cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5hqbzkhb5
title: Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes

description: Geographic isolation is the primary driver of speciation in many
 vertebrate lineages. This trend is exemplified by North American darters,
 a clade of freshwater fishes where nearly all sister species pairs are
 allopatric and separated by millions of years of divergence. One of the
 only exceptions is the Lake Waccamaw endemic Etheostoma perlongum and its
 riverine sister species E. maculaticeps, which have no physical barriers
 to gene flow. Here we show that lacustrine speciation of E. perlongum is
 characterized by morphological and ecological divergence likely
 facilitated by a large chromosomal inversion. While Etheostoma perlongum
 is phylogenetically nested within the geographically widespread E.
 maculaticeps, there is a sharp genetic and morphological break coinciding
 with the lake-river boundary in the Waccamaw River system. Despite recent
 divergence, an active hybrid zone, and ongoing gene flow, analyses using a
 de novo reference genome reveal a 9 Mb chromosomal inversion with elevated
 divergence between E. perlongum and E. maculaticeps. This region exhibits
 striking synteny with known inversion supergenes in two distantly related
 fish lineages, suggesting deep evolutionary convergence of genomic
 architecture. Our results illustrate that rapid, ecological speciation
 with gene flow is possible even in lineages where geographic isolation is
 the dominant mechanism of speciation.
DOI: 10.5061/dryad.7sqv9s4x5
title: High-resolution quasi-idealized experiments for future and present-day based upon composites from a decades-long set of recurving landfalling (RCL) North Atlantic ET cases

description: We present a high-resolution quasi-idealized experiment based upon
 composites from a decades-long set of recurving landfalling (RCL) North
 Atlantic extratropical transition (ET) cases. Following Jung and Lackmann
 (2021), we apply the track-based classification method of Colbert and
 Soden (2012) to the historical database (1979 to 2018) of North Atlantic
 RCL ET events; recurving landfalling tropical cyclones (TCs) are defined
 as those which cross 70°W north of 25°N or cross 65W north of 40N and
 threaten the U.S. East Coast. We use the Atlantic Hurricane Database
 (HURDAT2) best-track data (Landsea and Franklin 2013); the track-based
 classification procedure yields 37 RCL ET cases over the 40-year period.
 To minimize the spread of the selected ET cases in terms of time to
 complete transition, we apply a threshold of 36 h as in Jung and Lackmann
 (2021). As HURDAT2 only specifies when transition is complete but does not
 provide the timeline of the transition, we supplement it with the cyclone
 phase space (CPS) method of Hart (2003) to diagnose onset and completion
 times of ET; ET events are first identified by HURDAT2 and then we compute
 the CPS parameters to confirm the ET timeline for each event using the
 ERA5 reanalysis dataset (Hersbach et al. 2020). This filtering process
 yields 21 RCL ET cases. This dataset is initialized by randomized 15-case
 composites selected from the 21 RCL ET cases as in Jung and Lackmann
 (2021). This dataset was used to produce figures and tables in the
 manuscript of Jung and Lackmann (2023, in review).  Due to
 storage limitations, the full dataset is much too large to be published (~
 500GB). Instead, a subset consisting of 3-hourly atmospheric temperature
 at 17 vertical levels, zonal and meridional wind at 17 vertical levels, 3
 hourly accumulated precipitation, mean sea level pressure, 10-m zonal and
 meridional wind, sea surface temperature, and relative humidity at 17
 vertical levels is presented. If you wish to access the full dataset,
 please contact one of the authors. 
description: See Jung and Lackmann (2021, 2023) for details on the creation of
 this dataset. 
description: The Files included are in NetCDF format so the program or
 programming language used needs to be capable of processing it.
DOI: 10.5061/dryad.kd51c5bbg
title: Craniodental divergence associated with bite force between hybridizing pine squirrels (Tamiasciurus)

description: Bite force can be a limiting factor in foraging and can significantly
 affect the competitive ability and lifetime fitness of mammals.
 Tamiasciurus squirrels feed primarily on conifer seeds and have a strong
 bite force to mechanically extract seeds from conifer cones with their
 mouths. In the North Cascades region, Douglas squirrels (Tamiasciurus
 douglasii) and red squirrels (T. hudsonicus) occupy ecologically different
 forests with different hardnesses in conifer cones. The ranges of these
 species overlap in a narrow hybrid zone where these forests meet near the
 crest of the North Cascades. We examined interspecific divergence in
 dietary ecomorphology in allopatry, in sympatry within the hybrid zone,
 and between hybrids and each parental species. We focused on three
 craniodental traits, including the incisor-strength index as a proxy
 measure for maximal bite force, cranial-suture complexity, and mandible
 shape. We find that these sister squirrel species differ in bite force and
 suture complexity in allopatry and sympatry and that mandible shape
 changes with the expected hardness of accessed food items, but is not
 significantly different between species. Furthermore, we find that hybrids
 display morphologies that overlap with hybrid zone red squirrels but not
 with hybrid zone Douglas squirrels. This work shows how important
 ecological processes at shallow evolutionary timescales can impact the
 divergence of morphological traits in taxa with extreme conservation of
 craniomandibular shape.
description: Measurement data is presented as a .xls file. Raw landmark
 coordinates are presented as a .TPS file
DOI: 10.5061/dryad.4b8gththk
title: Supplementary materials for: Use and detection of a vitamin B1 degradation product yields new views of the marine B1 cycle and plankton metabolite exchange

description: Vitamin B1 (thiamin) is a vital nutrient for most cells in nature
 including marine plankton. Early and recent experiments show that B1
 degradation products instead of B1 can support the growth of marine
 bacterioplankton and phytoplankton. However, the use and occurrence of
 some degradation products remain uninvestigated – namely
 N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine (FAMP) – which has been
 a focus of plant oxidative stress research. We investigated the relevance
 of FAMP in the ocean. Experiments and global ocean meta-omic data indicate
 that eukaryotic phytoplankton, including picoeukaryotes and harmful algal
 bloom species, use FAMP while bacterioplankton appear more likely to use
 deformylated FAMP, 4-amino-5-aminomethyl-2-methylpyrimidine (AmMP).
 Measurements of FAMP in seawater and biomass revealed that it occurs at
 picomolar concentrations in the surface ocean, heterotrophic bacterial
 cultures produce FAMP in the dark – indicating non-photodegradation of B1
 by cells, and B1-requiring (auxotrophic) picoeukaryotic phytoplankton
 produce intracellular FAMP. Our results require an expansion of thinking
 about vitamin degradation in the sea, but also the marine B1 cycle – where
 it is now crucial to consider a new B1-related compound pool (FAMP) – as
 well as generation (dark degradation – likely via oxidation), turnover
 (plankton uptake), and exchange of the compound within networks of
 plankton.
DOI: 10.7280/d1q398
title: An updated cloud-overlap photolysis module for atmospheric chemistry models, UCI Cloud-J v8.0, with near-UV H2O absorption

description: This new data set (Cloud-J v8.0) includes near-UV cross sections for water
 vapor absoprtion that can be used to calculate photolysis rates in
 atmospheric chemistry models using the new photolysis code UCI Cloud-J
 version 8.0.  This data set and the code that uses it are updated
 and improved versions of the last published version 7.6c (Prather,
 Michael; Hsu, Juno, 2019, Solar-J and Cloud-J models version 7.6c, Dryad,
 Dataset, https://doi.org/10.7280/D1096P).  It cleans up some
 minor bugs (see notes) and now includes the option for water vapor
 absorption in the ultraviolet region 290-340 nm.  The new H2O
 cross sections are derived from Pei et al. (2019, Water vapor near‐UV
 absorption: Laboratory spectrum, field evidence, and atmospheric impacts.
 JGR-Atmos, 124, 14,310–14,324. doi: 10.1029/2019JD030724).  With
 these new H2O cross sections, more solar UV is absorbed in the lower
 atmomsphere and many major photolysis rates are reduced by 10% near the
 surface.  We estimate that the lifetime of methane will increase
 by 7%.    Note (30 May 2023).  An error in the
 calculation of Ice Water Path [IWP(L)] in the standalone driver code for
 Cloud-J versions 7.6 through 8.0 has been discovered.  This does
 not affect any of the results or example output archived here because the
 calculations of with and without UV H2O absorption were done with clear
 skies.  A corrected version 8.0c is posted. The corrected code
 line goes from "IWP(L) = 1000.d0*WIC(L)*PDEL*G100 / CLF(L)" to
 "IWP(L) = 1000.d0*WIC(L)*PDEL*G100"
description: The dataset was taken directly from the Pei et al. 2019 published
 tables and then re-mapped onto the Cloud-J wavelength bins.
description: The primary dataset (FJX_spec.dat) can be opened and read with
 any editor.  The use of this data to calculate photolysis rates (J-values)
 requires the Cloud-J v8.0 FORTRAN F90 source code and a FORTRAN compiler. 
 No special libraries are needed. A standalone version of the code and
 necessary data tables are provided in the Zenodo software archive linked
 to this Dryad data DOI.
DOI: 10.5061/dryad.fttdz08xz
title: Data of publications on environmental reproductive cues and reproductive phenological shifts

description: Males and females often desynchronise their mating activity during the
 breeding season (intersexual phenological asynchrony). This suggests that
 the two sexes differentially use environmental cues to initiate seasonal
 reproduction, and climate change may cause phenological shifts in a
 sex-specific manner, subsequently altering frequency distribution of
 mating attempts over time and influencing the emergence timing and
 recruitment success of juveniles. In this article, we tested these
 hypotheses through literature reviews and theoretical modelling. We found
 that the sex specificity of environmental cues and phenological shifts
 remain poorly understood in most sexually reproducing animal taxa because
 of sex-specific publication bias and data limitations. Meanwhile, our
 theoretical model predicted that the ecological consequences of
 phenological shifts are sexually asymmetric, with earlier mating onset of
 males having generally greater negative effects on population growth than
 that of females. We therefore suggest that further research is necessary
 to collect and incorporate sex-specific information on seasonal
 reproduction into the theory of phenological mismatch, for which previous
 work has mostly focused on interspecific trophic asynchrony. We also
 outline a future research agenda to better understand the consequences of
 sex-specific phenological shifts on seasonal population dynamics and
 long-term persistence of species.
DOI: 10.5061/dryad.59zw3r2cs
title: Food webs coupled in space: Consumer foraging movement affects both stocks and fluxes

description: The exchange of material and individuals between neighbouring food webs is
 ubiquitous and affects ecosystem functioning. Here, we explore animal
 foraging movement between adjacent, heterogeneous habitats and its effect
 on a suite of interconnected ecosystem functions. Combining dynamic
 food-web models with nutrient-recycling models, we study foraging across
 habitats that differ in fertility and plant diversity. We found that net
 foraging movement flowed from high to low fertility or high to low
 diversity and boosted stocks and flows across the whole loop of ecosystem
 functions including biomass, detritus, and nutrients in the recipient
 habitat. Contrary to common assumptions, however, the largest flows were
 often between the highest and intermediate fertility habitats rather than
 highest and lowest. The effect of consumer influx on ecosystem functions
 was similar to the effect of increasing fertility. Unlike fertility,
 however, consumer influx caused a shift towards highly predator-dominated
 biomass distributions, especially in habitats that were unable to support
 predators in the absence of consumer foraging. This shift resulted from
 both direct and indirect effects propagated through the interconnected
 ecosystem functions. Only by considering both stocks and fluxes across the
 whole loop of ecosystem functions do we uncover the mechanisms driving our
 results. In conclusion, the outcome of animal foraging movements will
 differ from that of dispersal and diffusion. Together we show how
 considering active types of animal movement and the interconnectedness of
 ecosystem functions can aid our understanding of the patchy landscapes of
 the Anthropocene.
description: This simulation dataset was simulated using a dynamic food-web
 model combined with a nutrient recycling model in Matlab. The code used to
 create this data is also provided.<br><br>The model simulated food
 web and nutrient dynamics in two habitats, with foraging
 movement of some consumer species between habitats. The
 habitats differed in number of basal species, with potential scenarios
 including low, medium, or high diversity of habitat 1 (div1 = 1, 2, or 3
 respectively) and low or high diversity of habitat 2 (div2 = 1 or 3). The
 habitats also differed in fertility, with potential scenarios including
 low, medium or high fertility (productivity) for habitat 1 or 2 (prod1 and
 prod2 respectively). We simulated scenarios with no, low, or high linkage
 (consumer movement) between habitats (link = 0, 1, or 2). There were 1000
 replicates for each scenario. The data here are the
 mean of the final 100 time steps (they were almost always at equilibrium
 by this point, but this removed the effect of any cycles). We report the
 coefficient of variation for each value, so any instances where the
 simulation was not at equilibrium should be easily identified.
DOI: 10.5061/dryad.rbnzs7hgb
title: Co-designing conservation interventions through participatory action research in the Indian Trans-Himalaya

description: Community-based conservation, despite being more inclusive than fortress
 conservation, has been criticized for being a top-down implementation of
 external ideas brought to local communities for conservation’s benefit.
 This is particularly true for Changpas, the pastoral people of Changthang
 in trans-Himalayan India who live alongside unique wildlife. Our main aim
 was to co-design conservation interventions through participatory action
 research. We worked with two Changpa communities, to understand issues
 faced by them. Subsequently, we co-designed context-sensitive
 interventions to facilitate positive human-nature interactions. We did so
 by integrating the PARTNERS (Presence, Aptness, Respect, Transparency,
 Empathy, Responsiveness, Strategic Support) principles with the Trinity of
 Voice (Access, Standing, and Influence). In Rupsho, we facilitated focus
 group discussions (FGDs) led by the community. We found livestock
 depredation by wildlife was primarily facilitated by the weather. This led
 to co-designing of a new corral design which was piloted with seven
 households, safeguarding 2,385 pashmina goat and sheep. Approximating the
 value of each sheep/goat to be USD125, this intervention amounts to a
 significant economic protection of USDc.42,500 for each household. This is
 along with intangible gains of trust, ownership, and improved self-esteem.
 In Tegazong, a restricted area adjoining the Indo-China border with no
 previous research records, we worked with 43 Changpa people to co-create
 research questions of mutual interest. Wildlife presence and reasons for
 livestock loss were identified as areas of mutual interest.  The
 herders suggested they would record data in a form of their choice, for
 six months, while they live in their winter pastures. This participatory
 community monitoring revealed nutrition and hypothermia to be a key cause
 of livestock death. Subsequently, we delimited two previously untested
 interventions: lamb cribs and provisioning of locally-sourced barley as
 feed supplement. The wildlife monitoring recorded the first record of
 Tibetan Gazelle Procapra picticuadata, outside of their known
 distribution, in Tegazong. We aim to highlight the benefits of
 co-designing projects with local communities that link research and
 conservation, while also discussing the challenges faced. Ultimately, such
 projects are needed to ensure ethical knowledge generation and
 conservation that aims to be decolonial and inclusive.
DOI: 10.5061/dryad.fbg79cp0f
title: Wildfire impacts on seedbank and vegetation dynamics in Calluna heath

description: Moorlands dominated by Calluna vulgaris (hereafter Calluna) are globally
 rare and under increasing threat of wildfires due to climate change. The
 soil seedbank is important for community resilience, but research on its
 contribution to regenerating vegetation after moorland fires has, to date,
 focused on prescribed fire or on the short-term (≤ 2 year) impacts of
 wildfire. To address the role of the seedbank in long-term vegetation
 regeneration, we studied a chronosequence of six wildfire sites within a
 Scottish moorland catchment, ranging from 2 to 64 years since burning. We
 recorded vegetation composition and sampled the seedbank. Calluna and
 Erica spp. comprised 66 % and 27 % of germinated seeds, respectively, and
 the majority of vegetation species were not represented in the seedbank.
 Canonical Correspondence Analysis (CCA) revealed that time since fire was
 a strong predictor of vegetation species composition, but it had no effect
 on seedbank composition, suggesting that the same species dominate the
 seedbank regardless of burning. Whilst total seed density was not affected
 by time since wildfire, the effect on the non-Calluna seedbank was more
 notable. The proportion of non-Calluna species decreased with time in both
 vegetation and seedbank as Calluna cover was re-established and the
 seedbank of other species became gradually depleted. Whilst relative
 non-Calluna cover in the vegetation was at a maximum in recently burnt
 areas and then declined with time since fire, the species richness and
 proportion of non-Calluna in the seedbank followed a unimodal pattern
 after fire and reached a peak after approximately 35 years. Our results
 contribute to the knowledge of how moorland ecosystems regenerate after
 severe disturbances, which are likely to become more common as the climate
 changes.
description: Raw seedbank and vegetation data originating from 1x1 m randomly
 placed quadrats in and around historical wildfire sites in Glen Tanar,
 Scotland. Vegetation species are given in percentage cover by visual
 estimate. Seedbank species are given in number of germinated seeds per
 sample (two seedbank samples were collected in different locations in each
 quadrat using a soil core of 6 cm diameter and 4 cm depth, resulting in a
 total soil volume of 226.2 cm3 collected from a total area of 56.5 cm2 in
 each quadrat.). We have also included species number, the number of total
 seeds and non-Calluna vulgaris seeds per square metre, and proportion of
 non-Calluna seeds. The seedbank dataset additionally includes
 environmental data of quadrats: elevation, aspect, slope, soil pH, soil
 bulk density, soil N, soil C, ratio of C to N, National Vegetation
 Classification (NVC) community and a broad habitat type (wet or dry
 moorland). Both datasets include years since fire and burning status,
 where B = burnt, U = unburnt.
DOI: 10.5061/dryad.6q573n631
title: Low conversion efficiency of flight power increases with speed in the migratory bat Nathusius’ pipistrelle

description: The efficiency with which flying animals convert metabolic fuel to
 mechanical power dictates an individual’s flight behaviour and energy
 requirements. Despite the significance of this parameter, we lack
 empirical data on conversion efficiency for most species. Furthermore, the
 assumption that efficiency is constant across flight speeds has yet to be
 empirically confirmed, revealing a major outstanding question in animal
 flight. We show, through direct measurements of metabolic and aerodynamic
 power, that conversion efficiency in the migratory bat (Pipistrellus
 nathusii) increases with flight speed between 7.0 and 10.4%. Our findings
 suggest that peak conversion efficiency in this species occurs near
 maximum range speed, where the cost of transport is minimized. A
 meta-analysis of 16 bird and 8 bat species revealed a strong scaling
 relationship between estimated conversion efficiency and body mass, with
 no discernible differences between bats and birds. This has profound
 consequences for modelling flight behaviour as estimates assuming 23%
 efficiency underestimate flight costs for P. nathusii by almost 50% on
 average (36-62%). Our findings suggest that conversion efficiency may vary
 around an ecologically relevant optimum speed and provides a crucial
 baseline for investigating how this may drive the variation in conversion
 efficiency between species.
description: Metabolic power input (P<sub>chem</sub>) was recorded
 in 8 <em>Pipistrellus nathusii </em>flying in a wind tunnel at
 various speeds. We using the <sup>13</sup>C-labelled sodium
 bicarbonate meathod to record CO2 production as a proxy for metabolic rate
 in flight. We converted CO2 production to watts (W) using a conversion
 factor of 20.1 W per ml CO2.  Mechanical power output
 (P<sub>mech</sub>) was calculated using tomographical particle
 image velocimetry (tomoPIV), also presented as W.
DOI: 10.5066/p1uosrnb
title: Cyanotoxin concentrations in extracts from Solid Phase Adsorption Toxin Tracking (SPATT) samplers and other water-quality data collected from the Salem River, New Jersey, July-October, 2020.

description: This data release presents cyanotoxin and multiparameter water-quality sonde data collected from July-October 2020, at eleven sites in the Salem River, New Jersey. Data-collection sites included seven flowing and four impounded reaches of the main stem Salem River. Solid Phase Adsorption Toxin Tracking (SPATT) samplers were deployed at 11 sampling locations during the study period and retrieved after 1-15 days. Discrete grab samples also were collected at each sampling location during SPATT deployment and retrieval. Physicochemical measurements were collected in-situ with a multiparameter water-quality sonde when the SPATT samplers were deployed and retrieved and include measurements of water temperature, pH, specific conductance, dissolved oxygen concentration, and turbidity. Because of analytical expenses, discrete cyanotoxin samples were analyzed at only 10 of the 11 discrete sampling locations, and toxin results from these analyses informed selection of only 4 of the 11 SPATT sampling locations for additional analyses. SPATT sampler extracts and discrete-grab samples were analyzed for four cyanotoxins (anatoxin-a, cylindrospermopsin, microcystin, saxitoxin) by enzyme-linked immunosorbent assay (ELISA).