cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6k630
title: Data from: Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds

description: Dry forest bird communities in South America are often fragmented by
 intervening mountains and rainforests, generating high local endemism. The
 historical assembly of dry forest communities likely results from dynamic
 processes linked to numerous population histories among codistributed
 species. Nevertheless, species may diversify in the same way through time
 if landscape and environmental features, or species ecologies, similarly
 structure populations. Here we tested whether six co-distributed taxon
 pairs that occur in the dry forests of the Tumbes and Marañón Valley of
 northwestern South America show concordant patterns and modes of
 diversification. We employed a genome reduction technique, double-digest
 restriction site-associated DNA sequencing, and obtained 4407–7186
 genomewide SNPs. We estimated demographic history in each taxon pair and
 inferred that all pairs had the same best-fit demographic model: isolation
 with asymmetric gene flow from the Tumbes into the Marañón Valley,
 suggesting a common diversification mode. Overall, we also observed
 congruence in effective population size (Ne) patterns where ancestral Ne
 were 2.9–11.0× larger than present-day Marañón Valley populations and
 0.3–2.0× larger than Tumbesian populations. Present-day Marañón Valley Ne
 was smaller than Tumbes. In contrast, we found simultaneous population
 isolation due to a single event to be unlikely as taxon pairs diverged
 over an extended period of time (0.1–2.9 Ma) with multiple nonoverlapping
 divergence periods. Our results show that even when populations of
 codistributed species asynchronously diverge, the mode of their
 differentiation can remain conserved over millions of years. Divergence by
 allopatric isolation due to barrier formation does not explain the mode of
 differentiation between these two bird assemblages; rather, migration of
 individuals occurred before and after geographic isolation.
description: G-PhoCS input files for
 Oswald et. al 2017G-PhoCS_files.tar.gzfastsimcoal2 input files for Oswald et al. 2017MarTum-fsc2_files.tgzSTRUCTURE input files for Oswald et al. 2017Note that the University of Florida samples are labeled with preparator numbers. These preparator numbers and associated FLMNH collection numbers and locality information for all individuals can be found in Oswald et al. 2017 Supplementary Table 1.Oswald et al. 2017_ME_Structure files.zip
DOI: 10.5061/dryad.bd08ft6
title: Data from: Speed-mediated properties of schooling

description: Collectively moving animals often display a high degree of synchronisation
 and cohesive group-level formations, such as elongated schools of fish.
 These global patterns emerge as the result of localised rules of
 interactions. However, the exact relationship between speed, polarisation,
 neighbour positioning and group structure has produced conflicting results
 and is largely limited to modelling approaches. This hinders our ability
 to understand how information spreads between individuals, which may
 determine the collective functioning of groups. We tested how speed
 interacts with polarisation and positional composition to produce the
 elongation observed in moving groups of fish as well as how this impacts
 information flow between individuals. At the local level, we found that
 increases in speed led to increases in alignment and shifts from lateral
 to linear neighbour positioning. At the global level, these increases in
 linear neighbour positioning resulted in elongation of the group.
 Furthermore, mean pairwise transfer entropy increased with speed and
 alignment, implying an adaptive value to forming faster, more polarised
 and linear groups. Ultimately, this research provides vital insight into
 the mechanisms underlying elongation of moving animal groups and
 highlights the functional significance of cohesive and coordinated
 movement.
description: deviation_bytrial.csvdataset used to calculate effect of speed on alignmentpropfront_bytrialdataset used to calculate effect of speed on proportion of group in front or behind focal individualKent et al_RcodeR code used for statistical analysisTE_trialavgdatasets used to calculate effect of speed and alignment on transfer entropyBN Trial ExcerptBN.mp4BR Trial ExcerptBR.mp4GC Trial ExcerptGC.mp4SC Trial ExcerptSC.mp4MD Trial ExcerptMD.mp4
DOI: 10.48656/nszr-w789
title: LiSa Open Data
title: LiSa Open Data
DOI: 10.48656/zzcp-4888
title: LiSa Open Data
title: LiSa Open Data
DOI: 10.5061/dryad.rb3b0d2p
title: Data from: Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm

description: Imprinting describes the differential expression of alleles based upon
 their parent of origin. Deep sequencing of RNAs from maize endosperm and
 embryo tissue 14 days after pollination was used to identify imprinted
 genes among a set of ~12,000 genes that were expressed and contained
 sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of
 parent-of-origin patterns of expression resulted in the identification of
 100 putative imprinted genes in maize endosperm including 54 maternally
 expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of
 these genes have been previously identified as imprinted while the
 remaining 97 genes represent novel imprinted maize genes. A genome-wide
 analysis of DNA methylation identified regions with reduced endosperm DNA
 methylation in, or near, 19 of the 100 imprinted genes. The reduced levels
 of DNA methylation in endosperm are caused by hypomethylation of the
 maternal allele for both MEGs and PEGs in all cases tested. Many of the
 imprinted genes with reduced DNA methylation levels also show
 endosperm-specific expression patterns. The imprinted maize genes were
 compared with imprinted genes identified in genome-wide screens of rice
 and Arabidopsis and at least 10 examples of conserved imprinting between
 maize and each of the other species were identified.
description: maize imprinting ms
 supplemental dataset1RPKM values for all
 maize genes in biological replicates of endosperm or embryo tissue
 isolated from B73 and Mo17 genotypesmaize imprinting ms
 supplemental dataset2Allele-specific
 expression values for all maize genes in biological replicates of
 endosperm or embryo tissue isolated from B73xMo17 hybrid
 genotypes.tpc092668_SupplementalDS2.xlsx
DOI: 10.5061/dryad.786r6
title: Data from: Techniques for estimating the size of low density gopher tortoise populations

description: The gopher tortoise (Gopherus polyphemus) is a candidate species for
 range-wide listing under the U.S. Endangered Species Act; hence reliable
 population estimates are required to aid management and guide policy
 needed to recover the species. Line transect distance sampling has been
 adopted as the preferred technique to estimate population size. However,
 when tortoise density is low, it can be challenging to obtain enough
 tortoise observations to reliably estimate the probability of detection, a
 vital component of the method. We suggest a modification to the method,
 based on counting usable tortoise burrows (which are more abundant than
 tortoises) and separately accounting for the proportion of burrows
 occupied by tortoises. The increased sample size generated by using
 burrows, rather than tortoises, can outweigh the additional uncertainty
 generated by needing to account for the proportion occupied. We
 demonstrate the method using surveys conducted within a 13,118 ha portion
 of the Gopher Tortoise Habitat Management Unit at Fort Gordon Army
 Installation, Georgia. An additional feature of these surveys was that we
 employed a systematic random design to obtain more precise estimates using
 a newly-developed systematic variance estimator. Individual transects
 consisted of pseudo-circuits, a design which greatly improved sampling
 efficiency on this large site. The burrow density was 0.091 ± 0.011
 burrows/ha (CV = 12.6%, 95% CI = 0.071-0.116); 25% of burrows were
 occupied by a tortoise (CV = 14.4%), yielding a tortoise density of 0.023
 ± 0.004 tortoise/ha (CV = 19.0%, 95% CI = 0.016-0.033) and corresponding
 population size of 297 (95% CI = 210-433). These techniques are applicable
 to other studies and species: surveying burrows or nests, rather than
 animals, can produce more reliable estimates when it leads to a
 significantly larger sample of detections and when the occupancy status
 can reliably be ascertained. Systematic line transect survey designs are
 practical to implement and, now, to analyze, and yield better precision.
description: FGtort_NE and NW
 datasetsTwo distance sample
 projects - Download Program distance at http://distancesampling.org/.
 Tutorial in the readme for loading data and running
 analysis.FGtort_data.zip
DOI: 10.5061/dryad.5b64r
title: Data from: Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

description: Gene sequence similarity due to shared ancestry after a duplication event,
 that is paralogy, complicates the assessment of genetic variation, as
 sequences originating from paralogs can be difficult to distinguish. These
 confounded sequences are often removed prior to further analyses, leaving
 the underlying loci uncharacterized. Salmonids have only partially
 rediploidized subsequent to a whole-genome duplication; residual
 tetrasomic inheritance has been observed in males. We present a
 maximum-likelihood-based method to resolve confounded paralogous loci by
 observing the segregation of alleles in gynogenetic haploid offspring and
 demonstrate its effectiveness by constructing two linkage maps for chum
 salmon (Oncorhynchus keta), with and without these newly resolved loci. We
 find that the resolved paralogous loci are not randomly distributed across
 the genome. A majority are clustered in expanded subtelomeric regions of
 14 linkage groups, suggesting a significant fraction of the chum salmon
 genome may be missed by the exclusion of paralogous loci. Transposable
 elements have been proposed as drivers of genome evolution and, in
 salmonids, may have an important role in the rediploidization process by
 driving differentiation between homeologous chromosomes. Consistent with
 that hypothesis, we find a reduced fraction of transposable element
 annotations among paralogous loci, and these loci predominately occur in
 the genomic regions that lag in the rediploidization process.
description: RAD seqeunces and
 genotypesRaw genotype data for
 all identified catalog entries. Each line gives genotypes for a single
 catalog entry, columns are individuals. The first 2 columns are metadata
 for each catalog entry and a header line is present. This is a zipped
 tab-delimited text file and line endings are in Unix format:
 "\n". This file is generated by Stacks v1.05 (Catchen, J.,
 Hohenlohe, P. A., Bassham, S., Amores, A. and Cresko, W. A. (2013),
 Stacks: an analysis tool set for population genomics. Mol Ecol, 22:
 3124–3140. doi:10.1111/mec.12354)RAD_genotypes.zipprimer-based (taqMan) genotypesThis file contains genotype data generated by primer- based genotyping. Each row is an individual, labeled in the first column. Each column past the first gives genotypes for a specific locus, labeled in the first row. Only haploid offspring are included and they are expected to be homozygous. Alleles are specified by 'X' and 'Y', uncalled genoyypes are specified with 'no call' or 'invalid'. This is a text file with Windows line endings: "\r\n"taqMan_genotypes.tsvCatalog sequencesThis is a zipped tab-delimited text file and line endings are in Unix format: "\n". This file is generated by Stacks v1.05 (Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A. and Cresko, W. A. (2013), Stacks: an analysis tool set for population genomics. Mol Ecol, 22: 3124–3140. doi:10.1111/mec.12354)Catalog.tags.zip
DOI: 10.5061/dryad.fj974
title: Data from: Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center

description: Since its establishment in 1966, the Duke Lemur Center (DLC) has
 accumulated detailed records for nearly 4200 individuals from over 40
 strepsirrhine primate taxa – the lemurs, lorises, and galagos. Here we
 present verified data for 3627 individuals of 27 taxa in the form of a
 life history table containing summarized species values for variables
 relating to ancestry, reproduction, longevity, and body mass, as well as
 the two raw data files containing direct and calculated variables from
 which this summary table is built. Large sample sizes, longitudinal data
 that in many cases span an animal’s entire life, exact dates of events,
 and large numbers of individuals from closely related yet biologically
 diverse primate taxa make these datasets unique. This single source for
 verified raw data and systematically compiled species values, particularly
 in combination with the availability of associated biological samples and
 the current live colony for research, will support future studies from an
 enormous spectrum of disciplines.
description: README - DLC Data Update
 Details Feb 2019This document contains
 details relating to the Duke Lemur Center (DLC) data update released in
 February 2019.DataRecord_1b_DLC_LH_Table_Analysis_05Feb2019The DLC Strepsirrhine Life History Summary Table contains 91 variables for 27 taxa. There are two versions of this file provided; they contain the same information but are formatted for different uses. The first, data record 1a, is a reference version, with all variables in character format in each of 91 rows, and 27 columns each referencing a different taxon. The reference version is designed to facilitate locations of particular data points for particular taxon that a user may be interested in and can be found in the HTML version of the associated manuscript. The second, data record 1b, is an analysis version that contains a mixture of character and numeric variables each in one of 91 columns, with a row for each of the 27 species. While it is perhaps more difficult to find a specific data point in this table, this version can be imported directly into analysis software for comparison of variables across taxa. Data record 1b is stored as comma separated values.DataRecord_2_DLC_Animal_List_05Feb2019The DLC Animal List data file, containing 32 variables for 3,749 individuals representing 27 taxa in all stages of life. These are the raw data used to calculate longevity and reproductive variables in the life history tables. This file is stored as comma separated values.DataRecord_3_DLC_Weight_File_05Feb2019The DLC Weight data file, containing 33 variables relating to 82,6109 weight measurements across 2270 individuals and 27 taxa. These are the raw data used to calculate body mass variables in the life history tables. This file is stored as comma separated values.
DOI: 10.5061/dryad.j4r4j13
title: Data from: Lepidosaurian diversity in the Mesozoic–Paleogene: the potential roles of sampling biases and environmental drivers

description: Lepidosauria is a speciose clade with a long evolutionary history, but
 there have been few attempts to explore its taxon-richness through time.
 Here we estimate patterns of terrestrial lepidosaur genus diversity for
 the Triassic–Paleogene (252–23 Ma), and compare observed and
 sampling-corrected richness curves generated using Shareholder Quorum
 Subsampling and classical rarefaction. Generalized least-squares
 regression (GLS) is used to investigate the relationships between
 richness, sampling and environmental proxies. We found low levels of
 richness from the Triassic until the Late Cretaceous (except in the
 Kimmeridgian–Tithonian of Europe). High richness is recovered for the Late
 Cretaceous of North America, which declined across the K–Pg boundary but
 remained relatively high throughout the Paleogene. Richness decreased
 following the Eocene–Oligocene Grande Coupure in North America and Europe,
 but remained high in North America and very high in Europe compared to the
 Late Cretaceous; elsewhere data are lacking. GLS analyses indicate that
 sampling biases (particularly the number of fossil collections per
 interval) are the best explanation for long-term face-value genus richness
 trends. The lepidosaur fossil record presents many problems when
 attempting to reconstruct past diversity, with geographic sampling biases
 being of particular concern, especially in the Southern Hemisphere.
description: SI Appendix 2 - all data
 and refsData processing script
 and termsScript and files that
 were used to filter out trace, oo- and marine taxa from the original PBDB
 download.
DOI: 10.15468/vuunxw
title: University of Georgia, Julian H. Miller Mycological Herbarium

description: The Julian H. Miller Mycological Herbarium (GAM) is an internationally recognized collection of fungi with an estimated 30,500 specimens that is a unit of the Georgia Museum of Natural History of the University of Georgia. The herbarium collections are especially strong in plant pathogenic ascomycetes; although, the majority of specimens are from Georgia and the southeastern USA. Specimens in the collection date back to the late 1800&rsquo;s, including exsiccati of J.B. Ellis and M.B. Everhart and A.B. Seymour and F. S. Earle. Other important collections are the Forest Disease Fungi acquired from the USDA Forest Service in Athens, which includes the rust collections of George Hepting and the Coleosporium collection of George Hedgcock, a large collection of Georgia myxomycetes and a collection of Georgia lichens.
DOI: 10.5061/dryad.rd250
title: Data from: Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of Atlantic cod Gadus morhua

description: Accurate prediction of species distribution shifts in the face of climate
 change requires a sound understanding of population diversity and local
 adaptations. Previous modeling has suggested that global warming will lead
 to increased abundance of Atlantic cod (Gadus morhua) in the ocean around
 Greenland, but the dynamics of earlier abundance fluctuations are not well
 understood. We applied a retrospective spatiotemporal population genomics
 approach to examine the temporal stability of cod population structure in
 this region and to search for signatures of divergent selection over a
 78-year period spanning major demographic changes. Analyzing &gt;900
 gene-associated single nucleotide polymorphisms in 847 individuals, we
 identified four genetically distinct groups that exhibited varying spatial
 distributions with considerable overlap and mixture. The genetic
 composition had remained stable over decades at some spawning grounds,
 whereas complete population replacement was evident at others.
 Observations of elevated differentiation in certain genomic regions are
 consistent with adaptive divergence between the groups, indicating that
 they may respond differently to environmental variation. Significantly
 increased temporal changes at a subset of loci also suggest that
 adaptation may be ongoing. These findings illustrate the power of
 spatiotemporal population genomics for revealing biocomplexity in both
 space and time and for informing future fisheries management and
 conservation efforts.
description: SNP_infoThis tab-separated file contains a complete list of the SNPs analyzed in the study. For each SNP we provide the linkage group and specific linkage map position (where available), the accession reference ID (dbSNP), the original publication for the SNP discovery (source), and any miscellaneous notes.Individual_info_and_genotypesThis tab-delimited file contains information on the sampling location and time, the available demographic data, and the observed SNP genotypes for all individuals analyzed in the study. See the readme file for descriptions of the variables. In the updated file, the weight data for the Icelandic samples have been corrected from grams to kilograms, and number-based sex encoding for these same samples have been changed to M and F. For the Icelandic samples the maturity key used is as follows: 1 is a resting fish, 2-6 indicates a maturing fish, &gt;6 (e.g. 22) means actively spawning.Genepop_GreenlandIcelandCanadaThe SNP genotype data from file "Individual_info_and_genotypes.txt" presented in Genepop format.EnvironmentalData_GreenlandThis tab-delimeted file contains the environmental data used in the BayEnv analysis of environment-allele frequency correlations. See the readme file for details.
DOI: 10.5061/dryad.mr0rg45
title: Data from: Diel predator activity drives a dynamic landscape of fear

description: A ‘landscape of fear’ (LOF) is a map that describes continuous spatial
 variation in an animal’s perception of predation risk. The relief on this
 map reflects, for example, places that an animal avoids to minimize risk.
 Although the LOF concept is a potential unifying theme in ecology that is
 often invoked to explain the ecological and conservation significance of
 fear, little is known about the daily dynamics of a LOF. Despite theory
 and data to the contrary, investigators often assume, implicitly or
 explicitly, that a LOF is a static consequence of a predator’s mere
 presence within an ecosystem. We tested the prediction that a LOF in a
 large-scale, free-living system is a highly-dynamic map with ‘peaks’ and
 ‘valleys’ that alternate across the diel (24-hour) cycle in response to
 daily lulls in predator activity. We did so with extensive data from the
 case study of Yellowstone elk (Cervus elaphus) and wolves (Canis lupus)
 that was the original basis for the LOF concept. We quantified the elk
 LOF, defined here as spatial allocation of time away from risky places and
 times, across nearly 1000-km2 of northern Yellowstone National Park and
 found that it fluctuated with the crepuscular activity pattern of wolves,
 enabling elk to use risky places during wolf downtimes. This may help
 explain evidence that wolf predation risk has no effect on elk stress
 levels, body condition, pregnancy, or herbivory. The ability of
 free-living animals to adaptively allocate habitat use across periods of
 high and low predator activity within the diel cycle is an
 underappreciated aspect of animal behavior that helps explain why strong
 antipredator responses may trigger weak ecological effects, and why a LOF
 may have less conceptual and practical importance than direct killing.
description: Kohl_etal_NorthernRangeCowElkData_2001thru2004This is GPS data collected by Dr. Mark Boyce and National Park Staff as part of the early monitoring efforts of elk following wolf reintroduction. Winter data (see paper for information) is cleaned and operational. Migration data and Summer is not. Fix intervals vary by individual so please contact Dan MacNulty at Utah State University for additional information pertaining to these schedules and any other pertinent information. These data were assembled from three different sources (Mao, Varley, Evans), so duplicated records may exists for some records.Kohl_etal_NorthernRangeElkData_2001thru2004.csvFinal Analysis Dataset for Matched-Case Control Elk Habitat SelectionFinalAnalysis_MCCDataset.csvSummary information for Historic Northern Yellowstone Elk DataKohl_etal_NorthernRangeElkData_SummaryInformation.xlsxDiel activity of wolvesWolf Diel Activity.xlsx