cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mgqnk98vt
title: Data from: Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

description: Plastid gene loss and pseudogenization has been widely documented in
 parasitic and mycoheterotrophic plants, which have relaxed selective
 constraints on photosynthetic function. More enigmatic are sporadic
 reports of degradation and loss of important photosynthesis genes in
 lineages thought to be fully photosynthetic. Here we report the complete
 plastid genome of Saniculiphyllum guangxiense, a critically endangered and
 phylogenetically isolated plant lineage, along with genomic evidence of
 reduced chloroplast function. We also report 22 additional plastid genomes
 representing the diversity of its containing clade Saxifragales,
 characterizing gene content and placing variation in a broader
 phylogenetic context. We find that the plastid genome of Saniculiphyllum
 has experienced pseudogenization of five genes of the NDH complex (ndhA,
 ndhB, ndhD, ndhF, and ndhK), previously reported in flowering plants with
 an aquatic habit, as well as the more surprising pseudogenization of two
 genes more central to photosynthesis (ccsA and cemA), contrasting with
 strong phylogenetic conservatism of plastid gene content in all other
 sampled Saxifragales. These genes participate in photooxidative
 protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs
 exist for all seven plastid pseudogenes, yet these are also unlikely to be
 functional. Saniculiphyllum appears to represent the greatest degree of
 plastid gene loss observed to date in any fully photosynthetic lineage,
 yet plastid genome length, structure, and substitution rate are within the
 variation previously reported for photosynthetic plants. These results
 highlight the increasingly appreciated dynamism of plastid genomes,
 otherwise highly conserved across a billion years of green plant
 evolution, in plants with highly specialized life history traits.
description: <strong>Alignments</strong>
 Individual alignments of chloroplast orthologs and the
 nuclear <em>Saniculiphyllum </em>paralogs are in the following
 files:  ndhK.fasta<br> ndhD.fasta<br>
 ndhF.fasta<br> cemA.fasta<br> ndhB.fasta<br>
 ccsA.fasta<br> ndhA.fasta<br>   The
 chloroplast tree alignment is chloroplast_alignment.phy, with the
 partition file at chloroplast_alignment_partition_FINAL.txt, and the
 resultant topology at RAxML_bipartitions.saniculiphyllum.tre. A version
 preserving the gene annotations is at
 allchloroplast_RAFedited.geneious.  
 <strong>Gene trees</strong> The
 plastid gene tree topologies with nuclear paralogs are at:
 RAxML_bipartitions.ndhA.reduced.tre<br>
 RAxML_bipartitions.ndhK.reduced.tre<br>
 RAxML_bipartitions.cemA.reduced.tre<br>
 RAxML_bipartitions.ccsA.reduced.tre<br>
 RAxML_bipartitions.ndhF.reduced.tre<br>
 RAxML_bipartitions.ccsA.tre<br>
 RAxML_bipartitions.ndhD.tre
DOI: 10.25338/b86p54
title: Differing, multi-scale landscape effects on genetic diversity and differentiation in eastern chipmunks

description: Understanding how habitat loss and fragmentation impact genetic variation
 is a major goal in landscape genetics, but to date, most studies have
 focused solely on the correlation between intervening matrix and genetic
 differentiation at a single spatial scale. Several caveats exist in these
 study designs, among them is the inability to include measures of genetic
 diversity in addition to differentiation. Both genetic metrics help
 predict population persistence, but are expected to function at differing
 spatial scales, which requires a multi-scale investigation. In this study,
 we sampled two distinct spatial scales in 31 independent landscapes along
 a gradient of landscape context (i.e., forest amount, configuration, and
 types of intervening matrix) to investigate how landscape heterogeneity
 influences genetic diversity and differentiation in the forest-associated
 eastern chipmunk (Tamias striatus). Overall, quality of intervening matrix
 was correlated with genetic differentiation at multiple spatial scales,
 whereas only configuration was associated with regional scale genetic
 diversity. Habitat amount, in contrast, did not influence genetic
 differentiation or diversity at either spatial scale. Based on our
 findings, landscape effects on genetic variation appears to differ based
 on spatial scale, the type of genetic response variable, and random
 variation among landscapes, making extrapolation of results from single
 scale, un-replicated studies difficult. We encourage landscape geneticists
 to utilize multi-scale, replicated landscapes with both genetic diversity
 and differentiation to gain a more comprehensive understanding of how
 habitat loss and fragmentation influence genetic variation.
description: These datafiles contain all landscape and genetic data for
 chipmunks sampled across the Upper Wabash Valley, Indiana, USA. Our
 analyses were conducted at two spatial scales: “Regional Scale” and “Local
 Scale”, so descriptions are provided for each datafile in the ReadMe.
 Please see FragStats documentation and manuscript text for further
 definitions of each landscape statistic.
DOI: 10.5061/dryad.d2547d7z5
title: An atypical mating system in a neotropical manakin

description: Most of the diversity of in the mating systems of birds and other animals
 come at higher taxonomic levels, such as across orders. Although divergent
 selective pressures should lead to animal mating systems that diverge
 sharply from those of close relatives, opportunities to examine the
 importance of such processes are scarce. We addressed this issue using the
 Araripe manakin (Antilophia bokermanni), a species endemic to a forest
 enclave surrounded by xeric shrublands in Brazil. Most manakins exhibit
 polygynous lekking mating systems that lack territoriality but exhibit
 strong sexual selection. In sharp contrast, we found that male Araripe
 manakins defended exclusive territories, and females nested within male
 territories. However, territoriality and offspring paternity were
 dissociated: males did not sire most young within their territories, and
 nonterritorial males sired numerous nestlings. Moreover, female polyandry
 was widespread, with most broods exhibiting mixed paternity. Apparently,
 territories in this species function differently from both lekking arenas
 and resource-based territories of monogamous species. The unexpected
 territoriality of Araripe manakins and its dissociation from paternity is
 a unique evolutionary development within the manakin clade. Collectively,
 our findings underscore how divergences in mating systems might evolve
 based on selective pressures from novel environmental
 contexts.  
description: Field data were collected in the Araripe plateau in northeastern
 Brazil. Birds were mist-netted and morphological measurements were taken.
 Blood samples were collected from all captured adults. Nests were found
 and monitored, and when nestlings hatched, blood samples were collected.
 We extracted DNA from blood samples using a standard extraction protocol
 (QIAGEN®) and sexed adults and nestlings with the primer set 2550F/2718R.
 We genotyped samples from chicks using 15 polymorphic microsatellite
 markers and ran paternity analysis in Cervus 3.0.0. Details are presented
 in the electronic supplementary material with the manuscript.
DOI: 10.5061/dryad.p5hqbzkkh
title: Migration takes extra guts for juvenile songbirds: energetics and digestive physiology during the first journey

description: Many birds undertake long migrations when they are only a few months of
 age. Although they are typically of adult body size, their performance and
 survival are often poor compared to adults. This differential performance
 could be due to lack of experience, selection against poor-performing
 cohort members, or inherent constraints of continuing physiological and
 morphological maturation of juveniles. Limited evidence suggests that
 digestive and muscle physiology of juveniles during their first migration
 may differ from that of adults. We compared body composition, metabolic
 rate, and digestive physiology between juvenile and adult passerines
 during fall migration. First, we measured fat and lean masses by
 quantitative magnetic resonance, and organ and muscle masses of salvaged
 carcasses of fall migrants from four passerine species. In general,
 juveniles had more lean mass and heavier digestive organs (especially
 liver) than adults in hermit thrushes (Catharus guttatus), Swainson’s
 thrushes (Catharus ustulatus), ovenbirds (Seiurus aurocapilla), and
 white-throated sparrows (Zonotrichia albicollis). Principal components
 analysis of all organs and muscles revealed that juveniles for three of
 four species had overall larger digestive components and smaller flight
 muscles than adults. We then used open-flow respirometry to measure basal
 metabolic rates (BMRs) of juvenile and adult Swainson’s thrushes and
 white-throated sparrows captured in fall at a migratory stopover site.
 Controlling for a significant effect of body mass, juveniles had 6% higher
 BMRs than adults in both species. We then conducted total collection mass
 balance feeding trials with fall migratory Swainson’s thrushes and
 white-throated sparrows. Juvenile thrushes had greater metabolizable
 energy intake than adults, which was achieved through higher food intake
 rather than greater utilization efficiency. Age classes of white-throated
 sparrows did not differ in these measures of digestive performance,
 although juveniles had greater food intake capacity at low lean body
 masses. We propose that age-related differences in foraging ecology, diet
 composition and energy requirements may be responsible for larger
 digestive organs of juvenile migrants. Larger guts may allow juveniles to
 consume more food or a more dilute diet, but may contribute to higher
 BMRs.
description: The data were collected from migrating birds in the field. They
 are measurements of body composition, metabolic rate and digestive
 parameters. There are 3 CSV files, each with a readme file.
DOI: 10.5061/dryad.73n5tb2s7
title: Data from: Nest association between two predators as a behavioral response to the low density of rodents

description: Many birds nest in association with aggressive birds of other species to
 benefit from their protection against predators. We hypothesized that the
 protective effect also could extend to foraging resources, whereby the
 resultant resource enriched habitats near a nest of aggressive raptors
 could be an alternative cause of associations between nesting bird species
 with non-overlapping foraging niches. In the Arctic, the Rough-legged Hawk
 (Buteo lagopus) and the Peregrine Falcon (Falco peregrinus) are 2 raptor
 species with non-overlapping food resources that have been reported to
 nest sometimes in close proximity. Since nesting Peregrine Falcons are
 very aggressive, they may protect the small rodent prey near their nests
 from predation, and Rough-legged Hawks could use these hot spots as a
 nesting territory. In 2 regions in low Arctic Russia we found that (1) the
 nesting territories of Peregrine Falcons were indeed enriched with small
 rodents as compared to control areas, (2) the probability of nest
 association between the 2 raptors increased when rodent abundance was
 generally low in the region where hawks did not use alternative prey, and
 (3) hawk reproductive success increased when nesting close to Peregrine
 Falcons. These results suggest that implications of aggressive nest site
 defense in birds in certain cases may involve more mechanisms than
 previously explored. A key ecological process in tundra, rodent population
 cycles, may explain the occurrence and adaptive significance of a specific
 behavior pattern, the nesting association between 2 raptor species.
DOI: 10.5061/dryad.v6wwpzgqw
title: Evolutionary rates are correlated between cockroach symbiont and mitochondrial genomes

description: Bacterial endosymbionts evolve under strong host-driven selection. Factors
 influencing host evolution might affect symbionts in similar ways,
 potentially leading to correlations between the molecular evolutionary
 rates of hosts and symbionts. Although there is evidence of rate
 correlations between mitochondrial and nuclear genes, similar
 investigations of hosts and symbionts are lacking. Here we demonstrate a
 correlation in molecular rates between the genomes of an endosymbiont
 (Blattabacterium cuenoti) and the mitochondrial genomes of their hosts
 (cockroaches). We used partial genome data for multiple strains
 of B. cuenotito compare phylogenetic relationships and
 evolutionary rates for 55 cockroach/symbiont pairs. The
 phylogenies inferred for B. cuenoti and the
 mitochondrial genomes of their hosts were largely congruent, as expected
 from their identical maternal and cytoplasmic mode of inheritance. We
 found a correlation between evolutionary rates of the two genomes, based
 on comparisons of root-to-tip distances and on comparisons of branch
 lengths of phylogenetically independent species pairs. Our results
 underscore the profound effects that long-term symbiosis can have on the
 biology of each symbiotic partner.
DOI: 10.25345/c5br8mw0b
title: MassIVE MSV000100605 - UV induces common cutaneous amyloid like aggregates derived from melanosomal proteins
title: We use immunostaining, electron microscopy, and mass spectrometry in primary human melanocytes, clinical samples, and a novel mouse model, to substantiate that alpha synuclein is also present in melanin-containing protein aggregates in a range of pigmentary disorders bound to many of the same proteins as in Parkinsons disease.
DOI: 10.5061/dryad.rxwdbrv40
title: Data from: Mortality and morphology in egg masses of unisexual and Jefferson Salamanders

description: Unisexual Ambystoma salamander egg masses have often been observed to
 exhibit very high rates of embryo mortality. The ecological consequences
 and underlying mechanisms are of great concern to researchers and managers
 studying these and other members of the species complex, all of which are
 listed as rare species throughout much of their range. Substantial embryo
 mortality is commonly used by field ecologists as an indicator that
 unisexual salamanders are present in a pond; egg masses of unisexual
 salamanders appear otherwise very similar to those of A. jeffersonianum
 (Jefferson Salamander). Early researchers suggested that elevated
 mortality among unisexual salamanders was due to lack of fertilization
 caused by sperm limitation. However, recent work has suggested that embryo
 failure is due to genetic errors particular to the unisexual salamander
 lineage. Our goals in this study were to (1) identify when during
 development embryonic mortality occurs in unisexual salamanders, and (2)
 to develop a morphological metric to distinguish egg masses of unisexual
 and Jefferson salamanders. Collecting from sites across western
 Massachusetts, we reared 356 eggs from 11 egg masses of known species
 identity in the laboratory, examined field photographs of 96 egg
 masses of known species identity (based on mitochondrial sequencing and 6
 microsatellite alleles), and examined 757 field photographs of egg masses
 of unknown species identity.  We developed a simple,
 scale-independent metric to distinguish Jefferson Salamander egg masses
 from those of co-occurring unisexual salamanders. Among developing embryos
 beyond the earliest stages, we found no difference in mortality rates
 between unisexual salamanders and Jefferson Salamanders. However, we
 observed a large pulse of embryo mortality in the earliest stages of
 development, followed by a trickle of additional mortality at later
 stages. Our results suggest that the primary cause of embryo mortality in
 Massachusetts populations of unisexual salamanders involves failure of
 embryos to initiate development.
DOI: 10.5061/dryad.kkwh70s15
title: Data from: Nanoaperture fabrication via colloidal lithography for single molecule fluorescence analysis

description: In single molecule fluorescence studies, background emission from labeled
 substrates often restricts their concentrations to non-physiological
 nanomolar values. One approach to address this challenge is the use of
 zero-mode waveguides (ZMWs), nanoscale holes in a thin metal film that
 physically and optically confine the observation volume allowing much
 higher concentrations of fluorescent substrates. Standard fabrication of
 ZMWs utilizes slow and costly E-beam nano-lithography. Herein, ZMWs are
 made using a self-assembled mask of polystyrene microspheres, enabling
 fabrication of thousands of ZMWs in parallel without sophisticated
 equipment. Polystyrene 1 μm dia. microbeads self-assemble on a glass slide
 into a hexagonal array, forming a mask for the deposition of metallic
 posts in the inter-bead interstices. The width of those interstices (and
 subsequent posts) is adjusted within 100–300 nm by partially fusing the
 beads at the polystyrene glass transition temperature. The beads are
 dissolved in toluene, aluminum or gold cladding is deposited around the
 posts, and those are dissolved, leaving behind an array ZMWs. Parameter
 optimization and the performance of the ZMWs are presented. By using
 colloidal self-assembly, typical laboratories can make use of
 sub-wavelength ZMW technology avoiding the availability and expense of
 sophisticated clean-room environments and equipment.
DOI: 10.5061/dryad.nvx0k6dn1
title: Presence-absence sampling for estimating plant density using survey data with variable plot size

description: 1. Presence-absence sampling is an important method for monitoring state
 and change of both individual plant species and communities. With this
 method only the presence or absence of the target species is recorded on
 plots and thus the method is straightforward to apply and less prone to
 surveyor judgment compared to other vegetation monitoring methods.
 However, in the basic setting all plots must be equally large or otherwise
 it is unclear how data should be analyzed. In this study we propose and
 evaluate five different methods for estimating plant density based on
 presence-absence registrations from surveys with variable plot sizes. 2.
 Using artificial plant population data as well as empirical data from the
 Swedish National Forest Inventory we evaluated the performance of the
 proposed methods. The main analysis was conducted through sampling
 simulation in the artificial populations, whereby bias and variance of
 density estimators for the different methods were quantified and compared.
 3. Both for state and change estimation of plant density, we found that
 the best method to handle variable plot size was to perform generalized
 least squares regression, using plot size as an independent variable.
 Methods where plots smaller than a certain threshold were excluded or
 their registrations recalculated were, however, almost as good. Using all
 registrations as if they were obtained from plots with the nominal plot
 size resulted in substantial bias. 4. Our findings are important for plant
 population studies in a wide range of environmental monitoring programmes.
 In these programmes plots are typically randomly laid out and may be
 located across boundaries between different land use or land cover
 classes, resulting in subplots of variable size. Such splitting of plots
 is common when large plots are used, e.g. with the 100 m2 plots used in
 the Swedish National Forest Inventory. Our methods overcome problems to
 estimate plant density from presence-absence data observed in plots that
 vary in size.
DOI: 10.15139/s3/slwvcv
title: Data Management and Sharing Plan for: Suppression of progesterone receptor signaling by heavy metals promotes tamoxifen resistance and metastasis or ER+ breast cancer

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.wdbrv15j4
title: Genomic relatedness and diversity of Swedish native cattle breeds

description: Background Native cattle breeds are important genetic resources given
 their adaptation to the local environment in which they are bred. However,
 the widespread use of commercial cattle breeds has resulted in a marked
 reduction in population size of several native cattle breeds worldwide.
 Therefore, conservation management of native cattle breeds requires urgent
 attention to avoid their extinction. To this end, we genotyped nine
 Swedish native cattle breeds with genome-wide 150K single nucleotide
 polymorphisms (SNPs) to investigate the level of genetic diversity and
 relatedness between these breeds. Results We used various SNP-based
 approaches on this dataset to connect the demographic history with the
 genetic diversity and population structure of these Swedish cattle breeds.
 Our results suggest that the Väne and Ringamåla breeds originating from
 southern Sweden have experienced population isolation and have a low
 genetic diversity, whereas the Fjäll breed has a large founder population
 and a relatively high genetic diversity. Based on the shared ancestry and
 the constructed phylogenetic trees, we identified two major clusters in
 Swedish native cattle. In the first cluster, which includes Swedish
 mountain cattle breeds, there was little differentiation among the Fjäll,
 Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster
 consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red.
 Interestingly, we also identified sub-structuring in the Fjällnära breed,
 which indicates different breeding practices on the farms that maintain
 this breed. Conclusions This study represents the first comprehensive
 genome-wide analysis of the genetic relatedness and diversity in Swedish
 native cattle breeds. Our results show that different demographic patterns
 such as genetic isolation and cross-breeding have shaped the genomic
 diversity of Swedish native cattle breeds and that the Swedish mountain
 breeds have retained their authentic distinct gene pool without
 significant contribution from any of the other European cattle breeds that
 were included in this study.