cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q2bvq83k9
title: Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans

description: The germ line produces gametes that transmit genetic and epigenetic
 information to the next generation. Maintenance of germ cells and
 development of gametes require germ granules—well-conserved membraneless
 and RNA-rich organelles. The composition of germ granules is elusive owing
 to their dynamic nature and their exclusive expression in the germ line.
 Using C. elegans germ granule, called P granule, as a model system, we
 employed a proximity-based labeling method in combination with mass
 spectrometry to comprehensively define its protein components. This set of
 experiments identified over 200 proteins, many of which contain
 intrinsically disordered regions. An RNAi-based screen identified factors
 that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two
 putative LOTUS-domain proteins. Loss of eggd-1 and eggd-2 results in
 separation of P granules from the nuclear envelope, germline atrophy and
 reduced fertility. We show that intrinsically disordered regions of EGGD-1
 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS
 domains are required to promote perinuclear localization of P granules.
 Together, our work expands the repertoire of P granule constituents and
 provides new insights into the role of LOTUS-domain proteins in germ
 granule organization.
description: See details in Materials and
 Methods
description: File "Figure 1-Source Data 1" Source data file for
 Figure 1B. File "Figure 1-Source Data
 2-uncropped_blot_images.zip" for uncropped blots of Figure
 1C. File "Figure 1-figure supplement 1-Source data
 1-uncropped_blot_images.zip" for uncropped blots of Figure 1—figure
 supplement 1B. File "Figure 2-Source Data 1"
 Source data file for Figure 2A. File "Figure
 2-Source Data 2" Source data file for Figure 2E and Figure
 2F. File "Figure 3-Source Data 1" Source data
 file for Figure 3D. File "Figure 3-Source Data
 2" Source data file for Figure 3E. File
 "Figure 3-Source Data 3" Source data file for Figure
 3F. File "Figure 3-Supplement 1-Source Data
 1" Source data file for Figure 3-Supplement 1E.
 File "Figure 4-Source Data 1" Source data file for
 Figure 4A and 4B. File "Figure 4-Source Data
 2" Source data file for Figure 4E.
DOI: 10.5061/dryad.z08kprrd5
title: Evolutionary history of quadrupedal walking gaits shows mammalian release from locomotor constraint

description: Vertebrates employ an impressive range of strategies for coordinating
 their limb movements while walking. Although this gait variation has been
 quantified and hypotheses for its origins tested in select tetrapod
 lineages, a comprehensive understanding of gait evolution in a
 macroevolutionary context is currently lacking. We used freely-available
 internet videos to nearly double the number of species with quantitative
 gait data and used phylogenetic comparative methods to test key hypotheses
 about gait origin and evolution. We find strong support for an ancestral
 Lateral-Sequence Diagonal-Couplet gait in gnathostomes, and this mode is
 remarkably conserved throughout tetrapod phylogeny. Evolutionary rate
 analyses show that mammals overcame this ancestral constraint, resulting
 in a greater range of gait values than any other tetrapod lineage.
 Diagonal-Sequence Diagonal-Couplet gaits are significantly associated with
 arboreality in mammals, though this relationship is not recovered for
 other tetrapod lineages. Notably, the Lateral-Sequence Lateral-Couplet
 gait, unique to mammals among extant tetrapods, is not associated with any
 traditional explanations. The complex drivers of gait diversification in
 mammals remain unclear, but our analyses suggest that their success was
 due, in part, to released from a locomotor constraint that has likely
 persisted in other extant tetrapod lineages for over 375 million years.
DOI: 10.25338/b8jp70
title: Annotated checklist of the vascular plants of Swanton Pacific Ranch

description: The Swanton Pacific Ranch (SPR) is located north of the town of Davenport,
 in Santa Cruz County, California, and is owned by California Polytechnic
 State University, San Luis Obispo. SPR is approximately 1,295 ha and
 contains areas of salt marsh, coastal prairie, coastal bluff scrub,
 northern coastal scrub, riparian forest, redwood forest, mixed evergreen
 forest, and chaparral. The property extends over an elevational gradient
 from 0 m to 420 m. In this study, we conducted a floristic inventory at
 SPR and documented 635 taxa. Between 2017 and 2019 we vouchered 546 taxa
 with 974 specimens. We were unable to locate 63 taxa that had been
 previously reported, 27 represented from historic collections and 36
 represented by personal observations but lacking vouchers.  We
 relocated, but did not collect, 26 taxa known from previous collections.
 Overall, we documented 93 families at SPR, with Asteraceae, Poaceae, and
 Fabaceae having the most species, respectively. California rare taxa,
 listed by the California Native Plant Society, made up 2.5% of the flora
 (N = 18). Locally rare taxa made up 10% of the flora (N = 65). Non-native
 taxa made up 26% of the flora (N = 169). We vouchered one new taxon for
 Santa Cruz County, Senecio aphanactis DC., which has a California Rare
 Plant Rank of 2B.2; documented a new occurrence of Hesperocyparis
 abramsiana (C.B. Wolf) Bartel var. abramsiana, a Federally Threatened
 conifer; and collected a form of Sanicula crassicaulis Poepp. ex DC that
 we believe should be recognized as a distinct variety. Overall, this
 relatively small coastal ranch contained approximately 10% of the flora of
 California. The 2020 CZU Lightning Complex Fire burned ca. 90% of SPR
 within a year of this study being completed. This opens the possibility
 for this study to be used as a baseline for future studies examining
 postfire shifts in plant diversity at a landscape scale.
description: This dataset was represents vascular plant species that have been
 collected and made into voucher speciemens or in some cases observed but
 not collected by the authors. Species were identified by the authors with
 the aid of experts when neccesary.
DOI: 10.5061/dryad.j3tx95xf2
title: Does lake eutrophication support biological invasions in rivers? A study on Dreissena polymorpha (Bivalvia) in lake-river ecotones

description: The zebra mussel (Dreissena polymorpha) has all traits required to
 effectively colonize the aquatic environment and consequently reduce the
 diversity of native bivalves We hypothesized that the zebra mussel chooses
 lake outlets characterized by medium current velocity and good food
 conditions. Here, we analyzed differences between bivalve abundances in
 lake outlets with varying environmental conditions such as the Carlson
 Index (trophy status), depth, width, current velocity, bed vegetation
 coverage, and type of bottom substrate. The results showed that the zebra
 mussel inhabits outlets that provide food (high trophy outlets) and have a
 mineral bed and a medium current velocity (ca. 0.2–0.3 m s-1). The
 following main factors seem to be favorable for colonizing such outlets:
 (1) easy access to high amounts of food due to the increased density of
 the suspension drifting from the lake and (2) easy transport of the zebra
 mussel larvae from the lake to the downstream. The zebra mussel larvae
 drifting with the current may colonize the downstream. An increase in lake
 trophy may indirectly cause an increase in biological invasions in rivers.
description: The study was performed in the catchment area of the Drawa River
 (GPS: 53°20ʹ25ʺ N; 15°46ʹ30ʺ E – the middle Drawa), which is a 190-km-long
 quaternary tributary of the Odra River. Samples of bivalves were collected
 from 55 lake outlets in July 2016. An area of approximately 50
 m<sup>2</sup> was selected for the study, starting from the
 shoreline of the lake downstream. Samples of macrozoobenthos were
 collected at the point where the water current changed from the cumulative
 to the rectilinear. The samples were collected using a Surber sampler
 (sampling surface 0.0625m<sup>2</sup>) by disturbing the
 bottom at 4 places: 2 places were located at the middle of the outlet and
 one at each shore. All samples were joined together as one sample. The
 abundance of the organisms was counted per square meter. We decided to use
 a Surber sampler because of the small size of Sphaeriidae clams. To avoid
 “double zeros,” an entire 50-m section of the outlet was checked for the
 absence of dreissenids.
DOI: 10.5061/dryad.np5hqbztd
title: From individual to population level: Temperature and snow cover modulate fledging success through breeding phenology in Greylag geese (Anser anser)

description: Local weather conditions may be used as environmental cues by animals to
 optimize their breeding behaviour, and could be affected by climate
 change. We measured associations between climate, breeding phenology, and
 reproductive output in greylag geese (Anser anser) across 29 years
 (1990-2018). The birds are individually marked, which allows accurate
 long-term monitoring of life-history parameters for all pairs within the
 flock. We had three aims: (1) identify climate patterns at a local scale
 in Upper Austria, (2) measure the association between climate and greylag
 goose breeding phenology, and (3) measure the relationship between climate
 and both clutch size and fledging success. Ambient temperature increased
 2°C across the 29-years study period, and higher winter temperature was
 associated with earlier onset of egg-laying. Using the hatch-fledge ratio,
 average annual temperature was the strongest predictor for the proportion
 of fledged goslings per season. There is evidence for an optimum time
 window for egg-laying (the earliest and latest eggs laid had the lowest
 fledging success). These findings broaden our understanding of
 environmental effects and population-level shifts which could be
 associated with increased ambient temperature and can thus inform future
 research about the ecological consequences of climate changes and
 reproductive output in avian systems.
description: Data were collected over 29 years, from 1990 to 2018, in the Alm
 valley, Austria, during which period the greylag geese flock consisted of
 on average 149.14 individuals (SD = 15.64). All data (egg-laying, clutch
 size, hatching success, fledging success) were recorded 2-3 times per week
 during the reproductive season of the geese (approx. mid Feb. to end of
 July). During the mating period, the breeding huts and the traditional
 nesting locations were checked every two days, eggs weighed, measured and
 numbered according to their laying sequence. Later on, during the rearing
 phase, individual families were monitored every two days and the number of
 the accompanying offspring (i.e., goslings) was documented. The start of
 egg-laying was calculated as follows: (a) at pair level, the ordinal date
 of the first laid egg was used; (b) at flock level, the ordinal date of
 the first egg laid by the first breeding pair was used. In addition to the
 timing of egg-laying, we recorded (c) clutch size, and (d) ‘gosling
 survival’ (i.e., the ratio between the number of fledged goslings and the
 number of hatched eggs).
DOI: 10.5061/dryad.xwdbrv1ds
title: 35,000-year record of pollen, charcoal and NPP from Bass Strait, southeast Australia

description: We reconstruct the last glacial vegetation (pollen record), fire (charcoal
 record) and lake levels (NPP record) for Bass Strait. Results show the
 Bass Strait area was characterized by Eucalyptus woodland and shrubland
 vegetation, with high fire activity and lake levels from 35,000 to 29,000
 years ago. Grassland expanded at the expense of woodland after this
 period, with a decline in fire activity and lake levels.
description: <b>Sediment core
 locations</b> Crystal Lagoon (-40.477381°,
 148.350799°, ~8 m asl), truwana/Cape Barren Island, Bass Strait, southeast
 Australia. <b>Methods</b> For pollen analysis, samples were taken from sediment cores at 2–4-cm intervals and samples were processed following standard pollen preparation procedures, which included HCl, KOH and acetolysis treatments. At least 300 terrestrial pollen grains were identified on slides except for a few depths (60 and 64 cm) with extremely low pollen concentrations in which at least 100 pollen grains were counted. Pollen and spores were identified using the Australasian Pollen and Spore Atlas (http://apsa.anu.edu.au/) and PalaeoWorks reference collections at the Australian National University’s Archaeology and Natural History Laboratory. Microscopic charcoal particles (&lt;125 µm) were also counted on pollen slides. For macrocharcoal ( &gt;125 µm) analysis, contiguous sediment samples were taken from core and analysed, following the method of Whitlock & Larsen (2001). Chronology is based on eight Accelerator Mass Spectrometry (AMS) <sup>14</sup>C dates and age-depth model was created using ‘rbacon’, with SHCal20 calibration curve. Reference Whitlock, C., & Larsen, C. (2001). Charcoal as fire proxy. In J. P., Smol, et al. (Eds.), <i>Tracking environmental change using lake sediments: terrestrial, algal, and siliceous indicators, </i>3. Kluwer Academic Publishers, Dordrecht, The Netherlands.
DOI: 10.5061/dryad.sj3tx965f
title: Data From: Fear conditioning potentiates the Hippocampal CA1 commissural pathway In vivo and increases awake phase sleep

description: The hippocampus is essential for spatial learning and memory. To assess
 learning we used contextual fear conditioning (cFC), where animals learn
 to associate a place with aversive events like foot-shocks. Candidate
 memory mechanisms for cFC are long-term potentiation and long-term
 depression, but there is little direct evidence of them operating in the
 hippocampus in vivo following cFC. Also, little is known about the
 behavioral state changes induced by cFC. To address these issues, we
 recorded local field potentials in freely behaving mice by stimulating in
 the left dorsal CA1 region and recording in the right dorsal CA1 region.
 Synaptic strength in the commissural pathway was monitored by measuring
 field excitatory postsynaptic potentials (fEPSPs) before and after cFC.
 After cFC, the commissural pathway’s synaptic strength was potentiated.
 Although recordings occurred during the wake phase of the light/dark
 cycle, the mice slept more in the post-conditioning period than in the
 pre-conditioning period. Relative to awake periods, in non-rapid eye
 movement (NREM) sleep the fEPSPs were larger in both pre- and
 post-conditioning periods. We also found a significant negative
 correlation between the animal’s speed and fEPSP size. Therefore, to avoid
 confounds in the fEFSP potentiation estimates, we controlled for
 speed-related and sleep-related fEPSP changes and still found that cFC
 induced long-term potentiation, but no significant long-term depression.
 Synaptic strength changes were not found in the control group that simply
 explored the fear-conditioning chamber, indicating that exploration of the
 novel place did not produce the measurable effects caused by cFC. These
 results show that following cFC, the CA1 commissural pathway is
 potentiated, likely contributing to the functional integration of the left
 and right hippocampi in fear memory consolidation. In addition, the cFC
 paradigm produces significant changes in an animal’s behavioral state,
 which are observable as proximal changes in sleep patterns.
description: The data were collected from mice during different behavioral
 states before and after fear conditioning. In vivo field recording was
 used to measure changes in field potentials (fEPSP). Data were processed
 in MATLAB and submitted here in .mat file extension.
description: Users should read the original research article associated with
 this dataset in order to understand this data set.
DOI: 10.5061/dryad.d51c5b03p
title: Experimental manipulation of photoperiod influences migration timing in a wild, long-distance migratory songbird

description: Previous laboratory studies have demonstrated the role of photoperiod in
 cueing the migration timing of small land birds; however, how migration
 timing of young birds in wild environments develops in relation to these
 cues have rarely been investigated. Such investigations can make important
 contributions to our developing understanding of the phenotypic plasticity
 of migration timing to new conditions with climate change, where changes
 in the timing of nesting may expose juvenile birds to different
 photoperiods. We investigated the impact of manipulating photoperiod
 during nestling development in a long-distance migratory songbird on the
 timing of post-breeding movements in the wild. Using programmable lighting
 installed in the nest-boxes of purple martins (Progne subis), we exposed
 developing nestlings, from hatch to fledge date, to an extended
 photoperiod that matched the day length of the summer solstice in
 Manitoba, Canada. We found that birds with a simulated, earlier
 photoperiod had a longer nesting period and later fledge and autumn
 departure dates than control group birds. This study demonstrates the
 phenotypic plasticity of first-year birds to the ontogenetic effect of
 their hatch date in the formation of the timing of their first
 post-breeding movements. Further, we discuss how these results have
 implications for the potential use of assisted evolution approaches to
 alter migration timing to match new conditions with climate change.
description: The dataset was collected during a breeding season of purple
 martin in Manitoba and has been processed by a series of generalized
 linear mixed models (R v. 3.6.1) to produce a MS accepted for publication
 in Proceedings of the Royal Society B.
description: date: the date of mounting tags on birds
 location: location of breeding colonies of purple
 martins cavity ID: the number of each nest
 cavity Motus:Motus tag number
 motustagID: the ID of each Motus tag
 treatment: two groups of extension light and control
 group t: giving numbers as codes to different
 groups first egg date: the date of the first egg of
 each cavity hatch date: the date of hatching eggs at
 each nest cavity Fledge date: the date of fledging of
 juveniles of each cavity Colony departure: the date of
 juveniles departed their colony nesting period:
 duration of nesting period of juveniles  duration of
 staying at the colony: the duration between fledge date and colony
 departure date weight: the weight of juveniles at the
 time of mounting tags on them tarsus: the length of the
 tarsus  of juveniles at the time of mounting tags on them
 wing: the wing length of juveniles at the time of mounting tags
 on them tail: the length of the tail of juveniles at
 the time of mounting tags on them fat: the score of
 fat of juveniles at the time of mounting tags on them
 nestmate numbers: number of nestlings at each nest cavity at the
 time of mounting tags site: giving numbers as codes to
 different sites
DOI: 10.5061/dryad.z34tmpgf0
title: Data from: Species Delimitation of Endemic Atlantic Forest Inga subnuda (Leguminosae, Caesalpinioideae, mimosoid clade) Subspecies Based on Morphological, Ecological and Palaeoecological Data

description: Inga subnuda Salzm. ex Benth. are one of 31 endemic species in the
 Brazilian Atlantic Forest. Intermixed leaf and floral traits have made
 morphological distinctiveness difficult, and its current taxonomic
 treatment considers I. subnuda as one species with two subspecies. We aim
 to explore different lines of evidence to disentangle and clarify species
 boundaries in these two subspecies. Morphological variation and
 bioclimatic data of the two subspecies of the complex were assessed by
 using multivariate morphometric analyses and ecological niche modeling.
 Morphological quantitative characters allowed the recognition of different
 groups. The climatic space was similar but not identical, and the recent
 climatic cycles that could have shaped the current distribution are
 discussed. The results of our integrative study suggest regard both
 subspecies as two different species. Moreover, we propose a change in
 status of I. subnuda subsp. luschnathiana to the rank of species. The new
 up-ranked taxon is described and illustrated.
description: Dataset S1.
 Dataset with nine leaf characters and 44
 individuals. Dataset S2.
 Dataset with nine floral characters and 24
 individuals. Dataset S3.
 Dataset with nine leaf characters log transformed (base 10) and 44
 individuals. Dataset S4.
 Dataset with nine floral characters log transformed (base 10) and 24
 individuals. 
 SYSBOT-D-20-00129_Supplemental_Material. Fig. S1, Fig. S2.
DOI: 10.25349/d9q02t
title: Analysis Data for "Identifying and characterizing pesticide use on 9,000 fields of organic agriculture"

description: We identify the location of ~9,000 organic fields from 2013 — 2019 using
 field-level crop and pesticide use data, along with state certification
 data, for Kern County, CA, one of the US’ most valuable crop producing
 counties. We parse apart how being organic relative to conventional
 affects decisions to spray pesticides and, if spraying, how much to spray.
 We show the expected probability of spraying any pesticides is reduced by
 about 30 percentage points for organic relative to conventional fields,
 across different metrics of pesticide use including overall weight applied
 and coarse ecotoxicity metrics. We report little difference, on average,
 in pesticide use for organic and conventional fields that do spray, though
 observe substantial crop-specific heterogeneity.
description: Please see description in manuscript & supplementary
 information. 
description: Please see README. The Stata code file is a supplementary data
 file associated with the manuscript. As noted in the README, missing
 values are represented by empty cells, per the syntax for Stata. See
 README for an explanation for why different variables have missing
 data.