cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j4315
title: Data from: Character evolution and the origin of Caimaninae (Crocodylia) in the New World Tropics: new evidence from the Miocene of Panama and Venezuela

description: Alligators and caimans share a close relationship, supported by both
 molecular and morphological characters. The divergence between alligators
 and caimans has been difficult to discern in the fossil record. Two basal
 taxa have recently been described from the Miocene of Panama and Venezuela
 but have not yet been presented in a joint phylogeny. Continued
 preparation of the type material of the Venezuelan Globidentosuchus
 brachyrostris Scheyer et al., 2013 has revealed new characters for scoring
 in a cladistic framework. In addition, the first lower jaw of the
 Panamanian Centenariosuchus gilmorei Hastings et al., 2013 is described
 herein, and additional characters were scored. In total, we conducted five
 cladistic analyses to better understand the character evolution involved
 in the establishment of Caimaninae. In each case, Globidentosuchus appears
 as the basal-most of the caimanine lineage, followed by Culebrasuchus
 mesoamericanus Hastings et al., 2013 from Panama. Stepwise character
 additions of synapomorphies define progressively more derived caimanines,
 but stratigraphic context creates ghost lineages extending from the
 Miocene to Paleocene. The persistence of two basal taxa into the Miocene
 of northern South America and Central America supports the concept of a
 relict basal population in this region. This further supports
 biogeographic hypotheses of dispersals in both directions between North
 and South America prior to full land connection.
description: Supplemental
 DataCladistic data
 matrixCladistic character
 listList of the characters
 used for the cladistic analyses of this study, modified only for format
 from Brochu et al. (2012)Hastings_etal_Appendix.pdf
DOI: 10.5061/dryad.c8k6q
title: Data from: Species identification and likely catch time period of whale bones from South Georgia

description: Skeletal remains of baleen whales killed during the onset of 20th century
 commercial whaling lie scattered across the shores and abandoned whaling
 stations of the subantarctic island of South Georgia. Here we report on
 genetic species identification of whale bones collected from South Georgia
 using standard historical DNA protocols. We amplified and sequenced short
 fragments of the mitochondrial DNA (mtDNA) control region from 281
 available bone samples. Of these, 231 provided mtDNA sequences of
 sufficient quality and length (174–194 bp) for species identification: 158
 bones were identified as humpback whale (Megaptera novaeangliae), 51 bones
 were identified as fin whale (Balaenoptera physalus), 18 bones were
 identified as blue whale (B. musculus), two bones were identified as sei
 whale (B. borealis), one bone was identified as a southern right whale
 (Eubalaena australis), and one bone was identified as a southern elephant
 seal (Mirounga leonina). The prominence of humpback, fin, and blue whale
 bones in the sample collection corresponds to the catch record of the
 early years of whaling on the island of South Georgia (pre-1915), prior to
 the depletion of these populations.
description: Sremba et al. Species ID
 alignmentAn aligned sequence file
 of mtDNA control region haplotypes with sample codes for all great whale
 species
DOI: 10.5061/dryad.pk78j
title: Data from: Shifting agriculture supports more tropical forest birds than oil palm or teak plantations in Mizoram, northeast India

description: Conversion of tropical forests and diverse multicrop agricultural land to
 commercial monocultures is a conservation concern worldwide. In northeast
 India, landscapes under shifting agriculture (or jhum) practiced by tribal
 communities are increasingly being replaced by monoculture plantations
 (e.g., teak, oil palm). We compared oil palm and teak plantations,
 shifting agricultural fields, and forest fallows (0–8 yr regeneration)
 with tropical rainforest edge and interior sites in Dampa Tiger Reserve,
 Mizoram, India. Twenty replicate transects were surveyed in each of the 5
 study strata for vegetation structure, bird species richness and density,
 bird abundance, and species composition. Tree density and canopy and
 vertical structure were lowest in oil palm plantations, intermediate in
 teak plantations and jhum, and highest in rainforest sites. Tree density
 in jhum (4.3 stems per 100 m2) was much higher than in oil palm
 plantations (0.5 stems per 100 m2), but lower than in rainforest (6.8–8.2
 stems per 100 m2), with bamboo absent in oil palm plantations and most
 abundant in regenerating jhum (25 culms per 50 m2). We recorded 107 bird
 species (94 forest species, 13 open-country species). Oil palm plantations
 had the lowest forest bird species richness (10 species), followed by teak
 plantations (38), while jhum (50) had only slightly lower species richness
 than the rainforest edge (58) and interior (70). Forest bird abundance in
 the jhum landscape was similar to that in rainforest, on average 304%
 higher than in oil palm plantations, and 87% higher than in teak
 plantations. Jhum sites were more similar in bird community composition to
 rainforest than were monocultures. Rapid recovery of dense and diverse
 secondary bamboo forests during fallow periods makes the shifting
 agricultural landscape mosaic a better form of land use for bird
 conservation than monocultures. Land use policy and conservation plans
 should provide greater support for shifting agriculture, while mandating
 better land use practices such as retention of forest remnants, native
 trees, and riparian vegetation in monoculture plantations.
description: Bird and vegetation data
 from Dampa landscape, Mizoram (from Mandal and Raman 2016)
 Please see
 ReadMe.txt file in the ZIP folder for more details. This dataset is from:
 Mandal, J. and Raman, T. R. S. 2016. Shifting agriculture supports more
 tropical forest birds than oil palm or teak plantations in Mizoram,
 northeast India. The Condor: Ornithological Applications 18: 345–359. URL:
 http://www.bioone.org/doi/abs/10.1650/CONDOR-15-163.1 CondorDataset.zip
  
description: Please refer Methods in: Mandal, J. and Raman,
 T. R. S. 2016. Shifting agriculture supports more tropical forest birds
 than oil palm or teak plantations in Mizoram, northeast India.
 <em>The Condor: Ornithological Applications</em> 18: 345–359.
 URL: http://www.bioone.org/doi/abs/10.1650/CONDOR-15-163.1
DOI: 10.5061/dryad.7h62c8t
title: Data from: Prey diversity, prey composition, and predator population dynamics in experimental microcosms

description: 1. Food‐web complexity‐stability relations are central to ecology, and
 many empirical studies show greater food‐web complexity leads to lower
 population stability. Here, predator population variability decreased with
 increasing prey diversity in aquatic microcosm experiments, an example of
 greater food‐web complexity leading to greater population stability. 2.
 Prey diversity as well as different sets of prey species within each level
 of prey diversity produced differences in predator population dynamics,
 demonstrating the importance of both prey composition and prey diversity
 in determining predator population stability. 3. Prey diversity can affect
 predator population dynamics through at least three groups of mechanisms:
 prey reliability, prey biomass, and prey composition mechanisms. The
 results suggest that greater prey reliability at higher prey diversities
 enhances predator stability and provide support for MacArthur (1955).
description: Population abundance
 dataday - the day of the
 experiment the observation in the row belongs to. jar - a number that
 uniquely identifies each experimental unit. prey.composition - a number
 that identifies the combination of prey species added to the jar.
 prey.richness - the number of prey species added to the jar. replicate - a
 replicate identifier, unique within prey composition. species - a numeric
 code for the species that the observation in the row belongs to. count -
 the number of individuals counted in the sample; used to calculate density
 per ml. Counts were made by eye, looking down a microscope. w1 - the
 volume of liquid in ml removed from the community for sampling abundance,
 used to calculate density per ml. w2 - the volume of diluent added to the
 volume sampled. w3 - the volume of the sub-sample taken of the mixture of
 diluent and sample removed (i.e. w1 + w2).dileptus_predator_prey_data.csv
DOI: 10.5061/dryad.6354b
title: Data from: Clonal relatedness between lobular carcinoma in situ and synchronous malignant lesions

description: INTRODUCTION: Lobular carcinoma in situ (LCIS) has been accepted as a
 marker of risk for the development of invasive breast cancer, yet modern
 models of breast carcinogenesis include LCIS as a precursor of low-grade
 carcinomas. We provide evidence favoring a clonal origin for LCIS and
 synchronous estrogen receptor-positive malignant lesions of the ductal and
 lobular phenotype. METHODS: Patients with prior LCIS undergoing mastectomy
 were identified preoperatively from 2003-2008. Specimens were widely
 sampled, and frozen blocks were screened for LCIS and co-existing
 malignant lesions, and subject to microdissection. Samples from 65
 patients were hybridized to the Affymetrix SNP 6.0 array platform. Cases
 with both an LCIS sample and an associated ductal carcinoma in situ (DCIS)
 or invasive tumor sample were evaluated for patterns of somatic copy
 number changes to assess evidence of clonal relatedness. RESULTS: LCIS was
 identified in 44 of the cases, and among these, a DCIS and/or invasive
 lesion was also identified in 21 cases. A total of 17 tumor pairs had
 adequate DNA/array data for analysis, including 9 pairs of LCIS/invasive
 lobular cancer (ILC), 4 pairs of LCIS/DCIS, and 4 LCIS/invasive ductal
 cancer (IDC). Overall, 7 pairs (41%) were judged to be clonally related;
 in 5 (29%), evidence suggested clonality but was equivocal, and 5 (29%)
 were considered independent. Clonal pairs were observed with all matched
 lesion types and low and high histological grades. We also show anecdotal
 evidence of clonality between a patient-matched triplet of LCIS, DCIS, and
 IDC. CONCLUSIONS: Our results support the role of LCIS as a precursor in
 the development of both high- and low-grade ductal and lobular cancers.
description: KingClonalityCodeThis file contains the R code used to preprocess the SNP array files (not submitted due to privacy issues) as well as the clonality analysis using the submitted log-ratio data.KingClonalityDataNumber log-ratio data for the 31 samples in the manuscript. It is a gzipped text file.
DOI: 10.5061/dryad.h174j
title: Data from: Species interactions mediate phylogenetic community structure in a hyper-diverse lizard assemblage from arid Australia

description: Evolutionary history can exert a profound influence on ecological
 communities, but few generalities have emerged concerning the
 relationships among phylogeny, community membership, and niche evolution.
 We compared phylogenetic community structure and niche evolution in three
 lizard clades (Ctenotus skinks, agamids, diplodactyline geckos) from arid
 Australia. We surveyed lizard communities at 32 sites in the northwestern
 Great Victoria Desert and generated complete species-level molecular
 phylogenies for regional representatives of the three clades. We document
 a striking pattern of phylogenetic evenness within local communities for
 all groups: pairwise correlations in species abundance across sites are
 negatively related to phylogenetic similarity. By modeling site
 suitability based on species' habitat preferences, we demonstrate
 that phylogenetic evenness generally persists even after controlling for
 habitat filtering among species. This phylogenetic evenness is coupled
 with evolutionary lability of habitat-associated traits, to the extent
 that closely related species are more divergent in habitat use than
 distantly related species. In contrast, lizard diets are phylogenetically
 conserved and pairwise dietary overlap between species is negatively
 related to phylogenetic distance in two of three clades. Our results
 suggest that contemporary and historical species interactions have led to
 similar patterns of community structure across multiple clades in one of
 the world's most diverse lizard communities.
description: AN52871_dataLG_phylogenies
DOI: 10.5061/dryad.h0649
title: Data from: Identifying targets of selection in mosaic genomes with machine learning: applications in Anopheles gambiae for detecting sites within locally adapted chromosomal inversions

description: Chromosomal inversions are important structural changes that may
 facilitate divergent selection when they capture co-adaptive loci in the
 face of gene flow. However, identifying selection targets within
 inversions can be challenging. The high degrees of differentiation between
 heterokaryotypes, as well as the differences in demographic histories of
 collinear regions compared with inverted ones, reduce the power of
 traditional outlier analyses for detecting selected loci. Here, we develop
 a new approach that uses discriminant functions informed from
 inversion-specific expectations to classify loci that are under selection
 (or drift). Analysis of RAD sequencing data we collected in a classic
 dipteran species with polymorphic inversion clines-Anopheles gambiae, a
 malaria vector species from sub-Saharan Africa-demonstrates the benefits
 of the approach compared with traditional outlier analyses. We focus
 specifically on two polymorphic inversions, the 2La and 2Rb arrangements
 that predominate in dry habitats and the 2L+(a) and 2R+(b) arrangements in
 wet habitats, which contrast with the minimal geographic structure of SNPs
 from collinear regions. With our approach, we identify two strongly
 selected regions within 2La associated with dry habitat. Moreover, we also
 show that the prevalence of selection is greater in the arrangement 2L+(a)
 that is associated with wet habitat (unlike presumed importance of
 selective divergence associated with the shift of the mosquitoes into dry
 habitats). We discuss the implications of these results with respect to
 studies of rapid adaptation in these malaria vectors, and in particular,
 the insights our newly developed approach offers for identifying not only
 potential targets of selection, but also the population that has undergone
 adaptive change.
description: msms_runningSettingsbootstrap ranges of parameters for 2La, 2Rb regions and msms simulation settings fileAll individuals vcfVCF file of SNPs of all individuals.allIndividuals.vcf.gzSampling InfoSampling location, species, karyotypes of all specimens.SamplingInfo.csvfastsimcoal_settingsfastsimcoal2 input files of different scenarios.Inversion_DAPCRegion_statsRegion statistics of 2La and 2Rb and posterior probability of predicted scenarios.
DOI: 10.5061/dryad.26pt6
title: Data from: Comparative support for the expensive tissue hypothesis: big brains are correlated with smaller gut and greater parental investment in Lake Tanganyika cichlids

description: The brain is one of the most energetically expensive organs in the
 vertebrate body. Consequently, the energetic requirements of
 encephalization are suggested to impose considerable constraints on brain
 size evolution. Three main hypotheses concerning how energetic constraints
 might affect brain evolution predict covariation between brain investment
 and i) investment into other costly tissues, ii) overall metabolic rate,
 and iii) reproductive investment. To date, these hypotheses have mainly
 been tested in homeothermic animals and the existing data are
 inconclusive. However, there are good reasons to believe that energetic
 limitations might play a role in large-scale patterns of brain size
 evolution also in ectothermic vertebrates. Here we test these hypotheses
 in a group of ectothermic vertebrates, the Lake Tanganyika cichlid fishes.
 After controlling for the effect of shared ancestry and confounding
 ecological variables, we find a negative association between brain size
 and gut size. Furthermore, we find that the evolution of a larger brain is
 accompanied by increased reproductive investment into egg size and
 parental care. Our results indicate that the energetic costs of
 encephalization may be an important general factor involved in the
 evolution of brain size also in ectothermic vertebrates.
description: data_tsuboi_etal_EvolutionData on body weight, brain right, gut length of Lake Tanganyika cichlids. Other information used in the study is presented as supplementary material.
DOI: 10.5061/dryad.rk987
title: Data from: Soil acidification exerts a greater control on soil respiration than soil nitrogen availability in grasslands subjected to long-term nitrogen enrichment

description: Terrestrial ecosystems worldwide are receiving increasing amounts of
 biologically reactive nitrogen (N) as a consequence of anthropogenic
 activities. This intended or unintended fertilization can have a
 wide-range of impacts on biotic communities and hence on soil respiration.
 Reduction in below-ground carbon (C) allocation induced by high N
 availability has been assumed to be a major mechanism determining the
 effects of N enrichment on soil respiration. In addition to increasing
 available N, however, N enrichment causes soil acidification, which may
 also affect root and microbial activities. The relative importance of
 increased N availability vs. soil acidification on soil respiration in
 natural ecosystems experiencing N enrichment is unclear. We conducted a
 12-year N enrichment experiment and a 4-year complementary acid addition
 experiment in a semi-arid Inner Mongolian grassland. We found that N
 enrichment had contrasting effects on root and microbial respiration. N
 enrichment significantly increased root biomass, root N content and
 specific root respiration, thereby promoting root respiration. In
 contrast, N enrichment significantly suppressed microbial respiration
 likely by reducing total microbial biomass and changing the microbial
 community composition. The effect on root activities was due to both soil
 acidity and increased available N, while the effect on microbes primarily
 stemmed from soil acidity, which was further confirmed by results from the
 acid addition experiment. Our results indicate that soil acidification
 exerts a greater control than soil N availability on soil respiration in
 grasslands experiencing long-term N enrichment. These findings suggest
 that N-induced soil acidification should be included in predicting
 terrestrial ecosystem C balance under future N deposition scenarios.
description: Nitrogen_and_Acid_additionNitrogen_and_acid_addition.xlsxChen_et_al_FE_2015Includes responses of extractable_Ca2+, extractable_Mg2+, extractable_Na+, and extractable_Al3+ to acid addition treatment.
DOI: 10.5061/dryad.d8p78
title: Data from: Learning of salient prey traits explains Batesian mimicry evolution

description: Batesian mimicry evolution entails an initial major mutation that produces
 a rough resemblance to the model, followed by smaller improving changes.
 To examine the learning psychology of this process, we applied established
 ideas about mimicry in Papilio polyxenes asterius of the model Battus
 philenor. We performed experiments with wild birds as predators and
 butterfly wings as semi-artificial prey. Wings of hybrids of P. p.
 asterius and P. machaon were used to approximate the first mutant, with
 melanism as the hypothesized first mimetic trait. Based on previous
 results about learning psychology and imperfect mimicry, we predicted
 that: melanism should have high salience (i.e., being noticeable and
 prominent), meaning that predators readily discriminate a melanistic
 mutant from appearances similar to P. machaon; the difference between the
 first mutant and the model should have intermediate salience, to allow
 further improvement of mimicry; and the final difference in appearance
 between P. p. asterius and B. philenor should have very low salience,
 causing improvement to level off. Our results supported both the
 traditional hypothesis and all our predictions about relative salience. We
 conclude that there is good agreement between long-held ideas about how
 Batesian mimicry evolves and recent insights from learning psychology
 about the role of salience in mimicry evolution.
description: READMEDiscrimination learning
 datadiscri_data.txtGeneralization test datagenerali_data.txtSalience test - discrimination learningsalience_data.txtColor proportion measurements of butterfly wingswing_data.txtScript to analyze discrimination learning datadiscri_ana.RScript to analyze generalization test datagenerali_ana.RScript to analyze salience test datasalience_ana.RScript to analyze wing datawing_ana.R
DOI: 10.5061/dryad.gm367
title: Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)

description: Atlantic salmon (Salmo salar) is one of the most extensively studied fish
 species in the world due to its significance in aquaculture, fisheries and
 ongoing conservation efforts to protect declining populations. Yet,
 limited genomic resources have hampered our understanding of genetic
 architecture in the species and the genetic basis of adaptation to the
 wide range of natural and artificial environments it occupies. In this
 paper, we describe the development of a medium density Atlantic salmon
 SNP-array based on Expressed Sequence Tags (ESTs) and genomic sequencing.
 The array was used in the most extensive assessment of population genetic
 structure performed to date in this species. A total of 6176 informative
 SNPs were successfully genotyped in 38 anadromous and freshwater wild
 populations distributed across the species natural range. Principal
 component analysis clearly differentiated European and North American
 populations, and within Europe, three major regional genetic groups were
 identified for the first time in a single analysis. We assessed the
 potential for the array to disentangle neutral and putative adaptive
 divergence of SNP allele frequencies across populations and among regional
 groups. In Europe, secondary contact zones were identified between major
 clusters where endogenous and exogenous barriers could be associated,
 rendering the interpretation of environmental influence on potentially
 adaptive divergence equivocal. A small number of markers highly divergent
 in allele frequencies (outliers) were observed between (multiple)
 freshwater and anadromous populations, between northern and southern
 latitudes, and when comparing Baltic populations to all others. We also
 discuss the potential future applications of the SNP-array for
 conservation, management and aquaculture.
description: Genotypes_Dryad6176 SNP genotypes for 1295 samples used in submitted analysis (all but Foyle River population). For access to genotypes from Foyle River samples, please contact Dr. Dennis Ensing at Agri-Food & Biosciences Institute, Fisheries & Aquatic Ecosystems Branch . See paper for information on genotyping and SNP discovery.Baltic_Cfit_InputInput file for Cfit software. Includes populations geographic distances along the Baltic-Atlantic continuum (see paper) and allele counts for each populations.Barents_Cfit_InputInput file for Cfit software. Includes geographic distances for populations along the Barents-Atlantic continuum (see paper) as well as allele counts for each populations.