that characterize the super-radiation
 of spiny-rayed fishes.
description: Landmark data for
 cichlid motion shapesLandmark data for
 cichlid motion shapes. File is in .tps format, which can be opened in the
 tps series of morphometric programs as well as the package geomorph in R
 (with the readland.tps function). Note that scale is not provided in this
 file and must be implemented separately, with the "scale" factor
 in the accompanying "strike info.txt" file.cichlid feeding
 LM.TPSSliding
 semilandmarksFile designating which
 cranial landmarks will be treated as "sliding semilandmarks"
 during shape alignment.sliding_semi.txtFeeding Strike InformationTable with information associated with each shape from feeding motions included in the "cichlid feeding LM.TPS" file.strike info.txtSample GM motion codeA sample of the code used to measure the magnitude of strike kinesis and kinematic efficiency. Files utilized in code: "cichlid feeding LM.TPS", "sliding_semi.txt", and "strike info.txt".sample GM motion code.Rkinesis & standard errors (by individual)Table of feeding kinesis averages and standard errors for each individual SPECIMEN analyzed in this study.Kinesis & standard errors (by species)Table of feeding kinesis averages and standard errors for each SPECIES analyzed in this study.kinesis & standard errors (by species).csv
DOI: 10.5061/dryad.v30f1
title: Data from: Bayesian morphological clock methods resurrect placoderm monophyly and reveal rapid early evolution in jawed vertebrates

description: The phylogeny of early gnathostomes provides an important framework for
 understanding one of the most significant evolutionary events, the origin
 and diversification of jawed vertebrates. A series of recent cladistic
 analyses have suggested that the placoderms, an extinct group of armoured
 fish, form a paraphyletic group basal to all other jawed vertebrates. We
 revised and expanded this morphological data set, most notably by sampling
 autapomorphies in a similar way to parsimony-informative traits, thus
 ensuring this data (unlike most existing morphological data sets)
 satisfied an important assumption of Bayesian tip-dated morphological
 clock approaches. We also found problems with characters supporting
 placoderm paraphyly, including character correlation and incorrect
 codings. Analysis of this data set reveals that paraphyly and monophyly of
 core placoderms (excluding maxillate forms) are essentially equally
 parsimonious. The two alternative topologies have different root positions
 for the jawed vertebrates but are otherwise similar. However, analysis
 using tip-dated clock methods reveals strong support for placoderm
 monophyly, due to this analysis favoring trees with more balanced rates of
 evolution. Furthermore, enforcing placoderm paraphyly results in higher
 levels and unusual patterns of rate heterogeneity among branches, similar
 to that generated from simulated trees reconstructed with incorrect root
 positions. These simulations also show that Bayesian tip-dated clock
 methods outperform parsimony when the outgroup is largely uninformative
 (e.g., due to inapplicable characters), as might be the case here. The
 analysis also reveals that gnathostomes underwent a rapid burst of
 evolution during the Silurian period which declined during the Early
 Devonian. This rapid evolution during a period with few articulated
 fossils might partly explain the difficulty in ascertaining the root
 position of jawed vertebrates.
description: Supplementary
 informationSupplementary figures,
 taxon list with sources and tip dates, character list, supplementary
 referencesSupplementary_information.pdfxmlxml files for BEAST analysesR functionsCode for R functions used for summarising tree and rate information. includes example scripts.MATRIXMesquite-formatted data matrixConsensus treeMaximum clade consensus tree with median node heights. From the combined post burn-in tree sample of four runs of the focal analysis.combinedmcc.treePosterior tree sampleFull posterior tree sample from four independent runs of the focal analysis (all burn-in removed).combined.treesCorrigendumAcknowledgement of Per Ahlberg concerning Figure 1.
DOI: 10.5061/dryad.62qn5
title: Data from: Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes

description: Adaptive radiation is thought to be responsible for the evolution of a
 great portion of the past and present diversity of life. Instances of
 adaptive radiation, characterized by the rapid emergence of an array of
 species as a consequence to their adaptation to distinct ecological
 niches, are important study systems in evolutionary biology. However,
 because of the rapid lineage formation in these groups, and occasional
 gene flow between the participating species, it is often difficult to
 reconstruct the phylogenetic history of species that underwent an adaptive
 radiation. In this study, we present a novel approach for species-tree
 estimation in rapidly diversifying lineages, where introgression is known
 to occur, and apply it to a multimarker data set containing up to 16
 specimens per species for a set of 45 species of East African cichlid
 fishes (522 individuals in total), with a main focus on the cichlid
 species flock of Lake Tanganyika. We first identified, using age
 distributions of most recent common ancestors in individual gene trees,
 those lineages in our data set that show strong signatures of past
 introgression. This led us to formulate three hypotheses of introgression
 between different lineages of Tanganyika cichlids: the ancestor of
 Boulengerochromini (or of Boulengerochromini and Bathybatini) received
 genomic material from the derived H-lineage; the common ancestor of
 Cyprichromini and Perissodini experienced, in turn, introgression from
 Boulengerochromini and/or Bathybatini; and the Lake Tanganyika
 Haplochromini and closely related riverine lineages received genetic
 material from Cyphotilapiini. We then applied the multispecies coalescent
 model to estimate the species tree of Lake Tanganyika cichlids, but
 excluded the lineages involved in these introgression events, as the
 multispecies coalescent model does not incorporate introgression. This
 resulted in a robust species tree, in which the Lamprologini were placed
 as sister lineage to the H-lineage (including the Eretmodini), and we
 identify a series of rapid splitting events at the base of the H-lineage.
 Divergence ages estimated with the multispecies coalescent model were
 substantially younger than age estimates based on concatenation, and agree
 with the geological history of the Great Lakes of East Africa. Finally, we
 formally tested the three hypotheses of introgression using a likelihood
 framework, and find strong support for introgression between some of the
 cichlid tribes of Lake Tanganyika.
description: nexussequence
 alignmentstreesphylogenetic
 treesMeyer et al.,
 supplementary informationMeyer_et_al_supplementary_information.pdf
DOI: 10.5061/dryad.v1q0524
title: Data from: Network analysis by simulated annealing of taxa and islands of Macaronesia (North Atlantic Ocean)

description: With the aim of explaining the role that taxa and island features have in
 biogeographical patterns, we processed presence-absence matrices of all
 the Macaronesian native species of ten different taxa (arthropods, birds,
 bryophytes, fungi, lichens, mammals, mollusks, pteridophytes, reptiles and
 spermatophytes) through simulated annealing analysis. Distribution
 patterns among the archipelagos were pinpointed, along with the different
 biogeographic roles played by islands and species groups. All the networks
 analysed resulted to be significantly modular and the structure of
 biogeographic modules reflects known past connections among the
 archipelagos and the current drivers of species distribution. The role
 assigned to the species supports some biological (ecological amplitude,
 degree of endemicity) and functional (long-distance dispersal and
 persistence abilities) traits of their respective biota and justifies
 their position in recent models of biogeographical distribution. Whereas
 it was expected that the modules identified by the spermatophytes and
 arthropods would reflect the compartmentalization of archipelagos quite
 well, this was also the case for much more vagile taxa, such as fungi or
 lichens. Conversely, results obtained for pteridophytes and bryophytes
 suggest that for those taxa geographic distance and/or macroclimatic
 conditions are less important than the size, age and orography of an
 island to determine the modularity of island groups. On the other hand,
 dry, species-poor islets, act as connectors, tending to cluster together
 for different taxa, independently of their archipelagic adscription,
 whereas large, high, humid islands tend to form network or module hubs
 representing regional centers of speciation and dispersal.
description: Annex1_MATRICES and
 Annex2_ROLESANNEX1 - Processed
 matrices of the considered Taxonomic Operational Unit (TOUs),
 corresponding to the presence/absence data from Macaronesia, available for
 the following organisms: arthropods, bryophytes, fungi, lichens,
 pteridophytes, spermatophytes, molluscs, reptiles, birds, mammals. ANNEX 2
 - Scatterplots of the processed data.Annex
 1_2.zip
DOI: 10.5061/dryad.93j174jd
title: Data from: New fossil penguins (Aves, Sphenisciformes) from the Oligocene of New Zealand reveal the skeletal plan of stem penguins

description: Three skeletons collected from the late Oligocene Kokoamu Greensand of New
 Zealand are among the most complete Paleogene penguins known. These
 specimens, described here as Kairuku waitaki gen. et sp. nov. and Kairuku
 grebneffi sp. nov., reveal for the first time the unique proportions of a
 giant fossil penguin and the morphology of many key elements of the stem
 penguin skeleton associated with underwater flight, including the first
 reasonably complete sternum, one of only two complete forelimbs and the
 first described pygostyle. Relative proportions of the trunk, flippers and
 hindlimbs can now be determined from a single individual, offering insight
 into the body plan of stem penguins and improved constraints on size
 estimates for 'giant' taxa. Kairuku is characterized by an
 elongate, narrow sternum, a short and flared coracoid, an elongate narrow
 flipper and a robust hindlimb. The pygostyle of Kairuku lacks the derived
 triangular cross-section seen in extant Spheniscidae, suggesting the
 rectrices attached in a more typical avian pattern and the tail may have
 lacked the propping function utilized by living penguins. New materials
 described here, along with restudy of previously described specimens,
 resolves several long-standing phylogenetic, biogeographic and taxonomic
 issues stemming from the inadequate comparative material of several of the
 first-named fossil penguin species. An array of partial associated
 skeletons from the Eocene-Oligocene of New Zealand historically referred
 to Palaeeudyptes antarcticus or Palaeeudyptes sp. are recognized as at
 least five distinct species: Palaeeudyptes antarcticus, Palaeeudyptes
 marplesi, Kairuku waitaki, Kairuku grebneffi and an unnamed Burnside
 Formation species
description: Kairuku JVP Dataset -
 nexus fileCombined phylogenetic
 dataset for penguin phylogeny. 245 morphological characters, sequence data
 from RAG-1, cytochrome b, 12SrDNA, 16SrDNA and COI. 58 penguin species, 15
 outgroup species. The revised nexus file contains no character scoring
 changes, but we have added the character descriptions directly to the file
 to assist those wishing to expand or reuse the matrix.Kairuku JVP Dataset
 (annotated).nexusKairuku JVP Dataset -
 supplementary dataCombined phylogenetic
 dataset for penguin phylogeny. 245 morphological characters, sequence data
 from RAG-1, cytochrome b, 12SrDNA, 16SrDNA and COI. 58 penguin species, 15
 outgroup species. The original character list contained a numbering error,
 resulting in several characters in the 201-208 range being out of order.
 The new version of the character list has been corrected to indicate the
 proper numbering.Kairuku JVP Dataset
 (corrected).pdf
DOI: 10.5061/dryad.126dg
title: Data from: Marine life in a greenhouse world: cephalopod biodiversity and biogeography during the early Late Cretaceous

description: Two end-member models are proposed to explain marine biotic responses to
 greenhouse conditions. Global warming and increasing sea level may: (1)
 promote dispersal of marine species, leading to larger geographic ranges
 and decreased speciation and biodiversity, or (2) form isolated
 epicontinental basins that host endemic radiations, leading to smaller
 geographic ranges and increased speciation and biodiversity. The
 Cenomanian–Turonian (C–T) interval, marked by greenhouse warming, sea
 level rise, ocean anoxia, and biotic turnover, presents an opportunity to
 test these two end-member models. In particular, how cephalopods responded
 to these global changes has not been clear. A global database of 7,262
 cephalopod occurrences was used to evaluate biodiversity changes through
 the C–T interval. Both species- and genus-level diversity peaked in the
 Late Cenomanian. The global diversity drop across the C/T boundary was
 modest; rather, diversity was low during the Middle Cenomanian and Middle
 Turonian, times of brief cooling. Regional variations in diversity
 responses may reflect the degree and timing of environmental perturbations
 within different oceanographic settings. Surprisingly, cephalopod faunas
 in the European Platform, Western Interior, and South Atlantic all shifted
 equatorward across the C/T boundary, whereas other regions saw no change
 in latitudinal distributions. Global generic geographic ranges did not
 change through the C–T interval, but the percentage of cosmopolitan genera
 did increase significantly across the C/T, both globally and within the
 Western Interior and Europe, whereas cosmopolitans dropped in the Pacific
 and South Atlantic. Neither end-member model for biodiversity change in a
 greenhouse world is supported for C–T cephalopods, as diversity increased
 without an associated increase in geographic range. It may be that sea
 level rise and global warming led to both endemic radiations in
 epicontinental basins and an increase in cosmopolitan taxa in some
 regions, demonstrating the importance of combining global and regional
 scale analyses.
description: Yacobucci_PBIO_Suppl_Table1Dataset of Cenomanian-Turonian cephalopod occurrences, derived from the Paleobiology Database and the M.S. thesis of Richard A. MacKenzie III (2007, Bowling Green State University, Bowling Green, OH, USA).Yacobucci_PBIO_Suppl_Table2This file contains tables of p-values from all Mann-Whitney U-tests run for this analysis, including comparisons of global and regional latitudinal distributions and geographic range sizes.Yacobucci_PBIO_AppendixThis Appendix describes the two datasets used in this paper, the Paleobiology Database dataset (PBDB) and Richard MacKenzie Database (MKDB), and provides citations for the original data sources for the Richard MacKenzie Database (MKDB).
DOI: 10.5061/dryad.28g16
title: Data from: Molecular phylogeny and dating reveal a terrestrial origin in the early Carboniferous for ascaridoid nematodes

description: Ascaridoids are among the commonest groups of zooparasitic nematodes
 (roundworms) and occur in the alimentary canal of all major vertebrate
 groups, including man. They have an extremely high diversity and are of
 major socio-economic importance. However, their evolutionary history
 remains poorly known. Here we performed a comprehensive phylogenetic
 analysis of the Ascaridoidea. Our results divided the Ascaridoidea into
 six monophyletic major clades, i.e. the Heterocheilidae, Acanthocheilidae,
 Anisakidae, Ascarididae, Toxocaridae and Raphidascarididae, among which
 the Heterocheilidae, rather than the Acanthocheilidae, represents the
 sister clade to the remaining ascaridoids. The phylogeny was calibrated
 using an approach that involves time priors from fossils of the
 co-evolving hosts, and dates the common ancestor of the Ascaridoidea back
 to the Early Carboniferous (approximately 360.47–325.27 Ma). The
 divergence dates and ancestral host types indicated by our study suggest
 that members of the Ascaridoidea first parasitized terrestrial tetrapods
 and subsequently extended their host range to elasmobranchs and teleosts.
 We also propose that the fundamental terrestrial-aquatic switches of these
 nematodes were affected by changes in sea-level during the Triassic to the
 Early Cretaceous.
description: Data of
 AscaridoideaData of Ascaridoidea
 Alignment, Phylogeny, and TimetreesSupplementary
 InformationThis is the
 Supplementary Information in addition to the main text, which includes
 nine tables (Tables S1-S9), one figure (Figure S1) and the literature
 cited (References) in this Supplementary Information.Supplementary
 material.pdf
DOI: 10.5061/dryad.723m1
title: Data from: MycoDB, a global database of plant response to mycorrhizal fungi

description: Plants form belowground associations with mycorrhizal fungi in one of the
 most common symbioses on Earth. However, few large-scale generalizations
 exist for the structure and function of mycorrhizal symbioses, as the
 nature of this relationship varies from mutualistic to parasitic and is
 largely context-dependent. We announce the public release of MycoDB, a
 database of 4,010 studies (from 438 unique publications) to aid in
 multi-factor meta-analyses elucidating the ecological and evolutionary
 context in which mycorrhizal fungi alter plant productivity. Over 10 years
 with nearly 80 collaborators, we compiled data on the response of plant
 biomass to mycorrhizal fungal inoculation, including meta-analysis metrics
 and 24 additional explanatory variables that describe the biotic and
 abiotic context of each study. We also include phylogenetic trees for all
 plants and fungi in the database. To our knowledge, MycoDB is the largest
 ecological meta-analysis database. We aim to share these data to highlight
 significant gaps in mycorrhizal research and encourage synthesis to
 explore the ecological and evolutionary generalities that govern
 mycorrhizal functioning in ecosystems.
description: READMEMycoDB_version4FungalTree_version2PlantTree_version2phylometa_2018
DOI: 10.5061/dryad.s3d45
title: Data from: Role of selection and gene flow in population differentiation at the edge vs. interior of the species range differing in climatic conditions

description: Evaluating the relative importance of neutral and adaptive processes as
 determinants of population differentiation across environments is a
 central theme of evolutionary biology. We applied the QST-FST comparison
 flanked by a direct test for local adaptation to infer the role of
 climate-driven selection and gene flow in population differentiation of an
 annual grass Avena sterilis in two distinct parts of the species range,
 edge and interior, which represent two globally different climates, desert
 and Mediterranean. In a multi-year reciprocal transplant experiment the
 plants of desert and Mediterranean origin demonstrated home advantage, and
 population differentiation in several phenotypic traits related to
 reproduction exceeded neutral predictions, as determined by comparisons of
 QST values with theoretical FST distributions. Thus variation in these
 traits likely resulted from local adaptation to desert and Mediterranean
 environments. The two separate common garden experiments conducted with
 different experimental design revealed that two population comparisons are
 likely to detect population differences in virtually every trait, but many
 of these differences reflect effects of local rather than regional
 environment. We detected a general reduction in neutral (SSR) genetic
 variation but not in adaptive quantitative trait variation in peripheral
 desert as compared with Mediterranean core populations. On the other hand,
 the molecular data indicated intensive gene flow from the Mediterranean
 core towards desert periphery. Although species range position in our
 study (edge vs. interior) was confounded with climate (desert vs.
 Mediterranean), the results suggest that the gene flow from the species
 core does not have negative consequences for either performance of the
 peripheral plants or their adaptive potential.
description: Data for
 depositingData for depositing -
 oat SSR dataData for depositing -
 field introductionField experiment
 data