cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sk792
title: Data from: Modeling avian biodiversity using raw, unclassified satellite imagery

description: Applications of remote sensing for biodiversity conservation typically
 rely on image classifications that do not capture variability within
 coarse land cover classes. Here, we compare two measures derived from
 unclassified remotely sensed data, a measure of habitat heterogeneity and
 a measure of habitat composition, for explaining bird species richness and
 the spatial distribution of 10 species in a semi-arid landscape of New
 Mexico. We surveyed bird abundance from 1996 to 1998 at 42 plots located
 in the McGregor Range of Fort Bliss Army Reserve. Normalized Difference
 Vegetation Index values of two May 1997 Landsat scenes were the basis for
 among-pixel habitat heterogeneity (image texture), and we used the raw
 imagery to decompose each pixel into different habitat components
 (spectral mixture analysis). We used model averaging to relate measures of
 avian biodiversity to measures of image texture and spectral mixture
 analysis fractions. Measures of habitat heterogeneity, particularly
 angular second moment and standard deviation, provide higher explanatory
 power for bird species richness and the abundance of most species than
 measures of habitat composition. Using image texture, alone or in
 combination with other classified imagery-based approaches, for monitoring
 statuses and trends in biological diversity can greatly improve
 conservation efforts and habitat management.
description: Avian point count data,
 image texture, and spectral unmixing fractionsThe dataset includes the
 avian count data as well as image texture measures of NDVI and spectral
 unmixing fractions that were used in the analysis. The avian count data
 were collected in New Mexico, USA, between 1996 and 1998. A complete
 description of the methodology is available in Pidgeon et al.
 (1996).Pidgeon AM, Radeloff VC, Mathews NE. 2003 Landscape-scale patterns
 of black-throated sparrow (Amphispiza bilineata) abundance and nest
 success. Ecol. Appl. 13, 530 –542.St-Louisetal_bird_texture.xls
DOI: 10.5061/dryad.hc967
title: Data from: The evolution of social monogamy in primates is not consistently associated with male infanticide

description: Comparative analyses suggest that monogamous breeding systems evolved in
 mammals where feeding competition reduces range overlap between breeding
 females, preventing males from guarding more than one female at at time.
 In contrast, a recent analysis for primates suggests that monogamy evolved
 as a form of paternal care that reduces the risk of male infanticide. Here
 we re-examine the distribution of monogamy in primates and attempt to
 explain the contrasting results of the two analyses.
description: SupplementDataTable1_Lukas&CluttonBrock_Monogamy in Primates_PNASInformation on behaviour (sociality, paternal care, infanticide), life history (weaning and lactation duration), and ranging (population density, home range overlap) for 359 primate speciesLukasCluttonBrock_MonogamyinPrimates_SupplementforPNAS_LetterSupplementary file describing the data collection and analyses. Please note that this file is not stored directly with the online publication at PNAS.
DOI: 10.5061/dryad.k20q2
title: Data from: Studying phenology by flexible modeling of seasonal detectability peaks

description: 1.Many animals and plant species have advanced spring phenology in
 response to climate warming. The majority of avian phenological studies
 are based on arrival dates. Consequently knowledge on bird phenology is
 mainly based on migratory species. In addition, arrival dates of migratory
 birds may be substantially affected by en-route climate conditions; thus
 failing to provide good indicators for spring phenology on the breeding
 grounds. Correlating arrival dates with other phenological data or with
 environmental covariates may be meaningless in these cases. 2.We propose
 the date of highest singing activity, quantified by detection probability,
 as a powerful proxy for breeding phenology that is applicable to migratory
 and sedentary bird species alike. In contrast to arrival dates, breeding
 phenology is mainly (non-migrants) or at least partially (migrants)
 influenced by conditions experienced within the breeding area. 3.We
 developed a new method for flexible estimation of peak detectability date
 in spring by combining multi-season site-occupancy with semi-parametric
 regression modeling (thin-plate splines). We applied our approach to
 opportunistic observations of 27 bird species (mostly passerines) in
 Switzerland. 4.We found substantial differences among species in the date
 of spring peak detectability: late February to mid-April in sedentary and
 short-distance migratory species and mid-April to late May in
 long-distance migrants. Among 10 species with data for &gt;9 years,
 five showed a trend in detectability peaks towards an earlier spring
 phenology by nine to 17 days within 10 years. The mean shift over all
 species was ~3.5 days per 10 years. 5.Our approach is widely applicable,
 especially for temporally and spatially large-scale data from monitoring
 or citizen-science programs. Besides using the detectability peak as
 measure of phenology, the estimated seasonal pattern in detectability can
 help designing monitoring programs for improved efficiency. Our approach
 may be applied to any species with pronounced acoustic displays or other
 behavioral traits strongly influencing detectability during the breeding
 period. We believe that it can contribute substantially to unraveling how
 species and communities respond to environmental change.
description: Species attribute
 fileattr.csvObservation dataThis file contains all observation data analyzed in our article «Studying phenology by flexible modeling of seasonal detectability peaks».obs_data.csv
DOI: 10.5061/dryad.n525j
title: Data from: The monophyly of Euparkeriidae (Reptilia: Archosauriformes) and the origins of Archosauria: a revision of Dorosuchus neoetus from the Mid-Triassic of Russia

description: Euparkeria capensis is resolved as the sister taxon to crown Archosauria
 in many cladistic phylogenies and provides a key outgroup which may
 approximate the ancestral archosaur morphology. Several other taxa have
 been referred to the family Euparkeriidae, but the monophyly of this taxon
 remains doubtful and largely untested. In order to test this monophyly,
 the archosauriform and putative euparkeriid Dorosuchus neoetus from the
 Mid-Triassic of Russia is reexamined in light of recent work on the
 evolution of stem archosaurs. Dorosuchus neoetus is found to possess a
 number of morphological features that place it close to Archosauria,
 including a sigmoidal femur with a clear attachment region for the m.
 caudifemoralis musculature, but no unambiguous archosaurian apomorphies.
 Dorosuchus neoetus is included for the first time in a numerical cladistic
 analysis, and is recovered as the sole sister taxon to
 Archosauria+Phytosauria. A monophyletic Euparkeriidae including D. neoetus
 and E. capensis is slightly less parsimonious. In addition, a mandible and
 pterygoid that were previously referred to D. neoetus subsequent to the
 original description of the species are also included separately within
 the phylogenetic analysis, and are recovered within crown Archosauria,
 possibly raising questions as to their correct taxonomic referral.
 However, this phylogenetic placement is based primarily on the absence of
 palatal teeth, but the presence or absence of palatal teeth exhibits
 considerable homoplasy within Archosauriformes. Based on other aspects of
 their morphology, we do not reject the referral of these elements to D.
 neoetus.
description: Appendix
 S1Appendix of measurements
 of specimens of Dorosuchus neoetus.Appendix
 S2Appendix of strict
 consensus trees from all analyses carried out.Appendix
 S3Unadjusted matrix
 including Dorosuchus neoetus in nexus format.Appendix
 S4Adjusted matrix
 including Dorosuchus neoetus in nexus format.
DOI: 10.5061/dryad.63fr7
title: Data from: Fitness dynamics within a poplar hybrid zone: I. Prezygotic and postzygotic barriers impacting a native poplar hybrid stand.

description: Hybridization and introgression are pervasive evolutionary phenomena that
 provide insight to the selective forces that maintain species boundaries,
 permit gene flow and control the direction of evolutionary change. Poplar
 trees (Populus L.) are well known for their ability to form viable hybrids
 and maintain their distinct species boundaries despite this interspecific
 gene flow. We sought to quantify the hybridization dynamics and
 postzygotic fitness within a hybrid stand of balsam poplar (Populus
 balsamifera L.), eastern cottonwood (P. deltoides Marsh.) and their
 natural hybrids to gain insight to the barriers maintaining this stable
 hybrid zone. We observed asymmetrical hybrid formation with P. deltoides
 acting as the seed parent, but with subsequent introgression biased
 towards P. balsamifera. Native hybrids expressed fitness traits
 intermediate to the parental species and were not universally unfit. That
 said, native hybrid seedlings were absent from the seedling population,
 which may indicate additional selective pressures controlling their
 recruitment. It is imperative that we understand the selective forces
 maintaining this native hybrid zone in order to quantify the impact of
 exotic poplar hybrids on this native system.
description: R code for analysis of
 fitness dataAll R code associated
 with the manuscript are included. The file has been extensively commented
 as well.All
 analysesNativePoplar_submit.RTree stand
 characteristicsThis file contains the
 tree height, diameter at breast height, age classification, and
 genotype.Stand_TreeData.csvBiomass and yield fitness traitsThis file contains the following biomass fitness traits: total catkin biomass, total seed biomass, 100 seed biomass, capsule biomass, stem biomass, and cotton biomass. It also contains the following yield measurements: capsules per catkin, seeds per capsule, and seeds per catkin.Biomass.csvGerminationThis file contains two measures of germination success, as well as tree genotype class: germination success and number of abnormal germinants.Disease SusceptibilityThis file contains the results of the controlled inoculation of trees with three fungal diseases: Melampsora larici-populina, M. medusae f.sp. deltoidae, and M. occidentalis. Susceptibility was measured by number of uredia by unit area.Inoculations.csvStructure file for genotype assignmentThis file contains the recoded SNP data for input into Structure to estimate admixture in each individual.BPSF_NativeOnly­_CompleteRef.xlsNew Hybrid data fileThe file contains the recoded genotype data for each tree for analysis in New Hybrids.BPSF_NativeOnly_NH.txt
DOI: 10.5061/dryad.b46qg
title: Data from: Local adaptation limits lifetime reproductive success of dispersers in a wild salmon metapopulation

description: Demographic and evolutionary dynamics in wild metapopulations are
 critically affected by the balance between dispersal and local adaptation.
 Where populations are demographically interconnected by migration, gene
 flow is often assumed to prevent local adaptation. However, reduced
 fitness of immigrants may limit gene flow between populations adapted to
 distinct habitat types, although direct quantification of the lifetime
 reproductive success of immigrants in the wild is lacking. Here, we show
 that dispersers between stream-spawning populations of sockeye salmon
 (Oncorhynchus nerka) had similar reproductive success to those that
 spawned in their natal stream, while dispersers from a different habitat
 (nearby lake beaches) produced half as many offspring. The stream- and
 beach-spawning ecotypes exhibited striking morphological differences
 despite their close spatial proximity, yet dispersal from the beach to the
 streams was more common than dispersal between streams, presenting
 empirical evidence that variation in immigrant reproductive success is
 important for the maintenance of intraspecific biodiversity.
description: AC0405080910_final_genotypes_with_tagging_dataIndividual genotype and observational data
DOI: 10.5061/dryad.9pq70
title: Data from: Modelling competition and dispersal in a statistical phylogeographic framework

description: Competition between organisms influences the processes governing the
 colonization of new habitats. As a consequence, species or populations
 arriving first at a suitable location may prevent secondary colonization.
 While adaptation to environmental variables (e.g., temperature, altitude,
 etc.) is essential, the presence or absence of certain species at a
 particular location often depends on whether or not competing species
 co-occur. For example, competition is thought to play an important role in
 structuring mammalian communities assembly. It can also explain spatial
 patterns of low genetic diversity following rapid colonization events or
 the “progression rule” displayed by phylogenies of species found on
 archipelagos. Despite the potential of competition to maintain populations
 in isolation, past quantitative analyses have largely ignored it because
 of the difficulty in designing adequate methods for assessing its impact.
 We present here a new model that integrates competition and dispersal into
 a Bayesian phylogeographic framework. Extensive simulations and analysis
 of real data show that our approach clearly outperforms the traditional
 Mantel test for detecting correlation between genetic and geographic
 distances. But most importantly, we demonstrate that competition can be
 detected with high sensitivity and specificity from the phylogenetic
 analysis of genetic variation in space.
description: Phyloland R package -
 version 1.0Phyloland is a package
 that implements the competition-dispersion model described in Ranjard et
 al. "Modelling competition and dispersal in a statistical
 phylogeographic framework". Systematic Biology,
 2014.PhyML -
 20140406Supporting
 Informationsupporting-information.pdf
DOI: 10.5061/dryad.62797
title: Data from: Climate-driven range shifts explain the distribution of extant gene pools and predict future loss of unique lineages in a marine brown alga

description: The climate-driven dynamics of species ranges is a critical research
 question in evolutionary ecology. We ask whether present intra-specific
 diversity is determined by the imprint of past climate. This is an ongoing
 debate requiring interdisciplinary examination of population genetic pools
 and persistence patterns across global ranges. Previously, contrasting
 inferences and predictions have resulted from distinct genomic coverage
 and/or geographical information. We aim to describe and explain the causes
 of geographical contrasts in genetic diversity and their consequences for
 the future baseline of the global genetic pool, by comparing present
 geographic distribution of genetic diversity and differentiation with
 predictive Species Distribution Modeling (SDM) during past extremes,
 present-time and future climate scenarios for a brown alga, Fucus
 vesiculosus. SDM showed that both atmospheric and oceanic variables shape
 the global distribution of intertidal species, revealing regions of
 persistence, extinction and expansion during glacial and postglacial
 periods. These explained the distribution and structure of present genetic
 diversity, consisting of differentiated genetic pools with maximal
 diversity in areas of long term persistence. Most of the present species
 range comprises postglacial expansion zones and, in contrast with highly
 dispersive marine organisms, expansions involved only local fronts,
 leaving distinct genetic pools at rear edges. Besides unraveling a complex
 phylogeographic history and showing congruence between genetic diversity
 and persistent distribution zones, supporting the hypothesis of niche
 conservatism, range shifts and loss of unique genetic diversity at the
 rear edge were predicted for future climate scenarios, impoverishing the
 global gene pool.
description: Microsatellite data for
 F. vesiculosus (9 loci)Assis_et_al_msat_per_site.txtOccurrences (presences) of F. vesiculosus throughout its range (Northern Atlantic). Information gathered from literature. File formate: TXT (Lon, Lat, References)Assis_et_al_literature_occurrences.txtInput files for modeling (raster files for environmental and tidal data)Environment.zipR code for modelingR_SDM.R
DOI: 10.5061/dryad.39fs7
title: Data from: Fine-scale spatial genetic dynamics over the life-cycle of the tropical tree Prunus africana

description: Studying fine-scale spatial genetic patterns across life stages is a
 powerful approach to identify ecological processes acting within tree
 populations. We investigated spatial genetic dynamics across five life
 stages in the insect-pollinated and vertebrate-dispersed tropical tree
 Prunus africana in Kakamega Forest, Kenya. Using six highly polymorphic
 microsatellite loci, we assessed genetic diversity and spatial genetic
 structure (SGS) from seed rain and seedlings, and different sapling stages
 to adult trees. We found significant SGS in all stages, potentially caused
 by limited seed dispersal and high recruitment rates in areas with high
 light availability. SGS decreased from seed and early seedling stages to
 older juvenile stages. Interestingly, SGS was stronger in adults than in
 late juveniles. The initial decrease in SGS was probably driven by both
 random and non-random thinning of offspring clusters during recruitment.
 Intergenerational variation in SGS could have been driven by variation in
 gene flow processes, overlapping generations in the adult stage or local
 selection. Our study shows that complex sequential processes during
 recruitment contribute to SGS of tree populations.
description: Genotypic data of five
 life stages of Prunus africanaGenalex input file, six
 microsatellite loci, five life stages, geographic locations, notes and
 explanations given in 2nd excel-sheetRawDataUpload.xlsx
DOI: 10.5061/dryad.n0r41
title: Data from: Evolutionary basis of mitonuclear discordance between sister species of mole salamanders (Ambystoma sp.)

description: Distinct genetic markers should show similar patterns of differentiation
 between species reflecting their common evolutionary histories yet there
 are increasing examples of differences in the biogeographic distribution
 of species-specific nuclear (nuDNA) and mitochondrial DNA (mtDNA) variants
 within and between species. Identifying the evolutionary processes that
 underlie these anomalous patterns of genetic differentiation is an
 important goal. Here we analyze the putative mitonuclear discordance
 observed between sister species of mole salamanders (Ambystoma barbouri
 and A. texanum) in which A. barbouri-specific mtDNA is found in animals
 located in the range of A. texanum. We test three hypotheses for this
 discordance (undetected range expansion, mtDNA introgression and
 hybridization) using nuDNA and mtDNA data analyzed with methods that
 varied in the parameters estimated and the timescales measured. Results
 from a Bayesian clustering technique (structure), bi-directional estimates
 of gene flow (migrate-n and IMa2), and phylogeny-based methods (*beast,
 bucky) all support the conclusion that the discordance is due to
 geographically restricted mtDNA introgression from A. barbouri into A.
 texanum. Limited data on species-specific tooth morphology match this
 conclusion. Significant differences in environmental conditions exist
 between sites where A. texanum with and without A. barbouri-like mtDNA
 occur, suggesting a possible role for selection in the process of
 introgression. Overall, our study provides a general example of the value
 of using complimentary analyses to make inferences of the directionality,
 time scale, and source of mtDNA introgression in animals.
description: IMa2_infileInfile for IMa2 analysisinfile.txtMrBayes Posterior TreesCollection of gene trees produced from 10 nuclear loci.Denton_DAPC resourcesInfile (genepop) and R code for unpublished DAPC results.Denton_Environmental PCA is SPSSSPSS data file that contains the environmental variables for PCA.Data from DIVA v.2_barb and outliers removed.savDenton_STRUCTUREInput and settings file for STRUCTURE analysis.STRUCTURE.zipBarbTex_StarBEASTParameter and data files associated with *BEAST analysis.Migrate_infile and parmfileRepresentative infile and parmfile for Migrate analysis. This file is for model #3.BUCKyFiles associated with BUCKy analysis.Denton_fasta files for sequencesFinal, aligned fasta files used as input for multiple analyses.
DOI: 10.5061/dryad.j444n
title: Data from: Learning multiple routes in homing pigeons

description: The aerial lifestyle of central-place foraging birds allows wide-ranging
 movements, raising fundamental questions about their remarkable navigation
 and memory systems. For example, we know that pigeons (Columba livia),
 long-standing models for avian navigation, rely on individually distinct
 routes when homing from familiar sites. But it remains unknown how they
 cope with the task of learning several routes in parallel. Here, we
 examined how learning multiple routes influences homing in pigeons. We
 subjected groups of pigeons to different training protocols, defined by
 the sequence in which they were repeatedly released from three different
 sites, either sequentially, in rotation or randomly. We observed that
 pigeons from all groups successfully developed and applied memories of the
 different release sites (RSs), irrespective of the training protocol, and
 that learning several routes in parallel did not impair their capacity to
 quickly improve their homing efficiency over multiple releases. Our data
 also indicated that they coped with increasing RS uncertainty by adjusting
 both their initial behaviour upon release and subsequent homing
 efficiency. The results of our study broaden our understanding of avian
 route following and open new possibilities for studying learning and
 memory in free-flying animals.
description: Flack et al_Biology
 Letters
DOI: 10.5061/dryad.gn376
title: Data from: Testing for universal common ancestry

description: A phylogenetic model selection test to quantify the evidence for the
 Universal Common Ancestry (UCA) of life forms was proposed recently
 (Theobald 2010a), based on the comparison of the statistical support,
 using likelihoods, the Akaike Information Criterion (AIC), or Bayes
 factors, for two different phylogenetic models representing the UCA and
 the independent origins (IOs) hypotheses (Sober and Steel 2002). In this
 test, the former is represented by a single phylogeny connecting all
 sequences, whereas the latter is depicted by several, independent
 phylogenetic trees (Fig. 1). Importantly, in the original UCA test, the
 same alignment was used to represent both hypotheses. When applied to a
 particular data set of 23 universally conserved proteins, the test
 strongly favored a UCA scenario.
description: Supplementary
 DataThis file contains the
 scripts developed as well as data sets necessary to reproduce all analyses
 described in the article, together with extra analyses and the R scripts
 that produce the figures in the manuscript and Supplementary Text. A
 README file with more information is included.SupplementaryData_20140512.tbzSupplementary TextThis is the supplementary text describing additional analyses and figures. All analyses reported here can be reproduced by downloading the accompanying Supplementary Data.SupplementaryText_20140512.pdf