cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.57025
title: Data from: Neogene sloth assemblages (Mammalia, Pilosa) of the Cocinetas Basin (La Guajira, Colombia): implications for the Great American Biotic Interchange

description: We describe sloth assemblages from the Cocinetas Basin (La Guajira
 peninsula, Colombia), found in the Neogene Castilletes and Ware
 formations, located in northernmost South America, documenting otherwise
 poorly known biotas. The tentative referral of a specimen to a small
 megatherioid sloth, Hyperleptus?, from the early–middle Miocene
 Castilletes Formation, suggests affinities of this fauna with the distant
 Santa Cruz Formation and documents a large latitudinal distribution for
 this taxon. The late Pliocene Ware Formation is much more diverse, with
 five distinct taxa representing every family of ‘ground sloths’. This
 diversity is also remarkable at the ecological level, with sloths spanning
 over two orders of magnitude of body mass and probably having different
 feeding strategies. Being only a few hundred kilometres away from the
 Isthmus of Panama, and a few hundred thousand years older than the
 classically recognized first main pulse of the Great American Biotic
 interchange (GABI 1), the Ware Formation furthermore documents an
 important fauna for the understanding of this major event in Neogene
 palaeobiogeography. The sloths for which unambiguous affinities were
 recovered are not closely related to the early immigrants found in North
 America before GABI 1.
description: Data matrix used for the
 phylogenetic analysis.This taxon/character
 matrix was built with Mesquite (3.04). It was used to perform a
 phylogenetic analysis aiming at resolving the position of the specimen MUN
 STRI 36643, an edentulous partial horizontal ramus of dentary coming from
 the Ware Formation (Cocinetas Basin, La Guajira peninsula, Colombia). The
 characters are from Gaudin [2004, Phylogenetic relationships among sloths
 (Mammalia, Xenarthra, Tardigrada): the craniodental evidence. Zoological
 Journal of the Linnean Society, 140, 255–305].Data_matrix.nex
DOI: 10.17630/3d6fde13-8bfe-491f-8233-32c5f4db6c5e
title: Controlled Introduction of Defects to Delafossite Metals by Electron Irradiation (dataset)
DOI: 10.5061/dryad.n1cg7
title: Data from: DNA barcodes from century-old type specimens using next generation sequencing

description: Type specimens have high scientific importance because they provide the
 only certain connection between the application of a Linnean name and a
 physical specimen. Many other individuals may have been identified as a
 particular species, but their linkage to the taxon concept is inferential.
 Because type specimens are often more than a century old and have
 experienced conditions unfavorable for DNA preservation, success in
 sequence recovery has been uncertain. The present study addresses this
 challenge by employing next generation sequencing (NGS) to recover
 sequences for the barcode region of the cytochrome c oxidase 1 gene from
 small amounts of template DNA. DNA quality was first screened in more than
 1800 century-old type specimens of Lepidoptera by attempting to recover
 164bp and 94bp reads via Sanger sequencing. This analysis permitted the
 assignment of each specimen to one of three DNA quality categories – high
 (164bp sequence), medium (94bp sequence), or low (no sequence). Ten
 specimens from each category were subsequently analyzed via a PCR-based
 NGS protocol requiring very little template DNA. It recovered sequence
 information from all specimens with average read lengths ranging from
 458bp to 610bp for the three DNA categories. By sequencing ten specimens
 in each NGS run, costs were similar to Sanger analysis. Future increases
 in the number of specimens processed in each run promise substantial
 reductions in cost, making it possible to anticipate a future where
 barcode sequences are available from most type specimens.
description: Sequence alignments and
 tree filesThe file contains
 sequence alignments of sequences generated using Sanger sequencing and
 next generation sequencing. The NJ tree files associated with Figures 3
 and 4 are also included in this file.ToDryad.zip
DOI: 10.6084/m9.figshare.30763463.v3
title: <b>Mild decade-warming shifts soil organic carbon composition without altering total stock in temperate and subtropical forests</b>

description: <b>Mild decade-warming shifts soil organic carbon composition without altering total stock in temperate and subtropical forests</b>
DOI: 10.5061/dryad.1m90s
title: Data from: Lianas abundance is positively related with the avian acoustic community in tropical dry forests

description: Dry forests are important sources of biodiversity where lianas are highly
 abundant given their ability to grow during times of drought and as a
 result of secondary growth processes. Lianas provide food and shelter for
 fauna such as birds, but there are no studies assessing the influence of
 liana abundance on birds in dry forests. Here we evaluate the influence of
 liana abundance on the avian acoustic community in the dry forests of
 Costa Rica at Santa Rosa National Park. We selected forest sites with
 different levels of liana abundance and set up automated sound recorders
 for data collection, analysis and estimation of the avian acoustic
 community. When the number of lianas increases, the avian acoustic
 community becomes more complex. Lianas could provide important direct and
 indirect resources for birds such as structure for shelter, protection,
 nesting and roosting, and food. The positive relationship that lianas have
 with birds is particularly important in dry forests where lianas are
 becoming highly abundant due to the level of forest disturbance and
 climate change, especially for some bird species that are restricted to
 this ecosystem. By validating the number of bird species detected in the
 recordings with the acoustic complexity index, we found that a higher
 acoustic complexity means higher species richness.
description: Data from: Lianas
 abundance is positively related with the avian acoustic community in
 tropical dry forestsThe file includes
 information about the name of the forest sites where we evaluated liana
 abundance and the avian acoustic community at Santa Rosa National Park,
 Costa Rica, and also data about the number of lianas (the number of lianas
 divided by the number of trees observed in each plot), the total number of
 sounds detected in recordings, the total number of bird species detected
 in recordings, the Acoustic Complexity Index (ACI) generated from
 recordings, Tree Basal Area, Tree Canopy Height, and Plant Area
 Index.Hilje_et_al_2017.xlsx
DOI: 10.5061/dryad.8n00jc6
title: Data from: Genetic structure and diversity among historic and modern populations of the Sumatran rhinoceros (Dicerorhinus sumatrensis)

description: The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across
 Southeast Asia, now consists of as few as 30 individuals within Sumatra
 and Borneo. To aid in conservation planning, we sequenced 218 bp of
 control region mitochondrial (mt) DNA, identifying 17 distinct
 mitochondrial haplotypes across modern (N = 13) and museum (N = 26)
 samples. Museum specimens from Laos and Myanmar had divergent mtDNA,
 consistent with the placement of western mainland rhinos into the distinct
 subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean
 rhinos were highly diverse, but dissimilar from those of other regions,
 supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos
 from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent
 with their traditional placement into a single subspecies D. s
 sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18
 microsatellite loci. Rhinos within Sumatra formed two sub-populations,
 likely separated by the Barisan Mountains, though with only modest genetic
 differentiation between them. There are so few remaining Sumatran
 rhinoceros that separate management strategies for subspecies or
 subpopulations may not be viable, while each surviving rhino pedigree is
 likely to retain alleles found in no other individuals. Given the low
 population size and low reproductive potential of Sumatran rhinos, rapid
 genetic erosion is inevitable, while an under-appreciated concern is the
 potential for fixation of harmful genetic variants. Both concerns
 underscore two overriding priorities for the species: (1) translocation of
 wild rhinos to ex situ facilities, and (2) collection and storage of
 gametes and cell lines from every surviving captive and wild individual.
description: Dsu
 MicrosatelliteSTR
 DataDsuManuData-Dryad.txtDloop_Hap_SeqHaplotype sequencesFinal All Dsu.fas
DOI: 10.5061/dryad.8jr0b76
title: Data from: Reciprocally-transplanted lizards along an elevational gradient match light-environment use of local lizards via phenotypic plasticity

description: 1. Thermoregulatory behaviour enables ectotherms to maintain preferred
 body temperatures across a range of environmental conditions, and it may
 buffer individuals against the effects of climate warming. In lizards, the
 mechanism underlying variation in thermoregulatory behaviour has long been
 assumed to be phenotypic plasticity, and while this assumption has been
 difficult to test using wild populations in natural habitat, it has
 critical implications for how variation in thermoregulation is
 incorporated in models designed to predict outcomes of climate change on
 ectotherms. 2. We continuously recorded one component of thermoregulatory
 behaviour, light-environment use, by two wild populations of desert
 short-horned lizards (Phrynosoma hernandesi) occurring at low (warm) and
 high (cool) elevations. We then reciprocally transplanted lizards and
 recorded their light-environment use when exposed to a novel climate at
 the transplant site. 3. Immediately following the reciprocal transplant to
 a novel climate, lizards from both populations adjusted their
 light-environment use and matched the light-environment use exhibited by
 local lizards at that site. 4. This study provides direct empirical
 evidence that lizards can immediately adjust light-environment use, one
 component of thermoregulatory behaviour, via phenotypic plasticity to
 match local the local environment. Our results provide hope that lizards
 may have some capacity to buffer against climate change by adjusting their
 light-environment use to compensate for warmer environmental temperatures.
description: proportion of time spent
 in different light environmentsProportion of time
 (sunrise - sunset) spent in each of 6 light environments (buried
 underground, sheltered under cover, in shade, in partial shade, in partial
 sun, in full sun) by adult Phrynosoma hernandesi originating from
 populations at two different elevations (low and high), when at their home
 site and when reciprocally transplanted (i.e.,
 treatment)lizard light data_better
 bins.csvproportion of morning,
 afternoon, evening spent in different light environmentsProportion of morning
 (sunrise - 1100h), afternoon (1101h - 1600h), and evening (1601h - sunset)
 spent in each of 6 light environments (buried underground, sheltered under
 cover, in shade, in partial shade, in partial sun, in full sun) by adult
 Phrynosoma hernandesi originating from populations at two different
 elevations (low and high), when at their home site and when reciprocally
 transplanted (i.e., treatment)lizard light data_time
 bins.csv
DOI: 10.5061/dryad.h6r7p2s
title: Data from: Statistically testing the role of individual learning and decision-making in trapline foraging

description: Trapline foraging, a behavior consisting of repeated visitation to
 spatially fixed resources in a predictable sequence, has been observed
 over diverse taxa and is important ecologically for efficient resource
 gathering. Despite this, few null models exist to test the significance of
 suspected traplines, particularly for studies interested in the role of
 individual decision-making in the formation of traplines versus the role
 of resource layouts and random movement patterns. Here we present a
 spatially explicit, individual-based null model, which may be used to test
 whether resource layout and realistic forager movement may account for
 sequence repeats in suspected traplines. In our model, we generate
 resource visitation sequences by modeling a forager without spatial memory
 using a random walk to discover and visit spatially-fixed resources. We
 quantify traplining using Determinism, a metric derived from recurrence
 quantification analysis. Using both simulated and empirical bee foraging
 data, we compared our model with two existing null models—a completely
 random model and a sample randomization model. The former creates null
 sequences by randomly selecting available resources, while the latter
 randomizes the order of visits in observed sequences. We found that our
 model has a higher propensity of being (correctly) rejected than a sample
 randomization model for trapliners, and a lower propensity of being
 (incorrectly) rejected for non-trapliners compared to a completely random
 model. The use of a spatially explicit individual-based null model to test
 the statistical significance of patterns in empirical data is a novel
 approach that may be useful for other spatial and individual-based
 processes.
description: Emory Bee Foraging
 SequencesThis dataset contains
 bee foraging sequences from a laboratory foraging enclosure at Emory
 University in Atlanta, GA. This dataset contains information for eight
 bees (numbered from one to eight) foraging on 32 artificial flowers
 (numbered from one to 32). Each row represents one flower visit, and the
 rows are sorted chronologically for each bee individual. In column one,
 "bee_num" represents the number of the bee individual. In column
 two "flower_id" represents the ID number of the flower visited,
 and in column three "source" represents the source of the data
 (Emory University).Emory_bee_foraging_sequences.csv
DOI: 10.5061/dryad.8415f
title: Data from: A conceptual framework for clutch size evolution in songbirds

description: Causes of evolved differences in clutch size among songbird species remain
 debated. I propose a new conceptual framework that integrates aspects of
 traditional life history theory, while including novel elements, to
 explain evolution of clutch size among songbirds. I review evidence that
 selection by nest predation on length of time that offspring develop in
 the nest creates a gradient in offspring characteristics at nest-leaving
 (fledging), including flight mobility, spatial dispersion, and
 self-feeding rate. I postulate that this gradient has consequences for
 offspring mortality rates and parental energy expenditure per offspring.
 These consequences then determine how reproductive effort is partitioned
 among offspring, while reproductive effort evolves from age-specific
 mortality effects. Using data from a long-term site in Arizona, as well as
 from the literature, I provide support for hypothesized relationships.
 Nestling development period consistently explains fledgling mortality,
 energy expenditure per offspring, and clutch size while accounting for
 reproductive effort (i.e., total energy expenditure) to thereby support
 the framework. Tests in this paper are not definitive, but they document
 previously unrecognized relationships and address diverse traits
 (developmental strategies, parental care strategies, energy requirements
 per offspring, evolution of reproductive effort, clutch size) that justify
 further investigations of hypotheses proposed here.
description: Arizona field
 dataField data from the
 Arizona site, including species name, proportion of adult wing chord size
 at fledging (propWCfldg), clutch size (cs), nestling period length in days
 (nstl), log10 nestling period, log10 adult mass, aerial foraging (0= no,
 1=yes).Az
 field data.xlsx
DOI: 10.5061/dryad.44954v8f
title: Data from: A taxonomic revision of the North American species of Lepraria s.l. that produce divaricatic acid, with notes on the type species of the genus L. incana.

description: The divaricatic acid-producing populations of Lepraria in North America
 north of Mexico are revised using traditional morphological characters,
 chemistry, ecology, biogeography, and ITS1, 5.8S, and ITS2 sequence data.
 Three taxa are accepted: L. cryophila, L. hodkinsoniana sp. nov., and L.
 pacifica sp. nov. Both Lepraria crassissima and L. incana are excluded
 from the study area. Non-cryptic, semi-cryptic, and fully-cryptic species
 concepts in Lepraria are discussed with a special emphasis on the
 practical integration of molecular characters into taxonomic frameworks
 based on non-molecular characters.
description: incana_data_filesThis is a compressed .zip folder containing three nexus formatted files of DNA sequence alignments used for the molecular phylogenetic analyses in this study. The MP and ML files were input into PAUP. The BI file into MrBayes. Refer to the methods section of the paper for additional explanation.
DOI: 10.5061/dryad.539j4
title: Data from: Emergence of long-term balanced polymorphism under cyclic selection of spatially variable magnitude

description: A fundamental question in evolutionary biology is what promotes genetic
 variation at non-neutral loci, a major precursor to adaptation in changing
 environments. In particular, balanced polymorphism under realistic
 evolutionary models of temporally varying environments in finite natural
 populations remains to be demonstrated. Here, we propose a novel mechanism
 of balancing selection under temporally varying fitnesses. Using
 forward-in-time computer simulations and mathematical analysis, we show
 that cyclic selection that spatially varies in magnitude, such as along an
 environmental gradient, can lead to elevated levels of non-neutral genetic
 polymorphism in finite populations. Balanced polymorphism is more likely
 with an increase in gene flow, magnitude and period of fitness
 oscillations, and spatial heterogeneity. This polymorphism-promoting
 effect is robust to small systematic fitness differences between competing
 alleles or to random environmental perturbation. Furthermore, we
 demonstrate analytically that protected polymorphism arises as spatially
 heterogeneous cyclic fitness oscillations generate a type of storage
 effect that leads to negative frequency-dependent selection. Our findings
 imply that spatially variable cyclic environments can promote elevated
 levels of non-neutral genetic variation in natural populations.
description: Heterogeneous cyclic
 selection simulatorThis C source code
 simulates evolutionary dynamics under heterogeneous cyclic selection in a
 subdivided population. Short description of input files is given in
 comments in the source code.HCS.csample trajectory - drifttrajectorysample parameter filepars1
DOI: 10.5061/dryad.1779g
title: Data from: Changes in area of shallow siliciclastic marine habitat in response to sediment deposition: implications for onshore-offshore paleobiologic patterns

description: Models presented here of shallow-marine siliciclastic deposition show that
 the widths of depth-defined regions differ markedly in response to
 sea-level change. These models add to recent studies that have emphasized
 the highly specific response of habitat area to sea-level change.
 Collectively, these studies indicate that a particular bathymetric zone on
 a particular margin may vary substantially in area during a sea-level
 change, while other such zones and margins may experience little or even
 opposite responses. In the models presented here, intermediate- depth and
 deep-water regions tend to show sinusoidal variations in width, with
 widening during relative falls in sea level and narrowing during relative
 rises. The shallow-water region displays markedly non-sinusoidal change
 and is consistently characterized by abrupt widening at the beginning of
 the highstand systems tract and an equally abrupt narrowing at the onset
 of sea-level fall at the beginning of the falling-stage systems tract.
 These onshore-offshore differences in how width and area change with sea
 level may explain why taxa in shallow- water settings tend to be more
 abundant, eurytopic, and widespread than those in deeper-water settings.
 Likewise, these models suggest that the evolution of novelty in nearshore
 habitats may be a response to wide variation in shallow-marine area during
 sea-level change.
description: R and Matlab code for
 Holland and Christie 2013Contains R and Matlab
 functions for simulating and measuring the changes in the width of
 depth-defined zones during changes in sea levelHollandChristieSupplementaryMaterials.rtf
DOI: 10.6084/m9.figshare.31157041
title: Appendix

description: This section of the appendices systematically presents the complete empirical data and analytical framework that support the conclusions of this paper. The research follows a multidimensional and systematic investigative approach, examining five key levels: the foundational evidence from literature, tourists' individual characteristics, the social environment, physical attributes, and other supplementary factors. Together, these provide a comprehensive exploration of the mechanisms influencing tourist experiences in historic commercial districts. The appendices are interconnected and progressively structured, forming a complete chain of evidence from literature review to empirical validation. This aims to offer solid data support and detailed insights for understanding and optimizing the cultural-tourism integration and scene creation in historic districts.
DOI: 10.5061/dryad.bv0kr
title: Data from: Revision, cladistic analysis and biogeography of Typhochlaena C. L. Koch, 1850, Pachistopelma Pocock, 1901 and Iridopelma Pocock, 1901 (Araneae, Theraphosidae, Aviculariinae)

description: Three aviculariine genera endemic to Brazil are revised. Typhochlaena C.
 L. Koch, 1850 is resurrected, including five species; Pachistopelma
 Pocock, 1901 includes two species; and Iridopelma Pocock, 1901, six
 species. Nine species are newly described: Typhochlaena amma sp. n.,
 Typhochlaena costae sp. n., Typhochlaena curumim sp. n., Typhochlaena
 paschoali sp. n., Pachistopelma bromelicola sp. n., Iridopelma katiae sp.
 n., Iridopelma marcoi sp. n., Iridopelma oliveirai sp. n. and Iridopelma
 vanini sp. n. Three new synonymies are established: Avicularia pulchra
 Mello-Leitão, 1933 and Avicularia recifiensis Struchen & Brändle,
 1996 are junior synonyms of Pachistopelma rufonigrum Pocock, 1901 syn. n.,
 and Avicularia palmicola Mello-Leitão, 1945 is a junior synonym of
 Iridopelma hirsutum Pocock, 1901 syn. n. Pachistopelma concolor
 Caporiacco, 1947 is transferred to Tapinauchenius Ausserer, 1871, making
 the new combination Tapinauchenius concolor (Caporiacco, 1947) comb. n.
 Lectotypes are newly designed for Pachistopelma rufonigrum Pocock, 1901 ,
 Iridopelma hirsutum Pocock, 1901 and Pachistopelma concolor Caporiacco,
 1947. Cladistic analyses using both equal and implied weights were carried
 out with a matrix comprising 62 characters and 38 terminal taxa. The
 chosen cladogram found with X-Pee-Wee and concavity 6 suggests they are
 monophyletic. All species are keyed and mapped and information on species
 habitat and area cladograms are presented. Discussion on biogeography and
 conservation is provided.
description: Bertani
 AviculariinaeMatrix for cladistic
 analysis having all Typhochlaena, Pachistopelma and Iridopelma
 (Aviculariinae) species as well as several other Theraphosidae
 genera