cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.76hdr7swf
title: Counts of two sperm types during migration in female Manduca sexta reproductive system after mating

description: During mating in the Lepidoptera (moths and butterflies), sperm are passed
 to the female via a copulation in which the male transfers a large and
 often complex spermatophore over the major part of an hour or more.
 Subsequently, over the course of an hour or often considerably more, the
 sperm exit the spermatophore and travel over a relatively complex route to
 the spermatheca, where the sperm are stored and then used as the eggs are
 laid. The process of spermatophore formation and migration of sperm in the
 female has been described in many Lepidoptera, but the mechanics involved
 have received less attention. Understanding these is important in
 discerning the relative roles of males and females in determining the
 outcome of matings. We describe how the spermatophore is formed, how the
 sperm migrate in the female, and the fate of the sperm in the spermatheca
 of the tobacco hornworm moth, Manduca sexta. We found that sperm movement
 from the spermatophore relied upon motility of the sperm, but further
 movement of the sperm to the spermatheca was dependent on female muscular
 action. After arriving in the spermatheca, the anucleate parasperm
 (apyrene sperm) separated into the lateral pouch of the spermatheca
 (lagena) and disappeared over 7 days, while the eusperm (eupyrene sperm)
 persisted in the central lumen of the spermatheca (utriculus). The
 relative persistence of these two sperm types could shed some light on
 what determines the proclivity of females to remate. Elucidation of these
 physiological mechanisms contributes to an understanding of the mechanisms
 of female choice and male competition in Lepidoptera.
description: Laboratory research with a laboratory colony of the tobacco
 hornworm moth, Manduca sexta.
DOI: 10.5061/dryad.pk0p2ngnf
title: Developmental transcriptomics reveals a gene network driving mimetic color variation in a bumble bee

description: A major goal of evolutionary genetics and evo-devo is to understand how
 changes in genotype manifest as changes in phenotype. Bumble bees display
 remarkable color pattern diversity while converging onto numerous regional
 Müllerian mimicry patterns, thus enabling exploration of the genetic
 mechanisms underlying convergent phenotypic evolution. In western North
 America, multiple bumble bee species converge onto local mimicry patterns
 through parallel shifts of midabdominal segments from red to black. It was
 previously demonstrated that a Hox gene, Abd-B, is the key regulator of
 the phenotypic switch in one of these species, Bombus melanopygus,
 however, the mechanism by which Abd-B regulates color differentiation
 remains unclear. Using tissue/stage-specific transcriptomic analysis
 followed by qRT-PCR validation, this study reveals a suite of genes
 potentially involved downstream of Abd-B during color pattern
 differentiation. The data support differential genes expression of not
 only the first switch gene Abd-B, but also an intermediate developmental
 gene nubbin, and a whole suite of downstream melanin and redox genes that
 together reinforce the observed eumelanin (black)-pheomelanin (red)
 ratios. These include potential genes involved in the production of insect
 pheomelanins, a pigment until recently not thought to occur in insects and
 thus lacking known regulatory enzymes. The results enhance understanding
 of pigmentation gene networks involved in bumble bee color pattern
 development and diversification, while providing insights into how
 upstream regulators such as Hox genes interact with downstream morphogenic
 players to facilitate this adaptive phenotypic radiation.
description: This dataset contains the additional data files and notes for
 RNA-seq and q-PCR analysis. For a detailed description of the methods,
 please refer to the methods section of "Developmental transcriptomics
 reveals a gene network driving mimetic color variation in a bumble
 bee" (Rahman et al. 2021; Genome Biology and Evolution;
 https://doi.org/10.1093/gbe/evab080).
description: The dataset contains four files. 1. RNA-seq
 data file (DEG list) (RNA-Seq_DEG_list.xlsx) 2. RNA-seq
 DESeq2 codes (DESeq2_script.txt) 3. q-PCR dataset for
 males (Males_qPCR_raw&analyzed.xlsx) 4. q-PCR
 raw dataset for Workers (Worker_qPCR_raw&analyzed.xlsx)
DOI: 10.5061/dryad.stqjq2c3d
title: Densities of mollusc species at different sites along the Chinese coast

description: Aim: Molluscs are important grazers, filter and deposit feeders,
 scavengers and predators, which in turn are food for shorebirds, fish and
 people. Some species, targeted as human food, have been cultured along the
 Chinese coast for hundreds of years. To examine whether aquacultural
 practices have meanwhile affected biodiversity gradients, we measured
 mollusc community structure along the coast of China in habitats which are
 intensively used by humans. Location: Chinese coast Methods: We sampled 21
 intertidal sites spanning 20 latitudinal degrees and 18,400 km of
 coastline. We assessed alpha diversity to verify whether mollusc
 communities exhibit the expected biodiversity gradient with latitude, and
 beta diversity gradients with distance. To examine whether human
 activities such as transportation and culturing could have affected these
 patterns, we distinguished commercial from non-commercial mollusc species
 and compared the differences in distribution, density, alpha diversity and
 beta diversity. Results: We found non-commercial species showed the
 expected biodiversity gradients. Commercial species (i) dominated the
 intertidal mollusc communities at 19 of the 21 sites, and compared with
 non-commercial species, (ii) exhibited wider geographical distributions,
 (iii) showed no significant change in Bray-Curtis index (abundance-based
 beta diversity) with either geographical or climatic distance, (iv)
 exhibited lower average dissimilarities, and (v) did not show a decrease
 in species richness and Shannon diversity with latitude. Combining all
 species, trends were the same as for the commercial species. Main
 conclusions: A few cultured species dominated the intertidal mollusc
 communities in high densities along the Chinese coastline, taking over the
 ecological roles of the native species but not driving them extinct. In
 this way aquacultural practices have exerted a homogenizing influence
 strong enough to erase basic biodiversity gradients. Since molluscs are
 food for the growing human population and the shrinking populations of
 migratory animals, coastal planning and management of both intertidal
 habitats and the exploitative activities employed need to incorporate
 these dimensions.
DOI: 10.5061/dryad.63xsj3v22
title: Three‐dimensional soil heterogeneity modulates responses of grassland mesocosms to an experimentally imposed drought extreme

description: Heterogeneity is an intrinsic characteristic of soils, which regulates
 plant diversity and ecosystem functioning. However, whether soil
 heterogeneity also modulates responses of plant communities to climate
 change, including climate extremes, remains largely an open question.
 Here, we explore responses of plant communities to drought extremes across
 four levels of spatial soil heterogeneity, with cell sizes varying from
 very small to very large, i.e. 0, 12, 24 and 48 cm. These were created in
 mesocosms by alternating nutrient-rich and nutrient-poor substrate in
 three dimensions. A seed mixture of 24 grassland species was evenly sown
 on each mesocosm in spring. In late summer, a three-week drought was
 imposed with a rainout shelter. During the drought, soil water content at
 the mesocosm scale decreased more at intermediate (12 and 24 cm) than at
 small or large (0 and 48 cm) cell sizes, which was reflected in increased
 senescence and drought-induced heat stress. These responses could be
 traced to greater plant biomass coupled with higher water demand at those
 intermediate cell sizes, likely related to between-cell access to
 nutrients and effects of diversity and community composition. Our results
 indicate that soil heterogeneity can modulate the impact of drought
 extremes on plant communities, though more research is needed on the
 transition between intermediate and extreme cell sizes, where
 heterogeneity effects seem to change most. We propose that soil
 heterogeneity be considered more explicitly in studies of changing
 precipitation regimes.
description: # Three‐dimensional soil heterogeneity modulates responses of grassland
 mesocosms to an experimentally imposed drought extreme
 [https://doi.org/10.5061/dryad.63xsj3v22](https://doi.org/10.5061/dryad.63xsj3v22) ## Description of the data and file structure SR_Drough_Final.xlsx
DOI: 10.5061/dryad.2jm63xsp7
title: Data from: Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli

description: Plasmid-mediated antimicrobial resistance is a major contributor to the
 spread of resistance genes within bacterial communities. Successful
 plasmid spread depends upon a balance between plasmid fitness effects on
 the host and rates of horizontal transmission. While these key parameters
 are readily quantified in vitro, the influence of interactions with other
 microbiome members is largely unknown. Here, we investigated the influence
 of three genera of lactic acid bacteria (LAB) derived from the chicken
 gastrointestinal microbiome on the spread of an epidemic narrow-range ESBL
 resistance plasmid, IncI1 carrying blaCTX-M-1, in mixed cultures of
 isogenic Escherichia coli strains. Secreted products of LAB decreased E.
 coli growth rates in a genus-specific manner but did not affect plasmid
 transfer rates. Importantly, we quantified plasmid transfer rates by
 controlling for density-dependent mating opportunities. Parametrization of
 a mathematical model with our in vitro estimates illustrated that small
 fitness costs of plasmid carriage may tip the balance towards plasmid loss
 under growth conditions in the gastrointestinal tract. This work shows
 that microbial interactions can influence plasmid success and provides an
 experimental-theoretical framework for further study of plasmid transfer
 in a microbiome context.
description: ReadMe files for raw and processed data and code, per
 figure: README_Fig1a
 README_Fig1b_SupplFig2 README_Fig1c
 README_Fig1d README_SupplFig1
DOI: 10.5061/dryad.dr7sqv9xx
title: Artificial selection for non‐reproductive host killing in a native parasitoid on the invasive pest, Drosophila suzukii

description: Establishment and spread of invasive species can be facilitated by lack of
 natural enemies in the invaded area. Host-range evolution of natural
 enemies augments their ability to reduce the impact of the invader and
 could enhance their value for biological control. We assessed the
 potential of
 the Drosophila parasitoid, Leptopilina
 heterotoma (Hymenoptera: Figitidae), to exploit the invasive
 pest Drosophila suzukii by focussing on three
 performance indices: (1) attack rate (2) host killing, consisting of
 killing rate and lethal attack rate (killing efficiency) and (3)
 successful offspring development (reproductive success). We found
 significant intra-specific variation in attack rate and killing rate and
 lethal attack rate among seven European populations, but offspring
 generally failed to successfully develop from the D.
 suzukii host. We crossed these European lines to create a
 genetically variable source population and performed a half-sib analysis
 to quantify genetic variation. Using a Bayesian animal model, we found
 that attack rate and killing rate had a heritability of , lethal
 attack rate a  and offspring development . We
 then artificially selected wasps with the highest killing rate
 of D. suzukii for seven generations to test whether
 host-killing could be improved. There was a small and inconsistent
 response to selection in the three selection lines. Realized heritability
 ( ) after four generations of selection was 0.17 but near zero
 after seven generations of selection. The genetic response might have been
 masked by an increased D. suzukii fitness resulting from
 adaptation to laboratory conditions. Our study reveals that native,
 European, L. heterotoma can attack the invasive
 pest, D. suzukii and significantly reduce fly survival
 and that different steps of the parasitization process need to be
 considered in the evolution of host-range. It highlights how evolutionary
 principles can be applied to optimize performance of native species for
 biological control.
description: Data was collected and analyzed as described in https://doi.org/10.1111/eva.13252
DOI: 10.5061/dryad.stqjq2c3f
title: Stability of rocky intertidal communities in response to species removal varies across spatial scales

description: Improving our understanding of stability across spatial scales is crucial
 in the current scenario of biodiversity loss. Still, most empirical
 studies of stability target small scales. Here we experimentally removed
 the local space-dominant species (macroalgae, barnacles, or mussels) at
 eight sites spanning more than 1000 km of coastline in north- and
 south-central Chile, and quantified the relationship between area (the
 number of aggregated sites) and stability in aggregate community variables
 (total cover) and taxonomic composition. Resistance, recovery, and
 invariability increased nonlinearly with area in both functional and
 compositional domains. Yet, the functioning of larger areas achieved a
 better, albeit still incomplete, recovery than composition. Compared with
 controls, smaller disturbed areas tended to overcompensate in terms of
 total cover. These effects were related to enhanced available space for
 recruitment (resulting from the removal of the dominant species), and to
 increasing beta diversity and decaying community-level spatial synchrony
 (resulting from increasing area). This study provides experimental
 evidence for the pivotal role of spatial scale in the ability of
 ecosystems to resist and recover from chronic disturbances. This knowledge
 can inform further ecosystem restoration and conservation policies.
DOI: 10.5061/dryad.mkkwh710d
title: How head shape and substrate particle size affect fossorial locomotion in lizards

description: Granular substrates ranging from silt to gravel cover much of the Earth’s
 land area, providing an important habitat for fossorial animals. Many of
 these animals use their heads to penetrate the substrate. Although there
 is considerable variation in head shape, how head shape affects fossorial
 locomotor performance in different granular substrates is poorly
 understood. Here, head shape variation for 152 species of fossorial
 lizards was quantified for head diameter, slope and pointiness of the
 snout. The force needed to penetrate different substrates was measured
 using 28 physical models spanning this evolved variation was constructed.
 Ten substrates were considered, ranging in particle size from 0.025 to 4mm
 in diameter and consisting of spherical or angular particles. Head shape
 evolved in a weakly correlated manner, with snouts that were gently sloped
 being blunter. There were also significant clade differences in head shape
 among fossorial lizards. Experiments with physical models showed that as
 head diameter increased, absolute penetration force increased but force
 normalized by cross-sectional area decreased. Penetration force decreased
 for snouts that tapered more gradually and were pointier. Larger and
 angular particles required higher penetration forces, although
 intermediate size spherical particles, consistent with coarse sand,
 required the lowest force. Particle size and head diameter effect were
 largest, indicating that fossorial burrowers should evolve narrow heads
 and bodies, and select relatively fine particles. However, variation in
 evolved head shapes and recorded penetration forces suggest that
 kinematics of fossorial movement are likely an important factor in
 explaining evolved diversity.
description: Head shape data were collected for 152 species of lizards from
 500 preserved museum specimens. We provide these data as well as a pruned,
 ultrametricized phylogeny from Zhang & Wiens (2016).
 Penetration force data were collected for four substrates and one
 physcial model of a lizard head for a range of container diameters and
 substrate depths to determine what container size and depth was needed to
 avoid edge effects. Penetration force data were
 collected for five glass bead and four natural rock substrates using 28
 physical models that varied in diameter, slope and pointiness, mimicking
 evolved variation in lizard heads. For each combingation of model and
 substrate, ten trials were collected. Please see the
 methods of the published work for further details.
description: The datasets described here are provided in three Excel
 spreadsheets. Each spreadsheet has a readme worksheet explaining each
 varaible in each dataset. Each spreadsheet contains multiple worksheets
 providing various aspects of the data.
DOI: 10.7280/d11h5p
title: Local-scale thermal history influences metabolic response of marine invertebrates

description: As climate change continues, anticipating species’ responses to rising
 temperatures requires an understanding of the drivers of thermal
 sensitivity, which itself may vary over space and time. We measured
 metabolic rates of three representative marine invertebrate species
 (hermit crabs Pagurus hirsutiusculus, periwinkle snails Littorina sitkana,
 and mussels Mytilus trossulus) and evaluated the relationship between
 thermal sensitivity (Q10) and thermal history. We tested the hypothesis
 that thermal history drives thermal sensitivity and quantified how this
 relationship differs over time (short-term to seasonal time scales) and
 between species. Organisms were collected from tide pools in Sitka, Alaska
 where we also recorded temperatures to characterize thermal history prior
 to metabolic rate assays. Using respirometry, we estimated mass-specific
 oxygen consumption (MO2) at ambient and increased temperatures for one
 individual per species per tide pool across three seasons. We evaluated
 relationships between thermal sensitivity and pool temperatures for time
 periods ranging from 1 day to 1 month prior to collection. For all
 species, thermal sensitivity was related to thermal history for the
 shorter time periods (1 day to 1 week). However, the direction of the
 relationships and most important thermal parameters (i.e., maximum, mean,
 or range) differed between species and seasons. We found that on average,
 P. hirsutiusculus and L. sitkana were more thermally sensitive than M.
 trossulus. These findings show that variability in thermal history over
 small spatial scales influences individuals’ metabolic response to warming
 and may be indicative of these species’ ability to acclimate to future
 climate change.
description: Temperature Data:<br>Temperature data was collected at the
 tide pool level using Onset ® HOBO TidbiT temperature loggers (±0.2
 accuracy) that recorded temperature consecutively every 5 min from
 December 2018 to September 2019. Temperature data were summarized for the
 1-month, 1-week, and 1-day periods preceding each collection. For each
 tidepool, we calculated the following thermal parameters: variance,
 minimum, mean daily minimum, 10<sup>th</sup> percentile,
 range, mean daily range, mean daily average, maximum, mean daily maximum,
 90<sup>th</sup> percentile, mean daily
 90<sup>th</sup> percentile, 95<sup>th</sup>
 percentile, and mean daily 95<sup>th</sup> percentile
 temperatures.<br><br>Oxygen Consumption Data:<br>Raw
 Oxygen data was collected using Pre-Sens PSt3 sensor spots (PreSens
 Precision Sensing, Germany) and a 10-channel OXY-10 SMA (G2) oxygen meter
 (PreSens Precision Sensing, Germany). Data were processed after visual
 inspection and fit with a linear regression of oxygen consumption over
 time (only slopes that had an R<sup>2</sup>&gt;0.90 were
 used in the analysis).
description: Please use README files on how to use these datasets.
DOI: 10.5061/dryad.8sf7m0cn2
title: Memory extinction and spontaneous recovery shaping parasitoid foraging behavior

description: Animals can alter their foraging behavior through associative learning,
 where an encounter with an essential resource (e.g. food or a reproductive
 opportunity) is associated with nearby environmental cues (e.g.
 volatiles). This can subsequently improve the animal’s foraging
 efficiency. However, when these associated cues are encountered again, the
 anticipated resource is not always present. Such an unrewarding
 experience, also called a memory-extinction experience, can change an
 animal’s response to the associated cues. Although some studies are
 available on the mechanisms of this process, they rarely focus on cues and
 rewards that are relevant in an animal’s natural habitat. In this study,
 we tested the effect of different types of ecologically relevant
 memory-extinction experiences on the conditioned plant volatile
 preferences of the parasitic wasp Cotesia glomerata that uses these cues
 to locate its caterpillar hosts. These extinction experiences consisted of
 contact with only host traces (frass and silk), contact with non-host
 traces or an oviposition in a non-host near host traces, on the
 conditioned plant species. Our results show that the lack of an
 oviposition, after contacting host traces, led to the temporary alteration
 of the conditioned plant volatile preference in C. glomerata, but this
 effect was plant species-specific. These results provide novel insights in
 how ecologically relevant memory-extinction experiences can fine-tune an
 animal’s foraging behavior. This fine-tuning of learned behavior can be
 beneficial when the lack of finding a resource accurately predicts
 current, but not future foraging opportunities. Such continuous
 re-evaluation of obtained information helps animals to prevent maladaptive
 foraging behavior.
DOI: 10.5061/dryad.qz612jmfb
title: Data from: Ecological and biogeographic drivers of biodiversity cannot be resolved using clade age-richness data

description: Estimates of evolutionary diversification rates – speciation and
 extinction – have been used extensively to explain global biodiversity
 patterns. Many studies have analysed diversification rates derived from
 just two pieces of information: a clade's age and its extant species
 richness. This "age-richness rate" (ARR) estimator provides a
 convenient shortcut for comparative studies, but makes strong assumptions
 about the dynamics of species richness through time. We demonstrate that
 use of the ARR estimator in comparative studies is problematic on both
 theoretical and empirical grounds. We prove mathematically that ARR
 estimates are non-identifiable: there is no information in the data for a
 single clade that can distinguish a process with positive net
 diversification from one where net diversification is zero. Using
 palaeontological time series, we demonstrate that the ARR estimator has no
 predictive ability for real datasets. These pathologies arise because the
 ARR inference procedure yields "point estimates" that have been
 computed under a saturated statistical model with zero degrees of freedom.
 Although ARR estimates remain useful in some contexts, they should be
 avoided for comparative studies of diversification and species richness.