cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31166782
title: Complete chloroplast genome of Rhaphiolepis species

description: <i>Rhaphiolepis</i> species are valued for their ornamental and medicinal properties. We assembled and annotated the chloroplast genomes of nine <i>Rhaphiolepis</i> species. The chloroplast genome was assembled using GetOrganelle v1.7.7 software. This study provides the complete chloroplast (cp) genomes of nine <i>Rhaphiolepis</i> species, characterized by a typical quadripartite circular architecture including LSC, SSC and IR regions. This study will also support the genetic improvement of these economically important plants via chloroplast genetic engineering techniques.
DOI: 10.6084/m9.figshare.31166782.v1
title: Complete chloroplast genome of Rhaphiolepis species

description: <i>Rhaphiolepis</i> species are valued for their ornamental and medicinal properties. We assembled and annotated the chloroplast genomes of nine <i>Rhaphiolepis</i> species. The chloroplast genome was assembled using GetOrganelle v1.7.7 software. This study provides the complete chloroplast (cp) genomes of nine <i>Rhaphiolepis</i> species, characterized by a typical quadripartite circular architecture including LSC, SSC and IR regions. This study will also support the genetic improvement of these economically important plants via chloroplast genetic engineering techniques.
DOI: 10.5061/dryad.9p8cz8wgz
title: Ultraviolet polarized light pollution responses by aquatic insects

description: This dataset contains data from a field-based experiment described in the
 paper: "Fraleigh, D., Barratt Heitman, J., Robertson, B.A. (2021)
 Ultraviolet polarized light pollution and evolutionary traps for aquatic
 insects. Animal Behaviour. October." The experiment investigates the
 ability of different families of aquatic insects to detect and move toward
 sources of ultraviolet polarized light. The experiment conducted adjacent
 to the Saw Kill River in Annandale-on-Hudson, NY and wild emergent aquatic
 insects were simultaneously exposed to five lighting treatments: 1)
 polarized visible wavelengths of light , 2) polarized visible and
 polarized ultraviolet light, 3) unpolarized visible light, 4) polarized
 ultraviolet light and unpolarized visible light, and 5) unpolarized
 visible and ultraviolet light. Insects attracted to a light source
 reflecting from a oil-filled tray would touch down upon the oil and become
 trapped. The main results of the experiments was that one family
 of aquatic insects seems to have the ability to see ultraviolet polarized
 light and use it as a nocturnal cue to the location of water bodies, while
 terrestrial insects showed no indication of responses to any type of
 polarized light. 
description: The data set was collected on seven evenings in the September of
 2016 on the campus of Bard College, NY, USA next to the Saw Kill River. We
 measured differential attraction to one treatment vs. another as a
 function of the relative captures of aquatic insect families in one tray
 vs. another. Raw capture data is avilable for each family, but we have
 also converted the data to the percentages of captures for each treatment
 within each capture session. Finally, we created columns for each family
 rounding each percentage to an integer for using Poisson and negative
 binomial regression.
description: The three types of data for each family of aquatic and
 terrestrial insect collected in the experiment are described above. To
 reiterate, they are 1) raw captures (# of individuals) for each family
 during a single capture session, 2) the conversion of raw capture data to
 the % of captures for that family during that session as a function of the
 total numbers of individuals of that family captured in all five
 treatments. This was done to standardize the relative preference of
 individuals for each of the five treatments within a sampling session.
 Finally, 3) each % value was rounded off to an integer value (e.g. 35.4%
 was converted to 34%) for the purpose of analysis using statistical
 approaches that rely upon integer data. All three types of data are
 available for each family, for each of the five treatments and for each of
 the seven sessions.
DOI: 10.5061/dryad.4j0zpc8bx
title: Can sensory drive explain the evolution of visual signal diversity in terrestrial species? A test with Anolis lizards

description: Animal signal colors evolve to efficiently stimulate conspecific visual
 systems. The sensory drive hypothesis proposes that species differences in
 habitat light conditions favor the evolution of color diversity. The
 strongest support comes from aquatic systems, while terrestrial systems
 offer fewer convincing examples. Anolis lizards occupy diverse habitats
 and signal with a colorful dewlap. Dewlap visibility depends on perceived
 chromatic contrast with the background. Visual-system modeling has shown
 that red dewlaps are most visible in most habitat types. However, a
 majority of species possess white or yellow dewlaps. In a recent
 behavioral study we showed that low light conditions can sometimes make
 yellow and white colors more visible, by altering chromatic contrast
 perception with the background. Using 17 Caribbean Anolis species we
 showed that cut-on wavelength, a measure of dewlap color in a white-to-red
 continuum, correlates with habitat light intensity. Pairwise comparisons
 revealed that red dewlaps are most visible in bright habitats, whereas
 yellow and white are more visible in darker habitats. We conclude that
 sensory drive has contributed to the evolution of dewlap color differences
 through the interactive effects of total habitat light intensity and
 chromatic contrast perception and may provide a mechanism for speciation
 among anoles.
description: Field data collection and computer modeling.
DOI: 10.6086/d1s689
title: Modeling phenological reaction norms over an elevational gradient reveals contrasting strategies of Dusky Flycatchers and Mountain Chickadees in response to early season temperatures

description: We developed an approach to distinguish among three alternative strategies
 birds may employ relating the timing of egg-laying across elevations to
 annual variation in spring temperature (phenological reaction norms),
 which we applied to analyze breeding phenology of two species over an
 elevational gradient in the Sierra Nevada, California. In a “simple
 offset” strategy, birds at different elevations initiate breeding relative
 to environmental temperature in a consistent manner, in that breeding
 onset is triggered by a critical temperature regardless of when it occurs
 in the spring. Elevation-specific reaction norms based on multiple years
 are offset (high-elevation birds start breeding later) but parallel. In a
 “delay” strategy, in cooler springs populations at higher elevations that
 are sensitive to early-season weather-related risks may delay laying onset
 relative to those at lower elevations, yielding a high-elevation reaction
 norm that diverges from a low-elevation one at cooler temperatures.
 Conversely, high-elevation populations in cooler springs that are
 sensitive to the risk of having insufficient time to complete a breeding
 cycle may advance laying onset relative to lower populations (“advance”),
 yielding a high-elevation reaction norm than converges with a
 low-elevation one. Both “delay” and “advance” strategies imply an
 elevation-dependent interaction between temperature and date (photoperiod)
 in influencing laying onset. Examined across three elevation
 groupings, phenological reaction norms of Mountain Chickadees (Poecile
 gambeli) were essentially parallel, consistent with “simple offset,”
 whereas Dusky Flycatchers (Empidonax oberholseri) relationships were more
 complex. In cooler springs, mid-elevation flycatchers bred comparatively
 late relative to lowest-elevation birds (“delay”), implying greater
 sensitivity to early season risks, but still with sufficient time to
 complete a breeding cycle. However, high-elevation flycatchers bred
 comparatively early relative to mid-elevation populations (“advance”);
 delaying at these highest elevations may not be an option. Our
 approach revealed differences in risk-sensitivity that were consistent
 with other ecological differences between the two species.
DOI: 10.5061/dryad.m63xsj42p
title: Data from: Biosystematics of Platanthera bifolia s.l. (Orchidaceae): Inferences from analysis of Scandinavian population samples

description: Over the years, various authors have (sub)divided the Eurasian moth
 pollinated Platanthera bifolia into several taxa. Advanced studies using
 multivariate morphometric analysis and/or genetic fingerprinting have all
 included regions where the situation appears particularly complex. With
 the aim to resolve variation patterns in a region where the situation
 seems less complex, we analysed morphometric and AFLP data from 13
 Scandinavian populations using a range of uni- and multivariate
 statistical methods. Variation was largely continuous, though with
 (individuals from) short-spurred and long-spurred populations,
 respectively, forming loose groups. Provided that successful pollinator
 shifts usually occur between moth species with small difference in
 proboscis length, this pattern is congruent with the hypothesis that spur
 length in P. bifolia s.l. has mainly evolved through pollinator shifts
 followed by selection in response to proboscis length of the prevailing
 local pollinator species. Acknowledging an important adaptive role of spur
 length, observing that spur length was among the main contributors to
 morphological variation, and noting this pattern to be congruent with both
 AFLP patterns and habitat requirements, we advocate the formal distinction
 between a short-spurred and a long-spurred taxon. Adopting the operational
 definitions of species, subspecies and variety provided in Flora Nordica,
 the two taxa should be recognized as P. bifolia var. bifolia and P.
 bifolia var. latissima, respectively. A key to the varieties is provided.
description: The dataset is described in detail in the ReadMe file.
DOI: 10.5061/dryad.31zcrjdm5
title: Growth rates of populations evolved and assayed at two temperatures for 6500 generations

description: Evolutionary biologists have long sought to understand what factors affect
 the repeatability of adaptive outcomes. To better understand the role of
 temperature in determining the repeatability of adaptive trajectories, we
 evolved populations of different genotypes of the ciliate Tetrahymena
 thermophila at low and high temperatures and followed changes in growth
 rate over 6,500 generations. As expected, growth rate increased with a
 decelerating rate for all populations; however, there were differences in
 the patterns of evolution at the two temperatures. The growth rates of the
 different genotypes tended to converge as evolution proceeded at both
 temperatures, but this convergence was quicker and more pronounced at the
 higher temperature. Additionally, over the first 4,000 generations we
 found greater repeatability of evolution, in terms of change in growth
 rate, among replicates of the same genotype at the higher temperature.
 Finally, we found limited evidence of trade-offs in fitness between
 temperatures, and an asymmetry in the correlated responses, whereby
 evolution in a high temperature increases growth rate at the lower
 temperature significantly more than the reverse. These results demonstrate
 the importance of temperature in determining the repeatability of
 evolutionary trajectories for the eukaryotic microbe Tetrahymena
 thermophila and may provide clues to how temperature affects evolution
 more generally.
description: Growth rate data was collected from evolving populations
 on <em>Tetrahymena thermophila. </em>Growth rate was measure
 in 96-well plates on a microplate reader and a r-script was used to an
 r-max to each curve.
description: Dataset includes generation 0 which is calculated by taking the
 mean of the measurements over the first 50 generations for each
 combination of genotype and assay temperature.
DOI: 10.5061/dryad.q573n5tjj
title: Cell-type specific responses to associative learning in the primary motor cortex

description: The primary motor cortex (M1) is known to be a critical site for movement
 initiation and motor learning. Surprisingly, it has also been shown to
 possess reward-related activity, presumably to facilitate reward-based
 learning of new movements. However, whether reward-related signals are
 represented among different cell types in M1, and whether their response
 properties change after cue-reward conditioning remains unclear. Here, we
 performed longitudinal in vivo two-photon Ca2+ imaging to monitor the
 activity of different neuronal cell types in M1 while mice engaged in a
 classical conditioning task. Our results demonstrate that most of the
 major neuronal cell types in M1 showed robust but differential responses
 to both cue and reward stimuli, and their response properties undergo
 cell-type specific modifications after associative learning. PV-INs’
 responses became more reliable to the cue stimulus, while VIP-INs’
 responses became more reliable to the reward stimulus. PNs only showed
 robust response to the novel reward stimulus, and they habituated to it
 after associative learning. Lastly, SOM-IN responses emerged and became
 more reliable to both conditioned cue and reward stimuli after
 conditioning. These observations suggest that cue- and reward-related
 signals are represented among different neuronal cell types in M1, and the
 distinct modifications they undergo during associative learning could be
 essential in triggering different aspects of local circuit reorganization
 in M1 during reward-based motor skill learning.
description: Using two-photon microscopy, we imaged subpopulations of neurons
 in awake and behaving mice on day 1 and day 7 of a head-fixed classical
 conditioning task where an auditory tone was paired with water rewards. We
 imaged pyramidal neurons, PV-INs, SOM-INs and VIP-INs in M1 to understand
 how M1 represents reward and reward-related cues. 
description: dF/F files show the change in GCaMP6f fluorescence and are saved
 as .mat files and behavioural data (acquired using wavesurfer) was saved
 as H5 files. H5 files log cue, reward and mouse lick timing. Imaging was
 performed at 30 fps.
DOI: 10.5061/dryad.h9w0vt4j5
title: Balanced polymorphisms and their divergence in a Heliconius butterfly

description: The evolution of mimicry in similarly defended prey is well described by
 Müllerian mimicry theory, which predicts the convergence of warning
 patterns in order to gain the most protection from predators. However,
 despite this prediction, we can find great diversity of color patterns
 amongst Müllerian mimics such as Heliconius butterflies in the neotropics.
 Furthermore, some species have evolved the ability to maintain multiple
 distinct warning patterns in single populations, a phenomenon known as
 polymorphic mimicry. The adaptive benefit of these polymorphisms is
 questionable since variation from the most common warning patterns is
 expected to be disadvantageous as novel signals are punished by predators
 naive to them. In this study we use artificial butterfly models throughout
 Central and South America to characterize the selective pressures
 maintaining polymorphic mimicry in Heliconius doris. Our results highlight
 the complexity of positive frequency-dependent selection, the principal
 selective pressure driving convergence amongst Müllerian mimics, and its
 impacts on interspecific variation of mimetic warning coloration. We
 further show how this selection regime can both limit and facilitate the
 diversification of mimetic traits.
description: We made artificial models of <em>Heliconius doris
 </em>butterflies, 100 of each of 4 morphs for a total of 400 per
 transect. These models were placed on leaves, trunks or twigs in visible,
 well-lit areas at 10m intervals along a 4 kilometer transect in each site.
 The placement of each model was carried out so as to mimic the natural
 perching behavior of <i>Heliconius</i> butterflies and provide
 a visible target for potential avian predators. The distinct model morphs
 were placed along the transect in a regular order. From 376 to 416 models
 were placed per site and left for 72 hours, after which, models were
 collected. Damage was clearly visible in the malleable wax bodies and
 paper wings of several models. Damages were catalogued as either (i)
 “invertebrate attack” when bearing the visible fine marks of arthropod
 mandibles, often on the wax bodies, (ii) “Avian Attack” when bearing the
 characteristic U or V shape marks on the wax or (iii) “Unknown Predator”
 when a severe attack was evident but a specific mark was not found, such
 as when wings were torn or wax bodies broken in pieces. Models that bore
 attack marks characteristic of invertebrates were not included in the data
 analysis (n= 97 out of 2,271), as there is currently no literature
 regarding invertebrates carrying the cognitive capacity necessary to make
 the associations between unpalatability and warning color patterns central
 to Müllerian mimicry. Furthermore, missing models were also excluded from
 the analyses as we are unable to determine if they were displaced by
 falling forest debris, human action or attacked by natural
 predators.
DOI: 10.5061/dryad.dz08kprz2
title: Data from: Genome-wide analysis reveals demographic and life history patterns associated with habitat modification in land-locked, deep-spawning sockeye salmon (Oncorhynchus nerka)

description: Human-mediated habitat fragmentation in freshwater ecosystems can
 negatively impact genetic diversity, demography and life history of native
 biota, while disrupting the behaviour of species that are dependent on
 spatial connectivity to complete their life cycles. In the Alouette River
 system (British Columbia, Canada), dam construction in 1928 impacted
 passage of anadromous sockeye salmon (Oncorhynchus nerka), with the last
 records of migrants occurring in the 1930’s. Since that time, O. nerka
 persisted as a resident population in Alouette Reservoir until
 experimental water releases beginning in 2005 created conditions for
 migration; two years later, returning migrants were observed for the first
 time in ~70 years, raising important basic and applied questions regarding
 life history variation and population structure in this system. Here, we
 investigated the genetic distinctiveness and population history of
 Alouette Reservoir O. nerka using genome-wide SNP data (n=7,709 loci)
 collected for resident and migrant individuals, as well as for
 neighbouring anadromous sockeye salmon and resident kokanee populations
 within the Fraser River drainage (n=312 individuals). Bayesian clustering
 and principal components analyses based on neutral loci revealed five
 distinct clusters, largely associated with geography, and clearly
 demonstrated that Alouette Reservoir resident and migrant individuals are
 genetically distinct from other O. nerka populations in the Fraser River
 drainage. At a finer-level, there was no clear evidence for
 differentiation between Alouette Reservoir residents and migrants;
 although we detected eight high-confidence outlier loci, they all mapped
 to sex chromosomes suggesting that differences were likely due to uneven
 sex ratios rather than life history. Taken together, these data suggest
 that contemporary Alouette Reservoir O. nerka represents a landlocked
 sockeye salmon population, constituting the first reported instance of
 deep-water spawning behaviour associated with this life history form. This
 finding punctuates the need for re-assessment of conservation status and
 supports on-going fisheries management activities in Alouette
 Reservoir. 
description: 7012_SNPs_neutral.vcf: genotypic data for 312 individuals at 7012
 SNPs (neutral only) generated via RADseq
 7709_SNPs_all.vcf: genotypic data for 312 individuals at 7709
 SNPs (all) generated via RADseq 7709_Loci.fa: Fasta
 file containing sequences for 7,709 loci
 7709_SNPs_mapped.txt: Loci and SNPs mapped to linkage
 groups metadata.txt: individual metadata including
 sample identifiers, location, migratory form and sex (where
 known)
DOI: 10.5061/dryad.w6m905qq4
title: Plant management but not fertilization mediates soil carbon emission and microbial community composition in subtropical Eucalyptus plantations

description: The diversity of plant functional groups in plantations affects soil
 carbon, but we have limited understanding of the underlying mechanisms for
 how plant management affects soil carbon dynamics. Here, we conducted a
 3-year manipulation experiment of plant functional groups that included
 understory removal, tree root trenching, and fertilization treatments in
 2-year-old and 6-year-old Eucalyptus plantations in the subtropical
 region. The results showed that soil respiration was significantly
 suppressed by understory removal (-38%), tree root trenching (-41%), and
 their interactions (-54%), but that fertilization alone and in
 interactions had no significant effect. The Chao1 indices for soil
 bacterial and fungal diversity significantly decreased with understory
 removal in the 2-year-old plantation and with tree root trenching in the
 6-year-old plantation. Soil bacterial and fungal communities were also
 affected by understory removal and tree root trenching. Soil respiration,
 physicochemical characteristics, microbial diversity, and community
 composition were significantly affected by plantation age. Reductions in
 soil carbon emissions were associated with reductions in plant functional
 groups and soil microbial groups, while increases in soil respiration were
 associated with soil physicochemical factors, soil temperature, and
 plantation age. Our findings highlight that plant managements are of great
 significance to the soil carbon emission processes in afforested
 plantations.
description: Soil respiration was measured by a Li-cor 8100 automated soil
 flux system (LI-COR Inc., Lincoln, NE, USA); Microbial analysis of soil
 samples was measured by the Majorbio Inc.