cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.djh9w0vwb
title: Influence of biological and environmental conditions on winter mortality risk of a northern ungulate: evidence for a late-winter survival bottleneck

description: 1. A relationship between winter weather and survival of northern
 ungulates has long been established, yet the possible roles of biological
 (e.g., nutritional status) and environmental (e.g., weather) conditions
 make it important to determine which potential limiting factors are most
 influential. 2. Our objective was to examine the potential effects of
 individual (body mass and age) and extrinsic (winter severity and snow
 melt conditions) factors on the magnitude and timing of mortality for
 adult (&gt;2.5 years old) female white-tailed deer (Odocoileus
 virginianus [Zimmerman, 1780] during February–May in the Upper Peninsula
 of Michigan, USA. 3. One hundred and fifty deer were captured and
 monitored during 2009–2015 in two areas with varying snowfall.
 February–May survival ranged from 0.24–0.89 (mean = 0.69) across years.
 Mortality risk increased 1.9% with each unit increase of cumulative winter
 severity index, decreased 8.2% with each cumulative snow free day, and
 decreased 4.3% with each kg increase in body mass. Age and weekly snow
 depth did not influence weekly deer survival. Predation, primarily from
 coyote (Canis latrans [Say, 1823]) and wolves (Canis lupus [L., 1758]),
 accounted for 78% of known-cause mortalities. 4. Our results suggest that
 cumulative winter severity, and possibly to a lesser degree deer condition
 entering winter, impacted deer winter survival. However, the timing of
 spring snow melt appeared to be the most influential factor determining
 late winter mortality of deer in our study. This supports the hypothesis
 that nutrition and energetic demands from weather conditions are both
 important to northern ungulate winter ecology. Under this model, a delay
 of several weeks in the timing of spring snow melt could exert a large
 influence on deer survival, resulting in a survival bottleneck.
DOI: 10.5061/dryad.6m905qfwb
title: Barn Swallow (Hirundo rustica) fledglings use crop habitat more frequently in relation to its availability than pasture and other habitat types

description: Populations of birds that forage on aerial insects have been declining
 across North America for several decades, but the main causes of and
 reasons for geographical variation in these declines remains unclear. We
 examined the habitat use and survival of post-fledging Barn Swallows
 (Hirundo rustica), near Vancouver, BC, Canada using VHF radio telemetry.
 We predicted that fledgling Barn Swallows hatched in higher quality natal
 habitat (pasture) would fledge at higher quality, stay closest to the
 nest, disproportionately use higher-quality habitat during the post-fledge
 stage and have higher survival rates in the region. Contrary to our
 predictions, we found that natal habitat (crop, pasture or
 non-agriculture) had no effect on fledgling quality or movement distance.
 Barn Swallow fledglings used crop habitat more frequently in relation to
 its availability than other habitat types, including pasture. Barn
 Swallows had low post-fledging survival rates (0.44; 95% CI: 0.35-0.57),
 which could negatively influence the population trend of the species in
 this region. While natal habitat had only minor effects, crop habitat
 appears to be important for fledgling Barn Swallows and therefore a
 decline in this habitat type could have further negative implications for
 an already declining species.
DOI: 10.5061/dryad.00000000r
title: Data from: Genome assembly of Chiococca alba uncovers key enzymes involved in the biosynthesis of unusual terpenoids

description: Chiococca alba (L.) Hitchc. (snowberry), a member of the Rubiaceae, has
 been used as a folk remedy for a range of health issues including
 inflammation and rheumatism and produces a wealth of specialized
 metabolites including terpenes, alkaloids, and flavonoids. We generated a
 558 Mb draft genome assembly for snowberry which encodes 28,707 high
 confidence genes. Comparative analyses with other angiosperm genomes
 revealed enrichment in snowberry of lineage-specific genes involved in
 specialized metabolism. Synteny between snowberry and Coffea canepehora
 Pierre ex A. Froehner (coffee) was evident, including the chromosomal
 region encoding caffeine biosynthesis in coffee, albeit syntelogs of
 N-methyltransferase were absent in snowberry. A total of 27 putative
 terpene synthase genes were identified, including 10 that encode diterpene
 synthases. Functional validation of a subset of putative terpene synthases
 revealed that combinations of diterpene synthases yielded access to
 products of both general and specialized metabolism. Specifically, we
 identified plausible intermediates in the biosynthesis of merilactone and
 ribenone, structurally unique antimicrobial diterpene natural products.
 Access to the C. alba genome will enable additional characterization of
 biosynthetic pathways responsible for health-promoting compounds in this
 medicinal species.
DOI: 10.5061/dryad.ksn02v70w
title: Differences in architecture and performance between two sub-canopy congeneric tropical tree species

description: We report architectural divergence between two congeneric tropical tree
 species coexisting in the same stratum which suggests different
 strategies: reducing self-shading and support costs, or maximizing light
 foraging. We found species-specific differential performance across light
 environments, suggesting that architectural differentiation could
 facilitate the coexistence of species with similar vertical habitat.
description: Data colection details are depicted in the related article.
description: Please, see the related article for details on the names,
 collection and usage of the data. Additional important notes are available
 in the "ReadMe" file.
DOI: 10.5061/dryad.08kprr4zd
title: A molecular phylogenetic evaluation of the Ramalina siliquosa complex, with notes on species circumscription and relationships within Ramalina

description: Lichens of the Ramalina siliquosa complex dominate
 seashore cliffs in Europe and Southeast Asia, but their taxonomy has been
 vigorously debated for over a century. On many cliffs, they exhibit a
 bewildering zonation of chemotypes that resembles the classic zonation of
 organisms that occupy the littoral zone below. Do the chemotypes represent
 separate species, or infraspecific variation? To better understand the
 systematics of this group, sequences from four genetic loci (ITS, IGS RPB1
 and RPB2) were obtained for 59 samples from Denmark, France, Iceland,
 Norway, the UK, Japan and Korea, including all major chemotypes. Maximum
 likelihood analysis of these sequences, together with sequences from 36
 other Ramalina species, reveals that the complex
 comprises two distinct phylogenetic lineages, each including multiple
 chemotypes. These two putative species-level lineages correspond to the
 currently accepted taxa R. cuspidata and R.
 siliquosa. There is no evidence that these two species are phylogenetic
 sister species. Because of this, the explanation of this chemotype complex
 as an example of “sibling speciation” is
 rejected.  Specimens traditionally called
 “R. siliquosa” from Southeast Asia form a third clade, identified
 here as R. semicuspidata, with an additional,
 divaricatic acid chemotype. Other results include a robustly supported
 clade of Ramalina species that produce medullary
 depsides and depsidones; this clade includes another well-supported clade
 of southeastern United States coastal plain and
 tropical Ramalina species. By contrast, large,
 strap-shaped Ramalina species that lack medullary
 depsides and depsidones occur in separate lineages. In addition, close
 relationships between the following groups of species are
 indicated: R. farinacea with R.
 subfarinacea; R. fraxinea with R.
 leptocarpha, R. menziesii and R.
 subleptocarpha; and R. sinensis with R.
 unifolia. Further, a new, variolaric-only chemotype is reported
 for R. farinacea; and a new, acid-deficient chemotype is
 reported for a more broadly circumscribed R. culbersoniorum.
DOI: 10.5061/dryad.15dv41nt5
title: Data from: Negative correlation between dispersal investment and canopy openness among populations of the ant-dispersed sedge, Carex lanceolata

description: Flowering plants exhibit a wide variation in the
 resources they invest in dispersal structures (dispersal effort), but the
 environmental correlates remain unclear in many plants. Canopy openness is
 predicted to be negatively correlated with dispersal effort, because
 selective pressures on increased dispersal effort, including host-specific
 natural enemies and the paucity and/or ephemerality of safe sites, will be
 more prevalent in shady sites. Here, we tested this prediction using an
 ant-dispersed sedge, Carex
 lanceolata (Cyperaceae). By comparing seven
 populations of C. lanceolata in central Japan,
 we found a negative correlation between dispersal effort and canopy
 openness, thus supporting the prediction. A subsequent cafeteria
 experiment showed that a large species of ant (Formica japonica)
 with relatively long seed-dispersal distances tended to prefer diaspores
 with greater dispersal efforts, while smaller ant species with shorter
 dispersal distances preferred diaspores with lower dispersal efforts.
 These results correspond with the assumption that greater dispersal
 efforts result in a greater dispersal ability and indicate that among-site
 variations in dispersal efforts actually reflect differentiation in seed
 dispersal strategy rather than a neutral variation. There were more signs
 of rust infection caused by Puccinia spp., one of the
 main natural enemies of C. lanceolata, on adult plant
 leaves in more shady sites. A seedling transplant experiment was also
 performed and revealed that rust severity in sedge offspring was
 considerably reduced by the typical seed dispersal distance (ca. 4 m)
 afforded by the large ant species, F. japonica. The
 increased rust severity at shady sites, combined with the narrow dispersal
 ranges of rusts, can partially explain the negative correlation of
 dispersal effort with canopy openness. These results support the
 importance of canopy openness as a factor underlying the variations in
 dispersal effort seen among flowering plants.
DOI: 10.5061/dryad.5qfttdz1p
title: Data from: Links between environment and stomatal size through evolutionary time in Proteaceae

description: The size of plant stomata (adjustable pores that determine uptake of CO2
 and loss of water from leaves) is considered to be evolutionarily
 important.  This study uses fossils from the major southern
 hemisphere family Proteaceae to test whether stomatal cell size responded
 to Cenozoic climate change.  We measured the length and abundance
 of guard cells (the cells forming stomata), the area of epidermal pavement
 cells, stomatal index and maximum stomatal conductance from a
 comprehensive sample of fossil cuticles of Proteaceae, and extracted
 published estimates of past temperature and atmospheric CO2.  We
 developed a novel test based on stochastic modelling of trait evolution to
 test correlations among traits.  Guard cell length increased, and
 stomatal density decreased significantly with decreasing
 palaeotemperature.  However, contrary to expectations, stomata
 tended to be smaller and more densely packed at higher atmospheric
 CO2.  Thus, associations between stomatal traits and paleoclimate
 over the last 70 MY in Proteaceae suggest that stomatal size is
 significantly affected by environmental factors other than atmospheric
 CO2.  Guard cell length, pavement cell area, stomatal density,
 stomatal index covaried in ways consistent with coordinated development of
 leaf tissues.
description: The data set includes stomatal and epidermal cell dimensions from
 leaves of fossil and extant species of Proteaceae. The extant species
 represent a phylogenetically and ecologically diverse sample of the
 family. The fossils are all suitably preserved fossils currently known of
 the family.
description: The data has two sections. One set of columns represent fossil
 data, the other data from extant species. The fossil data include some
 missing values.
DOI: 10.5061/dryad.9p8cz8wc5
title: Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data

description: Topological conflict or incongruence is widespread in phylogenomic data.
 Concatenation- and coalescent-based approaches often result in incongruent
 topologies, but the causes of this conflict can be difficult to
 characterize. We examined incongruence stemming from conflict between
 likelihood-based signal (quantified by the difference in gene-wise log
 likelihood score or ΔGLS) and quartet-based topological signal (quantified
 by the difference in gene-wise quartet score or ΔGQS) for every gene in
 three phylogenomic studies in animals, fungi, and plants, which were
 chosen because their concatenation-based IQ-TREE (T1) and quartet-based
 ASTRAL (T2) phylogenies are known to produce eight conflicting internal
 branches (bipartitions). By comparing the types of phylogenetic signal for
 all genes in these three data matrices, we found that 30% - 36% of genes
 in each data matrix are inconsistent, that is, each of these genes has
 higher log likelihood score for T1 versus T2 (i.e., ΔGLS &gt;0)
 whereas its T1 topology has lower quartet score than its T2 topology
 (i.e., ΔGQS &lt;0) or vice versa. Comparison of inconsistent and
 consistent genes using a variety of metrics (e.g., evolutionary rate, gene
 tree topology, distribution of branch lengths, hidden paralogy, and gene
 tree discordance) showed that inconsistent genes are more likely to
 recover neither T1 nor T2 and have higher levels of gene tree discordance
 than consistent genes. Simulation analyses demonstrate that removal of
 inconsistent genes from datasets with low levels of incomplete lineage
 sorting (ILS) and low and medium levels of gene tree estimation error
 (GTEE) reduced incongruence and increased accuracy. In contrast, removal
 of inconsistent genes from datasets with medium and high ILS levels and
 high GTEE levels eliminated or extensively reduced incongruence, but the
 resulting congruent species phylogenies were not always topologically
 identical to the true species trees.
description: This repository contains phylogenetic data matrices, multiple
 sequence alignments, phylogenetic trees, supplementary figures and tables,
 R codes, and the custom Perl scripts used in this study.
 1)    Each folder corresponds to each topic in our
 study.<br> 2)    Example_GLS&GQS_caculation can guide us to
 calculate gene-wise log-likelihood score (GLS) and gene-wise quartet score
 (GQS) for every gene Please let me know if you have any
 question about them at email: xingxingshen@zju.edu.cn.
DOI: 10.4231/5q71-rd12
title: Resonant scattering, metallicity, and redshift (Figures)

description: &lt;p&gt;The warmer gaseous component of the Large Scale Structure of the Universe emits primarily in the X-ray portion of the electromagnetic spectrum, mostly through thermal emission. Resonant scattering of X-ray background radiation by the Warm-Hot Intergalactic Medium (10&lt;sup&gt;5 &lt;/sup&gt;K &lt; T &lt; 10&lt;sup&gt;7&lt;/sup&gt; K), however, can contribute significantly to the amplitude of the resonant emission lines of selected ions (with an increment of more than a factor 30).&lt;/p&gt;

&lt;p&gt;Tables for the emission (thermal and resonant scattering) at different temperature, density, metallicity, and redshift are generated with Cloudy. The comparison between thermal emission and resonant scattering contributions is performed with Jupyter Notebooks.&lt;/p&gt;

&lt;p&gt;All the material related to the published paper is stored in four sets: &ldquo;Cloudy scripts&rdquo;, &ldquo;Jupyter scripts&rdquo;, &ldquo;Data&rdquo;, and &ldquo;Figures&rdquo;. Additional material, that extends beyond the initial investigation, will be stored at a later time (the description will be updated accordingly).&lt;/p&gt;

&lt;p&gt;Figures.&lt;/p&gt;

&lt;p&gt;The &quot;Maps&quot; subset contains the phase diagrams generated by the &ldquo;phase_diagrams&rdquo; script (&ldquo;fig_rho_T*.pdf&rdquo;) and the emission and ratio maps generated by the script &ldquo;Scattering_emission_maps_short&rdquo; (&ldquo;fig_ioname_*.pdf&rdquo;). If the original Cloudy data or the summary data is not required, it is faster to download the figures from this repository.&lt;/p&gt;

&lt;p&gt;The phase diagrams have no units (the pixels show the mass fractions normalized to 1 over the full image).&lt;/p&gt;

&lt;p&gt;The emission maps have units of erg cm&lt;sup&gt;-2&lt;/sup&gt; s&lt;sup&gt;-1&lt;/sup&gt; Hz&lt;sup&gt;-1&lt;/sup&gt;.&lt;/p&gt;

&lt;p&gt;The ratio maps have no units.&lt;/p&gt;

&lt;p&gt;&lt;br /&gt;
The &quot;Graphs&quot; contains one-dimensional cuts of the emission and ratio maps as a function on density, at various temperatures, metallicities, redshifts, and CXB models.&lt;/p&gt;

&lt;p&gt;&lt;br /&gt;
Graphs have the same units as the corresponding maps.&lt;/p&gt;
description: Investigation of the contribution of resonant scattering to the emission of the Warm-Hot gas (10^5 K &lt; T &lt; 10^7 K) in the large scale structure of the Universe. Assessment of the effect of metallicity and redshift.
DOI: 10.5061/dryad.kd51c5b2f
title: Conservation genetics of native and European-introduced Chinese Water Deer (Hydropotes inermis)

description: The Chinese water deer (Hydropotes inermis) belongs to a relatively
 early-divergence lineage of Cervidae and is thought to have retained some
 ancestral features of the group. This species is classified as Vulnerable
 on the IUCN Red List (accessed 2020), and populations in its native range
 have declined drastically in recent years.  However, a
 number of individuals were introduced to the UK about a century ago; these
 have flourished and now make up over 40% of global
 numbers.  To infer the population genetic structure and
 genetic diversity of Chinese water deer both in their native China and in
 populations introduced to the UK and France, mitochondrial DNA sequence
 variation was investigated (control region and cytochrome B) for near 100
 individuals. The distribution of haplotypes among the regions shows
 distinct geographic structure, and only one cytochrome B haplotype was
 common to both China and European populations. Our results reveal
 lower levels of genetic diversity in the British populations,
 differentiation between native and introduced populations, and that the
 source population of British deer is likely to be extinct. Some
 recommendations are made for the conservation of different populations.
DOI: 10.5061/dryad.dr7sqv9vb
title: Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation

description: Some of the most important insights into the ecological and evolutionary
 processes of diversification and speciation have come from studies of
 island adaptive radiations, yet relatively little research has examined
 how these radiations initiate. We suggest that Anolis sagrei is a
 candidate for understanding the origins of the Caribbean Anolis adaptive
 radiation and how a colonizing anole species begins to undergo
 allopatric diversification, phenotypic divergence and, potentially,
 speciation. We undertook a genomic and morphological analysis of
 representative populations across the entire native range of
 A. sagrei, finding that the species originated in the early
 Pliocene, with the deepest divergence occurring between western and
 eastern Cuba. Lineages from these two regions subsequently colonized the
 northern Caribbean. We find that at the broadest scale, populations
 colonizing areas with fewer closely related competitors tend to evolve
 larger body size and more lamellae on their toepads. This trend follows
 expectations for post‐colonization divergence from progenitors and
 convergence in allopatry, whereby populations freed from competition with
 close relatives evolve towards common morphological and ecological optima.
 Taken together, our results show a complex history of ancient and recent
 Cuban diaspora with populations on competitor‐poor islands evolving away
 from their ancestral Cuban populations regardless of their phylogenetic
 relationships, thus providing insight into the original diversification of
 colonist anoles at the beginning of the radiation. Our research also
 supplies an evolutionary framework for the many studies of this
 increasingly important species in ecological and evolutionary research.
DOI: 10.5061/dryad.tdz08kpw8
title: Morphological variation in the Vriesea procera complex (Bromeliaceae, Tillandsioideae) in the Brazilian Atlantic Rainforest, with recognition of new taxa

description: The family Bromeliaceae is essentially Neotropical, with high endemism and
 diversity in the Atlantic Rainforest Domain. Species circumscription is a
 major problem in the family systematics, especially in the most diverse
 genera. Species of the Vriesea procera complex, which occur in forests and
 restinga (coastal vegetation) along the South American Atlantic coast from
 Venezuela to southern Brazil, share the same basic vegetative and
 reproductive morphological patterns. However, they vary widely in the
 number and position of inflorescence branches as well as in the
 dimensions, position, and shape of the leaves and flowers in different
 populations. Here we aimed (i) to evaluate the morphological variation in
 the V. procera complex, through morphometric analyses of natural
 populations along the Brazilian Atlantic Rainforest; and (ii) to determine
 the taxonomic relationships among these species, establishing the validity
 and the limits of variation of the taxa through taxonomic treatment.
 Fourteen natural populations, 271 individuals and 36 morphometric
 variables were analyzed. Kruskal-Wallis tests and discriminant analyses
 were conducted to test statistical differences between previously
 established groups. Of an original three species and three varieties, our
 data allowed us to recognize six species, including three new taxa and one
 new name and status. The resulting taxa are distinguished by the
 inflorescence and leaf sizes and especially by floral characteristics such
 as the length of bracts, sepals, petals, stamens, and pistils, besides the
 petal apex posture and relative position of the stamen during anthesis.
 Recognition of cryptic species under the names V. procera and V.
 neoglutinosa is an important step toward a better understanding of the
 biodiversity of the Brazilian Atlantic Rainforest.